Assessment of transparency indicators in space medicine

Rosa Katia Bellomo; Emmanuel A. Zavalis; John P. A. Ioannidis

doi:10.1371/journal.pone.0300701

Peer Review History

Original SubmissionJanuary 8, 2024
5 Feb 2024 Decision Letter - Tadej Debevec, Editor PONE-D-24-00779Assessment of transparency indicators in Space MedicinePLOS ONE Dear Dr. Bellomo, 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 Mar 21 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. 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The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. Thank you for stating the following financial disclosure: "The work of John Ioannidis is supported by an unrestricted gift from Sue and Bob O’Donnell to Stanford. The work of Rosa Katia Bellomo is funded within the framework of the project “ExACT - European network staff eXchange for integrating precision health in the health Care sysTems” (Grant Agreement n. 823995) funded by the European Commission under the H2020 – Marie Slodowska Curie Action – RISE scheme." Please state what role the funders took in the study. If the funders had no role, please state: ""The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."" If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. 3. Please be informed that 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. 4. In this instance it seems there may be acceptable restrictions in place that prevent the public sharing of your minimal data. However, in line with our goal of ensuring long-term data availability to all interested researchers, PLOS’ Data Policy states that authors cannot be the sole named individuals responsible for ensuring data access (http://journals.plos.org/plosone/s/data-availability#loc-acceptable-data-sharing-methods). 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Please also provide details on how you will ensure persistent or long-term data storage and availability. Additional Editor Comments: As you will see below the manuscript has been reviewed by two referees and while ref#1 was rather scant, the points raised by reviewer #2 should be carefully and fully addressed in the revision to ensure the paper fully aligns with PLOS ONE’s publication [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: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes 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: Yes 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: There few comments to make because the paper is well preformed, described and discussed, however I would suggest to change the source of the papers, I am using OpenAlex, and the number of papers is much more bigger using similar seach query than the ones found by the use of PubMed OA, this could be an important bias for the conclusions. I would also liked to state specific aims of the work, Reviewer #2: The manuscript presented by Bellomo et al., is an interesting topic that certainly needs to be discussed in order to maintain scientific rigor. The writing (grammar and style) in general is good, a final proof read will pick up a couple of typos. I would like to thank the authors for an enjoyable read and ask that they consider several minor comments. Further I command them on their extensive work. While the title refers to Space Medicine, I found that the ms uses indicators of transparency that are maybe more applicable to other fields. By that I mean that in space medicine or space life science not all studies conducted require code and thus code sharing in this field will be reduced. How many papers in space medicine or space life sciences actually use code? Were any papers included where the code was noted as propriety and therefore could not be shared? Was there a reason that bed rest, head down tilt or dry immersion were not included in the search query? However, I do see from the chosen articles in supplementary material that some bed rest papers were included. How did the authors choose the time period (2013-2023) in which to select papers from? Including this justification in the paper would aid the reader. In terms of observing trends (Fig. 2) a longer time period would be of interest. Although I fully understand that increasing the time span is a significant undertaking that may not change the outcome of the paper. Many journals actually require conflict of interest and funding statements but obviously do not require the same for data /code sharing which very likely accounts for the higher % of COI and funding statements rather than authors trying to hide something. Can the authors add some information on why they feel these particular markers improve transparency? What is the end goal of data sharing? To double check the data or to start to encourage study replication? Can the authors provide any guidelines or recommendations on how to be more transparent? Does this stem from the journals or from the scientists? What kind of items/transparency indicators do the authors recommend become a mandatory requirement for publication? How do the authors interpret the meaningfulness of the selected 5 indicators in improving transparency in space life science research? Are these the most important or useful? It would be of interest to include how the subset of 200 articles chosen? ****** 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: Yes: Remedios Melero 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. https://doi.org/10.1371/journal.pone.0300701.r001
Revision 1
