X. Shen

Generative Neural Spike Prediction from Upstream Neural Activity via Behavioral Reinforcement

This paper develops a reinforcement learning framework to predict downstream neural spike trains from upstream activity using behavioral rewards, achieving better behavioral performance than existing methods.

YAP/TAZ enhance P-body formation to promote tumorigenesis

This study shows YAP/TAZ promote P-body formation in cancer cells, enhancing tumorigenesis, and suggests targeting P-bodies or PNRC1 could be therapeutic.

Mutation of phosphatidate phosphohydrolase genes confers broad-spectrum disease resistance in plants

The paper shows that mutating phosphatidate phosphohydrolase (PAH) genes in rice and Arabidopsis increases phosphatidic acid (PA) levels and broad-spectrum disease resistance.

Novel sex-biased outcomes in neuroblastoma are associated with distinct gene expression and chromosomal loss patterns.

The paper identifies sex-biased outcomes in neuroblastoma, showing female patients with MYCN non-amplified high-risk disease have worse survival than males, linked to H19/DLK1 expression and chromosome 11q retention.

Aquaporins enriched in endothelial vacuole membrane regulate the diameters of microvasculature in hyperglycemia

This study identifies aquaporins in endothelial cells that regulate microvascular diameter in hyperglycemia, suggesting they are potential targets for diabetes-related vascular therapy.

Global variation in prior exposure shapes antibody neutralization profiles of SARS-CoV-2 variants up to BA.2.86

The paper analyzes antibody neutralization data from multiple countries to assess how prior exposure to SARS-CoV-2 variants affects neutralization profiles of BA.2.86 and its descendants.

Resting natural killer cells promote the progress of colon cancer liver metastasis by elevating tumor-derived sSCF

The paper identifies resting NK cells that promote colon cancer liver metastasis by enhancing tumor-derived sSCF through cell-to-cell interactions.

Unraveling the Role of Urea Hydrolysis in Salt Stress Response during Seed Germination and Seedling Growth in Arabidopsis thaliana

This study shows that salt stress increases urea hydrolysis in Arabidopsis thaliana, raising cytoplasmic pH and inhibiting seed germination and seedling growth, challenging the traditional view of ammonium toxicity as the main cause.

Intermittent energy restriction inhibits tumor growth and enhances paclitaxel response in a transgenic mouse model of endometrial cancer

This study shows that intermittent energy restriction (IER) reduces tumor growth and improves paclitaxel response in a mouse model of endometrial cancer compared to low-fat diet.

Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease

This study tracks microbiome changes across four body sites in 86 participants over six years, revealing site-specific stability, individualized dynamics, and altered patterns in insulin-resistant individuals.

Germline-targeting SOSIP trimer immunization elicits precursor CD4 binding-site targeting broadly neutralizing antibodies in infant macaques.

This study shows that a multi-dose immunization with germline-targeting SOSIP vaccines induces precursor broadly neutralizing antibodies in infant macaques, similar to adult responses.

Hybrid hydrogel-extracellular matrix scaffolds identify distinct ligand and mechanical signatures in cardiac aging

The paper develops tunable hybrid scaffolds to study how ligand presentation and mechanical stiffness in ECM influence cardiac fibroblast behavior during aging.

The linear and non-linear effects of CYP2C19 metaboliser status on DNA methylation: a methylome-wide association study

This study investigates how CYP2C19 metaboliser status affects DNA methylation across the genome, finding 48 CpG sites associated with both linear and non-linear effects, linked to drug metabolism and inflammation.

Mutational basis of serum cross-neutralization profiles elicited by infection or vaccination with SARS-CoV-2 variants

The paper models cross-neutralization profiles of SARS-CoV-2 sera against variants by analyzing mutations and shows that a third dose of mRNA-1273 improves neutralization breadth.

Comprehensive Assessment of the Intrinsic Pancreatic Microbiome

This study profiles the pancreatic microbiome in patients with benign, precancerous, and cancerous conditions, finding a low-biomass, low-diversity microbiome that does not differ across disease states.

DePARylation is critical for S phase progression and cell survival

This study shows that dePARylation by PARG is essential for S phase progression and cell survival, with PARG inhibition causing cytotoxicity through pADPr accumulation.

Tailoring Tfh Profiles Enhances Antibody Persistence to a Clade C HIV-1 Vaccine in Rhesus Macaques

This study shows that inducing GC Tfh1 cells with MPLA+QS-21 adjuvant leads to higher and longer-lasting HIV-1 Env antibodies in rhesus macaques compared to CAF01.

Lipid-anchored Proteasomes Control Membrane Protein Homeostasis

This study identifies N-myristoylation of Rpt2 as a mechanism for proteasome-membrane interaction, showing its role in membrane protein homeostasis and its impact on cellular processes and tumor growth.

Asparagine synthetase and G-protein coupled estrogen receptor are critical responders to nutrient supply in KRAS mutant colorectal cancer

This study investigates how nutrient supply affects ASNS and GPER1 expression in KRAS mutant and wild-type colorectal cancer cells and their association with patient survival.

Dynamics of the epigenetic landscape during development and in response to drought stress in sorghum

This study identifies novel epigenomic features in sorghum, including H3K27me3 islands and the role of histone marks in regulating tissue-specific and stress-responsive genes.

Discovery of decreased ferroptosis in male colorectal cancer patients with KRAS mutations

This study identifies suppressed ferroptosis in male colorectal cancer patients with KRAS mutations, linking it to poorer survival outcomes.

Development of a Robust Consensus Modeling Approach for Identifying Cellular and Media Metabolites Predictive of Mesenchymal Stromal Cell Potency

The paper develops a consensus machine learning approach to identify metabolites predictive of mesenchymal stromal cell immunomodulatory function across multiple lines.

An efficient context-aware approach for whole slide image classification

The paper introduces WIT, a context-aware transformer model for whole slide image classification, achieving higher accuracy than baseline methods across multiple cancer datasets.

Gating interactions steer loop conformational changes in the active site of the L1 metallo-β-lactamase

The paper investigates how gating interactions between loops in the L1 metallo-β-lactamase affect active site conformational changes and identifies key residues critical for enzyme activity.

A Subtle Balance between Host Selection and Microbial Size Effect Mediates Plant Microbiome Assembly in Mulberry

The paper investigates plant microbiome assembly in mulberry, finding that host selection and microbial size influence biogeographic patterns and community dynamics.

On the fitness effects and disease relevance of synonymous mutations

The paper evaluates the fitness effects of synonymous mutations in yeast, refuting claims that they are largely neutral and showing they are often deleterious.

Dynamics, signals and influencing factors of CD4 T cell activation revealed by single cell RNA-seq

The paper uses single-cell RNA-seq to analyze factors influencing CD4 T cell activation and identifies distinct functional states and differentiation patterns.

Chromatin Remodeling in Patient-Derived Colorectal Cancer Models

This study compares chromatin remodeling in colorectal cancer patient-derived models and identifies transcription factors driving differences in growth and drug response.

An engineered xCas12i with high activity, high specificity and broad PAM range

This paper identifies and engineers a high-fidelity Cas12i variant with broad PAM recognition and minimal off-target activity for improved genome editing.

Regulation of pDC Fate Determination by Histone Deacetylase 3

This study shows HDAC3 is essential for pDC development and hematopoietic progenitor homeostasis, with HDAC3 repressing cDC1-associated genes to promote pDC differentiation.