[PRE REVIEW]: Analix: an external agent detection software based on magnetoelastic sensors

[editorialbot]

Submitting author: @andreatta-ale (Alessandro Josue da Silva Andreatta)
Repository: https://github.com/andreatta-ale/external-agents-detector
Branch with paper.md (empty if default branch): main
Version: v1
Editor: Pending
Reviewers: Pending
Managing EiC: Kevin M. Moerman

Status

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Software report:

github.com/AlDanial/cloc v 1.90  T=20.25 s (471.0 files/s, 179798.8 lines/s)
-----------------------------------------------------------------------------------
Language                         files          blank        comment           code
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Python                            9021         504264         744528        2021861
C                                   58           8148          34438         148217
CSV                                 47              0              0          47409
Cython                              86           6088           4355          38728
CSS                                 11           1422           1309          18698
C/C++ Header                        63           2068           3128          12514
JSON                                40            227              0          12362
Markdown                            12           1913              0           4910
SVG                                 12              1             12           4066
Jupyter Notebook                    10              0           4169           2760
Fortran 77                          22            124             54           2747
SQL                                  4              0              0           1405
HTML                                30            218             55           1372
reStructuredText                    23            394             90           1256
JavaScript                          11            144            115            913
Fortran 90                          49            107             82            826
C++                                  6            191            197            761
TOML                                 1             39            120            640
TeX                                  1             61             64            556
Windows Resource File                1             36             45            135
PowerShell                           1             50            344            108
XML                                  3              0              1            102
DOS Batch                            4             27              1             80
ASP                                  5             24              0             68
Meson                                2             13              3             65
IDL                                  1              4              0             62
INI                                  3              5              0             32
PO File                              1              5             10             32
Visual Basic Script                  3             10              4             31
XSLT                                 1              7             24             24
Bourne Shell                         3              6              1             22
make                                 1              3              2             19
YAML                                 1              1              4             18
Lua                                  1              0              1              2
Unity-Prefab                         1              0              0              2
-----------------------------------------------------------------------------------
SUM:                              9539         525600         793156        2322803
-----------------------------------------------------------------------------------

Commit count by author:

    24	Alê Andreatta

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 3337

✅ The paper includes a Statement of need section

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3390/ma13214708 is OK
- 10.1609/aimag.v27i4.1911 is OK
- 10.1080/01621459.2000.10474333 is OK

