Peer Review History
| Original SubmissionDecember 28, 2022 |
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PONE-D-22-33929Transparency of COVID-19-related research: A meta-research studyPLOS ONE Dear Ahmad Sofi-Mahmudi, DDS 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. The paper deals with the issue of transparency about the research generated in terms of derived scientific publications, especially after having experienced the Covid-19 pandemic. This has highlighted the need to quickly communicate the results generated, with transparency to ensure their reproducibility and facilitate their reuse. First, I would like to thank the 3 reviewers for their important comments. I have the following additional comments: - The introduction should better explain open science and open data scenario with data sharing practices (data deposited in repositories or data from supplementary material, etc.), as well as code sharing. It is about transparency but no comments on FAIR principles and research data are done even in discussion. - Related to the methods: Document search strategy needs better description. As I understood you have searched for Covid-19 publications in PubMed database. At this point which are the terms used for the search equation? -Also you have used LitCovid for searching articles and reviews and L.OVE platform for searching clinical trials, is that correct? With the merged PMIDs that you have obtained from the PubMed, LitCovid and L.OVE databases, a second search has been performed in Europe PubMed Central to obtain the full texts of the papers (can be difficult to understand even reading S1 text-deviations from the protocol). Subsequently an analysis of the total papers obtained from EPMC has been done for 5 transparency practices (and results are showed by type of document: research article, review or RCT). All this search strategy should be summarized at the beginning of the results to improve readers' understanding. Even a flow chart with the data obtained (database and number or results) would be interesting and would facilitate understanding. - The authors need to discuss their choice of database--and the fact that they only searched one database--as a limitation of their research. Why EPMC? Why not PMC for example? In the methodology, the tool that has been used should be better explained, because the manual validation that we can see in the supplementary excel is only for 100 documents. -Table 5 and supplementary tables needs to clarify. It is needed an explanation regarding the significance of Median (IQR) with/without. - In addition to the questions previously asked, as suggested by the 3 reviewers, please respond to each point that they have questioned. As far as I can see, I cannot promise acceptance, but I would reconsider an improved version of the current manuscript. Reviewer 1 The subject matter of the work presented is of great importance to the scientific community. Transparency is one of the fundamental pillars on which most emphasis is currently being placed by international organizations and funding agencies. In my opinion, I believe that the article is interesting and useful for the scientific community. However, it has some shortcomings that I believe should be addressed. 1. The paper mentions that the five practices that underpin transparency are data sharing, code sharing, COI disclosures, and protocol registration. Considering that not everyone is familiar with the concepts, I think a brief description of each in the enumeration of the concepts in the "Data extraction and synthesis" section of the methodology would be very useful. Based on this description, I believe that it should be further specified what is to be considered in this study for each element. This is particularly important in the case of data sharing since within this group it is not differentiated whether it is raw data or already processed material, as can be seen in the S7 Appendix for example in the open data statement of record 103787, which is not raw data. 2. On the other hand, I think that, in addition to documentary typology, it would be very interesting to add some information on the distribution at least by country or by discipline, as I think it would give a richer context to the study. The subject matter of COVID-19 is very broad and the disciplines that deal with it in one way or another are very diverse. It would be very useful to know which disciplines are carrying out transparency practices and how, for example, which ones are sharing more code, or which ones are sharing more data. This type of information would enrich the discussion, and more robust conclusions could be drawn, since as they stand they are quite generic and highlight aspects that are not novel. In other words, we already know that more transparency is crucial to ensure credibility and that society should benefit from it, but at this point, it would be interesting to sharpen the focus and find out, within the medical disciplines, who does what and how, since genetics and its tradition of sharing data (regardless of covid) have nothing to do with more clinical disciplines. Reviewer 2 This is a very descriptive study in which the results of other studies are commented on without a clear relationship with the study addressed in this work. Method 1.The authors rely on the results of the Europe PubMed Central database. Explain the reasons why they have chosen this source over others, as well as the possible biases that this may have produced. 2.Please, explain how do you measure the data sharing variable? 3.Describe what the tool used considers “valid” or considers dataset. Explain what the tool consists of. It is not enough just to cite it in the bibliography. For example, does it include supplementary material or just datasets? Results. 4.In this chapter it is striking that nothing is said about the journals in Table 3 and the publishers in Table 4. 5.Table 5 only includes citations and impact factor. Why is the h-index and the number of articles published in open access not included? Discussion 6.The discussion is poor in arguments and repeats again some of the results of the study. It seems to be unfinished or halfway through. 