The relationship between traditional village landscape genes and the geographical environment is closely intertwined, exhibiting notable spatial differences and cultural characteristics during scale transformations. To effectively elucidate the formation mechanisms of these landscape genes, it is essential to construct a multi-scale analytical framework that integrates multiple dimensions. This paper address these challenges by expanding the sample selection range and combining both qualitative and quantitative analyses of landscape genes across various scales.
View Article and Find Full Text PDFThe emergence and spread of pose a severe threat to public health, highlighting the urgent need for the next generation of therapeutics due to its increasing resistance to existing antibiotics. BfmR, a response regulator modulating virulence and antimicrobial resistance, shows a promising potential as a novel antimicrobial target. Developing BfmR inhibitors may propel a new therapeutic direction for intractable infection of resistant strains.
View Article and Find Full Text PDFTreatments of inflammatory bowel disease (IBD) are diverse, but their efficacy is limited, and it is therefore urgent to find better therapies. Controlling mucosal inflammation is a must in IBD drug treatment. The occurrence of anti-tumor necrosis factor α (TNF-α) monoclonal antibodies has provided a safer and more efficacious therapy.
View Article and Find Full Text PDFContemporary structure-based molecular generative methods have demonstrated their potential to model the geometric and energetic complementarity between ligands and receptors, thereby facilitating the design of molecules with favorable binding affinity and target specificity. Despite the introduction of deep generative models for molecular generation, the atom-wise generation paradigm that partially contradicts chemical intuition limits the validity and synthetic accessibility of the generated molecules. Additionally, the dependence of deep learning models on large-scale structural data has hindered their adaptability across different targets.
View Article and Find Full Text PDFInt J Environ Res Public Health
August 2022
Self-rated health status (SRHS) reflects individuals' social environment, and the difference between urban and rural areas in China further highlights the impact of social environment on health. This paper aimed to systematically analyze and compare the impact mechanism of the SRHS of urban and rural residents from multiple dimensions, i.e.
View Article and Find Full Text PDFComput Math Methods Med
August 2022
Colorectal cancer has a high incidence rate in all countries around the world, and the survival rate of patients is improved by early detection. With the development of object detection technology based on deep learning, computer-aided diagnosis of colonoscopy medical images becomes a reality, which can effectively reduce the occurrence of missed diagnosis and misdiagnosis. In medical image recognition, the assumption that training samples follow independent identical distribution (IID) is the key to the high accuracy of deep learning.
View Article and Find Full Text PDFThe past few years have witnessed enormous progress toward applying machine learning approaches to the development of protein-ligand scoring functions. However, the robust performance and wide applicability of scoring functions remain a big challenge for increasing the success rate of docking-based virtual screening. Herein, a novel scoring function named RTMScore was developed by introducing a tailored residue-based graph representation strategy and several graph transformer layers for the learning of protein and ligand representations, followed by a mixture density network to obtain residue-atom distance likelihood potential.
View Article and Find Full Text PDFDNA methyltransferase 3A (DNMT3A) has been regarded as a potential epigenetic target for the development of cancer therapeutics. A number of DNMT3A inhibitors have been reported, but most of them do not have good potency, high selectivity and/or low cytotoxicity. It has been suggested that a non-conserved region around the target recognition domain (TRD) loop is implicated in the DNMT3A activity under the allosteric regulation of the ATRX-DNMT3-DNMT3L (ADD) domain, but the molecular mechanism of the regulation of the TRD loop on the DNMT3A activity needs to be elucidated.
View Article and Find Full Text PDFAccurate estimation of the synthetic accessibility of small molecules is needed in many phases of drug discovery. Several expert-crafted scoring methods and descriptor-based quantitative structure-activity relationship (QSAR) models have been developed for synthetic accessibility assessment, but their practical applications in drug discovery are still quite limited because of relatively low prediction accuracy and poor model interpretability. In this study, we proposed a data-driven interpretable prediction framework called GASA (Graph Attention-based assessment of Synthetic Accessibility) to evaluate the synthetic accessibility of small molecules by distinguishing compounds to be easy- (ES) or hard-to-synthesize (HS).
View Article and Find Full Text PDFComput Math Methods Med
February 2022
As an effective tool for colorectal lesion detection, it is still difficult to avoid the phenomenon of missed and false detection when using white-light endoscopy. In order to improve the lesion detection rate of colorectal cancer patients, this paper proposes a real-time lesion diagnosis model (YOLOv5x-CG) based on YOLOv5 improvement. In this diagnostic model, colorectal lesions were subdivided into three categories: micropolyps, adenomas, and cancer.
