Dear Dr Andrews,

Thank you for submitting your manuscript entitled "All-cause and cause-specific mortality during and following incarceration in Brazil" for consideration by PLOS Medicine.

Your manuscript has now been evaluated by the PLOS Medicine editorial staff as well as by an academic editor with relevant expertise and I am writing to let you know that we would like to send your submission out for external peer review.

However, before we can send your manuscript to reviewers, we need you to complete your submission by providing the metadata that is required for full assessment. To this end, please login to Editorial Manager where you will find the paper in the 'Submissions Needing Revisions' folder on your homepage. Please click 'Revise Submission' from the Action Links and complete all additional questions in the submission questionnaire.

Please re-submit your manuscript within two working days, i.e. by May 26 2021 11:59PM.

Login to Editorial Manager here: https://www.editorialmanager.com/pmedicine

Once your full submission is complete, your paper will undergo a series of checks in preparation for peer review. Once your manuscript has passed all checks it will be sent out for review.

Feel free to email us at plosmedicine@plos.org if you have any queries relating to your submission.

Kind regards,

Callam Davidson

Associate Editor

PLOS Medicine

Dear Dr. Andrews,

Thank you very much for submitting your manuscript "All-cause and cause-specific mortality during and following incarceration in Brazil" (PMEDICINE-D-21-02293R1) for consideration at PLOS Medicine.

Your paper was evaluated by a senior editor and discussed among all the editors here. It was also discussed with an academic editor with relevant expertise, and sent to independent reviewers, including a statistical reviewer. The reviews are appended at the bottom of this email and any accompanying reviewer attachments can be seen via the link below:

[LINK]

In light of these reviews, we will not be able to accept the manuscript for publication in the journal in its current form, but we would like to consider a revised version that addresses the reviewers' and editors' comments. You will understand that we cannot make any decision about publication until we have seen the revised manuscript and your response, and we plan to seek re-review by one or more of the reviewers.

In revising the manuscript for further consideration, your revisions should address the specific points made by each reviewer and the editors. Please also check the guidelines for revised papers at http://journals.plos.org/plosmedicine/s/revising-your-manuscript for any that apply to your paper. In your rebuttal letter you should indicate your response to the reviewers' and editors' comments, the changes you have made in the manuscript, and include either an excerpt of the revised text or the location (eg: page and line number) where each change can be found. Please submit a clean version of the paper as the main article file; a version with changes marked should be uploaded as a marked up manuscript.

In addition, we request that you upload any figures associated with your paper as individual TIF or EPS files with 300dpi resolution at resubmission; please read our figure guidelines for more information on our requirements: http://journals.plos.org/plosmedicine/s/figures. While revising your submission, please upload your figure files to the 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. 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 PLOSMedicine@plos.org.

We hope to receive your revised manuscript by Jul 30 2021 11:59PM. Please email us (plosmedicine@plos.org) if you have any questions or concerns.

***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 ask every co-author listed on the manuscript to fill in a contributing author statement, making sure to declare all competing interests. If any of the co-authors have not filled in the statement, we will remind them to do so when the paper is revised. If all statements are not completed in a timely fashion this could hold up the re-review process. If new competing interests are declared later in the revision process, this may also hold up the submission. Should there be a problem getting one of your co-authors to fill in a statement we will be in contact. YOU MUST NOT ADD OR REMOVE AUTHORS UNLESS YOU HAVE ALERTED THE EDITOR HANDLING THE MANUSCRIPT TO THE CHANGE AND THEY SPECIFICALLY HAVE AGREED TO IT. You can see our competing interests policy here: http://journals.plos.org/plosmedicine/s/competing-interests.

Please use the following link to submit the revised manuscript:

https://www.editorialmanager.com/pmedicine/

Your article can be found in the "Submissions Needing Revision" folder.

To enhance the reproducibility of your results, we recommend that 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. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols

Please ensure that the paper adheres to the PLOS Data Availability Policy (see http://journals.plos.org/plosmedicine/s/data-availability), which requires that all data underlying the study's findings be provided in a repository or as Supporting Information. For data residing with a third party, authors are required to provide instructions with contact information for obtaining the data. PLOS journals do not allow statements supported by "data not shown" or "unpublished results." For such statements, authors must provide supporting data or cite public sources that include it.

We look forward to receiving your revised manuscript and please get in touch with any questions.

Sincerely,

Callam Davidson,

Associate Editor

PLOS Medicine

plosmedicine.org

-----------------------------------------------------------

Requests from the editors:

Title: Please update the title to match PLOS Medicine’s typical format (see https://journals.plos.org/plosmedicine/ for examples). ‘All-cause and cause-specific mortality during and following incarceration in Brazil: a registry linkage and modelling study’ or similar, for example.

