A novel home-use culture mechanism for identifying microbial load in urine samples

Monika Singh; Riya Sahai; Siddharth Pattnaik

doi:10.1371/journal.pone.0285881

Peer Review History

Original SubmissionAugust 9, 2022
6 Nov 2022 Decision Letter - Thippa Reddy Gadekallu, Editor 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-22-22330A novel home-use culture mechanism for identifying microbial load in urine samplesPLOS ONE Dear Dr. Pattnaik, 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. ACADEMIC EDITOR: The authors have to address the comments from the reviewers carefully. Please submit your revised manuscript by Dec 21 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: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled '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. 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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 https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. Please update your submission to use the PLOS LaTeX template. The template and more information on our requirements for LaTeX submissions can be found at http://journals.plos.org/plosone/s/latex. 3. Please ensure that you have specified (1) whether consent was informed and (2) what type you obtained (for instance, written or verbal, and if verbal, how it was documented and witnessed). If your study included minors, state whether you obtained consent from parents or guardians. If the need for consent was waived by the ethics committee, please include this information. 4. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section. 5. 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. [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: 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: In this work, the author proposed a novel home-use culture mechanism for identifying microbial load in urine samples. The comments are listed as follows: 1. The contribution should be summarized in several sentences in brief, which can help the reader better understand the significance of this paper. 2. The existing works should be summarized and presented with the time or logic order rather than the direct illustration, the reviewer thinks that one table for the current efforts comparison may be better. 3. What are the shortcomings or research gaps for the current related work? I think the authors should highlight them at the end of each subsection of the related work section. 4. Where is the source of the adopted data? Please add some explanations. 5. What are the detailed parameter settings for the adopted neural networks? The authors should add more details to the manuscript. 6. To broaden the scope of this paper, the authors should refer to some papers. For example, AoI optimization in the UAV-aided traffic monitoring network under attack: A Stackelberg game viewpoint; BSIF: Blockchain-based Secure, Interactive, and Fair Mobile Crowdsensing; Mixed Game-based AoI Optimization for Combating COVID-19 with AI Bots; Data Freshness Optimization Under CAA in the UAV-Aided MECN: A Potential Game Perspective. 7. This paper needs to be carefully proofed and polished before being accepted. Reviewer #2: The work is interesting and scientifically good. However, the structure of the article should be redesigned 1)The abstract should focus on problem and how it is solved. 2)The introduction part requires related and motivation. 3)The methodology must be explained in detail and the author should specify how their approach is different. 4)The results should be compared with existing works. 5)The threats to validity must also be present in detail 6)The conclusion and the future work should be presented in detail. Deep neural networks to predict diabetic retinopathy , be used to modify the structure of the paper. ****** 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. https://doi.org/10.1371/journal.pone.0285881.r001
Revision 1
20 Dec 2022 Author Response Dear Professor Gadekallu, Thank you so much for giving us an opportunity to make revision to our manuscript. We are really grateful to all the reviewers and editors for their comments and support. We have now addressed the major comments raised by the reviewers and have edited our manuscript accordingly. The changes have been tracked in the revision that we are submitting. In addition, we are also submitting a clean copy of the manuscript with the changes made. We hope that the changes are satisfactory to the editors. Below is a detailed description of each comment and our response to that: Reviewer #1: In this work, the author proposed a novel home-use culture mechanism for identifying microbial load in urine samples. The comments are listed as follows: 1. The contribution should be summarized in several sentences in brief, which can help the reader better understand the significance of this paper. - We are grateful to the reviewer for this comment. We have changed the last paragraph of our introduction in order to summarize the findings of this paper. We believe that this fits well with the flow of the introduction. 2. The existing works should be summarized and presented with the time or logic order rather than the direct illustration, the reviewer thinks that one table for the current efforts comparison may be better. 3. What are the shortcomings or research gaps for the current related work? I think the authors should highlight them at the end of each subsection of the related work section. - We would like to thank the reviewer for this comment. We have added the shortcomings of the existing works and have highlighted them in the introduction for reference. In addition, we have also added a detailed description of the research gaps of our work in the discussion section. 4. Where is the source of the adopted data? Please add some explanations. - We are grateful to the reviewer for pointing this out. We have added the source of the data used in the materials and methods and have also explained the parameters. 5. What are the detailed parameter settings for the adopted neural networks? The authors should add more details to the manuscript. - Again, we are thankful for this comment. We agree that the parameter settings were not clearly explained and we have added the setting details in the materials and methods. 6. To broaden the scope of this paper, the authors should refer to some papers. For example, AoI optimization in the UAV-aided traffic monitoring network under attack: A Stackelberg game viewpoint; BSIF: Blockchain-based Secure, Interactive, and Fair Mobile Crowdsensing; Mixed Game-based AoI Optimization for Combating COVID-19 with AI Bots; Data Freshness Optimization Under CAA in the UAV-Aided MECN: A Potential Game Perspective. - We would like to thank the reviewer for this comment. While we have used the papers to structure the manuscript now, we feel that the papers cannot be referred to since the scope of these works are very different from our current research. 7. This paper needs to be carefully proofed and polished before being accepted. Reviewer #2: The work is interesting and scientifically good. However, the structure of the article should be redesigned 1)The abstract should focus on the problem and how it is solved. - We would like to thank the reviewer for this comment. We agree that the abstract in our initial submission was limited. However, we have made it more elaborate to highlight the problem and how our proposed method alleviates the issue. 2)The introduction part requires related and motivation. - We are thankful to the reviewer for suggesting this. We have edited the paragraphs to be more connected and we hope that the different motivations are conveyed clearly by each paragraph. 3)The methodology must be explained in detail and the author should specify how their approach is different. - We have added more details to the methodology and we hope the details suffice to understand the methods used in quantification of the paper. 4)The results should be compared with existing works. - We would like to thank the reviewer for this comment. The results are quite unique in their own self. However, as suggested by reviewer 1, we have added a comparison table in the discussion section comparing existing works and our work. We have also added a detailed explanation of the same. 5)The threats to validity must also be present in detail - We understand the reviewer’s concerns. We have added the threats to validity in the discussion section in more detail and have also suggested what further studies need to be conducted to invalidate those threats to the work here. 6)The conclusion and the future work should be presented in detail. - Once again, we are grateful to the reviewer for pointing this out. We have edited the conclusion section to bring forth the future prospects of this system as well as plausible extension of the work described. Deep neural networks to predict diabetic retinopathy , be used to modify the structure of the paper. Once again, we are very grateful to you for your kind consideration and to the reviewers for diligently pointing out important gaps in our manuscript. We hope you find everything in order. Yours sincerely, Siddharth Pattnaik Corresponding author. Attachments Attachment Submitted filename: Response_to_reviewers.docx https://doi.org/10.1371/journal.pone.0285881.r002
3 Feb 2023 Decision Letter - Kwame Kumi Asare, Editor PONE-D-22-22330R1A novel home-use culture mechanism for identifying microbial load in urine samplesPLOS ONE Dear Dr. Pattnaik, 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. ============================== ACADEMIC EDITOR: Authors have to carefully address all the concerns raised by the reviewers. Please submit your revised manuscript by Feb 22 2023 11:59 PM. 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: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled '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, Kwame Kumi Asare, Ph.D 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: 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: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: 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 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: In this work, the author proposed a novel home-use culture mechanism for identifying microbial load in urine samples. The comments are listed as follows: 1. The contribution should be summarized in several sentences in brief, which can help the reader better understand the significance of this paper. 2. The existing works should be summarized and presented with the time or logic order rather than the direct illustration, the reviewer thinks that one table for the current efforts comparison may be better. 3. What are the shortcomings or research gaps for the current related work? I think the authors should highlight them at the end of each subsection of the related work section. 4. Where is the source of the adopted data? Please add some explanations. 5. What are the detailed parameter settings for the adopted neural networks? The authors should add more details to the manuscript. 6. To broaden the scope of this paper, the authors should refer to some papers. For example, AoI optimization in the UAV-aided traffic monitoring network under attack: A Stackelberg game viewpoint; BSIF: Blockchain-based Secure, Interactive, and Fair Mobile Crowdsensing; Mixed Game-based AoI Optimization for Combating COVID-19 with AI Bots; Data Freshness Optimization Under CAA in the UAV-Aided MECN: A Potential Game Perspective. 7. This paper needs to be carefully proofed and polished before being accepted. Reviewer #2: The work is interesting and scientifically good. However, the structure of the article should be redesigned 1)The abstract should focus on problem and how it is solved. 2)The introduction part requires related and motivation. 3)The methodology must be explained in detail and the author should specify how their approach is different. 4)The results should be compared with existing works. 5)The threats to validity must also be present in detail 6)The conclusion and the future work should be presented in detail. Deep neural networks to predict diabetic retinopathy , be used to modify the structure of the paper. ****** 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 ******** [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.0285881.r003
Revision 2
22 Apr 2023 Author Response Dear Professor Asare, Thank you so much for giving us an opportunity to make revision to our manuscript. We are really grateful to all the reviewers and editors for their comments and support. We have now addressed the major comments raised by the reviewers and have edited our manuscript accordingly. The changes have been tracked in the revision that we are submitting. In addition, we are also submitting a clean copy of the manuscript with the changes made. We hope that the changes are satisfactory to the editors. Below is a detailed description of each comment and our response to that: Reviewer #1: The authors have not well addressed all my comments, some important references are missing. The authors should refer to the previous comments for paper improvement again. We are grateful to the reviewer for their comments. We have now added the references as suggested by the reviewer in their previous comments. We hope that the reviewer finds the references in place. Reviewer #2: The authors have addressed all the suggestions provided in the previous review. I recommend the article to be accepted We are really grateful to the reviewer for their previous comments and for recommending our article for publication. Once again, we are very grateful to you for your kind consideration and to the reviewers for diligently pointing out important gaps in our manuscript. We hope you find everything in order. Yours sincerely, Siddharth Pattnaik Corresponding author. Attachments Attachment Submitted filename: Response_to_reviewers_1.docx https://doi.org/10.1371/journal.pone.0285881.r004
4 May 2023 Decision Letter - Kwame Kumi Asare, Editor A novel home-use culture mechanism for identifying microbial load in urine samples PONE-D-22-22330R2 Dear Dr. Siddharth Pattnaik, 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, Kwame Kumi Asare, 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 ******** 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: No ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No ****** 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 ****** 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: all comments have been well addressed, so it can be accepted. all comments have been well addressed, so it can be accepted.all comments have been well addressed, so it can be accepted. ****** 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 ******** https://doi.org/10.1371/journal.pone.0285881.r005
Formally Accepted
9 May 2023 Acceptance Letter - Kwame Kumi Asare, Editor PONE-D-22-22330R2 A novel home-use culture mechanism for identifying microbial load in urine samples Dear Dr. Pattnaik: 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. Kwame Kumi Asare Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0285881.r006

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