A method for miRNA diffusion association prediction using machine learning decoding of multi-level heterogeneous graph Transformer encoded representations.

MicroRNAs (miRNAs) are a key class of endogenous non-coding RNAs that play a pivotal role in regulating diseases. Accurately predicting the intricate relationships between miRNAs and diseases carries profound implications for disease diagnosis, treatment, and prevention. However, these prediction tasks are highly challenging due to the complexity of the underlying relationships.

Integrated Transcriptomic Landscape and Deep Learning Based Survival Prediction in Uterine Sarcomas.

Purpose: The genomic characteristics of uterine sarcomas have not been fully elucidated. This study aimed to explore the genomic landscape of the USs.

Materials And Methods: Comprehensive genomic analysis through RNA-sequencing was conducted.

BERT-5mC: an interpretable model for predicting 5-methylcytosine sites of DNA based on BERT.

DNA 5-methylcytosine (5mC) is widely present in multicellular eukaryotes, which plays important roles in various developmental and physiological processes and a wide range of human diseases. Thus, it is essential to accurately detect the 5mC sites. Although current sequencing technologies can map genome-wide 5mC sites, these experimental methods are both costly and time-consuming.

MSTL-Kace: Prediction of Prokaryotic Lysine Acetylation Sites Based on Multistage Transfer Learning Strategy.

As one of the most important post-translational modifications (PTM), lysine acetylation (Kace) plays an important role in various biological activities. Traditional experimental methods for identifying Kace sites are inefficient and expensive. Instead, several machine learning methods have been developed for Kace site prediction, and hand-crafted features have been used to encode the protein sequences.

Identification and Expression Analysis of and Families in Cotton.

Weeds seriously affect the yield and quality of crops. Because manual weeding is time-consuming and laborious, the use of herbicides becomes an effective way to solve the harm caused by weeds in fields. Both 5-enolpyruvyl shikimate-3-phosphate synthetase () and acetyltransferase genes (bialaphos resistance, ) are widely used to improve crop resistance to herbicides.

NeuroPpred-SVM: A New Model for Predicting Neuropeptides Based on Embeddings of BERT.

Neuropeptides play pivotal roles in different physiological processes and are related to different kinds of diseases. Identification of neuropeptides is of great benefit for studying the mechanism of these physiological processes and the treatment of neurological disorders. Several state-of-the-art neuropeptide predictors have been developed by using a two-layer stacking ensemble algorithm.

LBCE-XGB: A XGBoost Model for Predicting Linear B-Cell Epitopes Based on BERT Embeddings.

Accurately detecting linear B-cell epitopes (BCEs) makes great sense in vaccine design, immunodiagnostic test, antibody production, disease prevention and treatment. Wet-lab experiments for determining linear BCEs are both expensive and laborious, which are not able to meet the recognition needs of modern massive protein sequence data. Instead, computational methods can efficiently identify linear BCEs with low cost.

BERT-Kgly: A Bidirectional Encoder Representations From Transformers (BERT)-Based Model for Predicting Lysine Glycation Site for .

As one of the most important posttranslational modifications (PTMs), protein lysine glycation changes the characteristics of the proteins and leads to the dysfunction of the proteins, which may cause diseases. Accurately detecting the glycation sites is of great benefit for understanding the biological function and potential mechanism of glycation in the treatment of diseases. However, experimental methods are expensive and time-consuming for lysine glycation site identification.

m5Cpred-XS: A New Method for Predicting RNA m5C Sites Based on XGBoost and SHAP.

As one of the most important post-transcriptional modifications of RNA, 5-cytosine-methylation (m5C) is reported to closely relate to many chemical reactions and biological functions in cells. Recently, several computational methods have been proposed for identifying m5C sites. However, the accuracy and efficiency are still not satisfactory.

Identification and Characterization of the Biosynthetic Pathway of the Sulfonolipid Capnine.

