Mastodawn

Our workshop "Cross-government policy modelling of long-term health and wellbeing impacts" brought 5 #microsimulation teams together with policy makers, public sector and other researchers.

#HealthEconomics

SimPaths
https://www.microsimulation.ac.uk/jas-mine/simpaths/

SIPHER
https://www.gla.ac.uk/research/az/sipher/

WELLMOD
https://chanse.org/wellmod/

Sheffield Tobacco and Alcohol Policy Model
https://onlinelibrary.wiley.com/doi/full/10.1002/hec.3105

The event was part of our #UKRI #MRC funding
https://gtr.ukri.org/projects?ref=MR%2FX002837%2F1#/tabOverview

And a #PrePrint from our work:
https://eprints.whiterose.ac.uk/id/eprint/234125/

amplisci 4d ago

This preprint titled “Assessment of inter-individual variation in metabolism of flavonoids from bilberry and grape seed extracts using an in vitro digestion and faecal fermentation model“ by Dr. Teresa Grohmann et al attempts to identify gut-microbial candidates that are capable of metabolising flavonoids and anthocyanins in bilberry and grape seed extracts using the INFOGEST in vitro digestion model. Microbes that can metabolise these phytochemicals are expected to modulate metabolic and cardiovascular health outcomes by producing potent secondary metabolites.

The preprint can be accessed here: https://doi.org/10.64898/2026.03.02.709000

This manuscript was typeset by Typescholar.

#preprint #academia #openscience

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VelteropⓐⓊ🪂🇪🇺🇳🇱🇬🇧🇩🇪4d ago

@brembs @albertcardona
The thing funders COULD mandate is to always post a #preprint before, or simultaneously with, submitting to any journal.
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000273

Plan U: Universal access to scientific and medical research via funder preprint mandates

Preprint servers are a low-cost mechanism for providing free access to research findings, and can also significantly accelerate research itself by making results available immediately. This Perspective article proposes that funding agencies should mandate preprint posting to ensure universal free access to the world’s scientific output, as well as stimulate new peer review and research evaluation initiatives.

Benjamin S-B

Mar 24

🎉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

Rastair: an integrated variant and methylation caller

Cytosine methylation is a crucial epigenetic mark that impact tissue-specific chromatin conformation and gene expression. For many years, bisulfite sequencing (BS-seq), which converts all non-methylated cytosine (C) to thymine (T), remained the only approach to measure cytosine methylation at base resolution. Recently, however, several new methods that convert only methylated cytosines to thymine (mC→T) have become widely available. Here we present rastair, an integrated software toolkit for simultaneous SNP detection and methylation calling from mC→T sequencing data such as those created with Watchmaker's TAPS+ and Illumina's 5-Base chemistries. Rastair combines machine-learning-based variant detection with genotype-aware methylation estimation. Using NA12878 benchmark datasets, we show that rastair outperforms existing methylation-aware SNP callers and achieves F1 scores exceeding 0.99 for datasets above 30x depth, matching the accuracy of state-of-the-art tools run on whole-genome sequencing data. At the same time, rastair is significantly faster than other genetic variant callers, processing a 30x depth file takes less than 30 minutes given 32 CPU cores on an Intel Xeon, and half as long when a GPU is available. By integrating genotyping with methylation calling, rastair reports an additional 500,000 positions in NA12878 where a SNP turns a non-CpG reference position into a "de-novo" CpG. Vice-versa, rastair also identifies positions where a variant disrupts a CpG and corrects their reported methylation levels. Rastair produces standard-compliant outputs in vcf, bam and bed formats, facilitating integration into downstream analyses pipelines. Rastair is open-source and available via conda, Dockerhub, and as pre-compiled binaries from https://www.rastair.com. ### Competing Interest Statement Pascal Hertleif is a employee and owner of Softleif AB, a software development company. All other authors declare no competing financial interests. Ludwig Institute For Cancer Research

bioRxiv

Hacker News Mar 20

ArXiv Declares Independence from Cornell

https://www.science.org/content/article/arxiv-pioneering-preprint-server-declares-independence-cornell

#HackerNews #ArXiv #Independence #Cornell #Preprint #Server #Science #News

Dr. Korinna Allhoff Mar 18

🚨 new #preprint 🚨

The evolutionary emergence of #EcologicalNetworks has been studied for decades but usually focussing on one type of interaction at a time, even though organisms naturally engage in multiple interaction types simultaneously. The combined effect of different interaction types on diversification thus remains unclear - until now. 😜

I hope you enjoy reading this fascinating story about ecological #pleiotropy and how it shapes #diversification patterns!

https://www.biorxiv.org/content/10.64898/2026.03.16.712075v1

Between Friends and Foes: Evolutionary Diversification in Mutualistic-Antagonistic Networks

