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  • Oxford University Press (OUP)  (17)
  • 2020-2024  (17)
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  • Oxford University Press (OUP)  (17)
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  • 2020-2024  (17)
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  • 1
    In: Database, Oxford University Press (OUP), Vol. 2022 ( 2022-11-24)
    Abstract: Drug–target association plays an important role in drug discovery, drug repositioning, drug synergy prediction, etc. Currently, a lot of drug-related databases, such as DrugBank and BindingDB, have emerged. However, these databases are separate, incomplete and non-uniform with different criteria. Here, we integrated eight drug-related databases; collected, filtered and supplemented drugs, target genes and experimentally validated (highly confident) associations and built a highly confident drug–target (HCDT: http://hainmu-biobigdata.com/hcdt) database. HCDT database includes 500 681 HCDT associations between 299 458 drugs and 5618 target genes. Compared to individual databases, HCDT database contains 1.1 to 254.2 times drugs, 1.8–5.5 times target genes and 1.4–27.7 times drug–target associations. It is normative, publicly available and easy for searching, browsing and downloading. Together with multi-omics data, it will be a good resource in analyzing the drug functional mechanism, mining drug-related biological pathways, predicting drug synergy, etc. Database URL: http://hainmu-biobigdata.com/hcdt
    Type of Medium: Online Resource
    ISSN: 1758-0463
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2496706-3
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  • 2
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2020
    In:  Metallomics Vol. 12, No. 9 ( 2020-09-01), p. 1389-1399
    In: Metallomics, Oxford University Press (OUP), Vol. 12, No. 9 ( 2020-09-01), p. 1389-1399
    Abstract: Traditional Tibetan medicines containing β-HgS have been used to treat chronic ailments for thousands of years. However, there has recently been speculation regarding the safety of these medicines due to their high mercury content. Although the toxic effect of β-HgS has been previously investigated in vivo, the mechanism underlying the toxicity of this compound remains unclear. In this study, we investigate the mechanism of β-HgS cytotoxicity via experiments performed on rat adrenal gland tumor cells (PC-12). Specifically, we analyze the viability and intracellular oxidative stress state of PC-12 cells treated with varying concentrations of β-HgS. For comparison purposes, the effects of MeHgCl and HgCl2, two Hg-based compounds, on ROS generation and MDA, GSH/GSSG, Nrf2, NQO-1, and HO-1 levels are also determined. It should be noted that we used the small-molecule thiols of cell culture medium, such as cysteine, to increase the solubility of β-HgS and prepare a β-HgS solution to treat PC-12 cells. The obtained results show that β-HgS inhibits cell viability at concentrations of 200–1000 ng Hg mL−1 (48 h treatment). In the concentration range of 200–600 ng Hg mL−1 (24 h treatment), the inhibitory effect of β-HgS is stronger than that of MeHgCl; however, this trend is reversed at higher concentrations (800–1000 ng mL−1) and longer exposure times (48 h). Moreover, β-HgS significantly promotes MDA, but has no appreciable influence on cell apoptosis and ROS generation in PC-12 cells, which suggests that its inhibitory effect on cell viability might be related to the stimulation of ROS-independent oxidative stress. Notably, β-HgS and HgCl2 significantly increase the GSH content, GSH/GSSG ratio, NQO-1 mRNA expression, and HO-1 protein expression in PC-12 cells, indicating that the antioxidant protection against these compounds is triggered by Nrf2 activation. HPLC-AFS analysis shows that in β-HgS and HgCl2 solutions, mercury exists in the same form of Hg2+, but the cytotoxicity of the former is greater. This is probably due to the additional oxidative damage induced by the S2− ion in β-HgS. In conclusion, β-HgS induces ROS-independent oxidative stress in PC-12 cells, and thus, is obviously cytotoxic. At the same time, it promotes the antioxidant capacity of cells by activating the Nrf2 pathway.
    Type of Medium: Online Resource
    ISSN: 1756-5901 , 1756-591X
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2474317-3
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  • 3
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2023
    In:  Journal of Neuropathology & Experimental Neurology Vol. 82, No. 4 ( 2023-03-20), p. 324-332
    In: Journal of Neuropathology & Experimental Neurology, Oxford University Press (OUP), Vol. 82, No. 4 ( 2023-03-20), p. 324-332
    Abstract: Peripheral nerve injury induces motor and sensory defects and has serious impacts on patients’ quality of life. Schwann cells (SCs) are the major glial cells in the peripheral nervous system and play important roles in the repair and regeneration of peripheral nerves. Long noncoding RNA HAGLR has been reported to be highly expressed in neurons and to promote neuronal differentiation but its expression decreases after nerve injury, suggesting that HAGLR may be involved in the process of nerve injury repair. This study aimed to investigate the role and mechanism of HAGLR in neural repair functions of SCs. We found that HAGLR promoted SC proliferation and migration and facilitated the secretion of neurotrophic factors. Furthermore, HAGLR functions as a competing endogenous RNA to regulate CDK5R1 expression via sponging miR-204. Overexpression of miR-204 or silencing of CDK5R1 partially abolished the promoting effect of HAGLR on SCs. Moreover, overexpression of HAGLR promoted the functional recovery of sciatic nerve crush (SNC) model rats. In summary, HAGLR promoted SC proliferation, migration, neurotrophic factor production, and facilitated functional recovery of SNC rats via miR-204/CDK5R1. Therefore, it may provide a potential therapeutic target for peripheral nerve repair and regeneration.