Capnine (2-amino-3-hydroxy-15-methylhexadecane-1-sulfonate) and capnoids (-fatty acylated capnine derivatives) are sulfonolipids present in the outer membrane of gliding bacteria in the phylum Bacteroidetes and play a role in their unique gliding motility. They are structurally similar to sphingolipids and are thought to be biosynthesized via a similar pathway. Here we report the identification and biochemical characterization of the capnine biosynthetic enzymes cysteate synthase (CapA) and cysteate-C-fatty acyltransferase (CapB) from the pathogenic gliding bacterium and NAD(P)H-dependent dehydrocapnine reductase CapC from the avian pathogen .

An efficient and straightforward approach for accessing thionoesters palladium-catalyzed C-N cleavage of thioamides.

We report for the first time the coupling of activated thioamides with alcohols to efficiently form thionoesters a palladium-catalyzed C-N cleavage strategy. The new approach employs thioamides as a thioacylating reagent to give thionoesters in moderate to good yields. Notably, this methodology demonstrates a broad substrate scope, as alkyl/aryl alcohols are well tolerated, and this process might facilitate the synthesis of sulfur-containing compounds under simple and mild conditions.

Perceived Stress and Short-Form Video Application Addiction: A Moderated Mediation Model.

Nowadays, short-form video applications have become increasingly popular due to their strong appeal to people, especially among college students. With this trend, the phenomenon of short-form video application addiction (SVA) also become prominent, which is a great risk for individuals' health and adaptation. Against this background, the present study aimed to examine the association between perceived stress and SVA addiction, as well as its mechanism-the mediating role of self-compensation motivation (SCM) and the moderating role of shyness.

m5CPred-SVM: a novel method for predicting m5C sites of RNA.

Background: As one of the most common post-transcriptional modifications (PTCM) in RNA, 5-cytosine-methylation plays important roles in many biological functions such as RNA metabolism and cell fate decision. Through accurate identification of 5-methylcytosine (m5C) sites on RNA, researchers can better understand the exact role of 5-cytosine-methylation in these biological functions. In recent years, computational methods of predicting m5C sites have attracted lots of interests because of its efficiency and low-cost.

A transaldolase-dependent sulfoglycolysis pathway in Bacillus megaterium DSM 1804.

Sulfoquinovose (6-deoxy-6-sulfoglucose, SQ) is a component of sulfolipids found in the photosynthetic membranes of plants and other photosynthetic organisms, and is one of the most abundant organosulfur compounds in nature. Microbial degradation of SQ, termed sulfoglycolysis, constitutes an important component of the biogeochemical sulfur cycle. Two sulfoglycolysis pathways have been reported, with one resembling the Embden-Meyerhof-Parnas (sulfo-EMP) pathway, and the other resembling the Entner-Doudoroff (sulfo-ED) pathway.

A novel method for assessing arterial stiffness by a hydrostatic approach.

Arterial stiffness is an important index for cardiovascular events. The objective of this study is to examine possible parameters related to arterial stiffness that can be estimated during simple arm movements. An experiment was conducted on 32 subjects divided into two groups, one with an age of 26+/-4 years old, and the other 61+/-9.

A hydrostatic calibration method for the design of wearable PAT-based blood pressure monitoring devices.

Pulse arrival time (PAT) has been proposed for measuring blood pressure (BP) noninvasively and continuously. A challenge of the PAT-based BP measurement technique is to calibrate it individually. The objective of this study is to examine a previously proposed model-based calibration method utilizing hydrostatic pressure for BP estimation.

The changes in pulse transit time at specific cuff pressures during inflation and deflation.

The changes in pulse transit time (PTT) during the continuous slow deflation of brachial cuff were early reported; however, the PTTs obtained for specific cuff pressures during inflation or deflation have not been compared before. Therefore, the objective of this study is to examine the differences in PTT when cuff pressure (P(cuff)) was raised or deflated to the desired level. Sixteen subjects participated in this study and according to their systolic blood pressure (SBP) and diastolic blood pressure (DBF), 8 levels of P(cuff) were predetermined for them individually.