Steps for Therapeutics Manuscript Submission #738
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rando2
changed the title
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Hello everyone! I went through the commit history for the nutraceuticals and pharmaceuticals section. Our aim is to submit within the next two weeks (ideally Feb 8).
For the pharmaceuticals, I ended up having to use a bit of subjectivity in weighing contributions (how many lines of text is a figure comparable to?), so please let me know if you have any concerns. I'm attaching the commit log I used to try to get a reading on this for reference -- I believe I've removed all the nutraceuticals commits, but again, let me know if I missed something. I didn't categorize every single commit for people who had a lot -- when they are only 2-3 lines, they're typically edits. I also didn't put people on the named author list if they were just fixing typos in this section without making contributions to the ideas of the text.
Commit Log: gitlog.20.treatments.xlsx Acknowledgements:
Note: |
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Hello @rando2 ! For the therapeutics manuscript, I think I should just be in the acknowledgements, because I contributed very little and don't know enough about the therapeutics to be able to review it intelligently. But congratulations on your progress! |
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We are going to need to move the vaccines section to a new paper -- even without it, we are significantly over the requested word limit (which is 12,000 words-- without vaccines, we're currently at > 16,000)! I'll go through the commits to see how this changes the author list/order and provide updates here. The good news is that I believe the rest of the paper is pretty up-to-date, so we should be able to get a draft sent out to authors for approval very soon! |
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In case you're interested, in the nutraceuticals section you could cite a brief commentary in JASA regarding vitamin D: |
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People who are moving off this manuscript to the vaccines manuscript: I updated the table above to reflect other changes (i.e., I separated Casey & my commits for the two different manuscripts) |
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Hi everyone! I am still working on checking all the therapeutics are roughly up-to-date and that we don't say anything super outdated (e.g., #837). I'm hoping to finish this tomorrow and then send the docx out to all authors. If anyone is open to reviewing PRs tomorrow (or to updating your favorite drug!) this would be hugely helpful -- please let me know if you don't mind being tagged! I'm happy to review for anyone who has anything they want changed! Thank you all so much! |
2 tasks
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The build is going out to co-authors over email momentarily. I'm leaving this comment here in case people want to use emojis to indicate that they're comfortable submitting the manuscript in its current state! |
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Good luck!!👍
…On Tue, Feb 9, 2021 at 5:23 PM HM Rando ***@***.***> wrote:
The build is going out to co-authors over email momentarily. I'm leaving
this comment here in case people want to use emojis to indicate that
they're comfortable submitting the manuscript in its current state!
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Looks good👍 |
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Yes, good luck! |
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good luck!!
…On Fri, Jan 29, 2021, 4:34 PM HM Rando ***@***.***> wrote:
Hello everyone! I went through the commit history for the nutraceuticals
and pharmaceuticals section.
Our aim is to submit within the next two weeks (ideally Feb 8).
- As far as I can tell, @RLordan <https://github.com/RLordan> wrote
the nutraceuticals section almost entirely on his own, so that author
list is very short <#m_3988177908201061300_749> -- please let me know
ASAP if you think you were skipped over!
- Is anyone willing to draft a section explaining the
adenovirus-vectored vaccines? Or evaluating the status of the ones that are
known to be in development/being administered?
- Is anyone willing to review my mRNA vaccine PRs? I'm trying to get
them up-to-date today.
For the pharmaceuticals, I ended up having to use a bit of subjectivity in
weighing contributions (how many lines of text is a figure comparable to?),
so please let me know if you have any concerns. I'm attaching the commit
log I used to try to get a reading on this for reference -- I *believe*
I've removed all the nutraceuticals commits, but again, let me know if I
missed something. I didn't categorize every single commit for people who
had a lot -- when they are only 2-3 lines, they're typically edits. I also
didn't put people on the author list if they were just fixing typos in this
section without making contributions to the ideas of the text.
