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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 | The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types显示文摘The Genome Sequence Archive(GSA)is a data repository for archiving raw sequence data,which provides data storage and sharing services for worldwide scientific communities.Considering explosive data growth with diverse data types,here we present the GSA family by expanding into a set of resources for raw data archive with different purposes,namely,GSA(https://ngdc.cncb.ac.cn/gsa/),GSA for Human(GSA-Human,https://ngdc.cncb.ac.cn/gsa-human/),and Open Archive for Miscellaneous Data(OMIX,https://ngdc.cncb.ac.cn/omix/).Compared with the 2017 version,GSA has been significantly updated in data model,online functionalities,and web interfaces.GSA-Human,as a new partner of GSA,is a data repository specialized in human genetics-related data with controlled access and security.OMIX,as a critical complement to the two resources mentioned above,is an open archive for miscellaneous data.Together,all these resources form a family of resources dedicated to archiving explosive data with diverse types,accepting data submissions from all over the world,and providing free open access to all publicly available data in support of worldwide research activities. | Tingting Chen Xu Chen Sisi Zhang Junwei Zhu Bixia Tang Anke Wang Lili Dong Zhewen Zhang Caixia Yu Yanling Sun Lianjiang Chi Huanxin Chen Shuang Zhai Yubin Sun Li Lan Xin Zhang Jingfa Xiao Yiming Bao Yanqing Wang Zhang Zhang Wenming Zhao | 2021 | Genomics, Proteomics & Bioinformatics2021，19，4： | 38 |
| 3 | Nutritional and medicinal characteristics of Chinese giant salamander (Andrias davidianus) for applications in healthcare industry by artificial cultivation: A review显示文摘Andrias davidianus,i.e.Chinese giant salamander(CGS),is one of the largest and oldest amphibians existing in the world and is also one of the valuable biological resources of China.Wild CGS has been threatened with extinction in the past decades due to over capturing,deterioration of natural environment,the slow breeding and growth of the wild species in nature.However,in the past twenty years,with the breakthrough and progress of artificial breeding technology by artificial insemination,the number of artificially cultivated CGS has increased rapidly.Artificially cultivated CGS can either be released to the CGS living environment to increase the population in nature or legally applied in food and medicinal industry as a feedstock due to the unique nutritional and medicinal values of CGS as recorded historically.In this review,the nutritional components,bioactive components and medicinal activities of the artificially cultivated CGS will be summarized.The mucus,skin,meat and bone of CGS contain many different bioactive substances thereby having various medicinal activities including anti-aging,anti-fatigue,anti-tumor,therapy of burn and anti-infection and other physiological functions.This paper will further discuss the potential applications of the artificially cultivated CGS in healthcare industry and prospects of future technological development. | Dong He Wenming Zhu Wen Zenga Jun Lin Yang Ji Yi Wang Chong Zhang Yuan Lu Daoquan Zhao Nan Su Xin-Hui Xing | 2018 | Food Science and Human Wellness2018，7，1： | 28 |
| 4 | Cobalt single atom site catalysts with ultrahigh metal loading for enhanced aerobic oxidation of ethylbenzene显示文摘The oxidation of hydrocarbons to produce high value-added compounds(ketones or alcohols)using oxygen in air as the only oxidant is an efficient synthetic strategy from both environmental and economic views.Herein,we successfully synthesized cobalt single atom site catalysts(Co SACs)with high metal loading of 23.58 wt.%supported on carbon nitride(CN),which showed excellent catalytic properties for oxidation of ethylbenzene in air.Moreover,Co SACs show a much higher turn-over frequency(19.6 h^(−1))than other reported non-noble catalysts under the same condition.Comparatively,the as-obtained nanosized or homogenous Co catalysts are inert to this reaction.Co SACs also exhibit high selectivity(97%)and stability(unchanged after five runs)in this reaction.DFT calculations reveal that Co SACs show a low energy barrier in the first elementary step and a high resistance to water,which result in the robust catalytic performance for this reaction. | Yu Xiong Wenming Sun Yunhu Han Pingyu Xin Xusheng Zheng Wensheng Yan Juncai Dong Jian Zhang Dingsheng Wang Yadong Li | 2021 | Nano Research2021，14，7： | 20 |
| 5 | GSA:Genome Sequence Archive显示文摘With the rapid development of sequencing technologies towards higher throughput and lower cost, sequence data are generated at an unprecedentedly explosive rate. To provide an efficient and easy-to-use platform for managing huge sequence data, here we present Genome Sequence Archive(GSA; http://bigd.big.ac.cn/gsa or http://gsa.big.ac.cn), a data repository for archiving raw sequence data. In compliance with data standards and structures of the International Nucleotide Sequence Database Collaboration(INSDC), GSA adopts four data objects(Bio Project, Bio Sample,Experiment, and Run) for data organization, accepts raw sequence reads produced by a variety of sequencing platforms, stores both sequence reads and metadata submitted from all over the world,and makes all these data publicly available to worldwide scientific communities. In the era of big data, GSA is not only an important complement to existing INSDC members by alleviating the increasing burdens of handling sequence data deluge, but also takes the significant responsibility for global big data archive and provides free unrestricted access to all publicly available data in support of research activities throughout the world. | Yanqing Wang Fuhai Song Junwei Zhu Sisi Zhang Yadong Yang Tingting Chen Bixia Tang Lili Dong Nan Ding Qian Zhang Zhouxian Bai Xunong Dong Huanxin Chen Mingyuan Sun Shuang Zhai Yubin Sun Lei Yu Li Lan Jingfa Xiao Xiangdong Fang Hongxing Lei Zhang Zhang Wenming Zhao | 2017 | Genomics, Proteomics & Bioinformatics2017，15，1： | 13 |
| 6 | Insight into the Ebola virus nucleocapsid assembly mechanism: crystal structure of Ebola virus nucleoprotein core domain at 1.8 A resolution显示文摘 | Shishang Dong Peng Yang Guobang Li Baocheng Liu Wenming Wang Xiang Liu Boran Xia Cheng Yang Zhiyong Lou Yu Guo Zihe Rao | 2015 | Protein & Cell2015，6，5： | 6 |
| 7 | A survey on ensemble learning显示文摘Despite significant successes achieved in knowledge discovery,traditional machine learning methods may fail to obtain satisfactory performances when dealing with complex data,such as imbalanced,high-dimensional,noisy data,etc.The reason behind is that it is difficult for these methods to capture multiple characteristics and underlying structure of data.In this context,it becomes an important topic in the data mining field that how to effectively construct an efficient knowledge discovery and mining model.Ensemble learning,as one research hot spot,aims to integrate data fusion,data modeling,and data mining into a unified framework.Specifically,ensemble learning firstly extracts a set of features with a variety of transformations.Based on these learned features,multiple learning algorithms are utilized to produce weak predictive results.Finally,ensemble learning fuses the informative knowledge from the above results obtained to achieve knowledge discovery and better predictive performance via voting schemes in an adaptive way.In this paper,we review the research progress of the mainstream approaches of ensemble learning and classify them based on different characteristics.In addition,we present challenges and possible research directions for each mainstream approach of ensemble learning,and we also give an extra introduction for the combination of ensemble learning with other machine learning hot spots such as deep learning,reinforcement learning,etc. | Xibin DONG Zhiwen YU Wenming CAO Yifan SHI Qianli MA | 2020 | Frontiers of Computer Science2020，14，2： | 4 |
| 8 | The Tibetan Plateau Surface–Atmosphere Coupling System and Its Weather and Climate Effects: The Third Tibetan Plateau Atmospheric Science Experiment显示文摘The Tibetan Plateau(TP) is a key area affecting forecasts of weather and climate in China and occurrences of extreme weather and climate events over the world. The China Meteorological Administration, the National Natural Science Foundation of China, and the Chinese Academy of Sciences jointly initiated the Third Tibetan Plateau Atmospheric Science Experiment(TIPEX-Ⅲ) in 2013, with an 8–10-yr implementation plan. Since its preliminary field measurements conducted in 2013, routine automatic sounding systems have been deployed at Shiquanhe, Gaize, and Shenzha stations in western TP, where no routine sounding observations were available previously. The observational networks for soil temperature and soil moisture in the central and western TP have also been established. Meanwhile, the plateau-scale and regional-scale boundary layer observations, cloud–precipitation microphysical observations with multiple radars and aircraft campaigns, and tropospheric–stratospheric air composition observations at multiple sites, were performed. The results so far show that the turbulent heat exchange coefficient and sensible heat flux are remarkably lower than the earlier estimations at grassland, meadow, and bare soil surfaces of the central and western TP. Climatologically, cumulus clouds over the main body of the TP might develop locally instead of originating from the cumulus clouds that propagate northward from South Asia. The TIPEX-Ⅲ observations up to now also reveal diurnal variations, macro-and microphysical characteristics, and water-phase transition mechanisms, of cumulus clouds at Naqu station. Moreover, TIPEX-Ⅲ related studies have proposed a maintenance mechanism responsible for the Asian 'atmospheric water tower' and demonstrated the effects of the TP heating anomalies on African, Asian, and North American climates. Additionally, numerical modeling studies show that the Γ distribution of raindrop size is more suitable for depicting the TP raindrop characteristics compared to the M–P distribution, the overestimation of sensible heat flux can be reduced via modifying the heat transfer parameterization over the TP, and considering climatic signals in some key areas of the TP can improve the skill for rainfall forecast in the central and eastern parts of China. Furthermore, the TIPEX-Ⅲ has been promoting the technology in processing surface observations, soundings, and radar observations, improving the quality of satellite retrieved soil moisture and atmospheric water vapor content products as well as high-resolution gauge–radar–satellite merged rainfall products, and facilitating the meteorological monitoring, forecasting, and data sharing operations. | Ping ZHAO Yueqing LI Xueliang GUO Xiangde XU Yimin LIU Shihao TANG Wenming XIAO Chunxiang SHI Yaoming MA Xing YU Huizhi LIU La JIA Yun CHEN Yanju LIU Jian LI Dabiao LUO Yunchang CAO Xiangdong ZHENG Junming CHEN An XIAO Fang YUAN Donghui CHEN Yang PANG Zhiqun HU Shengjun ZHANG Lixin DONG Juyang HU Shuai HAN Xiuji ZHOU | 2019 | Journal of Meteorological Research2019，33，3： | 4 |
| 9 | Targeted energy transfer of a parallel nonlinear energy sink显示文摘A parallel nonlinear energy sink(NES) is proposed and analyzed. The parallel NES is composed of a vibro-impact(VI) NES and a cubic NES. The dynamical equation is given, and the essential analytical investigation is carried out to deal with the cubic nonlinearity and impact nonlinearity. Multiple time-scale expansion is introduced, and the zeroth order is derived to give a rough outline of the system. The underlying Hamilton dynamic equation is given, and then the optimal stiffness is expressed. The clearance is regarded as a critical factor for the VI. Based on the periodical impact treatment by analytical investigation, the relationships of the cubic stiffness, the clearance, and the zeroth-order attenuation amplitude of the linear primary oscillator(LPO) are obtained.A cubic NES under the optimal condition is compared with the parallel NES. Harmonic signals, harmonic signals with noises, and the excitation generated by a second-order?lter are considered as the potential excitation forces on the system. The targeted energy transfer(TET) in the designed parallel NES is shown to be more e?cient. | Yimin WEI Sha WEI Qianlong ZHANG Xinjian DONG Zhike PENG Wenming ZHANG | 2019 | Applied Mathematics and Mechanics(English Edition)2019，40，5： | 4 |