    Type of Medium: Online Resource
    ISSN: 0022-3069 , 1554-6578
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2033048-0
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  • 4
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2022
    In:  Nucleic Acids Research Vol. 50, No. 16 ( 2022-09-09), p. 9294-9305
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 50, No. 16 ( 2022-09-09), p. 9294-9305
    Abstract: The tripartite ParABS system mediates chromosome segregation in a wide range of bacteria. Dimeric ParB was proposed to nucleate on parS sites and spread to neighboring DNA. However, how properly distributed ParB dimers further compact chromosomal DNA into a higher-order nucleoprotein complex for partitioning remains poorly understood. Here, using a single-molecule approach, we show that tens of Bacillus subtilis ParB (Spo0J) proteins can stochastically multimerize on and stably bind to nonspecific DNA. The introduction of CTP promotes the formation and diffusion of the multimeric ParB along DNA, offering an opportunity for ParB proteins to further forgather and cluster. Intriguingly, ParB multimers can recognize parS motifs and are more inclined to remain immobile on them. Importantly, the ParB multimer features distinct capabilities of not only bridging two independent DNA molecules but also mediating their transportation, both of which are enhanced by the presence of either CTP or parS in the DNA. These findings shed new light on ParB dynamics in self-multimerization and DNA organization and help to better comprehend the assembly of the ParB-DNA partition complex.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2022
    In:  The Computer Journal Vol. 65, No. 2 ( 2022-02-14), p. 251-260
    In: The Computer Journal, Oxford University Press (OUP), Vol. 65, No. 2 ( 2022-02-14), p. 251-260
    Abstract: It is a hot spot in the field of computer application to diagnose complex brain diseases such as Asperger syndrome (AS) using machine learning technology. To identify AS patients and detect lesions, this paper proposes a novel clustering-evolutionary random support vector machine (SVM) ensemble (CERSVME) based on graph theory. Firstly, we extract graph theory indexes from the resting-state functional magnetic resonance imaging (fMRI) data as sample features and construct an ensemble learner by integrating multiple SVM classifiers. Secondly, the base learners with high redundancy and poor classification ability are deleted through clustering evolutions to improve the performance of the model. Then the CERSVME model is used to classify fMRI image of AS patients and healthy controls. According to the classification results, a multi-stage analysis scheme is designed to find the AS-related brain areas. We validate the proposed approach on 135 participants from autism brain imaging data exchange cohort. The highest accuracy reported by the CERSVME reaches 95.24%. More importantly, the diseased brain areas such as middle frontal gyrus, hippocampus and precuneus are found based on their contributions to classification performances of the CERSVME. Our study provides useful assistances for the clinical detection of patients with AS.
    Type of Medium: Online Resource
    ISSN: 0010-4620 , 1460-2067
    RVK:
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1477172-X
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  • 6
    In: National Science Review, Oxford University Press (OUP), Vol. 9, No. 9 ( 2022-09-26)
    Type of Medium: Online Resource
    ISSN: 2095-5138 , 2053-714X
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2745465-4
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  • 7
    In: Horticulture Research, Oxford University Press (OUP), Vol. 10, No. 7 ( 2023-07-04)
    Abstract: Mulberry is a fundamental component of the global sericulture industry, and its positive impact on our health and the environment cannot be overstated. However, the mulberry reference genomes reported previously remained unassembled or unplaced sequences. Here, we report the assembly and analysis of the telomere-to-telomere gap-free reference genome of the mulberry species, Morus notabilis, which has emerged as an important reference in mulberry gene function research and genetic improvement. The mulberry gap-free reference genome produced here provides an unprecedented opportunity for us to study the structure and function of centromeres. Our results revealed that all mulberry centromeric regions share conserved centromeric satellite repeats with different copies. Strikingly, we found that M. notabilis is a species with polycentric chromosomes and the only reported polycentric chromosome species up to now. We propose a compelling model that explains the formation mechanism of new centromeres and addresses the unsolved scientific question of the chromosome fusion-fission cycle in mulberry species. Our study sheds light on the functional genomics, chromosome evolution, and genetic improvement of mulberry species.
