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A genomic baseline for long-term monitoring of economically important aquatic species in the Netherlands

The paper establishes a genomic baseline for six aquatic species in the Netherlands using SNP data to assess population structure, diversity, and conservation priorities.

Stochastic population growth and its implications for mutation dynamics under carrying capacity constraints

This study introduces a stochastic logistic growth model with carrying capacity to analyze mutation dynamics in microbial populations, showing that random fluctuations significantly impact population variability near carrying capacity.

Chronic unpredictable stress induces negative cognitive bias in rats with sex-specific changes in neurogenesis and functional connectivity

Brain PDGFRβ+ cells exhibit diverse reactive phenotypes after stroke without requiring KLF4

This study shows brain PDGFRβ+ cells show diverse reactive phenotypes after stroke, and KLF4 is not required for their activation or scar formation.

SMFnet reveals principles of combinatorial transcription factor assembly

The paper introduces SMFNet and PRISM to analyze how transcription factor assemblies influence chromatin accessibility and identifies sequence-encoded principles of combinatorial TF assembly.

Epidemic Risks associated with high-temperature replicating infectious hematopoietic necrosis virus (IHNV) field isolates: from molecular characterization to host pathogen interactions

This study examines how rising water temperatures affect IHNV replication and host-pathogen interactions, identifying thermotolerant isolates and validating zebrafish larvae as a model for virulence assessment.

A novel proviral mechanism for the ISG, Shiftless, during human coronavirus infection

This study reveals that the ISG Shiftless (SHFL) has both antiviral and proviral functions during coronavirus infection, enhancing susceptibility while modulating IFN signaling.

Systematic analysis reveals an Mln1-dependent trade-off between metabolic flexibility and thermotolerance in Cryptococcus neoformans

This study identifies Mln1 as a regulator of metabolic flexibility and thermotolerance in Cryptococcus neoformans, revealing a trade-off between nutrient utilization and stress resistance.

The large conjugative plasmid pAB3 integrates into the chromosome of Acinetobacter baumannii ATCC 17978

The paper shows that the plasmid pAB3 integrates into the chromosome of Acinetobacter baumannii ATCC 17978, leading to chromosomal rearrangements and potential phenotypic changes.

DCAF: Unifying Data Validity, Evaluation Validity and Predictive Modeling for Single-cell Perturbation Simulation

DCAF improves single-cell perturbation simulation by addressing data, evaluation, and model validity, outperforming baselines in generalization and recapitulating regulatory heterogeneity in mouse brain.

Modular biofabrication of a vascularized skeletal muscle model through endothelialized microvascular seeds

This paper develops a modular biofabrication strategy to create a vascularized skeletal muscle model by separately maturing muscle and vascular compartments and then assembling them.

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.

Extending digital biology: bacterial survival and morphological heterogeneity under antibiotic stress

This study develops a workflow to generate morphological signatures of bacterial progeny under antibiotic stress, revealing distinct morphologies linked to survival and antibiotic type.

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.

Multi-scale haplotype signatures distinguish among evolutionary processes

SHADES, a deep learning framework, distinguishes evolutionary processes like neutrality, selection, and introgression using haplotype data from humans, outperforming existing methods.

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.

Automated multiscale high-content imaging connects plaque population heterogeneity to localized synapse loss

The paper develops an automated high-content imaging workflow to quantify synapse loss associated with amyloid beta plaques in mouse brains, finding that large cored plaques primarily drive synapse loss.

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.

Desmin Mutations Disrupt Filament Elongation and Drive Polymorphic Aggregation

This study examines how desmin mutations affect filament assembly and aggregation, finding that specific mutations disrupt filament maturation and lead to distinct aggregation pathways.

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.