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| 1 | clusterProfiler 4.0:A universal enrichment tool for interpreting omics data显示文摘Functional enrichment analysis is pivotal for interpreting highthroughput omics data in life science.It is crucial for this type of tool to use the latest annotation databases for as many organisms as possible.To meet these requirements,we present here an updated version of our popular Bioconductor package,clusterProfiler 4.0.This package has been enhanced considerably compared with its original version published 9 years ago.The new version provides a universal interface for functional enrichment analysis in thousands of organisms based on internally supported ontologies and pathways as well as annotation data provided by users or derived from online databases.It also extends the dplyr and ggplot2 packages to offer tidy interfaces for data operation and visualization.Other new features include gene set enrichment analysis and comparison of enrichment results from multiple gene lists.We anticipate that clusterProfiler 4.0 will be applied to a wide range of scenarios across diverse organisms. | Tianzhi Wu Erqiang Hu Shuangbin Xu Meijun Chen Pingfan Guo Zehan Dai Tingze Feng Lang Zhou Wenli Tang Li Zhan Xiaocong Fu Shanshan Liu Xiaochen Bo Guangchuang Yu | 2021 | The Innovation2021，2，3： | 40 |
| 2 | Phase 1 clinical trial demonstrated that MUC1 positive metastatic seminal vesicle cancer can be effectively eradicated by modified Anti-MUC1 chimeric antigen receptor transduced T cells显示文摘Recent progress in chimeric antigen receptor-modified T-cell(CAR-T cell) technology in cancer therapy is extremely promising, especially in the treatment of patients with B-cell acute lymphoblastic leukemia. In contrast, due to the hostile immunosuppressive microenvironment of a solid tumor, CAR T-cell accessibility and survival continue to pose a considerable challenge, which leads to their limited therapeutic efficacy. In this study, we constructed two anti-MUC1 CAR-T cell lines. One set of CAR-T cells contained SM3 single chain variable fragment(sc Fv) sequence specifically targeting the MUC1 antigen and co-expressing interleukin(IL) 12(named SM3-CAR). The other CAR-T cell line carried the SM3 sc Fv sequence modified to improve its binding to MUC1 antigen(named p SM3-CAR) but did not co-express IL-12. When those two types of CAR-T cells were injected intratumorally into two independent metastatic lesions of the same MUC1+ seminal vesicle cancer patient as part of an interventional treatment strategy, the initial results indicated no side-effects of the MUC1 targeting CAR-T cell approach, and patient serum cytokines responses were positive. Further evaluation showed that p SM3-CAR effectively caused tumor necrosis, providing new options for improved CAR-T therapy in solid tumors. | Fengtao You Licui Jiang Bozhen Zhang Qiang Lu Qiao Zhou Xiaoyang Liao Hong Wu Kaiqi Du Youcai Zhu Huimin Meng Zhishu Gong Yunhui Zong Lei Huang Man Lu Jirong Tang Yafen Li Xiaochen Zhai Xiangling Wang Sisi Ye Dan Chen Lei Yuan Lin Qi Lin Yang | 2016 | Science China(Life Sciences)2016，59，4： | 16 |
| 3 | mTOR/miR-145-regulated exosomal GOLM1 promotes hepatocellular carcinoma through augmented GSK-3b/MMPs显示文摘Golgi membrane protein 1(GOLM1/GP73)is a serum marker of hepatocellular carcinoma(HCC).We have previously shown that mTOR promoted tumorigenesis of HCC through stimulating GOLM1 expression.In this study,we demonstrated that the mammalian target of rapamycin(mTOR)was a negative regulator of microRNA-145(miR-145)expression.miR-145 inhibited GOLM1 expression by targeting a coding sequence of GOLM1 gene.GOLM1 and miR-145 were inversely correlated in human HCC tissues.GOLM1-enriched exosomes activated the glycogen synthase kinase-3β/matrix metalloproteinases(GSK-3β/MMPs)signaling axis of recipient cells and accelerated cell proliferation and migration.In contrast,miR-145 suppressed tumorigenesis and metastasis.We suggest that mTOR/miR-145/GOLM1 signaling pathway should be targeted for HCC treatment. | Xiaochen Gai Bufu Tang Fangming Liu Yuting Wu Fang Wang Yanling Jing Fuqiang Huang Di Jin Ling Wang Hongbing Zhang | 2019 | Journal of Genetics and Genomics2019，46，5： | 13 |
| 4 | Major advances in studies of the physical geography and living environment of China during the past 70 years and future prospects显示文摘The natural environment provides material essentials for human survival and development. The characteristics,processes, regional differentiation and forcing mechanisms of the elements of the natural environment(e.g. geomorphology,climate, hydrology, soil, etc.) are the main objects of research in physical geography. China has a complex natural environment and huge regional differentiation and therefore it provides outstanding reserach opportunities in physical geography. This review summarizes the most important developments and the main contributions of research in the physical geography and human living environment in China during the past 70 years. The major topics addressed are the uplift of the Tibetan Plateau and the evolution of its cryosphere, the development of fluvial systems, the acidification of the vast arid region of the Asian interior, variations in the monsoon and westerly climate systems on multiple timescales, the development of lakes and wetlands, the watershed system model, soil erosion, past human-environment interactions, biogeography, and physical geographic zonality. After briefly introducing international research developments, we review the history of research in physical geography in China, focusing on the major achievements and major academic debates, and finally we summarize the status of current research and the future prospects. We propose that in the context of the national demand for the construction of an ecological civilization, we should make full use of the research findings of physical geography, and determine the patterns and mechanisms of natural environmental processes in order to continue to promote the continued contribution of physical geography to national development strategies, and to further contribute to the theory of physical geography from a global perspective. | Fahu CHEN Bojie FU Jun XIA Duo WU Shaohong WU Yili ZHANG Hang SUN Yu LIU Xiaomin FANG Boqiang QIN Xin LI Tingjun ZHANG Baoyuan LIU Zhibao DONG Shugui HOU Lide TIAN Baiqing XU Guanghui DONG Jingyun ZHENG Wei YANG Xin WANG Zaijun LI Fei Wang Zhenbo HU Jie WANG Jianbao LIU Jianhui CHEN Wei HUANG Juzhi HOU Qiufang CAI Hao LONG Ming JIANG Yaxian HU Xiaoming FENG Xingguo MO Xiaoyan YANG Dongju ZHANG Xiuhong WANG Yunhe YIN Xiaochen LIU | 2019 | Science China Earth Sciences2019，62，11： | 11 |
| 5 | Microvascular protective role of pericytes in melatonin-treated spinal cord injury in the C57BL/6 mice显示文摘 | Jing Yingli Wu Qingbin Yuan Xiaochen Li Bingwei Liu Mingming Zhang Xiaoyan Liu Shuying Li Hongwei Xiu Ruijuan | 2014 | Chinese Medical Journal2014，，15： | 9 |
| 6 | Retrieval and Analysis of Coal Fire Temperature in Wuda Coalfield, Inner Mongolia, China显示文摘Coal fire burning around the world is an environmental catastrophe characterized by the emission of noxious gases, particulate matter, and condensation by-products. In this study, coal fire temperature is retrieved based on Landsat 5 TM images and Generalized Single-Channel Algorithm (GSCA), in Wuda coalfield, Inner Mongolia, China. Then coal fire zones are extracted by Jenks′ natural breaks and threshold methods based on temperature images. Changes of coal fire zones are analyzed from 1989 to 2008. The results are summarized as follows: 1) The coal fire temperature retrieval method based on Landsat 5 TM and the GSCA model is effective and feasible, because the temperature error is relatively small (from –2.9℃ to +2.6℃) between the measured temperature and the retrieved temperature. 2) The accuracy is relatively high to extract coal fire zones through the Jenks′ natural breaks and threshold methods, because 83.56% of surveyed area is located in the coal fire zones extracted in 2005. 3) The coal fire area increased 9.81 × 10 5 m 2 from 1989 to 2005, and the annual growth is about 6.1 × 10 4 m 2 , with an annual increasing rate of 2.48%. The area of coal fire decreased by 8.1 × 10 5 m 2 from 2005 to 2008. | JIANG Weiguo ZHU Xiaohua WU Jianjun GU Lei MA Guobin LIU Xiaochen | 2011 | Chinese Geographical Science2011，21，2： | 7 |
| 7 | Magnetic resonance imaging with three-dimensional fast imaging employing steady-state acquisition with phase-cycled and short T1 inversion recovery pulse sequence for evaluating brachial plexus injury显示文摘There is a large amount of fat in the postganglionic segment of the brachial plexus nerve.The use of short T1 inversion recovery pulse sequence may improve signal strength of the brachial plexus postganglionic segment.The present study revealed that the combination of three-dimensional fast imaging employing steady-state acquisition with phase-cycled and short T1 inversion recovery pulse sequence clearly displayed the anatomical morphology and structure of the brachial plexus nerve,together with maximum intensity projection,volume rendering and other three-dimensional reconstruction techniques.Our results suggested that this method is also suitable for providing accurate assessment and diagnosis of the site,severity and scope of brachial plexus injury. | Dianxiu Ning Meiyu Sun Bo Sun Li Zhao Weisheng Zhang Lijun Wang Shaowu Wang Ailian Liu Jianlin Wu Zhijin Lang Di Ning Guanfu Liu Xiaochen Ji Xiufeng Wang | 2011 | Neural Regeneration Research2011，6，14： | 7 |
| 8 | Comparison of nonhuman primates identified the suitable model for COVID-19显示文摘Identification of a suitable nonhuman primate(NHP)model of COVID-19 remains challenging.Here,we characterized severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)infection in three NHP species:Old World monkeys Macaca mulatta(M.mulatta)and Macaca fascicularis(M.fascicularis)and New World monkey Callithrix jacchus(C.jacchus).Infected M.mulatta and M.fascicularis showed abnormal chest radiographs,an increased body temperature and a decreased body weight.Viral genomes were detected in swab and blood samples from all animals.Viral load was detected in the pulmonary tissues of M.mulatta and M.fascicularis but not C.jacchus.Furthermore,among the three animal species,M.mulatta showed the strongest response to SARS-CoV-2,including increased inflammatory cytokine expression and pathological changes in the pulmonary tissues.Collectively,these data revealed the different susceptibilities of Old World and New World monkeys to SARS-CoV-2 and identified M.mulatta as the most suitable for modeling COVID-19. | Shuaiyao Lu Yuan Zhao Wenhai Yu Yun Yang Jiahong Gao Junbin Wang Dexuan Kuang Mengli Yang Jing Yang Chunxia Ma Jingwen Xu Xingli Qian Haiyan Li Siwen Zhao Jingmei Li Haixuan Wang Haiting Long Jingxian Zhou Fangyu Luo Kaiyun Ding Daoju Wu Yong Zhang Yinliang Dong Yuqin Liu Yinqiu Zheng Xiaochen Lin Li Jiao Huanying Zheng Qing Dai Qiangming Sun Yunzhang Hu Changwen Ke Hongqi Liu Xiaozhong Peng | 2020 | Signal Transduction and Targeted Therapy2020，5，1： | 5 |
| 9 | Nuclear m^(6)A reader YTHDC1 regulates the scaffold function of LINE1 RNA in mouse ESCs and early embryos显示文摘N^(6)-methyladenosine(m^(6)A)on chromosome-associated regulatory RNAs(carRNAs),including repeat RNAs,plays important roles in tuning the chromatin state and transcription,but the intrinsic mechanism remains unclear.Here,we report that YTHDC1 plays indispensable roles in the self-renewal and differentiation potency of mouse embryonic stem cells(ESCs),which highly depends on the m^(6)A-binding ability.Ythdcl is required for sufficient rRNA synthesis and repression of the 2-cell(2C)transcriptional program in ESCs,which recapitulates the transcriptome regulation by the LINE1 scaffold.Detailed analyses revealed that YTHDC1 recognizes m^(6)A on LINE1 RNAs in the nucleus and regulates the formation of the LINE1-NCL partnership and the chromatin recruitment of KAP1.Moreover,the establishment of H3K9me3 on 2C-related retrotrans-posons is interrupted in Ythdcl-depleted ESCs and inner cell mass(ICM)cells,which consequently increases the transcriptional activities.Our study reveals a role of m^(6)A in regulating the RNA scaffold,providing a new model for the RNA-chromatin cross-talk. | Chuan Chen Wenqiang Liu Jiayin Guo Yuanyuan Liu Xuelian Liu Jun Liu Xiaoyang Dou Rongrong Le Yixin Huang Chong Li Lingyue Yang Xiaochen Kou Yanhong Zhao You Wu Jiayu Chen Hong Wang Bin Shen Yawei Gao Shaorong Gao | 2021 | Protein & Cell2021，12，6： | 4 |
| 10 | Experimental investigations on cavity-actuated under-expanded supersonic oscillating jet显示文摘As one type of potential flow control actuators, cavity-actuated supersonic jet oscillators,which consist of a 2-D convergent nozzle and two face to face cavities, need to be investigated deeply to get the knowledge of their oscillating feature and underlying mechanism. Wind tunnel testing are conducted under different back pressures in a vacuum-type wind tunnel for two supersonic jet oscillators, to obtain their characteristics and the conditions for jet oscillating. The experimental results show that the continuous, nearly symmetric or asymmetric flipping between the two cavities appears over certain nozzle pressure ratio(NPR) range for both oscillators according to schlieren visualizations. Compared to the free jet, the oscillating jet with large exit achieves larger mixing; the oscillating jet with small exit has less mixing, based on the analysis of jet axial peak velocity and the entrainment. The cross-junction mode for estimating the resonance frequency in a pipe with two closed side branches is modified and obtained comparable estimations of the frequency of jet flipping with experimental data, but further investigations are needed to discover the underlying mechanism for the jet flipping. | Sun Bo Luo Xiaochen Feng Feng Wu Xiaosong | 2015 | Chinese Journal of Aeronautics2015，28，5： | 4 |
| 11 | Emission Characteristics of VOCs from Automobile Coating Industry in Chongqing City显示文摘To fully analyze emission characteristics of volatile organic compounds( VOCs) from automobile coating industry in Chongqing City,related enterprises in the city were investigated in detail. The results show that the emission of VOCs from the automobile industry in Chongqing City was approximately 20 000 t in 2012,and the contribution rate of automobile coating was 83%. Most VOCs discharged from automobile coating industry were mainly from the use of coatings,diluents,curing agents and other materials containing VOCs. During the process of automobile coating,VOCs were mainly produced during the processes of spraying and drying. Besides,VOCs are partly produced during the processes of mixing paint,gluing,waxing,and repairing. The major ingredients of VOCs discharged during the process of automobile coating were methylbenzene,dimethylbenzene,trimethylbenzene,cumene,ethyl acetate,butyl alcohol,n-butyl alcohol,isobutyl alcohol,formaldehyde,butanone,acetone,cyclohexanone,and methyl ethyl ketone. Besides,the ingredients of naphtha and aromatic hydrocarbon in VOCs need to be determined. The maximum ozone formation potential( OFP) of the above pollutants by the typical enterprises was 900-1 300 mg/m^3. The production of secondary organic aerosol( SOA) was 3 636-11 073 t/a,which didn't include the contribution of aldehydes,ketones,ethers and esters to SOA. This research could provide scientific reference for the establishment of emission standard,control technology and management methods of VOCs from automobile coating industry that accord with economic and social development in Chongqing City. | Zhou Zhi'en Fang Weikai Luo Qian Wang Xiaochen Wu Liping | 2017 | Meteorological and Environmental Research2017，8，3： | 3 |
| 12 | CRISPR/Cas9-mediated genome engineering of the ferret显示文摘 | Zhaohui Kou Qian Wu Xiaochen Kou Chonghai Yin Hong Wang Zhentao Zuo Yan Zhuo Antony Chen Shaorong Gao Xiaoqun Wang | 2015 | Cell Research2015，25，12： | 3 |
| 13 | Frequency-dependent random fatigue of panel-type structures made of ceramic matrix composites显示文摘The panel-type structures used in aerospace engineering can be subjected to severe highfrequency acoustic loadings in service. This paper evaluates the frequency-dependent random fatigue of panel-type structures made of ceramic matrix composites(CMCs) under acoustic loadings. Firstly, the high-frequency random responses from the broadband random excitation will result in more stress cycles in a deinite period of time. The probability density distributions of stress amplitudes will be different in different frequency bandwidths, though the peak stress estimations are identical. Secondly, the fatigue properties of CMCs can be highly frequency-dependent. The fatigue evaluation method for the random vibration case is adopted to evaluate the fatigue damage of a representative stiffened panel structure. The frequency effect through S-N curves on random fatigue damage is numerically veriied. Finally, a parameter is demonstrated to characterize the mean vibration frequency of a random process, and hence this parameter can further be considered as a reasonable loading frequency in the fatigue tests of CMCs to obtain more reliable S-N curves.Therefore, the inluence of vibration frequency can be incorporated in the random fatigue model from the two perspectives. | Yadong Zhou Xiaochen Hang Shaoqing Wu Qingguo Fei Natasa Trisovic | 2017 | Acta Mechanica Solida Sinica2017，30，2： | 2 |
| 14 | Epidemiology of foodborne disease outbreaks caused by Vibrio parahaemolyticus , China, 2003–2008显示文摘 | Yongning Wu Jian Wen Yi Ma Xiaochen Ma Yan Chen | 2014 | Food Control2014，，： | 2 |
| 15 | Study on the Control Strategy of Free Piston Expander-Linear Generator Used for Organic Rankine Cycle Waste Heat Recovery显示文摘This study presents a free piston expander-linear generator (FPE-LG) for engine waste heat recovery.The control strategies based on displacement (control strategy A) and valve timings (control strategy B) are proposed.The operation and output characteristics with different control strategies are conducted.The results show that control strategy has significant effect on the FPE-LG performance.When FPE-LG operates with control strategy A,the operation frequency is determined by the intake pressure,advanced exhaust duration,fixed position point and external load resistance,whereas it is only related with the intake/exhaust time and advanced exhaust duration (ta) for control strategy B.The external load resistance has slight influence on the stroke length for these two control strategies.For control strategy A,when advanced exhaust duration is more than 40 ms,the stroke length rises with the intake pressure,whereas it first rises and then reduces when advanced exhaust duration is less than 40 ms.There exist the optimal external load resistance and advanced exhaust duration to achieve the maximum power output with control strategy A,whereas the average power output reduces with the increasing advanced exhaust duration when using control strategy B.Stable operation and high power output can be obtained by using different control strategies and adjusting relevant operation parameters. | HOU Xiaochen ZHANG Hongguang ZHAO Tenglong SHI Xin XU Yonghong LI Jian GE Zhong ZHANG Jun WU Yuting | 2021 | Journal of Thermal Science2021，30，2： | 1 |
| 16 | Nano-TiO2/PEEK bioactive composite as a bone substitute material: in vitro and in vivo studies显示文摘 | Feng Deng Wei Guo Xiaochen Liu Wu | 2012 | International Journal of Nanomedicine . 2012 (defa)2012，，： | 1 |
| 17 | Data-aware clustering hierarchy for wireless sensor networks 显示文摘 | Wu Xiaochen Wang Peng | 2008 | Lecture Notes in Computer Science2008，5012，： | 1 |
| 18 | Pre-ribosomal RNA reorganizes DNA damage repair factors in nucleus during meiotic prophase and DNA damage response显示文摘In response to DNA double strand breaks(DSBs),DNA damage repair factors are recruited to DNA lesions and form nuclear foci.However,the underlying molecular mechanism remains largely elusive.Here,by analyzing the localization of DSB repair factors in the XY body and DSB foci,we demonstrate that pre-ribosomal RNA(pre-rRNA)mediates the recruitment of DSB repair factors around DNA lesions.Pre-rRNA exists in the XY body,a DSB repair hub,during meiotic prophase,and colocalizes with DSB repair factors,such as MDC1,BRCA1 and TopBP1.Moreover,pre-rRNA-associated proteins and RNAs,such as ribosomal protein subunits,RNase MRP and snoRNAs,also localize in the XY body.Similar to those in the XY body,pre-rRNA and ribosomal proteins also localize at DSB foci and associate with DSB repair factors.RNA polymerase I inhibitor treatment that transiently suppresses transcription of rDNA but does not affect global protein translation abolishes foci formation of DSB repair factors as well as DSB repair.The FHA domain and PST repeats of MDC1 recognize pre-rRNA and mediate phase separation of DSB repair factors,which may be the molecular basis for the foci formation of DSB repair factors during DSB response. | Xiaochen Gai Di Xin Duo Wu Xin Wang Linlin Chen Yiqing Wang Kai Ma Qilin Li Peng Li Xiaochun Yu | 2022 | Cell Research2022，32，3： | 1 |
| 19 | Covalently combi- ning carbon nanotubes with anticaneer agent: preparation and antitumor activity显示文摘 | Wu Wei Li RuTian Bian XiaoChen el al | 2009 | ACS Nano2009，3，9： | 1 |
| 20 | Effects of long-term chemical fertilization and organic amendments on dynamics of soil organic C and total N in paddy soil derived from barren land in subtropical China显示文摘 | Zhongpei Li Ming Liu Xiaochen Wu Fengxiang Han Taolin Zhang | 2009 | Soil & Tillage Research2009，，2： | 1 |
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