Position Person Total Lines Modified Wrote Text? Other contributions
1 @rando2 <https://github.com/rando2> 2814 Yes Project Administration
2 @nilswellhausen <https://github.com/nilswellhausen> 201 Yes Project
Administration, Visualization
3 @soumitagh <https://github.com/soumitagh> 246 Yes
4 @aadattoli <https://github.com/aadattoli> 207 Yes
4 @hufengling <https://github.com/hufengling> 191 Yes
5 @byrdjb <https://github.com/byrdjb> 126 Yes
5 @likhithakolla <https://github.com/likhithakolla> 116 Yes
5 @ajlee21 <https://github.com/ajlee21> 107 Yes
5 @dianerafi <https://github.com/dianerafi> 88 Yes PA
5 @kevinsunofficial <https://github.com/kevinsunofficial>
Visualization
5 @qiyanjun <https://github.com/qiyanjun> Visualization
6 @marouenbg <https://github.com/marouenbg> 64 Yes
6 @Jeff-Field <https://github.com/Jeff-Field> 47 Yes
6 @esell17 <https://github.com/esell17> 42 Yes
6 @nafisajadavji <https://github.com/nafisajadavji> Supervision,
Editing
7 @cbrueffer <https://github.com/cbrueffer> 51 PA
7 @RLordan <https://github.com/RLordan> 29 Yes
7 @anskelly <https://github.com/anskelly> Editing
7 @ypar <https://github.com/ypar> Yes Editing
8 @jinhui2 <https://github.com/jinhui2> 11 Yes
9 @dziakj1 <https://github.com/dziakj1> 2 Yes
10 @SiminaB <https://github.com/SiminaB> 1037 Project Administration,
Editing
11 @agitter <https://github.com/agitter> 144 Project Administration,
Visualization
12 @cgreene <https://github.com/cgreene> 563 Yes Project Administration,
Editing
Commit Log: gitlog.20.treatments.xlsx
<https://github.com/greenelab/covid19-review/files/5896353/gitlog.20.treatments.xlsx>
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Looks good to me! 🌈
…On Tue, Feb 9, 2021 at 5:58 PM soumitagh ***@***.***> wrote:
good luck!!
On Fri, Jan 29, 2021, 4:34 PM HM Rando ***@***.***> wrote:
> Hello everyone! I went through the commit history for the nutraceuticals
> and pharmaceuticals section.
>
> Our aim is to submit within the next two weeks (ideally Feb 8).
>
> - As far as I can tell, @RLordan <https://github.com/RLordan> wrote
> the nutraceuticals section almost entirely on his own, so that author
> list is very short <#m_3988177908201061300_749> -- please let me know
> ASAP if you think you were skipped over!
> - Is anyone willing to draft a section explaining the
> adenovirus-vectored vaccines? Or evaluating the status of the ones that
are
> known to be in development/being administered?
> - Is anyone willing to review my mRNA vaccine PRs? I'm trying to get
> them up-to-date today.
>
> For the pharmaceuticals, I ended up having to use a bit of subjectivity
in
> weighing contributions (how many lines of text is a figure comparable
to?),
> so please let me know if you have any concerns. I'm attaching the commit
> log I used to try to get a reading on this for reference -- I *believe*
> I've removed all the nutraceuticals commits, but again, let me know if I
> missed something. I didn't categorize every single commit for people who
> had a lot -- when they are only 2-3 lines, they're typically edits. I
also
> didn't put people on the author list if they were just fixing typos in
this
> section without making contributions to the ideas of the text.
