PONE-D-24-00457Integrating machine learning in endemic lily conservation: advanced micropropagation techniques for Lilium akkusianum R. GämperlePLOS ONE

Dear Dr. Tütüncü,

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We look forward to receiving your revised manuscript.

Kind regards,

Mojtaba Kordrostami, Ph.D.

Academic Editor

PLOS ONE

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Additional Editor Comments:

Thank you for submitting your manuscript titled Integrating machine learning in endemic lily conservation: advanced micropropagation techniques for Lilium akkusianum R. Gämperle to PLOS ONE. We have now completed the review of your manuscript, and after considering the feedback from 2 experts in the field, we believe that your study makes a valuable contribution to the knowledge on the micropropagation of Lilium akkusianum. However, before your manuscript can be considered for publication, it is necessary for you to address several important issues raised during the review process. Therefore, we invite you to resubmit your manuscript after making major revisions.

Reviewer 1 Comments:

Writing Quality: There are concerns about the clarity and quality of writing throughout the manuscript. It is recommended that you seek the assistance of an expert in scientific writing to improve the English language and presentation of your work.

Species Name Formatting: Please ensure that the species name, Lilium akkusianum, is presented in full and italicized upon its first mention in the abstract, and maintain correct formatting throughout the text.

Introduction Section: The introduction should focus specifically on research progress related to Lilium akkusianum rather than a broad overview of tissue culture in different species. Any comparison with other species should be moved to the discussion section.

Histological Sections: The relevance and quality of the histological sections presented are questioned. It is advised to remove these sections, except for Figure 3G, which was deemed valuable.

Formatting: Ensure that all instances of Latin names and terms such as in vitro/ex vitro are italicized throughout the manuscript.

Reviewer 2 Comments:

Title Revision: The current title misleadingly suggests that machine learning (ML) is a micropropagation technique. Since ML is used as an analysis method in your research, the title should be revised to accurately reflect its application in the study of Lilium akkusianum. A suggested revision could focus on the in vitro propagation of Lilium akkusianum and the application of ML in this context.

Conclusions: The conclusions need to be revisited to provide specific insights into the ML methods applied and their effectiveness in the study. General statements on the use of ML should be supplemented with concrete findings from your research.

General Recommendations:

Ensure consistent formatting for scientific names and terms throughout the manuscript.

Review and address the specific points for revision mentioned in the attached PDF by the second reviewer.

We appreciate the effort you have put into your research and believe that addressing these points will significantly enhance the quality and impact of your manuscript. Please submit your revised manuscript along with a detailed response to the reviewers' comments and a summary of the changes made.

We look forward to receiving your revised manuscript and are optimistic about its potential contribution to the field. Should you have any questions or require further clarification, please do not hesitate to contact the editorial office.

Sincerely,

Mojtaba Kordrostami

Editor, PLOS ONE

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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

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

Reviewer #1: N/A

Reviewer #2: Yes

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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

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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: No

Reviewer #2: Yes

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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: A primary adventitious buds and regeneration protocol was developed for micropropagation of Lilium akkusianum bulb explants.

They have finished callus induction, bud regeneration and transplantation process. Howerver, the writing has some problem and need improve.

It is hoped that the author will find an expert to revise the writing of the paper and improve the English level；

In the abstract, when the species name appears first, the full name is concerned;

In the introduction, there is no need to introduce the relevant research on the tissue culture of other species, as long as the research progress of that species is introduced, you can transplant them into the discussion to take the discussion, and introduce their similarities and differences；

Histological sections don't make any sense here, and they aren't done well; It is advisable to just keep Figure 3G;

Major latin requires italics, note spaces;

Reviewer #2: Minor Revision

General Comments

The study presents a suitable micropropagation method for Lilium akkusiamum, using various phytohormones.

This is the first study on this endemic species.

The genetic stability of regenerated plantlets was assessed as well by molecular markers.

Machine learning methods were evaluated as well.

The reference list is extended with recent manuscripts.

There are no unnecessary references.

A general comment is that in vitro/ex vitro etc and scientific names must be written in italics everywhere in the text.

Introduction

The background is OK. There are information relevant studies and in vitro methods in the genus Lilium. The aim is clearly presented.

Material and Methods

Well and clear presented.

Statistical methods, design and replications suitable for analysis.

Results

Well presented, including the necessary figures, tables and pictures.

Discussion

Well presented. It contains the necessary references.

There are some issues in the attached .pdf

To my opinion there are two points to be revised:

1. Title

“Integrating machine learning in endemic lily conservation: advanced micropropagation techniques for Lilium akkusianum R. Gämperle”

Comment:

Machine learning is not a micropropagation technique. It is an analysis method used in micropropagation research. The reports confirm the reliability and accuracy of artificial intelligence in micropropagation systems. On the other hand, they are methods of analyzing data. I mean that micropropagation techniques are meristem culture, embryo culture, callus culture e.t.c. Additionally the manuscript presents a valuable, conventional, micropropagation method by scales and various phytohormones on solid MS media. To my opinion, there have not been used advanced micropropagation techniques and the title should be revised. It is about an application of ML in in vitro propagation of endemic lily Lilium akkusianum R. Gämperle.

The title must be focused on in vitro propagation and the usage/application of ML.

2. Conclusions

Comment:

I think that they need revision. There are general comments on the use of ML. Did a suitable ML-method revealed?

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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.

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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

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[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.]

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Attachments

Attachment

Submitted filename: PONE-D-24-00457_reviewer.pdf

Attachment

Submitted filename: PONE-D-24-00457_reviewer_1_.pdf

PONE-D-24-00457R1Application of machine learning in in vitro propagation of endemic Lilium akkusianum R. GämperlePLOS ONE

Dear Dr. Tütüncü,

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 Jul 11 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,

Mojtaba Kordrostami, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Additional Editor Comments:

Dear colleagues,

Please revise the manuscript before the final acceptance.

Regards

M. Kordrostami

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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

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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

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

Reviewer #1: Yes

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

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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)

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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: After the author can revised the following mini errors in the text, the manuscript can be accepted.

Line 199 µ?

Line 199, subscript;

The second paragraph or others need to be preceded by a few spaces；

Between two numbers in the text, use “‒”;

Conclusion section, it's too long, reducing the numbers and condensing the content.

Reviewer #2: (No Response)

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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.

Attachments

Attachment

Submitted filename: PONE-D-24-00457_R1_reviewer.pdf

Application of machine learning in in vitro propagation of endemic Lilium akkusianum R. Gämperle

PONE-D-24-00457R2

Dear Dr. Tütüncü,

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.

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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,

Mojtaba Kordrostami, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: