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| 1 | rMVP: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool for Genome-wide Association Study显示文摘Along with the develoipment of high-throughput sequencing technologies,both sample size and SNP number are increasing rapidly in genome-wide association studies(GWAS),and the associated computation is more challenging than ever.Here,we present a memory-efficient,visualization-enhanced,and parallel-accelerated R package called“r MVP”to address the need for improved GWAS computation.r MVP can 1)effectively process large GWAS data,2)rapidly evaluate population structure,3)efficiently estimate variance components by Efficient Mixed-Model Association e Xpedited(EMMAX),Factored Spectrally Transformed Linear Mixed Models(Fa ST-LMM),and Haseman-Elston(HE)regression algorithms,4)implement parallel-accelerated association tests of markers using general linear model(GLM),mixed linear model(MLM),and fixed and random model circulating probability unification(Farm CPU)methods,5)compute fast with a globally efficient design in the GWAS processes,and 6)generate various visualizations of GWASrelated information.Accelerated by block matrix multiplication strategy and multiple threads,the association test methods embedded in r MVP are significantly faster than PLINK,GEMMA,and Farm CPU_pkg.r MVP is freely available at https://github.com/xiaolei-lab/r MVP. | Lilin Yin Haohao Zhang Zhenshuang Tang Jingya Xu Dong Yin Zhiwu Zhang Xiaohui Yuan Mengjin Zhu Shuhong Zhao Xinyun Li Xiaolei Liu | 2021 | Genomics, Proteomics & Bioinformatics2021，19，4： | 12 |
| 2 | TLR4 is essential for dendritic cell activation and anti-tumor T-cell response enhancement by DAMPs released from chemically stressed cancer cells显示文摘免疫疗法和化疗的联合为癌症的某些类型的治疗被认为是一条有希望的途径。然而,内在的机制需要充分被调查为癌症 chemoimmunotherapy 指导更有效的协议的设计。联系危险的分子的模式(阻尼) 能激活有免疫力的房间,是众所周知的,包括树枝状的房间(DC ) ,经由像使用费的受体(TLR ) ;然而,在有免疫力的反应的激活免除化学对待药的肿瘤房间的阻尼的角色需要进一步被阐明。这里,我们发现那 colorectal 与 oxaliplatin (OXA ) 对待的癌症(CRC ) 房间或 5 氟尿嘧啶(5-Fu ) 释放了高活动性的组盒子 1 的高水平(HMGB1 ) 和热吃惊蛋白质 70 (HSP70 ) 。在 OXA/5-Fu 治疗以后,也展出的 CRC 病人的 sera 增加了 HMGB1 和 HSP70 的层次,哪个是著名阻尼。与 OXA/5-Fu 对待的垂死的 CRC 房间的上层清液支持了老鼠和人的 DC 成熟,与 HLA 医生, CD80 和 CD86 表示和 IL-1β 的改进的 upregulation;, TNF-α, MIP-1α, MIP-1β, RANTES 和 IP-10 生产。由 DC 组成的疫苗与导致的化学上强调的 CRC 房间的上层清液搏动了更重要的 IFN-γ在 vitro 并且在 vivo 生产 Th1 反应。然而,化学上强调的 CRC 房间的上层清液没能在 TLR4 缺乏的 DC 导致 phenotypic 成熟和 cytokine 生产,显示在导致阻尼的 DC 成熟和激活的 TLR4 的一个必要角色。而且,有化学上强调的 CRC 房间的上层清液的 pulsing 高效地没导致 IFN-γ在 TLR4 缺乏的 DC 生产 Th1 反应。一起,这些结果证明免除化学上强调的癌症房间的阻尼能经由 TLR4 激活 DC 并且提高反肿瘤 T 房间有免疫力的回答的正式就职,描出一条临床上相关的免疫助手小径由阻尼被触发。 | Hongliang Fang Bing Ang Xinyun Xu Xiaohui Huang Yanfeng Wu Yanping Sun Wenying Wang Nan Li Xuetao Cao Tao Wan | 2014 | Cellular & Molecular Immunology2014，11，2： | 11 |
| 3 | BioNano Genome Map Resource for Oryza sativa ssp.japonica and indica and Its Application in Rice Genome Sequence Correction and Gap Filling显示文摘 | Ping Chen Xinyun Jing Baosheng Liao Yan Zhu Jiang Xu Renyi Liu Yinhong Zhao Xuan Li | 2017 | Molecular Plant2017，10，6： | 4 |
| 4 | The advancements,challenges,and future implications of the CRISPR/Cas9 system in swine research显示文摘Clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(CRISPR/Cas9)genome editing technology has dramatically influenced swine research by enabling the production of high-quality disease-resistant pig breeds,thus improving yields.In addition,CRISPR/Cas9 has been used extensively in pigs as one of the tools in biomedical research.In this review,we present the advancements of the CRISPR/Cas9 system in swine research,such as animal breeding,vaccine development,xenotransplantation,and disease modeling.We also highlight the current challenges and some potential applications of the CRISPR/Cas9 technologies. | Jinfu Zhang Emmanuel M.Khazalwa Hussein M.Abkallo Yuan Zhou Xiongwei Nie Jinxue Ruan Changzhi Zhao Jieru Wang Jing Xu Xinyun Li Shuhong Zhao Erwei Zuo Lucilla Steinaa Shengsong Xie | 2021 | Journal of Genetics and Genomics2021，48，5： | 2 |
