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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 | Seismic analysis of a LNG storage tank isolated by a multiple friction pendulum system显示文摘The seismic response of an isolated vertical, cylindrical, extra-large liquefi ed natural gas (LNG) tank by a multiple friction pendulum system (MFPS) is analyzed. Most of the extra-large LNG tanks have a fundamental frequency which involves a range of resonance of most earthquake ground motions. It is an effective way to decrease the response of an isolation system used for extra-large LNG storage tanks under a strong earthquake. However, it is diff icult to implement in practice with common isolation bearings due to issues such as low temperature, soft site and other severe environment factors. The extra-large LNG tank isolated by a MFPS is presented in this study to address these problems. A MFPS is appropriate for large displacements induced by earthquakes with long predominant periods. A simplifi ed fi nite element model by Malhotra and Dunkerley is used to determine the usefulness of the isolation system. Data reported and statistically sorted include pile shear, wave height, impulsive acceleration, convective acceleration and outer tank acceleration. The results show that the isolation system has excellent adaptability for different liquid levels and is very effective in controlling the seismic response of extra-large LNG tanks. | Zhang Ruifu Weng Dagen Ren Xiaosong | 2011 | Earthquake Engineering and Engineering Vibration2011，10，2： | 17 |
| 3 | Acoustic emission activity in directly tensile test on marble specimens and its tensile damage constitutive model显示文摘 | Ruifu Yuan Bowen Shi | 2018 | International Journal of Coal Science & Technology2018，5，3： | 11 |
| 4 | Trial of small gateroad pillar in top coal caving longwall mining of large mining height显示文摘Coal seams in Tashan Mine of Datong Coal Group in China average 15 m thick and have been mined by the top coal caving longwall mining method of large mining height. Mining height was 3.8 m and the top coal caving height was 11.2 m. The gateroad pillar between panels was 38 m. During retreat mining,serious bumps occurred in the gateroads on both sides of the pillar affecting safety production. Therefore,pillarless mining was experimented. Using numerical modeling and comparative study of cases of similar mining condition,it was decided to employ a 6 m wide pillar,rather than the previous 38 m wide pillar.Support system for the gateroads was designed and implemented. During gateroad development,pillar failure conditions and entry deformation were monitored. Hydraulic fracturing method was employed to cut off the K3 sandstone along the entry rib so as to reduce the abutment pressure induced during retreat mining. Support reinforcement method combining grouting and advanced reinforcement methods was proposed to insure stable gateroad ahead of mining. Methane drainage and nitrogen injection were implemented to eliminate hazards associated with mine fire and spontaneous combustion. Since the development of gateroad has just completed,and retreat mining has not begun,the effectiveness of the proposed methods is unknown at this point. However,monitoring will continue until after mining.The results will be published in a separate paper. | Li Huamin Syd Peng Li Huigui Xu Yongxiang Yuan Ruifu Yue Shuaishuai Li Kun | 2016 | International Journal of Mining Science and Technology2016，26，1： | 8 |
| 5 | An Ebola virus-encoded microRNA-like fragment serves as a biomarker for early diagnosis of Ebola virus disease显示文摘 | Zeliang Chen Hongwei Liang Xi Chen Yuehua Ke Zhen Zhou Mingjuan Yang Ke Zen Ruifu Yang Chao Liu Chen-Yu Zhang | 2016 | Cell Research2016，26，3： | 7 |
| 6 | Formation and regulation of Yersinia biofilms显示文摘Flea-borne transmission is a recent evolutionary adaptation that distinguishes the deadly Yersinia pestis from its progenitor Y.pseudotuberculosis,a mild pathogen transmitted via the food-borne route.Y.pestis synthesizes biofilms in the flea gut,which is important for fleaborne transmission.Yersinia biofilms are bacterial colonies surrounded by extracellular matrix primarily containing a homopolymer of N-acetyl-D-glucosamine that are synthesized by a set of specific enzymes.Yersinia biofilm production is tightly regulated at both transcriptional and post-transcriptional levels.All the known structural genes responsible for biofilm production are harbored in both Y.pseudotuberculosis and Y.pestis,but Y.pestis has evolved changes in the regulation of biofilm development,thereby acquiring efficient arthropod-borne transmission. | Dongsheng Zhou Ruifu Yang | 2011 | Protein & Cell2011，2，3： | 6 |