| 10 | eGPS 1.0: comprehensive software for multi-omic and evolutionary analyses显示文摘It has become increasingly challenging for researchers to analyze the exponentially expanding amount of multi-omic data.Here,we describe multi-functional software named evolutionary GenotypePhenotype Systems(eGPS)that enables users to perform comprehensive multiomic and evolutionary analyses.The eGPS combines the power of cloud computing and the advantage of desktop application,has a user-friendly graphic interface and is highly interactive. | Dalang Yu Lili Dong Fangqi Yan Hailong Mu Bixia Tang Xiao Yang Tao Zeng Qing Zhou Feng Gao Zhonghuang Wang Ziqian Hao Hongen Kang Yi Zheng Hongwei Huang Yuzhang Wei Wei Pan Yaochen Xu Junwei Zhu Shilei Zhao Ciran Wang Pengyu Wang Long Dai Mushan Li Li Lan Yiwei Wang Hua Chen Yi-Xue Li Yun-Xin Fu Zhen Shao Yiming Bao Fangqing Zhao Luo-Nan Chen Guo-Qing Zhang Wenming Zhao Haipeng Li | 2019 | National Science Review2019，6，5： | 4 |
| 11 | The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR显示文摘On January 22,2020,China National Center for Bioinformation(CNCB)released the 2019 Novel Coronavirus Resource(2019nCoVR),an open-access information resource for the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).2019nCoVR features a comprehensive integration of sequence and clinical information for all publicly available SARS-CoV-2 isolates,which are manually curated with value-added annotations and quality evaluated by an automated in-house pipeline.Of particular note,2019nCoVR offers systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global scale.It provides all identified variants and their detailed statistics for each virus isolate,and congregates the quality score,functional annotation,and population frequency for each variant.Spatiotemporal change for each variant can be visualized and historical viral haplotype network maps for the course of the outbreak are also generated based on all complete and high-quality genomes available.Moreover,2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on the coronavirus disease 2019(COVID-19),including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe PMC.Furthermore,by linking with relevant databases in CNCB,2019nCoVR offers data submission services for raw sequence reads and assembled genomes,and data sharing with NCBI.Collectively,SARS-CoV-2 is updated daily to collect the latest information on genome sequences,variants,haplotypes,and literature for a timely reflection,making 2019nCoVR a valuable resource for the global research community.2019nCoVR is accessible at https://bigd.big.ac.cn/ncov/. | Shuhui Song Lina Ma Dong Zou Dongmei Tian Cuiping Li Junwei Zhu Meili Chen Anke Wang Yingke Ma Mengwei Li Xufei Teng Ying Cui Guangya Duan Mochen Zhang Tong Jin Chengmin Shi Zhenglin Du Yadong Zhang Chuandong Liu Rujiao Li Jingyao Zeng Lili Hao Shuai Jiang Hua Chen Dali Han Jingfa Xiao Zhang Zhang Wenming Zhao Yongbiao Xue Yiming Bao | 2020 | Genomics, Proteomics & Bioinformatics2020，18，6： | 4 |
| 12 | Transport and humification of dissolved organic matter within a semi-arid floodplain显示文摘In order to understand the transport and humification processes of dissolved organic matter(DOM) within sediments of a semi-arid floodplain at Rifle,Colorado,fluorescence excitation–emission matrix(EEM) spectroscopy,humification index(HIX) and specific UV absorbance(SUVA) at 254 nm were applied for characterizing depth and seasonal variations of DOM composition.Results revealed that late spring snowmelt leached relatively fresh DOM from plant residue and soil organic matter down into the deeper vadose zone(VZ).More humified DOM is preferentially adsorbed by upper VZ sediments,while non-or lesshumified DOM was transported into the deeper VZ.Interestingly,DOM at all depths undergoes rapid biological humification process evidenced by the products of microbial by-product-like(i.e.,tyrosine-like and tryptophan-like) matter in late spring and early summer,particularly in the deeper VZ,resulting in more humified DOM(e.g.,fulvic-acid-like and humic-acid-like substances) at the end of year.This indicates that DOM transport is dominated by spring snowmelt,and DOM humification is controlled by microbial degradation,with seasonal variations.It is expected that these relatively simple spectroscopic measurements(e.g.,EEM spectroscopy,HIX and SUVA) applied to depth-and temporally-distributed pore-water samples can provide useful insights into transport and humification of DOM in other subsurface environments as well. | Wenming Dong Jiamin Wan Tetsu K.Tokunaga Benjamin Gilbert Kenneth H.Williams | 2017 | Journal of Environmental Sciences2017，29，7： | 3 |
