MiRS-HF: A Novel Deep Learning Predictor for Cancer Classification and miRNA Expression Patterns.

Cancer classification and biomarker identification are crucial for guiding personalized treatment. To make effective use of miRNA associations and expression data, we have developed a deep learning model for cancer classification and biomarker identification. To make effective use of miRNA associations and expression data, we have developed a deep learning model for cancer classification and biomarker identification.

Fine-scale genomic analysis of the tree endophyte sp. FPYF3050 producing monoterpene 1,8-cineole.

1,8-Cineole has a potential in control crop pests and biofuels. The endophytic fungus, sp. FPYF3050 (), can produce over 90% 1,8-cineole of relative area in its natural volatiles, possessed nematicide properties.

Discovering type I cis-AT polyketides through computational mass spectrometry and genome mining with Seq2PKS.

Type 1 polyketides are a major class of natural products used as antiviral, antibiotic, antifungal, antiparasitic, immunosuppressive, and antitumor drugs. Analysis of public microbial genomes leads to the discovery of over sixty thousand type 1 polyketide gene clusters. However, the molecular products of only about a hundred of these clusters are characterized, leaving most metabolites unknown.

Biobank-wide association scan identifies risk factors for late-onset Alzheimer's disease and endophenotypes.

Rich data from large biobanks, coupled with increasingly accessible association statistics from genome-wide association studies (GWAS), provide great opportunities to dissect the complex relationships among human traits and diseases. We introduce BADGERS, a powerful method to perform polygenic score-based biobank-wide association scans. Compared to traditional approaches, BADGERS uses GWAS summary statistics as input and does not require multiple traits to be measured in the same cohort.

AdenPredictor: accurate prediction of the adenylation domain specificity of nonribosomal peptide biosynthetic gene clusters in microbial genomes.

Microbial natural products represent a major source of bioactive compounds for drug discovery. Among these molecules, nonribosomal peptides (NRPs) represent a diverse class that include antibiotics, immunosuppressants, anticancer agents, toxins, siderophores, pigments, and cytostatics. The discovery of novel NRPs remains a laborious process because many NRPs consist of nonstandard amino acids that are assembled by nonribosomal peptide synthetases (NRPSs).

The use of physical restraints and PRN medications in adolescent psychiatric inpatient units.

Problem: Although physical restraint practices and psychotropic/sedative pro re neta (PRN, as needed) medications have been commonly used for managing inpatient aggression, little is known about the characteristics of adolescents who receive them in psychiatric adolescent inpatient units. We aimed to determine the relationship between the use of physical restraints and psychotropic/sedative PRN medications, and to characterize individual attributes, substance use, clinical factors, and time of the first restraint episodes of the use of physical restraints and psychotropic/sedative PRN medications.

Methods: A retrospective case-control study approach was used with the data from electronic health records at a pediatric psychiatric hospital in the United States.

Identification of ophiostomatalean fungi associated with infesting in Northeastern China.

Ophiostomatalean fungi usually facilitate bark beetles to infest tree hosts and seriously endanger the health of coniferous forests. Spessivtsev is a common endemic bark beetle in Asia and primarily threatens . species have similar morphology; however, they can be differentiated by their genetic characteristics through phylogenetic analyses.

Integrating pharmacokinetics and network analysis to investigate the mechanism of Moutan Cortex in blood-heat and blood stasis syndrome.

Background: Raw Moutan Cortex (RMC) has been used in China and other Asian countries for thousands of years. Its medical application is the treatment of cooling blood and promoting blood circulation. However, its therapeutic mechanism is still undefined.

PeTGA1 enhances disease resistance against Colletotrichum gloeosporioides through directly regulating PeSARD1 in poplar.

Basic leucine zipper (bZIP) proteins play important roles in responding to biotic and abiotic stresses in plants. However, the molecular mechanisms of plant resistance to pathogens remain largely unclear in poplar. The present study isolated a TGACG-binding (TGA) transcription factor, PeTGA1, from Populus euphratica.

TransDiscovery: Discovering Biotransformation from Human Microbiota by Integrating Metagenomic and Metabolomic Data.

The human microbiome is a complex community of microorganisms, their enzymes, and the molecules they produce or modify. Recent studies show that imbalances in human microbial ecosystems can cause disease. Our microbiome affects our health through the products of biochemical reactions catalyzed by microbial enzymes (microbial biotransformations).

Development of a novel chemokine signaling-based multigene signature to predict prognosis and therapeutic response in colorectal cancer.

Colorectal cancer (CRC) is the most lethal gastrointestinal cancer in both males and females worldwide (Sung et al., 2021). Because of the high heterogeneity of tumors, robust prognostic biomarkers are urgently needed in CRC management (Koncina et al.

Clinicopathological factors affecting the prognosis of massive hemorrhage after radiotherapy for patients having nasopharyngeal carcinoma.

Aims: The aim of the study is to investigate the clinicopathological factors that determine prognosis of nasopharyngeal hemorrhage after radiotherapy in patients with nasopharyngeal carcinoma (NPC).

Patients And Methods: The clinicopathological data of 539 patients with NPC, who received radiotherapy, were analyzed retrospectively. Parameters included gender; age; T-stage; N-stage; pathological type; type of radiotherapy; synchronous chemotherapy; secondary-course radiotherapy; radiation-induced skull base osteonecrosis; diabetes, hypertension, or other systemic diseases; results of nasopharyngeal bacterial culture; and nasopharyngeal tumor recurrence.

Bacterial and fungal communities of traditional fermented Chinese soybean paste (Doujiang) and their properties.

Soybean paste (Doujiang) is one of the traditional fermented foods from China, fermented by various microorganisms. However, the microflora of Doujiang keeps little known. In this study, the microbial communities of seven kinds of representative Doujiang samples were investigated by both culture-independent and culture-dependent methods.

