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Seed dispersal disruption limits tropical forest regrowth

In field records from 3026 tropical sites, modeled bird and mammal seed dispersal disruption predicts slower natural-regrowth carbon accumulation, an estimated 57% average loss at candidate restoration sites.

Complex genetic variation in nearly complete human genomes

Hybrid HiFi/ultra-long ONT assemblies of 65 diverse humans yield 130 haplotypes, 1,246 complete centromeres, and a pangenome panel enabling short-read genome inference at median QV 45.

Exercise training remodels inter-organ endocrine networks

Correlation-based endocrine network analysis of MoTrPAC rat multi-tissue omics shows 8-week endurance training reshapes inter-organ secretory crosstalk, centering subcutaneous adipose, extracellular matrix factors, and Wnt regulators.

A contextualised protein language model reveals the functional syntax of bacterial evolution

Trained on over 1.3 million bacterial genomes represented as ordered protein sequences, the transformer foundation model Bacformer predicts protein interactions, operons, essentiality, and phenotypes while generating trait-conditioned synthetic proteomes.

Can AI modelling of protein structures distinguish between sensor and helper NLR immune receptors?

AlphaFold 3 oligomer models separate paired plant NLRs: helpers score higher pTM and form funnel-shaped resistosomes unlike sensors, including some rice pairs lacking integrated-domain annotations.

OrthoFinder: scalable phylogenetic orthology inference for comparative genomics

OrthoFinder v3 splits orthogroups at duplications predating the species-tree root, raising OrthoBench accuracy, and assigns extra species to a core run, finishing 1024 species in 128 hours.

Scalable emulation of protein equilibrium ensembles with generative deep learning

BioEmu, a diffusion model trained on structures, molecular dynamics trajectories, and stability assays, samples protein equilibrium ensembles and folding free energies within ~1 kcal/mol in GPU-hours.

Novel strains of tomato spotted wilt orthotospovirus (TSWV) are transmitted by western flower thrips in a context-specific manner

Western flower thrips inoculated six TSWV strains across four sequential periods; males trended toward higher efficiency (87% vs 77% for resistance-breaking strains), but per-period differences were not significant.

Phylogenomics and metabolic engineering reveal a conserved gene cluster in Solanaceae plants for withanolide biosynthesis

Comparing nine Solanaceae genomes reveals a conserved withanolide gene cluster; three of its P450s, expressed in yeast and N. benthamiana, oxidise 24-methyldesmosterol toward the withanoside V aglycone.

Single Cell Spatial Transcriptomics Reveals Immunotherapy-Driven Bone Marrow Niche Remodeling in AML

CosMx spatial transcriptomics of bone marrow from 6 refractory/relapsed AML patients shows CD14+ monocytes rising in leukemia-cell neighborhoods after pembrolizumab in responders, dendritic cells in nonresponders.

Locomotor Trends Among Early Mammals Illuminated by Predictors of Arboreality from the Mammalian Appendicular Skeleton

Bayesian multilevel models of 69 appendicular skeletal metrics across 236 extant mammal species predict climbing at 95% accuracy and indicate that several Mesozoic therians, including Juramaia, were terrestrial ground-dwellers.

Gut Bacteria Encode Reductases that Biotransform Steroid Hormones

Gut bacteria encode 5β-reductase, fused 3β-HSDH/Δ5-4 isomerase and Δ6-3-ketosteroid reductase enzymes acting on steroid hormones; two of these genes are enriched in female gut metagenomes.

Non-invasive assessment of integrated cardiorespiratory network dynamics after physiological stress in humans

Transfer entropy network maps of seven breath-by-breath cardiorespiratory signals in 22 healthy adults differ by stressor; only exercise raised total transfer entropy, while hypoxia and sleep deprivation reshaped node roles.

YY1 Enhances the Stability of HIF-1α Protein by Interacting with NUSAP1 in Macrophages within the Prostate Cancer Microenvironment

In THP-1 cells, hypoxia drives Lyn-dependent YY1 phosphorylation and phase separation; YY1 and NUSAP1 SUMOylate and stabilize HIF-1α, and degrading YY1 curbs mouse prostate tumors.

Ambient Proteins: Training Diffusion Models on Low Quality Structures

Treating low-confidence AlphaFold structures as noisy data at pLDDT-dependent diffusion times lets a 16.7M-parameter model generate long proteins with higher diversity, designability and novelty than Proteína.

A Large Language Model-Powered Map of Metabolomics Research

PubMedBERT embeddings of 80,656 metabolomics abstracts, projected with t-SNE and grouped into 20 GPT-4o mini-labelled topics, map the field's domains and trends (1998 to early 2024), browsable online.

To Peck or Not To Peck: The influence of early-life social environment on response inhibition and impulsive aggression in Japanese quails

Japanese quails reared in groups of 15 versus five pecked a transparent cylinder less, but rearing group size did not change impulsive aggression in either context.

Disruption of riboflavin biosynthesis in mycobacteria establishes 5-amino-6-D-ribitylaminouracil (5-A-RU) as key precursor of MAIT cell agonists

Deleting early riboflavin genes (ribA2 in both species, ribG in M. smegmatis) sharply reduced MAIT cell activation, while ribH deletion raised recognition of M. tuberculosis only.

Medium-sized protein language models perform well at transfer learning on realistic datasets

Medium-sized protein language models (e.g. ESM C 600M) with mean embeddings nearly match ESM-2 15B and ESM C 6B in transfer learning on mutational scanning and PISCES data.

Decomposition of phenotypic heterogeneity in autism reveals distinct and coherent genetic programs

Mixture modeling of 239 phenotype features in 5,392 SPARK autistic children defines four replicable classes carrying distinct common and rare variant signatures and developmental gene-timing patterns.