mixed model

Elucidating the conformational dynamics of the mitochondrial localization signal, M3, of TDP-43 and accessing potential inhibitors using molecular docking and simulation

This study identifies vitamin D3 as a potential inhibitor of TDP-43's mitochondrial mis-localization through molecular docking and simulation of the M3 region.

Similar Fecal SCFA Patterns Despite Diverse Gut Microbiota in Polish and Japanese Children During the First Two Years of Life. The longitudinal, comparative, validated study.

The paper compares gut microbiota and short-chain fatty acid (SCFA) patterns in Polish and Japanese children, finding similar SCFA trajectories despite divergent microbial communities.

dFCExpert: Learning Dynamic Functional Connectivity Patterns with Modularity and State Experts

dFCExpert learns dynamic functional connectivity patterns from fMRI data using modularity and state experts, showing superior performance on large-scale datasets.

Mapping genetic effects on splicing in ten thousand post-mortem brain samples reveals novel mediators of neurological disease risk

The paper maps genetic effects on splicing in 10,725 brain samples, identifying 68,358 cis-sQTLs and 97 loci where splicing mediates neurological disease risk.

Age associations with cortical and subcortical brain structure in adolescents age 9-17

The paper uses an extended mixed-effects model to analyze age-related changes in brain structure across a large adolescent cohort, finding distinct developmental patterns in cortical and subcortical regions.

Predicting non-covalent interactions between antioxidants in biological membranes through molecular dynamics

This study uses molecular dynamics to predict non-covalent interactions between antioxidants in lipid bilayers, validating MD simulations as a tool for assessing antioxidant synergism.

Tunable Bias Signaling of the Angiotensin II Type 1 Receptor for Inotropy via C-Terminal Peptide Modifications and Allosteric Site Targeting

This study identifies AngII analogs with modified C-terminal peptides that selectively engage Gq or β-arrestin pathways, showing differential effects on cardiac function and blood pressure in rats.

LDAK-KVIK performs fast and powerful mixed-model association analysis of quantitative and binary phenotypes

LDAK-KVIK is a mixed-model association analysis tool that outperforms existing methods in power and efficiency for quantitative and binary phenotypes.

Digital Communication Preferences and Environmental Behavior: A Mixed-Methods Study of Youth Waste Management Education in Buddhist Bhutan

This study examines youth waste management education in Bhutan, finding high environmental awareness and preference for social media videos, with recommendations for improving infrastructure and culturally tailored communication.

Listening to children's and educators' experiences in long-term place-based conservation education sessions on southern Indian rocky outcrops

The paper evaluates long-term place-based conservation education sessions in southern India, finding short-term knowledge gains but no attitude changes, while highlighting strengths in relational values and challenges in pedagogy.

Aggregation-Prone Region Mapping in Olfactomedin Domain of Myocilin through Classical and Enhanced Sampling Molecular Dynamics Simulations

This study maps aggregation-prone regions in the myocilin OLF domain using molecular dynamics simulations to identify potential therapeutic targets for POAG.

Developing best practice rare disease diagnostic care models in a real-world rural/regional setting

The paper identifies challenges in rare disease diagnosis in Tasmania through stakeholder consultations and suggests establishing a Rare Care Centre to improve care.

Seed dispersal disruption limits tropical forest regrowth

In field records from 3026 tropical sites, modeled bird and mammal seed dispersal disruption predicts slower natural-regrowth carbon accumulation, an estimated 57% average loss at candidate restoration sites.

Novel strains of tomato spotted wilt orthotospovirus (TSWV) are transmitted by western flower thrips in a context-specific manner

Western flower thrips inoculated six TSWV strains across four sequential periods; males trended toward higher efficiency (87% vs 77% for resistance-breaking strains), but per-period differences were not significant.

Single Cell Spatial Transcriptomics Reveals Immunotherapy-Driven Bone Marrow Niche Remodeling in AML

CosMx spatial transcriptomics of bone marrow from 6 refractory/relapsed AML patients shows CD14+ monocytes rising in leukemia-cell neighborhoods after pembrolizumab in responders, dendritic cells in nonresponders.

