Downstream retraction of preprinted research in the life and medical sciences

Michele Avissar-Whiting

doi:10.1371/journal.pone.0267971

Peer Review History

Original SubmissionFebruary 21, 2022
16 Mar 2022 Decision Letter - Frederique Lisacek, Editor PONE-D-22-05282Downstream retraction of preprinted research in the life and medical sciencesPLOS ONE Dear Dr. Avissar-Whiting, 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 manuscript lacks referencing to related work. This topic has been and is discussed in a number of articles that are not sufficiently cited. Please submit your revised manuscript by April 25, 2022. 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. 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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. 4. 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 If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.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 If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: N/A ****** 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: In my opinion this paper is relevant because it gives light on the link between preprints, publications focusing on retracted papers. It is very relevant to know how journals manage retraction but also how preprint servers identify those retracted papers from journals. This paper addresses this questions and provide some responses. I have very few comments. The first one is related to the references. In general there is a very low number of references and a small effort should be done by the author on this. In fact, the introduction only has 6 references with some paragraphs with no reference I have some doubts on the classification on retracted papers, from table 1 you can see that a number of retractions (most of them) were due to misconduct, but some of them did not show misconduct. This is the case of case 17, where it was a journal mistake. Regarding IRB approval, though it is bad practice, it is not misconduct as such on how we understand publishing-related misconduct. I wonder if you could be more precise on this in your results and how you consider this case 17. From table 1. It should be included the journal and name of first author. I think that journals publishing retracted papers should be identified along with unethical authors. Methods. Second paragraph. A reference is needed here, because you are classifying misconduct. It this your own classification? There are other classifications published that could add more comparability to your results. Results. Line 122-126. The cases do not add 30, and they should. I guess that perhaps some retractions are classified in two categories. An explanation is needed here. You give importance on the number of retractions by preprint server. I suggest that a new table showing retractions per server and also retraction notice per server, along with time to notice or time to retraction would provide useful information on how these servers work when retractions are detected and their performance on this. Some more references are needed on the discussion. Professor Alberto Ruano-Ravina Reviewer #2: This work provides us with a convincing observation on the status of preprints and links between preprints and subsequent pubications. This is rather an opinion on a socio-political topic of great interest than an authentic research article, but it is worth communicating to the community ****** 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: Alberto Ruano-Ravina Reviewer #2: Yes:** Antoine Danchin [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.0267971.r001
Revision 1
21 Mar 2022 Author Response Dear Dr. Lisacek, I am very grateful to the referees for the time they invested in reviewing the manuscript and for their important feedback, which has led to important revisions that greatly improved the presentation. My point-by-point responses to the referees’ comments follow. --- Comments to the Author Reviewer #1: In my opinion this paper is relevant because it gives light on the link between preprints, publications focusing on retracted papers. It is very relevant to know how journals manage retraction but also how preprint servers identify those retracted papers from journals. This paper addresses this questions and provide some responses. I have very few comments. The first one is related to the references. In general there is a very low number of references and a small effort should be done by the author on this. In fact, the introduction only has 6 references with some paragraphs with no reference. Response: I agree that the manuscript was lacking sufficient references. I have now added six new relevant references, including in places where new information was added based on other suggestions by the reviewer. I have also added new citations to existing references where needed throughout the text. --- I have some doubts on the classification on retracted papers, from table 1 you can see that a number of retractions (most of them) were due to misconduct, but some of them did not show misconduct. This is the case of case 17, where it was a journal mistake. Regarding IRB approval, though it is bad practice, it is not misconduct as such on how we understand publishing-related misconduct. I wonder if you could be more precise on this in your results and how you consider this case 17. Response: While not all cases were defined as being due to misconduct in the original manuscript, the reviewer makes an excellent point that these categories should have been defined in a more standardized and clearer way. To clarify the categorization of these retractions, I have redesignated them based on the definitions of research misconduct provided by the Council of Science Editors. Three discrete designations have been used, and the following text has been added to the Methods section: “Misconduct in each case of retraction was categorized according to the areas defined by the Council of Science Editors [7] as follows: Mistreatment of research subjects (includes failure to obtain approval from an ethical review board or consent from human subjects before conducting the study and failure to follow an approved protocol); Falsification and fabrication of data; Piracy and plagiarism (including unauthorized use of third-party data or other breach of policy by authors); or No evidence of misconduct. The determination of presence and type of misconduct was based on information contained in the individual retraction notices as well as on the reasons for retraction briefly noted in the Retraction Watch database.” Note that this definitional change also changed the quantification of retractions in each category, so the numbers in the results have shifted slightly as a result. --- From table 1. It should be included the journal and name of first author. I think that journals publishing retracted papers should be identified along with unethical authors. Response: While I agree in principle with the referee’s comment, I could not include this information due to our agreement with the Center for Scientific Integrity, which limits the granularity of the data I could share in this publication. Additionally (and fortunately), the specifics of the individual studies are not relevant to the thesis of this study, which is focused more on the integrity of information propagation rather than the individual instances of retraction themselves. Thus, not identifying them here does not seem to undermine the fundamental premise of the work. On a related note, I have removed the Article Type and Country information from the table, as neither is discussed or relevant to the topic at hand. --- Methods. Second paragraph. A reference is needed here, because you are classifying misconduct. It this your own classification? There are other classifications published that could add more comparability to your results. Response: Thank you for this comment, which has now been addressed above. --- Results. Line 122-126. The cases do not add 30, and they should. I guess that perhaps some retractions are classified in two categories. An explanation is needed here. Response: Thank you for this comment. The reviewer is correct that retractions could fall into multiple categories. I have now acknowledged this clearly in this section. Note that substantial changes were made to this section due to the re-classification of research misconduct. --- You give importance on the number of retractions by preprint server. I suggest that a new table showing retractions per server and also retraction notice per server, along with time to notice or time to retraction would provide useful information on how these servers work when retractions are detected and their performance on this. Response: I’m grateful to the reviewer for this suggestion. I have added a table (new Table 1) that contains the server-specific information. I have left the retraction notice information in the larger table, however. --- Some more references are needed on the discussion. Response: I thank the reviewer for this suggestion. Six new references and four new citations to existing references have been added to the paper. --- Reviewer #2: This work provides us with a convincing observation on the status of preprints and links between preprints and subsequent pubications. This is rather an opinion on a socio-political topic of great interest than an authentic research article, but it is worth communicating to the community Response: I thank the reviewer for their comment and agree that there is certainly an element of opinion or “call to action” in this work. My hope is that I’ve provided sufficient empirical evidence to start a discussion and provide a foundation for future, more comprehensive, studies assessing the fidelity of information transfer between associated article types. More importantly, I hope it will convince the myriad stakeholders of the importance of strengthening these connections. This comment compelled me to add a statement regarding future studies to the end of the discussion. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0267971.r002
20 Apr 2022 Decision Letter - Frederique Lisacek, Editor Downstream retraction of preprinted research in the life and medical sciences PONE-D-22-05282R1 Dear Dr. Avissar-Whiting, 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, Frederique Lisacek 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 ******** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes ****** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The author has answered all my comments satisfactorily and I do not have more concerns on the contents of the manuscript ****** 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:** Alberto Ruano-Raviña https://doi.org/10.1371/journal.pone.0267971.r003
Formally Accepted
22 Apr 2022 Acceptance Letter - Frederique Lisacek, Editor PONE-D-22-05282R1 Downstream retraction of preprinted research in the life and medical sciences Dear Dr. Avissar-Whiting: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Frederique Lisacek Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0267971.r004

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