Peer Review History
| Original SubmissionAugust 11, 2020 |
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Transfer Alert
This paper was transferred from another journal. As a result, its full editorial history (including decision letters, peer reviews and author responses) may not be present.
PONE-D-20-25115 Validation and repurposing of the MSL-COVID-19 score for prediction of severe COVID-19 using simple clinical predictors in a triage setting: The Nutri-CoV score PLOS ONE Dear Dr. Aguilar-Salinas, 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 Nov 12 2020 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. Please include the following items when submitting your revised manuscript:
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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. We note that you state in your ethics statement in the online submission form "proceedings were approved by the INCMNSZ Research and Ethics Committee". Please clarify whether your ethics committee specifically approved this study and provide the full name of this committee. 3. Please include the date(s) on which you accessed the databases or records to obtain the data used in your study. 4. We note that you have indicated that data from this study are available upon request. PLOS only allows data to be available upon request if there are legal or ethical restrictions on sharing data publicly. For information on unacceptable data access restrictions, please see http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. 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We will update your Data Availability statement on your behalf to reflect the information you provide. 5. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. Please see the following video for instructions on linking an ORCID iD to your Editorial Manager account: https://www.youtube.com/watch?v=_xcclfuvtxQ 6. Please ensure that you refer to Figure 2 in your text as, if accepted, production will need this reference to link the reader to the figure. [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? 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 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 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 ********** 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: Yes ********** 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: I have a number of concerns regarding statistical design, analysis, and representation. I will try to go in order of line number. Line 112. It is unclear to me whether or not the univariate analyses influenced which variables were used in the multivariable model which used BIC for model selection. For example, were only variables that were considered significantly associated with the outcome (p<0.05) used in the multivariable analysis? Line 116-119. Was the data used to make/decide the 4 risk group stratification the same data that was used to validate it? Or was the validation set used to validate it? Line 120. For bootstrapping, I assume the ordinary bootstrap method was used. Which confidence interval was used for the provided metrics? Percentile? BCA? etc. It is worth mentioning that the validation functions in the rms package are not intended to be used in complicated modeling designs wherein decisions such as cutoffs for continuous variables, risk stratification, etc. with the same data that is used to validate it. The result, optimistic estimates for performance. Even if you use the bootstrap later because you are not including data-driven decisions in the bootstrap process. You will likely need to code the loop yourself to include these elements in the bootstrap process. Line 129 indicates that lambda is the tuning parameter of the Elastic-Net model, but this is only half true. Lambda is the penalty parameter in a LASSO model -- Elastic-Net adds in a mixture parameter, typically represented as alpha, that determines how much LASSO penalty and how much ridge penalty is used. Can the authors please tell me how much mix, if any between the two were used? This does not have to appear in the main paper, but some more details in an appendix or similar would be helpful. This includes how the hyperparameter optimization was done -- exhaustive grid search, randomly sampled xxx points from the hypergrid, etc. Line 131. glmnet instead of gmlnet. Line 132. For design, it appears that there may be a typo with regards to the number of folds, 20. If k is indeed 20, then within the CV routine 1/20th of the sample used as the test set at any given point. This amounts to about 58 patients, approximately 6 of which will be events. In my view, this is too few. I strongly recommend that the authors instead use a 10 fold or perhaps a 5 fold CV. Line 136. likelihood ratios instead of likelihood rations Line 174, 178, 187. why are the c-statistics and AUC different? did you have censoring? if so, the AUC might have been calculated using a method that ignores this. Line 190. Was the cutoff created in the training cohort only? Line 190 - 197. Are these estimates all from the validation cohort? Line 259 "thus increasing the external validity of our model" how? including more variables does not necessarily increase the external validity. would remove this. Line 268. "the model is likely to have adequate performance when applied in external datasets" you have no external data to suggest this. Missing limitation elements from discussion. For example, the study is skewed in the direction of your model because the data used to validate your model is very similar to the data used to fit/train your model. The other models under evaluation here were, if my understanding is correct, were derived using data from other institutions. If you compare how well their respective papers said they would perform and compare that to how well they performed on your data, you will likely see that their models did not perform as well. The limitations here as I see it is three-fold: 1) repeated misuse of the bootstrap method, specifically not including cutoff and risk stratification inside the validation; 2) too many folds. i suspect that you will be better off using 5-fold or some such CV. Repeating the CV routine many times (repeated k-fold CV) would be one step better than that.; 3) recognize in the discussion that your model will inherently do better than models that were created outside of your institution. Please also remake the plots a higher quality file as they are not legible in their current state. Reviewer #2: In their paper " Validation and repurposing of the MSL-COVID-19 score for prediction of severe COVID-19 using simple clinical predictors in a triage setting: The Nutri-CoV score", Bello-Chavolla et al. develop prediction scores for several aspects of the COVID-19 disease using time-to-event models and present applications. In principle, the analysis is sound. However, I have one major point the authors have to address and a couple of minor comments. Major point: - In time-to-event models it is very important to define the time-scale exactly. Time zero is not defined in the paper. The authors write "We included patients aged >18 years with complete clinical data from March 16th to June 4th, 2020 who were evaluated at triage at the Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMNSZ), a COVID-19 reference center in Mexico City...". I would therefore conclude that the timepoint of presentation is taken to be timepoint zero. This would be problematic as it creates an immortal time bias for the presenting population. The interpretation of the model would then only be applicable in a setting where the same pattern of presenting at the triag unit would be present. A more logical timepoint zero would be the onset of symptoms, a population that would be well-defined. At the very least the authors need to perform a sensitivy analysis for such model, using time-dependent covariates to account for the immortal time bias Minor points: - Wording l. 81: "all proceedings" is somewhat unclear (all analyses?) - l. 107: It is only meaningful to to perform the "outcome assessment" at several time horizons which need to be specified. It is not meaningful to use the data set "as is", i.e. only the presence of the outcome at any timepoint. - l. 112: As the assumptions are checked visually, the plot need to be supplied as a supplement. - l. 136 (and other places): The curves need to be evaluated at time horizons. These need to be clearly specified. - Some of the predictors are known to act non-linearly such as age. As penalized regression is used, the authors are advised to include non-linear termas, such as quadratic terms. - The authors should stress that the validation is internal and not external. The authors should also use test-data instead of validation data to avoid confusion when describing cross-validation (the cross-validation uses the validation data, evaluation is performed in the test data). - The model should be evaluated in a stratified way using the known risk groups, as this is highly relevant for practical application. - The authors need to provide a URL for the data set. ********** 6. 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: 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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Validation and repurposing of the MSL-COVID-19 score for prediction of severe COVID-19 using simple clinical predictors in a triage setting: The Nutri-CoV score PONE-D-20-25115R1 Dear Dr. Aguilar-Salinas, 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 for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. 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, Itamar Ashkenazi 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 ********** 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: Thank you for addressing the statistical concerns. I would just like to reiterate a concept that I including in my review of the paper. Which is that I suspect that even if this model were used at a similar institution, the efficacy observed will likely not agree with the efficacy reported in the paper. ********** 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: No |
| Formally Accepted |
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PONE-D-20-25115R1 Validation and repurposing of the MSL-COVID-19 score for prediction of severe COVID-19 using simple clinical predictors in a triage setting: The Nutri-CoV score Dear Dr. Aguilar-Salinas: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. 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. If we can help with anything else, please email us at plosone@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. Itamar Ashkenazi Academic Editor PLOS ONE |
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