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SIMULATION OF THE OIL SLICK MOVEMENT IN TIDAL WATER-WAYS

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Journal of Hydrodynamics 2010年第1期22卷 96-102页

作者： WUZhao-chun WANG Dao-zeng shanghai Institute of Applied Mathematics and Mechanics Shanghai University Shanghai 200072 China School of Construction and Safety Engineering Shanghai Institute of Technology Shanghai 200235 China

Based on particle approach and tidal flow model this article studies the behavior of the oil slick on the water surface in the Huangpu River, a tidal waterway in shanghai. In order to track the oil slick motion, a two-dimensional oil trajectory model is used. The dynamical properties of spilled oil characterized by advection, oil spreading and turbulent diffusion are considered in the model. The simulation results consistent with the flume experimental data show that the model is applicable. Both simulation and experiment illustrate that the tidal flow has a great influence on the oil slick motion. The calculated results can be used as a reference for the response to oil spill accidents in rivers.

关键词： particle approach track of oil slick numerical simulation

NUMERICAL SOLUTION FOR TIDAL FLOW IN OPENING CHANNEL USING COMBINED MACCORMACK-FINITE ANALYSIS METHOD

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Journal of Hydrodynamics 2009年第4期21卷 505-511页

作者： WU Zhao-chun WANG Dao-zeng shanghai Institute of Applied Mathematics and Mechanics Shanghai University Shanghai 200072 China School of Construction and Safety Engineering Shanghai Institute of Technology Shanghai 200235 China

A new numerical scheme for solving the tidal flow in an opening channel using the advective-diffusion shallow-water equations as the governing equations is proposed based on the combination of the MacCormack and the finite analysis methods. In the present scheme, the finite analysis method is used to discretize the momentum equation and the MacCormack technique is used to discretize the continuity equation in a single grid system. The matrix of the discretized momentum equation is characterized by predominantly main diagonal elements, which ensures favorable convergence and stability for the numerical simulation by the combined method. To verify the present method, hydraulics simulation is carried out for a section down mainstream of the Huangpu River. The computational results agree with the measured data. By use of orthogonal curvilinear coordinate system, the methods can be easily extended to the numerical simulation of the tidal flow in a tortuous channel.

关键词： MacCormack technique finite analysis method tidal flow shallow water equation numerical simulation

EMMA:An Efficient Massive Mapping Algorithm Using Improved Approximate Mapping Filtering

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Acta Biochimica et Biophysica Sinica 2006年第12期38卷 857-864页

作者： Xin ZHANG~1 Zhi-Wei CAO~2 Zhi-Xin LIN~3 Qing-Kang WANG~1* Yi-Xue LI~4 1 Institute of Micro/Nano Science and Technology,shanghai Jiaotong University,shanghai 200030,China 2 shanghai Center for Bioinformation Technology,shanghai 200235,China 3 College of Life Science and Technology,shanghai Jiaotong University,shanghai 200030,China 4 Bioinformation Center of shanghai Institutes for Biological Sciences,Chinese Academy of Sciences,shanghai 200031,China Institute of Micro/Nano Science and Technology Shanghai Jiaotong UniversityShanghai 200030 China shanghai Center for Bioinformation Technology Shanghai 200235 China College of Life Science and Technology Shanghai Jiaotong UniversityShanghai 200030 China Bioinformation Center of shanghai Institutes for Biological Sciences Chinese Academy of SciencesShanghai 200031 China

Efficient massive mapping algorithm (EMMA),an algorithm on efficiently mapping massivecDNAs onto genomic sequences,has recently been *** process of mapping massive cDNAsonto genomic sequences has been improved using more approximate mapping filtering based on an enhancedsuffix array coupled with a pruned fast hash table,algorithms of block alignment extensions,and *** compared with the classical BLAT software in this field,the computing of EMMA ranges fromtwo to forty-one times faster under similar prediction precisions.

关键词： cDNA mapping maximal exact match enhanced suffix array pruned fast hash table extension algorithm

SIMULATION OF LAGRANGIAN DISPERSION USING A LAGRANGIAN STOCHASTIC MODEL AND DNS IN A TURBULENT CHANNEL FLOW

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Journal of Hydrodynamics 2009年第6期21卷 767-773页

作者： LUO Jian-ping LU Zhi-ming LIU Yu-lu School of Mechanical and Automation Engineering Shanghai Institute of Technology Shanghai 200235 China shanghai Institute of Applied Mathematics and Mechanics Shanghai University Shanghai 200072 China

The mean square displacements of fluid particles in a turbulent channel flow at Reτ = 100 are investigated using a modified Langevin equation, and are compared with DNS results. Both the Lagrangian integral time scales directly obtained from DNS and the predicted values using an empirical relation between the Eulerian and the Lagrangian integral time scales are used in the modified Langevin equation to test the effects of integral time scales on the dispersion of particles. The results show that the slight variation of the Lagrangian integral time scale has little influence on the dispersion. The agreement between results of the model equation and those of DNS is satisfactory except the streamwise dispersion for intermediate times （ 20 〈 t^＋〈 300 ）, where the results of the model equation are slightly overestimated compared to those of DNS. The cause of such discrepancy is discussed.

