Classification of multicategory edible fungi based on the infrared spectra of caps and stalks

Rui Gao; Cheng Chen; Hang Wang; Chen Chen; Ziwei Yan; Huijie Han; Fangfang Chen; Yan Wu; Zhiao Wang; Yuxiu Zhou; Rumeng Si; Xiaoyi Lv

doi:10.1371/journal.pone.0238149

Peer Review History

Original SubmissionApril 26, 2020
8 Jul 2020 Decision Letter - Jie Zhang, Editor PONE-D-20-12067 Classification of Multicategory Edible Fungi based on the Infrared Spectra of Caps and Stalks PLOS ONE Dear Dr. Lv, 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. Specifically, please specify which version of Matlab was used and to italicise the biological genus and species names of the fungi. Please submit your revised manuscript by Aug 21 2020 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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols We look forward to receiving your revised manuscript. Kind regards, Jie Zhang Academic Editor PLOS ONE Journal Requirements: 1. We understand that you purchased mushrooms from local markets for this study. In your Methods section, please provide additional details regarding the source of this material. Please provide the geographic coordinates and names of the purchase locations (e.g., stores, markets), if available, as well as any further details about the purchased items (e.g., lot number, source origin, description of appearance) to ensure reproducibility of the analyses. Additional Editor Comments (if provided): [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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 very well written all the statistical analysis have been done with great rigour and very nicely presented. The manuscript is very easy to follow and targeted for chemometricians. My only comments is to specify which version of Matlab was used and to italicise the biological genus and species names of the fungi. Good job once again to all the authors involved in this publication. ****** 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: Yes:** Frederick Lia [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. 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Revision 1
10 Aug 2020 Author Response Subject: Revised version of the manuscript No.: PONE-D-20-12067 Title: Classification of Multicategory Edible Fungi based on the Infrared Spectra of Caps and Stalks Dear Editor and Reviewer: Thanks to the editor and reviewer for your patient review and important suggestion for our article. We have further revised your valuable suggestions. We have highlighted our manuscript changes through the use of red font in the revised manuscript. The revision was carried out as a result of the comments of the editor and the reviewer. The main corrections in the paper and the responds to the editor’s comments and the responds to the reviewer’s comments are as following: Editor : Response to comment (1): ( We understand that you purchased mushrooms from local markets for this study. In your Methods section, please provide additional details regarding the source of this material. Please provide the geographic coordinates and names of the purchase locations (e.g., stores, markets), if available, as well as any further details about the purchased items (e.g., lot number, source origin, description of appearance) to ensure reproducibility of the analyses.) Response-1: Many thanks to the editor for the suggestions. Based on your suggestions, we have supplemented the description of the source origin, names of the purchase locations and appearance of mushrooms in 2. Experimental methods to ensure reproducibility of the analyses. Thanks again to the editor for your valuable suggestions. The contents are as follows: Among them, Lentinus edodes are produced in Fujian Province of China, and purchased from Fuchang Food Limited Company, Fujian Province of China; club fungi are produced in Yunnan Province of China, purchased from Wuweijin Store, and Bachu mushrooms are produced in Bachu County, Xinjiang Province, and purchased from the most famous wholesale market in Urumqi -- Six Markets. The three kinds of mushrooms purchased are all dried. The caps of the three kinds of mushrooms are umbrella-shaped and dark brown. The stalks of club fungi are longer and those of Lentinus edodes and Bachu mushrooms are shorter. The three kinds of mushrooms are similar in appearance. The samples of the three types of edible fungi were purchased from the market. Reviewer #1: 1.Response to comment (1-4): Response: Thank you very much for the reviewer's agreement on our work, which will encourage us to do better work in the future. 2.Response to comment (5): ( The manuscript is very well written all the statistical analysis have been done with great rigour and very nicely presented. The manuscript is very easy to follow and targeted for chemometricians. My only comments is to specify which version of Matlab was used and to italicise the biological genus and species names of the fungi. Good job once again to all the authors involved in this publication.) Response-5: Thanks to the reviewer for the suggestions. We have supplemented the MATLAB version and italicised the biological genus and species names of the fungi in the article. Thank the reviewer and editor for your patient and careful review. I hope you have good health and success in your work. Sincerely yours, Dr. Xiaoyi Lv, Dr. Cheng Chen Attachments Attachment Submitted filename: Response to Reviewers.doc https://doi.org/10.1371/journal.pone.0238149.r002
11 Aug 2020 Decision Letter - Jie Zhang, Editor Classification of Multicategory Edible Fungi based on the Infrared Spectra of Caps and Stalks PONE-D-20-12067R1 Dear Dr. Lv, 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, Jie Zhang Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0238149.r003
Formally Accepted
13 Aug 2020 Acceptance Letter - Jie Zhang, Editor PONE-D-20-12067R1 Classification of Multicategory Edible Fungi based on the Infrared Spectra of Caps and Stalks Dear Dr. Lv: 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. Jie Zhang Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0238149.r004

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