An efficient 3D column-only P300 speller paradigm utilizing few numbers of electrodes and flashings for practical BCI implementation

Onur Erdem Korkmaz; Onder Aydemir; Emin Argun Oral; Ibrahim Yucel Ozbek

doi:10.1371/journal.pone.0265904

Peer Review History

Original SubmissionSeptember 15, 2021
7 Jan 2022 Decision Letter - M. Shamim Kaiser, Editor PONE-D-21-29800An efficient 3D column-only P300 speller paradigm utilizing few numbers of electrodes and flashings for practical BCI implementationPLOS ONE Dear Dr. korkmaz, 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. ============================== ACADEMIC EDITOR: Ensure the quality and legibility of all figures; use the citation whenever required; include the contribution in bullet format ============================== Please submit your revised manuscript by Feb 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. 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, M. Shamim Kaiser, PhD Academic Editor PLOS ONE Journal requirements: 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. 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 financial disclosure: “No” At this time, please address the following queries: a) Please clarify the sources of funding (financial or material support) for your study. List the grants or organizations that supported your study, including funding received from your institution. b) State what role the funders took in the study. If the funders had no role in your study, please state: “The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.” c) If any authors received a salary from any of your funders, please state which authors and which funders. d) If you did not receive any funding for this study, please state: “The authors received no specific funding for this work.” Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 3. Thank you for stating the following in your Competing Interests section: “NO authors have competing interests” 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. 4. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability. Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized. Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access. We will update your Data Availability statement to reflect the information you provide in your cover letter. [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: Partly Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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: No Reviewer #2: 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 Reviewer #2: 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: Please amend the title either on the online submission form or in your manuscript so that they are identical. Please explain the rationale for the development of your work, and clearly indicating which problem with existing approaches you are addressing. Also describe about the datasets used in this work briefly. Please clearly report at the beginning of your methods or results section which the key performance measures were to establish validity and utility of your new system. Reviewer #2: In Brain Computer Interfaces (BCI), an event of P300 potentials, positive waveforms in electroencephalography (EEG) signals are used often. There are many studies in this field where main focus is to improve performance. Special thanks to authors for choosing this kind of application oriented field. However, 1. Figure 1 should be clearer. 2. Data set references are needed. ****** 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 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. https://doi.org/10.1371/journal.pone.0265904.r001
Revision 1
15 Jan 2022 Author Response AUTHOR RESPONSES TO THE REVIEWERS Journal: PONE-D-21-29800 Title of the manuscript: An efficient 3D column-only P300 speller paradigm utilizing few numbers of electrodes and flashings for practical BCI implementation Authors: Onur Erdem Korkmaz, Onder Aydemir, Emin Argun Oral and Ibrahim Yucel Ozbek We would like to start by thanking the editor(s) and the reviewers for their useful comments and suggestions on how to further improve the quality of my manuscript. I have been able to incorporate changes to reflect all the suggestions provided by the reviewer. Here is a point-by-point response to the reviewer’s comments and concerns. Reviewer 1: 1. Asked: Please amend the title either on the online submission form or in your manuscript so that they are identical. 1. Answer: We amended the titles both on the online submission form and in our manuscript. 2. Asked: Please explain the rationale for the development of your work, and clearly indicating which problem with existing approaches you are addressing. Also describe about the datasets used in this work briefly. Please clearly report at the beginning of your methods or results section which the key performance measures were to establish validity and utility of your new system. 2. Answer: We are very grateful to reviewer for his valuable comment, which helped us to improve the quality of our manuscript. Based on his/her suggestion we explain the important points, including the problem which we addressed, dataset and achieved performance, in the subsection of The Proposed Method. The added sentences are also given below. In this study, we proposed a 3D column (3D-C) intensified based P300 speller system, which provided higher CA rate and lower user workload than the classical 2D-RC P300 speller paradigm. The EEG signals were recorded in both 3D and 2D paradigm procedures from ten healthy participants. In both procedures, 60 characters were presented to each participant during the data collection phase. The proposed 3D-C paradigm was successfully applied to the datasets and we achieved an average CA rate of 99.81% for binary classification (target-nontarget) and 99.2% character detection accuracy on the test data by the traditional two-layer artificial neural networks (ANN) model with a single output neuron. Please see The Proposed Method section on page 4. Moreover, we added a brief introduction at the beginning of The Results section as follows: In this study, we proposed an efficient 3D column-only P300 speller paradigm utilizing few numbers of electrodes and flashings for practical BCI implementation. In this section, we provided the experimental results including P300 detection and the target character recognition performances achieved by the traditional two-layer ANN model with a single output neuron. Please see the Results section on page 11. Reviewer 2: 1. Asked: Figure 1 should be clearer. 