#biorxiv — Public Fediverse posts

New preprint dropped: __Systemic diazepam alters local hippocampal CA1 circuits and differentially affects entorhinal and CA3 inputs__

Peterson et al. (2026) #bioRxiv

https://www.biorxiv.org/content/10.64898/2026.08.18.745488v1

Really cool and amazing results that systemic diazepam obliterates hippocampal #sharpWaveRipples in vivo, particularly during the post-task rest, and disrupts representations during running.

Implies important issues that diazepam's side effects on consolidation really ought to be looked at. (All the diazepam memory tests we could find in the literature are short-term tests, no one seems to have looked at long-term consolidation, but would love citations if people have them.)

PS. To be honest, though, my favorite figure is the proof-of-efficacy in Figure 2 where decreased spiking cross-correlation directly reveals diazepam's effects on inhibition. It's so clean!

#science #neuroscience #hippocampus

@mdziemann
I recently had some of the links for newly published preprints (from the mastodon biorxiv bot) leading nowhere. At the moment any manuscript on #BioRxiv goes to a cloudfare screen (“We have received a high number of requests from this session. To keep the service fast and reliable for everyone, this page will reload automatically in 30 seconds.”) looping forever.
Overload-by-AI requests/repeated content scraping? BioRxiv probably would be exposed to that quite heavily…

Rxiv mechanobio
@Rxiv_mechanobio • Joined: Nov 05, 2024

I toot papers from #PubMed and preprints from #bioRxiv & #arXiv that seem to pertain to mechanobiology.
My filter can be tested there on PubMed: https://link.infini.fr/mechanobiology_2022_11_07
Improvement suggestions in this filter welcome, both to add or remove spurious results: contact @jocelyn_etienne

#bot #BotsOfMastodon

@richardsever

If my "submit revision" area contains no "submit" button, does that mean I have to submit my revision as a completely new manuskript, or is this a bug? I've submitted numerous revisions and never had that problem!

#biorxiv

oh I really like bioRxiv's implementation of curvenote reader.

#biorxiv #AcademicPublishing

New science: Our preprint on #LocalFieldPotentials (#lfp) and E/I balance just dropped on #bioRxiv

We took direct measurements of excitatory and inhibitory firing (using large simultaneously-recorded neural ensembles allowing us to actually identify excitatory and inhibitory neurons!) and compared it to measurable features from local field potentials in four remarkable data sets (1 from rat mPFC, 1 from rat OFC, 1 from mouse hippocampus, and 1 from mouse VI).

We find that while 1/f slope and gamma oscillations showed region and context dependencies, broadband (6-80 Hz) and high gamma (80-150 Hz) power consistently correlated with E/I activity ratios, supporting their use as proxy measures.

#neuroscience

J. Rodriguez-Sanchez, G. W. Diehl, P. J. Cunningham, D. Pinotsis, R. A.Adams, A. D. Redish (2026) Measuring excitation/inhibition balance through field potentials. #bioRxiv.

https://www.biorxiv.org/content/10.64898/2026.07.16.738654v1

Wow, I've never seen this from #bioRxiv before!

What Happens to Preprints After Peer Review? Analysis of 72,000 Studies Finds Most Conclusions Hold Up

https://1ban.news/preprint-reliability-analysis-biorxiv-conclusions/
#1ban #preprint #reliability #analysis #biorxiv #science

🧠 What can a single neuron compute?

A new #bioRxiv #preprint introduces #TwinProp, using a differentiable digital twin to optimize synaptic strengths and locations in a detailed layer 5 #pyramidal #CellModel. One #neuron classified images and speech and even solved 10-bit parity with 91% accuracy. The key: distributed #dendritic nonlinearities, especially #NMDA-dependent integration:

📄 https://doi.org/10.64898/2026.06.08.730984

#CompNeuro #Neuroscience #Dendrites #NeuroAI @albertcardona https://mathstodon.xyz/@albertcardona/116764629463190653

#OMIO is fully #OpenSource:

👨‍💻 https://github.com/FabrizioMusacchio/omio/

Documentation, tutorials, example data, and a #bioRxiv #preprint are also available:

📚 https://omio.readthedocs.io/en/latest/
📈 https://zenodo.org/records/18078231
📑 https://doi.org/10.64898/2026.06.09.731118

#BioimageAnalysis #Microscopy #Neuroscience

🧵7/8

New preprint from the lab!