MISSING DOIs

- 10.1056/nejmp1409903 may be a valid DOI for title: Ebola 2014—new challenges, new global response and...
- No DOI given, and none found for title: History of Ebola Disease Outbreaks. Cases and Outb...
- No DOI given, and none found for title: Ebola and Marburg haemorrhagic fever
- No DOI given, and none found for title: Marburg
- 10.3201/eid2505.181076 may be a valid DOI for title: Nipah virus sequences from humans and bats during ...
- No DOI given, and none found for title: Nipah virus
- 10.3201/eid2308.170354 may be a valid DOI for title: Characteristics of dysphagia in infants with micro...
- No DOI given, and none found for title:  Zika Virus
- No DOI given, and none found for title: Crimean-Congo hemorrhagic fever: history, epidemio...
- 10.1093/med/9780198570028.003.0033 may be a valid DOI for title: Crimean-Congo haemorrhagic fever
- No DOI given, and none found for title: Covid-19
- No DOI given, and none found for title: Coronavirus (covid-19) Dashboard
- No DOI given, and none found for title: Boletim Epidemiológico Vol 52
- 10.1590/s0103-40142008000300005 may be a valid DOI for title: Dengue no Brasil: situação epidemiológica e contri...
- 10.2105/ccdml.2868.046 may be a valid DOI for title: Dengue
- 10.3390/s110302809 may be a valid DOI for title: Theory, instrumentation and applications of magnet...
- No DOI given, and none found for title: Novel sensors and sensing
- 10.1016/j.sna.2005.03.027 may be a valid DOI for title: Magnetoelastic sensor application in civil buildin...
- No DOI given, and none found for title: Optimization strategies for HPLC and CZE
- 10.1016/s0304-8853(01)00979-9 may be a valid DOI for title: High-frequency magnetoelastic materials for remote...
- 10.1016/s0925-4005(00)00599-2 may be a valid DOI for title: A remote query magnetoelastic pH sensor
- 10.1002/pssa.201000738 may be a valid DOI for title: Magneto-elasticity in amorphous ferromagnets: Basi...
- No DOI given, and none found for title: Handbook of giant magnetostrictive materials
- 10.1109/20.221036 may be a valid DOI for title: Coupled magnetoelastic theory of magnetic and magn...
- 10.1016/j.jmmm.2008.04.107 may be a valid DOI for title: Extended Jiles–Atherton model for modelling the ma...
- 10.1016/s0304-8853(00)00612-0 may be a valid DOI for title: Magnetoelasticity of fe–ga and fe–al alloys
- 10.1016/s0022-5096(01)00050-3 may be a valid DOI for title: A constrained theory of magnetoelasticity
- 10.3390/s20700294 may be a valid DOI for title: Wireless magnetoelastic resonance sensors: A criti...
- No DOI given, and none found for title: Metallic glasses and sensing applications
- 10.1109/tmag.1981.1061735 may be a valid DOI for title: Magnetomechanical coupling and permeability in tra...
- 10.1088/0964-1726/10/2/322 may be a valid DOI for title: A wireless micro-sensor for simultaneous measureme...
- 10.1109/jsen.2014.2356851 may be a valid DOI for title: A highly miniaturized low-power CMOS-based pH moni...
- 10.3390/ma14164486 may be a valid DOI for title: On the possibility of developing magnetostrictive ...
- 10.1007/s00542-017-3495-5 may be a valid DOI for title: A review on pH sensitive materials for sensors and...
- 10.1088/0964-1726/9/6/320 may be a valid DOI for title: The frequency response of magnetoelastic sensors t...
- 10.1002/adma.202005448 may be a valid DOI for title: A review of piezoelectric and magnetostrictive bio...
- No DOI given, and none found for title: Dartmouth summer research conference on artificial...
- No DOI given, and none found for title: A few useful things to know about machine learning
- No DOI given, and none found for title: The quest for artificial intelligence
- No DOI given, and none found for title: Pattern recognition and machine learning
- No DOI given, and none found for title: Um novo algoritmo de agrupamento semi-supervisiona...
- No DOI given, and none found for title: Machine Learning: what it is and why it matters
- 10.21275/art20203995 may be a valid DOI for title: Machine learning algorithms-a review
- No DOI given, and none found for title: Understanding machine learning: from theory to alg...
- No DOI given, and none found for title: Supervised and unsupervised machine learning algor...
- No DOI given, and none found for title: Conceitos sobre aprendizado de máquina
- No DOI given, and none found for title: Deep learning
- 10.1016/0925-2312(95)90026-8 may be a valid DOI for title: Neural networks: a comprehensive foundation
- No DOI given, and none found for title: Deep learning
- No DOI given, and none found for title: Hands-on Machine Learning with Scikit-Learn and Te...
- No DOI given, and none found for title: Data science from scratch: first principles with p...
- No DOI given, and none found for title: Bootstrap methods and their application
- No DOI given, and none found for title: Neural networks for pattern recognition
- No DOI given, and none found for title: Neural networks and deep learning
- No DOI given, and none found for title: Magnetoelastic sensors: detection method of extern...
- 10.1016/j.snb.2019.05.089 may be a valid DOI for title: Enhanced mass sensitivity in novel magnetoelastic ...
- No DOI given, and none found for title: Xgboost: A scalable tree boosting system
- No DOI given, and none found for title: INTRODUCTION to Boosted Trees
- 10.1088/1361-6501/ad1e1d may be a valid DOI for title: Role of extrinsic factors on magnetoelastic resona...