7.Some aspects to be considered and argued have to do with transparency, since transparency alone is not synonymous with quality. Authors should at least relate transparency practices to other indicators of article quality, such as the number of citations received, impact factor, journal citation Indicator and quartile, since, on the other hand, it has been mentioned in the method. 8.The fact that review articles receive less funding is obvious, since this type of work is not usually funded, as they are not research work sensu stricto. 9.What are the implications of the fact that "COI disclosures seemed to be more common in articles published in lower-impact journals? 10.Why "adherence to transparent practices was at a similar level in COVID-19-related literature than in other biomedical literature analyzed with the same methods"? References What do you mean by "Scientometrics. 2021 kesäkuu"? Reviewer 3 This article deals with the concept of transparency in works (research, RCT, reviews) published in PubMed indexed journals about COVID-19. My major concerns focus the lack of explanations. 1. The background section is too short, and it is excessively centered in transparency, omitting that concepts like data sharing go beyond transparency. Authors do not explain what is data sharing or code sharing and why they are so important for transparency, among other considerations. 2.The Methods section lacks of an explanation about why Europe PMC repository was selected, despite of the potential problems about this decision were included in the Discussion section. 3.Table 5 is not sufficiently understandable. Please submit your revised manuscript by Mar 31 2023 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, Rut Lucas-Dominguez, PhD 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. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section. 3. Thank you for stating the following financial disclosure: "The author(s) received no specific funding for this work." At this time, please address the following queries: a) Please clarify the sources of funding (financial or material support) for your study. List the grants or organizations that supported your study, including funding received from your institution. b) State what role the funders took in the study. If the funders had no role in your study, please state: “The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.” c) If any authors received a salary from any of your funders, please state which authors and which funders. d) If you did not receive any funding for this study, please state: “The authors received no specific funding for this work.” Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 4. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability. Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized. Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions 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. 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: Yes Reviewer #2: Yes Reviewer #3: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: 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 Reviewer #3: 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 Reviewer #3: 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 subject matter of the work presented is of great importance to the scientific community. Transparency is one of the fundamental pillars on which most emphasis is currently being placed by international organizations and funding agencies. In my opinion, I believe that the article is interesting and useful for the scientific community. However, it has some shortcomings that I believe should be addressed. The paper mentions that the five practices that underpin transparency are data sharing, code sharing, COI disclosures, and protocol registration. Considering that not everyone is familiar with the concepts, I think a brief description of each in the enumeration of the concepts in the "Data extraction and synthesis" section of the methodology would be very useful. Based on this description, I believe that it should be further specified what is to be considered in this study for each element. This is particularly important in the case of data sharing since within this group it is not differentiated whether it is raw data or already processed material, as can be seen in the S7 Appendix for example in the open data statement of record 103787, which is not raw data. On the other hand, I think that, in addition to documentary typology, it would be very interesting to add some information on the distribution at least by country or by discipline, as I think it would give a richer context to the study. The subject matter of COVID-19 is very broad and the disciplines that deal with it in one way or another are very diverse. It would be very useful to know which disciplines are carrying out transparency practices and how, for example, which ones are sharing more code, or which ones are sharing more data. This type of information would enrich the discussion, and more robust conclusions could be drawn, since as they stand they are quite generic and highlight aspects that are not novel. In other words, we already know that more transparency is crucial to ensure credibility and that society should benefit from it, but at this point, it would be interesting to sharpen the focus and find out, within the medical disciplines, who does what and how, since genetics and its tradition of sharing data (regardless of covid) have nothing to do with more clinical disciplines. Reviewer #2: PONE-D-22-33929 Transparency of COVID-19-related research: A meta-research study This is a very descriptive study in which the results of other studies are commented on without a clear relationship with the study addressed in this work. Method The authors rely on the results of the Europe PubMed Central database. Explain the reasons why they have chosen this source over others, as well as the possible biases that this may have produced. Please, explain how do you measure the data