Tootfinder

The Grammar of FAIR: A Granular Architecture of Semantic Units for FAIR Semantics, Inspired by Biology and Linguistics
Lars Vogt, Barend Mons
https://arxiv.org/abs/2509.26434 ht…

The Grammar of FAIR: A Granular Architecture of Semantic Units for FAIR Semantics, Inspired by Biology and Linguistics
The FAIR Principles aim to make data and knowledge Findable, Accessible, Interoperable, and Reusable, yet current digital infrastructures often lack a unifying semantic framework that bridges human cognition and machine-actionability. In this paper, we introduce the Grammar of FAIR: a granular and modular architecture for FAIR semantics built on the concept of semantic units. Semantic units, comprising atomic statement units and composite compound units, implement the principle of semantic modu…

My next bedtime book, is a big biology book; heck it's not light reading; it's 3kg!
(I got the older 5th edition for about ~£10 - the current edition is a fortune)
I suspect it'll take me a couple of years.
https://en.wikipedia.org/wiki/Molecula

Molecular Biology of the Cell (book) - Wikipedia

🧝‍♂️ Wie überstehen #Elfen lange Schichten in der Kälte mit Dauergrinsen? 🧝‍♀️
Laut einer #Anatomie-Professorin könnten sie über effiziente #Energienutzung, spezielle

An Anatomy Professor Explains The Bizarre Biology of Elves
As Christmas Eve draws near, we're reminded of the tireless elves behind the scenes, toiling in workshops to bring festive magic to life.

Nephrobase Cell : Multimodal Single-Cell Foundation Model for Decoding Kidney Biology
Chenyu Li, Elias Ziyadeh, Yash Sharma, Bernhard Dumoulin, Jonathan Levinsohn, Eunji Ha, Siyu Pan, Vishwanatha Rao, Madhav Subramaniyam, Mario Szegedy, Nancy Zhang, Katalin Susztak
https://arxiv.org/abs/2509.26223 …

Nephrobase Cell+: Multimodal Single-Cell Foundation Model for Decoding Kidney Biology
Background: Large foundation models have revolutionized single-cell analysis, yet no kidney-specific model currently exists, and it remains unclear whether organ-focused models can outperform generalized models. The kidney's complex cellular architecture further complicate integration of large-scale omics data, where current frameworks trained on limited datasets struggle to correct batch effects, capture cross-modality variation, and generalize across species. Methods: We developed Nephrobase …

Beyond technology and biology, he has a passion for agriculture, the science and beauty of which have encouraged him to start his own vegetable garden and plant dozens of fruit-bearing trees with fragrant and succulent, sweet and sour fruits.

Julia Platt was a brilliant scientist. #Science She made experimental breakthroughs in developmental biology from the late 1800s to the 1920s. She worked in universities in the U.S. and Europe. Her non-standard ideas and techniques were eventually accepted and shown to be correct by male scientists, after she died.
Here's a portrait of her after she was mayor of Pacific Grove, California. She h…

To portray a mind as a kind of high-powered survival machine orchestrated and controlled by genes is, then, fundamentally a misconceived picture of what minds are.
Ball, Philip. How Life Works: A User’s Guide to the New Biology (p. 427). (Function). Kindle Edition.

A general optimization framework for mapping local transition-state networks
Qichen Xu, Anna Delin
https://arxiv.org/abs/2509.26269 https://arxiv.org/pdf/2…

A general optimization framework for mapping local transition-state networks
Understanding how complex systems transition between states requires mapping the energy landscape that governs these changes. Local transition-state networks reveal the barrier architecture that explains observed behaviour and enables mechanism-based prediction across computational chemistry, biology, and physics, yet current practice either prescribes endpoints or randomly samples only a few saddles around an initial guess. We present a general optimization framework that systematically expand…

What does the tree of life look like as it grows? Evolution and the multifractality of time
Kevin Hudnall, Raissa D'Souza
https://arxiv.org/abs/2509.25615 https://

What does the tree of life look like as it grows? Evolution and the multifractality of time
By unifying three foundational principles of modern biology, we develop a mathematical framework to analyze the growing tree of life. Contrary to the static case, where the analogy between phylogenetic trees and the tree that grows in soil is drawn, our framework shows that the living tree of life is analogous to a Cantor dust where each branch is a distinct fractal curve. The system as a whole is therefore multifractal in the sense that it consists of many unique fractals. The three foundation…

@… at least, some proof of your existence.
"In a twist, the findings lend credence to the Australian folk hoax of the “drop bear,” a ferocious, carnivorous variety of koala said to fall upon its victims from the canopy. Paleontologists think Thylacoleo was an adept climber and ambush predator that could dive upon its prey from tree branches or roc…

[2025-10-01 Wed (UTC), no new articles found for q-bio.OT Other Quantitative Biology]
toXiv_bot_toot

my link log mostly works as an external memory, provided i can remember the keywords in the headline
i edit headlines to stuff in extra keywords that make them easier to retrieve: implicit tags without the hash
but sometimes it can be a little frustrating
just now i was trying to remember something to do with numerical? analogies? sizes? units?
took me about 10 minutes to remember the other key word was “bio”
after which i was reminded the key words i had not-qu…

Metaphors for Biology: Sizes
A series of quantitative metaphors on the sizes and shapes of biomolecules and organisms.

Q&A with Google DeepMind VP of Research Pushmeet Kohli on launching AlphaFold 2 five years ago, hallucinations, building an "AI co-scientist", and more (Sandro Iannaccone/Wired)
https://www.wired.com/story/alphafold-changed-science-after-…

AlphaFold Changed Science. After 5 Years, It’s Still Evolving
WIRED spoke with DeepMind’s Pushmeet Kohli about the recent past—and promising future—of the Nobel Prize-winning research project that changed biology and chemistry forever.

The new Zygote issue 39 is featuring stunning art by Kate MccGwire[1] and articles about:
Forward Motion: Robert J. Full’s Career of Discovery
Science of Seeing: Plant It and They Will Come
Cutting Without Cutting: Lessons from the Sawfly
Interview with Arindam Phani and Seonghwan (Sam) Kim
Building with Biology
Turning Bio-Inspired Ideas Into Patents
Biomimicry in Architecture

🐠 3D-printed helix shelters increase baby coral survival rates
#coral

3D-printed helix shelters increase baby coral survival rates
To dramatically increase coral survival rates, scientists at the University of Hawaiʻi at Mānoa Hawaiʻi Institute of Marine Biology (HIMB) have developed innovative 3D-printed ceramic structures that provide crucial protection for baby corals. These new designs offer a low-cost and scalable solution to enhance reef recovery worldwide.

"Experts urge canceling fossil fuel contracts to meet Paris climate goals"
#FossilFuels #Cliamte #ClimateChange

Experts urge canceling fossil fuel contracts to meet Paris climate goals
The countries participating in the UN Climate Change Conference (COP30), currently taking place in Brazil, must cancel fossil fuel concessions in order to keep the Paris Agreement alive. This is the main message of a paper published in the journal Nature and signed by experts Martí Orta, Gorka Muñoa and Marcel Llavero, from the Faculty of Biology and the Biodiversity Research Institute (IRBio) of the University of Barcelona, and Guillem Rius, from the Barcelona Institute for Global Health (IS…

(2015, PDF) The rehabilitative potential of auditory to visual sensory substitution devices for the blind https://las.touro.edu/media/schools-an

My department at California State University Northridge is hiring! We're looking for a new colleague studying microbiology or molecular/cellular biology. I'm not on the search committee, but happy to answer questions about the department and campus, and life in LA

Experts urge canceling fossil fuel contracts to meet Paris climate goals #climate

Experts urge canceling fossil fuel contracts to meet Paris climate goals
The countries participating in the UN Climate Change Conference (COP30), currently taking place in Brazil, must cancel fossil fuel concessions in order to keep the Paris Agreement alive. This is the main message of a paper published in the journal Nature and signed by experts Martí Orta, Gorka Muñoa and Marcel Llavero, from the Faculty of Biology and the Biodiversity Research Institute (IRBio) of the University of Barcelona, and Guillem Rius, from the Barcelona Institute for Global Health (IS…

GenVarFormer: Predicting gene expression from long-range mutations in cancer
David Laub, Ethan Armand, Arda Pekis, Zekai Chen, Irsyad Adam, Shaun Porwal, Bing Ren, Kevin Brown, Hannah Carter
https://arxiv.org/abs/2509.25573

GenVarFormer: Predicting gene expression from long-range mutations in cancer
Distinguishing the rare "driver" mutations that fuel cancer progression from the vast background of "passenger" mutations in the non-coding genome is a fundamental challenge in cancer biology. A primary mechanism that non-coding driver mutations contribute to cancer is by affecting gene expression, potentially from millions of nucleotides away. However, existing predictors of gene expression from mutations are unable to simultaneously handle interactions spanning millions of base pairs, the ext…

The offices at John Quackenbush’s lab at the Harvard T.H. Chan School of Public Health
were once full of postdoctoral fellows, graduate students, and interns.
Young scientists here worked on some of the most cutting-edge computational biology research in the world,
driving new discoveries and the creation of widely used big data tools, including one the National Cancer Institute named among the most important advances of 2024.
Today, the offices are rows of empty comp…

His lab was humming with discovery. After one year under Trump, it’s almost silent
John Quackenbush built a lab that is at the forefront of human genetics research and bioinformatics. Trump administration cuts have put it in danger of collapse.

Weekend #Plankton Factoid 🦠🦐
Tintinnids ("tinkling bells") are ciliates found in fresh and saltwater known for their characteristic vase-shaped shell called a lorica. These are formed of tough proteins, incorporating minerals from the water and vary considerably by species. The shell offers protection and optimizes feeding on phytoplankton, bacteria and flagellates. These small pro…

I've been reading biology related books and by sheer hubris and ADHD delusion I thought about switching careers*! Figuring out life's systems feels more fascinating than figuring out how IT systems should be working together.
Then I found out that Alan Turing has touched both fields. I did not know about that! So here I stand with interests between Turing machines and Turing patterns! Always pretty cool to find out about these connections between fields!
* I won’t!
…

Turing pattern - Wikipedia

“If our world survives, the next great challenge to watch out for will come — you heard it here first — when the curves of research and development in artificial intelligence, molecular biology and robotics all converge.”
– Thomas Pynchon [writing in 1984]

Branching Flows: Discrete, Continuous, and Manifold Flow Matching with Splits and Deletions
Hedwig Nora Nordlinder (Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet), Lukas Billera (Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet), Jack Collier Ryder (Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet), Anton Oresten (Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet), Aron St{\aa}lmarck (…

Biology-driven assessment of deep learning super-resolution imaging of the porosity network in dentin
Lauren Anderson, Lucas Chatelain, Nicolas Tremblay, Kathryn Grandfield, David Rousseau, Aur\'elien Gourrier
https://arxiv.org/abs/2510.08407

Biology-driven assessment of deep learning super-resolution imaging of the porosity network in dentin
The mechanosensory system of teeth is currently believed to partly rely on Odontoblast cells stimulation by fluid flow through a porosity network extending through dentin. Visualizing the smallest sub-microscopic porosity vessels therefore requires the highest achievable resolution from confocal fluorescence microscopy, the current gold standard. This considerably limits the extent of the field of view to very small sample regions. To overcome this limitation, we tested different deep learning …

Microsoft researchers say AI models can be used to design toxins that evade biosecurity systems used to screen DNA orders for potential biothreats (Antonio Regalado/MIT Technology Review)
https://www.technologyreview.com/2025/10/0…

Microsoft says AI can create “zero day” threats in biology
Artificial intelligence can design toxins that evade security controls.

i stumbled across a fragment of my online dating profile from two decades ago
I'm into Monk, chaos theory, Björk, Vermeer, Frosted Mini-Wheats, Wallace Stevens, Saint-Saëns, Tim O'Brien, Miro, evolutionary biology, Ravel, Gregory Corso, fresh berries, UFOs, Ellington, Bible comics, computational complexity, Nespresso, The Kinks, Diane DiPrima, fresh-squeezed OJ, Köln's Kompakt music label, Giacometti, Mingus, that sort of thing. I'm very curious and never bored.
s…

Was talking to an acquaintance at church yesterday and she mentioned that things are not good with her job. She’s a secondary school biology teacher. She said more by what she didn’t say. She just clammed up and looked lost. Next time I see her, I want to tell her that it doesn’t have to be that way. That she has transferable skills and can find work that pays the bills without destroying her soul. That there are other places that will value and support her.

Great RadioLab interview with Ella al-Shamahi, about her journey from religious anti-evolutionism into evolutionary biology. New perspective but also familiar if you (like me) grew up among Christian creationists; really moving on what faith, even "denialist" faith, means to people
#science #evolution

a beautifully weird mckenna-ish mystery: chinese mushrooms that reliably bring the little people, but don't seem to contain any psychoactive elements (& yet obviously do) https://nhmu.utah.edu/articles/experts-explore-new-mushroom-which-cau…

Experts Explore New Mushroom Which Causes Fairytale-Like Hallucinations
Between traditional folklore and modern biology, the wild forest floor and the sterile scientific laboratory, lies the story of the lilliputian mushroom.

🔦 Engineered protein switches may lead to safer, smarter medicines
#biology

Engineered protein switches may lead to safer, smarter medicines
A new way to potentially control when drugs are active or inactive in the body is introduced in a study reported Sept. 24 in Nature. The research showed that, instead of controlling how tightly proteins bind to partner molecules, scientists can now directly control how long they stay bound. This advance has broad implications for developing safer medicines.

from my link log —
Quantitative metaphors for sizes in biology.
https://press.asimov.com/articles/metaphors-size
saved 2025-11-05 https://

Metaphors for Biology: Sizes
A series of quantitative metaphors on the sizes and shapes of biomolecules and organisms.

Profluent, which wants to use AI for protein design in drug discovery, raised $106M led by Bezos Expeditions and Altimeter, bringing its total funding to $150M (Amy Feldman/Forbes)
http://www.forbes.com/sites/amyfeldman/20

Jeff Bezos Is Backing An AI Startup Aiming To Make Proteins Programmable
Profluent has raised $106 million to scale up use of its AI models for biology in drug development and agriculture.

SemCSE-Multi: Multifaceted and Decodable Embeddings for Aspect-Specific and Interpretable Scientific Domain Mapping
Marc Brinner, Sina Zarrie{\ss}
https://arxiv.org/abs/2510.11599

SemCSE-Multi: Multifaceted and Decodable Embeddings for Aspect-Specific and Interpretable Scientific Domain Mapping
We propose SemCSE-Multi, a novel unsupervised framework for generating multifaceted embeddings of scientific abstracts, evaluated in the domains of invasion biology and medicine. These embeddings capture distinct, individually specifiable aspects in isolation, thus enabling fine-grained and controllable similarity assessments as well as adaptive, user-driven visualizations of scientific domains. Our approach relies on an unsupervised procedure that produces aspect-specific summarizing sentences…

Neurons in auditory cortex integrate information within a constrained and context-invariant temporal window (in ferret auditory cortex) https://www.cell.com/current-biology/fulltext/S0960-9822(25)01479-4 integration windows in human auditory cortex "range from a…

Effectiveness of Quota Policies Across STEM, Biological, and Humanities Programs
Ricardo D. Matheus, Elmer M. Gennaro, Marcelo T. Yamashita
https://arxiv.org/abs/2510.08261 http…

Effectiveness of Quota Policies Across STEM, Biological, and Humanities Programs
We examine more than a decade of quota policy at Unesp, analyzing Physics, Biology, and Pedagogy as representative programs of distinct assessment styles. Quotas show little impact in Physics, where the admission barrier is low, and in Pedagogy, where high pass rates make it difficult to differentiate students, but they reveal systematic differences in Biology. Focusing the analysis on Calculus I - an introductory course in Physics and other Science, Technology, Engineering, and Mathematics (ST…

I'm gonna dip the Christmas tree in ranch dressing and eat it as a snack

Global weak martingale solutions to a stochastic two-sidedly degenerate aggregation-diffusion equation issued from biology
Mostafa Bendahmane, Mohamed Mehdaoui, Mouhcine Tilioua
https://arxiv.org/abs/2510.03947

Global weak martingale solutions to a stochastic two-sidedly degenerate aggregation-diffusion equation issued from biology
The purpose of this paper is to establish the well-posedness of martingale (probabilistic weak) solutions to stochastic degenerate aggregation--diffusion equations arising in biological and public health contexts. The studied equation is of a stochastic degenerate parabolic type, featuring a nonlinear two-sidedly degenerate diffusion term accounting for repulsion, a locally Lipschitz reaction term representing competitive interactions, and a stochastic perturbation term capturing environmental …

Towards Label-Free Biological Reasoning Synthetic Dataset Creation via Uncertainty Filtering
Josefa Lia Stoisser, Lawrence Phillips, Aditya Misra, Tom A. Lamb, Philip Torr, Marc Boubnovski Martell, Julien Fauqueur, Kaspar M\"artens
https://arxiv.org/abs/2510.05871

Towards Label-Free Biological Reasoning Synthetic Dataset Creation via Uncertainty Filtering
Synthetic chain-of-thought (CoT) traces are widely used to train large reasoning models (LRMs), improving generalization by providing step-level supervision. Yet most approaches require ground-truth labels to seed or filter these traces - an expensive bottleneck in domains like biology where wet-lab data are scarce. We propose a label-free alternative: uncertainty-based filtering, which uses a model's own confidence - quantified through established uncertainty metrics like self-consistency and …

Inhomogeneous continuous-time Markov chains to infer flexible time-varying evolutionary rates
Pratyusa Datta, Philippe Lemey, Marc A. Suchard
https://arxiv.org/abs/2510.11982 ht…

Inhomogeneous continuous-time Markov chains to infer flexible time-varying evolutionary rates
Reconstructing evolutionary histories and estimating the rate of evolution from molecular sequence data is of central importance in evolutionary biology and infectious disease research. We introduce a flexible Bayesian phylogenetic inference framework that accommodates changing evolutionary rates over time by modeling sequence character substitution processes as inhomogeneous continuous-time Markov chains (ICTMCs) acting along the unknown phylogeny, where the rate remains as an unknown, positiv…

Attosecond-level synchronisation of chip-integrated oscillators
Alexander E. Ulanov, Bastian Ruhnke, Thibault Wildi, Tobias Herr
https://arxiv.org/abs/2510.11630 https://…

Attosecond-level synchronisation of chip-integrated oscillators
Attosecond science provides a window to the fastest processes in chemistry, materials science, and biology. Accessing this time scale requires precisely synchronised oscillators. In free-electron X-ray lasers, which also provide sub-atomic resolution, synchronisation must be achieved across hundreds of meters. Current approaches to synchronisation based on mode-locked lasers deliver this level of performance but complexity, cost and size hinder their deployment in facility-wide multi-node netwo…

"Specialist" and "generalist" are surprisingly slippery categories— biology abhors a binary— but quantifying the shared evolutionary history of plants eaten by insects introduced to North America let these authors predict their plant-damaging impacts https://doi.org/10.1111/ele.70083

Replaced article(s) found for q-bio.QM. https://arxiv.org/list/q-bio.QM/new
[1/1]:
- BixBench: a Comprehensive Benchmark for LLM-based Agents in Computational Biology
Mitchener, Laurent, Andonian, Tenmann, Narayanan, Wellawatte, White, Sani, Rodriques

Probing Phase Diagrams of Ordered Two-Dimensional Ice
Bingzheng Wu, Jianming Wu, Sai Duan, Xin Xu
https://arxiv.org/abs/2510.07717 https://arxiv.org/pdf/25…

Probing Phase Diagrams of Ordered Two-Dimensional Ice
Water, a ubiquitous and fundamental substance, plays a critical role across a wide range of disciplines from physics and chemistry to biology and engineering. Despite theoretical predictions of several phases of two-dimensional (2D) ice confined between idealized hydrophobic walls, experimental validation has been limited to the square phase, whose structural origin remains controversial. Here, we propose a realistic nanoconfinement setup using wide-bandgap hexagonal boron nitride (h-BN) as the…

🦎 City lizards turn out to be surprisingly social
#lizards

City lizards turn out to be surprisingly social
Streets, walls, concrete—cities may seem like a harsh environment. Yet some animals adapt remarkably well. A new study published in Biology Letters from Bielefeld University shows that common wall lizards (Podarcis muralis) behave far more socially in urban areas than in the countryside.

Analyzing Computational Approaches for Differential Equations: A Study of MATLAB, Mathematica, and Maple
Arhonefe Joseph Ogethakpo, Ignatius Nkonyeasua Njoseh
https://arxiv.org/abs/2510.02346

Analyzing Computational Approaches for Differential Equations: A Study of MATLAB, Mathematica, and Maple
Differential equations are fundamental to modeling dynamic systems in physics, engineering, biology, and economics. While analytical solutions are ideal, most real-world problems necessitate numerical approaches. This study conducts a detailed comparative analysis of three leading computational software packages: MATLAB, Mathematica, and Maple in solving various differential equations, including ordinary differential equations (ODEs), partial differential equations (PDEs), and systems of differ…

A fluorescence microscopy platform for time-resolved studies of spin-correlated radical pairs in biological systems
Noboru Ikeya, Jonathan R. Woodward
https://arxiv.org/abs/2510.05600

A fluorescence microscopy platform for time-resolved studies of spin-correlated radical pairs in biological systems
The importance of spin-correlated radical pairs in biology is increasingly recognized, with roles in biological effects of weak magnetic fields and emerging quantum spin-based biomedical applications. Fluorescence microscopy offers sufficient sensitivity to study magnetic field effects on radical pair reactions in living cells, but conventional techniques cannot directly resolve their dynamics because most biologically relevant radical pairs are non-emissive. To overcome this challenge, we intr…

Efficient Learning-based Graph Simulation for Temporal Graphs
Sheng Xiang, Chenhao Xu, Dawei Cheng, Xiaoyang Wang, Ying Zhang
https://arxiv.org/abs/2510.05569 https://

Efficient Learning-based Graph Simulation for Temporal Graphs
Graph simulation has recently received a surge of attention in graph processing and analytics. In real-life applications, e.g. social science, biology, and chemistry, many graphs are composed of a series of evolving graphs (i.e., temporal graphs). While most of the existing graph generators focus on static graphs, the temporal information of the graphs is ignored. In this paper, we focus on simulating temporal graphs, which aim to reproduce the structural and temporal properties of the observed…

Dry ice baths as liquid nitrogen substitutes for physics demonstrations
David Marasco, Paolo Marasco
https://arxiv.org/abs/2510.09971 https://arxiv.org/pdf…

🧠 Brain organoids reveal potential neural basis of schizophrenia and bipolar disorder
https://medicalxpress.com/news/2025-09-brain-organoids-reveal-potential-neural.html

Brain organoids reveal potential neural basis of schizophrenia and bipolar disorder
Pea-sized brains grown in a lab have for the first time revealed the unique way neurons might misfire due to schizophrenia and bipolar disorder, psychiatric ailments that affect millions of people worldwide but are difficult to diagnose because of the lack of understanding of their molecular basis.

Information and the living tree of life: A theory of measurement grounded in biology
Kevin Hudnall
https://arxiv.org/abs/2510.00155 https://arxiv.org/pdf/2…

Information and the living tree of life: A theory of measurement grounded in biology
We extend a formal framework that previously derived time from the multifractal structure of biological lineages (Hudnall \& D'Souza, 2025). That work showed that time itself is multifractal -- not a universal background dimension, but an observer-dependent geometry. Here we develop the corresponding theory of measurement: showing that a multifractal conception of time not only permits measurement, but grounds it more rigorously in the structure of biology. The tree of life is modeled as the ou…

Two-Stage Trigonometric Regression for Modeling Circadian Rhythms
Michael T. Gorczyca, Jenna D. Li, Charissa M. Newkirk, Arjun S. Srivatsa, Hugo F. M. Milan
https://arxiv.org/abs/2510.08309

Two-Stage Trigonometric Regression for Modeling Circadian Rhythms
Gene expression levels, hormone secretion, and internal body temperature each oscillate over an approximately 24-hour cycle, or display circadian rhythms. Many circadian biology studies have investigated how these rhythms vary across cohorts, uncovering associations between atypical rhythms and diseases such as cancer, metabolic syndrome, and sleep disorders. A challenge in analyzing circadian biology data is that the oscillation peak and trough times for a phenomenon differ across individuals.…

Sample-based Quantum Diagonalization Methods for Modeling the Photochemistry of Diazirine and Diazo Compounds
Saurabh Shivpuje, Tanvi P. Gujarati, Richard Van, Frank C. Pickard IV, Triet Friedhoff, Ieva Liepuoniute, Wade Davis, Gavin O. Jones, Alexey Galda
https://arxiv.org/abs/2510.00484

Sample-based Quantum Diagonalization Methods for Modeling the Photochemistry of Diazirine and Diazo Compounds
Diazirines and diazo compounds are widely employed as photoreactive precursors for generating carbenes, key intermediates in chemical biology and materials science. However, computationally modeling their reaction pathways remains challenging due to a need for large active spaces and the requirement to accurately capture excited-state surfaces along with transition states and conical intersections. In this work, we utilize a hybrid quantum-classical workflow for investigating carbene formation …

A path towards AI-scale, interoperable biological data
Brian Aevermann, Andrea Califano, Chi-Li Chiu, Nathan Clack, William M. Clemons Jr., Jonah Cool Florence D. D'Orazi, Joseph L. DeRisi, Joshua E. Elias, Elizabeth Fahsbender, Scott E. Fraser, Carlos G. Gonzalez, Matthias Haury, Theofanis Karaletsos, Shana O. Kelley, Aly A. Khan, Alan R. Lowe, Emma Lundberg, Ryan A. McClure, Stephani Otte, Evan O. Paull, Lo\"ic A. Royer, Dana Sadgat, Sandra L. Schmid, Samantha Scovanner, Cat…

A path towards AI-scale, interoperable biological data
Biology is at the precipice of a new era where AI accelerates and amplifies the ability to study how cells operate, organize, and work as systems, revealing why disease happens and how to correct it. Organizations globally are prioritizing AI to accelerate basic research, drug discovery, personalized medicine, and synthetic biology. However, despite these opportunities, scientific data have proven a bottleneck, and progress has been slow and fragmented. Unless the scientific community takes a t…

🔥 Novel way to 'rev up' brown fat burns calories, limits obesity in mice
#biology

Novel way to 'rev up' brown fat burns calories, limits obesity in mice
Researchers at Washington University School of Medicine in St. Louis have identified a novel way brown fat—an energy-burning form of fat—can rev the body's metabolic engine, consuming cellular fuel and producing heat in a way that improves metabolic health. The study, in mice, reveals new avenues to exploit brown fat to treat metabolic diseases, such as insulin resistance and obesity.

Empirical partially Bayes two sample testing
Wanyi Ling, Wufang Hong, Nikolaos Ignatiadis
https://arxiv.org/abs/2510.00432 https://arxiv.org/pdf/2510.00432…

Empirical partially Bayes two sample testing
A common task in high-throughput biology is to test for differences in means between two samples across thousands of features (e.g., genes or proteins), often with only a handful of replicates per sample. Moderated t-tests handle this problem by assuming normality and equal variances, and by applying the empirical partially Bayes principle: a prior is posited and estimated for the nuisance parameters (variances) but not for the primary parameters (means). This approach has been highly successfu…

Behavioural Classification in C. elegans: a Spatio-Temporal Analysis of Locomotion
Nemanja Antonic, Monika Scholz, Aymeric Vellinger, Euphrasie Ramahefarivo, Elio Tuci
https://arxiv.org/abs/2510.00086 …