> Position Person Total Lines Modified Wrote Text? Other contributions
> 1 @rando2 <https://github.com/rando2> 2814 Yes Project Administration
> 2 @nilswellhausen <https://github.com/nilswellhausen> 201 Yes Project
> Administration, Visualization
> 3 @soumitagh <https://github.com/soumitagh> 246 Yes
> 4 @aadattoli <https://github.com/aadattoli> 207 Yes
> 4 @hufengling <https://github.com/hufengling> 191 Yes
> 5 @byrdjb <https://github.com/byrdjb> 126 Yes
> 5 @likhithakolla <https://github.com/likhithakolla> 116 Yes
> 5 @ajlee21 <https://github.com/ajlee21> 107 Yes
> 5 @dianerafi <https://github.com/dianerafi> 88 Yes PA
> 5 @kevinsunofficial <https://github.com/kevinsunofficial>
> Visualization
> 5 @qiyanjun <https://github.com/qiyanjun> Visualization
> 6 @marouenbg <https://github.com/marouenbg> 64 Yes
> 6 @Jeff-Field <https://github.com/Jeff-Field> 47 Yes
> 6 @esell17 <https://github.com/esell17> 42 Yes
> 6 @nafisajadavji <https://github.com/nafisajadavji> Supervision,
> Editing
> 7 @cbrueffer <https://github.com/cbrueffer> 51 PA
> 7 @RLordan <https://github.com/RLordan> 29 Yes
> 7 @anskelly <https://github.com/anskelly> Editing
> 7 @ypar <https://github.com/ypar> Yes Editing
> 8 @jinhui2 <https://github.com/jinhui2> 11 Yes
> 9 @dziakj1 <https://github.com/dziakj1> 2 Yes
> 10 @SiminaB <https://github.com/SiminaB> 1037 Project Administration,
> Editing
> 11 @agitter <https://github.com/agitter> 144 Project Administration,
> Visualization
> 12 @cgreene <https://github.com/cgreene> 563 Yes Project Administration,
> Editing
>
> Commit Log: gitlog.20.treatments.xlsx
> <
https://github.com/greenelab/covid19-review/files/5896353/gitlog.20.treatments.xlsx
>
>
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Looks good! 👍 |
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Super! Well done everyone! 👍 |
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Looks good! 👍
Get Outlook for iOS<https://aka.ms/o0ukef>
…________________________________
From: Ronan Lordan <[email protected]>
Sent: Tuesday, February 9, 2021 6:30:43 PM
To: greenelab/covid19-review <[email protected]>
Cc: Wang, Jinhui <[email protected]>; Mention <[email protected]>
Subject: [External] Re: [greenelab/covid19-review] Steps for Therapeutics Manuscript Submission (#738)
Super! Well done everyone! 👍
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Wonderful! 🥇 |
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Wonderful, Good luck!
… On 29 Jan 2021, at 16:34, HM Rando ***@***.***> wrote:
Hello everyone! I went through the commit history for the nutraceuticals and pharmaceuticals section.
Our aim is to submit within the next two weeks (ideally Feb 8).
As far as I can tell, @RLordan <https://github.com/RLordan> wrote the nutraceuticals section almost entirely on his own, so that author list is very short <x-msg://4/#749> -- please let me know ASAP if you think you were skipped over!
Is anyone willing to draft a section explaining the adenovirus-vectored vaccines? Or evaluating the status of the ones that are known to be in development/being administered?
Is anyone willing to review my mRNA vaccine PRs? I'm trying to get them up-to-date today.
For the pharmaceuticals, I ended up having to use a bit of subjectivity in weighing contributions (how many lines of text is a figure comparable to?), so please let me know if you have any concerns. I'm attaching the commit log I used to try to get a reading on this for reference -- I believe I've removed all the nutraceuticals commits, but again, let me know if I missed something. I didn't categorize every single commit for people who had a lot -- when they are only 2-3 lines, they're typically edits. I also didn't put people on the author list if they were just fixing typos in this section without making contributions to the ideas of the text.
