PONE-D-24-35376Machine Learning Model to Predict The Adherence of Tuberculosis Patients Experiencing Increased Level of Liver Enzymes in IndonesiaPLOS ONE

Dear Dr. Perwitasari,

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Academic Editor

PLOS ONE

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The author thank to Ministry of Education, Cultural, Research and Technology for the grant research Number 075/E5/PG.02.00.PL/2023 date12 April 2023; Number : 0254.8/LL5-INT/AL.04/2023 date 17 April 2023; and Number 004/WCR/LPPM UAD/IV/2023. 

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Author who received award: DAP

Funder: Ministry of Education, Cultural, Research and Technology for the grant research Number 075/E5/PG.02.00.PL/2023 date12 April 2023; Number : 0254.8/LL5-INT/AL.04/2023 date 17 April 2023; and Number 004/WCR/LPPM UAD/IV/2023. 

URL: https://dikti.kemdikbud.go.id/

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: No

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Dear authors,

Thank you for submitting your manuscript titled "Machine Learning Model to Predict the Adherence of Tuberculosis Patients Experiencing Increased Levels of Liver Enzymes in Indonesia." This is an important and timely topic with potential clinical implications. However, there are several areas that need further clarification and improvement, particularly in terms of language, methodology, and the presentation of results, to ensure the study's findings are clearly understood and supported, as follow below:

Abstract

• Needs to be re-written after the manuscript review

Introduction

• English review is needed

• Suggest to change the wording of “side effect” to “adverse drug reaction”

• Contextualize more the hepatic adverse drug reaction

• Revise this sentence: “The poor adherence may cause the adverse drug reaction (…)” – in fact, is the opposite.

• Rewrite the sentence: “The side effect experienced by the TB patients led the patients refused the treatment. This side effect might be worsening TB patients condition, and led the patients’ refusal to their treatment”

• Overall: needs improvement, English review, and better paragraphs linkage

Methods

• Where the study was conducted?

• Clarify the inclusion criteria – what clinical forms were considered? Which anti-TB drugs or anti-TB drugs combination defined the first line? Was it a fixed-dose combination?

• Define which were the “comorbidities which related to liver function were excluded”

• Question: why did the authors exclude the pregnant women? What was the age range for inclusion?

• Define this better: “We also collected other symptoms which were related to the side effect of TB treatment.” The adverse drug reaction symptoms are usually related to the organ system affected. Which organ system(s) considered? Only hepatic?

• It’s not clear which variables were included in the model and how they were selected.

• Review this paragraph “Separately, we also used SPSS (Version 27.0, IBM Corp) to assess the associations between variables and adherence. The methods in this study were carried out in accordance with relevant guidelines and regulations.”

• SPSS is the statistical software. What were the statistical tests used for the associations? Why? What was alfa value, .05?

Results

• Review and rewrite the first paragraph – it’s confusing and difficult to follow.

• Table 1 – please provide a footnote with abbreviation

• Question: what is IDR? Not previously defined. I suppose it’s the Indonesian currency, and I suggest to also provide the equivalency in dollars or euros, so the reader can have a better perception of the amount.

• The variables described are not previously defined – e.g., how level of education was evaluated?

• There is no descriptive statistics of the baseline variables, of the adverse drug reaction characteristics, median AST, ALT, Hb…

• There is a variable “TB medication” in table 1, which list different categories of TB treatment. Please define and clarify.

• Moreover, there is a category of “regular medication details”. I suggest grouping them by medication class, such as anti-hypertension, medication for diabetes, and so on.

• Table 2 is not informative, lacks a footnote with abbreviation, and the statistical test used to compare. E.g., what is F<21?

• Figure 1 – again, where are the statistical results? Which test was used to compare de proportions of non-adherence?

Discussion

• Review this sentence:

• “Our study finds that tuberculosis patients had a good adherence and knowledge” – there is no mention of how “knowledge” was handled.

• Review the other paragraphs according to the suggestions in methods and results sections

• Conclusion

• Invalid for now. The study did not assess the implementation of a prediction model, but a development of it.

General comment:

• Please avoid using “subjects” when referring to study participants. Prefer participants, volunteers, or study participants.

Final comment:

In summary, while your study addresses the important issue of adverse drug reaction during TB treatment, several areas require further attention before it can be considered for publication. The manuscript would benefit from a thorough review of English language and structure, clearer definitions of key variables, improved descriptions of the methods and statistical analyses, and more robust presentation of the results. Additionally, the discussion and conclusion sections need to be better aligned with the findings. I recommend a major revision to address these points and strengthen the overall clarity and rigor of the study.

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Reviewer #1: Yes: Felipe Ridolfi

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PONE-D-24-35376R1Machine Learning Model to Predict The Adherence of Tuberculosis Patients Experiencing Increased Level of Liver Enzymes in IndonesiaPLOS ONE

Dear Dr. Perwitasari,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Jan 10 2025 11:59PM. If you will need significantly more time to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Frederick Quinn

Academic Editor

PLOS ONE

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Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Partly

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Dear authors, thanks for sending back your revised manuscritp. It has improved after your revision. However, I believe it would benefit from one last very careful review of grammar and wording, as there are some repeated small inconsistences - e.g., in abstract, you mention "adverse reaction", while in text, "adverse drug reaction". Moreover, the letter style in the figures differ from the text.

And just one question: I did not see any grading criteria for the adverse drug reaction - if you did not use any, please specify in methods.

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Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: Yes: Felipe Ridolfi

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[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

Machine Learning Model to Predict The Adherence of Tuberculosis Patients Experiencing Increased Level of Liver Enzymes in Indonesia

PONE-D-24-35376R2

Dear Dr. Perwitasari,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Frederick Quinn

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: (No Response)

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: Yes: Felipe Ridolfi

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