INVALID DOIs

- https://doi.org/10.1016/j.pecs.2008.01.001 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.clet.2020.100032 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[editorialbot]

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[Kevin-Mattheus-Moerman]

@andreatta-ale thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points:

• Please study the above reference check ☝️ and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.
• Your project appears to lack contributing guidelines at the moment. Please work to add these and to mention/link to them in your README. You could for instance create a CONTRIBUTING.md file (see here for some examples: https://contributing.md/example/).
• The README does not seem to link to documentation. Does this project have dedicated documentation?
• The README does not seem to link to automated testing. Does this project feature automated testing?
• Can you explain your repository organisation/content? The above report shows millions of lines of code, and the repository contains many binary .exe file. Did you create these binaries? What aspects of the code are your original contribution?

[xuanxu]

@editorialbot check references
(testing new references report)

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.3390/ma13214708 is OK
- 10.1609/aimag.v27i4.1911 is OK
- 10.1080/01621459.2000.10474333 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: History of Ebola Disease Outbreaks. Cases and Outb...
- No DOI given, and none found for title: Ebola and Marburg haemorrhagic fever
- No DOI given, and none found for title: Marburg
- No DOI given, and none found for title: Nipah virus
- No DOI given, and none found for title:  Zika Virus
- No DOI given, and none found for title: Crimean-Congo hemorrhagic fever: history, epidemio...
- No DOI given, and none found for title: Covid-19
- No DOI given, and none found for title: Coronavirus (covid-19) Dashboard
- No DOI given, and none found for title: Boletim Epidemiológico Vol 52
- No DOI given, and none found for title: Novel sensors and sensing
- No DOI given, and none found for title: Optimization strategies for HPLC and CZE
- No DOI given, and none found for title: Handbook of giant magnetostrictive materials
- No DOI given, and none found for title: Metallic glasses and sensing applications
- No DOI given, and none found for title: Dartmouth summer research conference on artificial...
- No DOI given, and none found for title: A few useful things to know about machine learning
- No DOI given, and none found for title: The quest for artificial intelligence
- No DOI given, and none found for title: Pattern recognition and machine learning
- No DOI given, and none found for title: Um novo algoritmo de agrupamento semi-supervisiona...
- No DOI given, and none found for title: Machine Learning: what it is and why it matters
- No DOI given, and none found for title: Understanding machine learning: from theory to alg...
- No DOI given, and none found for title: Supervised and unsupervised machine learning algor...
- No DOI given, and none found for title: Conceitos sobre aprendizado de máquina
- No DOI given, and none found for title: Deep learning
- No DOI given, and none found for title: Deep learning
- No DOI given, and none found for title: Hands-on Machine Learning with Scikit-Learn and Te...
- No DOI given, and none found for title: Data science from scratch: first principles with p...
- No DOI given, and none found for title: Bootstrap methods and their application
- No DOI given, and none found for title: Neural networks for pattern recognition
- No DOI given, and none found for title: Neural networks and deep learning
- No DOI given, and none found for title: Magnetoelastic sensors: detection method of extern...
- No DOI given, and none found for title: Xgboost: A scalable tree boosting system
- No DOI given, and none found for title: INTRODUCTION to Boosted Trees

❌ MISSING DOIs

- 10.1056/nejmp1409903 may be a valid DOI for title: Ebola 2014—new challenges, new global response and...
- 10.3201/eid2505.181076 may be a valid DOI for title: Nipah virus sequences from humans and bats during ...
- 10.3201/eid2308.170354 may be a valid DOI for title: Characteristics of dysphagia in infants with micro...
- 10.1093/med/9780198570028.003.0033 may be a valid DOI for title: Crimean-Congo haemorrhagic fever
- 10.1590/s0103-40142008000300005 may be a valid DOI for title: Dengue no Brasil: situação epidemiológica e contri...
- 10.2105/ccdml.2868.046 may be a valid DOI for title: Dengue
- 10.3390/s110302809 may be a valid DOI for title: Theory, instrumentation and applications of magnet...
- 10.1016/j.sna.2005.03.027 may be a valid DOI for title: Magnetoelastic sensor application in civil buildin...
- 10.1016/s0304-8853(01)00979-9 may be a valid DOI for title: High-frequency magnetoelastic materials for remote...
- 10.1016/s0925-4005(00)00599-2 may be a valid DOI for title: A remote query magnetoelastic pH sensor
- 10.1002/pssa.201000738 may be a valid DOI for title: Magneto-elasticity in amorphous ferromagnets: Basi...
- 10.1109/20.221036 may be a valid DOI for title: Coupled magnetoelastic theory of magnetic and magn...
- 10.1016/j.jmmm.2008.04.107 may be a valid DOI for title: Extended Jiles–Atherton model for modelling the ma...
- 10.1016/s0304-8853(00)00612-0 may be a valid DOI for title: Magnetoelasticity of fe–ga and fe–al alloys
- 10.1016/s0022-5096(01)00050-3 may be a valid DOI for title: A constrained theory of magnetoelasticity
- 10.3390/s20700294 may be a valid DOI for title: Wireless magnetoelastic resonance sensors: A criti...
- 10.1109/tmag.1981.1061735 may be a valid DOI for title: Magnetomechanical coupling and permeability in tra...
- 10.1088/0964-1726/10/2/322 may be a valid DOI for title: A wireless micro-sensor for simultaneous measureme...
- 10.1109/jsen.2014.2356851 may be a valid DOI for title: A highly miniaturized low-power CMOS-based pH moni...
- 10.3390/ma14164486 may be a valid DOI for title: On the possibility of developing magnetostrictive ...
- 10.1007/s00542-017-3495-5 may be a valid DOI for title: A review on pH sensitive materials for sensors and...
- 10.1088/0964-1726/9/6/320 may be a valid DOI for title: The frequency response of magnetoelastic sensors t...
- 10.1002/adma.202005448 may be a valid DOI for title: A review of piezoelectric and magnetostrictive bio...
- 10.21275/art20203995 may be a valid DOI for title: Machine learning algorithms-a review
- 10.1016/0925-2312(95)90026-8 may be a valid DOI for title: Neural networks: a comprehensive foundation
- 10.1016/j.snb.2019.05.089 may be a valid DOI for title: Enhanced mass sensitivity in novel magnetoelastic ...
- 10.1088/1361-6501/ad1e1d may be a valid DOI for title: Role of extrinsic factors on magnetoelastic resona...

❌ INVALID DOIs

- https://doi.org/10.1016/j.pecs.2008.01.001 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.clet.2020.100032 is INVALID because of 'https://doi.org/' prefix

[andreatta-ale]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.3390/ma13214708 is OK
- 10.1016/j.pecs.2008.01.001 is OK
- 10.1609/aimag.v27i4.1911 is OK
- 10.1080/01621459.2000.10474333 is OK
- 10.1016/j.clet.2020.100032 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: History of Ebola Disease Outbreaks. Cases and Outb...
- No DOI given, and none found for title: Ebola and Marburg haemorrhagic fever
- No DOI given, and none found for title: Marburg
- No DOI given, and none found for title: Nipah virus
- No DOI given, and none found for title:  Zika Virus
- No DOI given, and none found for title: Crimean-Congo hemorrhagic fever: history, epidemio...
- No DOI given, and none found for title: Covid-19
- No DOI given, and none found for title: Coronavirus (covid-19) Dashboard
- No DOI given, and none found for title: Boletim Epidemiológico Vol 52
- No DOI given, and none found for title: Novel sensors and sensing
- No DOI given, and none found for title: Optimization strategies for HPLC and CZE
- No DOI given, and none found for title: Handbook of giant magnetostrictive materials
- No DOI given, and none found for title: Metallic glasses and sensing applications
- No DOI given, and none found for title: Dartmouth summer research conference on artificial...
- No DOI given, and none found for title: A few useful things to know about machine learning
- No DOI given, and none found for title: The quest for artificial intelligence
- No DOI given, and none found for title: Pattern recognition and machine learning
- No DOI given, and none found for title: Um novo algoritmo de agrupamento semi-supervisiona...
- No DOI given, and none found for title: Machine Learning: what it is and why it matters
- No DOI given, and none found for title: Understanding machine learning: from theory to alg...
- No DOI given, and none found for title: Supervised and unsupervised machine learning algor...
- No DOI given, and none found for title: Conceitos sobre aprendizado de máquina
- No DOI given, and none found for title: Deep learning
- No DOI given, and none found for title: Deep learning
- No DOI given, and none found for title: Hands-on Machine Learning with Scikit-Learn and Te...
- No DOI given, and none found for title: Data science from scratch: first principles with p...
- No DOI given, and none found for title: Bootstrap methods and their application
- No DOI given, and none found for title: Neural networks for pattern recognition
- No DOI given, and none found for title: Neural networks and deep learning
- No DOI given, and none found for title: Magnetoelastic sensors: detection method of extern...
- No DOI given, and none found for title: Xgboost: A scalable tree boosting system
- No DOI given, and none found for title: INTRODUCTION to Boosted Trees

