Inferring stimulation induced short-term synaptic plasticity dynamics using novel dual optimization algorithm

Alireza Ghadimi; Leon Amadeus Steiner; Milos R. Popovic; Luka Milosevic; Milad Lankarany

doi:10.1371/journal.pone.0273699

Peer Review History

Original SubmissionFebruary 6, 2022
15 May 2022 Decision Letter - Jun Ma, Editor PONE-D-22-01502Inferring Stimulation Induced Short-term Synaptic Plasticity Dynamics Using Novel Dual Optimization AlgorithmPLOS ONE Dear Dr. Lankarany, 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 Jun 26 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. 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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. Thank you for stating the following financial disclosure: This study was supported by the following grants and scholarships: AGEWELL, UofT FASE Graduate Student and Postdoctoral Award in Technology and Aging (A.G.); Deutsche Forschungsgemeinschaft (DFG, German Research Fundation) Project ID 424778381 TRR 295 (L.A.S.); Junior Clinician Scientist Program of the Berlin Institute of Health (L.A.S.); German Academic Exchange Service, DAAD (L.A.S.); Brain Canada Foundation (L.M.); Walter and Maria Schroeder Foundation (L.M.) Natural Sciences and Engineering Research Council of Canada, RGPIN-2020-05868 (M.L) 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. 4. Thank you for stating the following in your Competing Interests section: We do not report any original data. We tested the performance of our proposed algorithm on a previously published data (see reference 7 in the submitted manuscript). Please complete your Competing Interests on the online submission form to state any Competing Interests. If you have no competing interests, please state "The authors have declared that no competing interests exist.", as detailed online in our guide for authors at http://journals.plos.org/plosone/s/submit-now This information should be included in your cover letter; we will change the online submission form on your behalf. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Does the manuscript provide a valid rationale for the proposed study, with clearly identified and justified research questions? The research question outlined is expected to address a valid academic problem or topic and contribute to the base of knowledge in the field. Reviewer #1: Yes ******** 2. Is the protocol technically sound and planned in a manner that will lead to a meaningful outcome and allow testing the stated hypotheses? The manuscript should describe the methods in sufficient detail to prevent undisclosed flexibility in the experimental procedure or analysis pipeline, including sufficient outcome-neutral conditions (e.g. necessary controls, absence of floor or ceiling effects) to test the proposed hypotheses and a statistical power analysis where applicable. As there may be aspects of the methodology and analysis which can only be refined once the work is undertaken, authors should outline potential assumptions and explicitly describe what aspects of the proposed analyses, if any, are exploratory. Reviewer #1: Yes ****** 3. Is the methodology feasible and described in sufficient detail to allow the work to be replicable? Descriptions of methods and materials in the protocol should be reported in sufficient detail for another researcher to reproduce all experiments and analyses. The protocol should describe the appropriate controls, sample size calculations, and replication needed to ensure that the data are robust and reproducible. Reviewer #1: Yes ****** 4. Have the authors described where all data underlying the findings will be made available when the study is complete? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception, at the time of publication. 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 ****** 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 and, if applicable, provide comments about issues authors must address before this protocol can be accepted for publication. You may also include additional comments for the author, including concerns about research or publication ethics. You may also provide optional suggestions and comments to authors that they might find helpful in planning their study. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The paper is interesting. It is a great deal to fit a model to experimental data. I would suggest to describe this in more details in the Introduction. There were several books published in this field previously. See for instance: 1. Chaos and Its Reconstructions, New York: Nova Science Publishers; 2003. (Eds). G. Gouesbet, S. Meunier-Guttin-Cluzel, O. Ménard. 