Position Person Total Lines Modified Wrote Text? Other contributions
1 @rando2 <https://github.com/rando2> 2814 Yes Project Administration
2 @nilswellhausen <https://github.com/nilswellhausen> 201 Yes Project Administration, Visualization
3 @soumitagh <https://github.com/soumitagh> 246 Yes
4 @aadattoli <https://github.com/aadattoli> 207 Yes
4 @hufengling <https://github.com/hufengling> 191 Yes
5 @byrdjb <https://github.com/byrdjb> 126 Yes
5 @likhithakolla <https://github.com/likhithakolla> 116 Yes
5 @ajlee21 <https://github.com/ajlee21> 107 Yes
5 @dianerafi <https://github.com/dianerafi> 88 Yes PA
5 @kevinsunofficial <https://github.com/kevinsunofficial> Visualization
5 @qiyanjun <https://github.com/qiyanjun> Visualization
6 @marouenbg <https://github.com/marouenbg> 64 Yes
6 @Jeff-Field <https://github.com/Jeff-Field> 47 Yes
6 @esell17 <https://github.com/esell17> 42 Yes
6 @nafisajadavji <https://github.com/nafisajadavji> Supervision, Editing
7 @cbrueffer <https://github.com/cbrueffer> 51 PA
7 @RLordan <https://github.com/RLordan> 29 Yes
7 @anskelly <https://github.com/anskelly> Editing
7 @ypar <https://github.com/ypar> Yes Editing
8 @jinhui2 <https://github.com/jinhui2> 11 Yes
9 @dziakj1 <https://github.com/dziakj1> 2 Yes
10 @SiminaB <https://github.com/SiminaB> 1037 Project Administration, Editing
11 @agitter <https://github.com/agitter> 144 Project Administration, Visualization
12 @cgreene <https://github.com/cgreene> 563 Yes Project Administration, Editing
Commit Log: gitlog.20.treatments.xlsx <https://github.com/greenelab/covid19-review/files/5896353/gitlog.20.treatments.xlsx>
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:) good luck!
…On Tue, Feb 9, 2021 at 7:19 PM aadattoli ***@***.***> wrote:
Wonderful, Good luck!
> On 29 Jan 2021, at 16:34, HM Rando ***@***.***> wrote:
>
>
> Hello everyone! I went through the commit history for the nutraceuticals
and pharmaceuticals section.
>
> Our aim is to submit within the next two weeks (ideally Feb 8).
>
> As far as I can tell, @RLordan <https://github.com/RLordan> wrote the
nutraceuticals section almost entirely on his own, so that author list is
very short <x-msg://4/#749> -- please let me know ASAP if you think you
were skipped over!
> Is anyone willing to draft a section explaining the adenovirus-vectored
vaccines? Or evaluating the status of the ones that are known to be in
development/being administered?
> Is anyone willing to review my mRNA vaccine PRs? I'm trying to get them
up-to-date today.
> For the pharmaceuticals, I ended up having to use a bit of subjectivity
in weighing contributions (how many lines of text is a figure comparable
to?), so please let me know if you have any concerns. I'm attaching the
commit log I used to try to get a reading on this for reference -- I
believe I've removed all the nutraceuticals commits, but again, let me know
if I missed something. I didn't categorize every single commit for people
who had a lot -- when they are only 2-3 lines, they're typically edits. I
also didn't put people on the author list if they were just fixing typos in
this section without making contributions to the ideas of the text.
