Peer Review History

Original SubmissionNovember 30, 2023
Decision Letter - Sara Hemati, Editor

PONE-D-23-40119Differential impact of environmental factors on airborne live bacteria and inorganic particles in an underground walkwayPLOS ONE

Dear Dr. Yamaguchi,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Feb 18 2024 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.

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,

Sara Hemati

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

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2. Did you know that depositing data in a repository is associated with up to a 25% citation advantage (https://doi.org/10.1371/journal.pone.0230416)? If you’ve not already done so, consider depositing your raw data in a repository to ensure your work is read, appreciated and cited by the largest possible audience. You’ll also earn an Accessible Data icon on your published paper if you deposit your data in any participating repository (https://plos.org/open-science/open-data/#accessible-data).

3. Please note that PLOS ONE has specific guidelines on code sharing for submissions in which author-generated code underpins the findings in the manuscript. In these cases, all author-generated code must be made available without restrictions upon publication of the work. Please review our guidelines at https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-code and ensure that your code is shared in a way that follows best practice and facilitates reproducibility and reuse.

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. Thank you for stating the following financial disclosure: " This study was funded by a grant-in-aid for scientific research, KAKENHI (grant number

20K20613 to HY)."

Please state what role the funders took in the study.  If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."

If this statement is not correct you must amend it as needed.

Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf.

6. We note that your Data Availability Statement is currently as follows: "All relevant data are within the manuscript and its Supporting Information files."

Please confirm at this time whether or not your submission contains all raw data required to replicate the results of your study. Authors must share the “minimal data set” for their submission. PLOS defines the minimal data set to consist of the data required to replicate all study findings reported in the article, as well as related metadata and methods (https://journals.plos.org/plosone/s/data-availability#loc-minimal-data-set-definition).

For example, authors should submit the following data:

- The values behind the means, standard deviations and other measures reported;

- The values used to build graphs;

- The points extracted from images for analysis.

Authors do not need to submit their entire data set if only a portion of the data was used in the reported study.

If your submission does not contain these data, please either upload them as Supporting Information files or deposit them to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. For a list of recommended repositories, please see https://journals.plos.org/plosone/s/recommended-repositories.

If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially sensitive information, data are owned by a third-party organization, etc.) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent. If data are owned by a third party, please indicate how others may request data access.

7. Thank you for stating the following in the Acknowledgments Section of your manuscript: “We are grateful to the South African Medical Research Council and National Research Foundation for financial support.”

We note that you have provided funding information that is currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form.

Additional Editor Comments:

Manuscript Number: PONE-D-23-40119

Differential impact of environmental factors on airborne live bacteria and inorganic particles in an underground walkway

Dear Dr. Yamaguchi,

I hope this email finds you well.

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Feb 09 2024 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.

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,

Sara Hemati

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. 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

**********

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

Reviewer #1: I Don't Know

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: No

**********

5. Review Comments to the Author

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

Reviewer #1: The difference between this article and your article September 18, 2017 is not significant in terms of results. Was there a special reason for presenting this article? It is better to explain the necessity of doing research.

Reviewer #2: Dear Authors,

The manuscript was fully reviewed. The comments in the manuscript. The manuscript needs a major revision before any consideration. The view of the study is good but some concerns exist. Best

**********

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.

Attachments
Attachment
Submitted filename: Yamaguchi et al text 20231201.docx
Attachment
Submitted filename: PONE-D-23-40119.pdf
Revision 1

REPLIES TO REVIEWER’S COMMENTS

Ref. ID: PONE-D-23-40119

Differential impact of environmental factors on airborne live bacteria and inorganic particles in an underground walkway

Responses to Editor Comments:

Comment 1: 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.

Response: We have incorporated all reviewer comments and journal requirements into the revised version according to the editor's instructions.

Comment 2: Please submit your revised manuscript by Feb 09 2024 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.

Response: According to the instructions, we submitted the revised manuscript within the extended deadline (the end of March).

Comment 3: 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'.

Response: According to the instructions, we uploaded the response letter s a separate file labeled 'Response to Reviewers'..

Comment 4: 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'.

Response: According to the comment, we highlighted the corrections in red color and uploaded the revised manuscript as a separate file labeled 'Revised Manuscript with Track Changes'.

Comment 5: An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

Response: Yes, according to the instructions, we uploaded a unmarked revised manuscript as a separate file labeled 'Manuscript'.

Comment 6: If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter.

Response: Since this research is supported by a grant-in-aid for scientific research, KAKENHI (grant number 20K20613 to HY), the following sentence has been added in the section 'financial disclosure'. 'This research is supported by a grant-in-aid for scientific research, KAKENHI (grant number 20K20613 to HY). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript'. According to the comment, we wrote about the corrections in the cover letter.

Comment 7: Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

Response: We have verified that the figures and tables follow the guidelines. No revisions to figures or tables were requested from the reviewers.

Comment 7: 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.

Response: Thank you for recommending the deposit of protocols used this study to 'protocols.io'. On the other hand, the R commands used this study is not applicable as it is a general one.

Responses to Journal Requirements:

Comment 1: Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming.

Response: We have confirmed that it matches the journal style of PLOS ONE, including the file name.

Comment 2: Did you know that depositing data in a repository is associated with up to a 25% citation advantage? If you’ve not already done so, consider depositing your raw data in a repository to ensure your work is read, appreciated and cited by the largest possible audience. You’ll also earn an Accessible Data icon on your published paper if you deposit your data in any participating repository.

Response: Thank you for introducing us to 'Repository'. On the other hand, there is no huge amount of metadata this time, so we don't think it applies. On the other hand, all the raw data used have been summarized in a table as supporting information so that readers can check the reproducibility.

Comment 3: Please note that PLOS ONE has specific guidelines on code sharing for submissions in which author-generated code underpins the findings in the manuscript. In these cases, all author-generated code must be made available without restrictions upon publication of the work. Please review our guidelines at https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-code and ensure that your code is shared in a way that follows best practice and facilitates reproducibility and reuse.

Response: Thank you for your advice. The R commands we used in this paper are general and do not include any proprietary code. Also, all codes are disclosed in the text, so anyone can perform similar analysis.

Comment 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. Thank you for stating the following financial disclosure: " This study was funded by a grant-in-aid for scientific research, KAKENHI (grant number 20K20613 to HY)." Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf.

Response: Thank you for your advice. According to the comment, we have checked the funding information, and have declared the following sentence 'The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript' into the Financial Disclosure' of the revised manuscript.

Comment 6: We note that your Data Availability Statement is currently as follows: "All relevant data are within the manuscript and its Supporting Information files." Please confirm at this time whether or not your submission contains all raw data required to replicate the results of your study. Authors must share the “minimal data set” for their submission. PLOS defines the minimal data set to consist of the data required to replicate all study findings reported in the article, as well as related metadata and methods. For example, authors should submit the following data:

- The values behind the means, standard deviations and other measures reported;

- The values used to build graphs;

- The points extracted from images for analysis.

Authors do not need to submit their entire data set if only a portion of the data was used in the reported study. If your submission does not contain these data, please either upload them as Supporting Information files or deposit them to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. For a list of recommended repositories, please see https://journals.plos.org/plosone/s/recommended-repositories. If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially sensitive information, data are owned by a third-party organization, etc.) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent. If data are owned by a third party, please indicate how others may request data access.

Response: We have confirmed that all previously published paper data used for R analysis is listed in the supporting information.

Comment 7: Thank you for stating the following in the Acknowledgments Section of your manuscript: “We are grateful to the South African Medical Research Council and National Research Foundation for financial support.” We note that you have provided funding information that is currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form.

Response: According to the comment, we corrected it.

To Reviewer 1:

Comment 1 (line 38): in length? in width?

Response: Sorry for not explaining enough. It is a straight walking space with a length of 520m. we corrected it

Comment 2 and 3 (line 62~): Adding: inorganic particles and environmental factors

Response: According to the comment, We added these to the keywords of the revised manuscript.

Comment 4 (line 64~): The difference between this article and your article September 18, 2017 is not significant in terms of results. Was there a special reason for presenting this article? It is better to explain the necessity of doing research.

Response: We apologize for the lack of clarity in addressing your points. The novelty of this paper lies in its use of a mathematical model to clarify the interconnectedness of environmental factors. This elucidation was previously unclear based on field data alone. We've added an explanation to this point in the introduction of the revised manuscript, as suggested in the comment.

To Reviewer 2:

Comment 1: The whole text needs proofreading.

Response: According to the comment, the revised paper has been edited in English by Edanz, an English editing company, as suggested in the comment.

Comment 2: The novelty should be highlighted.

Response: The novelty of this paper lies in its use of a mathematical model to clarify the interconnectedness of environmental factors. This elucidation was previously unclear based on field data alone. We've added an explanation to this point in the abstract and introduction of the revised manuscript, as suggested in the comment.

Comment 3: Here you should mention the place and time of conducting the study.

Response: According to the comment, we mentioned the place and time of conducting the study in the abstract of the revised manuscript.

Comment 4: Introduction needs improvement. These papers are useful:

1.https://doi.org/10.1016/j.chemosphere.2023.140627

2.https://doi.org/10.1038/s41598-023-37647-3

3.https://doi.org/10.1016/j.envpol.2023.121854

Response: We have incorporated the suggested papers into the introduction of the revised manuscript, updating the reference numbers accordingly throughout.

Comment 5 (Materials and Methods): You should re-design this section as it can be repeated easily as a recipe.

Following the suggestion, we have redesigned the section, consolidating the command lines to make them easier for readers to repeat.

Comment 6 (Discussion): You should discuss your findings with new findings of relevant studies.

Response: Following comments, we have added an explanation of the novelty and usefulness of this study to the discussion of the revised manuscript.

Attachments
Attachment
Submitted filename: Response to Journal and Reviewers 20240229.doc
Decision Letter - Sara Hemati, Editor

Differential impact of environmental factors on airborne live bacteria and inorganic particles in an underground walkway

PONE-D-23-40119R1

Dear Dr. Yamaguchi,

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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at http://www.editorialmanager.com/pone/ and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, 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,

Sara Hemati

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

-

Reviewers' comments:

-

Formally Accepted
Acceptance Letter - Sara Hemati, Editor

PONE-D-23-40119R1

PLOS ONE

Dear Dr. Yamaguchi,

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.

At this stage, our production department will prepare your paper for publication. This includes ensuring the following:

* All references, tables, and figures are properly cited

* All relevant supporting information is included in the manuscript submission,

* There are no issues that prevent the paper from being properly typeset

If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps.

Lastly, 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 customercare@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. Sara Hemati

Academic Editor

PLOS ONE

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .