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| 1 | A complete sequence and comparative analysis of a SARS-associated virus(Isolate BJ01)显示文摘The genome sequence of the Severe Acute Respiratory Syndrome (SARS)-associated virus provides essential information for the identification of pathogen(s), exploration of etiology and evolution, interpretation of transmission and pathogenesis, development of diagnostics, prevention by future vaccination, and treatment by developing new drugs. We report the complete genome sequence and comparative analysis of an isolate (BJ01) of the coronavirus that has been recognized as a pathogen for SARS. The genome is 29725 nt in size and has 11 ORFs (Open Reading Frames). It is composed of a stable region encoding an RNA-dependent RNA polymerase (composed of 2 ORFs) and a variable region representing 4 CDSs (coding sequences) for viral structural genes (the S, E, M, N proteins) and 5 PUPs (putative uncharacterized proteins). Its gene order is identical to that of other known coronaviruses. The sequence alignment with all known RNA viruses places this virus as a member in the family of Coronaviridae. Thirty putative substitutions have been identified by comparative analysis of the 5 SARS- associated virus genome sequences in GenBank. Fifteen of them lead to possible amino acid changes (non-synonymous mutations) in the proteins. Three amino acid changes, with predicted alteration of physical and chemical features, have been detected in the S protein that is postulated to beinvolved in the immunoreactions between the virus and its host. Two amino acid changes have been detected in the Mprotein, which could be related to viral envelope formation. Phylogenetic analysis suggests the possibility of non-human origin of the SARS-associated viruses but provides noevidence that they are man-made. Further efforts should focus on identifying the etiology of the SARS-associated virus and ruling out conclusively the existence of otherpossible SARS-related pathogen(s). | QIN E'de ZHU Qingyu YU Man FAN Baochang CHANG Guohui SI Bingyin YANG Bao PENG Wenming JIANG Tao LIU Bohua DENG Yongqiang LIU Hong ZHANG Yu WANG Cui LI Yuquan GAN Yonghua LI Xiaoyu L Fushuang TAN Gang CAO Wuchun, YANG Ruifu Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China WANG Jian, LI Wei, XU Zuyuan, LI Yan, WU Qingfa, LIN Wei, CHEN Weijun, TANG Lin, DENG Yajun, HAN Yujun, LI Changfeng, LEI Meng, LI Guoqing, LI Wenjie, L Hong, SHI Jianping, TONG Zongzhong, ZHANG Feng, LI Songgang, LIU Bin, LIU Siqi, DONG Wei, WANG Jun, Gane K-S Wong, YU Jun & YANG Huanming* Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300 National Center for Genome Information, Beijing 101300, China | 2003 | Chinese Science Bulletin2003，48，10： | 121 |
| 2 | Anti-malaria drug chloroquine is highly effective in treating avian influenza A H5N1 virus infection in an animal model显示文摘 | Yiwu Yan Zhen Zou Yang Sun Xiao Li Kai-Feng Xu Yuquan Wei Ningyi Jin Chengyu Jiang | 2013 | Cell Research2013，23，2： | 36 |
| 3 | Function S-Rough sets and its applications显示文摘Based on S-rough sets(singular rough sets), t hi s paper presents function S-rough sets (function singular rough sets)and its ma thematical structures and features. Function S-rough sets has two forms: functi on one direction S-rough sets (function one direction singular rough sets) and function two direction S-rough sets (function two direction singular rough sets ). This paper advances the relationship theorem of function S-rough sets and S -rough sets. Function S-rough sets is the general form of S-rough sets, and S -rough sets is the special case of function S-rough sets. In this paper, appli cations of function S-rough sets in rough law mining-discovery of system are g iven. Function S-rough sets is a new research direction of rough sets and rough system. | Cui Yuquan Shi Kaiquan | 2006 | Journal of Systems Engineering and Electronics2006，17，2： | 25 |
| 4 | 5-Hydroxymethylcytosine signatures in cell-free DNA provide information about tumor types and stages显示文摘5-Hydroxymethylcytosine (5hmC ) 是被连接了到基因规定和癌症致病的重要哺乳动物的 DNA epigenetic 修正。这里,我们用定序途径的一枝敏感化学基于标签的低输入的猎枪在传播没有房间的 DNA (cfDNA ) 探索了 5hmC 的诊断潜力。我们从七种不同癌症类型的 49 个病人定序没有房间的 5hmC 并且发现了能被用来与高精确性预言癌症类型和阶段的不同特征。明确地,我们发现肺癌症在 cfDNA 导致 5hmC 的进步全球损失,而 hepatocellular 癌和胰腺的癌症在没有房间的 hydroxymethylome 导致疾病特定的变化。我们的 proof-of-principle 结果建议没有房间的 5hmC 签名可以潜在地被使用不仅识别癌症类型而且在一些癌症追踪肿瘤舞台。 | Chun-Xiao Song Senlin Yin Li Ma Amanda Wheeler Yu Chen Yan Zhang Bin Liu Junjie Xiong Weihan Zhang Jiankun Hu Zongguang Zhou Biao Dong Zhiqi Tian Stefanie S Jeffrey Mei-Sze Chua Samuel So Weimin Li Yuquan Wei Jiajie Diao Dan Xie Stephen R Quake | 2017 | Cell Research2017，27，10： | 17 |
| 5 | Wind tunnel test on the effect of metal net fences on sand flux in a Gobi Desert, China显示文摘The Lanzhou-Xinjiang High-speed Railway runs through an expansive windy area in a Gobi Desert, and sand-blocking fences were built to protect the railway from destruction by wind-blown sand. However, the shielding effect of the sand-blocking fence is below the expectation. In this study, effects of metal net fences with porosities of 0.5 and 0.7 were tested in a wind tunnel to determine the effectiveness of the employed two kinds of fences in reducing wind velocity and restraining wind-blown sand. Specifically, the horizontal wind velocities and sediment flux densities above the gravel surface were measured under different free-stream wind velocities for the following conditions: no fence at all, single fence with a porosity of 0.5, single fence with a porosity of 0.7, double fences with a porosity of 0.5, and double fences with a porosity of 0.7. Experimental results showed that the horizontal wind velocity was more significantly decreased by the fence with a porosity of 0.5, especially for the double fences. The horizontal wind velocity decreased approximately 65% at a distance of 3.25 m(i.e., 13 H, where H denotes the fence height) downwind the double fences, and no reverse flow or vortex was observed on the leeward side. The sediment flux density decreased exponentially with height above the gravel surface downwind in all tested fences. The reduction percentage of total sediment flux density was higher for the fence with a porosity of 0.5 than for the fence with a porosity of 0.7, especially for the double fences. Furthermore, the decreasing percentage of total sediment flux density decreased with increasing free-stream wind velocity. The results suggest that compared with metal net fence with a porosity of 0.7, the metal net fence with a porosity of 0.5 is more effective for controlling wind-blown sand in the expansive windy area where the Lanzhou-Xinjiang High-speed Railway runs through. | WANG Tao QU Jianjun LING Yuquan XIE Shengbo XIAO Jianhua | 2017 | Journal of Arid Land2017，9，6： | 15 |
| 6 | SHRIMP zircon U-Pb dating for gabbro from the Tiding ophiolite in Tibet显示文摘 | WANG Ran XIA Bin ZHOU Guoqing ZHANG Yuquan YANG Zhiqing LI Wenqian WEI Dongliang ZHONG Lifeng XU Lifeng | 2006 | Chinese Science Bulletin2006，51，14： | 14 |
| 7 | CCL5/CCR5 axis in human diseases and related treatments显示文摘To defense harmful stimuli or maintain the immune homeostasis, the body produces and recruits a superfamily of cytokines such as interleukins, interferons, chemokines etc. Among them, chemokines act as crucial regulators in defense systems. CCL5/CCR5 combination is known for facilitating inflammatory responses, as well as inducing the adhesion and migration of different T cell subsets in immune responses. In addition, recent studies have shown that the interaction between CCL5 and CCR5 is involved in various pathological processes including inflammation, chronic diseases, cancers as well as the infection of COVID-19. This review focuses on how CCL5/CCR5 axis participates in the pathological processes of different diseases and their relevant signaling pathways for the regulation of the axis. Moreover, we highlighted the gene therapy and chemotherapy studies for treating CCR5-related diseases, including the ongoing clinical trials. The barriers and perspectives for future application and translational research were also summarized. | Zhen Zeng Tianxia Lan Yuquan Wei Xiawei Wei | 2022 | Genes & Diseases2022，9，1： | 12 |
| 8 | Mitochondrial DNA in the regulation of innate immune responses显示文摘线粒体作为房间的精力工厂被知道,它也是一个唯一的哺乳动物的细胞器并且考虑超过 10 亿年以前从氧气的初核质被发展。Mitochondrial DNA,类似于它的细菌的祖先,由一个圆形的环组成并且作为 CpG 岛包含 unmethylated DNA 的重要数字。天生的免疫系统在哺乳动物的有免疫力的反应起一个重要作用。最近的研究证明了 mitochondrial DNA (mtDNA ) 激活包含发信号的 TLR9, NLRP3 和圈套的几条天生的有免疫力的小径,它在受动器回答贡献发信号的平台和结果。除了便于抗菌剂豁免并且调整抗病毒的发信号,装证据建议 mtDNA 贡献跟随细胞的损坏和应力的煽动性的疾病。除了它在细胞的新陈代谢和精力生产的欣赏得好的角色,因此, mtDNA 看起来在天生的免疫系统作为一个关键成员工作。这里,我们在天生的免疫加亮 mtDNA 的新兴的角色。 | Chunju Fang Xiawei Wei Yuquan Wei | 2016 | Protein & Cell2016，7，1： | 12 |
| 9 | JMJD3 in the regulation of human diseases显示文摘In recent years,many studies have shown that histone methylation plays an important role in maintaining the active and silent state of gene expression in human diseases.The Jumonji domain-containing protein D3(JMJD3),specifically demethylate di-and trimethyllysine 27 on histone H3(H3K27me2/3),has been widely studied in immune diseases,infectious diseases,cancer,developmental diseases,and aging related diseases.We will focus on the recent advances of JMJD3 function in human diseases,and looks ahead to the future of JMJD3 gene research in this review. | Xiangxian Zhang Li Liu Xia Yuan Yuquan Wei Xiawei | 2019 | Protein & Cell2019，10，12： | 10 |
| 10 | Resequencing of 145 Landmark Cultivars Reveals Asymmetric Sub-genome Selection and Strong Founder Genotype Effects on Wheat Breeding in China显示文摘Controlled pedigrees and the multi-decade timescale of national crop plant breeding programs offer a unique experimental context for examining how selection affects plant genomes.More than 3000 wheat cultivars have been registered,released,and documented since 1949 in China.In this study,a set of 145 elite cultivars selected from historical points of wheat breeding in China were re-sequenced.A total of 43.75 Tb of sequence data were generated with an average read depth of 17.94x for each cultivar,and more than 60.92 million SNPs and 2.54 million InDels were captured,based on the Chinese Spring RefSeq genome v1.0.Seventy years of breeder-driven selection led to dramatic changes in grain yield and related phenotypes,with distinct genomic regions and phenotypes tar-geted by different breeders across the decades.There are very clear instances illustrating how introduced Italian and otherforeign germplasm was integrated into Chinese wheat programs and reshaped the genomic landscape of local modern cultivars.Importantly,the resequencing data also highlighted significant asymmetric breeding selec-tion among the three sub-genomes:this was evident in both the collinear blocks for homeologous chromosomes and among sets of three homeologous genes.Accumulation of more newly assembled genes in newer cultivars implied the potential value of these genes in breeding.Conserved and extended sharing of linkage disequilibrium(LD)blocks was highlighted among pedigree-related cultivars,in which fewer haplotype differences were detected.Fixation or replacement of haplotypes from founder genotypes after generations of breeding was related to their breeding value.Based on the haplotype frequency changes in LD blocks of pedigree-related cultivars,we propose a strategy for evaluating the breeding value of any given line on the basis of the accumulation(pyramiding)of bene-ficial haplotypes.Collectively,our study demonstrates the influence of 'founder genotypes' on the output of breeding efforts over many decades and also suggests that founder genotype perspectives are in fact more dy-namic when applied in the context of modern genomics-informed breeding. | Chenyang Hao Chengzhi Jiao Jian Hou Tian Li Hongxia Liu Yuquan Wang Jun Zheng Hong Liu Zhihong Bi Fengfeng Xu Jing Zhao Lin Ma Yamei Wang Uzma Majeed Xu Liu Rudi Appels Marco Maccaferri Roberto Tuberosa Hongfeng Lu Xueyong Zhang | 2020 | Molecular Plant2020，13，12： | 9 |
| 11 | Modeling of multi-inclusion composites with interfacial imperfections:Micromechanical and numerical simulations显示文摘A micromechanical approach based on a two-layer built-in model and a numerical simulation based on boundary element method are proposed to predict the effective properties of the multi-inclusion composite with imperfect interfaces.The spring model is introduced to simulate the interface imperfection.These two methods are compared with each other,and good agreement is achieved.The effects of interface spring stiffness,volume ratio and stiffness of inclusions on the micro-and macro-mechanical behaviors of fiber-reinforced composites are investigated.It is shown that the developed micromechanical method is very comprehensive and efficient for fast prediction of effective properties of composites,while the numerical method is very accurate in detailed modeling of the mechanical behavior of composites with multiple inclusions. | CHEN WeiQiu 1,ZHU XingYi 2 &HUANG ZhiYi 2 1 Department of Engineering Mechanics,Yuquan Campus,Zhejiang University,Hangzhou 310027,China 2 Key Laboratory of Soft Soils and Geoenvironmental Engineering,Ministry of Education Department of Civil Engineering,Zijingang Campus,Zhejiang University,Hangzhou 310058,China | 2010 | Science China(Technological Sciences)2010，53，3： | 8 |
| 12 | Experimental research and numerical simulation of RC beams strengthened with bonded steel plates显示文摘It is a common method to strengthen the damaged RC structures with bonded steel plates. At present the ultimate bearing ca- pacity of RC structures strengthened with bonded steel plates is calculated mostly using the theory based on the test. Four beams, including one reference beam, two strengthened concrete beams in primary force and secondary force respectively, and one strengthened concrete beam which was not anchored enough, were tested under four-point bending (4PB) in order to get the data of strain of longitudinal bars, bonded bottom steel plate in tension and deflection of beams in the middle span. The experimental program was supported by a three-dimensioned finite analysis using ABAQUS. At the end of experiments and finite analysis, it is concluded that the investing strengthening technique can significantly improve the load-carrying capacity and the phenomenon of stress concentration at the end of interface, as well as the damage at interface, can be well simulated with cohesive element provided by ABAQUS. | LEI Dong CHEN GuangYuan CHEN YuQuan REN QingWen | 2012 | Science China(Technological Sciences)2012，55，12： | 8 |
| 13 | Epigenetic regulation of macrophages: from homeostasis maintenance to host defense显示文摘Macrophages are crucial members of the innate immune response and important regulators.The differentiation and activation of macrophages require the timely regulation of gene expression,which depends on the interaction of a variety of factors,including transcription factors and epigenetic modifications.Epigenetic changes also give macrophages the ability to switch rapidly between cellular programs,indicating the ability of epigenetic mechanisms to affect phenotype plasticity.In this review,we focus on key epigenetic events associated with macrophage fate,highlighting events related to the maintenance of tissue homeostasis,responses to different stimuli and the formation of innate immune memory.Further understanding of the epigenetic regulation of macrophages will be helpful for maintaining tissue integrity,preventing chronic inflammatory diseases and developing therapies to enhance host defense. | Siyuan Chen Jing Yang Yuquan Wei Xiawei Wei | 2020 | Cellular & Molecular Immunology2020，17，1： | 8 |
| 14 | Fast multipole boundary element analysis of 2D viscoelastic composites with imperfect interfaces显示文摘A fast multipole boundary element method(FMBEM)is developed for the analysis of 2D linear viscoelastic composites with imperfect viscoelastic interfaces.The transformed fast multipole formulations are established using the time domain method. To simulate the viscoelastic behavior of imperfect interfaces that are frequently encountered in practice,the Kelvin type model is introduced.The FMBEM is further improved by incorporating naturally the interaction among inclusions as well as eliminating the phenomenon of material penetration.Since all the integrals are evaluated analytically,high accuracy and fast convergence of the numerical scheme are obtained.Several numerical examples,including planar viscoelastic composites with a single inclusion or randomly distributed multi-inclusions are presented.The numerical results are compared with the developed analytical solutions,which illustrates that the proposed FMBEM is very efficient in determining the macroscopic viscoelastic behavior of the particle-reinforced composites with the presence of imperfect interfaces.The laboratory measurements of the mixture creep compliance of asphalt concrete are also compared with the prediction by the developed model. | ZHU XingYi 1 ,CHEN WeiQiu 2 ,HUANG ZhiYi 1* &LIU YiJun 3 1 Department of Civil Engineering,Zhejiang University,Zijingang Campus,Hangzhou 310058,China 2 Department of Engineering Mechanics,Zhejiang University,Yuquan Campus,Hangzhou 310027,China 3Department of Mechanical Engineering,University of Cincinnati,Cincinnati,Ohio 45221-0072,USA | 2010 | Science China(Technological Sciences)2010，53，8： | 7 |
| 15 | K-Ar age of the Cenozoic volcanic rocks in the Nangqen Basin, Qinghai Province and its geological significance显示文摘The Nangqen Basin is one of the typical shearing-extensional basins situated in the north part of the Hengduan Mts. Nine ages of the Cenozoic volcanic rocks from the basin by K-Ar isotope-dilution technique have been reported in the note. The apparent ages of whole rock and separated biotite range from 32.04 to 36.50 Ma. The 40Ar-K (%) correlation isochronal line shows that there existed neither argon excessing , nor radiogenetic argon loosing, i.e. the age represents the true diagenetic time. Volcanic activity in this area occurred in the post-collision environment and is controlled by lithosphere substantial thickening and violent intercontinental shearing-strike slip faults. There is age difference of the magmatic activity in the east, the west and the north Tibet. The multi-periodic eruption-intrusion of the magmatic melt since Cenozoic is a tracer showing the pulsating uplift of the Tibetan Plateau. | DENG Wanming SUN Hongjuan ZHANG Yuquan | 2000 | Chinese Science Bulletin2000，45，11： | 7 |
| 16 | CRISPR/Cas9-mediated correction of human genetic disease显示文摘The clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated(Cas) protein 9 system(CRISPR/Cas9) provides a powerful tool for targeted genetic editing. Directed by programmable sequence-specific RNAs,this system introduces cleavage and double-stranded breaks at target sites precisely. Compared to previously developed targeted nucleases, the CRISPR/Cas9 system demonstrates several promising advantages, including simplicity, high specificity,and efficiency. Several broad genome-editing studies with the CRISPR/Cas9 system in different species in vivo and ex vivo have indicated its strong potential, raising hopes for therapeutic genome editing in clinical settings. Taking advantage of non-homologous end-joining(NHEJ) and homology directed repair(HDR)-mediated DNA repair, several studies have recently reported the use of CRISPR/Cas9 to successfully correct disease-causing alleles ranging from single base mutations to large insertions. In this review, we summarize and discuss recent preclinical studies involving the CRISPR/Cas9-mediated correction of human genetic diseases. | Ke Men Xingmei Duan Zhiyao He Yang Yang Shaohua Yao Yuquan Wei | 2017 | Science China(Life Sciences)2017，60，5： | 7 |
| 17 | Molecular mechanisms and clinical management of cancer bone metastasis显示文摘As one of the most common metastatic sites of malignancies,bone has a unique microenvironment that allows metastatic tumor cells to grow and flourish.The fenestrated capillaries in the bone,bone matrix,and bone cells,including osteoblasts and osteoclasts,together maintain the homeostasis of the bone microenvironment.In contrast,tumor-derived factors act on bone components,leading to subsequent bone resorption or excessive bone formation.The various pathways involved also provide multiple targets for therapeutic strategies against bone metastases.In this review,we summarize the current understanding of the mechanism of bone metastases.Based on the general process of bone metastases,we specifically highlight the complex crosstalk between tumor cells and the bone microenvironment and the current management of cancer bone metastases. | Manni Wang Fan Xia Yuquan Wei Xiawei Wei | 2020 | Bone Research2020，8，3： | 7 |
| 18 | Quantifying the Cloud Water Resource:Basic Concepts and Characteristics显示文摘The water in the air is composed of water vapor and hydrometeors,which are inseparable in the global atmosphere.Precipitation basically comes from hydrometeors instead of directly from water vapor,but hydrometeors are rarely focused on in previous studies.When assessing the maximum potential precipitation,it is necessary to quantify the total amount of hydrometeors present in the air within an area for a certain period of time.Those hydrometeors that have not participated in precipitation formation in the surface,suspending in the atmosphere to be exploited,are defined as the cloud water resource(CWR).Based on the water budget equations,we defined 16 terms(including 12 independent ones)respectively related to the hydrometeors,water vapor,and total water substance in the atmosphere,and 12 characteristic variables related to precipitation and CWR such as precipitation efficiency(PE)and renewal time(RT).Correspondingly,the CWR contributors are grouped into state terms,advection terms,and source/sink terms.Two methods are developed to quantify the CWR(details of which are presented in the companion paper)with satellite observations,atmospheric reanalysis data,precipitation products,and cloud resolving models.The CWR and related variables over North China in April and August 2017 are thus derived.The results show that CWR has the same order of magnitude as surface precipitation(Ps).The hydrometers converted from water vapor(Cvh)during the condensation process is the primary source of precipitation.It is highly correlated with Ps and contributes the most to the CWR over a large region.The state variables and advection terms of hydrometeors are two orders of magnitude lower than the corresponding terms of water vapor.The atmospheric hydrometeors can lead to higher PE than water vapor(several tens of percent versus a few percent),with a shorter RT(only a few hours versus several days).For daily CWR,the state terms are important,but for monthly and longer-time mean CWR,the source/sink terms(i.e.,cloud microphysical processes)contribute the largest;meanwhile,the advection terms contribute less for larger study areas. | Yuquan ZHOU Miao CAI Chao TAN Jietai MAO Zhijin HU | 2020 | Journal of Meteorological Research2020，34，6： | 6 |
| 19 | All-optical manipulation of micrometer-sized metallic particles显示文摘Optical traps use focused laser beams to generate forces on targeted objects ranging in size from nanometers to micrometers. However, for their high coefficients of scattering and absorption, micrometer-sized metallic particles were deemed non-trappable in three dimensions using a single beam. This barrier is now removed. We demonstrate, both in theory and experiment, three-dimensional(3D) dynamic all-optical manipulations of micrometersized gold particles under high focusing conditions. The force of gravity is found to balance the positive axial optical force exerted on particles in an inverted optical tweezers system to form two trapping positions along the vertical direction. Both theoretical and experimental results confirm that stable 3D manipulations are achievable for these particles regardless of beam polarization and wavelength. The present work opens up new opportunities for a variety of in-depth research requiring metallic particles. | YUQUAN ZHANG XIUJIE Dou YANMENG DAI XIANYOU WANG CHANGJUN MIN AND XIAOCONG YUAN | 2018 | Photonics Research2018，6，2： | 6 |
| 20 | Enhancing plasmonic trapping with a perfect radially polarized beam显示文摘Strong plasmonic focal spots, excited by radially polarized light on a smooth thin metallic film, have been widely applied to trap various micro-and nano-sized objects. However, the direct transmission part of the incident light leads to the scattering force exerted on trapped particles, which seriously affects the stability of the plasmonic trap.Here we employ a novel perfect radially polarized beam to solve this problem. Both theoretical and experimental results verify that such a beam could strongly suppress the directly transmitted light to reduce the piconewton scattering force, and an enhanced plasmonic trapping stiffness that is 2.6 times higher is achieved in experiments.The present work opens up new opportunities for a variety of research requiring the stable manipulations of particles. | xianyou wang yuquan zhang yanmeng dai changjun min xiaocong yuan | 2018 | Photonics Research2018，6，9： | 5 |
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