>
> Position Person Total Lines Modified Wrote Text? Other contributions
> 1 @rando2 <https://github.com/rando2> 2814 Yes Project Administration
> 2 @nilswellhausen <https://github.com/nilswellhausen> 201 Yes Project
Administration, Visualization
> 3 @soumitagh <https://github.com/soumitagh> 246 Yes
> 4 @aadattoli <https://github.com/aadattoli> 207 Yes
> 4 @hufengling <https://github.com/hufengling> 191 Yes
> 5 @byrdjb <https://github.com/byrdjb> 126 Yes
> 5 @likhithakolla <https://github.com/likhithakolla> 116 Yes
> 5 @ajlee21 <https://github.com/ajlee21> 107 Yes
> 5 @dianerafi <https://github.com/dianerafi> 88 Yes PA
> 5 @kevinsunofficial <https://github.com/kevinsunofficial> Visualization
> 5 @qiyanjun <https://github.com/qiyanjun> Visualization
> 6 @marouenbg <https://github.com/marouenbg> 64 Yes
> 6 @Jeff-Field <https://github.com/Jeff-Field> 47 Yes
> 6 @esell17 <https://github.com/esell17> 42 Yes
> 6 @nafisajadavji <https://github.com/nafisajadavji> Supervision, Editing
> 7 @cbrueffer <https://github.com/cbrueffer> 51 PA
> 7 @RLordan <https://github.com/RLordan> 29 Yes
> 7 @anskelly <https://github.com/anskelly> Editing
> 7 @ypar <https://github.com/ypar> Yes Editing
> 8 @jinhui2 <https://github.com/jinhui2> 11 Yes
> 9 @dziakj1 <https://github.com/dziakj1> 2 Yes
> 10 @SiminaB <https://github.com/SiminaB> 1037 Project Administration,
Editing
> 11 @agitter <https://github.com/agitter> 144 Project Administration,
Visualization
> 12 @cgreene <https://github.com/cgreene> 563 Yes Project
Administration, Editing
> Commit Log: gitlog.20.treatments.xlsx <
https://github.com/greenelab/covid19-review/files/5896353/gitlog.20.treatments.xlsx
>
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Nice work! Thanks for all your hard work! Good luck! |
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Looks great! 🎉
…Sent from my iPhone
On Feb 9, 2021, at 9:10 PM, Nafisa Jadavji <[email protected]> wrote:
Nice work! Thanks for all your hard work! Good luck!
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Looking good! |
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@nilswellhausen I just realized -- did you still want to make updates to the neutralizing antibodies? I have not done a check on where that literature has gone! |
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I would love to but I dont want to stall the progress either. I am pretty swamped this week so it would certainly take a while to properly update this section. Another option is to wait what the reviewers would like to see included and then edit. |
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Would it help if we add a date to the neutralizing antibodies section to give readers and reviewers of sense of when this was written? Including "As of MONTH, 2020..." could clarify that this hasn't been updated to reflect the latest literature. |
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@cbrueffer just to check, do you need more time to approve this or are you OK with it being submitted sometime this week? I know I've been pinging you on about 3 different manuscripts this week! |
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No, all good @rando2! Sorry, should have stated that explicitly. |
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Wonderful. Looks good!
…
On Feb 10, 2021, at 05:51, Elizabeth (Ellie) Sell ***@***.***> wrote:
Looks great! 🎉
Sent from my iPhone
On Feb 9, 2021, at 9:10 PM, Nafisa Jadavji ***@***.***> wrote:
Nice work! Thanks for all your hard work! Good luck!
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Two notes pre-submission:
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Thanks!
From: HM Rando <[email protected]>
Sent: Wednesday, February 24, 2021 12:03 PM
To: greenelab/covid19-review <[email protected]>
Cc: Byrd, James (J. "Brian") <[email protected]>; Mention <[email protected]>
Subject: Re: [greenelab/covid19-review] Steps for Therapeutics Manuscript Submission (#738)
External Email - Use Caution
Two notes pre-submission:
1. I bumped @byrdjb<https://github.com/byrdjb> and @ajlee21<https://github.com/ajlee21> up to tier 4 based on feedback during the review process.
2. I'm manually editing the acknowledgements for submission: We thank Nick DeVito for assistance with the Evidence-Based Medicine Data Lab COVID-19 TrialsTracker data and Vincent Rubinetti and Daniel Himmelstein for feedback on and support with Manubot. We thank Yael Evelyn Marshall who contributed writing (original draft) as well as reviewing and editing of pieces of the text but who did not formally approve the manuscript, as well as Ronnie Russell, who contributed text to and helped develop the structure of the manuscript early in the writing process. We are grateful to Nadia Danilova, James Eberwine, Adam L MacLean, Lucy McGowan, and Tiago Lubiana for reviewing pieces of the text.
