DGLinker: flexible knowledge-graph prediction of disease-gene associations.

As a result of the advent of high-throughput technologies, there has been rapid progress in our understanding of the genetics underlying biological processes. However, despite such advances, the genetic landscape of human diseases has only marginally been disclosed. Exploiting the present availability of large amounts of biological and phenotypic data, we can use our current understanding of disease genetics to train machine learning models to predict novel genetic factors associated with the disease. To this end, we developed DGLinker, a webserver for the prediction of novel candidate genes for human diseases given a set of known disease genes. DGLinker has a user-friendly interface that allows non-expert users to exploit biomedical information from a wide range of biological and phenotypic databases, and/or to upload their own data, to generate a knowledge-graph and use machine learning to predict new disease-associated genes. The webserver includes tools to explore and interpret the results and generates publication-ready figures. DGLinker is available at https://dglinker.rosalind.kcl.ac.uk. The webserver is free and open to all users without the need for registration.

Evaluation of the quality grade of Congou black tea by the fusion of GC-E-Nose, E-tongue, and E-eye.

In the present study, the comprehensive quality of Congou black tea (CBT) including aroma, taste, and liquid color was investigated by a combination of gas chromatography electronic nose (GC-E-Nose), electronic tongue (E-tongue), and electronic eye (E-eye). An excellent discrimination of different quality grades of CBT was accomplished through the fusion of GC-E-Nose, E-tongue, and E-eye combined with orthogonal partial least squares discriminant analysis, with parameters of R2Y = 0.803 and Q2 = 0.740. Moreover, the quantitative evaluation of CBT quality was successfully achieved by partial least squares regression analysis, with the absolute error within 1.39 point, and the relative error within 1.62%. Additionally, 12 key variables were screened out by stepwise multiple linear regression analysis, which significantly contributed to the comprehensive quality score of CBT. Our results suggest that the fusion of multiple intelligent sensory technologies offers great potential and practicability in the quality evaluation of black tea.

Brand first? The effect of hotel online word-of-mouth on consumer brand sensitivity.

With the e-commerce development and changing of hotels' booking channels, the online word-of-mouth, as a new signal of quality, is becoming to attract more attention of consumers. Using the scenario experiment, this study explores the effect of online word-of-mouth on brand sensitivity of consumers during the decision making for hotel booking. The results show that if the information about hotels obtained is limited in the decision-making process, consumers would have a higher sensitivity to the hotel brand. Increasing information about the online word-of-mouth can effectively reduce consumers' brand sensitivity to hotels. Besides, the moderating effect of the hotel grade on the relationship between the online word-of-mouth and brand sensitivity is affected by the scale of the negative differences of word-of-mouth.

DGL-LifeSci: An Open-Source Toolkit for Deep Learning on Graphs in Life Science.

Graph neural networks (GNNs) constitute a class of deep learning methods for graph data. They have wide applications in chemistry and biology, such as molecular property prediction, reaction prediction, and drug-target interaction prediction. Despite the interest, GNN-based modeling is challenging as it requires graph data preprocessing and modeling in addition to programming and deep learning. Here, we present Deep Graph Library (DGL)-LifeSci, an open-source package for deep learning on graphs in life science. Deep Graph Library (DGL)-LifeSci is a python toolkit based on RDKit, PyTorch, and Deep Graph Library (DGL). DGL-LifeSci allows GNN-based modeling on custom datasets for molecular property prediction, reaction prediction, and molecule generation. With its command-line interfaces, users can perform modeling without any background in programming and deep learning. We test the command-line interfaces using standard benchmarks MoleculeNet, USPTO, and ZINC. Compared with previous implementations, DGL-LifeSci achieves a speed up by up to 6×. For modeling flexibility, DGL-LifeSci provides well-optimized modules for various stages of the modeling pipeline. In addition, DGL-LifeSci provides pretrained models for reproducing the test experiment results and applying models without training. The code is distributed under an Apache-2.0 License and is freely accessible at https://github.com/awslabs/dgl-lifesci.

Pharmacophore modeling and 3D-QSAR study for the design of novel α-synuclein aggregation inhibitors.

Alpha-synuclein (α-syn), as a highly soluble presynaptic protein expressed in the brain, plays an important role in recycling synaptic vesicles and regulating the synthesis, storage, and release of neurotransmitters. Accumulation of α-syn in Lewy bodies and Lewy neurites is the pathological hallmark of Parkinson's disease (PD), so inhibition of α-syn aggregation may provide a novel approach for treating PD. In this study, the 3D structure of α-syn was downloaded from Protein Data Bank (PDB ID: 2N0A). A ligand-based pharmacophore model was conducted on a set of 43 diverse α-syn ligands, and the results suggested that two hydrogen-bond acceptors, one hydrophobic group, and two aromatic rings were significant to the inhibition of α-syn aggregation. A ligand-based 3D-QSAR model was also established with good statistical significance (R2 = 0.920) and excellent predictive ability (Q2 = 0.752). Novel indolinone derivatives were designed and synthesized based on the pharmacophore model. Subsequently, the 3D-QSAR model was used to predict the inhibitory activities towards α-syn aggregation, and the actual inhibitory activities were evaluated by thioflavin-T assay in vitro with the best inhibitory activity reaching 45.08%. The fitting results indicated that the built pharmacophore and 3D-QSAR models provided better reliability and accuracy for compound modification and prediction of the activity thereof. A ligand-based pharmacophore modeling and 3D-QSAR study have been performed on a set of 43 diverse ligands for α-synuclein for the first time. Based on the best pharmacophore modeling, novel indolinone derivatives were designed and synthesized, and the inhibitory activities for α-synuclein aggregation were evaluated by thioflavin-T assay in vitro, which preliminary indicated that five pharmacophore sites (two hydrogen bond acceptors (A), a hydrophobic group (H), and two aromatic rings (R)) in compounds contribute to the inhibitory activities. In the study, the built pharmacophore modeling and 3D-QSAR provided better reliability and accuracy for compound modification and prediction of the activity thereof.