| 13 | Parametric identification of time-varying systems from free vibration using intrinsic chirp component decomposition显示文摘Time-varying systems are applied extensively in practical applications,and their related parameter identification techniques are of great significance for structural health monitoring of time-varying systems.To improve the identification accuracy for time-varying systems,this study puts forward a novel parameter identification approach in the time-frequency domain using intrinsic chirp component decomposition(ICCD).ICCD is a powerful tool for signal decomposition and parameter extraction,with good signal reconstruction capability in a high-noise environment.To maintain good identification effects for the time-varying system in a noisy environment,the proposed method introduces a redundant Fourier model for the non-stationary signal,including instantaneous frequency(IF)and instantaneous amplitude(IA).The accuracy and effectiveness of the proposed approach are demonstrated by a single-degree-of-freedom system with three types of time-varying parameters,as well as an example of a multi-degree-of-freedom system.The effects of different levels of measured noise on the identified results are also discussed in detail.Numerical results show that the proposed method is very effective in tracking the smooth,periodical,and non-smooth variations of time-varying systems over the entire identification time period even when the response signal is contaminated by intense noise. | Sha Wei Shiqian Chen Xingjian Dong Zhike Peng Wenming Zhang | 2020 | Acta Mechanica Sinica2020，36，1： | 3 |
| 14 | Effects of various metals and their loading methods on the mesopore formation in pitch-based spherical activated carbon显示文摘 | Zhichang Liu Licheng Ling Wenming Qiao Chunxiang Lu Dong Wu Lang Liu | 1999 | Carbon1999，37，8： | 1 |
| 15 | Modal identification of multi-degree-of-freedom structures based on intrinsic chirp component decomposition method显示文摘Modal parameter identification is a mature technology.However,there are some challenges in its practical applications such as the identification of vibration systems involving closely spaced modes and intensive noise contamination.This paper proposes a new time-frequency method based on intrinsic chirp component decomposition(ICCD)to address these issues.In this method,a redundant Fourier model is used to ameliorate border distortions and improve the accuracy of signal reconstruction.The effectiveness and accuracy of the proposed method are illustrated using three examples:a cantilever beam structure with intensive noise contamination or environmental interference,a four-degree-of-freedom structure with two closely spaced modes,and an impact test on a cantilever rectangular plate.By comparison with the identification method based on the empirical wavelet transform(EWT),it is shown that the presented method is effective,even in a high-noise environment,and the dynamic characteristics of closely spaced modes are accurately determined. | Sha WEI Shiqian CHEN Zhike PENG Xingjian DONG Wenming ZHANG | 2019 | Applied Mathematics and Mechanics(English Edition)2019，40，12： | 1 |
| 16 | Adsorption and desorption of radioiodine in a calcareous soil 显示文摘 | Wang Xiangke Dong Wenming Guo Zhijun Gao Huibin Du Jinzhou Tao Zuyi | 2001 | Adsorpt Sci Technol2001，19，9： | 1 |
| 17 | Comparative Study on Sorption/Adsorption of Radioeuropium on Alumina, Bentonite and Red Earth: Effects of pH, Ionic Strength, Fulvic Acid and Iron Oxids in Red Earth显示文摘 | Dong Wenming Wang Xiangke Bian Xiaoyan | 2001 | Appl Radiat Isot2001，54，： | 1 |
| 18 | Sorption and Desorption of Eu and Yb on Alumina:Mechanisms and Effect of Fulvic Acid显示文摘 | Wang Xiangke Dong Wenming Dai Xiongxin | 2000 | Appl Radiat Isot2000，52，： | 1 |
| 19 | Sorption and desorption characteristics of Eu(Ⅲ) on red earth 显示文摘 | DONG Wenming WANG Xiangke DU Jinzhou | 1999 | Journal of Radioanalytical and Nuclear Chemistry1999，242，3： | 1 |
| 20 | Sorption and desorption of Eu and Yb on alumina:Mechanisms and effect of fulvic acid显示文摘 | WANG Xiangke DONG Wenming DAI Xiongxin | | 0，，02： | 1 |
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