Peer Review History
| Original SubmissionMay 24, 2020 |
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PONE-D-20-15597 Accuracy of C-reactive protein, procalcitonin, serum amyloid A and neopterin for low-dose CT-scan confirmed pneumonia in elderly patients: a prospective cohort study PLOS ONE Dear Dr. Prendki, 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 find below the comments by the reviewers. In your revision, please provide point-by-point to their queries. We look forward to your revised manuscript. Please submit your revised manuscript by due date. 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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols We look forward to receiving your revised manuscript. Kind regards, Muhammad Adrish 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. In your Methods section, please provide additional details regarding the sample size calculation employed to justify the number of patients included in this study. 3. One of the noted authors is a group or consortium: PneumOldCT study group. In addition to naming the author group, please list the individual authors and affiliations within this group in the acknowledgments section of your manuscript. Please also indicate clearly a lead author for this group along with a contact email address. [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: This study used a sample of consecutive patients (65+) to assess the accuracy of index test in diagnosing pneumonia. The research question is clearly stated. The study design and statistical methods used are appropriate. I recommend publishing this study if the following comments are addressed. 1. The major concern I have is the classification criteria adopted for the usual and reference diagnosis. In both measures, the probability of pneumonia is measured using a three-level Likert scale – low, intermediate, and high. Intermediate and high are then combined to indicate “positive”. The definition of intermediate seems rather vague. It is not clear what “intermediate” actually mean as doctors may have their own subjective interpretations. And since this is then used as the only “gold standard” to construct the ROC curves, the coding scheme may have substantial impacts on the final results. I suggest the authors to report the percentage of intermediate and run a set of sensitivity analysis – that is, whether the AUC values will increase if only “high” is treated as positive case. If they indeed increase considerably, the discussions and conclusions should be revised accordingly. The coding effect needs to be discussed. 2. Although data on a range of clinical characteristics are collected, they are not used in combination with the index tests to improve diagnosis. I think the univariate analysis for sure can provide some important information. But given that the final diagnosis is based on multiple indicators, it is of interest to see whether adding the index tests information in addition to existing criteria can improve the accuracy. 3. Minor comments: a. In Page 5 Line 7, severity scores of what? b. In Page 4 Line 15, it is not clear what it means by after completion of the study. c. Please provide reference for the sample size calculation of the original study. Or add 1-2 sentence to elaborate. d. Please use the official citation of R: To cite R in publications use: R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/. e. I think the flow-chart is not necessary as the procedure is quite simple f. For table 1, please add a column to list the valid sample size for each variable. Reviewer #2: Summary: This paper examined the ability of serum CRP, PCT, SAA and NP, added to the usual panel of indicators, to improve the diagnostic accuracy of pneumonia in patients over 65 years of age. This is a prospective observational cohort analysis. Of the 899 patients who were screened for inclusion, 200 were eligible based on the presence of one respiratory symptom and one symptom or laboratory value suggestive of infection and a working diagnosis of pneumonia. An expert panel used all available clinical, laboratory and radiographic (all patients had CXR and LDCT) and classified pneumonia as present on 133 patients and absent in 67. A pathogen was identified in 41.4% of patients. The 30-day mortality was 7%. Previous studies suggested CRP and PCT as useful biomarkers for pneumonia in non-elderly population and SAA and NP were more newly suggested but less well studied biomarkers for pneumonia. None were useful in this study to improve diagnosis of pneumonia. MAJOR CRITICISM: This paper lacks a clearly stated hypothesis. This can be addressed easily in the Introduction using “hypothesized” in place of ‘aimed.” The rationale for examining these biomarkers is presented but could be more concise. These data are well presented and this population is understudied so the results are worthy of publication. The reliance on blood markers to diagnose a process that begins at the lung alveolar surface continues to leave investigators shorthanded. Nonetheless, the authors made a valiant effort and the negative result calls for examination of newer and different biomarkers. Perhaps the authors could comment on the fact that there were more smokers in the pneumonia group and if this could have confounded baseline measures of these biomarkers. MINOR: English usage could be improved at a few sides in the manuscript. Example Page 6 line 29: consider “…expert panel classified pneumonia as present in 133 patients and absent in 67….” In place of current sentence. P5 line 25-6: Consider removal of masculine pronoun and just say “The diagnosis of pneumonia was considered positive if the rated probability was “intermediate” or “high.” Pneumonia was considered negative if it was “low.” ********** 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 [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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Accuracy of C-reactive protein, procalcitonin, serum amyloid A and neopterin for low-dose CT-scan confirmed pneumonia in elderly patients: a prospective cohort study PONE-D-20-15597R1 Dear Dr. Prendki, 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, Muhammad Adrish Academic Editor PLOS ONE Additional Editor Comments (optional): You have satisfactorily addressed all the reviewer's queries. 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: Yes 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-20-15597R1 Accuracy of C-reactive protein, procalcitonin, serum amyloid A and neopterin for low-dose CT-scan confirmed pneumonia in elderly patients: a prospective cohort study Dear Dr. Prendki: 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. Muhammad Adrish Academic Editor PLOS ONE |
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