❌ MISSING DOIs

- 10.1056/nejmp1409903 may be a valid DOI for title: Ebola 2014—new challenges, new global response and...
- 10.3201/eid2505.181076 may be a valid DOI for title: Nipah virus sequences from humans and bats during ...
- 10.3201/eid2308.170354 may be a valid DOI for title: Characteristics of dysphagia in infants with micro...
- 10.1093/med/9780198570028.003.0033 may be a valid DOI for title: Crimean-Congo haemorrhagic fever
- 10.1590/s0103-40142008000300005 may be a valid DOI for title: Dengue no Brasil: situação epidemiológica e contri...
- 10.2105/ccdml.2868.046 may be a valid DOI for title: Dengue
- 10.3390/s110302809 may be a valid DOI for title: Theory, instrumentation and applications of magnet...
- 10.1016/j.sna.2005.03.027 may be a valid DOI for title: Magnetoelastic sensor application in civil buildin...
- 10.1016/s0304-8853(01)00979-9 may be a valid DOI for title: High-frequency magnetoelastic materials for remote...
- 10.1016/s0925-4005(00)00599-2 may be a valid DOI for title: A remote query magnetoelastic pH sensor
- 10.1002/pssa.201000738 may be a valid DOI for title: Magneto-elasticity in amorphous ferromagnets: Basi...
- 10.1109/20.221036 may be a valid DOI for title: Coupled magnetoelastic theory of magnetic and magn...
- 10.1016/j.jmmm.2008.04.107 may be a valid DOI for title: Extended Jiles–Atherton model for modelling the ma...
- 10.1016/s0304-8853(00)00612-0 may be a valid DOI for title: Magnetoelasticity of fe–ga and fe–al alloys
- 10.1016/s0022-5096(01)00050-3 may be a valid DOI for title: A constrained theory of magnetoelasticity
- 10.3390/s20700294 may be a valid DOI for title: Wireless magnetoelastic resonance sensors: A criti...
- 10.1109/tmag.1981.1061735 may be a valid DOI for title: Magnetomechanical coupling and permeability in tra...
- 10.1088/0964-1726/10/2/322 may be a valid DOI for title: A wireless micro-sensor for simultaneous measureme...
- 10.1109/jsen.2014.2356851 may be a valid DOI for title: A highly miniaturized low-power CMOS-based pH moni...
- 10.3390/ma14164486 may be a valid DOI for title: On the possibility of developing magnetostrictive ...
- 10.1007/s00542-017-3495-5 may be a valid DOI for title: A review on pH sensitive materials for sensors and...
- 10.1088/0964-1726/9/6/320 may be a valid DOI for title: The frequency response of magnetoelastic sensors t...
- 10.1002/adma.202005448 may be a valid DOI for title: A review of piezoelectric and magnetostrictive bio...
- 10.21275/art20203995 may be a valid DOI for title: Machine learning algorithms-a review
- 10.1016/0925-2312(95)90026-8 may be a valid DOI for title: Neural networks: a comprehensive foundation
- 10.1016/j.snb.2019.05.089 may be a valid DOI for title: Enhanced mass sensitivity in novel magnetoelastic ...
- 10.1088/1361-6501/ad1e1d may be a valid DOI for title: Role of extrinsic factors on magnetoelastic resona...