2. Bezruchko BP, Smirnov DA. Extracting Knowledge From Time Series: (An In- troduction to Nonlinear Empirical Modeling. New York: Springer; 2010. There could be some newer also. Please, rebuild all figures. The figures are of very bad quality and some of them even cannot be read. It is hard to understand why the Results section is placed before the Methods section, if this is journal's policy I can only pity all of us. What do the strikeout terms in Eq. (15,16,22,23) mean? Please, report details of both optimization algorithms used: Trust-Region optimization methods and Nelder-Mead algorithm. Some programming functions like "argmax" and "argmin" appear in the text, but they are not suitable there. They should be explained or, better, reformulated. In Eq. 28 both * and × were used, for what? I did not found how many series and individuals were evaluated. Maybe, I was inattentive, but this affects the robustness of outcomes. What is the variability of fitting results between different series and individuals? ******** 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: Yes:** Ilya V. Sysoev [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.0273699.r001
Revision 1
4 Jul 2022 Author Response We thank the reviewer for the constructive feedback. These comments are reproduced below in blue together with our responses in black. Major changes to the manuscript text are indicated in red. We have striven to address all concerns. We believe that our paper has been significantly improved by addressing the reviewer’s comments and we hope that it will now be considered suitable for publication in the prestigious Plos One Journal. Reviewer #1: The paper is interesting. It is a great deal to fit a model to experimental data. Re: Thank you. We appreciate your understanding about the importance of this methodology for neural data. • I would suggest to describe this in more details in the Introduction. There were several books published in this field previously. See for instance: 1. Chaos and Its Reconstructions, New York: Nova Science Publishers; 2003. (Eds). G. Gouesbet, S. Meunier-Guttin-Cluzel, O. Ménard. 2. Bezruchko BP, Smirnov DA. Extracting Knowledge From Time Series: (An Introduction to Nonlinear Empirical Modeling. New York: Springer; 2010. Re: We have added these references in Introduction. Thanks for your suggestions. • Please, rebuild all figures. The figures are of very bad quality and some of them even cannot be read. Re: The figures that were integrated in the PDF has reduced quality. The high-quality figures were attached to the document (in the "other" file). We request the reviewer to kindly consider that we used the figures within the text in the revised manuscript to enhance its reading, but it was the journal policy to keep figures away from the main body text. We will make sure all figures, with original high qualities, be used in the final structure for publication. This is why we provided "other" document including all figures within the text. We hope that the reviewer can access to this document to endorse the quality of original figures. • It is hard to understand why the Results section is placed before the Methods section, if this is journal's policy I can only pity all of us. Re: Yes, it was the journal policy to have the results prior to the method section. • What do the strikeout terms in Eq. (15,16,22,23) mean? Re: Required explanations were added to the revised manuscript. • Please, report details of both optimization algorithms used: Trust-Region optimization methods and Nelder-Mead algorithm. Re: These detials were added to the revised manuscript. • Some programming functions like "argmax" and "argmin" appear in the text, but they are not suitable there. They should be explained or, better, reformulated. Re: Required explanations were added to the revised manuscript. • In Eq. 28 both * and × were used, for what? Re: It was a typo and it is corrected in the revised manuscript. • I did not found how many series and individuals were evaluated. Maybe, I was inattentive, but this affects the robustness of outcomes. What is the variability of fitting results between different series and individuals? Re: Good observation. The data used in this work was from 1 individual, we used this data as for a proof of principal. Thank you. https://doi.org/10.1371/journal.pone.0273699.r002
14 Jul 2022 Decision Letter - Jun Ma, Editor PONE-D-22-01502R1Inferring Stimulation Induced Short-term Synaptic Plasticity Dynamics Using Novel Dual Optimization AlgorithmPLOS ONE Dear Dr. Lankarany, 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 27 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. 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, Jun Ma, Dr. 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. [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: 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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A ****** 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 ****** 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: Most raised issues were reasonably addressed. I have to comment two new points which appeared in the revised manuscript and were not present in the original paper. 