CVD Atlas: a multi-omics database of cardiovascular disease.

Cardiovascular disease (CVD) is the leading cause of illness and death worldwide. Numerous studies have been conducted into the underlying mechanisms and molecular characteristics of CVD using various omics approaches. However, there is still a need for comprehensive resources on CVD.

Crosslinking intensity modulates the reliability and sensitivity of chromatin conformation detection at different structural levels.

Formaldehyde (FA) is a chemical that facilitates crosslinking between DNA and proteins. It is widely used in various biochemical assays, such as chromosome conformation capture (3C) and Chromatin Immunoprecipitation (ChIP). While the concentration and temperature of FA treatment are recognized as crucial factors in crosslinking, their quantitative effects have largely remained unexplored.

GEPREP: A comprehensive data atlas of RNA-seq-based gene expression profiles of exercise responses.

Background: Physical activity can regulate and affect gene expression in multiple tissues and cells. Recently, with the development of next-generation sequencing, a large number of RNA-sequencing (RNA-seq)-based gene expression profiles about physical activity have been shared in public resources; however, they are poorly curated and underutilized. To tackle this problem, we developed a data atlas of such data through comprehensive data collection, curation, and organization.

Immune responses and transcription landscape of adults with the third dose of homologous and heterologous booster vaccines of COVID-19.

Background: Heterologous booster vaccines are more effective than homologous booster vaccines in combating the coronavirus disease 2019 (COVID-19) outbreak. However, our understanding of homologous and heterologous booster vaccines for COVID-19 remains limited.

Methods: We recruited 34 healthy participants from two cohorts who were primed with two-dose inactivated COVID-19 vaccine before, vaccinated with COVID-19 inactivated vaccine and adenovirus-vectored vaccine (intramuscular and aerosol inhalation of Ad5-nCoV) as a third booster dose.

Identify Non-mutational p53 Functional Deficiency in Human Cancers.

An accurate assessment of p53's functional statuses is critical for cancer genomic medicine. However, there is a significant challenge in identifying tumors with non-mutational p53 inactivation which is not detectable through DNA sequencing. These undetected cases are often misclassified as p53-normal, leading to inaccurate prognosis and downstream association analyses.

HaploSweep: Detecting and Distinguishing Recent Soft and Hard Selective Sweeps through Haplotype Structure.

Identifying soft selective sweeps using genomic data is a challenging yet crucial task in population genetics. In this study, we present HaploSweep, a novel method for detecting and categorizing soft and hard selective sweeps based on haplotype structure. Through simulations spanning a broad range of selection intensities, softness levels, and demographic histories, we demonstrate that HaploSweep outperforms iHS, nSL, and H12 in detecting soft sweeps.

Magnetic resonance imaging-based radiomics model for preoperative assessment of risk stratification in endometrial cancer.

Background: Preoperative risk stratification is significant for the management of endometrial cancer (EC) patients. Radiomics based on magnetic resonance imaging (MRI) in combination with clinical features may be useful to predict the risk grade of EC.

Aim: To construct machine learning models to predict preoperative risk stratification of patients with EC based on radiomics features extracted from MRI.

CRISPR screening uncovers nucleolar RPL22 as a heterochromatin destabilizer and senescence driver.

Dysfunction of the ribosome manifests during cellular senescence and contributes to tissue aging, functional decline, and development of aging-related disorders in ways that have remained enigmatic. Here, we conducted a comprehensive CRISPR-based loss-of-function (LOF) screen of ribosome-associated genes (RAGs) in human mesenchymal progenitor cells (hMPCs). Through this approach, we identified ribosomal protein L22 (RPL22) as the foremost RAG whose deficiency mitigates the effects of cellular senescence.

Comprehensive assessment of long-read sequencing platforms and calling algorithms for detection of copy number variation.

Copy number variations (CNVs) play pivotal roles in disease susceptibility and have been intensively investigated in human disease studies. Long-read sequencing technologies offer opportunities for comprehensive structural variation (SV) detection, and numerous methodologies have been developed recently. Consequently, there is a pressing need to assess these methods and aid researchers in selecting appropriate techniques for CNV detection using long-read sequencing.

Radiomic prediction for durable response to high-dose methotrexate-based chemotherapy in primary central nervous system lymphoma.

Background: The rarity of primary central nervous system lymphoma (PCNSL) and treatment heterogeneity contributes to a lack of prognostic models for evaluating posttreatment remission. This study aimed to develop and validate radiomic-based models to predict the durable response (DR) to high-dose methotrexate (HD-MTX)-based chemotherapy in PCNSL patients.

Methods: A total of 159 patients pathologically diagnosed with PCNSL between 2011 and 2021 across two institutions were enrolled.

Periodontitis prevalence and acceleration of biological aging: Insights from NHANES 2009-2014 and Mendelian randomization study.

Aim: This study aimed to investigate the association of periodontitis with biological aging and to assess potential causality using Mendelian randomization (MR).

Methods: A cross-sectional study with 9558 participants from the National Health and Nutrition Examination Survey (2009-2014) was conducted. Age acceleration (BioAgeAccel and PhenoAgeAccel) was calculated from clinical biomarkers and their discrepancies with chronological age.

The function of juvenile-adult transition axis in female sexual receptivity of .

Female sexual receptivity is essential for reproduction of a species. Neuropeptides play the main role in regulating female receptivity. However, whether neuropeptides regulate female sexual receptivity during the neurodevelopment is unknown.

Substrate specificity of a branch of aromatic dioxygenases determined by three distinct motifs.

The inversion of substrate size specificity is an evolutionary roadblock for proteins. The Duf4243 dioxygenases GedK and BTG13 are known to catalyze the aromatic cleavage of bulky tricyclic hydroquinone. In this study, we discover a Duf4243 dioxygenase PaD that favors small monocyclic hydroquinones from the penicillic-acid biosynthetic pathway.