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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 | 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 |
| 3 | 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 |
| 4 | 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 |
| 5 | 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 |
| 6 | 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 |
| 7 | 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 |
| 8 | 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 |
| 9 | Sub-cytotoxic concentrations of ionic silver promote the proliferation of human keratinocytes by inducing the production of reactive oxygen species显示文摘 | Xiaodong Duan Daizhi Peng Yilan Zhang Yalan Huang Xiao Liu Ruifu Li Xin Zhou Jing Liu | 2018 | Frontiers of Medicine2018，12，3： | 1 |
| 10 | Enhanced root colonization and biocontrol activity of Bacillus amyloliquefaciens SQR9 by abrB gene disruption显示文摘 | Jun Weng Yang Wang Juan Li Qirong Shen Ruifu Zhang | 2013 | Applied Microbiology and Biotechnology2013，，19： | 1 |
| 11 | Application of bio-organic fertilizer can control Fusarium wilt of cucumber plants by regulating microbial community of rhizosphere soil显示文摘 | Meihua Qiu Ruifu Zhang Chao Xue Shusheng Zhang Shuqing Li Nan Zhang Qirong Shen | 2012 | Biology and Fertility of Soils2012，，7： | 1 |
| 12 | Failure Process of Rock Sample Observed by AE Source Locating Technique under Uniaxial Compression 显示文摘 | YUANHUI LI RUIFU YUAN XINGDONG ZHAO | 2006 | Key Engineering Material2006，324，56： | 1 |
| 13 | Simultaneous biodegradation of methyl parathion and carbofuran by a genetically engineered microorganism constructed by mini-Tn5 transposon显示文摘 | Jiandong Jiang Ruifu Zhang Rong Li Ji-Dong Gu Shunpeng Li | 2007 | Biodegradation2007，，4： | 1 |
| 14 | Numerical simulation of tensile damage and blast crater in brittle rock due to underground explosion显示文摘 | WANG Zhiliang LI Yongchi SHEN Ruifu | 2007 | International Journal of Rock Mechanics & Mining Sciences2007，44，5： | 1 |
| 15 | Genetic and Functional Differences of Escherichia coli Strains from Colorectal Cancer Mucosal Tissues显示文摘Colorectal cancer(CRC)is the third leading cancer globally.Metagenomics has been widely used to analyze the association between the gut microbiota and CRC based on bacterial genus-or species-level comparisons,providing evidence of dysbiosis in CRC development.However,this kind of analysis is unable to provide strain-level information for understanding the individual role of a species in CRC.Here,we used culturomics to isolate CRC mucosal samples and selected 158 Escherichia coli strains to reveal their differences in both genomics and functions by means of phylogenetic analysis and inflammatory induction based on cell and animal experiments.Through genomic comparison,these strains were divided into five phylogroups.The representative strains of each phylogroup significantly induced different levels of cytokine secretion by human leukemic monocyte(THP-1 cell)-based Transwell and animal experiments.Further bioinformatic analysis revealed different profiles of single-nucleotide polymorphisms,genes,and metabolic pathways in the different phylogroups,which can improve the current understanding of the phenotypic differences between these strains.The strain differences revealed in both genomics and functions indicate that the microbiota’s function at the strain level should be investigated in order to understand the interacting mechanisms between hosts and gut bacteria. | Yuxiao Chang Xiang Li Lei Ding Chao Yang Zhiyuan Pan Ni Han Yujun Cui Fachao Zhi Ruifu Yang Hong Gao Yujing Bi | 2022 | Engineering2022，，9： | 0 |
| 16 | Single-cell transcriptomics of immune cells in lymph nodes reveals their composition and alterations in functional dynamics during the early stages of bubonic plague显示文摘Bubonic plague caused by Yersinia pestis is highly infectious and often fatal.Characterization of the host immune response and its subsequent suppression by Y.pestis is critical to understanding the pathogenesis of Y.pestis.Here,we utilized single-cell RNA sequencing to systematically profile the transcriptomes of immune cells in draining lymph nodes(d LNs)during the early stage of Y.pestis infection.Dendritic cells responded to Y.pestis within 2 h post-infection(hpi),followed by the activation of macrophages/monocytes(Mφs/Mons)and recruitment of polymorphonuclear neutrophils(PMNs)to d LNs at 24 hpi.Analysis of cell-to-cell communication suggests that PMNs may be recruited to lymph nodes following the secretion of CCL9 by Mφs/Mons stimulated through CCR1-CCL9 interaction.Significant functional suppression of all the three innate immune cell types occurred during the early stage of infection.In summary,we present a dynamic immune landscape,at single-cell resolution,of murine d LNs involved in the response to Y.pestis infection,which may facilitate the understanding of the plague pathogenesis of during the early stage of infection. | Yifan Zhao Tong Wang Ziyang Liu Yuehua Ke Ruoyan Li Hongyan Chen Yang You Gengshan Wu Shiyang Cao Zongmin Du Fan Bai Ruifu Yang | 2023 | Science China(Life Sciences)2023，66，1： | 0 |