How do brain progenitors choose between D1 and D2 medium spiny neurons? We find the *relative levels* of SP9 and DLX TFs tip the balance: SP9 activates D2 genes at promoters, and represses D1 enhancers via DLX/NuRD.

Proud of the team — combining sparse in vivo CRISPR, lineage barcoding, scRNA-seq, ChIP-seq, CUT&RUN and proteomics for mechanistic depth in in vivo functional genomics.

🔗 [https://doi.org/10.64898/2026.05.25.727662]

#newsmayerlab #Neuroscience #DevBio #Transcription #bioRxiv

///Biorxiv///
The preprint server for biology!
https://www.biorxiv.org/
More free resources at https://www.libresites.org
#server #preprints #resources #science #biology #biorxiv

///Biorxiv///
Le serveur de prépublications scientifiques pour la biologie !
https://www.biorxiv.org/
Plus de ressources libres sur https://www.libresites.org
#serveur #prépublications #scientifique #science #biologie #biorxiv

📢 We are pleased to announce that authors can now submit manuscripts directly from bioRxiv to CSBJ through the 𝗯𝗶𝗼𝗥𝘅𝗶𝘃-𝘁𝗼-𝗝𝗼𝘂𝗿𝗻𝗮𝗹 (B2J) transfer service.

🙏We sincerely thank Cold Spring Harbor Laboratory (CSHL) for integrating CSBJ into the B2J service.

#CSBJ #bioRxiv #AAAS #OpenScience #Preprints #SystemsBiology #StructuralBiology #Biotechnology #ComputationalBiology #Omics #Nanoscience #MedicalInformatics #Biomedicine #AdvancedMaterials #Biomaterials #QuantumBiology #Biophotonics

We're still doing science! New preprint dropped: *Hippocampal representations differentiate reactive and anticipatory responses during foraging under threat* (Damphousse et al. bioRxiv).

*** Fleeing from a predator is represented fundamentally differently than retreat from anxiety about that predator.

On our "run the gauntlet" version of the "robogator" task, the dorsal hippocampus represents the attack (behind it as it flees) more during retreat from an actual attack than when it retreats from an anxiety-related pause (no actual attack).

*** Note that this means representation during theta can be about the thing behind the rat that it is running from, not just goals ahead of it.

We also found that when rats pause (presumably out of anxious concern about being attacked), aborting the journey (mid-track aborts) represented the attack more than continuing the journey (mid-track continue on).

https://www.biorxiv.org/content/10.64898/2026.04.17.719234v1.full.pdf+html

#neuroscience #bioRxiv

🎉New preprint out today! We present rastair - an ultra-fast SNP and methylation caller for TAPS or 5-Base data. Rastair takes less than 1h to process e.g. a 50x 5-Base dataset, yet SNP call accuracy is nearly identical to GATK on WGS data 🔥

https://www.biorxiv.org/content/10.64898/2026.03.19.712983v1

#biorxiv #epigenetics #bioinformatics #science #preprint

Circlesquare: juggling DOIs when preprinting

https://quantixed.org/2026/02/17/circlesquare-juggling-dois-when-preprinting/

#computing #publishing #bioRxiv #DOI #github #zenodo

My first #vibecoding applications. In my research life I struggle with keeping up with the literature and organizing my lab notebook.

I made a customizable automated literature search tool that performs weekly searches of #pubmed and #biorxiv then uses Claude to summarize and give a priority ranking based on my current #research

Also built an experiment management system to keep me on track and my data organized

Thanks for the inspiration @kevin and @Casey

https://hazletonlab.com/software.html

Otro pequeño orgullo de nuestro laboratorio del #iibce ya está en @biorxiv_neursci .
Un importante volumen de trabajo sobre las conexinas en la reparación de la médula espinal.
Gran equipo #MadeInUruguay lo hizo posible, gracias a financiación extranjera de #WingsForLife.

