Risk factors associated with congenital anomalies among newborns in southwestern Ethiopia: A case-control study

Soressa Abebe; Girmai Gebru; Demisew Amenu; Zeleke Mekonnen; Lemessa Dube

doi:10.1371/journal.pone.0245915

Peer Review History

Original SubmissionJuly 25, 2020
7 Oct 2020 Decision Letter - Linglin Xie, Editor PONE-D-20-23170 Risk Factors Associated with Congenital Anomalies among Newborns in Southwestern Ethiopia: A case-control study PLOS ONE Dear Dr. Geneti, 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 12/06/2020. 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: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. 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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols We look forward to receiving your revised manuscript. Kind regards, Linglin Xie 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 https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. Please include additional information regarding the checklist and questionnaire used in the study and ensure that you have provided sufficient details that others could replicate the analyses. For instance, if you developed a questionnaire and/or checklist as part of this study and it is not under a copyright more restrictive than CC-BY, please include a copy, in both the original language and English, as Supporting Information. 3. Thank you for stating the following in the Competing Interests section: 'The authors, Mr. Soressa Abebe and Dr. Girmai Gebru receive salary from Addis Ababa University, Dr. Demisew Amanu, Professor Zeleke Mekonnen and Mr. Lemessa Dube receive salary from Jimma University. The authors have declared that no competing interests exist.' a. Please confirm that this does not alter your adherence to all PLOS ONE policies on sharing data and materials, by including the following statement: "This does not alter our adherence to PLOS ONE policies on sharing data and materials.” (as detailed online in our guide for authors http://journals.plos.org/plosone/s/competing-interests). If there are restrictions on sharing of data and/or materials, please state these. Please note that we cannot proceed with consideration of your article until this information has been declared. b. Please include your updated Competing Interests statement in your cover letter; we will change the online submission form on your behalf. Please know it is PLOS ONE policy for corresponding authors to declare, on behalf of all authors, all potential competing interests for the purposes of transparency. PLOS defines a competing interest as anything that interferes with, or could reasonably be perceived as interfering with, the full and objective presentation, peer review, editorial decision-making, or publication of research or non-research articles submitted to one of the journals. Competing interests can be financial or non-financial, professional, or personal. Competing interests can arise in relationship to an organization or another person. 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Authors’ affiliations should reflect the institution where the work was done (if authors moved subsequently, you can also list the new affiliation stating “current affiliation:….” as necessary). [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No ****** 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: 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 ****** 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: Major comments: This article is a retrospective study on the association between maternal exposure to risk factors during early pregnancy and the development of congenital anomalies. The study was conducted based on data collected from six selected hospitals in southwestern Ethiopia through two years. The data analysis provided exciting data and analysis on the possible correlation between possible risk factors and congenital anomalies. One issue with the experimental design is the sampling method to select the six hospitals. The authors mentioned that the hospitals were selected purposively based on their capacity to carry out the required assessment. This non-randomness of sampling may sharply limit the generalization of the conclusion to newborns in the whole area. This point has been mentioned in the “Limitation of the Study” section. But without providing more evidence that these hospitals can represent all the hospitals in the area, the authors should be more careful when they tried to generalize the conclusions. One major issue with the statistical analyses is that the author conducted multiple tests during their studies, while they used a threshold P-value of 0.05 for significance, which is a typical cut-off when doing a single test. I would suggest that they use an adjusted p-value instead to control the false positive rate for this multiple test case. Also, it would be more informative if a formula for the final regression model with corresponding coefficients was provided beside the descriptions. Also, there should be a separate section where data availability is described. The authors should show where the original questionnaire and raw data can be found for their readers. Minor comments: Table 7: It would be clearer if the variable name is in a separate column from the variable levels. ****** 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 [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. https://doi.org/10.1371/journal.pone.0245915.r001
Revision 1
10 Dec 2020 Author Response • A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled ‘Response to Reviewers.’ Comment accepted. The rebuttal letter that responds to each point raised by the academic editor and reviewer(s) is included. The letter is uploaded as a separate file and labeled ‘Response to Reviewers’ • A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled ‘Revised Manuscript with Track Changes’ � Comment accepted. The changes made to the original version is highlighted in orange color in the revised manuscript. The file is labeled as Revised Manuscript with Track Changes’. • An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled ’‘Manuscript'. � Comment accepted. The unmarked version of the revised paper without tracked changes labeled as ‘Manuscript’ • If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. The financial disclosure and updated statement included in the cover letter 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. Dear editor, � We thank you for reminding us to check our manuscript in lines with PLOS ONE's style requirements. We checked journal formats and corrected it accordingly. 2. Please include additional information regarding the checklist and questionnaire used in the study and ensure that you have provided sufficient details that others could replicate the analyses. For instance, if you developed a questionnaire and/or checklist as part of this study and it is not under copyright more restrictive than CC-BY, please include a copy, in both the original language and English, as Supporting Information. Dear editor, We uploaded the questionnaire written in English, Afaan Oromo, and Amharic languages as supporting information. � We confirm this does not alter our adherence to PLOS ONE policies on sharing data and materials. Funding This study obtained findings s from Addis Ababa University and Jimma University for data collection. The funding universities do not have any role in the study's design, data collection, analysis and interpretation of data and writing of the manuscript. b. Please include your updated Competing Interests statement in your cover letter; we will change the online submission form on your behalf. � We included the updated competing interest statement in our cover letter. � The corresponding author declared on behalf of all authors � The corresponding author linked his ORCID iD � We included the updated list of authors and their corresponding affiliation as per request. Response to Reviewers' comments: We thank you for your invaluable comments, suggestions and recommendations. We have amended the manuscript based on your constructive comments as follows: We thank you for raising this critical comment; although we mentioned purposive selection of the hospitals, we have included all hospitals except one. So, we feel it can be generalizable to the whole study area. Besides our indication of the limitations, we have now updated the revised manuscript indicating that almost all hospitals six out of seven in the study area were assessed. Thank you again for your constructive comment. We just considered P-value for candidate selection. We used the 95% CI interval for the final decision to minimize complications/false positive rate. If the confidence interval includes a null value, we declared not statistically significant. Thank you for the comment. We Now included the final regression formula as per your invaluable recommendation as follows. log⁡(odds of CA)=-1.997+1.234(drug use)+1.368 (pesticide exposure)+1.412 (passive smoker)-0.358 (folic acid)+1.349 (history of CA+0.729 (surface water)+1.082 (no antenatal care visits)+0.752 (1 to 3 antenatal care visit). � Thanks for the suggestion about the availability of data and materials. We uploaded all required documents as supporting information including consent form and questionnaire written in the English, Afaan Oromo, and Amharic languages. As per your recommendation and PLOS ONE standard of minimal data set, particularly in our manuscript, we a Availability of data and materials All relevant data are within the manuscript and its supporting information. We have corrected. Attachments Attachment Submitted filename: Reponse to Reviewers.docx https://doi.org/10.1371/journal.pone.0245915.r002
16 Dec 2020 Decision Letter - Linglin Xie, Editor PONE-D-20-23170R1 Risk factors associated with congenital anomalies among newborns in southwestern Ethiopia: A case-control study PLOS ONE Dear Dr. Geneti, 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 01/15/2021. 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: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. 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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols We look forward to receiving your revised manuscript. Kind regards, Linglin Xie 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 #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: N/A ****** 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 modifications are reasonable to all comments except the one for the multiple test issue. The multiple test issue would not be solved by replacing p-values with significance intervals. If a 95% CI is used, then significance level is still 5%. The authors should also adjust their significance levels and choose a more restrict CI to adjust for the multiple test issue. ****** 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. https://doi.org/10.1371/journal.pone.0245915.r003
Revision 2
7 Jan 2021 Author Response Dear editor, We thank you for your invaluable comments, suggestions and recommendations in our revised manuscript, Now we included responses and corrections as per your comments and suggestions for each point raised either by the editor or the reviewer’s as follows • A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. � The rebuttal letter is prepared and uploaded as a separate file and labeled ‘Response to Reviewers’ • A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes' � The changes made to the original version are highlighted in orange color in the revised manuscript. The file is labeled as ‘Revised Manuscript with Track Changes’. • An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. � The unmarked version of the revised paper without tracked changes labeled as ‘Manuscript’ • If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. � No changes made 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: N/A ________________________________________ 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 modifications are reasonable to all comments except the one for the multiple test issue. The multiple test issue would not be solved by replacing p-values with significance intervals. If a 95% CI is used, then significance level is still 5%. The authors should also adjust their significance levels and choose a more restrict CI to adjust for the multiple test issue. Comment accepted: Dear reviewer, we thank you for raising this critical comment. It is acceptable that instead of looking at the 95% CI, logistic regression analyses was repeated by using a narrower interval (e.g. 99% CI) to reduce the significance level from 0.05 to 0.01. Setting a higher significance threshold for individual comparisons to compensate for the number of inferences was being made. This is one way that we can reduce the probability of getting a false positive. Therefore, as per your invaluable comment, we corrected and adjusted the multiple tests to 99% confidence interval and significance level of 0.01(1%) and indicated it in the revised manuscript in (table 6 and 7) as well as in the text under independent predicator (risk factors) of congenital anomalies. Interdependent risk factors adjusted for multiple tests are indicated and uploaded as supporting information as S2 Table for your considerations. Best regards! Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0245915.r004
11 Jan 2021 Decision Letter - Linglin Xie, Editor Risk factors associated with congenital anomalies among newborns in southwestern Ethiopia: A case-control study PONE-D-20-23170R2 Dear Dr. Geneti, 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, Linglin Xie Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0245915.r005
Formally Accepted
18 Jan 2021 Acceptance Letter - Linglin Xie, Editor PONE-D-20-23170R2 Risk factors associated with congenital anomalies among newborns in southwestern Ethiopia: A case-control study Dear Dr. Abebe: 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. Linglin Xie Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0245915.r006

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