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View article: GPTAnno: Ontology-tree-guided hierarchical cell type annotation based on GPT models for single-cell data
GPTAnno: Ontology-tree-guided hierarchical cell type annotation based on GPT models for single-cell data Open
Cell type annotation is critical for interpreting single-cell transcriptomic data but remains challenging due to uncertain cellular clustering granularity and inconsistent labeling across studies. Here we present GPTAnno, an automated, ont…
View article: Causal effect analysis of serving performance using double machine learning
Causal effect analysis of serving performance using double machine learning Open
Serving performance is widely recognized as a critical factor influencing match outcomes in professional tennis. To evaluate its contribution to winning probability, this study analyzes ATP men’s singles matches (2013–2024) and estimates t…
View article: Oral microbial profile polymorphisms predict early Siewert II adenocarcinoma of esophagogastric junction
Oral microbial profile polymorphisms predict early Siewert II adenocarcinoma of esophagogastric junction Open
View article: Acute pancreatitis as the presenting manifestation of MYC/BCL6 double-hit diffuse large B-Cell lymphoma with metastasis: A case report
Acute pancreatitis as the presenting manifestation of MYC/BCL6 double-hit diffuse large B-Cell lymphoma with metastasis: A case report Open
View article: Clinical analysis of cerebral edema after aneurysm clipping in patients with aneurysmal subarachnoid hemorrhage
Clinical analysis of cerebral edema after aneurysm clipping in patients with aneurysmal subarachnoid hemorrhage Open
Background To explore the clinical analysis of cerebral edema in aneurysmal subarachnoid hemorrhage (aSAH) patients after aneurysm clipping. Methods The clinical data of 232 aSAH patients treated with aneurysm clipping in our hospital from…
View article: Disruption of the Clock Component BMAL1 in HDM-induced Asthma Causes GC Resistance in Airway Epithelial Cells by Regulating GR Phosphorylation through the DUSP4-p38MAPK Pathway
Disruption of the Clock Component BMAL1 in HDM-induced Asthma Causes GC Resistance in Airway Epithelial Cells by Regulating GR Phosphorylation through the DUSP4-p38MAPK Pathway Open
Circadian rhythm disruption has been increasingly implicated in asthma and glucocorticoid (GC) resistance. In this study, we discovered that disruption of the brain and muscle ARNT-like 1 (BMAL1), a significant activator of the circadian c…
View article: An Interpretable Deep Learning Framework for Biomarker Discovery in Complex Disease Survival Outcomes
An Interpretable Deep Learning Framework for Biomarker Discovery in Complex Disease Survival Outcomes Open
Identification of important biomarkers associated with complex disease survival outcomes is fundamental for gaining an in-depth understanding of disease mechanisms and advancing precision medicine in conditions such as cancer and cardiovas…
View article: Integration of Preclinical and Clinical Vaccine Safety and Immunogenicity Testing for Development of a Pediatric HIV Vaccine to Achieve Protective HIV Immunity Prior to Adolescence
Integration of Preclinical and Clinical Vaccine Safety and Immunogenicity Testing for Development of a Pediatric HIV Vaccine to Achieve Protective HIV Immunity Prior to Adolescence Open
An optimal HIV vaccine should provide protective immunity before sexual debut to prevent infection in adolescents and young adults, including acute infections in women of childbearing age. Such a vaccine will likely require multiple sequen…
View article: Effect of a pay-it-forward strategy on reducing HPV vaccine delay and increasing uptake among 15- to 18-year-old girls in China: A randomized controlled trial.
Effect of a pay-it-forward strategy on reducing HPV vaccine delay and increasing uptake among 15- to 18-year-old girls in China: A randomized controlled trial. Open
BACKGROUND: Catch-up human papillomavirus (HPV) vaccination is challenging in many low- and middle-income countries (LMICs). Pay-it-forward offers an individual a subsidized vaccine, then an opportunity to donate to help others access vacc…
View article: BCG Vaccination Potentially Modulates the Transcriptome of Infant CD4 T Cells in Addition to Age-Dependent Immune Ontogeny-Associated Changes
BCG Vaccination Potentially Modulates the Transcriptome of Infant CD4 T Cells in Addition to Age-Dependent Immune Ontogeny-Associated Changes Open
Background: The Bacille Calmette–Guérin (BCG) vaccine is part of the Extended Programme on Immunization (EPI) and as such is generally administered at birth. The global introduction of BCG not only protected many vaccinated infants against…
View article: 3Mont: A multi-omics integrative tool for breast cancer subtype stratification
3Mont: A multi-omics integrative tool for breast cancer subtype stratification Open
Breast Cancer (BRCA) is a heterogeneous disease, and it is one of the most prevalent cancer types among women. Developing effective treatment strategies that address diverse types of BRCA is crucial. Notably, among different BRCA molecular…
View article: Effect of a pay-it-forward strategy on reducing HPV vaccine delay and increasing uptake among 15- to 18-year-old girls in China: A randomized controlled trial
Effect of a pay-it-forward strategy on reducing HPV vaccine delay and increasing uptake among 15- to 18-year-old girls in China: A randomized controlled trial Open
Background Catch-up human papillomavirus (HPV) vaccination is challenging in many low- and middle-income countries (LMICs). Pay-it-forward offers an individual a subsidized vaccine, then an opportunity to donate to help others access vacci…
View article: Inadvertent Transfer of Murine VL30 Retrotransposons to CAR-T Cells
Inadvertent Transfer of Murine VL30 Retrotransposons to CAR-T Cells Open
For more than a decade, genetically engineered autologous T-cells have been successfully employed as immunotherapy drugs for patients with incurable blood cancers. The active components in some of these game-changing medicines are autologo…
View article: Pay-it-forward gonorrhoea and chlamydia testing among men who have sex with men in China: a randomised controlled trial
Pay-it-forward gonorrhoea and chlamydia testing among men who have sex with men in China: a randomised controlled trial Open
View article: BCG Vaccination Potentially Modulates the Transcriptome of Infant CD4 T Cells in Addition to Age-Dependent Immune Ontogeny-Associated Changes
BCG Vaccination Potentially Modulates the Transcriptome of Infant CD4 T Cells in Addition to Age-Dependent Immune Ontogeny-Associated Changes Open
Background: The Bacille Calmette–Guérin (BCG) vaccine is part of the Extended Programme on Immunization (EPI) and as such is generally administered at birth. The global introduction of BCG not only protected many vaccinated infants against…
View article: 3Mont: A multi-omics integrative tool for breast cancer subtype stratification
3Mont: A multi-omics integrative tool for breast cancer subtype stratification Open
Breast Cancer (BRCA) is a heterogeneous disease, and it is one of the most prevalent cancer types among women. Developing effective treatment strategies that address diverse types of BRCA is crucial. Notably, among different BRCA molecular…
View article: <i>MITScan</i> : Score-Based Genome-Wide Association Analysis of the Microbiome and Host Transcriptome
<i>MITScan</i> : Score-Based Genome-Wide Association Analysis of the Microbiome and Host Transcriptome Open
Microbiome research explores how microbial communities interact with the human body to influence health and well-being, offering insights for advancing personalized medicine and targeted treatments. Microbiome profiles can be measured, for…
View article: A deep learning semiparametric regression for adjusting complex confounding structures
A deep learning semiparametric regression for adjusting complex confounding structures Open
Deep Treatment Learning (deepTL), a robust yet efficient deep learning-based semiparametric regression approach, is proposed to adjust the complex confounding structures in comparative effectiveness analysis of observational data, e.g. ele…
View article: Research Progress on Performance Regulation and Application of Ti-Ni-Based, Fe-Based, and Cu-Based Shape Memory Alloys
Research Progress on Performance Regulation and Application of Ti-Ni-Based, Fe-Based, and Cu-Based Shape Memory Alloys Open
This paper reviews the system characteristics and application progress of shape memory alloys (SMAs). SMAs realize the shape memory effect (SME) and super-elasticity (SE) through solid-solid phase transformations (such as B2↔B19'), and the…
View article: Construction of a diagnostic model for early-stage postoperative complications after liver transplantation and molecular mechanism research
Construction of a diagnostic model for early-stage postoperative complications after liver transplantation and molecular mechanism research Open
Objectives This study aimed to identify risk factors, elucidate molecular mechanisms, and establish a prediction model for early complications following liver transplantation (LT). Methods This study analysed 99 patients who underwent thei…
View article: A deep neural network two-part model and feature importance test for semicontinuous data
A deep neural network two-part model and feature importance test for semicontinuous data Open
Semi-continuous data frequently arise in clinical practice. For example, while many surgical patients still suffer from varying degrees of acute postoperative pain (POP) sometime after surgery (i.e., POP score > 0), others experience none …
View article: On kernel machine learning for propensity score estimation under complex confounding structures
On kernel machine learning for propensity score estimation under complex confounding structures Open
Post marketing data offer rich information and cost-effective resources for physicians and policy-makers to address some critical scientific questions in clinical practice. However, the complex confounding structures (e.g., nonlinear and n…
View article: Permutation-based identification of important biomarkers for complex diseases via machine learning models
Permutation-based identification of important biomarkers for complex diseases via machine learning models Open
View article: Unbiased genetics identifies a glutamatergic signaling network as a mediator of daily sleep patterns
Unbiased genetics identifies a glutamatergic signaling network as a mediator of daily sleep patterns Open
Sleep is a fundamental, conserved behavior important for survival. In many species, sleep behavior is controlled by poorly understood interactions between a system of circadian rhythms (CR), which promote sleep at ecologically appropriate …
View article: High-dimensional Biomarker Identification for Interpretable Disease Prediction via Machine Learning Models
High-dimensional Biomarker Identification for Interpretable Disease Prediction via Machine Learning Models Open
MOTIVATION: Omics features, often measured by high-throughput technologies, combined with clinical features, significantly impact the understanding of many complex human diseases. Integrating key omics biomarkers with clinical risk factors…
View article: High-dimensional biomarker identification for interpretable disease prediction via machine learning models
High-dimensional biomarker identification for interpretable disease prediction via machine learning models Open
Motivation Omics features, often measured by high-throughput technologies, combined with clinical features, significantly impact the understanding of many complex human diseases. Integrating key omics biomarkers with clinical risk factors …
View article: PETScan: Score-Based Genome-Wide Association Analysis of RNA-Seq and ATAC-Seq Data
PETScan: Score-Based Genome-Wide Association Analysis of RNA-Seq and ATAC-Seq Data Open
High-dimensional sequencing data, such as RNA-Seq for gene expression and ATAC-Seq for chromatin accessibility, are widely used in studying systems biology. Accessible chromatin allows transcription factors and regulatory elements to bind …
View article: Author Correction: Pay-it-forward incentives for hepatitis virus testing in men who have sex with men: a cluster randomized trial
Author Correction: Pay-it-forward incentives for hepatitis virus testing in men who have sex with men: a cluster randomized trial Open
View article: Author Correction: Pay-it-forward incentives for hepatitis virus testing in men who have sex with men: a cluster randomized trial
Author Correction: Pay-it-forward incentives for hepatitis virus testing in men who have sex with men: a cluster randomized trial Open
View article: CT-based radiomics deep learning signatures for non-invasive prediction of metastatic potential in pheochromocytoma and paraganglioma: a multicohort study
CT-based radiomics deep learning signatures for non-invasive prediction of metastatic potential in pheochromocytoma and paraganglioma: a multicohort study Open