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C^3:Consensus Cancer Driver Gene Caller

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Genomics, Proteomics & Bioinformatics 2019年第3期17卷 311-318页

作者： Chen-Yu Zhu Chi Zhou yun-Qin Chen Ai-Zong Shen Zong-Ming Guo Zhao-Yi Yang xiang-yun Ye Shen Qu Jia Wei Qi Liu Department of Endocrinology&Metabolism Shanghai Tenth People’s HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200092China Department of Ophthalmology Ninghai First HospitalNinghai 315600China R&D Information Innovation Center ChinaAstraZenecaShanghai 201203China Shanghai Chest Hospital Shanghai Jiaotong UniversityShanghai 200240China Department of Pharmacy The First Affiliated Hospital of University of Science and Technology of ChinaHefei 230036China

Next-generation sequencing has allowed identification of millions of somatic mutations in human cancer cells.A key challenge in interpreting cancer genomes is to distinguish drivers of cancer development among available genetic *** address this issue,we present the first webbased application,consensus cancer driver gene caller(C^3),to identify the consensus driver genes using six different complementary strategies,i.e.,frequency-based,machine learning-based,functional bias-based,clustering-based,statistics model-based,and network-based *** application allows users to specify customized operations when calling driver genes,and provides solid statistical evaluations and interpretable visualizations on the integration results.C^3 is implemented in Python and is freely available for public use at http://***/c3.

关键词： Somatic mutation Cancer driver genes Consensus Data integration Web server

Farmers' Self-decision Right in New Countryside Construction——An interview with Lu Xueyi,a specialist on rural issues

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The Journal of Human Rights 2006年第6期5卷 4-6页

作者： yun xiang

Lu Xueyi graduated from the Philosophy Department of Beijing University in 1962. He pursued graduate studies at the Philosophy Institute of the Chinese Academy of Social Sciences during 1962-1965. He has long been engaged in the study of sociology, social structure and rural development. He worked once as director of the Sociology Institute of CASS. After 1998 he.. has served as member of the Academic Committee of CASS. In 1996 he became president of China Sociology Society. He was a deputy to the Eighth and Ninth National People＇s Congresses. He is author of The Chinese Countryside and Chinese Farmers amid Reforms, Chinese Society in a Transitional Period, Evolution of China＇s Social Structure and On Agriculture, the Countryside and Peasantry.

关键词： Self-decision Right in New Countryside Construction Farmers An interview with Lu Xueyi,a specialist on rural issues

Safeguarding Farmer Workers' Rights and Interests——An interview with Ye Jingyi, professor of Beijing University Law School

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The Journal of Human Rights 2007年第2期6卷 8-11页

作者： yun xiang

Farmer workers are a new powerful workforce that has sprung up amid China＇s reform and door opening and in the process of the country＇s industrialization and urbanization. They have made great contributions to urban prosperity, rural development and their country＇s modernization. At present, however, farmer workers face numerous difficulties and problems in income, work safety, social security, vocational training, the schooling of their children and living conditions. To safeguard the legitimate rights and interests of farmer workers, the State Council in March 2006 issued Ideas of the State Council on Solving Farmer Workers-related Problems. In the document, the State Council promises to strengthen and improve leadership over work regarding farmer workers and prioritize the solving of farmer workers-related problems.

关键词： work Rights and Interests Safeguarding Farmer Workers professor of Beijing University Law School An interview with Ye Jingyi

Phylogenetic conservatism in threatened species responses to climate change differs between functional types in the Gongga Mountains of China

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Journal of Mountain Science 2023年第12期20卷 3568-3581页

作者： ZU Kui-ling Nawal SHRESTHA JIANG Yong JIA Guo-qing PENG Shi-jia ZHU xiang-yun WANG Zhi-heng Key Laboratory of National Forestry and Grassland Administration on Forest Ecosystem Protection and Restoration of Poyang Lake Watershed College of ForestryJiangxi Agricultural UniversityNanchang 330045China Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education College of Urban and Environmental SciencesPeking UniversityBeijing 100871China State Key Laboratory of Plant Diversity and Specialty Crops Institute of BotanyChinese Academy of SciencesBeijing 100093China State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems College of EcologyLanzhou UniversityGansuLanzhou 730000China Administration of Gongga Mountain National Nature Reserve Kangding 626000China