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Hey all, I'm getting ready to send the new version of the manuscript out by email (hopefully tomorrow). I just wanted to make a note that based on the line edits made during revisions, I think it would make sense to bump @cbrueffer @RLordan up one spot each in the author list. @ajlee21 your line edits put you in group 4 but it seems like you were already there! |
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Just an update that an email with the new draft went out yesterday! If you have any questions or didn't receive it, please just let me know! I'm hoping to hear from everyone either with approval or edits (or a timeline for when you will be able to provide edits) by the end of next week -- let me know if this is an issue for you though, I know summer is hectic!
Note: some people on this thread wrote vaccines topics, and those will be going out separately -- I'm aiming for sending that email out in 2-3 weeks. |
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Approve! 👍 |
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I edited the life cycle/therapeutics figure. Besides that, I approve. |
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Approve! Thanks.
…________________________________
From: nilswellhausen ***@***.***>
Sent: Tuesday, August 3, 2021 10:06 AM
To: greenelab/covid19-review ***@***.***>
Cc: Wang, Jinhui ***@***.***>; Mention ***@***.***>
Subject: [External] Re: [greenelab/covid19-review] Steps for Therapeutics Manuscript Submission (#738)
I edited the life cycle/therapeutics figure. Besides that, I approve.
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I'm not really involved in this one but I approve. |
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If you haven't already, you might optionally want to cite or link to this living guideline that I read about this morning: |
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Approve. Thanks
…Sent from my iPhone
On Aug 3, 2021, at 10:33, John J. Dziak ***@***.***> wrote:
If you haven't already, you might optionally want to cite or link to this living guideline that I read about this morning:
https://www.who.int/publications/i/item/WHO-2019-nCoV-therapeutics-2021.2
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Approve. Thank you.
…On Tue, Aug 3, 2021 at 1:03 PM qiyanjun ***@***.***> wrote:
Approve. Thanks
Sent from my iPhone
> On Aug 3, 2021, at 10:33, John J. Dziak ***@***.***> wrote:
>
>
> If you haven't already, you might optionally want to cite or link to
this living guideline that I read about this morning:
>
https://www.who.int/publications/i/item/WHO-2019-nCoV-therapeutics-2021.2
>
> —
> You are receiving this because you were mentioned.
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--
Soumita Ghosh
University of Pensylvania
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Approve. Thank you so much! |
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Looks good to me. I approve! Thank you |
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Approve! Nice work!
Nafisa M. Jadavji, Ph.D.
www.jadavjilab.com
…On Tue, Aug 3, 2021 at 12:21 PM Alexandra Lee ***@***.***> wrote:
Looks good to me. I approve! Thank you
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approve. thanks
… On 5 Aug 2021, at 23:42, Nafisa Jadavji ***@***.***> wrote:
Approve! Nice work!
Nafisa M. Jadavji, Ph.D.
www.jadavjilab.com
On Tue, Aug 3, 2021 at 12:21 PM Alexandra Lee ***@***.***>
wrote:
> Looks good to me. I approve! Thank you
>
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> Reply to this email directly, view it on GitHub
> <#738 (comment)>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AO6TZUFWAGNA3D2EZ56KATTT3A6ULANCNFSM4VADGVXA>
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Approved, pending #997. Thanks everyone! |
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I approve and can help review the remaining therapeutics pull requests. |
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Here's what we need to do for this hefty manuscript! PR reviews or people willing to take a stab at opening PRs very, very welcome! I will update with PRs as they have numbers -- please consider reviewing!
Most Critical:
Determine whether we need to adjust Figure 1: Restructure files for new 6-paper format #734The text was updated successfully, but these errors were encountered: