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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 http://gffzz188fe103f8f1460as9kck5x9fn0oq69vn.ffgz.tsg.suse.edu.cn/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 | Modelling of dynamic recrystallization kinetics of 300M steel at high strain rates during hot deformation显示文摘The flow curves of 300M steel exhibit a transition from stress peak presence to stress peak absence as the strain rate increases. It is difficult to establish dynamic recrystallization(DRX) kinetics models suitable for strain rates where there are no stress peaks in the flow curves using the existing Avrami equation, and the optimal processing parameters for forging can be scarcely acquired.In this study, the high-temperature flow and DRX behavior of 300M steel are investigated by performing isothermal compression tests at temperatures between 1173–1423K with strain rates between 0.001–50 s-1. Distinct stress peaks can be found in the flow curves at low strain rates, and the average grain size decreases with the increase in the strain rate at the same temperature. The DRX mechanism is a discontinuous DRX, and the grain boundary migration plays an important role in the DRX process. In contrast, no stress peak is observed in the flow curves at high strain rates, and the average grain size no longer decreases with the strain rate increase at the same temperature. The DRX mechanism in this case is a continuous DRX. The demarcated strain rate is calculated based on the characteristics of the obtained flow curves and grain sizes. The recrystallization volume fraction model and prediction grain size model at high strain rates are established. In combination with the existing DRX kinetics models at low strain rates, the processing parameters can be optimized to produce components with excellent mechanical properties. | GUO Peng DENG Lei WANG XinYun LI JianJun | 2019 | Science China(Technological Sciences)2019，62，9： | 5 |
| 4 | 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 |
| 5 | Entropy correction of charged black hole via fermions tunneling beyond semi-classical approximation显示文摘Motivated by the idea of tunneling beyond semi-classical approximation of Majhi et al., we discuss entropy correction of Dirac particles tunneling from the Reissner-Nordstrm black hole with a global monopole. To get the corrections correctly, we regard the proportionality constants of quantum correction terms to the semi-classical term of action as the inverse of the square of the Planck Length but not that of the Planck Mass. Our study shows that corrections to the Bekenstein-Hawking entropy, namely the logarithmic term and the inverse area term, may be reproduced as the quantum effect is considered. | ZENG XiaoXiong 1 , LI Ling 2 & HU XinYun 3 1 Journal of Sichuan University of Arts and Science, Dazhou 635000, China 2 Department of Maths and Finance-Economics, Sichuan University of Arts and Science, Dazhou 635000, China 3 Library of Sichuan University of Arts and Science, Dazhou 635000, China | 2010 | Science China(Physics,Mechanics & Astronomy)2010，53，1： | 3 |
| 6 | Thermoplastic micro-formability of TiZrHfNiCuBe high entropy metallic glass显示文摘High entropy metallic glasses(MGs) have attracted tremendous attentions owing to high entropy that benefits the probing of new MG-forming systems. However, the micro-formability of high entropy MGs is lack of investigation in comparison with these conventional MG counterparts, which is crucial to the development of this kind of metallic alloys. In this work, the thermoplastic mciro-formability of TiZrHfNiCuBe high entropy MG was systemically investigated. Time-Temperature-Transformation(TTT)curve was first constructed based on isothermal crystallization experiments, which provides thermoplastic processing time of the supercooled high entropy MGs. By comparison with the deformation map,Newtonian flow was found beneficial to the thermoplastic formability. While the thermoplastic forming becomes arduous with reducing mould size to tens micrometer, because of the strong supercooled TiZrHfNiCuBe high entropy MG(fragility = 27). Fortunately, the micro-formability of TiZrHfNiCuBe high entropy MG could be improved by vibration loading, as demonstrated by finite-element-method simulation. Our findings not only systemically evaluate the thermoplastic micro-formability of high entropy MG, but also provide fundamental understanding of the phenomenon. | Xinyun Wang Wenlei Dai Mao Zhang Pan Gong Ning Li | 2018 | Journal of Materials Science & Technology2018，34，11： | 3 |
| 7 | 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 |