1. The only rat was considered. So, the model reconstruction was done only just as a proof of concept. In any case I do support this research. But this should be clearly stated in both abstract and Introduction. 2. The second derivative was calculated from the data. Experimental data are noisy and all numerical approaches are very sensitive to measurement noise. Please, comment what was done to minimize the effect of the noise (e.g. Savitzky–Golay filter). Also, please, take into account that in some recent papers the models integrated over time are preferred for identification, since this reduces number of differentiations, see e.g. [1] Mishchenko et al. Identification of Phase-Locked Loop System from Its Experimental Time Series. IEEE Transactions on Circuits and Systems II: Express Briefs, 2022. 69(3):854-858 doi: 10.1109/TCSII.2021.3122892 [2] Sysoev & Bezruchko. Noise robust approach to reconstruction of van der Pol-like oscillators and its application to Granger causality. Chaos 31, 083118 (2021); doi: 10.1063/5.0056901 Both these papers actually deal with some neuron-like models though this is not clear from the title. Please, study, whether reconstruction of integrated over time equations is theoretically possible for the considered system. ****** 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 ******** [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.0273699.r003
Revision 2
8 Aug 2022 Author Response We thank the reviewer for the constructive feedback. We hope that it will now be considered suitable for publication in the prestigious Plos One Journal. Reviewer #1: Most raised issues were reasonably addressed. I have to comment two new points which appeared in the revised manuscript and were not present in the original paper. 1. The only rat was considered. So, the model reconstruction was done only just as a proof of concept. In any case I do support this research. But this should be clearly stated in both abstract and Introduction. Re: Thank you. Your point is very true. We added this point in both the Abstract and the Introduction. Please see the revised version. 2. The second derivative was calculated from the data. Experimental data are noisy and all numerical approaches are very sensitive to measurement noise. Please, comment what was done to minimize the effect of the noise (e.g. Savitzky–Golay filter). Also, please, take into account that in some recent papers the models integrated over time are preferred for identification, since this reduces number of differentiations, see e.g. [1] Mishchenko et al. Identification of Phase-Locked Loop System from Its Experimental Time Series. IEEE Transactions on Circuits and Systems II: Express Briefs, 2022. 69(3):854-858 doi: 10.1109/TCSII.2021.3122892 [2] Sysoev & Bezruchko. Noise robust approach to reconstruction of van der Pol-like oscillators and its application to Granger causality. Chaos 31, 083118 (2021); doi: 10.1063/5.0056901 Both these papers actually deal with some neuron-like models though this is not clear from the title. Please, study, whether reconstruction of integrated over time equations is theoretically possible for the considered system. Re: Your point is reasonable, this is why we added a new sub-section to our Methodology part, sub-section 2.6.1, to address your point. We mainly put our focus to provide a context for the suggested references as they are suitable to deal with noise using numerical integration (rather than the differentiation). As well to justify why our algorithm can be reasonably robust to experimental noise, we considered the steady-state estimation of the TM model, which can be calculated from the recorded PSC over time (average). Please note that since the scope of this paper and proposed algorithm were not on the exploration of the impact of noise, we think that this sub-section can address the importance of noise in experimental data without diverging the focus of the paper. Thank you. https://doi.org/10.1371/journal.pone.0273699.r004
15 Aug 2022 Decision Letter - Jun Ma, Editor Inferring Stimulation Induced Short-term Synaptic Plasticity Dynamics Using Novel Dual Optimization Algorithm PONE-D-22-01502R2 Dear Dr. Lankarany, 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, Jun Ma, Dr. Academic Editor PLOS ONE Reviewer #1: All comments have been addressed ********** https://doi.org/10.1371/journal.pone.0273699.r005
Formally Accepted
7 Sep 2022 Acceptance Letter - Jun Ma, Editor PONE-D-22-01502R2 Inferring Stimulation Induced Short-term Synaptic Plasticity Dynamics Using Novel Dual Optimization Algorithm Dear Dr. Lankarany: 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. and Pro. Jun Ma Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0273699.r006

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