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Structural variants contribute to pangenome evolution of a plant pathogenic fungus [article]

Li Guo, Quanbin Dong, Bo Wang, Mengyao Guo, Kai Ye
2021 bioRxiv   pre-print
Genome biology 20(1): 224. 5 4 7 Alonge M, Wang X, Benoit M, Soyk S, Pereira L, Zhang L, Suresh H, 5 4 8 Ramakrishnan S, Maumus F, Ciren D, et al. 2020.  ...  https://doi.org/10.1101/2021.04.14.439764 doi: bioRxiv preprintThe authors declare no conflict of interest. 5 4 0 5 4 1 5 4 2 REFERENCES 5 4 3 5 4 4 Alonge M, Soyk S, Ramakrishnan S, Wang  ... 
doi:10.1101/2021.04.14.439764 fatcat:3bc4i67y5jej5bojv2vtyfiuyi

Investigation of Electromagnetic Pulse Compaction on Conducting Graphene/PEKK Composite Powder

Quanbin Wang, Deli Jia, Xiaohan Pei, Xuelian Wu, Fan Xu, Huixiong Wang, Minghao Cao, Haidong Chen
2021 Materials  
Polymer-composite materials have the characteristics of light weight, high load, corrosion resistance, heat resistance, and high oil resistance. In particular, graphene composite has better electrical conductivity and mechanical performance. However, the raw materials of graphene composite are processed into semi-finished products, directly affecting their performance and service life. The electromagnetic pulse compaction was initially studied to get the product Graphene/PEKK composite powder.
more » ... imultaneously, spark plasma sintering was used to get the bars to determine the electrical conductivity of Graphene/PEKK composite. On the basis of this result, conducting Graphene/PEKK composite powder can be processed by electromagnetic pulse compaction. Finite element numerical analysis was used to obtain process parameters during the electromagnetic pulse compaction. The results show that discharge voltage and discharge capacitance influence on the magnetic force, which is a main moulding factor affecting stress, strain and density distribution on the specimen during electromagnetic pulse compaction in a few microseconds.
doi:10.3390/ma14030636 pmid:33573144 fatcat:f2miydx3inewhntsfmi3fik4qu

High-quality Arabidopsis thaliana genome assembly with Nanopore and HiFi long reads [article]

Bo Wang, Yanyan Jia, Peng Jia, Quanbin Dong, Xiaofei Yang, Kai Ye
2021 bioRxiv   pre-print
Here, we report a high-quality (HQ) and almost complete genome assembly with a single gap and quality value (QV) larger than 60 of the model plant Arabidopsis thaliana ecotype Columbia (Col-0), generated using combination of Oxford Nanopore Technology (ONT) ultra-long reads, high fidelity (HiFi) reads and Hi-C data. The total genome assembly size is 133,877,291 bp (chr1: 32,659,241 bp, chr2: 22,712,559 bp, chr3: 26,161,332 bp, chr4: 22,250,686 bp and chr5: 30,093,473 bp), and introduces 14.73
more » ... (96% belong to centromere) novel sequences compared to TAIR10.1 reference genome. All five chromosomes of our HQ assembly are highly accurate with QV larger than 60, ranging from QV62 to QV68, which is significantly higher than TAIR10.1 referecne (44-51) and a recent published genome (41-43). We have completely resolved chr3 and chr5 from telomere-to-telomere. For chr2 and chr4, we have completely resolved apart from the nucleolar organizing regions, which are composed of highly long-repetitive DNA fragments. It has been reported that the length of centromere 1 is about 9 Mb and it is hard to assembly since tens of thousands of CEN180 satellite repeats. Based on the cutting-edge sequencing data, we assembled about 4Mb continuous sequence of centromere 1. We found different identity patterns across five centromeres, and all centromeres were significantly enriched with CENH3 ChIP-seq signals, confirming the accuracy of the assembly. We obtained four clusters of CEN180 repeats, and found CENH3 presented a strong preference for a cluster 3. Moreover, we observed hypomethylation patterns in CENH3 enriched regions. This high-quality assembly genome will be a valuable reference to assist us in the understanding of global pattern of centromeric polymorphism, genetic and epigenetic in naturally inbred lines of Arabidopsis thaliana.
doi:10.1101/2021.06.08.447650 fatcat:vtavukezdbbshnhbcqvceqn2ou

Fucoidan protects against dopaminergic neuron death in vivo and in vitro

Dingzhen Luo, Quanbin Zhang, Haomin Wang, Yanqiu Cui, Zuoli Sun, Jian Yang, Yan Zheng, Jun Jia, Fen Yu, Xuan Wang, Xiaomin Wang
2009 European Journal of Pharmacology  
Parkinson's disease is a neurodegenerative disorder of uncertain pathogenesis characterized by a loss of dopaminergic neurons in substantia nigra pars compacta, and can be modeled by the neurotoxin 1-methyl-4phenyl-1, 2, 3, 6-tetrahydropyridine (MPTP). Oxidative stress may contribute to MPTP-and Parkinson's disease-related neurodegeneration. Fucoidan is a sulfated polysaccharide extracted from brown seaweeds which possesses a wide variety of biological activities including potent antioxidative
more » ... ffects. Here we investigated the effect of fucoidan treatment on locomoter activities of animals, striatal dopamine and its metabolites and survival of nigral dopaminergic neurons in MPTP-induced animal model of Parkinsonism in C57/BL mice in vivo and on the neuronal damage induced by 1-methyl-4-phenylpyridinium (MPP + ) in vitro, and to study the possible mechanisms. When administered prior to MPTP, fucoidan reduced behavioral deficits, increased striatal dopamine and its metabolites levels, reduced cell death, and led to a marked increase in tyrosine hydroxylase expression relative to mice treated with MPTP alone. Furthermore, we found that fucoidan inhibited MPTP-induced lipid peroxidation and reduction of antioxidant enzyme activity. In addition, pre-treatment with fucoidan significantly protected against MPP + -induced damage in MN9D cells. Taken together, these findings suggest that fucoidan has protective effect in MPTP-induced neurotoxicity in this model of Parkinson's disease via its antioxidative activity.
doi:10.1016/j.ejphar.2009.06.015 pmid:19545563 fatcat:nfjn5tq5nfgkvahlj2hvqpdiw4

Is Electroacupuncture an Effective and Safe Treatment for Poststroke Depression? An Updated Systematic Review and Meta-Analysis

Xiafei Wang, Wa Cai, Yongpeng Wang, Song Huang, Quanbin Zhang, Feng Wang, Vida Demarin
2021 BioMed Research International  
] E: 40 C: 40 CCCD/CCMD/HAMD E: 30:96 ± 4:25 C: 30:65 ± 3:98 GV20, EX-HN1, EX-HN3, LR3, HT7, PC6, KI3, SP6, BL15; 30 min, once a day 20 mg/d fluoxetine 42 6 1 (1, 0, 0, 0) Wang  ...  15.6 -9.18 -11.77 -8.26 -15.41 -9.9 -9.8 Chen 2005 Chen 2012 Chu 2007 Dong 2007 Hong 2015 Kang 2014 Li 2013 Li 2015 Li 2015 Long 2004 Peng 2011 Guo 2011 Huang 2014 Xu 2015 Wang  ...  Xiafei Wang, Wa Cai, and Yongpeng Wang are the joint first authors.  ... 
doi:10.1155/2021/8661162 pmid:34485527 pmcid:PMC8410412 fatcat:ahzqb6x275ay3pnc5cpt53isku

Strength Development of Ternary System Portland Cement-Slag-Phosphogypsum

Yuxin Gao, Baojun Cheng, Shuo Wang, Peifei Ma, Quanbin Chen, Yaning Kong, Yao Bi, Jun Wang
2019 DEStech Transactions on Engineering and Technology Research  
., Chengdu, China Shuo Wang, China West Construction Group Co.  ... 
doi:10.12783/dtetr/icaen201/29060 fatcat:s7anspzbdjaq3dsxvccdcghpra

Low-molecular-weight fucoidan protects endothelial function and ameliorates basal hypertension in diabetic Goto-Kakizaki rats