View Article and Find Full Text PDFA spiro -clerodane homodimer with a rare 6/6/6/6/6-fused pentacyclic scaffold, spiroarborin (), together with four new monomeric analogues (-), were isolated from . Their structures were elucidated by comprehensive spectroscopic data analysis, quantum-chemical calculations, and X-ray diffraction. A plausible biosynthetic pathway of was proposed, and a biomimetic synthesis of its derivative was accomplished.
View Article and Find Full Text PDFThe Lower Cambrian black shales of the Sansui vanadium deposits, located in South China, host a thin accumulation of Ni, Mo, V, and platinum group of elements (PGE). However, among them, the origin of V-bearing deposits remains controversial. To characterize the enrichment process of V-bearing deposits, samples of the mineralized layer and surrounding rocks from the Sansui area, South China, were investigated through bulk geochemical analysis and scanning electron microscopy (SEM) and energy dispersive spectrometry (EDS) analyses.
View Article and Find Full Text PDFCellular inflammation is the underlying cause of several diseases and development of a safe and effective anti-inflammatory drug is need-of-the hour for treatment of diseases like lung inflammation. Callicarpa integerrima Champ. is a well-known herbal medicine with hemostatic and anti-inflammatory functions.
View Article and Find Full Text PDFNucleic Acids Res
January 2021
Inhibitors that form covalent bonds with their targets have traditionally been considered highly adventurous due to their potential off-target effects and toxicity concerns. However, with the clinical validation and approval of many covalent inhibitors during the past decade, design and discovery of novel covalent inhibitors have attracted increasing attention. A large amount of scattered experimental data for covalent inhibitors have been reported, but a resource by integrating the experimental information for covalent inhibitor discovery is still lacking.
View Article and Find Full Text PDFProteolysis-targeting chimeras (PROTACs), which selectively degrade targeted proteins by the ubiquitin-proteasome system, have emerged as a novel therapeutic technology with potential advantages over traditional inhibition strategies. In the past few years, this technology has achieved substantial progress and two PROTACs have been advanced into phase I clinical trials. However, this technology is still maturing and the design of PROTACs remains a great challenge.
View Article and Find Full Text PDFMethods: We collected and sorted out the white light endoscopic images of some patients undergoing colonoscopy. The convolutional neural network model is used to detect whether the image contains lesions: CRC, colorectal adenoma (CRA), and colorectal polyps. The accuracy, sensitivity, and specificity rates are used as indicators to evaluate the model.
View Article and Find Full Text PDFLeonurus japonicus (motherwort) has been widely used to treat gynecological disorders, in which estrogen is often dysregulated, for a long time in China and other Asian countries. However, the chemical constituents and mechanisms underlying the activity of this medicinal plant are not fully understood. Seventeen of forty-six tested natural products from L.
View Article and Find Full Text PDFJ Chem Theory Comput
June 2020
A large number of protein-protein interactions (PPIs) are mediated by the interactions between proteins and peptide segments binding partners, and therefore determination of protein-peptide interactions (PpIs) is quite crucial to elucidate important biological processes and design peptides or peptidomimetic drugs that can modulate PPIs. Nowadays, as a powerful computation tool, molecular docking has been widely utilized to predict the binding structures of protein-peptide complexes. However, although a number of docking programs have been available, the systematic study on the assessment of their performance for PpIs has never been reported.
View Article and Find Full Text PDFThe identification and optimization of lead compounds are inalienable components in drug design and discovery pipelines. As a powerful computational approach for the identification of hits with novel structural scaffolds, structure-based virtual screening (SBVS) has exhibited a remarkably increasing influence in the early stages of drug discovery. During the past decade, a variety of techniques and algorithms have been proposed and tested with different purposes in the scope of SBVS.
View Article and Find Full Text PDFFungal drug resistance is a major health threat, and reports of clinical resistance worldwide are becoming increasingly common. In a research program to discover new molecules to help overcome this problem, 14 new lanostane-type triterpenoids, gibbosicolids A-G (-) and gibbosic acids I-O (-), were isolated from the fruiting bodies of , along with seven known triterpenoid derivatives. These compounds featured high levels of oxidation, epimerization, and γ-lactonization.
View Article and Find Full Text PDFPremnafulvol A (1), a unique diterpenoid featuring a 6/5/7/3-fused tetracyclic carbon skeleton, with three biosynthetically related analogues, premnafulvols B-D (2-4), were isolated from the aerial parts of Premna fulva. Structures of 1-4 were established by a combination of extensive spectroscopic analyses, quantum chemical calculations, and X-ray crystallography. Plausible biosynthetic pathways of 1-4 were proposed.
View Article and Find Full Text PDFCirsitakaoside is a natural compound isolated from Premna szemaoensis. However, the anti-inflammatory effects of cirsitakaoside are poorly understood. We investigated the anti-inflammatory action of cirsitakaoside in lipopolysaccharide (LPS)-stimulated macrophages and mice in vivo.
View Article and Find Full Text PDF