sharing variable? Describe what the tool used considers “valid” or considers dataset. Explain what the tool consists of. It is not enough just to cite it in the bibliography. For example, does it include supplementary material or just datasets? Results. In this chapter it is striking that nothing is said about the journals in Table 3 and the publishers in Table 4. Table 5 only includes citations and impact factor. Why is the h-index and the number of articles published in open access not included? Discussion The discussion is poor in arguments and repeats again some of the results of the study. It seems to be unfinished or halfway through. Some aspects to be considered and argued have to do with transparency, since transparency alone is not synonymous with quality. Authors should at least relate transparency practices to other indicators of article quality, such as the number of citations received, impact factor, journal citation Indicator and quartile, since, on the other hand, it has been mentioned in the method. The fact that review articles receive less funding is obvious, since this type of work is not usually funded, as they are not research work sensu stricto. What are the implications of the fact that "COI disclosures seemed to be more common in articles published in lower-impact journals? Why "adherence to transparent practices was at a similar level in COVID-19-related literature than in other biomedical literature analyzed with the same methods"? References What do you mean by "Scientometrics. 2021 kesäkuu"? Reviewer #3: This article deals with the concept of transparency in works (research, RCT, reviews) published in PubMed indexed journals about COVID-19. My major concerns focus the lack of explanations. The background section is too short, and it is excessively centered in transparency, omitting that concepts like data sharing go beyond transparency. Authors do not explain what is data sharing or code sharing and why they are so important for transparency, among other considerations. The Methods section lacks of an explanation about why Europe PMC repository was selected, despite of the potential problems about this decision were included in the Discussion section. Table 5 is not sufficiently understandable. ********** 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 Reviewer #3: 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.
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| Revision 1 |
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PONE-D-22-33929R1Transparency of COVID-19-related research: A meta-research studyPLOS ONE Dear Dr. Sofi-Mahmudi, 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 Jul 02 2023 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, Rut Lucas-Dominguez, PhD 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. Additional Editor Comments: The paper has been improved following the recommendations of the academic editor and reviewers. It is important for the acceptation of the manuscript that the minor changes suggested will be taken into account. 1. Background. There are spaces in the text before citations 3 and 4 that need to be removed. 2. Background. The sentence: To facilitate rapid and collaborative scientific research, over 100 organizations…please could authors insert the reference to support this sentence. 3. Methods. At the end of Data sources and study selection it is mentioned: As we want to focus solely on RCTs that have been done, we applied two filters: “RCT” and “Reporting data,” on the L·OVE website and then downloaded the dataset with these characteristics. Again, we used PMIDs to merge datasets. Please, check if is correct that sentence? The PMIDs are used to recover the articles?, not datasets. In fact, authors are explaining in the next paragraph of Data extraction and synthesis: we assessed articles’ adherence to five transparent practices. 4. Methods. Regarding journal and article information in METHODS, please explain what IQM is and how is calculated. It appears in the tables of results many times. 5. Methods. In the table 5 Where did the citations come from? Are calculated through the Web of Science, since is the same table of JIF. Explain please. To clarify, authors may include citations and Impact index of the journals were obtained from JCR. Which edition of JCR are you using? Mainly because for the other impact indicators in the following table you are using SJR and h-index from another database (SJR). 6. Methods. Data analysis. Regarding the tables of results, appears in the legend of the tables SD: standard deviation. But never appears this acronym in the tables, so this may be confusing. 7. Results. Transparency practices. It appears figure 1, however authos have to correct writing figure 3, as well as Figure 3-right. 8. Results. At the end of table 4: Tables S2 and S3 show the results for RCTs and reviews. I can not see this supplementary tables. I only can see Table S4, Table S5 and S6 appendix in the submission files. 9. Results. Table 5. SD appears in the explanatory legend below the table: standard deviation. But this acronym does not appear in the table. For example, IQR appears in the table, and it is explained as inter quartile range. At this point, please explain the meaning/calculation of Median inter-quartile range (IQR) in methodology. 10. Results. Of 100 random articles for validation, 20 discrepancies (out of 500, 4%), could authors explain the meaning of: out of 500, 4%. 11. Results. (S7 Appendix). I cannot see S7 appendix. 