13 Feb 2024 Author Response 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 The manuscript was formatted as required. 2. Thank you for stating the following financial disclosure: "The work of John Ioannidis is supported by an unrestricted gift from Sue and Bob O’Donnell to Stanford. The work of Rosa Katia Bellomo is funded within the framework of the project “ExACT - European network staff eXchange for integrating precision health in the health Care sysTems” (Grant Agreement n. 823995) funded by the European Commission under the H2020 – Marie Slodowska Curie Action – RISE scheme." Please state what role the funders took in the study. If the funders had no role, please state: ""The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."" If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. We updated the cover letter according to your requirements. 3. Please be informed that 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. All funding related text was removed from the manuscript. 4. In this instance it seems there may be acceptable restrictions in place that prevent the public sharing of your minimal data. However, in line with our goal of ensuring long-term data availability to all interested researchers, PLOS’ Data Policy states that authors cannot be the sole named individuals responsible for ensuring data access (http://journals.plos.org/plosone/s/data-availability#loc-acceptable-data-sharing-methods). Data requests to a non-author institutional point of contact, such as a data access or ethics committee, helps guarantee long term stability and availability of data. Providing interested researchers with a durable point of contact ensures data will be accessible even if an author changes email addresses, institutions, or becomes unavailable to answer requests. Before we proceed with your manuscript, please also provide non-author contact information (phone/email/hyperlink) for a data access committee, ethics committee, or other institutional body to which data requests may be sent. If no institutional body is available to respond to requests for your minimal data, please consider if there any institutional representatives who did not collaborate in the study, and are not listed as authors on the manuscript, who would be able to hold the data and respond to external requests for data access? If so, please provide their contact information (i.e., email address). Please also provide details on how you will ensure persistent or long-term data storage and availability. The analyzed information dataset is available at OSF (www.doi.org/10.17605/OSF.IO/YXU9Q. Additional Editor Comments: As you will see below the manuscript has been reviewed by two referees and while ref#1 was rather scant, the points raised by reviewer #2 should be carefully and fully addressed in the revision to ensure the paper fully aligns with PLOS ONE’s publication 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: Yes 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes 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: Yes 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: There few comments to make because the paper is well preformed, described and discussed, however I would suggest to change the source of the papers, I am using OpenAlex, and the number of papers is much more bigger using similar seach query than the ones found by the use of PubMed OA, this could be an important bias for the conclusions. We recognize that different tools may yield different numbers of articles. We have added in the limitations section in the Discussion after the statement “Open access is in fact another dimension of transparency(9).” the following new text: “Second, our search aimed to have high specificity and thus retrieve articles that had a high likelihood of being relevant to space medicine. However, it did not capture all papers that pertain to space medicine. We used a search that focused on papers that have pertinent terms in their title, but many other papers may be relevant to space medicine without having these terms explicitly in their titles. Moreover, we focused on PubMed OA papers that could be readily text-mined, but other approaches for obtaining open access papers, e.g. OpenAlex, might have yielded some additional papers. There is no strong reason to believe, nevertheless, that these additional papers would have better transparency features.” I would also liked to state specific aims of the work, We have replaced the last sentence of the Introduction (previously: “In order to map the transparency of the space medicine literature, here we performed a meta-epidemiological assessment of these transparency indicators in articles regarding scientific research in space medicine.”) with the more explicit: “The aim of this work is to map the transparency of the space medicine literature by performing a meta-epidemiological assessment of transparency indicators in articles regarding scientific research in space medicine.” Reviewer #2: The manuscript presented by Bellomo et al., is an interesting topic that certainly needs to be discussed in order to maintain scientific rigor. The writing (grammar and style) in general is good, a final proof read will pick up a couple of typos. I would like to thank the authors for an enjoyable read and ask that they consider several minor comments. Further I command them on their extensive work. 1. While the title refers to Space Medicine, I found that the ms uses indicators of transparency that are maybe more applicable to other fields. By that I mean that in space medicine or space life science not all studies conducted require code and thus code sharing in this field will be reduced. How many papers in space medicine or space life sciences actually use code? Were any papers included where the code was noted as propriety and therefore could not be shared? We have added at the end of the paragraph in the Discussion that starts with “Regarding data sharing…” the following: “We recorded very low rates of code sharing, however it should be acknowledged that both in space medicine and in other fields, a large share of articles does not use any code anyhow, while a few papers may have proprietary code that cannot be shared.” 2. Was there a reason that bed rest, head down tilt or dry immersion were not included in the search query? However, I do see from the chosen articles in supplementary material that some bed rest papers were included. Thank you for your insightful question. Our paper focuses on space medicine and microgravity, encompassing both real space conditions and simulations achieved on Earth through experiments like bed rest, head down tilt, and dry immersion. While we didn't specifically include the terms "bed rest," "head down tilt," or "dry immersion" in our search query to avoid potential noise in the results, our search criteria were designed to capture all articles with medical or biological relevance in conditions that occur in space or simulate such environments. As a result, articles describing terrestrial experiments simulating microgravity, including those you mentioned, were indeed included in our research and some of them related to concepts such as bed rest. Please see also our reply to the first comment of reviewer 1 that explains that we used search terms with high specificity. 