| 8 | Bi-level optimization based two-stage market clearing model considering guaranteed accommodation of renewable energy generation显示文摘The existing electricity market mechanisms designed to promote the consumption of renewable energy generation complicate network participation in market transactions owing to an unfair market competition environment,where the low cost renewable energy generation is not reflected in the high bidding price of high cost conventional energy generation.This study addresses this issue by proposing a bi-level optimization based two-stage market clearing model that considers the bidding strategies of market players,and guarantees the accommodation of renewable energy generation.The first stage implements a dual-market clearing mechanism that includes a unified market for trading the power generations of both renewable energy and conventional energy units,and a subsidy market reserved exclusively for conventional generation units.A re-adjustment clearing mechanism is then proposed in the second stage to accommodate the power generation of remaining renewable energy units after first stage energy allocations.Each stage of the proposed model is further described as a bi-level market equilibrium problem and is solved using a co-evolutionary algorithm.Finally,numerical results involving an improved IEEE 39-bus system dem-onstrate that the proposed two-stage model meets the basic requirements of incentive compatibility and individual rationality.It can facilitate the rational allocation of resources,promote the economical operation of electric power grids,and enhance social welfare. | Qianya He Zhenjia Lin Haoyong Chen Xinyun Dai Yirui Li Xin Zeng | 2022 | Protection and Control of Modern Power Systems2022，7，1： | 2 |
| 9 | A pH Model for Calculating the pH Value of Mixed–Acid–Base Equilibria of Overhead Condensing Systems in Crude Distillation显示文摘A pH predictive model based on acid–base equilibria and ion equilibria was proposed to calculate the pH value of the overhead condensing system of crude distillation unit. The pH model could be used to predict the appropriate amounts of neutralizers by measuring the Cl-ion concentration of the overhead knockout drum. The pH values of various neutralized streams were estimated by this model. The results showed that the predicted pH values were in good agreement with the experimental ones. The trend of the corrosion inhibition efficiency decreases in the following order: ethylenediamine > N,Ndimethylethanolamine> triethylamine > 3-methoxypropylamine > morpholine. The difficulty in the accurate control of corrosion was solved, and a good instruction was provided for mitigating corrosion in refinery. | Wang Haibo Li Yun Cheng Guangxu Wu Wei Chen Xuan Zhang Yaoheng Li Xinyun | 2017 | China Petroleum Processing & Petrochemical Technology2017，19，4： | 2 |
| 10 | Use of Support Vector Regression Based on Mean Impact Value Model to Identify Active Compounds in a Combination of Curcuma longa L.and Glycyrrhiza extracts显示文摘A support vector regression based on the mean impact value (MIV) model was constructed to identify the bioactive compounds inhibiting proliferation of He La cells in a combination of turmeric (Curcuma longa L.)and liquorice (Glycyrrhiza) extracts.The quantitative chemical fingerprint from 50 batches of turmeric and liquorice extracts was established using high performance liquid chromatography hyphenated to an ultraviolet visible detector.Qualitative results were obtained using ultra performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry.A total of 46 peaks (peaks 1–15 from turmeric and 16–46 from liquorice) were selected as 'common peaks' for analysis.The inhibitory effect of the combined extracts on He La cells was measured by MTT (3- (4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay.It was found that 15 compounds (peaks:8,12,30,24,46,11,14,9,3,1,44,18,7,45 and 43)possessing high absolute MIV exhibited a significant correlation with the cytotoxicity against He La cells; most of these have already been confirmed with potential cytotoxicity in previous research.The important potential application of the present model can be extended to help discover active compounds from complex herbal medicine prior to traditional bioassay-guided separation.It is considered that this could be a useful tool for redeveloping herbal medicine based on the use of these active compounds. | Jianlan Jiang Qingjie Tan Weifeng Li Xinyun Du Ningzhi Liu | 2017 | Transactions of Tianjin University2017，23，3： | 2 |
| 11 | The microRNA,miR-29c,participates in muscle development through targeting the YY1 gene and is associated with postmortem muscle pH in pigs显示文摘Previous studies indicated that miR-29c is important for muscle development in mice and human,but its role in pigs is unknown.In this study,we detected the expression of miR-29c in Meishan longissimus lumborum(LL)muscle.The results showed that miR-29c was gradually upregulated during development of skeletal muscle in pig.Moreover,the expression of YY1 and Akt3 genes,which were confirmed to be targeted by miR-29c in mice,was decreased along with muscle development.Furthermore,the expression level of miR-29c was significantly higher in adult Meishan pigs than Large White pigs,while the expression of YY1 and Akt3 genes was significantly lower in Meishan pigs.These results indicated that the expression pattern of miR-29c was opposite to that of YY1 and Akt3 genes in pigs.Also,the luciferase assay indicated that miR-29s can target the YY1 gene in pigs.In addition,we identified a T to C mutation in the primary transcript of miR-29c,which was associated with the postmortem muscle pH in pigs.Based on these results,we concluded that miR-29c is also important in skeletal muscle development of pigs. | Weiya ZHANG Wei WEI Yuanyuan ZHAO Shuhong ZHAO Xinyun LI | 2015 | Frontiers of Agricultural Science and Engineering2015，2，4： | 2 |
