A heterogeneous information network learning model with neighborhood-level structural representation for predicting lncRNA-miRNA interactions.

Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are closely related to the treatment of human diseases. Traditional biological experiments often require time-consuming and labor-intensive in their search for mechanisms of disease. Computational methods are regarded as an effective way to predict unknown lncRNA-miRNA interactions (LMIs).

Identification and characterization of related substances in DTX-AI via LC-QTOF-HRMS.

10-O-4-Ketonephenyl carbamate docetaxel (DTX-AI) is a synthetic taxane compound that exerts antitumor effects by inhibiting microtubule depolymerization and promoting microtubule dimer synthesis. Owing to the poor water solubility of DTX-AI, the liposomal formulation for injection was developed and prepared. In vitro experiments showed that DTX-AI and its liposomal formulation outperformed DTX in terms of antitumor efficacy at much lower concentrations, with correspondingly lower toxicity.

Consensus representation of multiple cell-cell graphs from gene signaling pathways for cell type annotation.

Background: Recent advancements in single-cell RNA sequencing have greatly expanded our knowledge of the heterogeneous nature of tissues. However, robust and accurate cell type annotation continues to be a major challenge, hindered by issues such as marker specificity, batch effects, and a lack of comprehensive spatial and interaction data. Traditional annotation methods often fail to adequately address the complexity of cellular interactions and gene regulatory networks.

Interpretable identification of cancer genes across biological networks via transformer-powered graph representation learning.

Graph representation learning has been leveraged to identify cancer genes from biological networks. However, its applicability is limited by insufficient interpretability and generalizability under integrative network analysis. Here we report the development of an interpretable and generalizable transformer-based model that accurately predicts cancer genes by leveraging graph representation learning and the integration of multi-omics data with the topologies of homogeneous and heterogeneous networks of biological interactions.

Capturing short-range and long-range dependencies of nucleotides for identifying RNA N6-methyladenosine modification sites.

N-methyladenosine (mA) plays a crucial role in enriching RNA functional and genetic information, and the identification of mA modification sites is therefore an important task to promote the understanding of RNA epigenetics. In the identification process, current studies are mainly concentrated on capturing the short-range dependencies between adjacent nucleotides in RNA sequences, while ignoring the impact of long-range dependencies between non-adjacent nucleotides for learning high-quality representation of RNA sequences. In this work, we propose an end-to-end prediction model, called mASLD, to improve the identification accuracy of mA modification sites by capturing the short-range and long-range dependencies of nucleotides.

Toward Multilabel Classification for Multiple Disease Prediction Using Gut Microbiota Profiles.

Advancements in high-throughput technologies have yielded large-scale human gut microbiota profiles, sparking considerable interest in exploring the relationship between the gut microbiome and complex human diseases. Through extracting and integrating knowledge from complex microbiome data, existing machine learning (ML)-based studies have demonstrated their effectiveness in the precise identification of high-risk individuals. However, these approaches struggle to address the heterogeneity and sparsity of microbial features and explore the intrinsic relatedness among human diseases.

scPriorGraph: constructing biosemantic cell-cell graphs with prior gene set selection for cell type identification from scRNA-seq data.

Cell type identification is an indispensable analytical step in single-cell data analyses. To address the high noise stemming from gene expression data, existing computational methods often overlook the biologically meaningful relationships between genes, opting to reduce all genes to a unified data space. We assume that such relationships can aid in characterizing cell type features and improving cell type recognition accuracy.

Knowledge Graph Neural Network With Spatial-Aware Capsule for Drug-Drug Interaction Prediction.

Uncovering novel drug-drug interactions (DDIs) plays a pivotal role in advancing drug development and improving clinical treatment. The outstanding effectiveness of graph neural networks (GNNs) has garnered significant interest in the field of DDI prediction. Consequently, there has been a notable surge in the development of network-based computational approaches for predicting DDIs.

Retrospective charts for reporting, analysing, and evaluating disaster emergency response: a systematic review.

Objective: Given the frequency of disasters worldwide, there is growing demand for efficient and effective emergency responses. One challenge is to design suitable retrospective charts to enable knowledge to be gained from disasters. This study provides comprehensive understanding of published retrospective chart review templates for designing and updating retrospective research.

Electrochemical Deconstructive and Ring-Expansion Functionalization of Unstrained Cycloalkanols.

An efficient and sustainable electrochemical method for the synthesis of cyclic ethers and acyclic aldehydes from alkanols has been reported. This strategy has been successfully applied to cycloalkanols bearing different ring sizes and different types of nucleophiles. In addition, mechanistic investigations show that the reactions undergo sequential processes, including anodic oxidation, β-scission, and nucleophilic addition.

