mixed model

The Impact of Pathogenic and Artificial Mutations on Claudin-5 Selectivity from Molecular Dynamics Simulations

The paper uses molecular dynamics simulations to study how pathogenic and artificial mutations affect ion selectivity in Claudin-5 paracellular pores, identifying structural models that align with experimental observations.

The application of mixed linear models for the estimation of functional effects on bovine stature based on SNP summary statistics from a whole-genome association study

The paper estimates the functional effects of KEGG pathways on bovine stature using SNP summary statistics from GWAS and mixed linear models.

A microbial community growth model for dynamic phenotype predictions

This paper introduces CommPhitting, a dynamic model that predicts microbial community phenotype abundances and growth kinetics using experimental data and optimization.

Challenges of Proper Disposal of Old Long-Lasting Insecticidal Nets and its Alternative Uses in Rural South-Eastern Tanzania

This study examines alternative uses and poor disposal practices of retired long-lasting insecticidal nets in rural Tanzania, finding low awareness of WHO guidelines and high rates of burning, landfilling, and repurposing.

Exploring the potential of using simulation games for engaging with sheep farmers about lameness recognition

This study evaluates a simulation game designed to help sheep farmers recognize lameness, finding no link between game performance and real-life experience but noting potential for future development.

Anti-proliferative effect of potential LSD1/CoREST inhibitors based on molecular dynamics model for treatment of SH-SY5Y neuroblastoma cancer cell line

The paper identifies four potent LSD1/CoREST inhibitors with anti-proliferative activity against SH-SY5Y neuroblastoma cells and low toxicity to normal fibroblasts using molecular dynamics and in-silico screening.

Global Biobank Meta-analysis Initiative: powering genetic discovery across human diseases

Meta-analysis of harmonized GWAS from up to 18 biobanks (six ancestry groups) across 14 endpoints replicated 320 known loci and identified 188 apparently novel loci.

In silico conformational features of botulinum toxins A1 and E1 according to the intraluminal acidification

This study uses molecular dynamics simulations to analyze conformational changes in botulinum toxins A1 and E1 under different pH conditions, revealing domain movements and structural dynamics.

Molecular dynamics analysis of fast-spreading severe acute respiratory syndrome coronavirus 2 variants and their effects in the interaction with human angiotensin-converting enzyme 2

The paper uses molecular dynamics simulations and SPR assays to analyze how SARS-CoV-2 variants bind to the ACE2 receptor and how this affects viral spread.

Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4

Marker genes for 26,970 species-level genome bins, 4,992 defined only by metagenome-assembled genomes, let MetaPhlAn 4 quantify uncharacterized species and beat MetaPhlAn 3, mOTUs and Bracken on synthetic benchmarks.

Identification of key interactions of benzimidazole resistance-associated amino acid mutations in Ascaris β-tubulins by molecular docking simulations

The paper identifies key amino acid interactions in Ascaris β-tubulins that influence benzimidazole resistance through molecular docking and simulations.

Understanding The Role of Heparinoids on the SARS-CoV-2 Spike Protein through Molecular Dynamics Simulations

This study uses molecular dynamics simulations to investigate how heparinoids interact with the SARS-CoV-2 spike protein and ACE2 receptor, revealing mechanisms behind their inhibitory effects.

Covalent Docking and Molecular Dynamics Simulations Reveal the Specificity-Shifting Mutations Ala237Arg and Ala237Lys in TEM Beta-Lactamase

The paper identifies two mutations in TEM beta-lactamase that shift drug specificity through salt bridges, validated by simulations and experiments.

Identification of upstream transcription factor binding sites in orthologous genes using mixed Student's t-test statistics

This paper introduces a tool called Grit for identifying transcription factor binding sites using a mixed Student's t-test method, showing improved performance over existing tools on ChIP-Atlas datasets.

Improved prediction of bacterial CRISPRi guide efficiency from depletion screens through mixed-effect modeling and data integration

The paper develops a mixed-effect random forest model to predict CRISPRi guide efficiency using data from depletion screens and gene-specific features, outperforming existing methods.

Effects of Body Mass on Leg and Vertical Stiffness in Running Humans

This study examines how leg and vertical stiffness scale with body mass in humans, finding isometric scaling overall but slight negative allometry in vertical stiffness for females at certain speeds.

Public exams decrease anxiety and facilitate deeper conceptual thinking

This study evaluates public exams as an assessment method, finding they reduce anxiety and promote deeper conceptual thinking without worsening outcome disparities.

Driving Forces underlying Selectivity Filter Gating in the MthK Potassium Channel

This study investigates selectivity filter gating in the MthK potassium channel and its V55E mutant using electrophysiology and simulations, revealing structural and functional differences compared to KcsA.

Molecular Dynamic Investigation of H5N1 Influenza Virus Dual H274Y-I222K Mutation Resistance to Peramivir

This study uses molecular dynamics to analyze how mutations in H5N1 influenza virus neuraminidase affect Peramivir binding, finding that mutations reduce binding stability and drug efficacy.

A molecular dynamic investigation of Human Rhinovirus 3C Protease Drug Target: Insights towards the design of potential Inhibitors

The paper uses molecular dynamics to compare binding affinities of two HRV-3C protease inhibitors, identifying key residues involved in ligand-enzyme interactions.

Predicted binding interface between coronavirus nsp3 and nsp4

The paper predicts a binding interface between coronavirus nsp3 and nsp4 that is membrane-associated, conserved, and stable, suggesting a model for DMV pore formation.

FinnGen: Unique genetic insights from combining isolated population and national health register data

Finnish-enriched low-frequency variants, often coding, underlie many GWAS signals across 1,932 register endpoints in 218,792 Finns; a 15-disease meta-analysis with Estonian and UK biobanks adds 30 unreported associations.

Evaluation of Postgraduate Educational Environment of Doctors Training in Psychiatry: a mixed method study

This study evaluates the educational environment for psychiatry postgraduate training in Ireland using mixed methods, finding a generally positive environment with areas needing improvement.

A multi-dimensional integrative scoring framework for predicting functional variants in the human genome

The paper introduces MACIE, a framework for predicting functional variants by integrating diverse annotations, and applies it to fine-mapping using GWAS data.

An Improved Linear Mixed Model for Multivariate Genome-Wide Association Studies

This paper introduces an improved linear mixed model for multivariate genome-wide association studies that handles incomplete data and reduces computational complexity.

Specificity of Loxosceles α clade phospholipase D enzymes for choline-containing lipids: role of a conserved aromatic cage

The paper investigates the role of an aromatic cage in the lipid specificity of Loxosceles α clade phospholipase D enzymes using molecular dynamics simulations and experimental validation.

Programming Cell-Free Biosensors with DNA Strand Displacement Circuits

This paper develops DNA strand displacement circuits to enhance biosensors by enabling fine-tuning of reaction kinetics and faster response times, creating binary outputs that encode target molecule concentrations.

Pore structure controls stability and molecular flux in engineered protein cages

This study investigates how pore structure affects stability and molecular flux in engineered protein cages through design, structural analysis, and simulations.

Cell Type Composition Analysis: Comparison of statistical methods

The paper compares statistical methods for cell type composition analysis in single-cell RNA-Seq, finding that some methods perform better than others while highlighting the importance of accounting for sample variability.

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

In 5,959 Finns with genotypes and stool metagenomes, GWAS found 583 independent SNP-taxon associations; dairy intake modified LCT effects on Bifidobacterium, and ABO-linked Faecalicatena lactaris tracked secretor status.