| 5 | Severe hypersensitivity dermatitis and liver dysfunction induced by occupational exposure to trichloroethylene 显示文摘 | Xinyun XU Rongxing YANG Nan WU | 2009 | Ind Health2009，47，2： | 1 |
| 6 | Oxidative stress and inducible nitric oxide synthase expression in human hepatocytes treated with trichlomethylene显示文摘 | XU Xinyun WU Peiqino KE Yuebin | 2010 | Toxicol Environ Chem2010，92，4： | 1 |
| 7 | Severe hypersensitivity dermatitis and liver dysfunction induced by occupational exposure to trichloroethylene显示文摘 | Xinyun XU Rongxing YANG Nan WU | 2009 | Ind Health2009，47，2： | 1 |
| 8 | Severe Hypersensitivity Dermatitis and Liver Dysfunction Induced by Occupational Exposure to Trichloroethylene显示文摘 | Xinyun Xu Rongxing Yang Nan Wu | 2009 | Ind Health2009，47，2： | 1 |
| 9 | Oxidative stress and inducible nitric oxide synthase expression in human hepatocytes treated with trichloroethylen 显示文摘 | XU Xinyun WU Peiqiao KE Yuebin | 2010 | Toxicological & Environmental Chemistry2010，92，4： | 1 |
| 10 | Epigenetic regulation mechanism of ABCG2 induced drug-resistant phenotype显示文摘The aim of this study is to investigate epigenetic mechanism of ABCG2 induced drug-resistance.It is not only expatiate for drug-resistance regulation mechanism in all-round,but also to provide scientific experimental basis for selecting target to reverse its drug-resistance.Apply methylation-specific PCR(MSP) to have tested methylation of ABCG2 promoter region -359 to -353 specific positions in breast cancer tissues and paired adjacent tissue of 22 cases,and test their methylation positions with MSP products for sequencing;and adopt fluorescent quantitation RT-PCR to test expression level DNMT1,DNMT3A,DNMT3B and ABCG2;to make analysis on relationship between them with statistical spearman correlation.Specific positions of ABCG2 gene promoter region of 18 cases among the 22 cases with breast cancer(18/22,82%) existed high methylation(P<0.05),MSP products sequencing proved methylation of the specific position,and mRNA expression level was relative higher in remarkable positive correlation(P<0.05).ABCG2,DNMT1,DNMT3A,DNMT3B mRNA expression levels in breast cancer tissues were obviously higher than adjacent tissues(P<0.01),and DNMT3B expression level was obviously higher than DNMT1 and DNMT3A(P<0.01) in negative correlation with ABCG2 gene expression(P=0.001).-359 to -353 positions of promoter regions of ABCG2 gene existed high methylation capable to push expression of this gene in beast cancer tissue.DNMT3B is involved in expression regulation in ABCG2 gene,and provides new scientific basis for drug-resistance target as reverse ABCG2 | Yuan Jianhui Zhou Jianmeng JiNana Xu Xinyun Liu Jianjun Ke Yuebin Cheng Jinquan. Zhuang Zhixiong | 2011 | Journal of Medical Colleges of PLA(China)2011，26，5： | 1 |
| 11 | Altered expression of hepatic metabolic enzyme and apoptosis-related gene transcripts in human hepatocytes treated with trichloroethylene 显示文摘 | Xinyun XU Yuefeng LIU Jiyan MAO et a/ | 2012 | Human Exp Toxicol2012，31，9： | 1 |
| 12 | Oxidative stress and inducible nitric oxide synthase expression in human hepatocytes treated with trichloroethylene显示文摘 | Xinyun XU Peiqiao WU Yuebin KE | 2010 | Toxicol Environ Chem2010，92，4： | 1 |
| 13 | Severe Hypersensitivity Dermatitis and Liver Dysfunction Induced by Occupational Exposure to Trichloroethylene显示文摘 | Xinyun XU Rongxing YANG Nan WU et ol | 2009 | Ind Health2009，47，2： | 1 |
