@sliverdaemon.bsky.social
43 followers 290 following 120 posts
"Then how should I begin To spit out all the butt-ends of my days and ways? And how should I presume?" - TS Eliot, Love Song of J. Alfred Prufrock I like ML, quantitive biology, and medicine.
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laurahelmuth.bsky.social
Bacteria from a Yellowstone hot spring do something no other organism has been found to do: breathe oxygen and sulfur at the same time. 🧪 It's both aerobic and anaerobic, a beautiful freaky creature from a beautiful freaky place
The Cells That Breathe Two Ways | Quanta Magazine
In a hot spring at Yellowstone National Park, a microbe does something that life shouldn’t be able to do: It breathes oxygen and sulfur at the same time.
www.quantamagazine.org
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socdevbio.bsky.social
🐌💫 Snail embryos never looked so fabulous!
Tubulin (white), phospho-histone H3 (pink), and F-Actin (cyan) light up this early stage like a cytoskeletal disco ball.
Image from Clemens Cabernard & Adam von Barnau Sythoff 🪩🧬 #FluorescenceFriday
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jcb.org
Aceitón, Riobó, Del Valle Batalla, Yuseff et al show that B cells respond to mechanical cues at the immune synapse through ATAT1-dependent microtubule acetylation to coordinate cytoskeletal dynamics & lysosome positioning, enhancing antigen extraction and presentation rupress.org/jcb/article/...
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frankschnorrer.bsky.social
Microtubules: the architect of muscles. Watch how microtubules transport mitochondria in proximity to energy consuming sarcomeres in muscles of flies and mice. @jeromeavellaneda.bsky.social @nunoluis.bsky.social @ibdm.bsky.social with @gomeslabo.bsky.social www.sciencedirect.com/science/arti...
sliverdaemon.bsky.social
using interpretability methods to extract biological hypotheses hidden in the model and then validating the most promising ones in the wet lab. some datasets are strong enough to establish the existence of a mechanism, but observing the mechanism in action will ultimately be needed to settle debates
sliverdaemon.bsky.social
where the authors examine the model gradients (cf. "Identifying important regions and regulators" to guess which TF motifs interact with genes. From Fig1 of the paper, it's clear the model is inacurrate in many scenarios, and accurate in just as many. but they found a new biological fact from it
sliverdaemon.bsky.social
(stops *at benchmarks) ... rarely applies interpretability to extract possible mechanisms (causal relationships), ie biological truths, that the model has learned to work in certain contexts. a good example of this interpretability is (www.nature.com/articles/s41...)
sliverdaemon.bsky.social
"causal" has several technical definitions, eg referenced authors' vs your own, and considering only one to be a appropriate works for debating, but ignores other fields of study. however, this thread made me realize that ML culture stops and benchmarks, and rarely applies interpretability
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onenimesa.bsky.social
Have you ever thought about inflating tissues?
Or maybe quickly deflating those inflated tissues?

New #EpithelialMechanics pre-print: doi.org/10.1101/2025...
🧵 with pressure control, multiscale buckling, controlled wrinkling
sliverdaemon.bsky.social
what a time to be alive! (you know, as far image processing is concerned)
haesleinhuepf.bsky.social
New in #biabob 0.29.0: Code insertions in @jupyter.org Cells! 🥳
If you know how to start your image analysis, and how to visualize the results, just put %bob in between and let the AI do the hard coding work. Also provide hints as comments to guide the AI 😉
github.com/haesleinhuep...
sliverdaemon.bsky.social
sorry, thanks for correcting. causal methods do exist for deconfounding of observational data (eg propensity matchng), but agree that interventions (eg crispr screens) are preferable, best is RNA + ATAC (www.nature.com/articles/s41...) tho can RNA also b informative (www.nature.com/articles/s41...)
sliverdaemon.bsky.social
dogma now absurd first
slavov-n.bsky.social
When science advances:

"... 𝘢𝘵 𝘵𝘩𝘢𝘵 𝘵𝘪𝘮𝘦, 𝘯𝘰𝘣𝘰𝘥𝘺 𝘤𝘰𝘶𝘭𝘥 𝘪𝘮𝘢𝘨𝘪𝘯𝘦 𝘵𝘩𝘢𝘵 𝘵𝘩𝘦 𝘱𝘩𝘰𝘴𝘱𝘩𝘰𝘳𝘺𝘭𝘢𝘵𝘪𝘰𝘯 𝘰𝘧 𝘢𝘯 𝘦𝘯𝘻𝘺𝘮𝘦 𝘤𝘰𝘶𝘭𝘥 𝘣𝘦 𝘪𝘯𝘷𝘰𝘭𝘷𝘦𝘥 𝘪𝘯 𝘪𝘵𝘴 𝘳𝘦𝘨𝘶𝘭𝘢𝘵𝘪𝘰𝘯."

-- Eddy Fischer
Nobel Prize in Physiology or Medicine 1992
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epiellie.bsky.social
I am once again reminded of my favorite @edyong209.bsky.social quote:

“…a tiny wise decision can do exponential good.”
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mobydickatsea.bsky.social
Queequeq, my fine friend, does this sort of thing often happen?
sliverdaemon.bsky.social
disagree that trans reg. models always end up just doing weighted nearest neighbors & they do not learn biology, but agree current cis models generalize better. perturbation data is not sequences but still is biology. for me GRN models a "virtual cell" more directly than sequence (my bias). 💯thead
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rabihalameddine.bsky.social
The inferno of the living is not something that will be; if there is one, it is what is already here, the inferno where we live every day, that we form by being together. There are two ways to escape suffering it.
1/3
sliverdaemon.bsky.social
nerve cells give their mitochondria to cancer cells. yeah, really.

www.nature.com/articles/s41...

🤯
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plantcellatlas.bsky.social
Meet The Speakers of the Single-Cell Approaches in Plant Biology GRC Conference!

To Apply to the GRC: lnkd.in/gvkMxuKR

To Learn More About Dr. Shahan's Research: sites.lifesci.ucla.edu/mcdb-shahan/

@rachelmshahan.bsky.social
Promotional image for the "Single-Cell Approaches in Plant Biology GRC Conference" focusing on meeting the speakers. This promo includes an image of Dr. Rachel Shahan from UCLA with a short bio on Dr. Shahan.
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jeanmichelane.bsky.social
If we can develop cheap, effective and stable inoculants... Effect of Arbuscular Mycorrhyzal Fungi in Improving Soybean Growth in Ultisol Soil | Applied Research in Science and Technology
Effect of Arbuscular Mycorrhyzal Fungi in Improving Soybean Growth in Ultisol Soil
Background: Soybean is one of the most popular agricultural commodities in Indonesia, but its production is still low. Thus, it is necessary to make efforts to expand its agriculture in the form of marginal land development. Aims: This study aims to examine the effect and obtain the best treatment dose of arbuscular mycorrhizal fungi (AMF) in ultisol soil to increase the growth of soybean plants (Glycine max (L.) Merill). Methods: This experimental study employed a complete randomized design (CRD) with the treatment of arbuscular mycorrhizal fungi (AMF). The AMF treatment comprised five levels: no AMF, 4 g/polibag, 8 g/polibag, 12 g/polibag and 16 g/polibag. Each treatment was repeated four times, resulting in 20 experimental units and each experimental unit comprised three polybags so that this study used 60 polybags. The data were analyzed using Analysis of Variance (ANOVA) and continued with Duncan's New Multiple Range Test (DNMRT) at the 5% level. Result: AMF treatment is able to increase the growth of soybean plants in the parameters of plant height, number of productive branches, flowering age, number of flowers, and harvest age. The AMF treatment dose of 12 g/polybag is proven to give the best results in increasing the growth of soybean plants. The use of AMF can be an effective strategy in optimizing soybean production, especially on marginal lands.
sco.lt
sliverdaemon.bsky.social
authors say bc genetic perturbation had smaller dataset:
"performance gains over mean baselines were notably larger on Tahoe-100Million[...] and Parse-PBMC, which includes 10 million [...], as compared to [...] genetic perturbation datasets conducted in just a few cell lines." about 3 million cells