Peer Review History
| Original SubmissionJuly 18, 2025 |
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PONE-D-25-38965-->-->Can physiological network mapping reveal pathophysiological insights into emerging diseases? Lessons from COVID-19-->-->PLOS ONE?> Dear Dr. Mani, 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 Oct 13 2025 11:59PM. If you will need more time than this 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.
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Kind regards, Siddharth Gosavi, MBBS, MD Internal Medicine,DNB Internal Medicine Academic Editor PLOS ONE Journal requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and 2. In the online submission form, you indicated that [Data will be made available upon reasonable request.]. All PLOS journals now require all data underlying the findings described in their manuscript to be freely available to other researchers, either 1. In a public repository, 2. Within the manuscript itself, or 3. Uploaded as supplementary information. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If your data cannot be made publicly available for ethical or legal reasons (e.g., public availability would compromise patient privacy), please explain your reasons on resubmission and your exemption request will be escalated for approval. 3. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. Additional Editor Comments: The study is well written and addresses a clinically relevant question with network analyses of clinical data. Targeted revisions are required to ensure reproducibility, interpretability, and statistical rigour. 1. Network construction and reproducibility • Correlation networks and the Bonferroni edge-selection rule are described. Specify which correlation coefficient was used (for example Pearson or Spearman), any preprocessing applied before correlation, the missing-data policy, and the effective sample size for each network and each δ-axis. If pairwise deletion was used, report edgewise sample sizes. This allows readers to judge robustness and reproducibility. • Age-matched and O₂-matched networks are described, and a prior method is cited. For reproducibility in this cohort, add a summary of the implementation: matching approach and ratio, calliper or tolerance used, balance diagnostics (for example pre- and post-match standardised mean differences and the balance criterion), matched sample sizes and any excluded cases, and confirmation that panels labelled as matched used only the matched sets. These choices determine which patients are retained and can change which correlations pass the edge rule. • Define the admission “consciousness” scale and coding, since it appears in tables and as a δ-axis. • Make figure captions self-contained by adding sample sizes, correlation type, the edge-selection criterion or threshold, and whether the panel shows unmatched data or which matched set. This improves interpretability for readers consulting figures independently of the text. 2. Survival and prognostic analyses • Pre-specify multiplicity control and report adjusted p values within families, for example BH-FDR or Holm. Treat the four Mann-Whitney tests as one family and the four Cox tests as a second, and indicate which results remain significant after adjustment. This ensures that reported findings are robust to multiple testing. • State the time origin for survival analyses, censoring rules, and whether follow-up is complete to 30 days. This is required for reproducibility and correct interpretation. • δ is analysed in univariable Cox models, with some sensitivity checks (for example age- and O₂-matched networks). These do not replace multivariable adjustment. If an independent prognostic claim is to be retained, run multivariable Cox models for each retained δ-axis, adjusting for a small, pre-specified set of clinical covariates such as age, an oxygenation measure, and a renal function measure. Check the proportional hazards assumption and report hazard ratios with 95% confidence intervals. This establishes whether δ adds prognostic information beyond basic clinical factors. • If predictive language is to be retained, add internal validation using bootstrap or k-fold methods, and report discrimination and calibration (for example C index or time-dependent AUC at 30 days, plus a calibration plot or Brier score). Clarify whether δ was computed in-sample or against a fixed reference and avoid information leakage by computing δ within folds or using a fixed reference. If validation is not added, temper wording to association and avoid terms such as “predicts” or “independent predictor”. I congratulate the authors for this research and manuscript which describes the application of a novel network analysis tool (Parenclitic Network Analysis) to the dataset of COVID-19 patients in Iran. Authors have employed this tool to assess the physiological network connectivity/deviation of a group of patients with COVID-19 and the association with survival. Authors reported that overall, COVID-19 patients that survived after 30 days have similar physiological network connectivity compared to those that did not survive although these survivor groups showed different clusters. Specifically, survivors’ serum potassium level which may reflect acid-base balance amongst other physiology is more related to arterial pH in survivors while in non-survivors, the Blood Urea Nitrogen (BUN) is the main driver of serum potassium level with less deviation in survivors along the BUN-potassium axis. I have some comments Major 1. Methods, Parenclitic deviation section: It is not clear whether the survivors or the non-survivors were used as reference population. Please rephrase or clarify. Also, in this session, please consider referencing various recent works that have used similar techniques with in-depth description and representation of the parenclitic analysis for clarity. 2. Table 2: It is not clear how consciousness was measured. Please include a definition or description of this in the methodology or as supplementary material. Also, include the unit of measurement for the variables presented. 3. The authors have not performed any analysis to assess whether the difference in correlation or physiological network deviation is linked with 30-day survivor. Please clarify why as this is a major step that would have confirmed whether the techniques is suitable for predicting mortality. 4. Also, the data on mechanical ventilation is jot Minor 1. It is not explicitly clear in the methods section about the population that the study population are either patients admitted to the ICU or otherwise. Please make this clear. 2. Please include the full spellings of the abbreviations in the tables below the tables for clarity. 3. Table 1: consider the convention of providing the counts (%) for categorical variables. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? Reviewer #1: Partly Reviewer #2: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: No Reviewer #2: Yes ********** 3. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: No Reviewer #2: Yes ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes ********** Reviewer #1: The study is well written and addresses a clinically relevant question with network analyses of clinical data. Targeted revisions are required to ensure reproducibility, interpretability, and statistical rigour. 1. Network construction and reproducibility • Correlation networks and the Bonferroni edge-selection rule are described. Specify which correlation coefficient was used (for example Pearson or Spearman), any preprocessing applied before correlation, the missing-data policy, and the effective sample size for each network and each δ-axis. If pairwise deletion was used, report edgewise sample sizes. This allows readers to judge robustness and reproducibility. • Age-matched and O₂-matched networks are described, and a prior method is cited. For reproducibility in this cohort, add a summary of the implementation: matching approach and ratio, calliper or tolerance used, balance diagnostics (for example pre- and post-match standardised mean differences and the balance criterion), matched sample sizes and any excluded cases, and confirmation that panels labelled as matched used only the matched sets. These choices determine which patients are retained and can change which correlations pass the edge rule. • Define the admission “consciousness” scale and coding, since it appears in tables and as a δ-axis. • Make figure captions self-contained by adding sample sizes, correlation type, the edge-selection criterion or threshold, and whether the panel shows unmatched data or which matched set. This improves interpretability for readers consulting figures independently of the text. 2. Survival and prognostic analyses • Pre-specify multiplicity control and report adjusted p values within families, for example BH-FDR or Holm. Treat the four Mann-Whitney tests as one family and the four Cox tests as a second, and indicate which results remain significant after adjustment. This ensures that reported findings are robust to multiple testing. • State the time origin for survival analyses, censoring rules, and whether follow-up is complete to 30 days. This is required for reproducibility and correct interpretation. • δ is analysed in univariable Cox models, with some sensitivity checks (for example age- and O₂-matched networks). These do not replace multivariable adjustment. If an independent prognostic claim is to be retained, run multivariable Cox models for each retained δ-axis, adjusting for a small, pre-specified set of clinical covariates such as age, an oxygenation measure, and a renal function measure. Check the proportional hazards assumption and report hazard ratios with 95% confidence intervals. This establishes whether δ adds prognostic information beyond basic clinical factors. • If predictive language is to be retained, add internal validation using bootstrap or k-fold methods, and report discrimination and calibration (for example C index or time-dependent AUC at 30 days, plus a calibration plot or Brier score). Clarify whether δ was computed in-sample or against a fixed reference and avoid information leakage by computing δ within folds or using a fixed reference. If validation is not added, temper wording to association and avoid terms such as “predicts” or “independent predictor”. 3. Data availability • PLOS ONE requires that data needed to reproduce the findings be publicly available at publication, with rare, justified exceptions. The current “available on request” statement does not comply. Revise the Data Availability Statement to provide a public repository link with a persistent identifier for a de-identified dataset and, where applicable, the analysis code. If legal or ethical constraints apply, describe them, provide a controlled-access route, and make a minimal dataset publicly available. This aligns the manuscript with the journal’s open-data policy and enables verification and reuse. Reviewer #2: I congratulate the authors for this research and manuscript which describes the application of a novel network analysis tool (Parenclitic Network Analysis) to the dataset of COVID-19 patients in Iran. Authors have employed this tool to assess the physiological network connectivity/deviation of a group of patients with COVID-19 and the association with survival. Authors reported that overall, COVID-19 patients that survived after 30 days have similar physiological network connectivity compared to those that did not survive although these survivor groups showed different clusters. Specifically, survivors’ serum potassium level which may reflect acid-base balance amongst other physiology is more related to arterial pH in survivors while in non-survivors, the Blood Urea Nitrogen (BUN) is the main driver of serum potassium level with less deviation in survivors along the BUN-potassium axis. I have some comments Major 1. Methods, Parenclitic deviation section: It is not clear whether the survivors or the non-survivors were used as reference population. Please rephrase or clarify. Also, in this session, please consider referencing various recent works that have used similar techniques with in-depth description and representation of the parenclitic analysis for clarity. 2. Table 2: It is not clear how consciousness was measured. Please include a definition or description of this in the methodology or as supplementary material. Also, include the unit of measurement for the variables presented. 3. The authors have not performed any analysis to assess whether the difference in correlation or physiological network deviation is linked with 30-day survivor. Please clarify why as this is a major step that would have confirmed whether the techniques is suitable for predicting mortality. 4. Also, the data on mechanical ventilation is jot Minor 1. It is not explicitly clear in the methods section about the population that the study population are either patients admitted to the ICU or otherwise. Please make this clear. 2. Please include the full spellings of the abbreviations in the tables below the tables for clarity. 3. Table 1: consider the convention of providing the counts (%) for categorical variables. ********** 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: No Reviewer #2: 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.] 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. |
| Revision 1 |
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Can physiological network mapping reveal pathophysiological insights into emerging diseases? Lessons from COVID-19 PONE-D-25-38965R1 Dear Dr. Mani, 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. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact billing support . 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, Siddharth Gosavi, MBBS, MD Internal Medicine,DNB Internal Medicine Academic Editor PLOS ONE Additional Editor Comments (optional): Thank you for your response.I am happy personally with the justifications you have provided. Reviewers' comments: |
| Formally Accepted |
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PONE-D-25-38965R1 PLOS ONE Dear Dr. Mani, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. 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. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Siddharth Gosavi Academic Editor PLOS ONE |
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