Sleeping pattern and activities of daily living modulate protein expression in AMD

Kaushal Sharma; Ramandeep Singh; Suresh Kumar Sharma; Akshay Anand

doi:10.1371/journal.pone.0248523

Peer Review History

Original SubmissionSeptember 17, 2020
6 Nov 2020 Decision Letter - Alfred S Lewin, Editor PONE-D-20-29337 Sleeping pattern and activities of daily living modulate protein expression in AMD PLOS ONE Dear Dr. Anand, 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 evaluate the role of epigenetic changes in the onset and progression of AMD. Please submit your revised manuscript by Dec 21 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. 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We will update your Data Availability statement on your behalf to reflect the information you provide. 5.Thank you for stating the following in the Acknowledgments Section of your manuscript: [Department of Biotechnology (No. BT/PR17550/MED/30/1755/2016), New Delhi, India. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.] We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. 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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 ****** 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: The manuscript is interesting and well organized. The methods selected and applied for the analyzes are correct and adequate. As the rationale of the paper evaluates "Sleeping pattern and activities of daily living" it is also crucial to discuss the possible role of epigenetics in the onset and progression of AMD. Numerous papers have been published in the literature describing a possible role of epigenetic mechanisms in the etiopathogenesis of the disease. This topic should be included in both the introduction and discussion with the aim of improving the originality of the manuscript. To date, when studying multifactorial diseases it is very important to take into account the role of epigenetics. ****** 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.0248523.r001
Revision 1
26 Jan 2021 Author Response PONE-D-20-29337 Sleeping pattern and activities of daily living modulate protein expression in AMD Dear Editor We have addressed all the comments raised by the reviewers and modified the manuscript as per journal requirements. Please see revised manuscript for your kind consideration. Please evaluate the role of epigenetic changes in the onset and progression of AMD. Response: We have added the requisite literature to support our results of the manuscript. Thanks for valuable comment. Sincerely Akshay Anand, PhD Professor Neuroscience Research lab Department of Neurology PGIMER, Chandigarh, India. 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 Response: Thanks for comment. Manuscript has been changed as per the template provided. 2. In your Methods section, please provide additional information about the participant recruitment method and the demographic details of your participants. Please ensure you have provided sufficient details to replicate the analyses such as: a) the recruitment date range (month and year), b) a description of any inclusion/exclusion criteria that were applied to participant recruitment, c) a table of relevant demographic details, d) a statement as to whether your sample can be considered representative of a larger population, e) a description of how participants were recruited, and f) descriptions of where participants were recruited and where the research took place. Response 2: a) the recruitment date range (month and year) Response: The methodology has been updated as per the reviewer comment. b). a description of any inclusion/exclusion criteria that were applied to participant recruitment. Response: We have expanded the inclusion criteria of the manuscript, based on which we have recruited the participants. c) a table of relevant demographic details Response: Thanks for the comment. We have mentioned the socio-demographic characteristics of the recruited participants in Table 1, 2 and 3. Please see for your kind consideration. d) a statement as to whether your sample can be considered representative of a larger population. Response: We have added the statement as reviewer suggested. Please see ‘Recruitment of participants’ section of the manuscript. e) a description of how participants were recruited. Response: The recruitment of the participants was done as per the inclusion and exclusion criteria of the study as mentioned in the ‘inclusion criteria and recruitment of participants’ sections of the manuscript. f) descriptions of where participants were recruited and where the research took place. Response: The recruitment of participants and clinical examination were done from Department of Ophthalmology, PGIMER, Chandigarh, India and experiments were conducted in Neuroscience Research Lab, Dept of Neurology, Post Graduate Institute of medical Education and Research, Chandigarh, India. We have updated the recruitment of participants section as per the reviewer comment. 3. We suggest you thoroughly copyedit your manuscript for language usage, spelling, and grammar. If you do not know anyone who can help you do this, you may wish to consider employing a professional scientific editing service. Response: We have substantially edited the manuscript with native English to enhance the readability of the same. We have also acknowledges the same in the ‘acknowledgment section’ of the manuscript. Thanks for your comment. Upon resubmission, please provide the following: • The name of the colleague or the details of the professional service that edited your manuscript • A copy of your manuscript showing your changes by either highlighting them or using track changes (uploaded as a supporting information file) • A clean copy of the edited manuscript (uploaded as the new manuscript file) Response: Dr Pramod Avti, associate Professor, Department of Biophysics, Post Graduate Institute of Medical Education and Research has help us in editing of the manuscript. We are thankful and acknowledged the same in the manuscript. 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. Response: We have already published an article on genetic analysis which is accessible in the pubmed portal without any restriction (doi:10.1016/j.ygeno.2020.09.044). In your revised cover letter, please address the following prompts: a) If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially identifying or sensitive patient information) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent. Response: Not applicable. b) If there are no restrictions, please upload the minimal anonymized data set necessary to replicate your study findings as either Supporting Information files or to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. Please see http://www.bmj.com/content/340/bmj.c181.long for guidelines on how to de-identify and prepare clinical data for publication. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. We will update your Data Availability statement on your behalf to reflect the information you provide. Response: We have recently published an article and could be used as data source for current manuscript (doi: 10.1016/j.ygeno.2020.09.044). Meanwhile, we will initiate the process to upload the data in public repository. 5. Thank you for stating the following in the Acknowledgments Section of your manuscript: [Department of Biotechnology (No. BT/PR17550/MED/30/1755/2016), New Delhi, India. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.] We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: [The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.] Response: We have removed the funding statement from the manuscript as per the suggestion of the reviewer. Please include your amended statements within your cover letter; we will change the online submission form on your behalf. Response: Please write the funding statement as “Department of Biotechnology (No. BT/PR17550/MED/30/1755/2016), New Delhi, India and no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript”. Reviewers' comments: Reviewer's Responses to Questions Reviewer #1: The manuscript is interesting and well organized. The methods selected and applied for the analyzes are correct and adequate. As the rationale of the paper evaluates "Sleeping pattern and activities of daily living" it is also crucial to discuss the possible role of epigenetics in the onset and progression of AMD. Numerous papers have been published in the literature describing a possible role of epigenetic mechanisms in the etiopathogenesis of the disease. This topic should be included in both the introduction and discussion with the aim of improving the originality of the manuscript. To date, when studying multifactorial diseases it is very important to take into account the role of epigenetics. Response: Thanks for valuable comment. We have updated the manuscript by discussing the significance of epigenetic modification and its implication in genetic and pathological complexity of AMD. Please see introduction and discussion sections of the manuscript. Attachments Attachment Submitted filename: Rebuttal letter.docx https://doi.org/10.1371/journal.pone.0248523.r002
1 Mar 2021 Decision Letter - Alfred S Lewin, Editor Sleeping pattern and activities of daily living modulate protein expression in AMD PONE-D-20-29337R1 Dear Dr. Anand, 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, Alfred S Lewin, Ph.D. Section 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: (No Response) ****** 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 https://doi.org/10.1371/journal.pone.0248523.r003
Formally Accepted
21 May 2021 Acceptance Letter - Alfred S Lewin, Editor PONE-D-20-29337R1 Sleeping pattern and activities of daily living modulate protein expression in AMD Dear Dr. Anand: 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. Alfred S Lewin Section Editor PLOS ONE https://doi.org/10.1371/journal.pone.0248523.r004

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