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#preprint

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Mikolaj Kocikowski, PhD

🐶 New preprint: DoggifAI

🤖 We built a transformer model that translates antibodies from mouse/human to dog “protein language” - preserving structure while reducing immunogenicity.

📂 Open model, code + dataset of 430k canine antibody sequences (largest to date): biorxiv.org/content/10.1101/20

#bioinformatics #AI #immunotherapy #OpenScience #preprint #comparativeoncology #dogs #OpenData, #cancerresearch

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Dr. Ramesh Glückler

It's been fantastic to attend the #PAGES Open Science Meeting 2025 last week in #Shanghai, together with @Iza_bai!

This key conference in the field of (not just) #paleoecology is only organized every four years, and when I joined and presented there for the first time in 2021, it had to be online due to the pandemic. Now, I could finally meet many great researchers who I've been following from around the world in person!

It's also been great to present my research on long-term #wildfire dynamics to an expert audience and discuss diverse ideas. I took with me many creative ideas and an extended and deepened network! Thanks to the conveners of Session 15 for the chance to present my work, and to the local organizing committee from Tongji University and everyone else who made this conference happen!

The study I presented is currently in review, but a #preprint is available here: lnkd.in/g-Fp2JGM

@academicchatter @paleofire @academicsunite #science

Me and Izabella Baisheva standing in front of a conference banner.
Me standing in front of a big screen showing the first slide of my conference presentation.
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ASAPbio

Need an idea for your next Journal Club? Discuss a #preprint!
💪 Help the authors strengthen their work
🗣️ Discuss science as it happens
🥼 Help raise your and your group’s profile
📰 No restrictions on papers to include
🧪 Focus on the science

Share this and other ASAPbio Infographics with your friends!

Visit the ASAPbio Preprint Resource Center to find English, Spanish, French, Portuguese, Italian, and Polish infographics!
asapbio.org/focus-areas/prepri

#OpenScience
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ScienceOpen

'Trends in use, spending, and prices of doxepin for insomnia' - a #REPO4EU #Research article #Preprint open for review on #ScienceOpen: drugrepocentral.scienceopen.co

ScienceOpenTrends in use, spending, and prices of doxepin for insomnia<p xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" class="first" dir="auto" id="d30465e99">Doxepin has been prescribed since the 1960s at daily doses ranging from 25-300mg as a tricyclic antidepressant. More recently, low-dose doxepin (3-6mg/day) was found to be safe and effective for treating insomnia. In 2010, the FDA approved low-dose doxepin under a new brand name (Silenor); generic versions became available in 2020. But total use of low-dose doxepin remained lower than use of capsules. In 2023, there were 2.6 million 30-day supplies of doxepin for insomnia, which was greater than DORAs (895,000), similar to melatonin agonists (2.6 million) and less than benzodiazepine receptor agonists (29.2 million) and trazodone (70.1 million). Mean prices per 30-day supply were $526 for brand name low-dose tablets, $252 for generic low-dose tablets, $11 for 10mg capsules, and $7 for liquid. If low-dose doxepin tablets had been available at the same per-milligram price as liquid doxepin, spending would have been reduced by $73.9 million dollars (98%). Despite generic competition, low-dose doxepin tablets approved for insomnia have substantially higher prices and less use than similar doses of capsules or liquid doxepin which can be used off-label to treat insomnia. Well-intentioned repurposing of generic medications like doxepin can be hindered if the repurposing requires doses that are not interchangeable with original versions, allowing manufacturers to set high prices for the new version that can limit patient access. </p>
Replied in thread
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Georg Krammer

@briannosek.bsky.social

A word of caution on my end. It relates to something I touch upon that in a recent #preprint on open data: doi.org/10.31219/osf.io/hk786_

There is a striking resemble to things recommended and backed by Big #Tabacco vs #Science some decades ago.
Ironically, they demanded what we in #OpenScience demand nowadays, but with a very different aim... :(

