High-quality gene/disease embedding in a multi-relational heterogeneous graph after a joint matrix/tensor decomposition.

Motivation: Node embedding of biological entity network has been widely investigated for the downstream application scenarios. To embed full semantics of gene and disease, a multi-relational heterogeneous graph is considered in a scenario where uni-relation between gene/disease and other heterogeneous entities are abundant while multi-relation between gene and disease is relatively sparse. After introducing this novel graph format, it is illuminative to design a specific data integration algorithm to fully capture the graph information and bring embeddings with high quality.

Optical Cell Tagging for Spatially Resolved Single-Cell RNA Sequencing.

Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for profiling gene expression of distinct cell populations at the single-cell level. However, the information of the positions of cells within the multicellular samples is missing in scRNA-seq datasets. To overcome this limitation, we herein develop OpTAG (optical cell tagging) as a new chemical platform for attaching functional tags onto cell surfaces in a spatially resolved manner.

SIGNET: single-cell RNA-seq-based gene regulatory network prediction using multiple-layer perceptron bagging.

High-throughput single-cell RNA-seq data have provided unprecedented opportunities for deciphering the regulatory interactions among genes. However, such interactions are complex and often nonlinear or nonmonotonic, which makes their inference using linear models challenging. We present SIGNET, a deep learning-based framework for capturing complex regulatory relationships between genes under the assumption that the expression levels of transcription factors participating in gene regulation are strong predictors of the expression of their target genes.

Molecular Detection and Genotyping of in Black Goats () in Yunnan Province, Southwestern China.

is a fungus-like protist that can parasitize in the intestines of humans and various animals causing a threat to public health. However, there has been no data for prevalence and genotypes in black goats in Yunnan Province, Southwestern China. In this study, 907 fecal samples were collected from black goats in 5 counties from Yunnan Province.

Mobile Detection and Alarming Systems for Hazardous Gases and Volatile Chemicals in Laboratories and Industrial Locations.

The leakage of hazardous gases and chemical vapors is considered one of the dangerous accidents that can occur in laboratories, workshops, warehouses, and industrial sites that use or store these substances. The early detection and alarming of hazardous gases and volatile chemicals are significant to keep the safety conditions for the people and life forms who are work in and live around these places. In this paper, we investigate the available mobile detection and alarming systems for toxic, hazardous gases and volatile chemicals, especially in the laboratory environment.

PET imaging of brain aromatase in humans and rhesus monkeys by C-labeled cetrozole analogs.

Aromatase is an estrogen synthetic enzyme that plays important roles in brain functions. To quantify aromatase expression in the brain by positron emission tomography (PET), we had previously developed [C]cetrozole, which showed high specificity and affinity. To develop more efficient PET tracer(s) for aromatase imaging, we synthesized three analogs of cetrozole.

The Data Use Ontology to streamline responsible access to human biomedical datasets.

Human biomedical datasets that are critical for research and clinical studies to benefit human health also often contain sensitive or potentially identifying information of individual participants. Thus, care must be taken when they are processed and made available to comply with ethical and regulatory frameworks and informed consent data conditions. To enable and streamline data access for these biomedical datasets, the Global Alliance for Genomics and Health (GA4GH) Data Use and Researcher Identities (DURI) work stream developed and approved the Data Use Ontology (DUO) standard.

Loss of RNA-Binding Protein HuR Leads to Defective Ependymal Cells and Hydrocephalus.

Multiciliated ependymal cells line the ventricle wall and generate CSF flow through ciliary beating. Defects in ependymal cells cause hydrocephalus; however, there are still significant gaps in our understanding the molecular, cellular and developmental mechanisms involved in the pathogenesis of hydrocephalus. Here, we demonstrate that specific deletion of RNA-binding protein (RBP) Hu antigen R (HuR) in the mouse brain results in hydrocephalus and causes postnatal death.

H, C and N resonance assignments and solution structures of the two RRM domains of Matrin-3.

Matrin-3 is a multifunctional protein that binds to both DNA and RNA. Its DNA-binding activity is linked to the formation of the nuclear matrix and transcriptional regulation, while its RNA-binding activity is linked to mRNA metabolism including splicing, transport, stabilization, and degradation. Correspondingly, Matrin-3 has two zinc finger domains for DNA binding and two consecutive RNA recognition motif (RRM) domains for RNA binding.

Water quality and climate variability of urban and tourism areas in Thailand and northern Vietnam: correlations and possible influences on nearby coastal shrimp farms.

This research explored the long-term relationships of climate parameters and coastal water quality nearby shrimp farms in two countries. In Thailand, two sampling points in canals located in Bangkok and Trang provinces were selected as the urban and tourism areas, respectively. In northern Vietnam, the canals located in Thai Binh and Quang Ninh provinces were used as the urban and tourism areas, respectively.

Majonoside-R2 Postconditioning Protects Cardiomyocytes Against Hypoxia/Reoxygenation Injury by Attenuating the Expression of HIF1 and Activating RISK Pathway.

Reoxygenation of hypoxic cardiac myocytes can paradoxically induce myocardial injury and affect the recovery processes. Pharmacological postconditioning is an efficient strategy used in clinical practice that protects cardiomyocytes from hypoxia/reoxygenation (HR) injury. Natural products or foods have been known to possess effective cardioprotective properties.

Case Report: Lenalidomide as a Second-Line Treatment for Bortezomib-Ineffective Nephrotic Syndrome Caused by LCDD: 2 Case Reports and a Literature Review.

