Mental chronometry in big noisy data

Edmund Wascher; Fariba Sharifian; Marie Gutberlet; Daniel Schneider; Stephan Getzmann; Stefan Arnau

doi:10.1371/journal.pone.0268916

Peer Review History

Original SubmissionNovember 29, 2021
7 Mar 2022 Decision Letter - Wajid Mumtaz, Editor PONE-D-21-37772Mental chronometry in big noisy dataPLOS ONE Dear Dr. Edmund Wascher, 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 Apr 21 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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If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.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 (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: This is an interesting paper. It deals with important methodological issues and it provides a beautiful overview of some recent approaches to handle big data. The issue of ERPs moreover is a timely topic with a lot of interest for cognitive neuroscience. The whole idea of “mental chronometry”, therefore, is quite challenging. The paper as a whole is well written, with a sound methodology, and some interesting and convincing results, but the readability and understandability of the technical matters could be a problem for the common readership of PLoS One, which consists not only of highly trained neuroscientists. I therefore suggest to add more intuitive descriptions of technical terms and to be more explicit in the description of some methodological procedures. In order to provide a critical-constructive review, I list below some general remarks and detailed comments. I propose to accept the paper for publication on condition that the remarks and comments are addressed appropriately. General remarks � The English use is OK and is quite idiomatic. The explanation of the basic concepts of the paper should be explained in more intuitive terms at their first appearance. This can be very short, but it is important that non-informed readers can have an intuition of the meaning of the terms (see below for detailed comments). � Concepts as peak latency, fractional area latency and jackknife procedure need a better intuitive description, given their importance for the whole paper. Even if these are common terms for trained neuroscientists, they are not easily understandable for readers outside of the field. An additional figure to illustrate the intuition behind the terms could also be helpful here. � The methodology seems to be sound and very strict, nut is not easy to understand. Some more elaborate digression in the methodology section should be welcome so as to guide the reader somewhat through the paper. � There are some very interesting results. Perhaps some additional explaining text about the role and measurement of the grand averages could add additional value to these findings and could make the take home message stronger. � The use of quality criteria is not clear and should be explained more in detail. � The paper as a whole is very technical. This is a strength, but somewhat at the cost of understandability and readability. A better description of some technicalities would increase the impact of the paper. Detailed comments � page 8: there are no keywords � page 9, 1st paragraph: here the concept of peak latency is first introduced. Provide a very short description of the intuitive meaning of the term. � page 9, 2nd paragraph: same remark with respect to the term “connectome” � page 10: same remark with respect to the three focal concepts of peak latencies, fractional area latencies (give the percentages), and jackknifing procedure. Especially the latter is not sufficiently explained. Also the motivation for the N-1 subject average is not sufficiently clear. Please provide the motivation behind this procedure. � page 11, 2nd par.: trial count would never be are than 26: not clear, explain better � page 12,3rd par.: fractional area latencies: explain better the point that divides the area into two regions (equal size: 50 %, or another division). This is given later in the paper, but it should be given here at first appearance. A possible example of a short intuitive description could be: “fractional area latencies measure the area within a time window and finds the time point that divides the area into a specific fraction.” Such short intuitive explanations can do a lot to improve the overall readability of a technical paper. � page 15, 1st par.: explain better how you came to the number of 132 trials. � page 15, 2nd par.: explain a little more in detail what is meant with alternate draw analysis (can be very short). This paragraph as a whole is difficult to understand. Please be clearer here. � page 15, last par.: ICA: I guess this means Independent component analysis? Please write in full with the abbreviation between brackets at first appearance. � page 17, last par.: this whole paragraph about quality criteria is not clear. Explain better what is meant with quality criteria and what the aim is of this paragraph. Explain also how to understand the pruned dataset. � page 18, last par.: explain the concept of split-reliability in more intuitive terms. � page 19: fig. 2: caption: the four splits are not clear. Please explain better, either in the main text or in the figure caption. Try to avoid that readers must invest too much time in deciphering the figures. � page 20: perhaps a stupid question, but how to interpret the F-value of the table. What has been tested? What kind of statistical significance? The table seems to be very rich in content, but it is quite difficult to do the interpretation. Some guidance for the reader should be welcome. ****** 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 [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.0268916.r001
Revision 1
31 Mar 2022 Author Response Action letter revision “Mental chronometry in big noisy data” Please ensure that your manuscript meets PLOS ONEs style requirements Style has been checked. References have been corrected. We note that you have indicated that data from this study are available upon request. Data as requested are now available at https://osf.io/73f8u/ 4. Please include your full ethics statement in the ‘Methods’ section of your manuscript file. ethics statement is added 5. Please review your reference list Done Comments to the Author Review Comments to the Author Reviewer #1: This is an interesting paper. It deals with important methodological issues and it provides a beautiful overview of some recent approaches to handle big data. The issue of ERPs moreover is a timely topic with a lot of interest for cognitive neuroscience. The whole idea of “mental chronometry”, therefore, is quite challenging. The paper as a whole is well written, with a sound methodology, and some interesting and convincing results, but the readability and understandability of the technical matters could be a problem for the common readership of PLoS One, which consists not only of highly trained neuroscientists. I therefore suggest to add more intuitive descriptions of technical terms and to be more explicit in the description of some methodological procedures. General remarks � The English use is OK and is quite idiomatic. The explanation of the basic concepts of the paper should be explained in more intuitive terms at their first appearance. This can be very short, but it is important that non-informed readers can have an intuition of the meaning of the terms (see below for detailed comments). � Concepts as peak latency, fractional area latency and jackknife procedure need a better intuitive description, given their importance for the whole paper. Even if these are common terms for trained neuroscientists, they are not easily understandable for readers outside of the field. An additional figure to illustrate the intuition behind the terms could also be helpful here. A new figure 1 is added with the symbolic presentation of peak latency and fractional area latency. Additionally, the problem of high frequency noise is part of the presentation Figure 1. Simulated data for two subsets of a typical posterior waveshape (black and red lines), reflecting a P3 component. Both, peak latencies and 50% fractional area latencies were extracted. Peak latencies denote a single moment of maximal voltage within the designated measurement window. Fractional area latency denotes the moment when the cumulative area under the curve exceeds a defined criterion, here 50% of the overall area. Despite the high similarity of morphology across the two subsets, peak latencies would show an effect of more than 50 ms due to high frequency noise (solid vertical lines), that did not affect fractional area latency to the same amount (dashed vertical lines). Also the jackknifing procedure is described now more extensively. � The methodology seems to be sound and very strict, but is not easy to understand. Some more elaborate digression in the methodology section should be welcome so as to guide the reader somewhat through the paper. A paragraph was added, describing the rationale for the processing pipeline. Arguments for single processing steps are added. � There are some very interesting results. Perhaps some additional explaining text about the role and measurement of the grand averages could add additional value to these findings and could make the take home message stronger. We did not really understand this point. The grand average is just a overall average for presentation that is not subject to measurement. � The use of quality criteria is not clear and should be explained more in detail. See detailed comments � The paper as a whole is very technical. This is a strength, but somewhat at the cost of understandability and readability. A better description of some technicalities would increase the impact of the paper. We hope that we managed to make descriptions clearer Detailed comments � page 8: there are no keywords Keywords are added � page 9, 1st paragraph: here the concept of peak latency is first introduced. Provide a very short description of the intuitive meaning of the term. We added a better description of the measures used and a conceptual graph that should make the concepts better to understand � page 9, 2nd paragraph: same remark with respect to the term “connectome” The “human connectome project” is described now in more detail � page 10: same remark with respect to the three focal concepts of peak latencies, fractional area latencies (give the percentages), and jackknifing procedure. Especially the latter is not sufficiently explained. Also the motivation for the N-1 subject average is not sufficiently clear. Please provide the motivation behind this procedure. Motivations and descriptions for procedures are added � page 11, 2nd par.: trial count would never be are than 26: not clear, explain better Is explained now in detail � page 12,3rd par.: fractional area latencies: explain better the point that divides the area into two regions (equal size: 50 %, or another division). This is given later in the paper, but it should be given here at first appearance. A possible example of a short intuitive description could be: “fractional area latencies measure the area within a time window and finds the time point that divides the area into a specific fraction.” Such short intuitive explanations can do a lot to improve the overall readability of a technical paper. The concept of fractional area latency is described 2 pages before. Now furthermore, an additional figure illustrates it. � page 15, 1st par.: explain better how you came to the number of 132 trials. Has been made explicit � page 15, 2nd par.: explain a little more in detail what is meant with alternate draw analysis (can be very short). This paragraph as a whole is difficult to understand. Please be clearer here. Added � page 15, last par.: ICA: I guess this means Independent component analysis? Please write in full with the abbreviation between brackets at first appearance. Done � page 17, last par.: this whole paragraph about quality criteria is not clear. Explain better what is meant with quality criteria and what the aim is of this paragraph. Explain also how to understand the pruned dataset. This small chapter is revised � page 18, last par.: explain the concept of split-reliability in more intuitive terms. Is now more explicitly named and also described in the method section more explicitly � page 19: fig. 2: caption: the four splits are not clear. Please explain better, either in the main text or in the figure caption. Try to avoid that readers must invest too much time in deciphering the figures. Caption of fig.2 (which is now figure 3), has been revised accordingly � page 20: perhaps a stupid question, but how to interpret the F-value of the table. What has been tested? What kind of statistical significance? The table seems to be very rich in content, but it is quite difficult to do the interpretation. Some guidance for the reader should be welcome. Information about statistics is added in the table capture as well as in the method section While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool All figures were tested by PACE Attachments Attachment Submitted filename: Action noisy data_v2.docx https://doi.org/10.1371/journal.pone.0268916.r002
11 May 2022 Decision Letter - Wajid Mumtaz, Editor Mental chronometry in big noisy data PONE-D-21-37772R1 Dear Dr. Edmund Wascher, 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, Wajid Mumtaz Academic Editor PLOS ONE Additional Editor Comments (optional): 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: (No Response) ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: (No Response) ****** 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: (No Response) ****** 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: (No Response) ****** 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: (No Response) ****** 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 https://doi.org/10.1371/journal.pone.0268916.r003
Formally Accepted
24 May 2022 Acceptance Letter - Wajid Mumtaz, Editor PONE-D-21-37772R1 Mental chronometry in big noisy data Dear Dr. Wascher: 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. Wajid Mumtaz Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0268916.r004

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