3. How did the authors choose the time period (2013-2023) in which to select papers from? Including this justification in the paper would aid the reader. In terms of observing trends (Fig. 2) a longer time period would be of interest. Although I fully understand that increasing the time span is a significant undertaking that may not change the outcome of the paper. Many journals actually require conflict of interest and funding statements but obviously do not require the same for data /code sharing which very likely accounts for the higher % of COI and funding statements rather than authors trying to hide something. The choice of the time period (2013-2023) was made to observe trends and ensure a sufficient number of publications for meaningful analysis. Before 2013, the number of relevant papers was too low to infer any trends in transparency indicators with any certainty. The adoption of platforms like Github in the research community also began around that time. The revised manuscript now states: “The choice of the time period was made to observe trends and ensure a sufficient number of publications for meaningful analysis. Before 2013, the number of relevant papers was too low to infer any trends in transparency indicators with any certainty.” 4. Can the authors add some information on why they feel these particular markers improve transparency? In the Introduction, following “In this regard, transparency features, such as sharing of data and code, availability of pre-registered protocols, as well as reporting of conflicts of interest and funding, are important to assess to evaluate the rigor of evidence obtained in biomedical research in this field(8–10)”, we have added: “Data and code sharing facilitate replication studies, allow checking for errors, and enable reuse of the data in secondary analyses and meta-analyses. Pre-registration allows comparing notes between protocols and published results. Reporting of conflicts of interest and funding also help to put the work in context and increase trust.” What is the end goal of data sharing? To double check the data or to start to encourage study replication? As above, we have clarified that “Data and code sharing facilitate replication studies, allow checking for errors, and enable reuse of the data in secondary analyses and meta-analyses.” 5. Can the authors provide any guidelines or recommendations on how to be more transparent? Does this stem from the journals or from the scientists? What kind of items/transparency indicators do the authors recommend become a mandatory requirement for publication? Transparency and reproducibility are becoming more and more important in scientific research as article production is becoming incredibly extensive and prolific. We have added in the Discussion at the end of the Conclusions that “Multiple stakeholders, including funding agencies, journals, scientific societies and grassroot movements from scientists may help make research more transparent. These stakeholders may coordinate efforts and reach greater consensus on best research practices, including what items and transparency indicators should be mandatory for publication.” We would prefer to avoid making recommendations and guidelines just by ourselves. 6. How do the authors interpret the meaningfulness of the selected 5 indicators in improving transparency in space life science research? Are these the most important or useful? We have added in the Discussion a new paragraph, which is now the 4th paragraph in this section: “The selection of the 5 assessed indicators was based on their broad applicability and recognized effectiveness in improving transparency across various fields. While they may not be equally relevant to all studies in space life science, they address key aspects that enhance research quality and credibility. Furthermore, we based the selection of those indicators following previous studies performed using the same R package, in order to be able to compare the results across different fields. This also allows to draw conclusions by comparing results and assess how transparency changes across different fields.” 7. It would be of interest to include how the subset of 200 articles chosen? The subset of 200 articles was selected through a random sampling method in R. Manuscript integrated accordingly at line 169 “selected through a random sampling method in R,”. 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: Yes: Remedios Melero 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. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0300701.r002
5 Mar 2024 Decision Letter - Tadej Debevec, Editor Assessment of transparency indicators in Space Medicine PONE-D-24-00779R1 Dear Dr. Bellomo, 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, Tadej Debevec, Ph.D. Academic 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 Reviewer #2: 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 Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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 Reviewer #2: 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 Reviewer #2: 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: I think all issues/questions raised by reviewers have been accomplished, and responded by the authors. Reviewer #2: I would like to thank you for addressing my comments, I wish you all the best with your future work ****** 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: Yes: Remedios Melero Reviewer #2: No ******** https://doi.org/10.1371/journal.pone.0300701.r003
Formally Accepted
23 Mar 2024 Acceptance Letter - Tadej Debevec, Editor PONE-D-24-00779R1 PLOS ONE Dear Dr. Bellomo, 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. Tadej Debevec Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0300701.r004

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