Wentong Cui, Yuanyuan Zheng, Quanbin Zhang, Jing Wang, Limin Wang, Wenzhe Yang, Chenyang Guo, Weidong Gao, Xiaomin Wang, Dali Luo
2014 Laboratory Investigation  
Endothelial dysfunction, characterized by impairment of endothelial nitric oxide synthase (eNOS) and nitric oxide (NO) bioavailability, has been implicated in diabetic cardiovascular pathogenesis. In this study, low-molecular-weight fucoidan (LMWF), which has multiple biological activities including anti-inflammatory and anti-oxidative properties, was investigated for its protective effect against endothelial dysfunction in Goto-Kakizaki type 2 diabetic rats. LMWF (50, 100, or 200 mg/kg/day) or
more » ... probucol (100 mg/kg/day) were given to diabetic rats for 12 weeks. Basal blood pressure, acetylcholine-or flow-mediated relaxation of mesenteric and paw arteries, endothelium-dependent dilation of aorta, eNOS phosphorylation, and NO production were measured using laser Doppler flowmetry, force myograph, hematoxylin and eosin staining, western blot analysis, and an NO assay. We found that LMWF robustly ameliorated the basal hypertension and impairment of endothelium-dependent relaxation in the aorta, as well as mesenteric and paw arteries in diabetic rats. In addition, the reduction in eNOS phosphorylation at Ser1177, eNOS expression, and NO production because of diabetes were partially reversed by LMWF treatment. However, probucol, a lipid-modifying drug with antioxidant properties, displayed only mild effects. Moreover, LMWF induced, in a dose-dependent manner, endotheliumdependent vasodilation and eNOS phosphorylation at Ser1177 in normal aorta, and also promoted Ser1177 phosphorylation and NO synthesis in primary cultured vasoendothelial cells. Thus, these data demonstrate for the first time that fucoidan protects vasoendothelial function and reduces basal blood pressure in type 2 diabetes rats via, at least in part, preservation of eNOS function. Fucoidan is therefore a potential candidate drug for protection of endothelium in diabetic cardiovascular complications. Diabetic patients are at high risk of endothelial dysfunction and vascular lesions, because of multiple harmful stimuli, such as hyperglycemia, hyperlipidemia, and oxidative stress. These patients are susceptible to atherosclerosis, hypertension, and peripheral vascular disease. 1,2 It is well established that endothelium-derived nitric oxide (NO) maintains vascular homeostasis and health through vasodilation and protection of vasculature from various damaging agents. 3-5 Loss of NO induces increased activity of proinflammatory transcription factors, such as nuclear factor kappa B, resulting in expression of leukocyte adhesion molecules and production of chemokines and cytokines, which further promote endothelial inflammation and atherosclerosis. 5,6 Therefore, the endothelial dysfunction caused by imbalance of NO bioavailability in early-stage diabetes has been implicated as a sign or a predictor of a future cardiovascular event. 6-8 Mechanistically, a disturbance in endothelial NO synthase (eNOS) activity, referred to as uncoupling of eNOS and downregulation of eNOS expression, 2,9 has been identified as an important pathogenic
doi:10.1038/labinvest.2014.12 pmid:24614196 fatcat:tr7mlou4lbcrbph3fdpozrcrby

Ensemble Decision for Spam Detection Using Term Space Partition Approach

Ying Tan, Quanbin Wang, Guyue Mi
2018 IEEE Transactions on Cybernetics  
This paper proposes an ensemble decision approach which combines global and local features of e-mails together to detect spam effectively. In the proposed method, a special feature construction method named term space partition (TSP) is utilized to divide the whole term space into several subspaces and adopt different feature construction strategies on each of them, respectively. This method can make each term play a distinct and important role when conducting detection. This method is utilized
more » ... and extended by introducing the sliding window technique to extract local features from e-mails. The global classifier and local classifiers are constructed on a global feature vector set and local feature vector sets, respectively, and together make the ensemble decision by adopting the voting technique. The principles of the TSP-based approach and mechanism of the ensemble decision method are presented in detail. Five different and standard benchmark corpora are applied to experiments for performance evaluation of this proposed method. Comprehensive experimental results show that the proposed method brings significant performance improvement and better robustness on the basis of the TSP-based approach. In addition, the proposed method outperforms the current prevalent and state-of-the-art approaches, especially when a comprehensive consideration of performance, efficiency, and robustness is taken. This endows it with flexible capability and adaptivity in the real-world applications.
doi:10.1109/tcyb.2018.2868794 pmid:30273168 fatcat:jqre5hgrnbbl3ovhvurwhe7axe

MiR-363 suppresses cell migration, invasion, and epithelial-mesenchymal transition of osteosarcoma by binding to NOB1

Yongtao Zhang, Fang Wang, Lina Wang, Quanbin Zhang
2020 World Journal of Surgical Oncology  
Wang et al. demonstrated similar findings; miR-363 inhibited lung adenocarcinoma cell proliferation, colony formation, and tumor growth [13] .  ...  A similar finding by Wang et al. demonstrated that miR-363 inhibited lung adenocarcinoma cell proliferation, colony formation, and tumor growth [13] .  ...  Fang Wang as the second author contributed to the analyses. Lina Wang as the third author helped perform the analysis with constructive discussions.  ... 
doi:10.1186/s12957-020-01859-y pmid:32357945 fatcat:yjk45ro5pnelhauiwb736qcgi4

Preparation and Neuroprotective Activity of Glucuronomannan Oligosaccharides in an MPTP-Induced Parkinson's Model

Yingjuan Liu, Weihua Jin, Zhenzhen Deng, Jing Wang, Quanbin Zhang
2020 Marine Drugs  
(Zhang, Zhang, Wang, Shi and Zhang, 2009 ).  ... 
doi:10.3390/md18090438 pmid:32842556 pmcid:PMC7551172 fatcat:3qiblfjrevcc5dvqpryq7xiu6y