Abstract: Please add a final line to the ‘Methods and Findings’ section of the abstract that begins “The limitations of this study are” and summarises the main limitations. Please also ensure any conclusions are written in the past tense.

References: Please format these to remove and bold or italicised text and list the first six authors before ‘et al.’.

Please remove the ‘Author contributions’ section from the end of the manuscript as, in the event of publication, this information is presented in the metadata based on your responses to the submission form.

If a protocol or statistical analysis plan were prepared in advance of the study, please can these be provided as supplementary materials and referenced appropriately in the methods (if an analysis plan was prepared, please highlight any analyses that were not pre-specified).

Please include an ‘Author Summary’ section as outlined here https://journals.plos.org/plosmedicine/s/revising-your-manuscript

Please consider whether the term ‘sex’ would be more appropriate than ‘gender’ throughout the manuscript.

Please include line numbering in the margin.

Comments from the reviewers:

Reviewer #1: This is a useful and well-conducted study on all-cause and cause-specific mortality during and following incarceration in Brazil. The study design, datasets, and statistical methods and analyses are mostly adequate. However, there are still a few issues needing attention.

1) It said all rates were age-standardised, but why not both age and sex standardised as there were female prisoners too?

2) In statistical analysis section, it says "Deaths of individuals under 18 years of age were excluded from rates analysis due to missing age structure information for those under 18". As the main analyses were on rates, does this mean the study cohort should be defined as those over18 years old? It's a bit confusing throughout the paper, in text, tables and figures that some are on 18+, some on 15+ and some on 16+?

3) There is no table at all in the main text. Need a comprehensive and informative table 1 on summary of the dataset on baselines (age, sex, and etc) and possibly outcomes of interests.

4) Regarding figures, Figure 2 can be moved to supplementary as mainly details on data linkage. Figure 4 presents the main results of the paper but why there was no "closed prison (women)"?

5) The deaths trend analysis after release as shown in Figure 5 is very interesting but lacks of solid interpretation on the reasons behind the trend which should be supported by the literature and statistics of trends in risk factors.

6) In conclusions in the abstract, it says "The cause-specific trends and risk of incarceration-associated mortality in Brazil differ from those reported in high-income countries...". However, this is not a comparative study, and can't compare like for like, therefore it's not adequate to conclude this as a key conclusion of the study.

Reviewer #2: "All-cause and cause-specific mortality during and following incarceration in Brazil."

This is an interesting and relevant study examining mortality rates among criminal justice-involved populations in the Brazilian state, Mato Grosso do Sul. The authors find elevated mortality rates among this population, with particularly alarming rates of death due to violence both while under supervision and post-release.

1. My main issues with the manuscript as it stands lie in the framing of the study and the discussion of findings.

a. With regard to the former, the paper is framed as a study of "incarceration-associated mortality" (see abstract and introduction). However, this is a misnomer in a couple of ways. For one, the paper does not and cannot trace deaths to being caused by or related to incarceration itself. These are death rates among justice-involved persons- NOT incarceration-associated mortality. Second, the study also includes mortality rates of those in police stations. Is this being defined as incarceration as well? Please clarify.

b. As for the latter, and this is a similar issue to the one abovementioned, the discussion makes problematic statements, but most notably:

"These disparities [in mortality] may be partially explained by pre-existing vulnerabilities in system-impacted populations, but likely also reflect the long-term negative effects of incarceration due to communicable diseases, chronic stress, social deprivation, malnutrition, and/or medical neglect, as well as the social conditions associated with previous incarceration, such as stigma, poverty, and barriers to housing, healthcare and employment."

First, the author cannot establish causality between exposure to carceral settings and death, or causes of death. Second, the study does not speaks to this swath of potential hypotheses and variables. Third, things like communicable diseases were actually pretty comparable across post-release and general populations in the findings.

Importantly, the authors should acknowledge that they cannot establish causality, let alone speculate about underlying reasons for causality. Also, justice-involved populations exhibit riskier lifestyles, including violent behavior, gang involvement, and substance use - all of which may contribute to these disparities in mortality.

2. The causes of death while incarcerated piqued my curiosity in terms of the validity and reliability of these data. It strikes me that prison administrators and criminal justice organizations might have incentive to manipulate the data in this case - for example, claiming a death was a suicide rather than due to violence perpetrated by another prisoner or by a guard. Can the authors speak a little bit more about whether there might be reliability or validity issues of this nature?

3. I would appreciate more discussion of the differences between data culled from DEPEN vs. SIGO. By that I do not mean how well records were matched, but more so - do these agencies have different missions, responsibilities, how do they collect these data similarly/differently?

4. It strikes me that this research runs counter to some work on United States prison populations, which finds that being in prison can be protective for some populations in terms of mortality. This might be worth a discussion. For example, please see the work of Chris Wildeman and Evelyn Patterson.