Light-chain deposition disease (LCDD) is a rare systemic disorder characterized by the deposition of monoclonal light chains in organs. The kidney is a prominent target of light-chain deposition, with a median time to end-stage renal disease (ESRD) of 2.7 years and 5-year ESRD-free survival of 37%.

Loss of FBXO31-mediated degradation of DUSP6 dysregulates ERK and PI3K-AKT signaling and promotes prostate tumorigenesis.

FBXO31 is the substrate receptor of one of many CUL1-RING ubiquitin ligase (CRL1) complexes. Here, we show that low FBXO31 mRNA levels are associated with high pre-operative prostate-specific antigen (PSA) levels and Gleason grade in human prostate cancer. Mechanistically, the ubiquitin ligase CRL1 promotes the ubiquitylation-mediated degradation of DUSP6, a dual specificity phosphatase that dephosphorylates and inactivates the extracellular-signal-regulated kinase-1 and -2 (ERK1/2).

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Vitamins play an important role in many processes in the human organism. The detection of insufficient supply of vitamins is therefore of particular importance to avoid significant effects for human health. An increasing number of tests is only possible with suitable automated procedures.

C3 glomerulonephritis associated with monoclonal gammopathy: a retrospective case series study from a single institute in China.

Objective: To investigate the demographic and clinicopathological features and renal outcomes of Chinese patients with C3 glomerulonephritis in the setting of monoclonal gammopathy.

Methods: Patients with renal biopsy-proven C3 glomerulonephritis and detectable serum and/or urine monoclonal immunoglobulin from 2006 to 2018 in Peking University First Hospital were included, their clinical data, renal pathology type, treatment, and prognosis were collected and analyzed.

Results: Nineteen patients were enrolled, accounting for 24% of C3GN patients in the study period.

O-JMeSH: creating a bilingual English-Japanese controlled vocabulary of MeSH UIDs through machine translation and mutual information.

Previous approaches to create a controlled vocabulary for Japanese have resorted to existing bilingual dictionary and transformation rules to allow such mappings. However, given the possible new terms introduced due to coronavirus disease 2019 (COVID-19) and the emphasis on respiratory and infection-related terms, coverage might not be guaranteed. We propose creating a Japanese bilingual controlled vocabulary based on MeSH terms assigned to COVID-19 related publications in this work.

Constructing Japanese MeSH term dictionaries related to the COVID-19 literature.

The coronavirus disease 2019 (COVID-19) pandemic has led to a flood of research papers and the information has been updated with considerable frequency. For society to derive benefits from this research, it is necessary to promote sharing up-to-date knowledge from these papers. However, because most research papers are written in English, it is difficult for people who are not familiar with English medical terms to obtain knowledge from them.

Barnase encapsulation into submicron porous CaCO particles: studies of loading and enzyme activity.

The present study focuses on the immobilization of the bacterial ribonuclease barnase (Bn) into submicron porous calcium carbonate (CaCO) particles. For encapsulation, we apply adsorption, freezing-induced loading and co-precipitation methods and study the effects of adsorption time, enzyme concentration and anionic polyelectrolytes on the encapsulation efficiency of Bn. We show that the use of negatively charged dextran sulfate (DS) and ribonucleic acid from yeast (RNA) increases the loading capacity (LC) of the enzyme on CaCO particles by about 3-fold as compared to the particles with Bn itself.

Divergent degeneration of creA antitoxin genes from minimal CRISPRs and the convergent strategy of tRNA-sequestering CreT toxins.

Aside from providing adaptive immunity, type I CRISPR-Cas was recently unearthed to employ a noncanonical RNA guide (CreA) to transcriptionally repress an RNA toxin (CreT). Here, we report that, for most archaeal and bacterial CreTA modules, the creA gene actually carries two flanking 'CRISPR repeats', which are, however, highly divergent and degenerated. By deep sequencing, we show that the two repeats give rise to an 8-nt 5' handle and a 22-nt 3' handle, respectively, i.

The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background.

Background: The lymphatic and the blood vasculature are closely related systems that collaborate to ensure the organism's physiological function. Despite their common developmental origin, they present distinct functional fates in adulthood that rely on robust lineage-specific regulatory programs. The recent technological boost in sequencing approaches unveiled long noncoding RNAs (lncRNAs) as prominent regulatory players of various gene expression levels in a cell-type-specific manner.

Region-specific H3K9me3 gain in aged somatic tissues in Caenorhabditis elegans.

Epigenetic alterations occur as organisms age, and lead to chromatin deterioration, loss of transcriptional silencing and genomic instability. Dysregulation of the epigenome has been associated with increased susceptibility to age-related disorders. In this study, we aimed to characterize the age-dependent changes of the epigenome and, in turn, to understand epigenetic processes that drive aging phenotypes.

Isoleucine Enhances Plant Resistance Against via Jasmonate Signaling Pathway.

Amino acids are the building blocks of biomacromolecules in organisms, among which isoleucine (Ile) is the precursor of JA-Ile, an active molecule of phytohormone jasmonate (JA). JA is essential for diverse plant defense responses against biotic and abiotic stresses. is a necrotrophic nutritional fungal pathogen that causes the second most severe plant fungal disease worldwide and infects more than 200 kinds of monocot and dicot plant species.

Technical considerations in Hi-C scaffolding and evaluation of chromosome-scale genome assemblies.

The recent development of ecological studies has been fueled by the introduction of massive information based on chromosome-scale genome sequences, even for species for which genetic linkage is not accessible. This was enabled mainly by the application of Hi-C, a method for genome-wide chromosome conformation capture that was originally developed for investigating the long-range interaction of chromatins. Performing genomic scaffolding using Hi-C data is highly resource-demanding and employs elaborate laboratory steps for sample preparation.