| 7 | Shiga toxin-producing Escherichia coli O104:H4: An emerging 0important pathogen in food safety显示文摘In 2011, Shiga toxin-producing Escherichia coli O104 : H4 resulted in a large outbreak of bloody diarrhea and hemolytic uremic syndrome (HUS) in Germany and 15 other countries in Europe and North America. This event raised a serious public health crisis and caused more than two billion US dollars in economic losses. In this review, we describe the classification of E. coli, the Germany outbreak, and the characteristics and epidemical source-tracing of the causative agent. We also discuss the genomics analysis of the outbreak organism and propose an open-source genomics analysis as a new strategy in combating the emerging infectious diseases. | CUI YuJun LI DongFang YANG RuiFu | 2013 | Chinese Science Bulletin2013，58，14： | 5 |
| 8 | IL-17A-dependent gut microbiota is essential for regulating diet-induced disorders in mice显示文摘The gut microbiota plays a key role in obesity and related metabolic disorders, and multiple factors including diet, host genotype, and age regulate it. Many studies have examined the contribution of extrinsic factors to the regulation of the gut microbiota, but the importance of the host genetic constitution cannot be ignored. Interleukin 17A(IL-17A), a pro-inflammatory cytokine, is important in the defense against infection and diseases. Here, we investigated the association among IL-17, a high-fat diet(HFD), and the gut microbiota. Mice deficient in IL-17A were resistant to diet-induced obesity and related diseases. Compared with the Ⅱ-17^(-/-)mice, wild-type(WT) mice challenged with HFD showed obvious weight fluctuations, such as those seen in type 2 diabetes, and hematological changes similar to those associated with metabolic syndrome. However, housing WT mice and Ⅱ-17a^(-/-)mice together significantly alleviated these symptoms in the WT mice. A metagenomic analysis of the mouse feces indicated that the microbial community compositions of these two groups differed before HFD feeding. The HFD mediated shifts in the gut microbial compositions, which were associated with the mouse phenotypes.We also identified potentially beneficial and harmful species present during this period, and drew networks of the most abundant species. A functional analysis indicated pathway changes in the WT and Ⅱ-17a^(-/-)mice when fed the HFD. Collectively, these data underscore the importance of the host factor IL-17 A in shaping and regulating the gut microbiota, which conversely, influences the host health. | Yujing Bi Chunxiao Li Lin Liu Jiyuan Zhou Zhengchao Li Huimin Deng Chunyan Wu Yanping Han Yajun Song Yafang Tan Xiaoyi Wang Zongmin Du Yujun Cui Yanfeng Yan Fachao Zhi Guangwei Liu Nan Qin Heping Zhang Ruifu Yang | 2017 | Science Bulletin2017，62，15： | 5 |
| 9 | Alterations in gut microbiota and metabolites associated with altitude-induced cardiac hypertrophy in rats during hypobaric hypoxia challenge显示文摘The gut microbiota is involved in host responses to high altitude.However,the dynamics of intestinal microecology and their association with altitude-related illness are poorly understood.Here,we used a rat model of hypobaric hypoxia challenge to mimic plateau exposure and monitored the gut microbiome,short-chain fatty acids(SCFAs),and bile acids(BAs)over 28 d.We identified weight loss,polycythemia,and pathological cardiac hypertrophy in hypoxic rats,accompanied by a large compositional shift in the gut microbiota,which is mainly driven by the bacterial families of Prevotellaceae,Porphyromonadaceae,and Streptococcaceae.The aberrant gut microbiota was characterized by increased abundance of the Parabacteroides,Alistipes,and Lactococcus genera and a larger Bacteroides to Prevotella ratio.Trans-omics analyses showed that the gut microbiome was significantly correlated with the metabolic