Pearceconnolly9407

All in all, this review provided guidance for researchers engaged in pharmacometabonomics and metabolomics, and it would promote the wide application of metabolomics in drug research and personalized medicine.Accurate predictions of druggability and bioactivities of compounds are desirable to reduce the high cost and time of drug discovery. KRT-232 MDM2 inhibitor After more than five decades of continuing developments, quantitative structure-activity relationship (QSAR) methods have been established as indispensable tools that facilitate fast, reliable and affordable assessments of physicochemical and biological properties of compounds in drug-discovery programs. Currently, there are mainly two types of QSAR methods, descriptor-based methods and graph-based methods. The former is developed based on predefined molecular descriptors, whereas the latter is developed based on simple atomic and bond information. In this study, we presented a simple but highly efficient modeling method by combining molecular graphs and molecular descriptors as the input of a modified graph neural network, called hyperbolic relational graph convolution network plus (HRGCN+). The evaluation results show that HRGCN+ achieves state-of-the-art performance on 11 drug-discovery-related datasets. We also explored the impact of the addition of traditional molecular descriptors on the predictions of graph-based methods, and found that the addition of molecular descriptors can indeed boost the predictive power of graph-based methods. The results also highlight the strong anti-noise capability of our method. In addition, our method provides a way to interpret models at both the atom and descriptor levels, which can help medicinal chemists extract hidden information from complex datasets. We also offer an HRGCN+'s online prediction service at https//quantum.tencent.com/hrgcn/.Elucidating compensatory mechanisms underpinning phonemic fluency (PF) may help to minimize its decline due to normal aging or neurodegenerative diseases. We investigated cortical brain networks potentially underpinning compensation of age-related differences in PF. Using graph theory, we constructed networks from measures of thickness for PF, semantic, and executive-visuospatial cortical networks. A total of 267 cognitively healthy individuals were divided into younger age (YA, 38-58 years) and older age (OA, 59-79 years) groups with low performance (LP) and high performance (HP) in PF YA-LP, YA-HP, OA-LP, OA-HP. We found that the same pattern of reduced efficiency and increased transitivity was associated with both HP (compensation) and OA (aberrant network organization) in the PF and semantic cortical networks. When compared with the OA-LP group, the higher PF performance in the OA-HP group was associated with more segregated PF and semantic cortical networks, greater participation of frontal nodes, and stronger correlations within the PF cortical network. We conclude that more segregated cortical networks with strong involvement of frontal nodes seemed to allow older adults to maintain their high PF performance. Nodal analyses and measures of strength were helpful to disentangle compensation from the aberrant network organization associated with OA.The prediction of genes related to diseases is important to the study of the diseases due to high cost and time consumption of biological experiments. Network propagation is a popular strategy for disease-gene prediction. However, existing methods focus on the stable solution of dynamics while ignoring the useful information hidden in the dynamical process, and it is still a challenge to make use of multiple types of physical/functional relationships between proteins/genes to effectively predict disease-related genes. Therefore, we proposed a framework of network impulsive dynamics on multiplex biological network (NIDM) to predict disease-related genes, along with four variants of NIDM models and four kinds of impulsive dynamical signatures (IDSs). NIDM is to identify disease-related genes by mining the dynamical responses of nodes to impulsive signals being exerted at specific nodes. By a series of experimental evaluations in various types of biological networks, we confirmed the advantage of multiplex network and the important roles of functional associations in disease-gene prediction, demonstrated superior performance of NIDM compared with four types of network-based algorithms and then gave the effective recommendations of NIDM models and IDS signatures. To facilitate the prioritization and analysis of (candidate) genes associated to specific diseases, we developed a user-friendly web server, which provides three kinds of filtering patterns for genes, network visualization, enrichment analysis and a wealth of external links (http//bioinformatics.csu.edu.cn/DGP/NID.jsp). NIDM is a protocol for disease-gene prediction integrating different types of biological networks, which may become a very useful computational tool for the study of disease-related genes.In this letter, we explain how intuitive and explainable methods inspired from human physiology and computational biology can serve to simplify and ameliorate the way we process and generate knowledge resources.Acupuncture is an important part of Chinese medicine that has been widely used in the treatment of inflammatory diseases. During the coronavirus disease 2019 (COVID-19) epidemic, acupuncture has been used as a complementary treatment for COVID-19 in China. However, the underlying mechanism of acupuncture treatment of COVID-19 remains unclear. Based on bioinformatics/topology, this paper systematically revealed the multi-target mechanisms of acupuncture therapy for COVID-19 through text mining, bioinformatics, network topology, etc. Two active compounds produced after acupuncture and 180 protein targets were identified. A total of 522 Gene Ontology terms related to acupuncture for COVID-19 were identified, and 61 pathways were screened based on the Kyoto Encyclopedia of Genes and Genomes. Our findings suggested that acupuncture treatment of COVID-19 was associated with suppression of inflammatory stress, improving immunity and regulating nervous system function, including activation of neuroactive ligand-receptor interaction, calcium signaling pathway, cancer pathway, viral carcinogenesis, Staphylococcus aureus infection, etc.