AlGaN/GaN MIS-HEMT with PECVD SiNx, SiON, SiO2 as Gate Dielectric and Passivation Layer

Kuiwei Geng, Ditao Chen, Quanbin Zhou, Hong Wang
2018 Electronics  
Three different insulator layers SiNx, SiON, and SiO2 were used as a gate dielectric and passivation layer in AlGaN/GaN metal–insulator–semiconductor high-electron-mobility transistors (MIS-HEMT). The SiNx, SiON, and SiO2 were deposited by a plasma-enhanced chemical vapor deposition (PECVD) system. Great differences in the gate leakage current, breakdown voltage, interface traps, and current collapse were observed. The SiON MIS-HEMT exhibited the highest breakdown voltage and Ion/Ioff ratio.
more » ... SiNx MIS-HEMT performed well in current collapse but exhibited the highest gate leakage current density. The SiO2 MIS-HEMT possessed the lowest gate leakage current density but suffered from the early breakdown of the metal–insulator–semiconductor (MIS) diode. As for interface traps, the SiNx MIS-HEMT has the largest shallow trap density and the lowest deep trap density. The SiO2 MIS-HEMT has the largest deep trap density. The factors causing current collapse were confirmed by Photoluminescence (PL) spectra. Based on the direct current (DC) characteristics, SiNx and SiON both have advantages and disadvantages.
doi:10.3390/electronics7120416 fatcat:s55tpdzkefexlpiusis7l4pbj4

The Protective Effect of Fucoidan in Rats with Streptozotocin-Induced Diabetic Nephropathy

Jing Wang, Huaide Liu, Ning Li, Quanbin Zhang, Hong Zhang
2014 Marine Drugs  
Preparation of Natural Polysaccharides FPS was extracted according to the modified method of Wang et al. [27] .  ... 
doi:10.3390/md12063292 pmid:24886867 pmcid:PMC4071577 fatcat:3sfxvecn7jazvf5rpr2lckkyka

Application of Unsupervised Transfer Technique Based on Deep Learning Model in Physical Training

Quanbin Zhao, Hanqi Wang, Vijay Kumar
2022 Computational Intelligence and Neuroscience  
The research purpose is to study the standardization and scientizing of physical training actions. Stacking denoising auto encoder (SDAE), a BiLSTM deep network model (SDAL-DNM) (a kind of training action model), and an unsupervised transfer model are used to deeply study the action problem of physical training. Initially, the physical training action discrimination model adopted here is a combination of stacked noise reduction self-encoder and bidirectional depth network model. Then, this
more » ... can collect data for five actions in physical training and further analyze the importance of action standardization for physical training. Afterward, the SDAL-DNM implemented here fully integrates the advantages of SDAE and BiLSTM. Finally, the unsupervised transfer model adopted here is based on SDAL-DNM deep learning (DL). The movement data of the physical training crowd are collected, and then the unsupervised transfer model is trained. According to the movement characteristics of physical training, the data difference between trainers is calculated so that the actions of each trainer can be continuously adapted according to the model, and finally, the benefits of effectively distinguishing the training actions can be achieved. The research shows that before and after unsupervised learning, the average decline of the model used is 1.69%, while the average decline of extreme learning machine (ELM) is 5.5%. The conclusion is that the unsupervised transfer model can improve the discrimination accuracy of physical training actions and provide theoretical support to effectively correct mistakes in physical training actions.
doi:10.1155/2022/8679221 pmid:35463226 pmcid:PMC9023208 fatcat:ylb5rmgor5fy5j5crxgp3c4p4y

Structural and mechanistic insights into Mps1 kinase activation

Wei Wang, Yuting Yang, Yuefeng Gao, Quanbin Xu, Feng Wang, Songcheng Zhu, William Old, Katheryn Resing, Natalie Ahn, Ming Lei, Xuedong Liu
2008 Journal of Cellular and Molecular Medicine  
doi:10.1111/j.1582-4934.2008.00605.x pmid:19120698 pmcid:PMC2829362 fatcat:5rrqagksvndhfgvr6uuuvhocei

Roles of Endovascular Calyx Related Enzymes in Endothelial Dysfunction and Diabetic Vascular Complications

Zhi Li, Ning Wu, Jing Wang, Quanbin Zhang
2020 Frontiers in Pharmacology  
., 2016; Wang et al., 2016; Sieve et al., 2018a) .  ...  Furthermore, a previous paper pointed out that human platelets contain hyaluronidase 2, while other cells contain HYAL1 and HYAL2 (Wang G.-H. et al., 2019) .  ...  Copyright © 2020 Li, Wu, Wang and Zhang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).  ... 
doi:10.3389/fphar.2020.590614 pmid:33328998 pmcid:PMC7734331 fatcat:4byljsjuszditkvyyivj5nvxla
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