Spectrometer-Less Remote Sensing Image Classification Based on Gate-Tunable van der Waals Heterostructures.

Remote sensing technology, which conventionally employs spectrometers to capture hyperspectral images, allowing for the classification and unmixing based on the reflectance spectrum, has been extensively applied in diverse fields, including environmental monitoring, land resource management, and agriculture. However, miniaturization of remote sensing systems remains a challenge due to the complicated and dispersive optical components of spectrometers. Here, m-phase GaTeSe with wide-spectral photoresponses (250-1064 nm) and stack it with WSe are utilizes to construct a two-dimensional van der Waals heterojunction (2D-vdWH), enabling the design of a gate-tunable wide-spectral photodetector.

LiViT-Net: A U-Net-like, lightweight Transformer network for retinal vessel segmentation.

The intricate task of precisely segmenting retinal vessels from images, which is critical for diagnosing various eye diseases, presents significant challenges for models due to factors such as scale variation, complex anatomical patterns, low contrast, and limitations in training data. Building on these challenges, we offer novel contributions spanning model architecture, loss function design, robustness, and real-time efficacy. To comprehensively address these challenges, a new U-Net-like, lightweight Transformer network for retinal vessel segmentation is presented.

Motif-Aware miRNA-Disease Association Prediction via Hierarchical Attention Network.

As post-transcriptional regulators of gene expression, micro-ribonucleic acids (miRNAs) are regarded as potential biomarkers for a variety of diseases. Hence, the prediction of miRNA-disease associations (MDAs) is of great significance for an in-depth understanding of disease pathogenesis and progression. Existing prediction models are mainly concentrated on incorporating different sources of biological information to perform the MDA prediction task while failing to consider the fully potential utility of MDA network information at the motif-level.

Dual-channel hypergraph convolutional network for predicting herb-disease associations.

Herbs applicability in disease treatment has been verified through experiences over thousands of years. The understanding of herb-disease associations (HDAs) is yet far from complete due to the complicated mechanism inherent in multi-target and multi-component (MTMC) botanical therapeutics. Most of the existing prediction models fail to incorporate the MTMC mechanism.

Discovering Consensus Regions for Interpretable Identification of RNA N6-Methyladenosine Modification Sites via Graph Contrastive Clustering.

As a pivotal post-transcriptional modification of RNA, N6-methyladenosine (m6A) has a substantial influence on gene expression modulation and cellular fate determination. Although a variety of computational models have been developed to accurately identify potential m6A modification sites, few of them are capable of interpreting the identification process with insights gained from consensus knowledge. To overcome this problem, we propose a deep learning model, namely M6A-DCR, by discovering consensus regions for interpretable identification of m6A modification sites.

Biocaiv: an integrative webserver for motif-based clustering analysis and interactive visualization of biological networks.

Background: As an important task in bioinformatics, clustering analysis plays a critical role in understanding the functional mechanisms of many complex biological systems, which can be modeled as biological networks. The purpose of clustering analysis in biological networks is to identify functional modules of interest, but there is a lack of online clustering tools that visualize biological networks and provide in-depth biological analysis for discovered clusters.

Results: Here we present BioCAIV, a novel webserver dedicated to maximize its accessibility and applicability on the clustering analysis of biological networks.

DeepCMI: a graph-based model for accurate prediction of circRNA-miRNA interactions with multiple information.

Recently, the role of competing endogenous RNAs in regulating gene expression through the interaction of microRNAs has been closely associated with the expression of circular RNAs (circRNAs) in various biological processes such as reproduction and apoptosis. While the number of confirmed circRNA-miRNA interactions (CMIs) continues to increase, the conventional in vitro approaches for discovery are expensive, labor intensive, and time consuming. Therefore, there is an urgent need for effective prediction of potential CMIs through appropriate data modeling and prediction based on known information.

iGRLDTI: an improved graph representation learning method for predicting drug-target interactions over heterogeneous biological information network.

Motivation: The task of predicting drug-target interactions (DTIs) plays a significant role in facilitating the development of novel drug discovery. Compared with laboratory-based approaches, computational methods proposed for DTI prediction are preferred due to their high-efficiency and low-cost advantages. Recently, much attention has been attracted to apply different graph neural network (GNN) models to discover underlying DTIs from heterogeneous biological information network (HBIN).

A novel cuproptosis-related diagnostic gene signature and differential expression validation in atherosclerosis.

Atherosclerosis (AS) is a major contributor to morbidity and mortality worldwide. However, the molecular mechanisms and mediator molecules involved remain largely unknown. Copper, which plays an essential role in cardiovascular disease, has been suggested as a potential risk factor.