benchmarking

Crowding distorts features, not objects: structured target confusions in a 4AFC conjunction task

The paper investigates visual crowding by analyzing feature-specific errors in a conjunction-report task, finding that orientation and luminance reports are independently impaired by similar flankers.

Hypoxia Disrupts Multiple Processes Supporting Spatial Navigation

This study examines how continuous and intermittent hypoxia affect spatial navigation and resting-state EEG in healthy adults, finding impairments in navigation and specific EEG features.

ScreenDMT reveals metabolites replicably associated with sleep disorders across three human cohorts

ScreenDMT identifies metabolites consistently linked to sleep disorders across three human cohorts, revealing replicable associations with insomnia, sleep duration, and daytime sleepiness.

Reciprocal effective conductance-based inference of protein-protein relationships delineates protein network hubs and macromolecular properties

The paper uses effective conductance to infer protein-protein relationships and identifies network hubs and macromolecular interactions using a new tool called CoBRAA.

LOCALE: Local-Alignment Embeddings for Noise-Robust DNA Search at Scale

LOCALE improves DNA sequence search by learning variation-robust embeddings, outperforming existing methods on benchmark datasets and real biological variance tasks.

It runs in the family: New extinct species from charismatic clades are more likely to be published in high-impact journals than those from non-charismatic clades

Among 8,331 new extinct species named in thirteen journals since 2000, avemetatarsalians and mammaliamorphs exceed 50% of species in Nature and Science but are under 15% in paleontology journals.

SCAMP - an open-source tool for the quantification of calcification in fish larvae

SCAMP quantifies calcification in fish larvae by straightening the notochord and generating standardized mineralization profiles, revealing genotype-specific differences and the effects of inorganic pyrophosphate and methylene blue.

Integrating morphological and molecular approaches to assess photosynthetic species diversity in the Venice Lagoon

The paper identifies 81 taxa in the Venice Lagoon using morphological and molecular methods, finding non-indigenous Sporobolus anglicus more prevalent than native S. maritimus.

Cell Painting PLUS reveals phenotypic signatures for nephrotoxicity profiling in human RPTEC/TERT1

This study uses Cell Painting PLUS to identify nephrotoxicity-related morphological signatures in human RPTEC/TERT1 cells by analyzing over 300 compounds.

Species ecology, behavior, and substrate type shape eDNA detection of mammals at savanna waterholes

This study investigates factors influencing eDNA detection of mammals at savanna waterholes using camera trapping and eDNA metabarcoding, finding that trophic level, behavior, and substrate type significantly affect detection probabilities.

Grid cells are not a parsimonious source of the hexadirectional signal

The paper shows grid-cell firing alone cannot explain hexadirectional modulation and proposes an improved framework for future studies.

Multistage AI Crop Inspection and Segmentation Framework (MACISF)

MACISF is a deep learning framework for automated fruit quality evaluation, achieving high accuracy in classification, health detection, and defect localization.

A Multiverse Approach to Brain Age Prediction: Exploring the Impact of Modality, Bias Adjustment, and Atlas

This study evaluates how different data modalities, bias adjustment methods, and brain atlases affect brain age prediction using neuroimaging data from 560 healthy adults.

REMAG: recovery of eukaryotic genomes from metagenomic data using non-contrastive self-supervised learning

REMAG improves eukaryotic genome recovery from metagenomic data by using non-contrastive self-supervised learning, outperforming existing tools in producing near-complete genomes.

HERO: A hierarchy-aware analysis pipeline for reducing and refining whole-brain atlas-mapped cellular datasets

HERO reduces and refines whole-brain atlas-mapped cellular datasets by performing hierarchy-aware selection, refinement, and visualization, improving interpretability and reproducibility.

Postprandial hypertriglyceridemia activates microglia to promote satiety via an ASC dependent signaling.

This study shows that postprandial hypertriglyceridemia activates microglia to promote satiety via an ASC-dependent signaling pathway, which is sexually dimorphic and disrupted in obesity.

An androgen-derived transcriptional state reveals signaling and mitochondrial vulnerabilities in cancer

The paper identifies an androgen-derived transcriptional state in cancer cells and links it to drug resistance and mitochondrial vulnerabilities.

Response representation shapes AlphaGenome enhancer-gene prediction in human astrocytes

The paper evaluates how response representation affects enhancer-gene prediction in human astrocytes using CRISPR-interference data and finds that whole-enhancer deletion responses improve prediction performance.

Ancestral State Reconstruction under Localized Evolutionary Change: Error Patterns and Their Control by Tree Partitioning

This study examines how localized evolutionary changes affect ancestral state reconstruction and shows that tree partitioning can reduce errors in these reconstructions.

Nucleic acid 3D structure search and alignment with GTalign

The paper extends GTalign to support nucleic acid structures, improving alignment accuracy and reducing runtime for large-scale 3D structure comparisons.

Investigating the pathogenicity of missense spliceogenic variants using whole-genome sequencing, RNA-sequencing, and proteomics data from population and clinical research cohorts

The paper investigates missense spliceogenic variants (MSVs) using genomic and proteomic data, finding they are common and can cause disease through splicing disruption, often missed by protein-centric tools.

A split-control criterion for few-shot adaptation in single-cell perturbation prediction

This paper introduces SafeDelta, a split-control criterion for few-shot adaptation in single-cell perturbation prediction, showing it improves reproducibility and identifies biological programs.

Community assembly dynamics in a regulated stream: Insights from environmental DNA

The paper uses eDNA metabarcoding to study fish community dynamics in a regulated stream, finding higher diversity downstream and increased detection of rare species compared to traditional methods.

RNA evidence supports clinical stage antibody drug targets in oncology

The paper evaluates whether single-cell RNA-seq improves the prioritization of antibody-based oncology targets by combining tumor specificity, normal safety, and blood sink features.

When can site-specific glycoform compositions resolve biosynthetic rates?

This paper evaluates when site-specific glycoform compositions can resolve biosynthetic rates, showing that sufficient panel size, separable responses, and model fit are required for accurate inference.

Beyond Conveyance: Assessing the Contribution of Process-Critical Bacteria from Urban Sewer Systems to Wastewater Treatment Plants

The paper quantifies biomass loads from sewer systems to wastewater treatment plants using microbial community data and mass balances, showing gravity sewers produce higher biomass loads than pressure systems.

Funding deadlines act as a zeitgeber for science

The paper shows that NIH grant deadlines influence the timing of preprint publications, with a peak in submissions before deadlines.

Benchmarked sequencing methods reveal hidden mosaic variation in the human brain

The paper benchmarks sequencing methods to recover mosaic variants in human brain tissue and introduces RIVER to enhance variant detection across methods.

Hubness and local scaling in paired T cell receptor distance spaces

The paper quantifies hubness in T cell receptor distance spaces and evaluates local scaling as a correction, showing improvements in retrieval accuracy but no universal solution.

Stemness overcomes IFNγ-induced antitumour exhaustion in human macrophages

This study shows that inducing stemness in human macrophages prevents IFNγ-induced exhaustion, enhancing their antitumour activity and persistence in vivo.