5. In general, the findings section was hard to follow and seemed unstructured/disorganized. I recommend cutting back on the amount of acronyms used and to organize the discussion of findings in order of interesting or meaningful comparisons. For example, a paragraph about gender differences, a paragraph about differences across recently vs. not recently incarcerated persons, a paragraph about differences across facility types, etc.

6. The authors should not claim that their findings from one state in Brazil could be generalizable (see conclusion). This is simply incorrect from a methodological standpoint. Also, bolstering this claim by saying that the mortality rates in prison are similar to other places in Brazil is a misleading justification of this point.

Reviewer #3: The following paper is ambitious in its goal to provide overall and cause-specific estimates of death rates during and following incarceration in Brazil. These estimates were compared to non-incarcerated residents Nevertheless, by linking the national mortality database and prison records, the authors found that deaths in custody were more than twice as high as deaths reported. While I commend the authors for breadth of the work, I found myself confused at times, regarding which populations were included or excluded from the analyses. Further, the methodology utilized to undertake the analysis requires much more detail than provided in the manuscript. To this end, citations would be helpful. My general recommendation is that the authors focus on mortality during incarceration (or after incarceration), but not both in the same paper. I found it overwhelming, and limiting it to such would allow the authors to dedicate more space to providing details regarding the methodology and underlying assumptions. Regardless, the findings add to this literature and I did think the results of the mortality levels during and after incarceration increase the knowledge to the general area. I enumerate my specific concerns regarding the manuscript below.

1. Describe how you projected the formerly incarcerated population in more detail. Right now, I understand that the authors stratified person-years by release year of the cohort, but I do not know anything about how or why a person exited the formerly incarcerated population.

2. Relatedly, it is not clear how the authors distinguished formerly incarcerated individuals with recent incarceration from the comparison group of the general population.

3. Please explain more details regarding the estimation of the age structure.

4. For the formerly incarcerated persons, the population only seems to change over time when persons die. However, there is certainly the risk of reincarceration. You mention this as means for individuals to be censored in the Pre-processing of SIGO incarceration database section, but it is not clear. I am guessing that the prison data contained this information at the individual level, however, my understanding is that you used summary level data. Please help me understand.

5. The differences in causes of death by facility make me question the assumption regarding each facility having the same age structure. Is there another option? That is, do you have wide age bins for each facility type?

6. I noted above that at times I got lost regarding the population included or excluded in analyses. I think this can easily be solved if the authors reiterate the population included/excluded. It would also be helpful, if the authors decide to keep both analyses, to partition the details of each piece in the data & methods and results sections. For example, describe the data and methods for the estimation of rates during incarceration, and then separately describe the data and methods for the post-incarceration mortality. It may be that the majority of my concerns can be taken care of by doing this.

7. I keep coming back to the decision to censor individuals upon movement to a different facility. It makes sense when thinking about facility specific death rates. However, part of the argument regarding deaths relates to the exposure to the settings, which makes me wonder about cumulative exposure in correctional settings. Further, one of the issues above regarding the formerly incarcerated population becomes less clear. For each population, does the movement censor the observation? It cannot because there are the release cohorts. I think I just need clearer depiction in the text.

8. In the abstract, the authors use the term "excess incarceration-associated mortality". When I read the term excess with mortality, I immediately think of deaths in excess of the expected. I do not think the authors seek to communicate such primarily because they do not do such, my understanding is that their study sets the foundation for future work. That is, this study serves as a baseline. I understand that the death rates found exceed that reported by the government, but as the authors also state, this is due to underreporting and insufficient data.

Any attachments provided with reviews can be seen via the following link:

[LINK]

Dear Dr. Andrews,

Thank you very much for re-submitting your manuscript "All-cause and cause-specific mortality during and following incarceration in Brazil: a retrospective cohort study" (PMEDICINE-D-21-02293R2) for review by PLOS Medicine.

I have discussed the paper with my colleagues and the academic editor and it was also seen again by the reviewers. I am pleased to say that provided the remaining editorial and production issues are dealt with we are planning to accept the paper for publication in the journal.

The remaining issues that need to be addressed are listed at the end of this email. Any accompanying reviewer attachments can be seen via the link below. Please take these into account before resubmitting your manuscript:

[LINK]

***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.***

In revising the manuscript for further consideration here, please ensure you address the specific points made by each reviewer and the editors. In your rebuttal letter you should indicate your response to the reviewers' and editors' comments and the changes you have made in the manuscript. Please submit a clean version of the paper as the main article file. A version with changes marked must also be uploaded as a marked up manuscript file.

Please also check the guidelines for revised papers at http://journals.plos.org/plosmedicine/s/revising-your-manuscript for any that apply to your paper.

