Peer Review History
| Original SubmissionMay 22, 2021 |
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PONE-D-21-16900Developing a machine learning-based tool to extend the usability of the NICHD BPD Outcome Estimator to the Asian populationPLOS ONE Dear Dr. Chou, 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 22 2022 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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Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access. We will update your Data Availability statement to reflect the information you provide in your cover letter. 4. Please include your full ethics statement in the ‘Methods’ section of your manuscript file. In your statement, please include the full name of the IRB or ethics committee who approved or waived your study, as well as whether or not you obtained informed written or verbal consent. If consent was waived for your study, please include this information in your statement as well. 5. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. [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: Partly ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: I Don't Know 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: Yes ********** 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: The article "Developing a machine learning-based tool to extend the usability of the NICHD Outcome Calculator to the Asian population," by Sandhu et al is an interesting application of the BPD Estimator to a local population of infants of Asian descent. Given disparities in outcomes based on racial demographics in infants with BPD, this idea is novel and may be useful in counseling families of Asian descent who have premature infants at risk for BPD. The developed model seems to have good predictive capability at 36 and 37 weeks', but there are some general concerns the authors should address. 1) Abstract: The objective of the study seems to be to apply the Estimator to an Asian demographic and evaluate its performance. However, the hypothesis and goal is unclear and should be revised. 2) Introduction: In general, when making statements about the incidence of BPD or inflammation as an etiology of BPD etc, references should be stated. Many BPD experts would argue about inflammation as being the most common cause of BPD, as it is largely considered to be of multi-factorial origin. Additionally, the authors claim the most significant intervention in preventing mortality and the incidence of BPD are systemic steroids. Although there is some evidence to support this claim, there was also a large NICHD study (Watterburg et al) that does not support this claim. On the whole, the authors should focus the introduction more on what is known about predictors of BPD in an Asian population, and the overall incidence in this group, to support their hypothesis more clearly. Methods: There should be a statement regarding approval by an Institutional Review Board. The methods are a little unclear. It seems that the Asian patient population was entered into the BPD Estimator using surrogate races, and that the prediction of the calculator was then compared to the observed outcomes at 36, 37 and 40 weeks'? The authors should clarify the approach some in the Methods section. How Asian descent was determined is an important factor in this study. Results: The validity of the model is enhanced by having a training and testing set. It could be further strengthened by testing it on an independent data set outside the institution if that is available. It may be interesting to evaluate the performance of the model based on the surrogate race/ethnicity used as input. For example, was there one race/ethnicity that is already in the calculator that performed well in the Asian descent population? Discussion: The tool included in the Discussion is useful. The authors should address how to apply this in a clinical setting. They should also include confidence limits around the point estimate. Reviewer #2: This interesting study assessed whether outcome prediction for Asian preterm born infants is possible using information hidden in prediction results for the other major racial groups in het NICHD BPD Outcome Estimator. Prediction of BPD development is an important topic, and investigating whether the risk can be predicted in infants with other descent then is used now in the Estimator is interesting. After reading the manuscript, I have some addition questions and comments. 1. In the methods section the authors described a retrospective study with prospective data collection, although at the end they describe that retrospective data collection was approved by the institutional review board. So it is unclear whether the data was collected prospectively or retrospectively? And where any exclusion criteria used for this study? 2. In the methods section the authors describe the part of machine learning-bases model development. First of all, good that the authors have performed internal validation (train and test set) as part of model development, however no information is presented whether the authors performed shrinkage of the predictor weights or regression coefficients. In addition, it is not clear which specific variables were used for model development. Are only the five severity categories are used? Or also the demographic data on GA, BW, respiratory support etc. And in case these demographic data is used, from which timepoint are these? 3. In the methods section no information is presented about the usage of any guidelines for development of prediction models? And no information is presented about how the authors dealed with missing data? 4. In the results section the authors described the inclusion of 842 premature newborns with a gestational age equal or less to 30 weeks and 6 days, although the inclusion criteria for this study described in the methods section, stated GA 30 weeks or less. 5. There is no information about how many infants developed BPD in the study cohort. 6. Table 3 missed information about which variables are included in the model. 7. In the results section information about the comparison of the outcomes from the machine-based learning models and the outcomes from the NICHD BPD Outcome Estimator is missing. In my opinion this is necessary to underlie the conclusion that extending the use of the Estimator to Asian population is feasible. In addition, no information is presented regarding the final predictor weights? 8. It can be suggested to add a calibration plot of model performances from both the train and test model in the results section. 9. From the discussion, no clear conclusion is presented. Only in the Abstract, a clear conclusion is presented. ********** 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: Yes: Michelle Romijn [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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PONE-D-21-16900R1Developing a machine learning-based tool to extend the usability of the NICHD BPD Outcome Estimator to the Asian populationPLOS ONE Dear Dr. Chou, 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 Jun 16 2022 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:
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, Jose Palma, Ph.D. Academic Editor PLOS ONE Journal Requirements: 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. [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 #1: (No Response) ********** 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: The authors have done a good job at addressing most Reviewer comments. However, there are still a few minor points that need to be addressed. Abstract: 1. The sentence that the Estimator does not apply to infants of Asian descent should be modified to say that is not known if it can be applied (I think this is the hypothesis)? 2. Is the hypothesis that the respiratory outcomes are interconnected between respiratory groups, or that the Estimator can be safely used to predict outcomes in infants of Asian descent? I think it is the latter? There is a grammatical error in this sentence. Introduction 1. Neonatology on Page 4 does not need to be capitalized. 2. There are grammatical errors in the Introduction. 3. The hypothesis needs to be clarified (as stated for the Abstract). Results 1. It may be important to know how many infants had missing race information on the facesheet as that may introduce some sampling bias. 2. On page 10, the word “had” should be removed from the sentence “At 37 and 40 weeks, CGA …” Discussion 1. The national pediatric hospitalization dataset should be capitalized if it is a specific dataset that is being named. 2. The statement “The use of LFNC indicates…residual resolving pulmonary hypertension associated with BPD” is misleading. Level of respiratory support alone is not used to determine PH risk. 3. The authors should carefully proofread the manuscript and correct grammatical errors prior to acceptance. ********** 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 [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 2 |
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Developing a machine learning-based tool to extend the usability of the NICHD BPD Outcome Estimator to the Asian population PONE-D-21-16900R2 Dear Dr. Chou, 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, Jose Palma, Ph.D. 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 #3: 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 #3: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #3: 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 ********** 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 ********** 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: The issues raised by the reviewer have been adequately addressed and the article is now ready for publication. ********** 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 ********** |
| Formally Accepted |
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PONE-D-21-16900R2 Developing a machine learning-based tool to extend the usability of the NICHD BPD Outcome Estimator to the Asian population Dear Dr. Chou: 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 Mr. Jose Palma Academic Editor PLOS ONE |
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