abnormalities of SCFAs and BAs in feces,suggesting an interaction network remodeling of the microbiome-metabolome after the hypobaric hypoxia challenge.Interestingly,the transplantation of fecal microbiota significantly increased the diversity of the gut microbiota,partially inhibited the increased abundance of the Bacteroides and Alistipes genera,restored the decrease of plasma propionate,and moderately ameliorated cardiac hypertrophy in hypoxic rats.Our results provide an insight into the longitudinal changes in intestinal microecology during the hypobaric hypoxia challenge.Abnormalities in the gut microbiota and microbial metabolites contribute to the development of high-altitude heart disease in rats. | Zhiyuan Pan Yichen Hu Zongyu Huang Ni Han Yan Li Xiaomei Zhuang Jiye Yin Hui Peng Quansheng Gao Wenpeng Zhang Yong Huang Yujun Cui Yujing Bi Zhenjiang Zech Xu Ruifu Yang | 2022 | Science China(Life Sciences)2022，65，10： | 5 |
| 10 | Theoretical and experimental analysis on the mechanism of the Kaiser effect of acoustic emission in brittle rocks显示文摘The Kaiser effect is formally described as the absence of detectable acoustic emission(AE)events until the load imposed on the material exceeds the previous applied level and is usually used to estimate geostress.By focusing on the heterogeneity of rock material,the mechanism of the Kaiser effect under cyclic loading is analyzed based on statistic damage mechanics.Two groups of granite specimens have been cyclically loaded with two different loading paths to verify the theoretical results.The heterogeneity of rock is the real reason that causes irrecoverable damage on the Kaiser effect of acoustic emission in cyclic loading.The Kaiser effect reflects the damaged state in rocks rather than the previous stress imposed on it.Applications for using the Kaiser effect to estimate geostress were discussed here.It is shown that the commonly used uniaxiai loading method for estimating geostress is not in accor- dance with the theoretical and experimental results.The analysis is of importance to use the Kaiser effect correctly for estimating geostress or in other fields. | Ruifu Yuan Yuanhui Li | 2008 | Journal of University of Science and Technology Beijing2008，15，1： | 4 |
| 11 | Heat-fluid-solid coupling model for gas-bearing coal seam and numerical modeling on gas drainage promotion by heat injection显示文摘Improving the absorbed gas to active desorption and seepage and delaying gas drainage attenuation are considered as key methods for increasing drainage efficiency and gas output.According to the solid mechanics theory,the nonlinear Darcy seepage theory and thermodynamics,the heat-fluid-solid coupling model for gassy coal has been improved.The numerical model was founded from the improved multi-field coupling model by COMSOL Multiphysics and gas drainage by borehole down the coal seam enhanced by heat injection was modelled.The results show that the heatfluid-solid model with adsorption effects for gassy coal was well simulated by the improved multi-field model.The mechanism of coal seam gas desorption seepage under the combined action of temperature,stress and adsorption can be well described.Gas desorption and seepage can be enhanced by heat injection into coal seams.The gas drainage rate was directly proportional to the temperature of injected heat in the scope of 30-150 ℃ and increasing in the whole modelleddrainage process (0-1000 d).The increased level was maximum in the initial drainage time and decreasing gradually along with drainage time.The increasing ratio of drainage rate was maximum when the temperature raised from 30 to 60 ℃.Although the drainage rate would increase along with increasing temperature,when exceeding 60 ℃,the increasing ratio of drainage rate with rising temperature would decrease.Gas drainage promotion was more effective in coal seams with lower permeability than with higher permeability.The coal seam temperature in a 5 m distance surrounding the heat injection borehole would rise to around 60 ℃ in 3 months.That was much less than the time of gas drainage in the coal mines in sites with low permeability coal seams.Therefore,it is valuable and feasible to inject heat into coal seams to promote gas drainage,and this has strong feasibility for coal seams with low permeability which are widespread in China. | Ruifu Yuan Chunling Chen Xiao Wei Xiaojun Li | 2019 | International Journal of Coal Science & Technology2019，6，4： | 4 |