12. Discussion. Due to the manuscript has many tables, it would be great if the authors could synthetize in brief short lines at the beginning of the discussion the results obtained.Please insert comments here and delete this placeholder text when finished. [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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PONE-D-22-33929R2Transparency of COVID-19-related research: A meta-research studyPLOS ONE Dear Dr. Sofi-Mahmudi, 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. ============================== Dear authors, thank you for sending the responses to the comments we raised and the corrections developed in the manuscript. However, we have recently received the reviewer's comments for your manuscript in the context of statistics, focused on methods and reporting of the manuscript, which I am enclosing herewith. I think it is important that you take into consideration and respond the questions and suggestions. Major 1) The authors assume that all studies can share data. That is not the case. Many studies would use patient level registers and it would be gross misconduct in terms of the GDPR (which is not even mentioned in the paper, data security in general) if the data was available for everyone to download. So if the authors want to do this, they need to separate between studies that CAN and do not share data (population level, or aggregate freely available date) and analyses of practice level registries that cannot share data. Overall, this domain is deeply problematic and perhaps it should be discussed very carefully, if the authors want to keep it. 2) A second, not as problematic domain is the protocol registration. this is standard for RCTs and meta-analyses but not much else. of course it's good practice, but it is not expected in observational studies. so can the authors expand the introduction to provide more information on why this is needed and on any evidence on that leading to better work? 3) the data tool used is central to the work. The authors should provide performance metric for the tool, previously published (when the tool is described), in addition to their random sample. 4) I don't understand why the authors use piecemeal univariable analyses rather than use a regression model (linear or ordinal logistic) to examine factors associated with transparency, as they define it. the predictors can be JIF, year etc. this should overcome multiple testing issues and Type-I error inflation, if they use a single model. Minor 1) Report uncertainty in all the reported estimates (e.g. percentages in the abstract). 2) I found this to be unclear, please rephrase: "We used the interquartile range (the third quartile (Q3) – the first quartile (Q1)) when the data were skewed." Used for what purpose. ============================== Please submit your revised manuscript by Jul 10 2023 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, Rut Lucas-Dominguez, PhD Academic Editor PLOS ONE 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 #4: (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 #4: Partly ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #4: No ********** 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 #4: 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 #4: 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 #4: As the statistical reviewer I will focus on methods and reporting. The authors should note this is the first time I see the paper. Major 1) The authors assume that all studies can share data. That is not the case. Many studies would use patient level registers and it would be gross misconduct in terms of the GDPR (which is not even mentioned in the paper, data security in general) if the data was available for everyone to download. So if the authors want to do this, they need to separate between studies that CAN and do not share data (population level, or aggregate freely available date) and analyses of practice level registries that cannot share data. Overall, this domain is deeply problematic and perhaps it should be discussed very carefully, if the authors want to keep it. 2) A second, not as problematic domain is the protocol registration. this is standard for RCTs and meta-analyses but not much else. of course it's good practice, but it is not expected in observational studies. so can the authors expand the introduction to provide more information on why this is needed and on any evidence on that leading to better work? 3) the data tool used is central to the work. The authors should provide performance metric for the tool, previously published (when the tool is described), in addition to their random sample. 4) I don't understand why the authors use piecemeal univariable analyses rather than use a regression model (linear or ordinal logistic) to examine factors associated with transparency, as they define it. the predictors can be JIF, year etc. this should overcome multiple testing issues and Type-I error inflation, if they use a single model. Minor 1) Report uncertainty in all the reported estimates (e.g. percentages in the abstract). 2) I found this to be unclear, please rephrase: "We used the interquartile range (the third quartile (Q3) – the first quartile (Q1)) when the data were skewed." Used for what purpose. ********** 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 #4: 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 3 |
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Transparency of COVID-19-related research: A meta-research study PONE-D-22-33929R3 Dear Dr. Ahmad Sofi-Mahmudi, 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, Rut Lucas-Dominguez, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): All comments suggested by the reviewers have been addressed by the authors. 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 #4: 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 #4: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #4: 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 #4: (No Response) ********** 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 #4: 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 #4: I am satisfied with the authors' responses. I am satisfied with the authors' responses. I am satisfied with the authors' responses. ********** 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 #4: No ********** |
| Formally Accepted |
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PONE-D-22-33929R3 Transparency of COVID-19-related research: A meta-research study Dear Dr. Sofi-Mahmudi: 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 Prof. Rut Lucas-Dominguez Academic Editor PLOS ONE |
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