statistical model

MC1R residue 223 is a convergent target for coat-colour lightening in domestic and wild bovids

The paper investigates the molecular evolution of grey coat color in cattle and identifies MC1R residue 223 as a recurrent target for coat-color lightening in both domestic and wild bovids.

Reduced cerebral blood flow and metabolic rate trigger an adaptive mitochondrial remodeling program in a Down syndrome mouse model

In Dp16 Down syndrome mice, MRI shows reduced cerebral blood flow and oxygen metabolism (significant in males), while brain mitochondrial respiratory capacity stays largely intact and oxidative phosphorylation genes rise.

COMBO-RATE: An experimentally validated bioinformatic tool to identify promiscuous HLA restrictions

COMBO-RATE identifies promiscuous HLA restrictions by analyzing immune response data, outperforming existing tools and revealing broader HLA allele coverage for T cell epitopes.

The Braarudosphaera bigelowii genome reveals cellular remodeling around a nitrogen-fixing organelle

This paper presents the genome of Braarudosphaera bigelowii, revealing genomic and metabolic adaptations associated with its symbiotic nitrogen-fixing organelle.

Stage-resolved dynamics of antibiotic resistance genes and mobile genetic elements in full-scale anaerobic digestion systems

The paper analyzes antibiotic resistance genes and mobile genetic elements in anaerobic digestion systems, finding that pH and ammonia levels influence their abundance and that network analysis reveals dynamic associations across stages.

Measurement-Dependent Parameter Recoverability in Neural Cardiovascular LPN Inference

The paper evaluates parameter recoverability in cardiovascular LPN inference using a probabilistic neural framework, showing that accurate hemodynamic prediction does not guarantee correct parameter recovery.

Enzymes can activate and mobilize the cytoplasmic environment across scales

This study shows that enzymes in biomolecular condensates enhance catalytic activity through crowding-induced conformational changes and enable increased mobility despite environmental viscosity.

Predicting Pathway Dependency in Head and Neck Squamous Cell Carcinoma from Hallmark Transcriptomic Features

The paper develops a transcriptome-based framework to predict pathway dependency in HNSCC using Hallmark features, finding HPV+ tumors show higher dependency in seven pathways.

Feedback control via H3K9 methylation and siRNA biogenesis autonomously maintains RNAi heterochromatin through continuous low-level transcription

A tale of two states: AlphaFold binding pockets on the apo-holo continuum

The paper analyzes AlphaFold's predicted binding pockets to determine their similarity to apo or holo states, finding most are holo-like and showing how state affects docking success.

Differing patterns in community composition and diversity of biofilm-forming bacteria and fungi along a large salinity gradient

The paper examines how bacterial and fungal biofilm communities respond to salinity gradients, finding distinct patterns in diversity and environmental drivers between the two groups.

Genomic heterogeneity inflates the performance of variant pathogenicity predictions

The paper evaluates AI models for predicting pathogenic variants, finding that performance is inflated by genomic heterogeneity in pathogenic variant prevalence.

Pre-stress functional brain connectivity is associated with subsequent anxiety during war-related stress

The paper examines pre-stress functional brain connectivity in relation to anxiety during war-related stress and finds lower baseline connectivity between the right nucleus accumbens and right amygdala is linked to higher subsequent anxiety.

Representation learning of somatic missense mutation landscapes across cancer types

This paper introduces MMRL, a framework for learning representations of somatic missense mutations across cancer types, showing improved prognostic discrimination and identification of mutation subtypes.

Protein co-scientist aided simulations of the structural and functional impact of O-GlcNAc Transferase TPR domain deletions and amino acid substitutions associated with X-Linked Intellectual Disability

The paper uses computational methods to model structural and functional impacts of TPR domain deletions and amino acid substitutions in OGT linked to X-Linked Intellectual Disability.

The globally dispersed sun-coral species is _Tubastraea coccinea_ (Cnidaria: Anthozoa)

The paper resolves taxonomic confusion in sun corals by combining molecular phylogenetics and genome assemblies, revealing T. coccinea as the cosmopolitan species and T. tagusensis as endemic to the Galapagos.

Whole genome duplication uncouples cell volume scaling from mitochondrial homeostasis

This study shows that polyploidy leads to reduced mitochondrial scaling and impaired metabolic function, with conserved effects across yeast and human cells.

CNVSIM: an interpretable copy-number reference atlas for cancer subtyping

CNVSIM creates a reference atlas of copy-number variations for cancer subtyping, identifying 112 subtypes across 19 cancer types using the Progenetix dataset.

Speed judgments during smooth pursuit reflect low gain efference copy

The paper investigates how efference copy affects motion perception during smooth pursuit by analyzing perceptual and oculomotor responses to speed perturbations.

A spin glass representation of hierarchical gene regulation and the partial resolution of frustration

This paper develops a multicellular Ising model to study frustration in gene regulatory networks and shows how intercellular communication affects frustration resolution.

Neural mechanisms for resilient sensory computation under metabolic stress

The paper investigates how food-restricted mice maintain visual discrimination performance by analyzing neural noise structure and decision time changes.

Comparative Proteomics Reveals Cell-Type-Specific Heterogeneity of Human Neural Cell-Derived Extracellular Vesicles

The paper compares proteomic profiles of extracellular vesicles from different human neural cell types to identify cell-type-specific cargo and functional roles.

Specialisation of photosynthetic biochemistry in C4 chloroplasts potentiates distinct cell-specific functionality of different chloroplast-to-nucleus retrograde signalling pathways.

The paper shows that chloroplast-to-nucleus retrograde signalling pathways are cell-specific in C4 plants, correlating with photosynthetic specialisation in mesophyll and bundle sheath cells.

Goat land degradation reduces richness and reshapes the functional composition of an ant community in a tropical dry forest

This study examines how goat grazing affects ant community richness and functional traits in a tropical dry forest, finding reduced species richness and shifts in functional composition with higher degradation.

RankMap: Rank-based reference mapping for fast and robust cell type annotation in spatial and single-cell transcriptomics

RankMap improves cell type annotation in spatial and single-cell transcriptomics by using rank-based representations and multinomial regression, achieving competitive accuracy and faster runtime.

Measuring conscious tactile perception without report: pupil, blink, and microsaccade signatures of a tactile no-report paradigm

This paper develops a no-report tactile paradigm using eye tracking to detect conscious tactile perception without behavioral reports, finding that pupil dilation and blinking distinguish perceived from unperceived stimuli.

Bridging Sensory Extraction and Decision Dynamics: Face Pareidolia Emergent from Bottom-Up and Top-Down Interactions

This study investigates face pareidolia by analyzing EEG data during RSVP streams, showing that it results from both feedforward and top-down processes.

Rapid switching of in-phase and anti-phase interhemispheric rhythms within a single theta cycle: a mechanistic explanation

The paper explains how the granular retrosplenial cortex exhibits rapid switching between in-phase and anti-phase interhemispheric rhythms within a single theta cycle using computational models.

Pattern-triggered immunity induced by dsRNA against plant viruses involves two distinct branches, one of which depends on Coronatine insensitive1 (COI1)

This study shows dsRNA-induced PTI in plants restricts virus movement and replication, with a JA signaling-dependent branch involving COI1 and callose deposition.

Mapping long-distance jump dispersal risk by leveraging transport infrastructure data and sampling bias correction: a case study with the invasive spotted lanternfly (Lycorma delicatula)

The paper identifies high-risk areas for invasive species spread by analyzing transport infrastructure and correcting sampling bias using historical data on Lycorma delicatula.