Peer Review History

Original SubmissionFebruary 7, 2024
Decision Letter - Filomena de Nigris, Editor

PONE-D-24-04991Effect of chemotherapy on prognosis in patients with primary pancreatic signet ring cell carcinoma: A large real-world study based on machine learningPLOS ONE

Dear Dr. Huang,

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.

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Filomena de Nigris, Ph.D.

Academic Editor

PLOS ONE

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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: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: I Don't Know

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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

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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

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: The manuscript is well presented, the topics well described. The tables and graphs are clear and sufficient. Only a few aspects would need to be revised by the authors:

• The work has no innovative features. Authors are requested to emphasize the new aspects considered in comparison with the following work: Nie, D., Lan, Q., Huang, Y. et al. Epidemiology and prognostic analysis of patients with pancreatic signet ring cell carcinoma: a population-based study. BMC Gastroenterol 22, 458 (2022). 10.1186/s12876-022-02543-z

• Authors should specify how they intend to overcome the bias of their study in the discussion.

• Authors should review the bibliography (ex: 4-5)

Reviewer #2: In the paper by Yunshen He et al., the role of chemotherapy as a prognostic factor of primary pancreatic singet ring cell carcinoma, a rare pancreatic ductal adenocarcinoma, is investigated through a statistical analysis. the paper is well written but:

- The introduction is too short and does not delve into any topic about pancretic cancer or PSRCC. It is not satisfactory for a student reader and very poor for an academic reader.

- Statistical analysis does not make any histological classification - Statistical analysis does not mention the different treatment groups, but in general chemotherapy it is not easy to understand if there is an effect of radiotherapy. The author should be able to take the effect of radiotherapy or a particular radiotherapy protocol in combination or individually.

Although the idea of the proposed analysis may be interesting, it is presented in a very superficial way, leaving unresolved many aspects about the variability of treatments, staging, etc.

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Reviewer #1: No

Reviewer #2: No

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Revision 1

23th Mar, 2024

PONE-D-24-04991

Effect of chemotherapy on prognosis in patients with primary pancreatic signet ring cell carcinoma: A large real-world study based on machine learning.

Dear editors,

Thank you for your thoughtful review of our manuscript and the helpful comments from the reviewers. We agree with the reviewers’ suggestions. Here below a point-by-point reply to the comments. Major changes are marked in the revised manuscript. Hopefully you will find the revised manuscript improved and suitable for publication in PLOS ONE.

Reviewer 1

Q1:

The manuscript is well presented, the topics well described. The tables and graphs are clear and sufficient. Only a few aspects would need to be revised by the authors: The work has no innovative features. Authors are requested to emphasize the new aspects considered in comparison with the following work: Nie, D., Lan, Q., Huang, Y. et al. Epidemiology and prognostic analysis of patients with pancreatic signet ring cell carcinoma: a population-based study. BMC Gastroenterol 22, 458 (2022). 10.1186/s12876-022-02543-z; Authors should specify how they intend to overcome the bias of their study in the discussion.

Response:

We have meticulously reviewed the study by Nie et al., which centers on investigating the epidemiology of PSRCC. However, the content regarding prognostic analysis is relatively limited, and it does not specifically target the analysis of the value of chemotherapy. Furthermore, the outcome measures in this article are limited to Overall Survival (OS) only. In addition, the baseline characteristics of patients are not comprehensively presented in the comparison between chemotherapy and non-chemotherapy groups. In contrast, in this study, we aimed to specially investigate the prognostic value of chemotherapy in PSRCC. The patients’ demographics and tumor characteristics stratified by chemotherapy are detailedly summarized in Table 1. Also, the main outcomes in this study were cancer-specific survival (CSS) and OS, which enhances the reliability of the results. Further, we independently used univariate and multivariate Cox regression, LASSO, and Random Survival Forest model to analyze the prognostic factors for survival and also used subgroup analysis to adjust all other variables affecting the prognosis, making our conclusions more reliable and stable.

Notably, in addition to the aforementioned aspects, we have also utilized machine learning algorithms to optimize the methodology.

Q2:

Authors should review the bibliography (ex: 4-5).

Response:

We have meticulously reviewed all the references in the full manuscript and confirmed their accuracy. For references 4 and 5, we have downloaded the PDF documents and uploaded them as supplementary materials.

Reviewer 2

Q1:

The introduction is too short and does not delve into any topic about pancretic cancer or PSRCC. It is not satisfactory for a student reader and very poor for an academic reader.

Response:

We have made relevant additions and revisions to the introduction section.

Q2:

Statistical analysis does not make any histological classification

Response:

PSRCC is an extremely rare histologic variant of pancreatic cancers with the code of “ICD‑O‑3 Hist/behave, malignant” stated as ‘8490/3: Signet ring cell carcinoma’. In this study, we exclusively focus on a specific histological type of pancreatic cancers to investigate the influence of chemotherapy on prognosis. Consequently, the statistical analysis does not involve any other histological classification.

Q3:

Statistical analysis does not mention the different treatment groups, but in general chemotherapy it is not easy to understand if there is an effect of radiotherapy. The author should be able to take the effect of radiotherapy or a particular radiotherapy protocol in combination or individually. Although the idea of the proposed analysis may be interesting, it is presented in a very superficial way, leaving unresolved many aspects about the variability of treatments, staging, etc.

Response:

In our study, we not only utilized the standard univariate and multivariate Cox regression models and LASSO regression model for prognostic variable analysis but also employed the Random Survival Forest model and Survival Analysis for Subgroups. The Random Survival Forest model is advantageous as it lacks the constraint of the Proportional Hazards Assumption and prevents overfitting through its dual random sampling processes. On the other hand, Survival Analysis for Subgroups allows for the observation of chemotherapy's impact on patient prognosis at various subgroup levels after adjusting for the influence of other variables. This comprehensive statistical approach enhances the robustness of our findings and provides a nuanced understanding of how chemotherapy may affect outcomes within specific patient populations. ( Fig 5)

Attachments
Attachment
Submitted filename: A rebuttal letter.docx
Decision Letter - Filomena de Nigris, Editor

Effect of chemotherapy on prognosis in patients with primary pancreatic signet ring cell carcinoma: A large real-world study based on machine learning

PONE-D-24-04991R1

Dear Dr Huang

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.

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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,

Filomena de Nigris, 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

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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: I Don't Know

**********

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: The authors have responded clearly and comprehensively to the comments raised in the first revision, therefore the manuscript is suitable for publication

Reviewer #2: the author's answers are exhaustive within the scope of the paper's objective even if some remain perplexed about the validity of the paper's idea.

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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
Acceptance Letter - Filomena de Nigris, Editor

PONE-D-24-04991R1

PLOS ONE

Dear Dr. Huang,

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.

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Kind regards,

PLOS ONE Editorial Office Staff

on behalf of

Prof. Filomena de Nigris

Academic Editor

PLOS ONE

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