| 12 | Transcriptomic Response to Yersinia pestis:RIG-I Like Receptor Signaling Response Is Detrimental to the Host against Plague显示文摘Bacterial pathogens have evolved various mechanisms to modulate host immune responses for successful infection.In this study,RNAsequencing technology was used to analyze the responses of human monocytes THP1 to Yersinia pestis infection.Over 6000 genes were differentially expressed over the 12 h infection.Kinetic responses of pathogen recognition receptor signaling pathways,apoptosis,antigen processing,and presentation pathway and coagulation system were analyzed in detail.Among them,RIG-I-like receptor(RLR) signaling pathway,which was established for antiviral defense,was significantly affected.Mice lacking MAVS,the adaptor of the RLR signahng pathway,were less sensitive to infection and exhibited lower IFN-P production,higher Thl-type cytokines IFN-y and IL-12 production,and lower Th2-type cytokines EL-4 and IL-13 production in the serum compared with wild-type mice.Moreover,infection of pathogenic bacteria other than Y.pestis also altered the expression of the RLR pathway,suggesting that the response of RLR pathway to bacterial infection is a universal mechanism. | Zongmin Du Huiying Yang Yafang Tan Guang Tian Qingwen Zhang Yujun Cui Yanfeng Yan Xiaohong Wu Zuyun Chen Shiyang Cao Yujing Bi Yanping Han Xiaoyi Wang Yajun Song Ruifu Yan | 2014 | Journal of Genetics and Genomics2014，41，7： | 2 |
| 13 | Transcriptional regulation of the waaAE-coaD operon by PhoP and RcsAB in Yersinia pestis biovar Microtus显示文摘亲爱的编辑, | Lei Liu Nan Fang Yicheng Sun Huiying Yang Yiquan Zhang Yanping Han Dongsheng Zhou Ruifu Yang | 2014 | Protein & Cell2014，5，12： | 2 |
| 14 | Changes in biochemical and microbiological parameters during the period of rapid composting of dairy manure with rice chaff显示文摘 | Liu Dongyang Zhang Ruifu Wu Hongsheng | 2011 | Bioresource Technology2011，102，19： | 1 |
| 15 | Pandora of Ebola virus: are we ready?显示文摘在 2014 年 3 月 23 日,畿尼的健康的部通知了在东南的 forested 区域的 Ebola 病毒疾病(EVD ) 的很快传播的爆发,并且 4 ? 天以后,疾病被证实被传给 Conakry,畿尼的首都。疾病很快也传播了到利比里亚,尼日利亚和塞拉利昂。2014 年 7 月 27 日,累积数字证实(909 ) ,可能(276 ) 并且在上述四个国家的嫌疑犯(138 ) EVD 盒子到达了 1,323,包括 729 死亡(与 55.1 的死亡率 ?%)(http://gffzz36b398b81f8a4a4choub06w050bc66of0.ffgz.tsg.suse.edu.cn/csr/don/2014_07_31_ebola/en/) 。这是 EVD 的最大的爆发直到现在并且第一次疾病在韦斯特检测了非洲。 | Ruifu Yang | 2014 | Chinese Science Bulletin2014，59，32： | 1 |
| 16 | Distinctness of spore and vegetative cellular fatty acid profiles of some aerobic endospore-forming bacilli显示文摘 | SONG Yajun YANG Ruifu GUO Zhaobiao | 2000 | J Microbiol Methods2000，39，3： | 1 |
| 17 | Changes in biochemical and microbiological parameters during the period of rapid composting of dairy manure with rice chaff显示文摘 | Dongyang Liu Ruifu Zhang Hongsheng Wu Dabing Xu Zhu Tang Guanghui Yu Zhihui Xu Qirong Shen | 2011 | Bioresource Technology2011，，19： | 1 |
| 18 | Detection of Francisella tularensis by the polymerase chain reaction 显示文摘 | Zhai Junhui Yang Ruifu Lu Jianchun | 1996 | J Med Microbiol1996，45，： | 1 |
| 19 | Experimen- tal Investigation of Flow Resistance and Convection Heat Transfer of CO2 at Supercritical Pressures in a Vertical Porous Tube 显示文摘 | JIANG Peixue Shi Ruifu Xu Yijun | 2006 | The Journal of Supercritical Fluids2006，38，： | 1 |
| 20 | Seven facts and five initiatives for gut microbiome research显示文摘The gut microbiome has attracted increasing attention over the past 15 years.Along with the fast-growing body of research literature and media reports,the public's opinions on the gut microbiome have begun to appear polarized.Some believe that the gut microbiome is at the core of human health and is related to every single disease.To the opposite,some people question the scientific basis of gut microbiome studies and criticize that many of them are farfetched;there is even a joke spreading in the biomedical research field—'keeping gut microbiome in mind,no mechanism is hard to find'. | Danyi Li Chunhui Gao Faming Zhang Ruifu Yang Canhui Lan Yonghui Ma Jun Wang | 2020 | Protein & Cell2020，11，6： | 1 |
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