Dear Prof. Mirasso,

Thank you very much for submitting your manuscript "Modeling circuit mechanisms of opposing cortical responses to visual flow perturbations" for consideration at PLOS Computational Biology. As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. The reviewers appreciated the attention to an important topic. Based on the reviews, we are likely to accept this manuscript for publication, providing that you modify the manuscript according to the review recommendations.

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Sincerely,

Lyle Graham

Section Editor

PLOS Computational Biology

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Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: The authors have studied the circuit and dynamical mechanisms underlying the different responses of the primary visual cortex to visual stimuli. Using a biologically realistic model of V1, the authors have tried to explain how the incoming excitatory stimuli from LGN can depolarize some excitatory neurons in layer 2/3 while hyperpolarizing the other ones. The authors have shown that how differential excitatory inputs from LGN combined with the recurrent inhibition give rise to this observation. The structural and dynamical aspects of the problem have been extensively studied.

I found the manuscript well-written and clear and the results are interesting. Using a detailed biological model is an advantage of the study and can help for more future researches using these type of models. I can recommend publication of the manuscript after addressing some points that I list below. Most of all, I think the Methods section needs a revision with taking more care.

Figure 1: The quality of the figure should be improved. Text in A cannot be read.

Model is general, is a little bit vague. It seems that it is better to first introduce general model including second part of Eq. 1 and then Eq. 2. The first part of Eq. 1 (ASC) should be defined after Eq 2. Furthermore, ACS should be explained in more details since it is not known for the most people in the field and is not exactly explained.

Eq. 3 also looks imprecise. In the equations, t should be the time of the firing of the presynaptic neurons. Therefore, it seems more precise that instead of time t, write it in the form of (t-t_sp) where t_sp is the time of firing of the presynaptic neuron or external input.

Again, in Eq. 5 I_e(t) is written in another form. I think there is some discrepancy in writing the methods. I understand what the authors meant, but for being comprehensible for general reader and for being reproducible a more coherent and precise format in needed.

Fig. 3: In the caption please note what are different columns in part A.

Line 325: “ hVf neurons lack direct connections to the LGN” should it be from LGN?

Line 326: “This discovery aligns with” might be “this observation aligns with”.

Lines 332-337: I do not agree that this is a rich-club structure. Indeed this is more looks like a modular structure. In rich-club structure there is a subset of the nodes in different modules that are more strongly connected to each other. Please write this part with more care.

Lines 349-355: I would suggest moving this part to a relevant position in Discussion section.

From line 391: appearance of these three subtitles here without any prior explanations is not appropriate. Please write and explanations before them why they are chosen for more detailed analysis.

Reviewer #2: uploaded as attachmentt

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Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: None

Reviewer #2: No: On the manuscript it states: Data and code will be accessible via gitHub

Code was not available during the review process

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Reviewer #1: Yes: Alireza Valizadeh

Reviewer #2: No

Figure Files:

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References:

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.

Attachments

Attachment

Submitted filename: Fraileetal2023-ModelOfPredictiveCoding.docx

Dear Prof. Mirasso,

We are pleased to inform you that your manuscript 'Modeling circuit mechanisms of opposing cortical responses to visual flow perturbations' has been provisionally accepted for publication in PLOS Computational Biology.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests.

Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated.

IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript.

Should you, your institution's press office or the journal office choose to press release your paper, you will automatically be opted out of early publication. We ask that you notify us now if you or your institution is planning to press release the article. All press must be co-ordinated with PLOS.

Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Computational Biology. 

Best regards,

Lyle J. Graham

Section Editor

PLOS Computational Biology

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Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: I have no further comment.

Reviewer #2: The authors have addressed all my concerns satisfactorily. I believe the manuscript is suitable for publication in its current form. I thank the authors for this useful research.

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Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —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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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: Alireza Valizadeh

Reviewer #2: No