clustering

An Integrated Multiphoton Imaging Workflow for Quantitative Analysis of Aortic Tissue Microstructure

This paper introduces a workflow for quantitative analysis of aortic tissue microstructure using multiphoton imaging, providing measurements of elastic lamellae, collagen organization, and cell morphology.

Discovery of microbial intergenic features with genomic language modeling and multimodal search

The paper identifies microbial intergenic features using a sparse autoencoder and multimodal search, revealing previously uncharacterized regulatory DNA and structured RNA elements.

SRPK1 is a determinant of chemoresistance to Docetaxel in prostate cancer

This study identifies SRPK1 as a key regulator of docetaxel resistance in prostate cancer by modulating splicing and apoptosis pathways.

Developmental Cerebellar Pathology in Mouse Models of SCN2A Premature Termination Codon Variants

This study examines cerebellar development in mouse models with SCN2A premature termination codon variants, finding age- and position-dependent effects on cerebellar structure and function.

Transplantation reveals birthdate-dependent post-mitotic competence in cortical neurons

This study shows that post-mitotic cortical neurons retain birthdate-dependent differentiation potential, with early-born neurons maintaining a broader repertoire than late-born neurons.

Functional capacities drive recruitment of bacteria into plant root microbiota

The paper investigates how Arabidopsis, Barley, and Lotus plants recruit specific bacteria from synthetic communities, finding that functional capacities drive microbiota assembly.

Cognitive control networks in human and macaque

This study compares cognitive control networks in humans and macaques using fMRI, finding similarities in the MD network but differences in lateral frontal cortex activation patterns.

Functional organization and natural scene responses across mouse visual cortical areas revealed with encoding manifolds

The paper uses encoding manifolds to analyze how mouse visual cortical areas represent natural scenes and static gratings, revealing layer-specific and cell-type-specific response patterns.

Developmental remodeling uncouples neural stem cell function from niche anatomy

This study shows neural stem cells can maintain function outside their normal anatomical niche, revealing plasticity in stem-cell environment relationships.

Differentiation protocol and maturation shape the axial identity and synaptic state in human iPSC-derived spinal motor neurons

This study compares two protocols for generating human iPSC-derived spinal motor neurons, finding that the extended protocol produces more mature, spinal-specific neurons with enhanced synaptic features.

Neural encoding of grasp and object properties in the posterior parietal and motor cortices of the cortical grasping network in tetraplegic humans

This study investigates how grasp and object properties are encoded in the cortical grasping network of tetraplegic humans, showing separable neural representations in different brain regions that could improve brain-machine interface performance.

Apoptotic Quality Control of Cellular Competence Limits Cryptic Germinal Center B Cell States

This study shows that mitochondrial apoptosis limits non-proliferating and defective B cell states in germinal centers without affecting affinity maturation.

Nitrotoxin metabolism in bacteria may have emerged from a diverse oxidoreductase reservoir

The paper identifies a diverse oxidoreductase reservoir in bacteria for nitrotoxin metabolism, showing that 3NPA-responsive bacteria are widespread and use oxidoreductases beyond canonical NMOs.

Spatially resolved gene expression and tumour-microenvironment interactions across malignant transformation in IDH-mutant glioma

The paper analyzes spatial gene expression and tumor-microenvironment interactions in IDH-mutant gliomas across malignant transformation, finding reduced proliferation at the infiltrative margin in higher-grade tumors.

Rsearch: An R interface to VSEARCH supporting visualization and parameter tuning

Rsearch runs VSEARCH from R with quality plots, trimming optimizers and phyloseq conversion; on a 16S mock community it matched DADA2's abundance accuracy with fewer, more prevalent OTUs.

Division-Specific Organization of a Shared Functional Scaffold in the Early-Life Human Brain

This paper develops a fine-grained whole-brain functional parcellation framework for early human development and identifies a shared functional scaffold with division-specific organization.

RamiGlyph Captures Microglial Morphological Diversity and Predicts Functional States in Ischemia Reperfusion and Amyloid Pathology

Microdomes: Micro-engineered Microdome arrays enable standardised and shear-free 3D biology with full-spectrum optical imaging compatibility

The paper introduces Microdomes, a 3D biology platform that enables shear-free handling and full-spectrum optical imaging of spheroids and organoids.

HaloUMI: Physics-informed analysis of inhibition halo assays

HaloUMI provides an automated tool for analyzing microbial inhibition assays, improving accuracy by accounting for irregular zones and varying microbial density.

Chemically modified CRISPR enzymes for multi-organ genome editing in vivo

This paper introduces PERCEPT, a CRISPR delivery platform that enables multi-organ genome editing in vivo by chemically modifying CRISPR enzymes for targeted and efficient delivery.

Divergent specializations for motion-driven representations in higher lateral and dorsal visual areas

The paper investigates how artificial neural networks trained on motion-related tasks develop representations that align with brain activity and support object categorization using motion cues.

A moving front of osteoblast maturation scales regenerating zebrafish bone

The paper identifies a moving front of osteoblast maturation that controls proliferation during zebrafish scale regeneration, explaining size scaling through regulated cell dynamics.

fishROI: A specialized workflow for semi-automated muscle morphometry analysis in teleosts

The paper introduces a FIJI2 plugin for semi-automated muscle morphometry analysis in zebrafish, combining cytoplasmic staining and deep learning for accurate quantification and visualization.

Biofilms promote tolerance and stability in gut bacterial communities during bile acid stress

This study investigates how biofilms in multispecies gut microbiota communities enhance tolerance and stability during bile acid stress.

mAIcrobe: an open-source framework for high-throughput bacterial image analysis

mAIcrobe provides an open-source framework for bacterial image analysis using deep learning models, enabling analysis of diverse bacterial species and microscopy modalities.

Analysis of motor-based transport in primary cilia by dynamic mode decomposition of live-cell imaging data

The paper uses dynamic mode decomposition to analyze live-cell imaging data and investigates KIF13B's role in ciliary transport, finding it does not affect IFT velocity or frequency in a deletion mutant.

pTRIP, a novel integration plasmid for Listeria monocytogenes

The paper introduces pTRIP, a new integrative plasmid for Listeria monocytogenes that allows stable gene integration without antibiotic selection.

Engineering phenotypic heterogeneity for functional organization in microbial populations

This paper introduces PROMETEO, a genetic-circuit framework that programs microbial population composition through asymmetric circuits, enabling functional organization and efficient biotransformation.

Fixation-evoked potentials reveal neural signatures of hierarchical value-integration during decision-making

This study uses EEG and eye-tracking with a computational model to identify neural signatures of value-integration during decision-making under naturalistic conditions.

Concurrent Supervised-Unsupervised Representative Subspace Clustering (CSU-RSC)

CSU-RSC identifies sex-dominant subgroups in psychosis by integrating supervised and unsupervised clustering on neuroimaging data, revealing sex-specific biological heterogeneity.