Locomotor Trends Among Early Mammals Illuminated by Predictors of Arboreality from the Mammalian Appendicular Skeleton

Bayesian multilevel models of 69 appendicular skeletal metrics across 236 extant mammal species predict climbing at 95% accuracy and indicate that several Mesozoic therians, including Juramaia, were terrestrial ground-dwellers.

Medium-sized protein language models perform well at transfer learning on realistic datasets

Medium-sized protein language models (e.g. ESM C 600M) with mean embeddings nearly match ESM-2 15B and ESM C 6B in transfer learning on mutational scanning and PISCES data.

Structural and dynamic study of fungal cell wall degrading fungal chitinase and its interaction with chitooligosaccharide

This study uses molecular modeling and simulation to analyze the structure and dynamics of a fungal chitinase and its interaction with chitotriose, revealing key residues and stability mechanisms.

Modality specific memory enhancement in Heliconius butterflies

Heliconius butterflies retain odour associations over eight days no better than outgroup Heliconiini, contrasting with their superior visual long-term memory, consistent with a modality-specific memory enhancement.

Significant variations in tolerance to clothianidin and pirimiphos-methyl in Anopheles gambiae and Anopheles funestus populations during a dramatic malaria resurgence despite sustained indoor residual spraying in Uganda

In Tororo, Uganda, An. funestus tolerated clothianidin-sprayed walls better than An. gambiae yet was killed on pirimiphos-methyl walls up to 7 months post-spray, implicating it in the malaria resurgence.

Increased Inflammation as well as Decreased Endoplasmic Reticulum Stress and Translation Differentiate Pancreatic Islets of Pre-symptomatic Stage 1 Type 1 Diabetes and Non-diabetic Cases

Laser-microdissected islets of 3 multiple-autoantibody-positive stage 1 type 1 diabetes donors versus matched controls show 202 altered proteins: immune and glycolytic up, translation and ER-stress proteins down.

Ammonia-mediated Conformational Dynamics in SCAP for SREBP Activation

This study uses molecular dynamics simulations to show ammonia induces conformational changes in SCAP that activate the SREBP pathway by promoting dissociation from Insig.

REV-ERBβ Binding Pocket Dynamics with Implications for Rational Design of Small Molecule Modulators

This study uses molecular dynamics simulations to analyze REV-ERBβ ligand-binding domain dynamics and antagonist effects on NCoR peptide binding, informing rational drug design.

ChromMovie: A Molecular Dynamics Approach for Simultaneous Modeling of Chromatin Conformation Changes from Multiple Single-Cell Hi-C Maps

ChromMovie models 3D chromatin structure changes across cellular trajectories using single-cell Hi-C data and cell cycle information.

Sumatran orangutan mothers differ in the extent and trajectory of their expression of maternal behaviour

After controlling for confounders, 15 wild Sumatran orangutan mothers differed consistently in average expression of four of six maternal behaviours and in age-related plasticity for three.

Experimental and Computational Insights into the Structural Dynamics of the Fc Fragment of IgG1 Subtype from Biosimilar VEGF-Trap

This study presents near-physiological structures of the Fc fragment from a biosimilar VEGF-Trap and shows structural plasticity through molecular dynamics simulations.

Investigating the genetic architecture of biotic stress response in stone fruit tree orchards under natural infections with a multi-environment GWAS approach

Multi-environment GWAS of 206 peach and 150 apricot accessions under natural infection finds mostly environment-specific or interactive loci, 60 high confidence QTLs and 87 candidate genes.

Functional connectomics reveals general wiring rule in mouse visual cortex

Functionally similar neurons in mouse visual cortex connect preferentially across layers and areas, including feedback, and feature tuning, not receptive-field position, predicts synapses beyond axon-dendrite proximity.

A Proposed Statistical Approach for Conducting Longitudinal Assessment of Circulating Tumor DNA

This paper proposes a statistical framework using hierarchical mixed-effects models to analyze ctDNA dynamics in liquid biopsy data, finding that a hierarchical linear spline model best captures patient-level ctDNA evolution.

Perception of Mangrove Ecosystem Conservation: A Case of Silvofishery in East Kalimantan, Indonesia

This study examines farmers' perceptions of mangroves and their impact on shrimp aquaculture in Berau, Indonesia, using mixed methods to identify challenges and strategies for sustainable integration.