1. Answer: Based on the reviewer’s suggestion, we improved the readability of Figure 1. 2. Asked: Data set references are needed. 2. Answer: We are very grateful to the reviewer pointing out this issue. The datasets presented in this study were used for the first time in the literature. Therefore, this paper will be cited by the researchers, who will use these datasets. On the other hand, in the section of Introduction, we cited other datasets which were presented by other researchers. Comment from the editor: Asked: 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. Answer: We mentioned the Data Availability in the section of Acknowledgement as follows: On the other hand, the datasets, which were presented in this study, could be available for the researchers by contacting the corresponding author via e-mail. Please see the section of Acknowledgement on page 15. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0265904.r002
18 Feb 2022 Decision Letter - M. Shamim Kaiser, Editor PONE-D-21-29800R1An Efficient 3D Column-Only P300 Speller Paradigm Utilizing Few Numbers of Electrodes and Flashings for Practical BCI ImplementationPLOS ONE Dear Dr. korkmaz, 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. ============================== ACADEMIC EDITOR: Please check the title of the paper in the system There are typos in the article, please read the paper very carefully. The font size in the figures must be same. Also mention the impact and reproducibility of this work. Please submit your revised manuscript by Apr 04 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, M. Shamim Kaiser, PhD 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 Reviewer #2: 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 Reviewer #2: Yes ****** 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 ****** 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: 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: Explaination and overall writing is good. Keep doing this type of work and contribute more in this field. Reviewer #2: Brain computer interface (BCI) is a methodical system that interfaces the brain to a wide variety of electronic devices including computer, robotic arm, and mobile phone. Authors did a good work on this arena. They proposed a new 3D column flashing based P300 speller paradigm (3D-C). It increases 377 the CA rates. Moreover, it provides lower user workload. Their proposed speller paradigm 378 is specially useful in BCI systems designed for less EEG electrode usage. Furthermore, they showed that their proposed 379 paradigm performs better with less flashings compared to the classical 2D-RC paradigm. Significantly, it is mentioned that the best 380 average CA performance for P8 electrode for 1, 3 and 15 flashings improved to 9.69%, 4.72%, and 1.73%, 381 respectively. ****** 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. https://doi.org/10.1371/journal.pone.0265904.r003
Revision 2
19 Feb 2022 Author Response AUTHOR RESPONSES TO THE ACADEMIC EDITOR Journal: Plos One Title of the manuscript: An Efficient 3D Column-Only P300 Speller Paradigm Utilizing Few Numbers of Electrodes and Flashings for Practical BCI Implementation Manuscript ID: PONE-D-21-29800R1 Authors: Onur Erdem Korkmaz, Onder Aydemir, Emin Argun Oral and Ibrahim Yucel Ozbek We would like to start by thanking the editor(s) and the reviewers for their useful comments and suggestions on how to further improve the quality of my manuscript. We have been able to incorporate changes to reflect all the suggestions provided by the academic editor. Here is a point-by-point response to the academic editor. Academic Editor: 1. Asked: Please check the title of the paper in the system. 1. Answer: We checked the title of the paper in the system. We realized that while the first letters of the words were not written in capital letters in the manuscript, but they were given with capital letters in the system. Therefore, we edited the manuscript with capital letters. 2. Asked: There are typos in the article, please read the paper very carefully. 2. Answer: We read the paper very carefully and corrected the typos. 3. Asked: The font size in the figures must be same. 3. Answer: We set the font sizes same in the figures. 4. Asked: Also mention the impact and reproducibility of this work. 4. Answer: We mentioned the impact and reproducibility of this work at the end of the Conclusion section. The added statement is also given below: We believe that the proposed method has a great potential to achieve higher performance for improving the BCI spelling systems. On the other hand, we make the entire dataset publicly available to the community to encourage the reproducibility of this work. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0265904.r004
10 Mar 2022 Decision Letter - M. Shamim Kaiser, Editor An Efficient 3D Column-Only P300 Speller Paradigm Utilizing Few Numbers of Electrodes and Flashings for Practical BCI Implementation PONE-D-21-29800R2 Dear Dr. korkmaz, 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, M. Shamim Kaiser, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Please read the article very carefully to eliminate typos. Reviewers' comments: https://doi.org/10.1371/journal.pone.0265904.r005
Formally Accepted
4 Apr 2022 Acceptance Letter - M. Shamim Kaiser, Editor PONE-D-21-29800R2 An Efficient 3D Column-Only P300 Speller Paradigm Utilizing Few Numbers of Electrodes and Flashings for Practical BCI Implementation. Dear Dr. Korkmaz: 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. M. Shamim Kaiser Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0265904.r006

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .