A review of deep learning models for the prediction of chromatin interactions with DNA and epigenomic profiles.

Advances in three-dimensional (3D) genomics have revealed the spatial characteristics of chromatin interactions in gene expression regulation, which is crucial for understanding molecular mechanisms in biological processes. High-throughput technologies like ChIA-PET, Hi-C, and their derivatives methods have greatly enhanced our knowledge of 3D chromatin architecture. However, the chromatin interaction mechanisms remain largely unexplored.

Enhancement of adult liver regeneration in mice through the hepsin-mediated epidermal growth factor receptor signaling pathway.

Given the widespread use of partial hepatectomy for treating various liver pathologies, understanding the mechanisms of liver regeneration is vital for enhancing liver resection and transplantation therapies. Here, we demonstrate the critical role of the serine protease Hepsin in promoting hepatocyte hypertrophy and proliferation. Under steady-state conditions, liver-specific overexpression of Hepsin in adult wild-type mice triggers hepatocyte hypertrophy and proliferation, significantly increasing liver size.

Tacrolimus regulates extracellular vesicle secretion from T cells via autophagy-lysosomal pathway.

Extracellular vesicles (EVs) derived from T cells have been proposed to mediate intercellular communication and orchestrate immune responses. The immunosuppressive drug, tacrolimus (TAC), suppresses T cell activity; however, the impact of TAC on T cell-derived EVs remains primarily unexplored. In this study, human primary T cells purified from healthy donors were used to investigate TAC-mediated regulation of EV secretion by T cells.

Genome-Wide Dissection of Selection on microRNA Target Genes Involved in Rice Flower Development.

Although genome-wide studies have identified a number of candidate regions evolving under selection in domesticated animals and cultivated plants, few attempts have been made, from the point of a definite biological process, to assess sequence variation and characterize the regimes of the selection on miRNA-associated motifs. Here, we performed a genome-wide dissection of nucleotide variation and selection of miRNA targets associated with rice flower development. By sampling and resequencing 26 miRNA targets for globally diverse representative populations of Asian cultivated rice and wild relatives, we found that purifying selection has reduced genetic variation at the conserved miRNA binding sites on the whole, and highly conserved miRNA binding sequences were maintained in the studied rice populations.

Sixteen-Frame Gated Myocardial Perfusion SPECT as a Surrogate for Equilibrium Radionuclide Angiography in Measurement of Systolic and Diastolic Indices: A Cross-Sectional Study.

 Equilibrium radionuclide angiography (ERNA) has long been assumed as the preferred method to assess cardiac volumes as well as left ventricular systolic and diastolic indices. ERNA was used to diagnose subtle changes in cardiac function during chemotherapy or early stages of heart failure. Gated myocardial perfusion SPECT (GMPS) was introduced as a more feasible and versatile alternative to ERNA, but the precision of GMPS to assess systolic and diastolic indices has not yet been fully reviewed.

Mechanosensing regulates pDC activation in the skin through NRF2 activation.

Plasmacytoid DCs (pDCs) infiltrate the skin, chronically produce type I interferon (IFN-I), and promote skin lesions and fibrosis in autoimmune patients. However, what controls their activation in the skin is unknown. Here, we report that increased stiffness inhibits the production of IFN-I by pDCs.

Altered X-chromosome inactivation of the TLR7/8 locus and heterogeneity of pDCs in systemic sclerosis.

Systemic sclerosis (SSc) is an autoimmune disease that has a strong female predominance. Both the X-linked TLR7 and TLR8 can induce type I IFN (IFN-I) by plasmacytoid DCs (pDCs), which can promote fibrosis. We identified five subclusters of pDCs, including ISGhigh clusters that were over-represented in SSc patients.

Complete chloroplast genome sequence of the medicinal plant (Rubiaceae) and phylogenetic analysis.

Lour. 1790, valued for ornamental and medicinal properties, has been extensively utilized in traditional medicinal in Vietnam. This study assembled and characterized the first chloroplast of consisted of 155,333 bp with a GC content of 37.

Investigation of pH-dependent H NMR urine metabolite profiles for diagnosis of obesity-related disordering.

Background: Human urine is highly favorable for H NMR metabolomics analyses of obesity-related diseases, such as non-alcoholic fatty liver, type 2 diabetes, and hyperlipidemia (HL), due to its non-invasiveness and ease of large-scale collection. However, the wide range of intrinsic urine pH (5.5-8.

Suppressed oncogenic molecules involved in the treatment of colorectal cancer by fecal microbiota transplantation.

Dysbiosis of the intestinal microbiota is prevalent among patients with colorectal cancer (CRC). This study aims to explore the anticancer roles of the fecal microbiota in inhibiting the progression of colorectal cancer and possible mechanisms. The intestinal microbial dysbiosis in CRC mice was significantly ameliorated by fecal microbiota transplantation (FMT), as indicated by the restored ACE index and Shannon index.

Allele frequency of genetic variations related to the gene-drug pair in a group of Iranian population.

Objectives: The efficacy and safety of drug treatments vary widely due to genetic variations. Pharmacogenomics investigates the impact of genetic variations on patient drug response. This research investigates the frequency of genetic variations in the Iranian population, comparing them with global data to provide insights into the pharmacogenomic approach in the Iranian population.

Recognition of GCK Homozygote missense (His424Tyr) variant in a female patient with neonatal hyperglycemia.

Introduction: Heterozygous mutations in the GCK gene result in mildly elevated glucose levels from birth, and the homozygous loss-of-function mutations leads to permanent neonatal diabetes. In the present study we aim to investigate the cause of diabetes in an adult female patient with unusual course of diabetes.

Case Presentation: We evaluate a female patient who previously encountered significant hyperglycemia during the infancy and subsequently experienced a relatively uneventful childhood.

Cellular signatures in human blood track bone mineral density in postmenopausal women.

Osteoclasts are the sole bone-resorbing cells and are formed by the fusion of osteoclast precursor cells (OCPs) derived from myeloid lineage cells. Animal studies reveal that circulating OCPs (cOCPs) in blood travel to bone and fuse with bone-resident osteoclasts. However, the characteristics of human cOCPs and their association with bone diseases remain elusive.

Identification of apelin/APJ signaling dysregulation in a human iPSC-derived granulosa cell model of Turner syndrome.

The interaction between germ cells and somatic cells in the ovaries plays a crucial role in establishing the follicle reserve in mammals. Turner syndrome (TS) predominantly affects females who have a partial or complete loss of one X chromosome. Our understanding of the role that granulosa cells (GCs) play in TS disease progression and pathogenesis remains limited.

Meta-analysis reveals an inverse relationship between Alzheimer's disease and cancer.

Recent reports have suggested an inverse relationship between Alzheimer's disease (AD) and cancer, although the underlying mechanism remains unclear. We performed an epidemiological meta-analysis to assess cancer likelihood in AD patients and vice versa and explored the role of APOE in tumor immunity across 33 The Cancer Genome Atlas (TCGA) cancer types. Our analysis revealed that people with AD are epidemiologically less likely to develop cancer than individuals without AD (RR: 0.