❌ INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@andreatta-ale can you please respond to my queries above ☝️

[andreatta-ale]

Dear Kevin, I apologize for the delay in my response. I am still in the process of familiarizing myself with this review procedure. Regarding the inquiries: 1. I have addressed some of the DOI issues and am currently revising the references. Many of these sources are books or government websites, which do not have DOIs available for citation. 2. As per your suggestion, I have created a Contributing.md file, which I will push alongside the new README. Upon reviewing the current README file, I noticed that many of the comments within it serve as part of our documentation. Consequently, I am also in the process of rewriting the README to better reflect this. 3. We had proposed documentation on how to run the code in the previous README, and I am revising this as well. 4. The project does not include automated testing. 5. The 'app' folder contains the core code. There are only three original Jupyter Notebooks: Classifier.ipynb, I_am_here_to_test_the_model.ipynb, and analysis_script.ipynb. Additionally, the folder contains source data, which is essential for anyone who wishes to test the entire project codebase. The remaining files consist of the packages and resources I utilized during the project's development and execution, such as Python packages and the virtual environment. I assumed it would be beneficial to include all relevant components in the repository. However, I seek your guidance on whether the repository should contain only the original artifacts. Thank you in advance for your insights and contributions. Best regards, Alessandro

…

________________________________ From: Kevin Mattheus Moerman ***@***.***> Sent: Wednesday, August 28, 2024 06:44 To: openjournals/joss-reviews ***@***.***> Cc: Alê Andreatta ***@***.***>; Mention ***@***.***> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: Analix: an external agent detection software based on magnetoelastic sensors (Issue #7116) @andreatta-ale<https://github.com/andreatta-ale> can you please respond to my queries above ☝️ — Reply to this email directly, view it on GitHub<#7116 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AG2V43ETBTL6JR46ZDCTFTLZTWLXVAVCNFSM6AAAAABMXSQFPKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMJUHA2DEMZRHA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[Kevin-Mattheus-Moerman]

@andreatta-ale thanks for working on some of the points I listed. Your response indicated some work is still in progress. Can you confirm this work is now completed? If not I would recommend we reject this submission at the moment and you may resubmit in the future once the work has been completed.

[Kevin-Mattheus-Moerman]

@andreatta-ale please confirm if all points have now been addressed.

[Kevin-Mattheus-Moerman]

@andreatta-ale after reviewing your comments above in more detail, I have come to the conclusion that this submission is not suitable for JOSS as it stands. The project lacks (automated) testing, consists of only 3 original Jupyter notebooks (which is not sufficient to pass our substantial scholarly effort criteria), and the project organisation is not well done. Hence we will now proceed to reject this submission from JOSS.

It may be possible to consider a future re-submission. If you did the following:

• Clean the repository so only the original codes written by the authors is provided. Hence purge the project from things like the binaries added at the moment.
• Extend the project functionality and establish maturity such that the project conforms to our substantial scholarly effort criteria.
• Add automated testing
• Add detailed documentation, including how to set-up the environment etc.
• Data can be included in the project if it is small enough. However, it may be better to house data in a separate repository, or to house it elsewhere e.g. e.g. ZENODO or similar, especially if this concerns a lot of data.

Note that one possible alternative to JOSS is to follow GitHub's guide on how to create a permanent archive and DOI for your software. This DOI can then be used by others to cite your work.

[Kevin-Mattheus-Moerman]

@editorialbot reject

[editorialbot]

Paper rejected.

[andreatta-ale]

Hello, @Kevin-Mattheus-Moerman.
Thank you for your attention in reviewing the paper. I will work on the suggested improvements to address all issues before resubmission.