Peer Review History
Original SubmissionSeptember 25, 2023 |
---|
PONE-D-23-30773Caffeinated Beverages Intake and Risk of Deep Vein Thrombosis: A Mendelian Randomization StudyPLOS ONE Dear Dr. Lin, 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 Feb 11 2024 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 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: 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, Eyüp Serhat Çalık 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 2. Note from Emily Chenette, Editor in Chief of PLOS ONE, and Iain Hrynaszkiewicz, Director of Open Research Solutions at PLOS: Did you know that depositing data in a repository is associated with up to a 25% citation advantage (https://doi.org/10.1371/journal.pone.0230416)? If you’ve not already done so, consider depositing your raw data in a repository to ensure your work is read, appreciated and cited by the largest possible audience. You’ll also earn an Accessible Data icon on your published paper if you deposit your data in any participating repository (https://plos.org/open-science/open-data/#accessible-data). 3. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. Please see the following video for instructions on linking an ORCID iD to your Editorial Manager account: https://www.youtube.com/watch?v=_xcclfuvtxQ Additional Editor Comments: Congratulations to the authors for their valuable study and efforts. Your manuscript has been evaluated by two reviewers and their suggestions are given below. Please respond to these suggestions point by point and make the necessary edits to your manuscript. In addition, I would like to know; in the conclusion section of your article, you say that higher coffee intake is associated with a slight increase in DVT, but in the results section, can you give a measure of this higher coffee intake? Is there such a measure in genetic variants? Can you specify? Finally, please have your manuscript professionally edited for language. [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: No 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: First of all, I want to congratulate the group of Lin and co-workers for their efforts! And I want to thank the journal respectively editor for the allowance to review this interesting manuscript. In the following I will go through the following points step by step: relevance, formals / language, material and methods, results, table, figures, conceptualization, conclusion of this review. Relevance: For my understanding the author's tackle a topic of relevance. Formals / Language: I am not a native speaker; therefore, I usually consult native speakers or language polishing services to have the English checked. I personally feel like, that such a revision of the English would improve the manuscript. For example, at some points there are redundancies, typos, and at least for my feeling potentially misleading phrasings. One example for the phrasing issue can be found in the lines 47 to 49. I am uncertain whether the wording should be "performed U-shaped relationship" or "observed an U-shaped relationship". One example for a typo can be found in line 92, as I think it should be history instead of “History”. The abbreviation “VTE” is not correctly introduced. The abbreviation is used first in line 45, and introduced in line 48. Several abbreviations are introduced repeatedly. One example is “IV” for instrumental variables. Once it is introduced in line 54. Second, it is introduced again in line 118. Please, check this. Material and Methods: Yet, I don't have experience in using Mendelian Randomization. Thus, I do not think, that I am competent enough to comment on this. In line 91 and 92 the authors write “currently, there are established risk factors for DVT, such as obesity, cancer, history of venous thromboembolism and so on”. Why do we find this sentence in the material and methods section? There is no further reference to this in this section of the manuscript. Results: For my personal feeling very limited results for complete original article (all results are displayed in 24 lines, 1 table, and 2 figures). Table: No comment. Figures: Figure 1 – How can be assumend, only looking on an single nucleotide polymorphism level, there only is one mediation – knowing all the risk factos pointed out in the manuscript. For my personal understanding of such a complex entity as deep vein thrombosis, such an assumption is at least a questionable simplification. Conceptualization: From a general pathological point of view, the analyses performed must be scrutinized. The authors point out several times, that their study provides information on causality (e.g., lines 10, 15, 59, 197). But, they only assess. Furthermore, they underline that there are known (and for my feeling important) risk factors for deep vein thrombosis such as cancer or obesity. From my perspective, these are potential confounders respectively mediators are only partially addressed on the level of single nucleotide polymorphisms (SNP). Thus, for my understanding, the statement of providing “causality” overestimates the results of the study. Conclusion of this review: Taken together I would recommend a rejection and reconceptualization of the study. I truly believe, that there is important information in this approach, but how it is at least reported in this manuscript it is for my feeling not suitable at the moment. The concise and narrowly circumscribed results, for my feeling, would fit something like, for example a “short communication” (or whatever the respective journal names it). Reviewer #2: 1. The authors of this study investigated the potential causal relationship between coffee and tea intake and the risk of deep vein thrombosis (DVT) using Mendelian randomization (MR) analysis. The research design is appropriate! Nevertheless, I am a bit concerned about the statistical analysis. In particular, the authors reported for the OR =1.001 for the coffee intake and 95% CI = (1.001, 1.015) with p-value .025. The CI is an open interval meaning the endpoints are not part of the CI. Perhaps, this can be explained by the round-off error. Therefore, I would recommend reporting more decimal digits. 2. While the statistical significance can be supported by the p-value, I am wondering if the finding is practically significant. 3. The statements in Lines 141-144 need rephrasing. 4. Lines 288-289: Why did the authors capitalize the title. Furthermore, the year is 1997 not "n.d." ********** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No ********** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. |
Revision 1 |
Caffeinated Beverages Intake and Risk of Deep Vein Thrombosis: A Mendelian Randomization Study PONE-D-23-30773R1 Dear Dr. Lin, 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, Eyüp Serhat Çalık Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
Formally Accepted |
PONE-D-23-30773R1 PLOS ONE Dear Dr. Lin, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, 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 customercare@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. Eyüp Serhat Çalık Academic Editor PLOS ONE |
Open letter on the publication of peer review reports
PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.
We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.
Learn more at ASAPbio .