mixed model

What works to improve species conservation state? An analysis of species whose state has improved and the actions responsible

Across 67,217 IUCN-assessed animal species, deteriorations in Red List category outnumber improvements sixfold; reintroductions and invasive species control are most consistently linked to recovery.

Disrupting Viral Replication in Human Metapneumovirus: Targeting Key Proteins with Unani Phytochemicals through Structural Dynamics and Energetics

This study evaluates Unani phytochemicals against HMPV using computational methods, finding strong binding affinities and stability for Crocin, Quercetin, and Oleuropein.

Exploring FDA-Approved Antiviral Drugs for Human Metapneumovirus Treatment: Integrative Computational Insights

This study identifies Remdesivir and Peramivir as promising FDA-approved antiviral drugs for HMPV treatment using computational methods.

Assessing the helical stability of polyXYs at the boundaries of Intrinsically Disordered Regions with MD simulations

The paper uses MD simulations to study helical stability in polyXY sequences at IDR boundaries, finding they form dynamic helices that may aid in protein flexibility.

A Molecular Dynamics Protocol for Rapid Prediction of EGFR Overactivation and Its Application to the Rare Mutations S768I, S768N, D761N

This paper develops a molecular dynamics protocol to predict EGFR mutation effects and applies it to three rare mutations, showing how they alter structural dynamics and activity.

Structural conformations of intrinsically disordered proteins of podocyte slit-diaphragm

The paper investigates the structural dynamics of slit-diaphragm proteins using molecular docking and simulations, revealing conformational adaptations and subunit-sharing mechanisms in health and disease.

Bacteriophage Kil peptide folds into a predicted helix-turn-helix structure to disrupt Escherichia coli cell division

The paper identifies the minimal functional region of the Kil peptide and shows it forms a helix-turn-helix structure to disrupt FtsZ ring assembly in E. coli.

Mixture of Experts Enable Efficient and Effective Protein Understanding and Design

AIDO.Protein is a mixture-of-experts model for protein understanding and design, achieving state-of-the-art performance with improved efficiency.

Molecular dynamics simulations provide insights into ULK-101 potency and selectivity toward autophagic kinases ULK1/2

This study uses molecular dynamics simulations to analyze how ULK-101 binds to ULK1/2 kinases, revealing structural features that explain its potency and selectivity.

Phytochemicals from Daucus carota have therapeutic potential against Triple-Negative Breast Cancer PDK1 and PLK1.

This study identifies eight bioactive compounds from Daucus carota that bind to PDK1 and PLK1 ATP sites, showing potential for TNBC treatment through computational analysis.

A site-wise reliability analysis of the ABCD diffusion fractional anisotropy and cortical thickness: impact of scanner platforms

The paper evaluates test-retest reliability of brain imaging metrics across multiple sites and scanners, finding significant differences in reliability between scanner types.

A survey of the mentor-mentee relationship in early career research (ECR): Implications for publishing and career advancement in the STEMM disciplines

This study surveys ECRs and mentors in STEMM to understand how mentor-mentee relationships affect publishing and career development, finding that clear communication and mutual respect are key.

Regulators of health and lifespan extension in genetically diverse mice on dietary restriction

In 937 genetically diverse female mice, caloric restriction and intermittent fasting extended lifespan, yet bodyweight resilience, immune and red-cell traits, not metabolic improvements, predicted longevity.

Family-GWAS reveals effects of environment and mating on genetic associations

Family-based GWAS meta-analysis of 34 phenotypes shows standard GWAS effects carry sizeable confounding uncorrelated with direct genetic effects, while assortative mating likely inflates SNP heritability and genetic correlations.

Insights from Molecular Docking and Dynamics Simulations of P2RX7-????Syn Complex

This paper uses molecular docking and dynamics simulations to study the interaction between P2RX7 and alpha-synuclein, identifying binding sites and structural changes involved in neuronal damage.

Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics

This study uses Gaussian accelerated MD simulations to improve tunnel sampling in enzymes, revealing new transient tunnels and their functional relevance.

PIPI-C: A combinatorial optimization framework for identifying post-translational modification crosstalks in mass spectrometry data

PIPI-C identifies PTM crosstalks in mass spectrometry data using a combinatorial optimization framework, revealing upregulated PTM patterns in cancer datasets.

Impact of aging on the GABAB receptor-mediated connectome

This paper investigates how aging affects GABAB receptor interactions and membrane lipid composition in rat cerebella, revealing reduced GABAB2 expression and altered lipid profiles that impact protein-protein interactions.

Investigating Medin Cleavage Accessibility in MfgE8: Conformational Insights Derived from Molecular Dynamics Simulations and AlphaFold2 Models

This study uses molecular dynamics simulations and AlphaFold2 models to investigate MfgE8 conformations and how they affect medin cleavage site accessibility.

Diversity and Scale: Genetic Architecture of 2,068 Traits in the VA Million Veteran Program

Population-stratified GWAS of 2,068 traits in 635,969 Million Veteran Program participants, 29% genetically non-European, yields 98,485 associations and 57,601 fine-mapped signals with largely shared cross-population architecture.

Efficient and accurate mixed model association tool for single-cell eQTL analysis

SAIGE-QTL is a tool for single-cell eQTL analysis that directly maps eQTLs without pseudobulk aggregation and improves power for detecting rare variants.

Differential gene expression analysis of spatial transcriptomic experiments using spatial mixed models

This study applies spatial mixed models to differential gene expression analysis in spatial transcriptomics, showing they reduce type-I error and improve model fit compared to non-spatial methods.

Optimal Phylogenetic Reconstruction of Insertion and Deletion Events

This paper introduces a Mixed-Integer Programming approach to optimally reconstruct indel events in phylogenetic trees, outperforming existing methods in accuracy and efficiency.

Atomic insights into the signaling landscape of E. coli PhoQ Histidine Kinase from Molecular Dynamics simulations

The paper uses Molecular Dynamics simulations and AlphaFold2 to study PhoQ signaling, revealing three conformations and insights into its activation mechanism.

A novel multi-omics mendelian randomization method for gene set enrichment and its application to psychiatric disorders

This paper introduces MR-GSE, a multi-omics Mendelian randomization method for gene set enrichment in psychiatric disorders, showing increased detection of significant gene sets compared to non-MR methods.

Investigating the Structural Impact and Conformational Dynamics of a Sequence Variant (c.242G>A) in TMIE Gene Provoking Usher Syndrome

This study uses molecular dynamics simulations to show that the c.242G>A variant in TMIE causes structural instability and conformational changes leading to Usher syndrome.

How does perception of zoo animal welfare influence public attitudes, experiences, and behavioural intentions? A mixed-methods systematic review

This review identifies factors influencing public perceptions of zoo animal welfare and their effects on attitudes, experiences, and behaviors, recommending improvements for future research.

Empowering future scientists: Mentors employ various strategies to engage students in professional science disciplinary literacy practices

The paper examines how mentors support students in developing professional science disciplinary literacy practices through writing and publishing research.

Pan-UK Biobank GWAS improves discovery, analysis of genetic architecture, and resolution into ancestry-enriched effects

Meta-analyzing per-ancestry GWAS of 7,266 UK Biobank traits across six genetic ancestry groups adds 14,676 loci missed by European-only analysis, including ancestry-enriched CAMK2D and G6PD signals.

Molecular dynamics of outer membrane-embedded polysaccharide secretion porins reveals closed resting-state surface gates targetable by virtual fragment screening for drug hotspot identification

The paper uses molecular dynamics to study porin structures and identifies drug targets for inhibiting polysaccharide secretion.