We hope to receive your revised manuscript within 1 week. Please email us (plosmedicine@plos.org) if you have any questions or concerns.

We ask every co-author listed on the manuscript to fill in a contributing author statement. If any of the co-authors have not filled in the statement, we will remind them to do so when the paper is revised. If all statements are not completed in a timely fashion this could hold up the re-review process. Should there be a problem getting one of your co-authors to fill in a statement we will be in contact. YOU MUST NOT ADD OR REMOVE AUTHORS UNLESS YOU HAVE ALERTED THE EDITOR HANDLING THE MANUSCRIPT TO THE CHANGE AND THEY SPECIFICALLY HAVE AGREED TO IT.

Please ensure that the paper adheres to the PLOS Data Availability Policy (see http://journals.plos.org/plosmedicine/s/data-availability), which requires that all data underlying the study's findings be provided in a repository or as Supporting Information. For data residing with a third party, authors are required to provide instructions with contact information for obtaining the data. PLOS journals do not allow statements supported by "data not shown" or "unpublished results." For such statements, authors must provide supporting data or cite public sources that include it.

To enhance the reproducibility of your results, we recommend that 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. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols

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.

Please note, when your manuscript is accepted, an uncorrected proof of your manuscript will be published online ahead of the final version, unless you've already opted out via the online submission form. If, for any reason, you do not want an earlier version of your manuscript published online or are unsure if you have already indicated as such, please let the journal staff know immediately at plosmedicine@plos.org.

If you have any questions in the meantime, please contact me or the journal staff on plosmedicine@plos.org.  

We look forward to receiving the revised manuscript by Aug 30 2021 11:59PM.   

Sincerely,

Callam Davidson,

Associate Editor 

PLOS Medicine

plosmedicine.org

------------------------------------------------------------

Requests from Editors:

Please state that your study did not have a pre-specified analysis plan in the methods section.

Please include your study design (retrospective cohort study) in both your abstract and methods, as it currently only appears in your title and your conclusions.

Line 45: The final line of the background section of your abstract should clearly state the study question. Please add an additional line to this effect.

Line 114: Please remove the second bullet point in the ‘What do these findings mean?’ section of your author summary, as I feel it is too broad a statement to be included here and is better placed in the discussion where a more nuanced approach can be taken.

Line 566: Please include ‘to our knowledge’ whenever making claims of primacy (‘As the first systematic study’).

Figure S9: Please define what your error bars show in the figure legend.

References 20, 28, and 35: Insufficient material is presented to allow the reader to locate these sources – please provide more detail and cite using Vancouver style (see guidelines here: https://journals.plos.org/plosmedicine/s/submission-guidelines#loc-references)

Reference 52: Please cite preprints per the guidelines here -https://journals.plos.org/plosmedicine/s/submission-guidelines#loc-references

Please ensure that the study is reported according to the STROBE guideline, and include the completed STROBE checklist as Supporting Information. Please add the following statement, or similar, to the Methods: "This study is reported as per the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) guideline (S1 Checklist)."

The STROBE guideline can be found here: http://www.equator-network.org/reporting-guidelines/strobe/

When completing the checklist, please use section and paragraph numbers, rather than page numbers.

Comments from Reviewers:

Reviewer #1: Many thanks authors for their great effort to improve the manuscript. The authors have addressed my comments professionally. I am satisfied with the response and revision. Only a minor point, for table 1. all the categorical variables need to be summarised as count and percentage e.g. xx (yy%). Please just correct this and no need to come back to me. No other issues needing attention and I recommend publicaiton of the paper.

Reviewer #2: I appreciate the authors' attention to my comments, especially my concerns about causality. I am satisfied with the revisions they have carried out.

Any attachments provided with reviews can be seen via the following link:

[LINK]

Dear Dr Andrews, 

On behalf of my colleagues and the Academic Editor, Dr Vikram Patel, I am pleased to inform you that we have agreed to publish your manuscript "All-cause and cause-specific mortality during and following incarceration in Brazil: a retrospective cohort study" (PMEDICINE-D-21-02293R3) in PLOS Medicine.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. Please be aware that it may take several days for you to receive this email; during this time no action is required by you. Once you have received these formatting requests, please note that your manuscript will not be scheduled for publication until you have made the required changes.

In the meantime, please log into Editorial Manager at http://www.editorialmanager.com/pmedicine/, click the "Update My Information" link at the top of the page, and update your user information to ensure an efficient production process. 

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To enhance the reproducibility of your results, we recommend that 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. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols

Thank you again for submitting to PLOS Medicine. We look forward to publishing your paper. 

Sincerely, 

Callam Davidson 

Associate Editor 

PLOS Medicine