In Silico Prediction of Metabolic Epoxidation for Drug-like Molecules via Machine Learning Methods.

Epoxidation is one of the reactions in drug metabolism. Since epoxide metabolites would bind with proteins or DNA covalently, drugs should avoid epoxidation metabolism in the body. Due to the instability of epoxide, it is difficult to determine epoxidation experimentally. In silico models based on big data and machine learning methods are hence valuable approaches to predict whether a compound would undergo epoxidation. In this study, we collected 884 epoxidation data manually from various sources, and finally got 829 unique sites of epoxidation. Three types of molecular fingerprints with different lengths (1024, 2048 or 4096 bits) were used to describe the reaction sites. Six machine learning methods were used to build the classification models. The training set and test set were randomly divided into 8 : 2, and 54 models were constructed and evaluated. Four best models were selected for feature selection. The features were then chosen and verified by external validation set. The resulted optimal model had the accuracy and AUC (area under the curve) values at 0.873 and 0.944 for the test set, 0.838 and 0.987 for the external validation set, respectively. The models built in this study could accurately predict whether a compound will undergo epoxidation and which part is most susceptible to epoxidation, which is of great significance for drug design.

Development of Novel N-hydroxypyridone Derivatives as Potential Anti-Ischemic Stroke Agents.

Our previous study had identified ciclopirox (CPX) as a promising lead compound for treatment of ischemic stroke. To find better neuroprotective agents, a series of N-hydroxypyridone derivatives based on CPX were designed, synthesized, and evaluated in this study. Among these derivatives, compound 11 exhibits significant neuroprotection against oxygen glucose deprivation and oxidative stress-induced injuries in neuronal cells. Moreover, compound 11 possesses good blood-brain barrier permeability and superior antioxidant capability. In addition, a complex of compound 11 with olamine-11·Ola possesses good water solubility, negligible hERG inhibition, and superior metabolic stability. The in vivo experiment demonstrates that 11·Ola significantly reduces brain infarction and alleviates neurological deficits in middle cerebral artery occlusion rats. Hence, compound 11·Ola is identified in our research as a prospective prototype in the innovation of stroke treatment.

Experimental study of blood pressure and its impact on spontaneous hypertension in rats with Xin Mai Jia.

AIM: The aim of this study was to evaluate the antihypertensive effect of Xin Mai Jia (XMJ) and to explore the mechanism of its hypotensive effect. METHODS: A total of 50 spontaneously hypertensive rats (SHR) were randomised into five groups. A total of 30 Wistar-Kyoto rats were randomised into three groups, comprising the control group. All of the rats were administered medicine through a gastrogavage once a day for 8 weeks. The tail-cuff method was applied to their monitor blood pressure. After 8 weeks of treatment, serum NO, SOD activity, MDA level, ET, ALD, AngII, RE, and CGRP in the serum were detected in all of the rats. Pathological changes in the aorta were observed via haematoxylin-eosin (HE) and immunohistochemical staining. Vasodilation function was assessed by measuring acetylcholine-induced vessel relaxation in the rats' organ chambers. The function of the mesenteric arteries was measured using DMT wire myography. Human aortic smooth muscle cells (HASMCs) and human umbilical vein endothelial cells (HUVECs) injury models were induced by hydrogen peroxide (H2O2). HASMCs and HUVECs were injured by H2O2 and then exposed to various drugs. HASMC and HUVEC migration was evaluated using the cell scratch test. The expression of the AT1 receptors (AT1R) in the HASMCs was detected via immunofluorescence (IFC) assay. RESULTS: After 8 weeks of treatment, XMJ reduced the systolic blood pressure of the SHR. XMJ significantly reduced the serum RE, AngII, ALD, and ET-1 levels and increased the content of CGRP and NO in the SHR, upregulated the SOD content, and downregulated MDA level of the SHR. XMJ improved pathological damage of the aorta to varying degrees, decreased the expression of AT1R in the SHR aortic vessels, and improved the mesenteric microvascular relaxation of the SHR. Cell experiments confirmed that XMJ inhibited the migration of the HUVECs and HASMCs induced by H2O2 and the expression of AT1R in the HASMCs. CONCLUSION: XMJ had satisfactory hypotensive action on the SHR in this study. Its mechanism may be associated with inhibiting RAAS activity and improving RAAS function, inhibiting hypertensive-induced vascular diastolic dysfunction, and improving vascular endothelial function.