Here a quick summary:
"Long before today’s #Open #Science movements, the Executive Committee of the Sound Science Coalition (1994; cited in Ong & Glantz, 2001) published guidelines that align with what Open Science practices advocate today. For example:
(1) The study design should inform about all hypotheses,
(2) after the study was conducted, the data should be analyzed as described in the study design, and
(3) if the data does not support the hypotheses, no further analyses are necessary.
Shockingly, in 1994 these recommendations were motivated by the fact that parts of the #tobacco industry aimed to #discredit research and researchers on a large scale, with the goal that it could not be legally established that smoking increases the risk of lung #cancer (Drope, 2001; Muggli et al., 2001; Ong & Glantz, 2001). Along this line, one may accuse researchers as having been naive to the vested interests aligning with scientific rigour by non-researchers."

doi.orgOSF
Replied in thread
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Georg Krammer

@UlrikeHahn
We as researchers are just super naive. If you ask me, those things go back to Big #Tabacco vs #Science
Ironically, they demanded what we in #OpenScience demand nowadays, but with a very different aim... :(

I touch upon that in a recent #preprint on open data: doi.org/10.31219/osf.io/hk786_

"Long before today’s #Open #Science movements, the Executive Committee of the Sound Science Coalition (1994; cited in Ong & Glantz, 2001) published guidelines that align with what Open Science practices advocate today. For example:
(1) The study design should inform about all hypotheses,
(2) after the study was conducted, the data should be analyzed as described in the study design, and
(3) if the data does not support the hypotheses, no further analyses are necessary.
Shockingly, in #1994 these recommendations were motivated by the fact that parts of the #tobacco industry aimed to #discredit research and researchers on a large scale, with the goal that it could not be legally established that smoking increases the risk of lung #cancer (Drope, 2001; Muggli et al., 2001; Ong & Glantz, 2001). Along this line, one may accuse researchers as having been naive to the vested interests aligning with scientific rigour by non-researchers."

doi.orgOSF
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Benjamin Carr, Ph.D. 👨🏻‍💻🧬

#MIT Asks #arXiv To Take Down #Preprint Paper On #AI and Scientific Discovery

"MIT has no confidence in the provenance, reliability or validity of the data and has no confidence in the veracity of the research contained in the paper. Based upon this finding, we also believe that the inclusion of this paper in arXiv may violate arXiv's Code of Conduct."
The paper by Aidan Toner-Rodgers, investigated #AI-driven materials discovery by 1,018 #scientists in a U.S. R&D lab.
economics.mit.edu/news/assurin

economics.mit.eduAssuring an accurate research record | MIT Economics
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Bibliolater 📚 📜 🖋

:bitcoin: **Bitcoin, Currencies, and Fragility**

_“In its current version, in spite of the hype, bitcoin failed to satisfy the notion of “currency without government” (it proved to not even be a currency at all), can be neither a short nor long term store of value (its expected value is no higher than), cannot operate as a reliable inflation hedge, and, worst of all, does not constitute, not even remotely, a safe haven for one's investments, a shield against government tyranny, or a tail protection vehicle for catastrophic episodes.”_

Taleb, N.N. (2021) 'Bitcoin, currencies, and fragility,' arXiv (Cornell University) [Preprint]. doi.org/10.48550/arxiv.2106.14.

#Bitcoin #Currency #Money #Wealth #Economics #Finance #Academia #Academic #Preprint #arXiv @economics

arXiv.orgBitcoin, Currencies, and FragilityThis discussion applies quantitative finance methods and economic arguments to cryptocurrencies in general and bitcoin in particular -- as there are about $10,000$ cryptocurrencies, we focus (unless otherwise specified) on the most discussed crypto of those that claim to hew to the original protocol (Nakamoto 2009) and the one with, by far, the largest market capitalization. In its current version, in spite of the hype, bitcoin failed to satisfy the notion of "currency without government" (it proved to not even be a currency at all), can be neither a short nor long term store of value (its expected value is no higher than $0$), cannot operate as a reliable inflation hedge, and, worst of all, does not constitute, not even remotely, a safe haven for one's investments, a shield against government tyranny, or a tail protection vehicle for catastrophic episodes. Furthermore, bitcoin promoters appear to conflate the success of a payment mechanism (as a decentralized mode of exchange), which so far has failed, with the speculative variations in the price of a zero-sum maximally fragile asset with massive negative externalities. Going through monetary history, we show how a true numeraire must be one of minimum variance with respect to an arbitrary basket of goods and services, how gold and silver lost their inflation hedge status during the Hunt brothers squeeze in the late 1970s and what would be required from a true inflation hedged store of value.
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petersuber