Biotic interactions can drive evolutionary diversification, but the underlying mechanisms differ depending on the type of interaction. For instance, Ehrlich and Raven's escape-and-radiate coevolution provides a pathway of diversification in antagonistic interactions, whereas in mutualistic networks, coevolution is hypothesized to result in trait convergence rather than diversification. The combined effect of mutualism and antagonism on diversification remains unclear, even though organisms naturally engage in multiple types of interactions simultaneously. Using an eco-evolutionary simulation model, we investigate diversification in tripartite ecological networks such as plant-pollinator-herbivore networks. We find that diversification patterns vary according to the way mutualism and antagonism are connected on the trait level. If the two interactions are governed by uncorrelated plant traits, we observe little diversification in the mutualistic and substantial diversification in the antagonistic subnetwork. By contrast, if the same plant trait mediates both mutualism and antagonism (an example of 'ecological pleiotropy'), diversification rates in all guilds become interdependent. In this case, even the mutualistic guild diversifies considerably when antagonism is strong, while strong mutualism restricts diversification also in the antagonistic guild. Our study underlines that the inclusion of multiple interaction types is necessary to advance our understanding of evolutionary dynamics in ecological networks. ### Competing Interest Statement The authors have declared no competing interest. Deutsche Forschungsgemeinschaft, https://ror.org/018mejw64, AL 2563/3‑1 German National Academic Foundation

bioRxiv

sayzard Mar 17

Kimi.ai (@Kimi_Moonshot)

arXiv에 새 연구 논문이 업로드되었다는 간단 공지와 arXiv 링크를 공유한 트윗입니다. 트윗 본문은 상세 설명 없이 arXiv 링크만 포함되어 있어, 논문 제목과 내용은 링크(https://arxiv.org/abs/2603.15031)를 통해 확인해야 합니다. 연구 발표·사전 공개(preprint) 알림으로 개발자와 연구자 대상의 새 연구 결과 공개를 의미합니다.

https://x.com/Kimi_Moonshot/status/2033796781327454686

#arxiv #research #preprint #paper

Attention Residuals

Residual connections with PreNorm are standard in modern LLMs, yet they accumulate all layer outputs with fixed unit weights. This uniform aggregation causes uncontrolled hidden-state growth with depth, progressively diluting each layer's contribution. We propose Attention Residuals (AttnRes), which replaces this fixed accumulation with softmax attention over preceding layer outputs, allowing each layer to selectively aggregate earlier representations with learned, input-dependent weights. To address the memory and communication overhead of attending over all preceding layer outputs for large-scale model training, we introduce Block AttnRes, which partitions layers into blocks and attends over block-level representations, reducing the memory footprint while preserving most of the gains of full AttnRes. Combined with cache-based pipeline communication and a two-phase computation strategy, Block AttnRes becomes a practical drop-in replacement for standard residual connections with minimal overhead. Scaling law experiments confirm that the improvement is consistent across model sizes, and ablations validate the benefit of content-dependent depth-wise selection. We further integrate AttnRes into the Kimi Linear architecture (48B total / 3B activated parameters) and pre-train on 1.4T tokens, where AttnRes mitigates PreNorm dilution, yielding more uniform output magnitudes and gradient distribution across depth, and improves downstream performance across all evaluated tasks.

arXiv.org

VelteropⓐⓊ🪂🇪🇺🇳🇱🇬🇧🇩🇪Mar 14

Anecdotal information seems to suggest that the cost of posting a #preprint is less than 0.25% of the cost of a typical APC. In other words, publishing in a typical peer reviewed journal is some 400 times more expensive than posting a preprint. Does pre-publication peer review really improve scientific information by a factor of 400? Might post-publication perhaps offer more cost-efficient possibilities to assess the integrity of the scientific record?

ScienceOpen Mar 13

🏆 #PreprintOfTheWeek on #ScienceOpen "Europe's Problem Child : The Turkish Path to Europeanisation"

Congrats from the Editors of ScienceOpen Preprints to the author Andreas Savva.

Discover the full #preprint and join the discussion.
🔗Link in the first comment.
#Turkey #EU

Ellen Euler ✅Mar 9

Quantitative Metriken setzen falsche Anreize. Was in vielen Disziplinen längst ein strukturelles Problem ist, hat die #Rechtswissenschaft noch nicht erfasst. Sie kann #Bewertungslogiken sowie #Publikationsinfrastruktur noch so gestalten, dass diese den epistemischen Anforderungen der Disziplin entsprechen & eine belastbare Grundlage für #Forschungsbewertung schaffen.

Wie? Dazu habe ich mit @philippfalkenburg bei #IntRechtDok ein #Preprint veröffentlicht:
https://doi.org/10.17176/20260309-114602-0
#CoARA #DOA #OA