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#preprint

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Check out our latest #preprint in which we use a combination of #clumped and #oxygen #isotope measurements to reconstruct extreme summer temperatures experienced by #fossil #rudist bivalves from the Late #Cretaceous in Oman. All feedback is welcome!
egusphere.copernicus.org/prepr

egusphere.copernicus.orgLiving on the edge: Response of rudist bivalves (Hippuritida) to hot and highly seasonal climate in the low-latitude Saiwan site, OmanAbstract. Earth’s climate history serves as a natural laboratory for testing the effect of warm climates on the biosphere. The Cretaceous period featured a prolonged greenhouse climate characterized by higher-than-modern atmospheric CO2 concentrations and mostly ice-free poles. In such a climate, shallow seas in low latitudes probably became very hot, especially during the summers. At the same time, life seems to have thrived there in reef-like ecosystems built by rudists, an extinct group of bivalve molluscs. To test the seasonal temperature variability in this greenhouse period, and whether temperature extremes exceed the maximum tolerable temperatures of modern marine molluscs, we discuss a detailed sclerochronological (incrementally sampled) dataset of seasonal scale variability in shell chemistry from fossil rudist (Torreites sanchezi and Vaccinites vesiculosus) and oyster (Oscillopha figari) shells from the late Campanian (75-million-year-old) low latitude (3° S paleolatitude) Saiwan site in present-day Oman. We combine trace element data and microscopy to screen fossil shells for diagenesis, before sampling well-preserved sections of a Torreites sanchezi rudist specimen for clumped isotope analysis. Based on this specimen alone, we identify a strong seasonal variability in temperature of 19.2 ± 3.8 °C to 44.2 ± 4.0 °C in the seawater at the Saiwan site. The oxygen isotopic composition of the seawater (δ18Osw) varied from -4.62 ± 0.86 ‰ VSMOW in winter to +0.86 ± 1.6 ‰ VSMOW in summer. We use this information in combination with age modelling to infer temperature seasonality from incrementally sampled oxygen isotope profiles sourced from the literature, sampling multiple shells and species in the assemblage. We find that, on average, the Saiwan seawater experienced strong seasonal fluctuations in monthly temperature (18.7 ± 3.8 to 42.6 ± 4.0 °C seasonal range) and water isotopic composition (-4.33 ± 0.86 to 0.59 ± 1.03 ‰ VSMOW). The latter would strongly bias the interpretation of stable oxygen isotopes in shell carbonate without independent control on either temperature or seawater composition. Combining our seasonal temperature estimates with shell chronologies based on seasonal cyclicity in stable isotope records and daily variability in trace element data, we show that T. sanchezi rudists record temperatures during the hottest periods of the year as well as during the winters, which were characterized by cooler temperatures and enhanced influx of freshwater. Both O. figari and V. vesiculosus plausibly stopped growing during these seasonal extremes. This study aims to demonstrate how high-resolution geochemical records through fossil mollusc shells can shed light on the variability in past warm ecosystems and open the discussion about the limits of life in the shallow marine realm during greenhouse climates. Future work should apply the clumped isotope paleothermometer on incrementally sampled bio-archives to explore the upper-temperature limits experienced by calcifiers in different environments throughout geological history.

🐶 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

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: doi.org/10.1101/2025.03.14.643

@academicchatter @paleofire @academicsunite #science

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

'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

@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

@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

Reimagining peer review: new #spotLights episode discussing the Fast & Fair peer review initiative launched by @BiologyOpen

Dan, Alejandra & Jonathan discuss early insights, now published as a #bioRxiv #preprint, and how you can get involved.

Listen below ⬇️ 🎧
youtu.be/mM6mZIubZaw

youtu.be- YouTubeEnjoy the videos and music you love, upload original content, and share it all with friends, family, and the world on YouTube.

#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

Led by Samuel Campos, the IMB565 class #ImmunobiologyUA has preLighted recent #immunology preprints.

“Resident Killers: Tonsil resident NK cells show potential against early HIV-1 infection.” #preprint from David Perea, Maria Buzon & team

#preLight prepared by Sukirti Shivpuri, Jared Alvarez & Vanessa Brizuela ⬇️

prelights.biologists.com/highl

preLightsEarly resident NK cell response to local HIV infection in lymphoid tissue - preLightsResident Killers: Tonsil resident NK cells show potential against early HIV-1 infection.

Four weeks ago, my first co-authored @EuroGeosciences #preprint « #Reviews and syntheses: Best practices for the application of #marine #GDGTs as proxy for paleotemperatures: sampling, processing, analyses, interpretation, and archiving protocols » went online!
doi.org/10.5194/egusphere-2025
#Science #ScienceMastodon #AcademicMastodon
#Review #Consensus
#EGUsphere
#isoGDGTs #brGDGTs #TeamArchaea #TeamBacteria
#archaeal #bacterial #tetraether #lipids
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