| 17 | Research on evolution of mining pressure field and fracture field and gas emission features显示文摘The relation betweenmining pressure field-fracture field and gas emission of working face is analyzed,and the concept that there is a stress point (or strain point) among permeability of coal is presented.It is believed that the mutation of coal permeability caused by the sudden loading or unloading of working face roof as periodic weighting occurs is the main reason that a lot of gas pour into the working face.Based on the above concept,the relation is established among abutment pressure during periodic weighting,permeability of coal seam and gas emission,and relation graph is drawn.Then the loading and unloading features of coal at the moment of fracture and non-fracture of main roof are revealed.And finally it is presented that the process of sudden loading or unloading as periodic weighting occurs plays an important role in rupture propagation of coal,analytical movement of gas and gas emission. | Li Huamin Xiong Zuqiang Li Dongyin Yuan Ruifu Wang Wen | 2012 | Engineering Sciences2012，10，2： | 0 |
| 18 | 高产酒精肺炎克雷伯菌引起的非酒精性脂肪肝病显示文摘文章简介非酒精性脂肪肝(NAFLD)具有进展为肝硬化和肝细胞癌的风险,其潜在病因多种多样,目前认为NAFLD与肠道微生物群的变化有关,然而,它们之间的因果关系尚不清楚。研究团队发现肠道菌群中高产酒精的肺炎克雷伯菌(HiAlc Kpn)可能是NAFLD的一个病因。在NAFLD患者人群中,高达60%的患者肠道菌群中含有HiAlc Kpn。 | 袁静 Chen Chen Jinghua Cui Jing Lu Chao Yan Xiao Wei Xiangna Zhao NanNan Li Shaoli Li Guanhua Xue Weiwei Cheng Boxing Li Huan Li Weishi Lin Changyu Tian Jiangtao Zhao Juqiang Han Daizhi An Qiong Zhang Hong Wei Minghua Zheng Xuejun Ma Wei Li Xiao Chen Zheng Zhang Hui Zeng Sun Ying JianXin Wu Ruifu Yang 刘翟 | 2020 | 科学新闻2020，，2： | 0 |
| 19 | Subsoil tillage enhances wheat productivity,soil organic carbon and available nutrient status in dryland fields显示文摘Tillage practices during the fallow period benefit water storage and yield in dryland wheat crops.However,there is currently no clarity on the responses of soil organic carbon(SOC),total nitrogen(TN),and available nutrients to tillage practices within the growing season.This study evaluated the effects of three tillage practices(NT,no tillage;SS,subsoil tillage;DT,deep tillage)over five years on soil physicochemical properties.Soil samples at harvest stage from the fifth year were analyzed to determine the soil aggregate and aggregate-associated C and N fractions.The results indicated that SS and DT improved grain yield,straw biomass and straw carbon return of wheat compared with NT.In contrast to DT and NT,SS favored SOC and TN concentrations and stocks by increasing the soil organic carbon sequestration rate(SOCSR)and soil nitrogen sequestration rate(TNSR)in the 0-40 cm layer.Higher SOC levels under SS and NT were associated with greater aggregate-associated C fractions,while TN was positively associated with soluble organic nitrogen(SON).Compared with DT,the NT and SS treatments improved soil available nutrients in the 0-20 cm layer.These findings suggest that SS is an excellent practice for increasing soil carbon,nitrogen and nutrient availability in dryland wheat fields in North China. | Qiuyan Yan Linjia Wu Fei Dong Shuangdui Yan Feng Li Yaqin Jia Jiancheng Zhang Ruifu Zhang Xiao Huang | 2024 | Journal of Integrative Agriculture2024，23，1： | 0 |
| 20 | Biosynthesis and Immunological Evaluation of a Dual-Antigen Nanoconjugate Vaccine Against Brucella melitensis显示文摘Brucellosis,caused by Brucella,is one of the most common zoonosis.However,there is still no vaccine for human use.Although some live attenuated vaccines have been approved for animals,the protection effect is not ideal.In this study,we developed a dual-antigen nanoconjugate vaccine containing both polysaccharide and protein antigens against Brucella.First,the antigenic polysaccharide was covalently coupled to the outer membrane protein Omp19 using protein glycan coupling technology,and then it was successfully loaded on a nano-carrier through the SpyTag/SpyCatcher system.After confirming the efficient immune activation and safety performance of the dual-antigen nanoconjugate vaccine,the potent serum antibody response against the two antigens and remarkable protective effect in non-lethal and lethal Brucella infection models were further demonstrated through different routes of administration.These results indicated that the dual-antigen nanoconjugate vaccine enhanced both T helper 1 cell(Th1)and Th2 immune responses and protected mice from Brucella infection.Furthermore,we found that this protective effect was maintained for at least 18 weeks.To our knowledge,this is the first Brucella vaccine bearing diverse antigens,including a protein and polysaccharide,on a single nanoparticle.Thus,we also present an attractive technology for co-delivery of different types of antigens using a strategy applicable to other vaccines against infectious diseases. | Jing Huang Yufei Wang Kangfeng Wang Shulei Li Peng Sun Yan Guo Jiankai Liu Ruifu Yang Ming Zeng Chao Pan Hengliang Wang Li Zhu | 2023 | Engineering2023，，10： | 0 |
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