clustering

Genetic drivers shape TREM2-dependent myeloid responses and glioblastoma progression

This study shows TREM2's role in glioblastoma depends on genetic context and timing, with different effects in Nf1-silenced/Ras-driven and PDGFB-driven models.

Increasing Cancer Stemness Drives Prostate Cancer Progression, Plasticity, Therapy Resistance and Poor Patient Survival

This study quantifies cancer stemness in prostate cancer across progression stages, showing its association with therapy resistance, poor survival, and lineage plasticity.

FennoTraits: Dataset of plant functional traits and community composition in northern European flora

The paper introduces FennoTraits, a dataset of plant functional traits and community composition from northern European flora, highlighting trait patterns and species distribution across seven study areas.

Cornealia: automated collective order analysis reveals density-dependent reorganization of donor corneal endothelium

Cornealia analyzes collective order in donor corneal endothelium, revealing density-dependent reorganization and mechanical responses not captured by traditional metrics.

A historical specimen of False Lingzhi (Ganoderma lucidum) resolves a 245-year-old confusion within an important medicinal mushroom group

The paper resolves a 245-year-old taxonomic confusion between Ganoderma lingzhi and G. lucidum using a historical specimen and genomic analysis, showing they diverged over 12 million years ago.

Systematic genome analysis enables long-overdue taxonomic reorganization of genus Orthoflavivirus; potential assignment of over 50 new species

The paper proposes a genetic divergence threshold for demarcating orthoflavivirus species, identifying 25 new Euflavivirus and 33 new Fusivirus species.

Climate-associated genomic variation across life stages reveals population-specific signals of local adaptation in European beech

The paper identifies climate-associated genomic variation in European beech across life stages, revealing population-specific adaptive responses to temperature and precipitation changes.

Beyond the Billion: Dose-Response Immunophenotyping and Machine Learning Classification of Live versus Heat-Inactivated Gram-Positive Probiotic Strains in Human Peripheral Blood Mononuclear Cells

This study challenges assumptions about probiotic efficacy by showing heat-treated strains can match live strains in immunological activity at higher doses, using flow cytometry and machine learning to classify probiotic strains.

Dissociating Resting-State Networks of Pedohebephilic Preference and Child Sexual Offending Using Network-Based Prediction

The paper distinguishes pedohebephilic preference from child sexual offending using resting-state functional connectivity and network-based prediction, identifying distinct neural network alterations.

CULTURE AND ISOLATION OF BACTERIA ASSOCIATED WITH MEDITERRANEAN CORALS

The paper isolates and cultures bacteria from four Mediterranean corals, identifying 84 pure isolates, including novel species, to better understand their roles in the coral holobiont.

Single-cell multiomics reveals archetypal regulatory programs shared across CD4 and CD8 T cell subsets in viral infection

Quantitative assessment of mesoscale cellular order and organization in the mouse hippocampus

The paper quantifies mesoscale cellular organization in the mouse hippocampus using a new software tool, revealing cell-type-specific nuclear shape variations and positionally ordered but orientationally disordered dense regions.

Immune-Epithelial Interactions via TGF-β Orchestrates Stem-Cell Niche Formation and Morphogenesis

This study shows immune cells influence stem-cell niche formation and organoid development through TGF-β signaling in a 3D breast organoid model.

Rapid thermoforming of polycarbonate cell culture accessories from 3D printed molds

This paper introduces a method to rapidly create customized, autoclavable cell culture accessories using polycarbonate thermoforming from 3D printed molds, demonstrating compatibility with human iPSC culture and differentiation.

Cardiomyocyte Identity Crisis Without Regenerative Re-entry: A Multi-Scale Atlas of Incomplete Dedifferentiation and Intercellular Communication Rewiring in the Infarcted Human Heart

The paper constructs a multi-scale atlas of cardiomyocyte changes in infarcted hearts, showing partial identity loss without regenerative proliferation and altered intercellular communication.

Development of py-mea-span for comprehensive analysis of multi-electrode array data and its application to LGI2-deficient neurons

Open-source Python package parses Axion spk files directly and matches NeuralMetric Tool outputs, then reveals burst and network burst hyperexcitability, without synchrony change, in LGI2-knockdown human iPSC neurons.

Large-scale integrated single-cell analysis reveals molecular subtypes and microenvironmental remodeling in cutaneous T cell lymphoma

This study integrates a large scRNA-seq dataset of CTCL to identify molecular subtypes and microenvironmental changes with clinical relevance.

A Pan-Cancer Benchmark of Clustering Strategies for Patient-Specific Gene Regulatory Networks

The paper benchmarks clustering strategies for patient-specific gene regulatory networks across 9,778 cancer samples, finding that standard deviation-based feature selection with k-means performs best.

Live-cell imaging of fetal microglia reveals time-dependent sex differences in their responsiveness to prenatal maternal stress

This study uses live-cell imaging to show sex-specific differences in fetal microglial responses to prenatal maternal cold stress, revealing time-dependent changes in morphology, motility, and phagocytic behavior.

Thalamo-insular basis for updating physiological needs

This study shows that thalamic inputs to the insular cortex update representations of physiological needs like thirst and hunger, and that inhibiting these inputs prevents such updates.

Understanding cognitive function in post-COVID-19 condition with fatigue: an interdisciplinary multimodal investigation

This study investigates cognitive symptoms in post-COVID-19 condition with fatigue, finding subtle neurobiological changes not captured by standard assessments.

Overcoming segmentation bottlenecks in brain tissue for spatial proteomic inference at population scale

The paper introduces SPInfer, a workflow for spatial proteomic inference that improves cell segmentation in human brain tissue, enabling better biological discovery at population scale.

Multi-scale histology reveals localized ageing signatures in normal human colon

This paper uses multi-scale histology to identify localized age-related changes in normal human colon tissue using H&E images and machine learning.

A clinically annotated proteomic and histological resource of 1,000 colorectal cancers

Deep proteomics of 997 treatment-naïve colorectal cancers defines six subgroups, splitting chromosomally unstable tumors into three and revealing a rare adverse subgroup, with H&E slide benchmarks.

OCTRON - a general purpose segmentation and tracking pipeline for behavioral experiments

OCTRON provides a segmentation and tracking pipeline for behavioral experiments, validated across species and setups.

Parvalbumin interneuron maturation reorganizes cortical population activity structure during development

This study shows that parvalbumin interneurons drive cortical network desynchronization and increased population activity dimensionality during development.

Sequential invasion under disturbance drives functional homogenisation of lake benthos

The paper examines how sequential invasion under different disturbance histories affects functional diversity in lake benthos, finding that non-native species dominate and reduce native functional richness.

Strong habitat-associated differentiation of microbial communities across a fine-scale land-water interface

The paper examines microbial community differentiation across a land-water interface, finding strong habitat-associated differences between terrestrial and aquatic samples.

Pediatric brain charts reveal ADHD biotypes with distinct developmental, molecular, and therapeutic profiles

The paper identifies two distinct ADHD biotypes using brain imaging and transcriptomic data, showing different developmental, molecular, and treatment responses.

Evolution of CTCF underlies the establishment of loop extrusion as a predominant chromatin folding mechanism in vertebrates

The paper investigates the evolution of CTCF's role in chromatin organization across species, finding that vertebrate CTCF enables loop extrusion but requires additional factors for full genome architecture.