Peer Review History
| Original SubmissionAugust 5, 2021 |
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Transfer Alert
This paper was transferred from another journal. As a result, its full editorial history (including decision letters, peer reviews and author responses) may not be present.
PONE-D-21-24615Oncologist Phenotypes and Associations with Response to a Machine Learning-Based Intervention to Increase Advance Care Planning: Secondary Analysis of a Randomized Clinical TrialPLOS ONE Dear Dr. Parikh, 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. I want to apologize for the length of time it took to review this manuscript. As you can see we obtained reviews from 3 independent reviewers including one biostatistician. The overall tenor of the reviews is positive and I believe the comments/suggestions provided are reasonable. Please submit your revised manuscript by Dec 10 2021 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:
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Kimple 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 you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. 3. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. Please see the following video for instructions on linking an ORCID iD to your Editorial Manager account: https://www.youtube.com/watch?v=_xcclfuvtxQ 4. 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: Partly Reviewer #2: Partly Reviewer #3: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: I Don't Know Reviewer #2: No 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: No Reviewer #2: No Reviewer #3: No ********** 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: In this secondary analysis of a randomized clinical trial that tested an intervention to increase ACP at a tertiary cancer hospital, the authors performed an analysis of oncologist phenotype to assess whether that impacted the likelihood of increasing ACP discussions. I have 1 major issue with the article and several minor ones below. Mostly, it is very unclear how the phenotypes of the physicians are actually defined. For example, why were there some specialists listed in the generalist phenotype and it is unclear how low volume specialists versus high volume specialists were exactly defined. This makes it very difficult to truly understand the difference between the groups. Minor issues: 1) Why was the initial analysis only done on patient with >10% risk of mortality, with sensitivity analysis on the entire cohort? Why not just do the initial analysis on the entire cohort. 2) In the abstract (page 2 line 36) please add the word patients' when explaining the multivariable analysis variables. 3) When explaining the statistics behind the oncologist phenotyping please explain why you decided to focus on patient volume rather than other provider characteristics (main center versus satellite, age, number of years in practice, etc.) Seems like the authors did have an underlying hypothesis when choosing patient volume as the phenotype to test. 4) Please clarify if the 78 clinicians studied were only in the intervention group of the randomized trial, and if so, shouldn't there only have been 12,170 patient encounters? If both groups were analyzed shouldn't there have been more physicians? 5) As already stated above in the major issues, why were there 3 specialty oncology physicians in the generalists phenotype (how the phenotypes were defined needs to be made more clear). 6) The wording in the response section when describing the difference in response rates between the specialists needs to be a more little more careful. The authors were not studying the individual doctor response rates. Rather they were testing whether the patients were listed as having an SIC and comparing that between the doctor phenotypes. It may seem irrelevant, but it is important statistically as it implies that the individual doctors were being tested for how well they responded to the intervention which is not the case. The statistics were done on a patient level. 7) Discussion: "our analysis suggests that bandwidth and volume are key drivers of response to interventions intended to improve advance care planning and clinician-patient interaction." Please be careful here with your wording. Your analysis does not suggest that these items are key drivers, rather it suggests that they "may be a driver of". Youre multivariate model only included one phenotypic characteristic of physicians (all of the other variables were patient variables). Therefore, you have no idea whether patient volume or other provider variables may be the actual driver. Maybe patient volume is associated with another physician variable (like training programs, gender, etc.) that are the actual drivers. This analysis did not look at that and therefore cannot claim this one provider variable is the key driver. 8) Discussion: "Targeted deployment of ML-based interventions in the future to clinicians most likely or able to respond, while mitigating alert fatigue or workflow interruptions for clinicians less likely to respond, is a viable strategy for future deployment of ML-based clinician decision support tools." One could also argue that an intervention that cannot be implemented by the physicians that are seeing the majority of the patients is probably not a good intervention. If only the doctors who are seeing the least number of patients can intervene than the majority of patients will not be helped by the intervention. Reviewer #2: Thank you to the authors for their hard work and submission and for the opportunity to review this study. This is an interesting secondary analysis of a recently reported trial investigating the use of machine learning to direct behavioral nudges for advanced care planning discussions. This study explores practitioner characteristics to identify potential groups where the intervention may have had a greater effect on practice. Overall, the study is important, a good idea, and interesting. The investigators should be applauded for their work in this area, though I do have a number of comments for clarification, particularly around study design and the conclusions drawn by the authors. Major comments: 1) Overall comment: the use of LPA is creative to try to define clusters/groups of physicians that respond differently to the intervention. However, this is overall less interpretable and more complex, which is reflected in the discussion. Overall, it seems like the investigators' primary objective is to identify characteristics associated with response. To that end, a logistic regression model across characteristics may be the most helpful tool, and I believe it should be included in the study even if it does not end up as a point of emphasis. Otherwise, conclusions are discussed in the context of clusters whose names are potentially overly simplified (comments regarding this challenge below). Rather than generating logistic regression models summarizing physician features with the LPA, it may be more clear to do so with physician characteristics themselves. It may also reduce some of the challenges with small categories caused by the LPA approach. The overall advantage of using the less-transparent LPA approach feels a bit unclear (and less practically useful). 2) LPA: I have a couple of questions for clarification - continuous data is on multiple scales (in this study for instance, clinic days/week versus % new patients versus patient encounters/week). Were these data standardized? Were baseline ACP rates ascertainable from Clarity? 3) The authors used AIC/BIC/entropy approaches to determine the best fit model. More on this decision making process should be discussed (balancing AIC/BIC, etc). AIC/BIC approaches do also have limitations that have been well-discussed in the statistical literature. The concept of "clinical interpretability" should also be discussed further. It is possible that due to the small sample sizes - particularly in the distribution of some characteristics (which result in imbalanced classes) may not allow the generation of highly distinct classes and that the 1 or 2 class models may not be as overfit as the 3 class model. 4) While the results appear to make sense, I think the authors should discuss the limitations of small sample sizes more. Using only 5 oncologists to define a group limits its external generalizability. Only 6 oncologists in the study were generalists, and only 5 were classified into the "low-volume specialists group." While the overall diversity of the general trial (as the authors have highlighted in the discussion) are an overall credit, this also reduces the sizes of each group and makes it more challenging to characterize the subgroups (increasing the brittleness of each group and potential bias). For instance, conclusions drawn on those 6 generalists is highly dependent on those few oncologists; they would also be expected to cluster together as a small group among specialists. Conclusions drawn here may not reflect differences that would be detected if this study was performed exclusively among generalists for instance. I think this limitation may contribute to comment #2 with regards to the models that had fewer classes. 5) On a related note, the "high-volume generalists" category feels like it may be a misnomer - all 6 of the generalists are in this group (which would be expected as a small minority group), but specialists still make up a fair number in the group. Similarly, the small "low-volume specialists" group also has a particularly high baseline ACP rate and fewer years in practice. Limiting the names to specific dimensions loses the resolution/benefit of including all of the variables in the LPA process. Again, logistic regression would help distill some of these features out (such as volume-based metrics). 6) I think there may be an error in line 197 - I think that 82% may be miscalculated. 7) Data availability - I agree that the patient data may not be available, though with 42 oncologists analyzed, I feel like deidentified individual level data should be potentially available for sharing, and I encourage the authors to consider exploring this given the PLOS Data policy. Minor comments: - I think that the "number of oncology clinicians" in Table 1 is a bit misleading as the analysis is based on dyads rather than individual clinicians. - While the authors indicate primacy in line 327-329 in the discussion, I don't believe this is necessarily true. There have been a number of studies now investigating clinician trust and use of AI, particularly in the radiology space. Some of those findings have similar findings as in this study - for instance more junior/trainee radiologists are more likely to follow clinical decision support tools/computer aided diagnosis systems. This historical work should be included and placed in context. Reviewer #3: A secondary analysis of a clinical trial aimed to evaluate associations between phenotypes and response to machine learning based intervention to prompt earlier advance care planning for cancer patients. High-volume specialists had greater response to intervention when compared to low-volume specialists and high-volume generalists. Minor revisions: 1- Line 197: Provide a measure of dispersion, perhaps interquartile range or range, for the median number of years in practice. 2- Line 198: Provide standard deviations for days oncologist spent in clinic and patients seen per week. 3- Line 199-200: Provide a measure of dispersion for these medians. ********** 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. |
| Revision 1 |
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PONE-D-21-24615R1Oncologist Phenotypes and Associations with Response to a Machine Learning-Based Intervention to Increase Advance Care Planning: Secondary Analysis of a Randomized Clinical TrialPLOS ONE Dear Dr. Parikh, 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 pay particular attention to the request to relabel clusters and the request for an additional regression model. Please submit your revised manuscript by Feb 28 2022 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, Randall J. Kimple Academic Editor PLOS ONE [Note: HTML markup is below. Please do not edit.] 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: (No Response) Reviewer #2: (No Response) Reviewer #3: 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: Partly Reviewer #3: (No Response) ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: No Reviewer #3: (No Response) ********** 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 Reviewer #3: (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 #1: Yes Reviewer #2: Yes Reviewer #3: (No Response) ********** 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 appreciate the authors responses to my questions and concerns. I have just one minor revision that I think is important for the interpretability of this paper. 1) Although I understand why the authors labelled the physician clusters (as they wanted to make the clusters easier to interpret), I believe by labelling the clusters in the way that they did they actually made their results and analysis more misleading which in my opinion is a graver sin then making the results more difficult to interpret clinically. I would highly recommend that the authors change the labels of the clusters to cluster 1, cluster 2, and cluster 3 and simply explain what the doctors in the clusters tended to have in common rather than labelling them with demographics that the physicians tended to have in common. I think this would be a critical step in making sure that casual readers will better understand the methods and not misinterpret the results. Reviewer #2: Thank you again for the authors for their hard work, comments, and revisions. I appreciate the effort they've taken in their thoughtful responses, though still have one primary concern around original comments #1 and 5 focused on supplementing their use of LPA to draw the conclusions highlighted in the manuscript. As the authors have indicated in their response, I think heterogeneity is a reasonable goal, but it feels a little inconsistent with the language used throughout the manuscript which really focuses specifically on the phenotypes themselves (as emphasized in the title and with discussion centered around the specialization/volume characteristics specifically). I think a regression model should hopefully be a limited amount of additional effort for the authors to supplement their current results, and I think is needed to draw the specific conclusions around these characteristics. I completely agree with the authors that the LPA can capture complex interactions across variables to generate classifications, but for this same reason, the conclusions and naming of the clusters in the manuscript is a bit discordant and oversimplify these same complex interactions. Drawing conclusions around volume and specialization without a more interpretable approach as supplementation (as emphasized in the abstract) risks the reader drawing incorrect conclusions about the data. For example, as stated in comment #5, the high-volume generalist cluster does not clearly show that high-volume generalists have a greater response, but rather there is a phenotypic group (which still has a substantial 33% representation by specialists) has a greater response to the intervention. I would really suggest to the authors to include simple regression models to help support their conclusions around these characteristics - this is also a common practice in computational health to provide simpler comparator models. Alternatively, I'd suggest the conclusions should otherwise be framed around the heterogeneous classes rather than the simpler specific volume/time availability characteristics. Reviewer #3: (No Response) ********** 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: 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. |
| Revision 2 |
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Oncologist Phenotypes and Associations with Response to a Machine Learning-Based Intervention to Increase Advance Care Planning: Secondary Analysis of a Randomized Clinical Trial PONE-D-21-24615R2 Dear Dr. Parikh, 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, Randall J. Kimple 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: (No Response) ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: (No Response) ********** 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: No Reviewer #2: (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 #1: Yes Reviewer #2: (No Response) ********** 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: (No Response) Reviewer #2: (No Response) ********** 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: No Reviewer #2: No |
| Formally Accepted |
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PONE-D-21-24615R2 Oncologist Phenotypes and Associations with Response to a Machine Learning-Based Intervention to Increase Advance Care Planning: Secondary Analysis of a Randomized Clinical Trial Dear Dr. Parikh: 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. Randall J. Kimple Academic Editor PLOS ONE |
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