PONE-D-19-21939

Safety and efficacy of N-acetylcysteine in hospitalized patients with HIV-associated tuberculosis: an open-label, randomized, phase II trial (RIPENACTB Study)

PLOS ONE

Dear Dr. Lacerda,

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.

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We look forward to receiving your revised manuscript.

Kind regards,

Delia Goletti, M.D., Ph.D.

Academic Editor

PLOS ONE

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2. We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed:

https://www.thelancet.com/journals/lanhiv/article/PIIS2352-3018(19)30154-7/fulltext

https://academic.oup.com/cid/advance-article-abstract/doi/10.1093/cid/ciz152/5365529?redirectedFrom=fulltext

The text that needs to be addressed is in the Introduction section.

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Additional Editor Comments (if provided):

the manuscript is interesting. It opens new insights in the treatment of HIV-TB patients.

Please, answer the referees' major points regarding:

1. safety issues

2. lenght of recruitment of the patients

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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

Reviewer #2: Partly

Reviewer #3: Yes

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

Reviewer #1: No

Reviewer #2: No

Reviewer #3: Yes

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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

Reviewer #2: No

Reviewer #3: 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

Reviewer #2: No

Reviewer #3: 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: 1. My main criticism of this manuscript is that you have not shown that the treatment condition is safe, only that it is not unsafe. You are arguing that not rejecting the null hypothesis implies the groups are similar, i.e., absence of evidence is evidence of absence. By this logic, I could test two people in each group and conclude the treatment group is "safe". This is a huge oversight and, as a statistician, very disappointing to see this. To conclude these groups are "similar", you would need to perform equivalence testing or noninferiority testing (provided you are able to set a margin for noninferiority).

2. Given the low sample sizes of the groups, I would recommend not using asymptotic tests, such as Pearson's Chi-squared. I would switch to either permutation tests or Fisher's Exact Test. Also, if you use one of those, you can tests for differences between groups with small numbers of events…provided that hypothesis fits with your goals.

3. The same is true for the logistic regression as I would recommend exact logistic regression. I also don't entirely understand the purpose of the regression models as all that I see mentioned in the text is the p-value. There seems to be no interest in the odds ratios, except in the figures.

4. Also, while the small sample size is a limitation, that is made all the much worse by using binary outcomes. Certainly, some are binary by nature, but some like hepatotoxicity could have the quantitative values analyzed. Research suggests the loss of power after dichotomizing is large (e.g., https://doi.org/10.1002/pst.331). There may be industry standards about how to cut an outcome. Fair, but this seems like a really good opportunity to analyze the quantitative values.

Reviewer #2: 1. Reference, for instance, reference 1, can be more updated.

2. Your underlying data regarding your manuscript cannot be found from the given URL.

3. Is it necessary to conduct the study in hospitalized patients? As we can have more participants without this criterion. It also quite a surprise to see not many participants in the study given 1.5 years of study duration even Brazil is one of the countries with the highest burden of TB and TB with HIV.

4. The study design was a phase II clinical trial to see the safety of the intervention. One should rather select less severe participants. However, in this study, one of the inclusion criteria was being hospitalized patient which was relatively severe.

5. The section "Results" was far too short. It needs more detail e.g., detail of liver function profiles at weeks 1, 2, 4, 6 and 8.

6. The culture conversion rate can also be calculated using hazard ratio as you mentioned in the definition that "The rate of culture conversion was defined as the time elapsed from day 1 to the first negative culture".

7. In this RCT, you can interpret your findings using relative risk or hazard ratio

8. For Table 1, mean with SD or median with IQR should be provided together with each continuous variable rather than just the stratified values. For viral load, you might consider presenting your information with the logarithm of viral load.

9. You stated to use logistic regression analysis, however, its results did not appear in the results.

10. Your conclusion was over claim for the benefit of NAC given the sample size of less than 40.

11. Given your Figure 1, it is quite interesting to see such a high rate of drug resistance tuberculosis; 5 out of 50 in both arms.

Reviewer #3: Some sentences needs revision to be fully understandable. you do not need to use long and confusing sentences in discussion. Break them to small and clear sentences.

This is a useful study in this field, similar to our study, that is not published yet.

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: Yes: Nasser Vahdati-Mashhadian

[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 to be viewed.]

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 us at figures@plos.org. Please note that Supporting Information files do not need this step.

PONE-D-19-21939R1

Safety and efficacy of N-acetylcysteine in hospitalized patients with HIV-associated tuberculosis: an open-label, randomized, phase II trial (RIPENACTB Study)

PLOS ONE

Dear dr LACERDA, deep apologies for the delay.

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.

==============================

ACADEMIC EDITOR:

the manuscript has been revised by additional two statisticians.

Few comments are needed:

1- Clarify that the adverse event RATES were similar in the two arms.

2- Statistical Analysis Section:

A. Differences in categorical variables were TESTED using Fisher’s exact test.

B. This statement is unclear, “generalized linear regression with log binomial.” More fully explain the statistical methods associated with the general linear regression model.

C. Remove “Differences with” in the sentence “Differences with p-values < 0.05 were  considered statistically significant.

3- Replace NS with numeric p-values.

4- Figure 2: Indicate the type of test used to generate the p-value.

5- State and justify the study’s target sample size with a pre-study statistical power calculation. thank you for being patient.

==============================

We would appreciate receiving your revised manuscript by Jun 28 2020 11:59PM. When you are 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.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter.

To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

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). This letter should be uploaded as separate file and labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'.

Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out.

We look forward to receiving your revised manuscript.

Kind regards,

Delia Goletti, M.D., Ph.D.

Academic Editor

PLOS ONE

[Note: HTML markup is below. Please do not edit.]

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 #3: (No Response)

Reviewer #4: (No Response)

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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 #3: Yes

Reviewer #4: Partly

**********

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

Reviewer #3: Yes

Reviewer #4: 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 #3: Yes

Reviewer #4: 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 #3: Yes

Reviewer #4: 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 #3: (No Response)

Reviewer #4: A phase II randomized two-arm controlled clinical trial was conducted to assess the safety and tolerability of N-acetylcysteine (NAC) in HIV patients with tuberculosis. The adverse event rates were similar in the two arms, and no evidence was found to refute that NAC was unsafe.

Minor revisions:

1- Clarify that the adverse event RATES were similar in the two arms.

2- Statistical Analysis Section:

A. Differences in categorical variables were TESTED using Fisher’s exact test.

B. This statement is unclear, “generalized linear regression with log binomial.” More fully explain the statistical methods associated with the general linear regression model.

C. Remove “Differences with” in the sentence “Differences with p-values < 0.05 were considered statistically significant.

3- Replace NS with numeric p-values.

4- Figure 2: Indicate the type of test used to generate the p-value.

5- State and justify the study’s target sample size with a pre-study statistical power calculation.

**********

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 #3: No

Reviewer #4: No

[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 to be viewed.]

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 us at figures@plos.org. Please note that Supporting Information files do not need this step.

Safety and efficacy of N-acetylcysteine in hospitalized patients with HIV-associated tuberculosis: an open-label, randomized, phase II trial (RIPENACTB Study)

PONE-D-19-21939R2

Dear Dr. Marcus VG Lacerda, 

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,

Delia Goletti, M.D., Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

The authors answered the questions raised.

Reviewers' comments: