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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://gffzz188fe103f8f1460asqcv0w6096vnn6obf.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 | Precision forging technology for aluminum alloy显示文摘 | Lei DENG Xinyun WANG Junsong JIN Juchen XIA | 2018 | Frontiers of Mechanical Engineering2018，13，1： | 6 |
| 4 | 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 |
| 5 | 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 |
| 6 | MULTIPOINT BLANK HOLDER FORCE CONTROL IN HYDROFORMING OF FUEL TANK显示文摘力量(BHF ) 控制的多点的空白的持有者的学习外面被得到 forhydroforming 一辆复杂形状摩托车燃料坦克。由有限元素方法(女性) 模拟,多点的空白的持有者柱体的配置和本地 BHF 的设置被优化,并且多点的 BHF 在上的影响流体力学的深绘画和 conventionalhydroforming 进程被学习。需要的液体压力和整个 BHF 为流体力学的深绘画过程被预言。最后,模拟结果被形成实验证明,并且他们在同意很好。 | WU Yousheng WANG Xinyun XIA Juchen HU Guoan SUN Yousong YANG Lin | 2006 | Chinese Journal of Mechanical Engineering2006，19，2： | 4 |
| 7 | 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 |
| 8 | HDL impairs osteoclastogenesis and induces osteoclast apoptosis via upregulation of ABCG1 expression显示文摘 | Xinyun Huang Yuan Lv Panpan He Zongbao Wang Fang Xiong Linhao He Xilong Zheng Dawei Zhang Qi Cao Chaoke Tang | 2018 | Acta Biochimica et Biophysica Sinica2018，50，9： | 3 |
| 9 | 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 |
| 10 | 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 |
| 11 | 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 |
| 12 | EFFECTS OF INJECTION STRATEGY ON D.I. DIESEL ENGINE COMBUSTION显示文摘Experiments are conducted to develop an understanding of how split injections can affect the combustion and emission characteristics of a D.I. diesel engine with a common-rail injection system. The ratio of the amount of fuel injected between two injection pulses and the injection interval is varied keeping the injected fuel quantity constant. Results show that under the 70D90-10 injection pattern, the engine achieves the lower NOx-smoke emissions and BSFC compared with the single injection pattern. The heat release rate and the temperature show that the split injections increase the initial premixed burn and retards the diffusion burn. With the balance of these two effects, the maximum in-cylinder temperature decreases while the 50% heat release point is held at almost the same crank angle. Therefore, both NOx emission and BSFC are improved while keeping the smoke emission at the same level. | ZI Xinyun JIANG Dahai DENG Chenglin OUYANG Minggao YANG Fuyuan | 2007 | Chinese Journal of Mechanical Engineering2007，20，3： | 2 |
| 13 | Research Progress of Microbial Degradation of Organophosphorus Pesticides显示文摘In recent years,the extensive use of organophosphorus pesticides,especially the unreasonable use,has brought great safety risks to the environment.Organic phosphorus pollution has become a hotspot,and there are a large number of microorganisms in the soil and water body that can degrade organophosphorus pesticides.The extensive degradation performance of pesticides is applied to a variety of pollution remediation practices.This paper summarizes the current situation of organophosphorus pesticide use and pesticide residues,the species of organophosphorus pesticide degrading bacteria and its separation and screening and degradation of pesticide characteristics of the research progress. | Weixia Tang Hongming Ji Xinyun Hou | 2018 | Progress in Applied Microbiology2018，1，1： | 2 |
| 14 | 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 |
| 15 | Polymersome-mediated cytosolic delivery of cyclic dinucleotide STING agonist enhances tumor immunotherapy显示文摘Cyclic dinucleotides(CDNs)as stimulator of interferon genes(STING)agonists capable of inducing strong antitumor innate immune response are highly promising for tumor immunotherapy.The efficacy of these CDNs is,however,reduced greatly by their fast clearance,poor cell uptake and inefficient cytosolic transportation.Here,we report that reduction-responsive biodegradable chimaeric polymersomes(CPs)markedly enhance tumor retention and cytosolic delivery of a synthetic CDN,ADU-S100,and bolster STING pathway activation in the tumor microenvironment and tumor draining lymph nodes,giving significantly better tumor repression and survival of B16F10 melanoma-bearing mice compared with free CDN control.The superiority of CPs-mediated CDN delivery is further verified in combination therapy with low-dose fractionated radiation,which brings about clearly stronger and longer-term immunotherapeutic effects and protection against tumor re-challenge.The development of nano-STING agonists that are able to overcome the delivery barriers of CDNs represents an effective strategy to potentiate cancer immunotherapy. | Huan Zheng Beibei Guo Xinyun Qiu Yifeng Xia Yan Qu Liang Cheng Fenghua Meng Zhiyuan Zhong | 2022 | Bioactive Materials2022，7，10： | 2 |
| 16 | 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 |
| 17 | Stepwise 3D-spatio-temporal magnesium cationic niche: Nanocomposite scaffold mediated microenvironment for modulating intramembranous ossification显示文摘The fate of cells and subsequent bone regeneration is highly correlated with temporospatial coordination of chemical,biological,or physical cues within a local tissue microenvironment.Deeper understanding of how mammalian cells react to local tissue microenvironment is paramount important when designing next generation of biomaterials for tissue engineering.This study aims to investigate that the regulation of magnesium cationic(Mg^2+)tissue microenvironment is able to convince early-stage bone regeneration and its mechanism undergoes intramembranous ossification.It was discovered that moderate Mg^2+content niche(~4.11 mM)led to superior bone regeneration,while Mg^2+-free and strong Mg^2+content(~16.44 mM)discouraged cell adhesion,proliferation and osteogenic differentiation,thereby bone formation was rarely found.When magnesium ions diffused into free Mg zone from concentrated zone in late time point,new bone formation on free Mg zone became significant through intramembranous ossification.This study successfully demonstrates that magnesium cationic microenvironment serves as an effective biochemical cue and is able to modulate the process of bony tissue regeneration.The knowledge of how a Mg^2+cationic microenvironment intertwines with cells and subsequent bone formation gained from this study may provide a new insight to develop the next generation of tissuerepairing biomaterials. | Jie Shen Bo Chen Xinyun Zhai Wei Qiao Shuilin Wu Xuanyong Liu Ying Zhao Changshun Ruan Haobo Pan Paul K.Chu Kenneth M.C.Cheung Kelvin W.K.Yeung | 2021 | Bioactive Materials2021，6，2： | 2 |
| 18 | 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 |
| 19 | SnRK1 Phosphorylates and Destabilizes WRKY3 to Enhance Barley Immunity to Powdery Mildew显示文摘Plants recognize pathogens and activate immune responses,which usually involve massive transcriptional reprogramming.The evolutionarily conserved kinase,Sucrose non-fermenting-related kinase 1(SnRK1),functions as a metabolic regulator that is essential for plant growth and stress responses.Here,we identify barley SnRK1 and a WRKY3 transcription factor by screening a cDNA library.SnRK1 interacts with WRKY3 in yeast,as confirmed by pull-down and luciferase complementation assays.Förster resonance energy transfer combined with noninvasive fluorescence lifetime imaging analysis indicates that the interaction occurs in the barley nucleus.Transient expression and virus-induced gene silencing analyses indicate that WRKY3 acts as a repressor of disease resistance to the Bgh fungus.Barley plants overexpressing WRKY3 have enhanced fungal microcolony formation and sporulation.Phosphorylation assays show that SnRK1 phosphorylates WRKY3 mainly at Ser83 and Ser112 to destabilize the repressor,and WRKY3 non-phosphorylation-null mutants at these two sites are more stable than the wild-type protein.SnRK1-overexpressing barley plants display enhanced disease resistance to Bgh.Transient expression of SnRK1 reduces fungal haustorium formation in barley cells,which probably requires SnRK1 nuclear localization and kinase activity.Together,these findings suggest that SnRK1 is directly involved in plant immunity through phosphorylation and destabilization of the WRKY3 repressor,revealing a new regulatory mechanism of immune derepression in plants. | Xinyun Han Ling Zhang Lifang Zhao Pengya Xue Ting Qi Chunlei Zhang Hongbo Yuan Lixun Zhou Daowen Wang Jinlong Qiuand Qian-Hua Shen | 2020 | Plant Communications2020，1，4： | 2 |
| 20 | Inversion of site effects and attenuation parameters of seismic wave using Lg wave data 显示文摘 | Zhu Xinyun Chen Yuntai | 2007 | Acta Seismologica Siniea2007，29，6： | 1 |
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