Climate change has become one of the most critical threats to global ***,whether phylogenetically related species respond to climate change in similar ways remains *** answer to this question is crucial for understanding the impacts of climate change and the conservation on the tree of *** integrating species distribution models with a molecular phylogeny of 50 threatened plant species from one of the global biodiversity hotspots,Gongga Mountains(***)in southwest China,we evaluated the responses of threatened plant species to future climate change,and estimated whether species responses are phylogenetically *** reconstruction was used to calculate the phylogenetic distance and null model to verify the reliability of the *** found that correlations between responses of different species to future climate change decreased with the increase in their phylogenetic distance in the monocotyledonous or herbaceous species,but not in the dicotyledonous and woody *** results suggested that the responses of herbaceous and monocotyledonous threatened species in *** to future climate change tend to be phylogenetically conserved,while the responses of woody and dicotyledonous threatened species are *** study provides evidence for the existence of phylogenetically non-random extinction in the monocotyledonous herbs in *** and highlights the importance of integrating phylogenetic information and evolutionary history into conservation *** also provide theoretical basis and technical support for designing effective conservation schemes for the protection of biodiversity under anthropogenic climate change.

关键词： Conservation strategies Climate suitability Mountain plants Phylogenetic distance Species distribution models

Gold nanolabels and enzymatic recycling dual amplification-based electrochemical immunosensor for the highly sensitive detection of carcinoembryonic antigen

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Science China Chemistry 2011年第11期54卷 1770-1776页

作者： ZHANG YuYong xiang yun CHAI YaQin YUAN Ruo QIAN XiaoQing ZHANG HaiXia CHEN Ying SU Jiao XU Jin Education Ministry Key Laboratory on Luminescence and Real-Time Analysis School of Chemistry and Chemical EngineeringSouthwest UniversityChongqing 400715China

A sensitive electrochemical immunoassay system for the detection of a protein tumor biomarker through a dual amplified strategy was reported. Firstly, this protocol involves in the electropolymerization of o-aminobenzoic acid (o-ABA) on a glass carbon electrode (GCE). Subsequently, capture anti-CEA (Abl) is covalently linked to poly(o-ABA) (PAB) film, via N-(3-dimethylamminopropyl)-N'-ethylcarbodiimide hydrochloride (EDC), and N-hydroxysulfosuccinimid sodium salt (NHS) activation of the carboxyl groups and surface blocking with ethanolamine. Later, the target, carcinoembryonic antigen (CEA), is sandwiched between an electrode surface confined Ab1 and the alkaline phosphatase-labeled signal anti-CEA antibodies conjugated with gold nanoparticles (Ab2-ALP-AuNP bioconjugates). The dual biocatalytic signal amplification for CEA monitoring is achieved by coupling the numerous enzymes loaded on the AuNPs with redox-recycling of the enzymatic products in the presence of the secondary enzyme and the corresponding substrate. The novel dramatic signal amplification strategy, exhibits a good linearity at the studied concentration range from 0.005 to 50 ng mL-1 towards CEA with a detection limit of 2 pg mL-1 (S/N=3). There is a 5-100-fold improvement in detection limit compared to other similar studies. The developed dual signal amplified strategy shows good selectivity, regeneration, stability and acceptable reproducibility. Therefore, the signal amplification approach holds great potential applications in detection of ultra-trace protein biomarkers.

关键词： amplification electrochemical immunosensor carcinoembryonic antigen redox-recycling

Ab initio free energy simulations come of age

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Ab initio free energy simulations come of age

Structure effect of nucleotides in terbium(Ⅲ)-nucleotide fluorescent reaction—-New evidence for the binding sites of terbium(Ⅲ) on nucleotides

中国化学会第29届学术年会

作者： yun xiang State Key Laboratory of Precision Spectroscopy Department of Physics Institute of Theoretical and Computational Science East China Normal University

Recent progress in simulation methodology and computer power has made free energy calculations of chemical and biological processes in the condensed phase based on ab initio potentials largely *** this talk,I will report our work on computational enzymology using ab initio QM/MM molecular dynamics simulation combined with polarizable force field to elucidate both the reaction mechanism in the active site of enzymes and the orgin of their catalytic *** interesting enzymatic systems we will discuss include the ribozyme ribosome and the protein enzyme DNA polymerase?.Multidimensional free energy surfaces obtained directly from density functional theory calculations will be *** importantly,our study has led to the finding that proteins’electronic polarization contributes significantly to their catalytic functions.

关键词：

来源： cnki会议评论

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cnki会议

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Chinese Journal of Chemistry 1993年第6期11卷 524-531页

作者： LI Yuan-Zong CHANG Wen-Bao CI yun-xiang Department of Chemistry Beijing UniversityBeijing 100871

Upon addition of Tb^(3+) to 16 nucleotides and homopolynucleotides, all of them showed a characteristic green emission from Tb^(3+), but with much different intensity, upon excitation in the aromatic region of bases. The result suggested that nucleotides with at least one carbonyl group in nucleotide bases are better enhancers to the fluorescence of Tb3+. The complexes of ATP, GDP and GTP with T5^(3+) are synthesized as two types of models. Guanine tpye nucleotides with one carbonyl group in the bases are the best enhancers, while adenine type nucleotides with no carbonyl group in the bases are poorest enhancers to the fluorescence of Tb^(3+). Comparing the IR spectra of ATP, GTP, GDP and their Tb^(3+) complexes suggested that C-6 carbonyl group in GTP and GDP may be involved in complex formation, which may be responsible for the effective energy transfer. This is further supported by comparing the UV spectra of ATP, Poly(A), GTP, and Poly(G) with their Tb^(3+) complexes in water solution.

关键词： nucleotide fluorescent reaction Structure effect of nucleotides in terbium New evidence for the binding sites of terbium

Novel THP algorithms with minimum BER criterion for MIMO broadcast communications

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The Journal of China Universities of Posts and Telecommunications 2009年第4期16卷 71-77页

作者： yun xiang,L Tie-jun School of Information and Communication Engineering,Beijing University of Posts and Telecommunications,Beijing 100876,China [a]School of Information and Communication Engineering Beijing University of Posts and Telecommunications Beijing 100876 China

In this article, two novel Tomlinson-Harashima precoding （THP） algorithms are proposed at the downlink broadcast channel of multi-user multiple-input multiple-output （MIMO） systems. The optimality criterion is the minimization of the bit error rate （BER） at the receiver with a constraint on the overall transmitted power. In these algorithms, transmit power allocation （TPA） matrix is introduced to the traditional THP algorithms as part of the precoding matrix. This leads to a power loading operation based on substreams signal to interference-plus-noise ratio （SINR） and results in improvement of the error rate performance compared with traditional THP algorithms. When the precoding loss factor is considered, further performance improvement is achieved by the enhanced algorithm.

关键词： MIMO system THP minimum bit-error rate (MBER) broadcast communication

Subacute toxicity of exogenous manganese on rat hippocampal neurons Examination by MRI and optical microscopy

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Neural Regeneration Research 2008年第5期3卷 550-553页

作者： Xiaoli Xu yun xiang Min Yang School of Medicine ＆ Life Science Jianghan University Wuhan 430056 Hubei Province China

BACKGROUND： Manganism may cause learning and memory impairment by influencing the normal function of the hippocampus, however, this effect requires further examination. OBJECTIVE： To investigate the effects of manganism on the rat hippocampus using immunohistochemistry and MRI examination. DESIGN, TIME AND SETTING： A randomized controlled study, performed in the School of Medicine and Life Science, Jianghan University and the State Key Laboratory of Atomic ＆ Molecular Physics and Spectroscopy, Chinese Academy of Science, from July to September 2005. MATERIALS： Fourteen healthy SD rats aged two months were selected for this study. MnCl2 4H2O （BHD, UK）（batch number： 9791325）; glial fibrillary acidic protein （GFAP） staining kit （Beijing Zhongshan Biotechnology）; Biospec 4.7T/30 animal MRI formatter （Bruker, Germany）. METHODS： Fourteen rats were randomly divided into a control group （n =7） and a manganism group （n = 7）. Rats in the manganism group received intraperitoneal injection of MnCl2 · 4H2O （50 mg/kg）, once a day, for four successive days. Rats in the control group were injected according to the manganism regimen, but using saline instead of manganese solution. MAIN OUTCOME MEASURES： Twenty-four hours after the last injection, rats were examined using MRI. Immunohistochemically stained GFAP and hematoxylin-eosin stained hippocampal sections were observed under optical microscopy. RESULTS： Fourteen rats were included in the final analysis. After manganese treatment, T1 weighted image and inversion recovery MR1 demonstrated that the signal intensity was significantly enhanced in hippocampus, compared to controls. Neuronal necrosis was not observed in the hippocampus after HE staining. As compared to the control group, GFAP expression was markedly enhanced in the hippocampus of the manganism group. CONCLUSION： Within the rat brain, manganese preferentially localizes to the hippocampus and can induce astroctye activation.

关键词： manganism hippocampus rats MRI glial fibrillary acidic protein