Prioritization of the concepts and skills in quantitative education for graduate students in biomedical science

Louis J. Gross; Rachel Patton McCord; Sondra LoRe; Vitaly V. Ganusov; Tian Hong; W. Christopher Strickland; David Talmy; Albrecht G. von Arnim; Greg Wiggins

doi:10.1371/journal.pone.0284982

Peer Review History

Original SubmissionAugust 20, 2022
10 Feb 2023 Decision Letter - Yaser Mohammed Al-Worafi, Editor PONE-D-22-21390Prioritization of the concepts and skills in quantitative education for graduate students in biomedical sciencePLOS ONE Dear Prof. Louis Joseph Gross, 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 Mach, 10 If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. 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We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: “Burroughs Wellcome Fund Quantitative and Statistical Thinking in the Life Sciences Award #1018963 to the University of Tennessee and the National Science Foundation through Award DBI-1300426 to the University of Tennessee. “ Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 3. 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 If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.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 If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.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: No ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: No ****** 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: No ****** 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: Summary: The article entitled Prioritization of the concepts and skills in quantitative education for graduate students in biomedical science elevates a long-standing question of aligning graduate student preparedness with program-based curricular. This work situates the current/historical perspectives of how program curriculum may vary by school, and department levels, and the implications of graduate student readiness and/or requirement for tailored curriculum. The novel approach of using faculty survey of literature and identifying preferential requisites necessary for graduate students in their prospective fields offers and opportunity for best practices in curriculum design in the biomedical sciences. Overall and very nice article worthy of publication. Minor comments: Methodology and Statistics: The methodology implemented was well-designed and sample size and statistics used were of strong rigor. Results: Results are well present allowing for clear interpretation of author’s findings including supplemental data shown. Minor concern: The reviewer would appreciate further discussion as it relates to how alignment of student needs locally can be expanded to discipline across institutions. Reviewer #2: The idea is not clear The sample size was 160 and no details on how it was obtained or tge technique used The concepts arenot clear Chi2 was mentioned in tge analysis but not clear in the results All results are figures with no tables No clear scaling system was used to quantify the data as likert scale Most of the references used were old ****** 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: Yes: Ghada Omer Hamad Abd El-Raheem ******** [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: PLOS review_11282022.docx https://doi.org/10.1371/journal.pone.0284982.r001
Revision 1
26 Mar 2023 Author Response The comments below are included in the Response to Reviewers letter - that letter is duplicated here. We thank the editor and reviewers for helpful comments that allowed us to enhance the submission. We here respond to each review comment, using red to denote our response. We have updated the manuscript to use the PLOS ONE formatting guidelines. As noted by the editor, we have removed all acknowledgement of financial support from the Acknowledgements section of the manuscript. The statement that is already in the Funding Statement of the online submission form is appropriate and need not be changed. Reviewer #1: Summary: The article entitled Prioritization of the concepts and skills in quantitative education for graduate students in biomedical science elevates a long-standing question of aligning graduate student preparedness with program-based curricular. This work situates the current/historical perspectives of how program curriculum may vary by school, and department levels, and the implications of graduate student readiness and/or requirement for tailored curriculum. The novel approach of using faculty survey of literature and identifying preferential requisites necessary for graduate students in their prospective fields offers and opportunity for best practices in curriculum design in the biomedical sciences. Overall and very nice article worthy of publication. Minor comments: Methodology and Statistics: The methodology implemented was well-designed and sample size and statistics used were of strong rigor. Results: Results are well present allowing for clear interpretation of author’s findings including supplemental data shown. Minor concern: The reviewer would appreciate further discussion as it relates to how alignment of student needs locally can be expanded to discipline across institutions. We appreciate the kind comments of Reviewer #1 and their thoughtful summary of the main objective of the paper. We appreciate their suggestion as to how local needs might be expanded to recommendations across the discipline. Our manuscript had discussed expansion of the approach we suggested to different areas of life science outside biomedical areas. Based on the reviewer’s comment though, we have added a couple of sentences to that paragraph in the Conclusions with a suggestion that a professional society for a particular life science sub-discipline might encourage some of the training programs at different institutions to carry out an analysis similar to ours, and then use these to provide overall guidance on quantitative concepts for their sub-discipline. 1. Is the manuscript technically sound, and do the data support the conclusions? Reviewer #1: Yes Reviewer #2: No 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: No 3. Have the authors made all data underlying the findings in their manuscript fully available? Reviewer #1: Yes Reviewer #2: Yes 4. Is the manuscript presented in an intelligible fashion and written in standard English? Reviewer #1: Yes Reviewer #2: No Reviewer #2: The idea is not clear The sample size was 160 and no details on how it was obtained or tge technique used The concepts arenot clear Chi2 was mentioned in tge analysis but not clear in the results All results are figures with no tables No clear scaling system was used to quantify the data as likert scale Most of the references used were old We appreciate the concerns of Reviewer #2 and have modified the manuscript in many places to respond to the various concerns. The reviewer did not provide much guidance in their comments to assist our response but we suggest that the modifications made enhance the paper. The idea is not clear We have expanded and modified the introduction section to put our effort in a broader context regarding quantitative education and to point out how it connects to a recent workshop report. The sample size was 160 and no details on how it was obtained or tge technique used We are not sure why the reviewer suggests that there was a sample size of 160. The only place we mention this number is as an approximate number of total graduate students in the various programs, which has no connection to how we carried out our study. There was no sampling of students or interaction with students in these programs associated with this study. The study was based on analysis of a set of 48 journal articles suggested by the faculty. We have modified the manuscript in the Materials and Methods section to emphasize how these papers were chosen based on submissions from the faculty, and we have also attempted to further clarify the objectives of this study in the introduction. The concepts arenot clear We are not certain here as to whether the reviewer is referring to the overall objective and conceptual foundations of the paper or whether the reference is to our use of “concepts” to refer to general quantitative concepts. If it is the former, we have modified the introduction to clarify the objectives further. If the reviewer is referring to our use of the term “concepts” associated with quantitative concepts, we have modified the manuscript to perhaps ameliorate this by consistently using the term “general concepts” and referring to the underlying skills they encompass that are listed in Table S2. Chi2 was mentioned in tge analysis but not clear in the results In the first paragraph of the Statistical data analysis section we have added clarification of the objective of the use of this statistical test. We have also explicitly added mention to these tests in the Results section. All results are figures with no tables The paper does include two Tables that lists the papers and concepts. Presumably the reviewer means data tables that would duplicate the results that we have illustrated in the figures. It is not clear to us how adding tables of these data would enhance comprehension of the paper. As the reviewer responded “yes” to the Question “Have the authors made all data underlying the findings in their manuscript fully available?” we don’t see the necessity of adding these for the purposes of reproducibility. No clear scaling system was used to quantify the data as likert scale We expect that the reviewer is referring here to how the evaluations were assigned by each evaluator to each concept or skill. We have further modified the manuscript to make it even clearer that the assessment of the presence and importance of each concept for each paper was based on the assessment of those from the team with the greatest knowledge of the particular field of the article. There is not a Likert scale here – there is no assumption (as in Likert scaling) of equi-distance between responses along the set of assessments. Rather, these are categorical responses and they cannot be “averaged” in the way Likert scaling might. Our analysis treats the results as discrete categorical values in both the chi-squared tests and in the power analysis we carried out. Most of the references used were old Indeed, we emphasize that though there has been a plethora of recent work on undergraduate quantitative life science education, there has been very little for graduate education. We did add a reference to the recent workshop report on quantitative education that is specifically on graduate life science programs. We added a section in the introduction on this report and how the methods in this paper align with recommendations from that report. We have also added a reference to a recent paper on preprint reviews to enhance education and how this approach can enhance quantitative comprehension through journal clubs. Attachments Attachment Submitted filename: ResponseToReviewers.docx https://doi.org/10.1371/journal.pone.0284982.r002
13 Apr 2023 Decision Letter - Yaser Mohammed Al-Worafi, Editor Prioritization of the concepts and skills in quantitative education for graduate students in biomedical science PONE-D-22-21390R1 Dear Dr. Louis, 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, Yaser Mohammed Al-Worafi Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0284982.r003
Formally Accepted
18 Apr 2023 Acceptance Letter - Yaser Mohammed Al-Worafi, Editor PONE-D-22-21390R1 Prioritization of the concepts and skills in quantitative education for graduate students in biomedical science Dear Dr. Gross: 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 Professor Yaser Mohammed Al-Worafi Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0284982.r004

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