Autoencoder-Transformed Transcriptome Improves Genotype-Phenotype Association Studies.

Transcriptome-wide association study (TWAS) is an emerging model leveraging gene expressions to direct genotype-phenotype association mapping. A key component in TWAS is the prediction of gene expressions; and many statistical approaches have been developed along this line. However, a problem is that many genes have low expression heritability, limiting the performance of any predictive model.

Apollo: a comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell.

Modern sequencing instruments bring unprecedented opportunity to study within-host viral evolution in conjunction with viral transmissions between hosts. However, no computational simulators are available to assist the characterization of within-host dynamics. This limits our ability to interpret epidemiological predictions incorporating within-host evolution and to validate computational inference tools.

Combined effects of quinic acid and isochlorogenic acid B on LPS-induced inflammation and pyroptosis in MAC-T cells and mouse mammary glands.

Introduction: Quinic acid (QA) and isochlorogenic acid B (ICAB) have been demonstrated to possess antioxidant, anticancer, and anti-inflammatory properties. However, their combined efficacy in protection against mastitis requires further investigation. This study aims to examine the inhibitory effects and mechanisms of QA and ICAB combination on lipopolysaccharide (LPS)-induced inflammation and pyroptosis in bovine mammary epithelial cells (MAC-T) and mouse mammary tissue.

Linking DNA methylation in brain regions to Alzheimer's disease risk: a Mendelian randomization study.

Aim: DNA methylation in brain regions represents a potential mechanism linking genetic variation to Alzheimer's disease (ad) risk, yet most studies have focused on blood-derived methylation markers. In this study, we conducted a systematic Mendelian randomization (MR) study to evaluate associations between predicted brain region-specific DNA methylation levels and ad risk, using methylation quantitative trait loci (mQTL) as genetic instruments.

Methods: We analyzed mQTLs from five human brain regions: cerebellum (CRBLM), frontal cortex (FCTX), causal pons (PONS), and temporal cortex (TCTX) from 600 individuals in Gibbs et al's study, as well as mQTLs from dorsolateral prefrontal cortex (DLPFC) of 543 participants in the Religious Orders Study and the Rush Memory and Aging Project (ROSMAP).

Recrystallization-Driven High-Performance Optical Nonlinearity Recovery of Layered van der Waals NbOCl.

van der Waals crystal NbOCl has attracted considerable interest owing to its spontaneous parametric downconversion properties, but challenges remain due to its degradation and reduced optical nonlinearity under ambient conditions. Here, we show that high-temperature vacuum annealing can recover and even enhance second harmonic generation (SHG) in degraded NbOCl via recrystallization. During degradation, the second-order nonlinearity decreases, accompanied by changes in the crystal structure of NbOCl.

Biochar doping of synthesized mordenite improves adsorption and oxidation in As(III) removal: Experiments and DFT calculations.

In this study, a composite material was synthesized through the co-pyrolysis of biochar doped with synthetic mordenite. The adsorption experiments conducted with BC@ASM on As(III) facilitated the determination of the optimal mass ratio of 20:1 (ASM: Yak dung) and a pyrolysis temperature of 500 °C. The adsorption properties of ASM and BC@ASM were examined through batch adsorption experiments and a range of characterization techniques.

Enhancing disease risk gene discovery by integrating transcription factor-linked trans-variants into transcriptome-wide association analyses.

Transcriptome-wide association studies (TWAS) have been successful in identifying disease susceptibility genes by integrating cis-variants predicted gene expression with genome-wide association studies (GWAS) data. However, trans-variants for predicting gene expression remain largely unexplored. Here, we introduce transTF-TWAS, which incorporates transcription factor (TF)-linked trans-variants to enhance model building for TF downstream target genes.

N-coordinated iron sites dispersed in porous carbon frameworks to activate peroxymonosulfate for efficient sulfisoxazole degradation and real hospital wastewater decontamination.

Herein, an N-coordinated Fe site dispersed in porous carbon frameworks (Fe-NC) fabricated from zeolitic imidazolate frameworks encapsulated with iron acetylacetonate (Fe(acac) @ZIFs) was employed to activate peroxymonosulfate (PMS) for the attenuation of sulfisoxazole (SIZ) and treating real hospital wastewater. The constructed Fe-NC/PMS system exhibited good catalytic stability for SIZ degradation, maintaining excellent degradation performance over multiple cycles with virtually no leaching. The quenching experiments, electron paramagnetic resonance (EPR) capture analyses, and semi-quantitative measurements showed that singlet oxygen (O) and high-valent metal-oxo species were mainly responsible for SIZ degradation by Fe-NC/PMS.

Apollo: A comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell.

Modern sequencing instruments bring unprecedented opportunity to study within-host viral evolution in conjunction with viral transmissions between hosts. However, no computational simulators are available to assist the characterization of within-host dynamics. This limits our ability to interpret epidemiological predictions incorporating within-host evolution and to validate computational inference tools.

Large-scale integration of omics and electronic health records to identify potential risk protein biomarkers and therapeutic drugs for cancer prevention and intervention.

Identifying risk protein targets and their therapeutic drugs is crucial for effective cancer prevention. Here, we conduct integrative and fine-mapping analyses of large genome-wide association studies data for breast, colorectal, lung, ovarian, pancreatic, and prostate cancers, and characterize 710 lead variants independently associated with cancer risk. Through mapping protein quantitative trait loci (pQTL) for these variants using plasma proteomics data from over 75,000 participants, we identify 365 proteins associated with cancer risk.

The development of brain pericytes requires expression of the transcription factor nkx3.1 in intermediate precursors.

Brain pericytes are one of the critical cell types that regulate endothelial barrier function and activity, thus ensuring adequate blood flow to the brain. The genetic pathways guiding undifferentiated cells into mature pericytes are not well understood. We show here that pericyte precursor populations from both neural crest and head mesoderm of zebrafish express the transcription factor nkx3.

Preparation of a Novel Lignocellulose-Based Aerogel by Partially Dissolving Medulla Tetrapanacis via Ionic Liquid.

A novel lignocellulosic aerogel, MT-LCA, was successfully prepared from MT by undergoing partial dissolution in an ionic liquid, coagulation in water, freezing in liquid nitrogen, and subsequent freeze-drying. The MT-LCA preserves its original honeycomb-like porous structure, and the newly formed micropores contribute to increased porosity and specific surface area. FT-IR analysis reveals that MT, after dissolution and coagulation, experiences no chemical reactions.

An expression-directed linear mixed model discovering low-effect genetic variants.

Detecting genetic variants with low-effect sizes using a moderate sample size is difficult, hindering downstream efforts to learn pathology and estimating heritability. In this work, by utilizing informative weights learned from training genetically predicted gene expression models, we formed an alternative approach to estimate the polygenic term in a linear mixed model. Our linear mixed model estimates the genetic background by incorporating their relevance to gene expression.

Effect of montmorillonite modified straw biochar on transfer behavior of lead and copper in the historical mining areas of dry-hot valleys.

Due to the rapid development of human beings, heavy metals are occurred in the Yunnan-Guizhou Plateau and Panxi Plateau, the special dry and hot climate areas. Pb and Cu can be quickly transferred through water-plant-animal, further harm to human health by food chain. Therefore, the study of heavy metal treatment is imminent.

A statistical method for image-mediated association studies discovers genes and pathways associated with four brain disorders.

Brain imaging and genomics are critical tools enabling characterization of the genetic basis of brain disorders. However, imaging large cohorts is expensive and may be unavailable for legacy datasets used for genome-wide association studies (GWASs). Using an integrated feature selection/aggregation model, we developed an image-mediated association study (IMAS), which utilizes borrowed imaging/genomics data to conduct association mapping in legacy GWAS cohorts.

Enhancing Disease Risk Gene Discovery by Integrating Transcription Factor-Linked Trans-located Variants into Transcriptome-Wide Association Analyses.

Transcriptome-wide association studies (TWAS) have been successful in identifying disease susceptibility genes by integrating cis-variants predicted gene expression with genome-wide association studies (GWAS) data. However, trans-located variants for predicting gene expression remain largely unexplored. Here, we introduce transTF-TWAS, which incorporates transcription factor (TF)-linked trans-located variants to enhance model building.

Effect of 3D Printing Process Parameters and Heat Treatment Conditions on the Mechanical Properties and Microstructure of PEEK Parts.

Fused deposition modeling (FDM) processed Poly-ether-ether-ketone (PEEK) materials are widely used in aerospace, automobile, biomedical, and electronics industries and other industries due to their excellent mechanical properties, thermal properties, chemical resistance, wear resistance, and biocompatibility, etc. However, the manufacture of PEEK materials and parts utilizing the FDM process faces the challenge of fine-tuning a list of process parameters and heat treatment conditions to reach the best-suiting mechanical properties and microstructures. It is non-trivial to make the selection only according to theoretical analysis while counting on a vast number of experiments is the general situation.

Interaction-integrated linear mixed model reveals 3D-genetic basis underlying Autism.

Genetic interactions play critical roles in genotype-phenotype associations. We developed a novel interaction-integrated linear mixed model (ILMM) that integrates a priori knowledge into linear mixed models. ILMM enables statistical integration of genetic interactions upfront and overcomes the problems of searching for combinations.

Integrating transcription factor occupancy with transcriptome-wide association analysis identifies susceptibility genes in human cancers.

Transcriptome-wide association studies (TWAS) have successfully discovered many putative disease susceptibility genes. However, TWAS may suffer from inaccuracy of gene expression predictions due to inclusion of non-regulatory variants. By integrating prior knowledge of susceptible transcription factor occupied elements, we develop sTF-TWAS and demonstrate that it outperforms existing TWAS approaches in both simulation and real data analyses.

Stick, stretch, and scan imaging method for DNA and filaments.

Biomolecules and organelles usually undergo changes to their structure or form as a result of mechanical stretching or stimulation. It is critical to be able to observe these changes and responses, which trigger mechano-chemical coupling or signal transduction. Advanced techniques have been developed to observe structure and form during manipulation; however, these require sophisticated methods.

Low dielectric resins derived from hyperbranched carbosilane oligmers functionalized by benzocyclobutene groups.

Polycarbosilanes have been considered as potential materials used in electronic packaging and circuit boards owing to their excellent low-dielectric performance. In this work, we prepared new hyperbranched carbosilane oligomers (HCBOs) which were functionalized by benzocyclobutene (BCB) groups. HCBOs can be thermally cured to produce transparent (HCBRs) with low dielectric constant and high thermostability.

Reconstructing SARS-CoV-2 infection dynamics through the phylogenetic inference of unsampled sources of infection.

The COVID-19 pandemic has illustrated the importance of infection tracking. The role of asymptomatic, undiagnosed individuals in driving infections within this pandemic has become increasingly evident. Modern phylogenetic tools that take into account asymptomatic or undiagnosed individuals can help guide public health responses.

Disentangling genetic feature selection and aggregation in transcriptome-wide association studies.

The success of transcriptome-wide association studies (TWAS) has led to substantial research toward improving the predictive accuracy of its core component of genetically regulated expression (GReX). GReX links expression information with genotype and phenotype by playing two roles simultaneously: it acts as both the outcome of the genotype-based predictive models (for predicting expressions) and the linear combination of genotypes (as the predicted expressions) for association tests. From the perspective of machine learning (considering SNPs as features), these are actually two separable steps-feature selection and feature aggregation-which can be independently conducted.