Improved prediction of swimming talent through random forest analysis of anthropometric and physiological phenotypes.

Unlabelled: The field of competitive swimming lacks broadly applicable predictive models for talent identification across various age groups of adolescent swimmers. This study aimed to construct a predictive model for athletic talent using machine learning methods based on anthropometric and physiological data. Baseline data were collected from 5444 participants aged 10-18 in Shanghai, China, between 2015 and 2018, with 4969 completing a 3-year follow-up.

Effects of physical exercise on cardio-respiratory health of young adults during short-term exposure to varying air pollution levels.

Background: Air pollution (AP) has become a substantial environmental issue affecting human cardiorespiratory health. Physical exercise (PE) is widely accepted to promote cardiorespiratory health. There is a paucity of research on the point at which the level of polluted environment engaged in PE could be used as a preventive approach to compensate for the damages of AP.

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.

Reprogramming of 3D genome structure underlying HSPC development in zebrafish.

Background: Development of hematopoietic stem and progenitor cells (HSPC) is a multi-staged complex process that conserved between zebrafish and mammals. Understanding the mechanism underlying HSPC development is a holy grail of hematopoietic biology, which is helpful for HSPC clinical application. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision; however, its dynamic and role in HSPC development is poorly investigated.

Exercise-Mediated Protection against Air Pollution-Induced Immune Damage: Mechanisms, Challenges, and Future Directions.

Air pollution, a serious risk factor for human health, can lead to immune damage and various diseases. Long-term exposure to air pollutants can trigger oxidative stress and inflammatory responses (the main sources of immune impairment) in the body. Exercise has been shown to modulate anti-inflammatory and antioxidant statuses, enhance immune cell activity, as well as protect against immune damage caused by air pollution.

Prediction Model for Tight Gas Wells with Time-Dependent Mechanism and Stress Sensitivity Effect.

In the production process of tight gas wells, reservoir fluid distribution and gas-water relative permeability vary with time. However, traditional models fail to handle the time-dependent mechanism and stress sensitivity effect in the reservoir, leading to significant errors in the dynamic analysis results. To address this issue, this article presents a prediction model for fractured well production in tight gas reservoirs.

Decomposition and humification process of domestic biodegradable waste by black soldier fly (Hermetia illucens L.) larvae from the perspective of dissolved organic matter.

Black soldier fly larvae (Hermitia illucens L.) (BSFL) bioconversion is a promising technology for domestic biodegradable waste (DBW) management and resource recovery. However, little is known about the DBW biodegradation during the BSFL bioconversion from the perspective of dissolved organic matter (DOM).

Exercise Promotes Bone Marrow Microenvironment by Inhibiting Adipsin in Diet-Induced Male Obese Mice.

Obesity is a growing global epidemic linked to many diseases, including diabetes, cardiovascular diseases, and musculoskeletal disorders. Exercise can improve bone density and decrease excess bone marrow adipose tissue (BMAT) in obese individuals. However, the mechanism of exercise regulating bone marrow microenvironment remains unclear.

Cell cycle arrest explains the observed bulk 3D genomic alterations in response to long-term heat shock in K562 cells.

Heat shock is a common environmental stress, although the response of the nucleus to it remains controversial in mammalian cells. Acute reaction and chronic adaptation to environmental stress may have distinct internal rewiring in the gene regulation networks. However, this difference remains largely unexplored.

A Pan-Cancer Analysis of Predictive Methylation Signatures of Response to Cancer Immunotherapy.

Recently, tumor immunotherapy based on immune checkpoint inhibitors (ICI) has been introduced and widely adopted for various tumor types. Nevertheless, tumor immunotherapy has a few drawbacks, including significant uncertainty of outcome, the possibility of severe immune-related adverse events for patients receiving such treatments, and the lack of effective biomarkers to determine the ICI treatments' responsiveness. DNA methylation profiles were recently identified as an indicator of the tumor immune microenvironment.

Association Between the Severity of Diabetic Retinopathy and Optical Coherence Tomography Angiography Metrics.

Diabetic retinopathy, the most serious ocular complication of diabetes, imposes a serious economic burden on society. Automatic and objective assessment of vessel changes can effectively manage diabetic retinopathy and prevent blindness. Optical coherence tomography angiography (OCTA) metrics have been confirmed to be used to assess vessel changes.

DeNOPA: decoding nucleosome positions sensitively with sparse ATAC-seq data.

As the basal bricks, the dynamics and arrangement of nucleosomes orchestrate the higher architecture of chromatin in a fundamental way, thereby affecting almost all nuclear biology processes. Thanks to its rather simple protocol, assay for transposase-accessible chromatin using sequencing (ATAC)-seq has been rapidly adopted as a major tool for chromatin-accessible profiling at both bulk and single-cell levels; however, to picture the arrangement of nucleosomes per se remains a challenge with ATAC-seq. In the present work, we introduce a novel ATAC-seq analysis toolkit, named decoding nucleosome organization profile based on ATAC-seq data (deNOPA), to predict nucleosome positions.

The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos.

Background: Pigs are important animals for agricultural and biomedical research, and improvement is needed for use of the assisted reproductive technologies. Determining underlying mechanisms of epigenetic reprogramming in the early stage of preimplantation embryos derived from in vitro fertilization (IVF), parthenogenesis, and androgenesis will not only contribute to assisted reproductive technologies of pigs but also will shed light into early human development. However, the reprogramming of three-dimensional architecture of chromatin in this process in pigs is poorly understood.

IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data.

Genome reannotation aims for complete and accurate characterization of gene models and thus is of critical significance for in-depth exploration of gene function. Although the availability of massive RNA-seq data provides great opportunities for gene model refinement, few efforts have been made to adopt these precious data in rice genome reannotation. Here we reannotate the rice (Oryza sativa L.

Decoding topologically associating domains with ultra-low resolution Hi-C data by graph structural entropy.

Submegabase-size topologically associating domains (TAD) have been observed in high-throughput chromatin interaction data (Hi-C). However, accurate detection of TADs depends on ultra-deep sequencing and sophisticated normalization procedures. Here we propose a fast and normalization-free method to decode the domains of chromosomes (deDoc) that utilizes structural information theory.

Characteristic arrangement of nucleosomes is predictive of chromatin interactions at kilobase resolution.

High-throughput chromosome conformation capture (3C) technologies, such as Hi-C, have made it possible to survey 3D genome structure. However, obtaining 3D profiles at kilobase resolution at low cost remains a major challenge. Therefore, we herein present an algorithm for precise identification of chromatin interaction sites at kilobase resolution from MNase-seq data, termed chromatin interaction site detector (CISD), and a CISD-based chromatin loop predictor (CISD_loop) that predicts chromatin-chromatin interactions (CCIs) from low-resolution Hi-C data.

An efficient and assumption-free method to approximate protein level distribution in the two-states gene expression model.

Stochastic fluctuations at each step of gene expression might influence protein levels distributions across cell populations. However, current methods to model protein distribution of intrinsic gene expression dynamics are either computationally inefficient or rely on ad hoc assumptions, e.g.