| 12 | NES1/KLK10 and hNIS gene therapy enhanced iodine-131 internal radiation in PC3 proliferation inhibition显示文摘NES1 gene is thought to be a tumor-suppressor gene.Our previous study found that overexpression of NES1 gene in PC3 cell line could slow down the tumor proliferation rate,associated with a mild decrease in BCL-2 expression.The BCL-2 decrease could increase the sensitivity of radiotherapy to tumors.Thus,we supposed to have an“enhanced firepower”effect by combining overexpressed NES1 gene therapy and 131I radiation therapy uptake by overexpressed hNIS protein.We found a weak endogenous expression of hNIS protein in PC3 cells and demonstrated that the low expression of hNIS protein in PC3 cells might be the reason for the low iodine uptake.By overexpressing hNIS in PC3,the radioactive iodine uptake ability was significantly increased.Results of in vitro and in vivo tumor proliferation experiments and 18F-fluorothymidine(18F-FLT)micro-positron emission tomography/computed tomography(micro-PET/CT)imaging showed that the combined NES1 gene therapy and 131I radiation therapy mediated by overexpressed hNIS protein had the best tumor proliferative inhibition effect.Immunohistochemistry showed an obvious decrease of Ki-67 expression and the lowest BCL-2 expression.These data suggest that via inhibition of BCL-2 expression,overexpressed NES1 might enhance the effect of radiation therapy of 131I uptake in hNIS overexpressed PC3 cells. | Jiajia Hu Wenbin Shen Qian Qu Xiaochun Fei Ying Miao Xinyun Huang Jiajun Liu Yingli Wu Biao Li | 2019 | Frontiers of Medicine2019，13，6： | 1 |
| 13 | Optimization of Ultrasonic Extraction and Clean-up Protocol for the Determination of Polycyclic Aromatic Hydrocarbons in Marine Sediments by High-performance Liquid Chroma-tography Coupled with Fluorescence Detection显示文摘The procedures of ultrasonic extraction and clean-up were optimized for the determination of polycyclic aromatic hydrocarbons (PAHs) in marine sediments. Samples were ultrasonically extracted, and the extracts were purified with a miniaturized silica gel chromatographic column and analyzed with high performance liquid chromatography (HPLC) with a fluorescence detector. Ultrasonication with methanol-dichloromethane (2:1, v/v) mixture gave higher extraction efficiency than that with dichloromethane. Among the three elution solvents used in clean-up step, dichloromethane-hexane (2:3, v/v) mixture was the most satisfactory. Under the optimized conditions, the recoveries in the range of 54.82% to 94.70% with RSDs of 3.02% to 23.22% for a spiked blank, and in the range of 61.20% to 127.08% with RSDs of 7.61% to 26.93% for a spiked matrix, were obtained for the 15 PAHs studied, while the recoveries for a NIST standard reference SRM 1941b were in the range of 50.79% to 83.78% with RSDs of 5.24% to 21.38%. The detection limits were between 0.75 ng L-1 and 10.99 ng L-1for different PAHs. A sample from the Jiaozhou Bay area was examined to test the established methods. | PENG Xuewei YAN Guofang LI Xianguo GUO Xinyun ZHOU Xiao WANG Yan | 2012 | Journal of Ocean University of China2012，11，3： | 1 |
| 14 | Molecular characterization, induced expression, and transcriptional regulation of porcine S100A12 gene显示文摘 | Hongbo Chen Lei Cheng Songbai Yang Xiangdong Liu Ying Liu Juan Tang Xinyun Li Qigai He Shuhong Zhao | 2010 | Molecular Immunology2010，，7： | 1 |
| 15 | Porcine S100A8 and S100A9 : Molecular characterizations and crucial functions in response to Haemophilus parasuis infection显示文摘 | Hongbo Chen Joan K. Lunney Lei Cheng Xinyun Li Jianhua Cao Mengjin Zhu Shuhong Zhao | 2010 | Developmental and Comparative Immunology2010，，4： | 1 |
| 16 | Intercalation of Two-dimensional Layered Materials显示文摘Two-dimensional(2D)layered materials have attracted great attention due to their unique electrical,optical,thermal and mechanical properties.2D layered materials have miique van der Waals gaps,thus the foreign substance,such as atoms,molecules and ions,can be inserted into the gaps to change the physical and chemical properties of 2D layered materials,which is conducive to realize their multi-fimctional application.Herein,we present a critical review of recent research progress of 2D intercalated materials,including the synthesizing metliods,theoretical calculation,characterization and multifunctional application.Finally,we will summarize llie current challenges and future opportunities in the development of 2D intercalated materials. | ZHOU Xinyun YANG Juehan ZHONG Mianzeng XIA Qinglin LI Bo DUAN Xidong WEI Zhongming | 2020 | Chemical Research in Chinese Universities2020，36，4： | 1 |
| 17 | Demonstration program of population‐based lung cancer screening in C hina: Rationale and study design显示文摘 | Qinghua Zhou Yaguang Fan Ning Wu Yunchao Huang Ying Wang Lu Li Jiewei Liu Xinyun Wang Weimin Li Youlin Qiao | 2014 | Thoracic Cancer2014，，3： | 1 |
| 18 | Effect of isothermal extrusion parameters on mechanical properties of Al–Si eutectic alloy显示文摘 | Lei Deng Xinyun Wang Juchen Xia Jianjun Li | 2011 | Materials Science & Engineering A2011，，21： | 1 |
| 19 | 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 |
| 20 | Porcine S100A8 and S100A9 : Molecular characterizations and crucial functions in response to Haemophilus parasuis infection显示文摘 | Hongbo Chen Joan K. Lunney Lei Cheng Xinyun Li Jianhua Cao Mengjin Zhu Shuhong Zhao | 2010 | Developmental and Comparative Immunology2010，，4： | 1 |
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