    Type of Medium: Online Resource
    ISSN: 2052-7276
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2781828-7
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  • 8
    In: Journal of Antimicrobial Chemotherapy, Oxford University Press (OUP), Vol. 75, No. 7 ( 2020-07-01), p. 1756-1765
    Abstract: To investigate the prevalence and transmission of mcr-3 among Salmonella enterica serotype Typhimurium and 1,4,[5],12:i:−. Methods A total of 4724 clinical Salmonella isolates were screened for the presence of mcr-3 in China during 2014–19. The clonal relationship of the mcr-3-positive isolates and their plasmid contents and complete sequence were also characterized based on WGS data from the Illumina and MinION platforms. Results We identified 10 mcr-3-positive isolates, and all were MDR, mostly resistant to colistin, cefotaxime, ciprofloxacin, doxycycline and florfenicol. mcr-3 was co-present with blaCTX-M-55-qnrS1 on hybrid ST3-IncC-FII conjugatable plasmids (n = 6) and an ST3-IncC non-conjugatable plasmid (n = 1) and embedded into a pCHL5009T-like IncFII plasmid on the Salmonella chromosome (n = 3). Four distinctive genetic contexts surrounded mcr-3 and all but one were closely related to each other and to the corresponding region of IncFII plasmid pCHL5009T. IS15DI was most likely the vehicle for integration of mcr-3-carrying IncFII plasmids into ST3-IncC plasmids and the chromosome and for shaping the MDR regions. In addition, a phylogenetic tree based on the core genome revealed a unique Salmonella lineage (≤665 SNPs) that contained these 10 mcr-3-positive isolates and another 38 (33 from patients) mcr-3-positive Salmonella from five countries. In particular, most of the 51 mcr-3-positive isolates belonged to ST34 and harboured diverse antibiotic resistance genes (ARGs), including mcr-3-blaCTX-M-55-qnrS1, and possessed similar ARG profiles. Conclusions Our findings revealed global clonal spread of MDR ST34 Salmonella from clinical isolates co-harbouring mcr-3 with blaCTX-M-55 and qnrS1 and a flexibility of mcr-3 co-transmittance with other ARGs mediated by mobile genetic elements.
    Type of Medium: Online Resource
    ISSN: 0305-7453 , 1460-2091
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 1467478-6
    SSG: 15,3
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  • 9
    In: Clinical Infectious Diseases, Oxford University Press (OUP), Vol. 71, No. 3 ( 2020-07-27), p. 622-629
    Abstract: China is thought to be a hotspot for zoonotic influenza virus emergence, yet there have been few prospective studies examining the occupational risks of such infections. Methods We present the first 2 years of data collected from a 5-year, prospective, cohort study of swine-exposed and -unexposed participants at 6 swine farms in China. We conducted serological and virological surveillance to examine evidence for swine influenza A virus infection in humans. Results Of the 658 participants (521 swine-exposed and 137 swine-unexposed), 207 (31.5%) seroconverted against at least 1 swine influenza virus subtype (swine H1N1 or H3N2). Swine-exposed participants’ microneutralization titers, especially those enrolled at confined animal feeding operations (CAFOs), were higher against the swine H1N1 virus than were other participants at 12 and 24 months. Despite elevated titers, among the 187 study subjects for whom we had complete follow-up, participants working at swine CAFOs had significantly greater odds of seroconverting against both the swine H1N1 (odds ratio [OR] 19.16, 95% confidence interval [CI] 3.55–358.65) and swine H3N2 (OR 2.97, 95% CI 1.16–8.01) viruses, compared to unexposed and non-CAFO swine workers with less intense swine exposure. Conclusions While some of the observed increased risk against swine viruses may have been explained by exposure to human influenza strains, study data suggest that even with elevated preexisting antibodies, swine-exposed workers were at high risk of infection with enzootic swine influenza A viruses.
    Type of Medium: Online Resource
    ISSN: 1058-4838 , 1537-6591
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2002229-3
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  • 10
    In: Bioinformatics, Oxford University Press (OUP), Vol. 36, No. 8 ( 2020-04-15), p. 2561-2568
    Abstract: The multimodal data fusion analysis becomes another important field for brain disease detection and increasing researches concentrate on using neural network algorithms to solve a range of problems. However, most current neural network optimizing strategies focus on internal nodes or hidden layer numbers, while ignoring the advantages of external optimization. Additionally, in the multimodal data fusion analysis of brain science, the problems of small sample size and high-dimensional data are often encountered due to the difficulty of data collection and the specialization of brain science data, which may result in the lower generalization performance of neural network. Results We propose a genetically evolved random neural network cluster (GERNNC) model. Specifically, the fusion characteristics are first constructed to be taken as the input and the best type of neural network is selected as the base classifier to form the initial random neural network cluster. Second, the cluster is adaptively genetically evolved. Based on the GERNNC model, we further construct a multi-tasking framework for the classification of patients with brain disease and the extraction of significant characteristics. In a study of genetic data and functional magnetic resonance imaging data from the Alzheimer’s Disease Neuroimaging Initiative, the framework exhibits great classification performance and strong morbigenous factor detection ability. This work demonstrates that how to effectively detect pathogenic components of the brain disease on the high-dimensional medical data and small samples. Availability and implementation The Matlab code is available at https://github.com/lizi1234560/GERNNC.git.
    Type of Medium: Online Resource
    ISSN: 1367-4803 , 1367-4811
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 1468345-3
    SSG: 12
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