Peer Review History

Original SubmissionNovember 9, 2019
Decision Letter - Nadia M Hamdy, Editor

PONE-D-19-31278

Gene Polymorphisms of Patatin-like phospholipase domain containing 3 (PNPLA3), Adiponectin, Leptin in Diabetic Obese Patients

PLOS ONE

Dear Dr Hafez,

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.

We would appreciate receiving your revised manuscript by Feb 01 2020 11:59PM. When you are 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.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter.

To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

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). This letter should be uploaded as separate file and labeled 'Response to Reviewers'.
  • A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'.
  • An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'.

Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out.

We look forward to receiving your revised manuscript.

Kind regards,

Nadia M Hamdy, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments:

Dear

English language needs revision and paragraphs need rephrasing as well

More details are required in the methods

Limitations and future prospective are to be there

Journal Requirements:

When submitting your revision, we need you to address these additional requirements:

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Reviewers' comments:

[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 to be viewed.]

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 us at figures@plos.org. Please note that Supporting Information files do not need this step.

Attachments
Attachment
Submitted filename: Dear.pdf
Revision 1

Gene Polymorphisms of Patatin-like phospholipase domain containing 3 (PNPLA3), Adiponectin, Leptin in Diabetic Obese Patients

1. Comment: ʺEnglish language needs revision and paragraphs need rephrasing as wellʺ

Response: the whole manuscript starting from the title was revised by English native speaker and many paragraphs were rephrased or almost rewritten.

2. Comment: ʺMore details are required in the methodsʺ

Response: each protocol for each parameter was written as a separate item with separate title and the details for each technique was added including principle, steps, kit manufacturer and the machine used.

3. Comment: ʺLimitations are to be thereʺ

Response: a title of (Limitations of the study) was added after the conclusion section and all expected limitations were mentioned under this section.

4. Comment: ʺFuture prospective are to be thereʺ

Response: a title of (Future Prospective) was added after the limitations of the study section and all recommended future work was mentioned under this section.

*All changes done in the manuscript according to reviewer comments are highlighted in yellow and English language and grammar revisions are done but not highlighted as they are frequent.

Attachments
Attachment
Submitted filename: Respnse to reviewers.docx
Decision Letter - Nadia M Hamdy, Editor

PONE-D-19-31278R1

Gene Polymorphisms of Patatin-like phospholipase domain containing 3 (PNPLA3), Adiponectin, Leptin in Diabetic Obese Patients

PLOS ONE

Dear Dr Hafez,

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.

In addition to the Academic Editor's comments from the previous decision, we have now obtained an assessment from an external reviewer. Please find their comments included below.

We would appreciate receiving your revised manuscript by May 10 2020 11:59PM. When you are 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.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter.

To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

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). This letter should be uploaded as separate file and labeled 'Response to Reviewers'.
  • A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'.
  • An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'.

Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out.

We look forward to receiving your revised manuscript.

Kind regards,

Artur Arikainen, Associate Editor, PLOS ONE

on behalf of

Nadia M Hamdy, Ph.D.

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: (No Response)

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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: (No Response)

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: (No Response)

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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: (No Response)

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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: (No Response)

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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: 1. English editing is highly recommended throughout the manuscript.

2. Abstract:

- Rephrase line 35-37.

3. Introduction:

- Add more references on PNPLA3, lane 76

4. Methods:

- “Fresh venous blood samples” explain what do you mean by “fresh” this is not an accurate word here, explain?? And rephase.

- Add references for PNPLA3 amplification and genotyping sections.

- A figure for PNPLA3 results should be added.

5. Results:

- include a table with the demographic data of all participants.

- Rephrase lines from 190-194 to be more simple and comprehensive.

-

6. Discussion:

- Authors should compare results of genotypes distribution of the genes with other studies in Egypt, specially in controls.

- Authors should compare polymorphism results of all genes with those of other studies.

7. Limitations of the study:

- State clearly that the small sample numbers is a limitation in the study of polymorphism of these genes in the herein study.

8.

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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 to be viewed.]

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 us at figures@plos.org. Please note that Supporting Information files do not need this step.

Attachments
Attachment
Submitted filename: REPLY.docx
Revision 2

Response to Reviewers

Gene Polymorphisms of Patatin-like phospholipase domain containing 3 (PNPLA3), Adiponectin, Leptin in Diabetic Obese Patients

1. Comment: English editing is highly recommended throughout the manuscript ʺ

Response: the whole manuscript was revised.

2. Comment: ʺAbstract: Rephrase line 35-37ʺ

Response: lines 34-37 were rephrased.

3. Comment: ʺIntroduction: Add more references on PNPLA3, line 76ʺ

Response: 3 more references were added, lines 78, 79.

4. Comment: ʺ Methods: Fresh venous blood samples” explain what do you mean by “fresh” this is not an accurate word here, explain?? And rephraseʺ

Response: it was written by mistake and it is modified into five ml

5. Comment: ʺ Methods: “Add references for PNPLA3 amplification and genotyping sections. ʺ

Response: the reference is added (Dutta, 2011) line 128

6. Comment: ʺ Methods: “A figure for PNPLA3 results should be added.ʺ

Response: the gel electrophoresis pictures were added (figure 1 for PCR product at line 134) and (figure 2 for genotying, line 153).

7. Comment: ʺResults: include a table with the demographic data of all participants ʺ

Response: We put it at the supporting information files.

8. Comment: ʺResults: Rephrase lines from 190-194 to be more simple and comprehensive ʺ

Response: most of results paragraphs were made simpler and more comprehensive

9. Comment: ʺDiscussion: Authors should compare results of genotypes distribution of the genes with other studies in Egypt, especially in controls.

Response: for PNPLA3 genotyping there is only one study was done in Egypt which was on Hepatitis C infection and liver fibrosis. We added citation for this study in discussion section with comparison between control groups of this study and our study. So this is the first time to assess PNPLA3 genotype frequency in diabetic obese patients in Egypt. ADIPOQ and LEP gene polymorphism which were done in Egypt were targeting other sites other than our target on ADIPOQ rs266729 and Leptin rs2167270.

10. Comment: ʺ Discussion: Authors should compare polymorphism results of all genes with those of other studies ʺ

Response: Regarding PNPLA3 genotyping, we compared among our study and other different studies but there are very few studies which performed this polymorphism in diabetic obese patients but we mentioned them in discussion. Regarding ADIPOQ and LEP genotyping, were compared with different mentioned studies in the discussion with new citations.

11. Comment: ʺLimitations of the study: State clearly that the small sample numbers is a limitation in the study of polymorphism of these genes in the herein studyʺ

Response: the small sample size limitation is stated and recommendations were restated.

*All changes done in the manuscript according to reviewer comments are highlighted in blue and English language and grammar revisions are done.

Attachments
Attachment
Submitted filename: Respnse to reviewers.docx
Decision Letter - Nadia M Hamdy, Editor

Gene Polymorphisms of Patatin-like phospholipase domain containing 3 (PNPLA3), Adiponectin, Leptin in Diabetic Obese Patients

PONE-D-19-31278R2

Dear Dr. Hafez,

We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements.

Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication.

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With kind regards,

Nadia M Hamdy, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Formally Accepted
Acceptance Letter - Nadia M Hamdy, Editor

PONE-D-19-31278R2

Gene Polymorphisms of Patatin-like phospholipase domain containing 3 (PNPLA3), Adiponectin, Leptin in Diabetic Obese Patients

Dear Dr. Hafez:

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

Professor Nadia M Hamdy

Academic Editor

PLOS ONE

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