Automated scoring of nematode nictation on a textured background

Patrick D. McClanahan; Luca Golinelli; Tuan Anh Le; Liesbet Temmerman

doi:10.1371/journal.pone.0289326

Peer Review History

Original SubmissionMay 3, 2023
4 Jul 2023 Decision Letter - Ebrahim Shokoohi, Editor PONE-D-23-13383Automated scoring of nematode nictation on a textured backgroundPLOS ONE Dear Dr. McClanahan, 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 Aug 18 2023 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. 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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. Thank you for stating the following in the Acknowledgments Section of your manuscript: "We would like to thank Anthony Fouad, Zihao Li, and Andre Brown for useful discussions concerning the design of the tracking and behavior classification algorithms; and Junho Lee, Heeseung Lee, Bram Cockx, and William Schafer for useful discussions regarding the project. N2 was provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440)." We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. 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Reviewer #1: 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: The manuscript contains very exciting information about nictation in free living nematodes. However, minor changes before acceptance needs to be addressed. 1-the English's style need to be revised. the comment's are attached. 2-What factors included in the behavior of nictation? What temperature, humidity, etc.? 3-What is the capability of in vivo application of this study? 4-Does it beneficial only to nematode behavior's? 5-How the nictation in the nature affect the behavior's of EPN and free living nematodes? ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). 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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: manuscript-revised.docx https://doi.org/10.1371/journal.pone.0289326.r001
Revision 1
12 Jul 2023 Author Response Response to editor comments: 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. We have reviewed the PLOS One formatting guidelines and set heading to the appropriate heading level as well as changed citations to the PLOS One style (reference numbers in brackets). 2. We note that you have provided funding information [in the Acknowledgements Section] that is not 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. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Please include your amended statements within your cover letter; we will change the online submission form on your behalf. Thank you for pointing out this error. We have removed the funding source of the CGC from the Acknowledgments section of our manuscript (lines 724-728 with tracked changes visible) and requested that this information be included in the Funding Statement instead (please see cover letter). Dear Authors Please check the English style, and it must be significantly revised. The comments from the Referee also must be address. The revised version is attached for your reference. One of the author comment on the MS left before the submission. We thank the editor for his comments. Our manuscript has been reviewed by a native speaker of English (see below). Response to reviewer comments: The manuscript contains very exciting information about nictation in free living nematodes. However, minor changes before acceptance needs to be addressed. We thank the reviewer for their support and enthusiasm and for pointing out various ways we could improve our manuscript. 1-the English's style need to be revised. the comment's are attached. We thank the reviewer for their observations and corrections. Our revised manuscript has been checked by a native speaker of English. Based on their advice, we chose to keep these corrections in the revised manuscript, and also corrected several other grammatical and spelling errors. All these corrections can be seen as tracked changes in the 'revised_manuscript_with_changes_highlighted.docx' document appended to this submission. 2-What factors included in the behavior of nictation? What temperature, humidity, etc.? We agree that many factors may affect nictation behavior. This is why we performed all experiments in a climate-controlled room on microdirt arenas fabricated under controlled conditions. For S. carpocapsae, the temperature of the room was held between 23-24 °C and for C. elegans, 20-21 °C. For both, the humidity in the room was 30-45% (lines 578-579 of the revised manuscript). During all experiments, the arena was kept inside a sealed, humidified Petri dish (lines 586-588) and the same trans illumination system was used for recording (lines 554-559). 3-What is the capability of in vivo application of this study? We thank the reviewer for wondering about further potential applications of our system. Our study describes a behavioral assay performed on whole, living animals. As such, it could be used to assess the effects of a variety of interventions, in vivo in the nematodes. These include for example targeted mutations, transgene expression, gene knockdowns, compound interventions, varying environmental influences, etc. We have now mentioned such applications in the revised Discussion (lines 494-497). 4-Does it beneficial only to nematode behavior's? Our analysis pipeline is designed to score nictation in nematodes. However, it may be possible to apply the pipeline to other behaviors in other model organisms, provided they have a cylindrical shape whose posture can be represented as a spline (e.g. fruit fly larvae or zebrafish). This suggestion is included in the Discussion section of the revised manuscript (lines 504-509). 5-How the nictation in the nature affect the behavior's of EPN and free living nematodes? Nictation is a means for nematodes to attach themselves to larger animals, such as insects. EPNs and free-living nematodes differ in that for EPNs, the host is the food source, whereas for free-living nematodes, the host is a means of transport to a food source. We discuss this distinction in the manuscript Introduction (lines 35-40). How natural conditions such as CO2, air movement, and host cues affect this behavior is an important question, especially for biocontrol. Several studies have investigated the effects of various environmental conditions on nictation (cited in lines 389-391). We believe that our platform could be adapted to study these manipulations systematically in controlled conditions, and have added this to the revised discussion (lines 496-497). We thank the editor and reviewer for their feedback. Additionally, we have corrected the y-tick labels on Fig 5C, which we noticed were wrong in our initial submission, and uploaded a new image files for that figure as well as the other figures after processing thru the PACE tool. https://doi.org/10.1371/journal.pone.0289326.r002
17 Jul 2023 Decision Letter - Ebrahim Shokoohi, Editor Automated scoring of nematode nictation on a textured background PONE-D-23-13383R1 Dear Dr. McClanahan, 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, Ebrahim Shokoohi Academic Editor PLOS ONE Additional Editor Comments (optional): The authors addressed the questions raised by Referees and AE, as possible. Reviewers' comments: No comments https://doi.org/10.1371/journal.pone.0289326.r003
Formally Accepted
24 Jul 2023 Acceptance Letter - Ebrahim Shokoohi, Editor PONE-D-23-13383R1 Automated scoring of nematode nictation on a textured background Dear Dr. McClanahan: 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. Ebrahim Shokoohi Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0289326.r004

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