Behavioural Classification in C. elegans: a Spatio-Temporal Analysis of Locomotion
The 1mm roundworm C. elegans is a model organism used in many sub-areas of biology to investigate different types of biological processes. In order to complement the n-vivo analysis with computer-based investigations, several methods have been proposed to simulate the worm behaviour. These methods extract discrete behavioural units from the flow of the worm movements using different types of tracking techniques. Nevertheless, these techniques require a clear view of the entire worm body, which …

Hierarchical self-assembly of Brownian particle-like pulses in a modelocked laser
Aladin \c{S}ura, F. \"Omer Ilday
https://arxiv.org/abs/2510.05344 https://

Hierarchical self-assembly of Brownian particle-like pulses in a modelocked laser
Passive modelocking involves self-locking of thousands of frequency modes to form ultrashort pulses. In fundamental modelocking, a single intracavity pulse provides high stability and reproducibility, but limits the repetition rate. Harmonic modelocking can overcome this by supporting multiple pulses, but suffers from instabilities and poor reproducibility, with specific states achievable only sporadically. Biology exploits hierarchy to organise complexity, which has inspired hierarchical self-…

Effect of Attachment Surface on Biofilm Response and the Dissipation of PAHs and nitrogen in Submerged Plant System under the application of Bactericide and Algaecide
Xiabinchen Zhao, Liling Xia, Zhenhua Zhao
https://arxiv.org/abs/2510.03357

Effect of Attachment Surface on Biofilm Response and the Dissipation of PAHs and nitrogen in Submerged Plant System under the application of Bactericide and Algaecide
The biofilms response on active attachment surfaces (submerged plant leaves) and inert attachment surfaces (biomimetic plant glass attachment surfaces) and their effects on PAHs and nitrogen transformation under the application conditions of bactericide, algaecide and PAHs were investigated by lab simulated hydroponics and high-throughput molecular biology methods in Vallisneria natans (VN), Hydrilla verticillata (HV) and biomimetic plants (BP) systems. Results showed that the introduction of b…

Mapping gene expression dynamics to developmental phenotypes with information entropy analysis
Ben Ansbacher, Malachy Guzman, Jordi Garcia-Ojalvo, Arjendu K Pattanayak
https://arxiv.org/abs/2510.04101 …

Mapping gene expression dynamics to developmental phenotypes with information entropy analysis
The development of multicellular organisms entails a deep connection between time-dependent biochemical processes taking place at the subcellular level, and the resulting macroscopic phenotypes that arise in populations of up to trillions of cells. A statistical mechanics of developmental processes would help to understand how microscopic genotypes map onto macroscopic phenotypes, a general goal across biology. Here we follow this approach, hypothesizing that development should be understood as…

🥁 Blink to the beat: Scientists discover that when we listen to music, we unconsciously blink our eyes
https://medicalxpress.com/news/2025-11-scientists-music-unconsciously-eyes.html

Blink to the beat: Scientists discover that when we listen to music, we unconsciously blink our eyes
Yi Du and colleagues from the Chinese Academy of Sciences published an article in the open access journal PLOS Biology detailing their findings about a new way our bodies naturally respond to music. Given a steady beat, our eyes blink in synchrony.

I feel a bit out of the loop with hashtags at the moment.
Could someone enlighten me what the current general purpose and biology/animal science specific academic hashtags are?
Since guppee shut down, my feed feels quite empty.
And it took me far too long to even notice that 😅
#AcademicMastodon #AcademicChatter ##PostdocLife #FediTip

♨️ Underwater thermal vents may have given rise to the first molecular precursors of life
https://phys.org/news/2025-10-underwater-thermal-vents-molecular-precursors.html

Underwater thermal vents may have given rise to the first molecular precursors of life
A study published in the Journal of the American Chemical Society has recreated in the laboratory chemical reactions that may have occurred on Earth about four billion years ago, producing the first molecular precursors for the emergence of life.

Single-cell sequencing of trophoblasts in preeclampsia and chemical hypoxia in BeWo b30 cells reveals EBI3, COL17A1, miR-27a-5p, and miR-193b-5p as hypoxia-response markers
Evgeny Knyazev (Faculty of Biology and Biotechnology, HSE University, Moscow, Russia, Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia), Timur Kulagin (Faculty of Biology and Biotechnology, HSE Universi…

Single-cell sequencing of trophoblasts in preeclampsia and chemical hypoxia in BeWo b30 cells reveals EBI3, COL17A1, miR-27a-5p, and miR-193b-5p as hypoxia-response markers
Background. Preeclampsia (PE) complicates 2-8% of pregnancies and is marked by placental hypoxia and HIF-pathway activation, especially in early-onset PE (eoPE). Integrating patient tissue analyses with experimental models may reveal common molecular markers of trophoblast hypoxia. Methods. We analyzed scRNA-seq data from 10 eoPE, 7 late-onset PE (loPE), and corresponding control placentas, identifying villous cytotrophoblast (VCT), syncytiotrophoblast (SCT), and extravillous trophoblast (EVT…

Replaced article(s) found for q-bio.OT. https://arxiv.org/list/q-bio.OT/new
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- Open and Sustainable AI: challenges, opportunities and the road ahead in the life sciences (Octob...
Gavin Farrell, et al.