| 14 | Engineering of hollow polymeric nanosphere-supported imidazolium-based ionic liquids with enhanced antimicrobial activities显示文摘The design of stable,efficient and processable bactericidal materials represents a significant challenge for combating multidrugresistant bacteria in a variety of engineering fields.Herein,we report a facile strategy for the preparation of hollow polymeric nanosphere(HPN)-supported imidazolium-based ionic liquids(denoted as HPN-ILs)with superior antimicrobial activities.HPNILs were tailored by moderate Friedel−Crafts polymerization followed by the sequential covalent bonding of imidazole and bromoalkene.The resultant HPN-ILs have uniform hollow spherical morphology,an adequate surface area,and excellent physicochemical stability.Furthermore,they are highly active against both Gram-positive and Gram-negative bacteria and exhibit typical time/dosage-dependent antibacterial activities.The rational combination of porous HPNs and antibacterial ILs to generate an all-in-one entity may open new avenues for the design and fabrication of efficient bacteriostatic agents.Moreover,HPN-ILs have good biocompatibility and can also be loaded onto diverse matrices,and thus could extend their practical bactericidal application in the potential biomedical-active field. | Yu Zhang Shuwei Li Yixin Xu Xinyun Shi Mingxin Zhang Yingning Huang Ying Liang Yaqiong Chen Wanli Ji Jung Rae Kim Wenliang Song Deng-Guang Yu Il Kim | 2022 | Nano Research2022，15，6： | 1 |
| 15 | Oxidative stress and inducible nitric oxide synthase expression in human hepatocytes treated with trichloroethylene显示文摘 | Xinyun XU Peiqiao WU Yuebin KE | 2010 | Toxicol Environ Chem2010，92，4： | 1 |
| 16 | Altered expressionof hepatic metabolic enzyme and apoptosis-related gene transcriptsin human hepatocytes treated with trichloroethylene显示文摘 | Xu Xinyun Liu Yuefeng Mao Jiyan | 2012 | Hum ExpToxicol2012，31，9： | 1 |
| 17 | Severehypersensitivity dermatitis and liver dysfunction induced byoccupational exposure to trichloroethylene 显示文摘 | XU Xinyun YANG Rongxing WU Nan | 2009 | Ind Health2009，47，2： | 1 |
| 18 | Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features显示文摘Background:A large number of pig breeds are distributed around the world,their features and characteristics vary among breeds,and they are valuable resources.Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved pig breeds.Results:In this study,we performed GWAS using a standard mixed linear model with three types of genome variants(SNP,InDel,and CNV)that were identified from public,whole-genome,sequencing data sets.We used 469 pigs of 57 breeds,and we identified and analyzed approximately 19 million SNPs,1.8 million InDels,and 18,016 CNVs.We defined six biological phenotypes by the characteristics of breed features to identify the associated genome variants and candidate genes,which included coat color,ear shape,gradient zone,body weight,body length,and body height.A total of 37 candidate genes was identified,which included 27 that were reported previously(e.g.,PLAG1 for body weight),but the other 10 were newly detected candidate genes(e.g.,ADAMTS9 for coat color).Conclusion:Our study indicated that using GWAS across a modest number of breeds with high density genome variants provided efficient mapping of complex traits. | Jingya Xu Yuhua Fu Yan Hu Lilin Yin Zhenshuang Tang Dong Yin Mengjin Zhu Mei Yu Xinyun Li Yang Zhou Shuhong Zhao Xiaolei Liu | 2021 | Journal of Animal Science and Biotechnology2021，12，2： | 1 |
| 19 | Oxidative stress and inducible nitric oxide synthase expression in human hepatocytes treated with trichloroethylene显示文摘 | Xinyun XU Peiqiao WU Yuebin KE | 2010 | Toxicol Environ Chem2010，92，4： | 1 |
| 20 | Oxidative stress and inducible nitric oxide synthase expression in human hepatocytes treated with trichloroethylene 显示文摘 | XU Xinyun WU Peiqiao KE Yuebin | 2010 | Toxicological & Environmental Chemistry2010，92，4： | 1 |
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