I like this idea for a #LettersToTheEditor #preprint server.
link.springer.com/article/10.1

"Such a preprint server would offer three major benefits…: format-free ease of swift communication, increased author visibility and accountability, and avoiding the homelessness of unpublished [letters]."

PS: I've sent letters to journals that had policies not to publish them, but without saying so anywhere. Once I sent a letter to a new journal that had never received or published one and needed time to think about it. Right now #SocialMedia takes up this slack and does a pretty good job. But posting letters as preprints would give authors more space, prevent even published letters from languishing behind #paywalls, and offer better opportunities for #PIDs, #metadata, and #discoverability.

SpringerLinkReinventing the Letter to the Editor in Science: A Dedicated Preprint Server - Publishing Research QuarterlyAlthough letters to the editor (LTEs, or Correspondence) have a wide range of communicative functions within science, they also present several drawbacks, three of which we highlight: editorial ambiguity, technological limitations and skewed perceptions about their format. An assessment of Scopus (September 16, 2023) indicated that letters account for 1.7% to 3.2% per year, relative to articles and reviews, suggesting that the LTE field is undeveloped. We argue that the creation of a new preprint server, which we name CoArXiv or LettersArXiv, would allow LTEs—with timely and valuable knowledge and insight—to be posted in much the same way as other preprints, and would be one way to overcome needed reform of LTE-publishing culture, ultimately expanding the range of science communication channels for multidisciplinary research. We consider that such a preprint server would offer three major benefits for scientific research: format-free ease of swift communication, increased author visibility and accountability, and avoiding the homelessness of unpublished LTEs.
#ScholComm
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LucCogZest

Now on ResearchGate: A free #preprint of an article describing the theory behind the #cognitiveShuffle is available on ResearchGate. It's called the somnolent information processing theory. It will be in the upcoming #CambridgeUniversityPress book on sleep theories edited by Daniel Kay:
researchgate.net/publication/3 #sleep #insomnia

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Bibliolater 📚 📜 🖋

🔴 **Long-term hunter-gatherer continuity in the Rhine-Meuse region was disrupted by local formation of expansive Bell Beaker groups**

“_We document an exception to this pattern in the wider Rhine-Meuse area in communities in the wetlands, riverine areas, and coastal areas of the western and central Netherlands, Belgium and western Germany, where we assembled genome-wide data for 109 people 8500-1700 BCE. Here, a distinctive population with high hunter-gatherer ancestry (∼50%) persisted up to three thousand years later than in continental European regions, reflecting limited incorporation of females of Early European Farmer ancestry into local communities._”

Olalde, I. et al. (2025) 'Long-term hunter-gatherer continuity in the Rhine-Meuse region was disrupted by local formation of expansive Bell Beaker groups,' bioRxiv (Cold Spring Harbor Laboratory) [Preprint]. doi.org/10.1101/2025.03.24.644.

#Preprint #Science #Biology #Genetics #Archaeology #Archaeodons #Anthropology #Europe @archaeodons

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Nick Byrd, Ph.D.

🔔 In Religious Studies: Analytic #Atheism & Analytic Apostasy...

Steve Stich, Justin Sytsma, and I studied >70k people across the globe.

Apostates were more reflective thinkers.

That explained links between reflection and #religion.

#Preprint + audio: byrdnick.com/archives/28471/up

The final typeset version is also freely available (#openAccess) via #CambridgeUP; doi.org/10.1017/S0034412525000

Nick Byrd, Ph.D. · Why do atheists tend to do better on critical thinking tests?Apostates seem to score better than others. And they tend to be atheists. So "analytic atheism" seems to be explained by analytic APOSTASY.
#psychology#psychometrics#cogSci
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