@constanzasilvera

#neuroscience #neuromastodon #medulaeespinal #conexinas #neurociencia #biology #biologia #investigacion #ciencia #Uruguay #spinalcordinjury #spinalcord #research #pedeciba @SocNeuroUy #preprint #biorxiv

https://www.biorxiv.org/content/10.64898/2026.01.16.699895v1.full.pdf+html

@jonmsterling

They explain that there are simply too many ultra-low quality reviews posted.

#bioRxiv has not been accepting to archive reviews for years already (at least since 2017). Their FAQ says it's irrelevant as #preprint because they're not novel in themselves, but I believe part of the reason is also that there's a flooding of dodgy reviews.

#arXiv

https://www.nature.com/articles/d41586-025-03664-7

https://web.archive.org/web/20170419045045/https://www.biorxiv.org/about/FAQ

Thank you #biorxiv staff for processing the pre-prints so quickly and nicely. Our latest manuscript addresses a rather specialized, albeit important, question in mRNA degradation in yeast. To what extent the Lsm1-7/Pat1 complex is involved in the degradation of mRNA by decapping activation ? By using a degron strain allowing rapid depletion of Lsm1, we find a slight impact of the complex on decapping, including changes in #NMD substrate levels.

https://www.biorxiv.org/content/10.64898/2025.12.17.694855v1

#RNA #decapping

#OpenRxiv just added an #AI #PeerReview feature for #preprints on #bioRxiv and #medRxiv. At the moment, they're using the #qedscience tool.
https://www.nature.com/articles/d41586-025-03909-5

The bioRxiv announcement makes clear that AI review is optional for authors and that authors might be able to choose from other AI tools in the future.
https://connect.biorxiv.org/news/2025/11/04/qed_review_tool

PS: My experiments lead me to think that AI isn't good enough to do peer review yet -- even if (1) it's getting better, (2) it can already help human reviewers, and (3) many human reviewers are worse. Journals that allow it too large a role are abdicating their responsibility and might be deceiving authors and readers. Referees who give it too large a role are abdicating their responsibility and might be deceiving journals, authors, and readers. If you lean in the same direction, let me suggest that these objections don't carry over to preprint servers making AI review an #FWIW option for authors. This kind of AI review doesn't pretend to be more than it is. When it happens, it's a voluntary decision by authors. Of course authors could have gotten AI feedback on their own, with the AI tools of their choice, and without the preprint-server mediation. But giving them another option for the same kind of feedback is harmless and convenient. Moreover, it creates a training ground to monitor the quality and improvement of the AI tools.

@sfmatheson @steveroyle @neuralreckoning @biorxivpreprint

#biorxiv is very strict about experimental only. I have never been able to get a paper without a methods section past biorxiv.

I want a preprint server that people will look at. So just putting it up on a website isn't good enough for me. I think of OSF and zenodo as places for data, not manuscripts.

Still have no freakin' clue what #arxiv is smokin' here.

Open to ideas.

So if preprint servers reject papers editorially without review or possibility of appeal, how are they different from gatekeeping journals, except without peer review or editorial responsibility.

(The editors at #arxiv and #biorxiv are unclear, unknown, and apparently answer to no one?)

#AcademicPublishing #preprints

Still doing #neuroscience.

Our #orbitofrontalcortex (#OFC) paper published in _Neuron_ today. (Also available in #biorxiv.)

Paul Cunningham, A. David Redish (2025) Opposing, multiplexed information in lateral and ventral orbitofrontal cortex guides sequential foraging decisions in rats Neuron.

https://www.cell.com/neuron/abstract/S0896-6273(25)00467-2

Key insights:

1. VO and LO are doing opposite things: LO is about immediate value, while VO is about opportunity costs.

2. OFC neurons are representing both task state (through which neurons are active) and value (as the total activity).

Talking about #arXiv #bioRxiv, one weakness is that there is no "flag" to indicate whether PDF is a #preprint or the post- #peerReview #postprint. I am surprised at the lack of attention on this.

Although I have my reservations on the quality of #peerReviewing in general, I believe it should be a point of attention of an institutional archive to make sure the file is post-peer review, or, if that version is under paywall only (which is a problem), state it at least.

@sebastienmaret @hal_fr