A Ferroptosis-Related Gene Signature Identified as a Novel Prognostic Biomarker for Colon Cancer.

Background: Colon cancer (CC) is a common gastrointestinal malignant tumor with high heterogeneity in clinical behavior and response to treatment, making individualized survival prediction challenging. Ferroptosis is a newly discovered iron-dependent cell death that plays a critical role in cancer biology. Therefore, identifying a prognostic biomarker with ferroptosis-related genes provides a new strategy to guide precise clinical decision-making in CC patients.

Chinese chestnut yellow crinkle disease influence microbiota composition of chestnut trees.

Context: Candidatus-phytoplasma castaneae has been found as the causal agent of the Chinese chestnut yellow crinkle disease. However, the ecological impact of the disease on microbiota of chestnut trees is unknown.

Aims: The study aim was to clarify difference attributes in microbial community structure of asymptomatic and symptomatic chestnut leaves and twigs for chestnut tree health in orchard.

Nine absorbed components pharmacokinetic of raw and processed Moutan Cortex in normal and blood-heat and hemorrhage syndrome model rats.

Raw Moutan Cortex (RMC) and Processed Moutan Cortex (PMC) have a long history of use in China and other Asian countries. In this study, a rapid and accurate ultra-high-pressure liquid chromatography coupled with diode array detector (UHPLC-DAD) method was developed and validated for the simultaneous determination of nine absorbed compounds of RMC/PMC. After extraction by protein precipitation with methanol from plasma, the analytes were separated on an Acquity UPLC® BEH Shield RP column (2.

Effects of GABA and Vigabatrin on the Germination of Chinese Chestnut Recalcitrant Seeds and Its Implications for Seed Dormancy and Storage.

Recalcitrant chestnut seeds are rich in γ-aminobutyric acid (GABA), which negatively regulates adventitious root development by altering carbon/nitrogen metabolism. However, little is known regarding the role of this metabolite in chestnut seeds. In this study, we investigated the effects of GABA changes on the germination of chestnut seeds treated with exogenous GABA and vigabatrin (VGB, which inhibits GABA degradation).

Distinctive Gene Expression Profiles and Effectors Consistent With Host Specificity in Two Formae Speciales of .

The knowledge on the host specificity of a pathogen underlying an interaction is becoming an urgent necessity for global warming. In this study, the gene expression profiles and the roles of effectors in host specificity were integrally characterized with two formae speciales, multigermtubi and monogermtubi, of a hemibiotrophic pathogen when they were infecting respective susceptible poplar hosts. With a functional genome comparison referring to a transcriptome of and Pathogen-Host Interaction database functional annotations, the multigermtubi strain showed abundant and significant differentially expressed unigenes (DEGs) (more than 40%) in colonizing the initial invasion stage and in the necrotrophic stage.

An Endophytic Produces Monoterpenes with Inhibitory Activity against Phytopathogenic Fungi.

Volatile organic compounds (VOCs) from endophytic fungi are becoming a potential antibiotic resource. The inhibitive effects of VOCs produced by an endophytic fungus in were investigated on plant pathogens in this study. Using standard morphological methods and multigene phylogeny, the fungus was identified as strain FPYF 3052.

Organs, Cultivars, Soil, and Fruit Properties Affect Structure of Endophytic Mycobiota of Pinggu Peach Trees.

Pinggu peach ( (L.)) has great economic and ecological value in north China. As a plant, the peach is naturally colonized by a variety of endophytic fungi, which are very important for tree growth and health.

Comparative Proteomic Analysis of Plant-Pathogen Interactions in Resistant and Susceptible Poplar Ecotypes Infected with .

Poplar are important forestry species in China, but the pathogen causes serious economic losses worldwide. To identify candidate resistance proteins and explore the molecular mechanisms involved in poplar-pathogen interactions, proteomic responses of stem samples from resistant and susceptible poplar ecotypes to were investigated using nanoflow liquid chromatography-tandem mass spectrometry with label-free quantitative analysis. We identified 588 proteins, divided into 21 biological process categories including 48 oxidoreductases, 72 hydrolytic enzymes, 80 metabolic enzymes, and 29 proteins of unknown function.

Epstein-Barr Virus Infection and Increased Sporadic Breast Carcinoma Risk: A Meta-Analysis.

Objective: An association of Epstein-Barr virus (EBV) infection with breast carcinoma (BC) risk has so far been disputed in the literature. Therefore, we performed a meta-analysis to clarify this relationship.

Materials And Methods: An electronic database search for eligible case-control studies was performed using PubMed, Embase, Web of Science, the Cochrane Library, CNKI, and Wanfang Data until May 17, 2018.

Taxonomy, virulence genes and antimicrobial resistance of Aeromonas isolated from extra-intestinal and intestinal infections.

Background: Clinical characteristics (taxonomy, virulence genes and antimicrobial resistance ) of Aeromonas in isolated from extra-intestinal and intestinal infections were investigated to describe epidemiology, associated virulence factors and optimal therapy options.

Methods: Clinical samples (n = 115) of Aeromonas were collected from a general hospital in Beijing between the period 2015 and 2017. Taxonomy was investigate by Multilocus phylogenetic analysis (MLPA), 10 putative virulence factors by use of polymerase chain reaction (PCR) and antimicrobial resistance to 15 antibiotics by use of the microbroth dilution method.

Incorporating Deep Features in the Analysis of Tissue Microarray Images.

Tissue microarray (TMA) images have been used increasingly often in cancer studies and the validation of biomarkers. TACOMA-a cutting-edge automatic scoring algorithm for TMA images-is comparable to pathologists in terms of accuracy and repeatability. Here we consider how this algorithm may be further improved.