Review Request A. K. Diem

[alexdiem]

DIEM

Dear @ReScience/editors,

I request a review for the following replication:

Original article

Title: A bidirectional model for communication in the neurovascular unit
Author(s): Witthoft A, Karniadakis GE
Journal (or Conference): Journal of Theoretical Biology
Year: 2012
DOI: https://doi.org/10.1016/j.jtbi.2012.07.014
PDF: http://www.sciencedirect.com/science/article/pii/S0022519312003487

Replication

Author(s): Diem AK
Repository: https://github.com/akdiem/ReScience-submission/tree/Diem-2017
PDF: https://github.com/akdiem/ReScience-submission/blob/Diem-2017/article/Diem-2017.pdf
Keywords: neurovascular unit, neurovascular signalling, neurovascular coupling, astrocyte signalling
Language: Python 3.5.3
Domain: Neurovascular coupling

Results

• Article has been fully replicated
• Article has been partially replicated
• Article has not been replicated

I believe the original results have been almost fully reproduced as explained in the accompanying article.

---

EDITOR

• Editor acknowledgment June 28, 2017
• Reviewer 1 started (@ChristophMetzner) July 4, 2017
• Reviewer 2 (@TiinaManninen July 7, 2017
• Review 1 decision [accept] September 6, 2017
• Review 2 decision [accept] August 31, 2017
• Editor decision [accept] September 6, 2017

[rougier]

@akdiem Thanks for your submission, we'll assign an editor soon. Do you have a link to an open-access version of the original article ?

[rougier]

Dear @ReScience/associate-editors

Can someone edit this submission (domain is Biology / Neurovascular coupling)?

[alexdiem]

@rougier The original authors have a pdf on their website
https://www.brown.edu/research/projects/crunch/sites/brown.edu.research.projects.crunch/files/uploads/Alix_bidirectional.pdf I didn't upload it into my repository because I did not want to infringe on the journal copyright.

[rougier]

Thanks, a link is perfect !

[alexdiem]

Is it acceptable to make small changes to the manuscript at this point? I have just realised that I forgot to add a detail for implementing one of the equations, which I only got to know about by contacting the original authors.

[rougier]

No problem, you can

[rougier]

@akdiem Just to let you know I did not forget you, an editor will be assigned soon hopefully.

[rougier]

@benoit-girard Can you edit this submission ?

[benoit-girard]

Yes

[benoit-girard]

@ChristophMetzner Do you think you can review this submission?

[ChristophMetzner]

@benoit-girard At first glance it seems a little bit out of my comfort zone. I will have a closer look this evening and reply tomorrow the latest.

[ChristophMetzner]

@benoit-girard Had a closer look and, although I am not an expert on the topic, I feel confident to review.

[benoit-girard]

@ChristophMetzner OK, great, thank you.
It is difficult to find someone fully comfortable with the topic, given our current set of reviewers. I have been contacting potential reviewers by mail, without much success up to now. I am waiting for answers, that's why we will have to wait a bit before we have a second reviewer.

[benoit-girard]

A second reviewer is expected to join soon. Thanks for your patience.

[alexdiem]

@benoit-girard Ok, thanks for the update!

[alexdiem]

I just modified eq 23.

[TiinaManninen]

@ChristophMetzner @benoit-girard

@akdiem Because of the change in the equation, the result plots that the new codes produce are different than earlier, but you still have the old figures in your manuscript. Mostly the results vary just a bit, but new Figure 6b plotted from the new code is very different compared to the earlier version.

[alexdiem]

It seems that the best set of changes was to leave eqs 5 and 23 as in the original publication, but change the definition of J_trpv to positive sign and J_Ca negative.

[TiinaManninen]

@ChristophMetzner @benoit-girard

@akdiem The signs in your version of Equation 23 in the manuscript do not match the signs in your code. Please correct in the manuscript.

[alexdiem]

Thanks for carefully checking, there's always the one spot.

[TiinaManninen]

@ChristophMetzner @benoit-girard

@akdiem Thanks for making the last modification! The signs were already confusing in the original manuscript, but if you plan still to make errata with the original authors, I would kindly suggest to pay attention to the signs that they are given biologically correct. I have now accepted the submission. Congratulations!

[benoit-girard]

@ChristophMetzner @akdiem
If I correctly followed the discussion, the last point standing concerns the signs of J_BK and J_KIR currents?
@ChristophMetzner : do you still have a concern about that?

[ChristophMetzner]

@benoit-girard @akdiem No, this issue has been resolved.

[benoit-girard]

@ChristophMetzner are you now ready to make a final decision [accept/reject] on this paper?

[ChristophMetzner]

@benoit-girard @akdiem My final decision is to accept the paper.

[benoit-girard]

@akdiem Congratulations, I hereby accept the submission for publication!
@ChristophMetzner , @TiinaManninen thank you for your reviews!

[benoit-girard]

@akdiem could you provide a list of keywords?

[alexdiem]

Thank you for accepting my submission! Please use these keywords: neurovascular modelling, neurovascular unit, chemical signalling, astrocytes, neuroscience

[benoit-girard]

EDITOR

This submission has been accepted for publication, and has been published at
http://rescience.github.io/read/

[rougier]

@benoit-girard Don't forget to update Volume 3 - Issue 1 file as well

[benoit-girard]

@rougier I did and just submitted the corresponding PR (hopefuly).

[benoit-girard]

When the last step of the "publication process" states "Close the PR without merging", it refers to the PR initiated by the author in ReScience-submission? Meaning, in this case, the PR #33 where this comment appears?

[khinsen]

Exactly! Just push the "close pull request" button below.

[rougier]

I cannot see your PR. Do you see it on your side ? Do you have a pointer ?

[benoit-girard]

@khinsen Will close it now
@rougier Finally managed to do the PR (sorry for the delay)