Brilliant source of 19.2 attosecond soft X-ray pulses below the atomic unit of time
Fernando Ardana-Lamas, Seth L. Cousin, Juliette Lignieres, Jens Biegert
https://arxiv.org/abs/2510.04086

Brilliant source of 19.2 attosecond soft X-ray pulses below the atomic unit of time
Electronic correlations occur on attosecond timescales, dictating how chemical bonds form, energy flows, and materials respond to light. Capturing such many-body processes requires light pulses of similar duration. The soft X-ray water window is vital because it encompasses the principle absorption edges of carbon, nitrogen, and oxygen that underpin chemistry, biology, and materials science. However, generating and characterising isolated attosecond pulses that reach into the soft X-ray water w…

🪸 Tree rings of the sea: How environmental conditions influence microalgae and coral communities
https://phys.org/news/2025-11-tree-sea-environmental-conditions-microalgae.html

Tree rings of the sea: How environmental conditions influence microalgae and coral communities
An international research team led by marine biologist Prof. Dr. Maren Ziegler from Justus Liebig University Giessen (JU) has developed an innovative method for reconstructing the past of corals and their symbiosis with algae by drilling into coral skeletons. The results, published in Global Change Biology, offer new insights into changes in symbiotic single-celled algae species that are crucial to the survival of coral reefs.

[2025-10-15 Wed (UTC), 1 new article found for q-bio.OT Other Quantitative Biology]
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Replaced article(s) found for q-bio.OT. https://arxiv.org/list/q-bio.OT/new
[1/1]:
- Charting dissipation across the microbial world
Tommaso Cossetto, Jonathan Rodenfels, Pablo Sartori

Predicting cell-specific gene expression profile and knockout impact through deep learning
Yongjian He, Vered Klein, Orr Levy, Xu-Wen Wang
https://arxiv.org/abs/2510.03359 https…

Predicting cell-specific gene expression profile and knockout impact through deep learning
Gene expression data is essential for understanding how genes are regulated and interact within biological systems, providing insights into disease pathways and potential therapeutic targets. Gene knockout has proven to be a fundamental technique in molecular biology, allowing the investigation of the function of specific genes in an organism, as well as in specific cell types. However, gene expression patterns are quite heterogeneous in single-cell transcriptional data from a uniform environme…

[2025-10-14 Tue (UTC), 4 new articles found for q-bio.OT Other Quantitative Biology]
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[2025-10-13 Mon (UTC), no new articles found for q-bio.OT Other Quantitative Biology]
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Crosslisted article(s) found for q-bio.OT. https://arxiv.org/list/q-bio.OT/new
[1/1]:
- The Software Observatory: aggregating and analysing software metadata for trend computation and F...
Eva Mart\'in del Pico, Josep Llu\'is Gelp\'i, Salvador Capella-Guti\'errez

[2025-10-10 Fri (UTC), 1 new article found for q-bio.OT Other Quantitative Biology]
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[2025-10-09 Thu (UTC), no new articles found for q-bio.OT Other Quantitative Biology]
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Crosslisted article(s) found for q-bio.OT. https://arxiv.org/list/q-bio.OT/new
[1/1]:
- Automated Genomic Interpretation via Concept Bottleneck Models for Medical Robotics
Zijun Li, Jinchang Zhang, Ming Zhang, Guoyu Lu

[2025-10-08 Wed (UTC), 1 new article found for q-bio.OT Other Quantitative Biology]
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Crosslisted article(s) found for q-bio.OT. https://arxiv.org/list/q-bio.OT/new
[1/1]:
- Building the EHR Foundation Model via Next Event Prediction
Zekai Chen, Arda Pekis, Kevin Brown

[2025-10-07 Tue (UTC), no new articles found for q-bio.OT Other Quantitative Biology]
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[2025-10-06 Mon (UTC), no new articles found for q-bio.OT Other Quantitative Biology]
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[2025-10-03 Fri (UTC), 2 new articles found for q-bio.OT Other Quantitative Biology]
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[2025-10-02 Thu (UTC), 1 new article found for q-bio.OT Other Quantitative Biology]
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