关键词： turbulent channel flow Lagrangian dispersion Lagrangian stochastic model

Research on Hierarchical Supervision System and Emergency Engineering for Pudong Industrial Zone in shanghai

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Research on Hierarchical Supervision System and Emergency En...

Comparative Analysis of Two-component Signal Transduction System in Two Streptomycete Genomes

首届风险分析与危机反应国际学术研讨会

作者： WANG Xiao-qun ZHANG Xing-rong (shanghai Institute of Technology shanghai 200235 P. R. China)

＜正＞In order to strengthen the macroscopic supervision of dangerous sources in enterprises,hierarchical supervision systems must be built up in modern industrial *** article describes the present condition of production safety management in Pudong Industrial Zone,,and investigates a hierarchical monitoring system that is suitable for all enterprises in the industrial *** a hierarchical supervision system is explored by taking into account situations wherever production safety should be *** establishment of this system is based on the evaluation and calculation with the scientific safety evaluation method （hierarchy gray assessment method）.The purpose of hierarchical supervision is not only to prevent serious accidents but to minimize harm when an accident ***,the emergency engineering is also studied as an auxiliary measure.

关键词： Industrial Zone Hierarchical Supervision Evaluation System Hierarchy Gray Assessment Method Emergency

来源： cnki会议评论

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Acta Biochimica et Biophysica Sinica 2007年第5期39卷 317-325页

Species of the genus Streptomyces are major bacteria responsible for producing most natural antibiotics. Streptomyces coelicolor A3(2) and Streptomyces avermitilis were sequenced in 2002 and 2003, respectively. Two-component signal transduction systems (TCSs), consisting of a histidine sensor kinase (SK) and a cognate response regulator (RR), form the most common mechanism of transmembrane signal transduction in prokaryotes. TCSs in S. coelicolor A3(2) have been analyzed in detail. Here, we identify and classify the SK and RR of S. avermitilis and compare the TCSs with those of S. coelicolor A3(2) by computational approaches. Phylogenetic analysis of the cognate SK-RR pairs of the two species indicated that the cognate SK-RR pairs fall into four classes according to the distribution of their orthologs in other organisms. In addition to the cognate SK-RR pairs, some potential partners of non-cognate SK-RR were found, including those of unpaired SK and orphan RR and the cross-talk between different components in either strain. Our study provides new clues for further exploration of the molecular regulation mechanism of streptomycetes with industrial importance.

关键词： Streptomyces two-component system cross-talk phylogenetic analysis

Semantic Search among Heterogeneous Biological Databases Based on Gene Ontology

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Acta Biochimica et Biophysica Sinica 2004年第5期36卷 365-370页

作者： Shun-Liang CAO, Lei QIN1, Wei-Zhong HE1, Yang ZHONG2, Yang-Yong ZHU, and Yi-Xue LI1,3* Department of Computing and Information Technology, Fudan University, shanghai 200433, China shanghai Center for Bioinformation 1 Technology, shanghai 200235, China School of Life Sciences, Fudan University, shanghai 200433, China Bioinformation Center of shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, shanghai 200031, China Department of Computing and Information Technology Fudan University Shanghai 200433 China shanghai Center for Bioinformation Technology shanghai 200235 China School of Life Sciences Fudan University Shanghai 200433 China Bioinformation Center of shanghai Institutes for Biological Sciences the Chinese Academy of Sciences Shanghai 200031 China

Semantic search is a key issue in integration of heterogeneous biological databases. In this paper, we present a methodology for implementing semantic search in BioDW, an integrated biological data warehouse. Two tables are presented: the DB2GO table to correlate Gene Ontology (GO) annotated entries from BioDW data sources with GO, and the semantic similarity table to record similarity scores derived from any pair of GO terms. Based on the two tables, multifarious ways for semantic search are provided and the corresponding entries in heterogeneous biological databases in semantic terms can be expediently searched.

关键词： Gene Ontology semantic search BioDW

Functional analysis of schistosomes EF-hand domain-containing tegument proteins

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Chinese Science Bulletin 2007年第15期52卷 2100-2107页

作者： YU FuDong1,2,3,KANG Bin1,3,LI YuanYuan3,4 & LI YiXue1,3 1 Bioinformatics Center,Key Laboratory of Systems Biology,shanghai Institutes for Biological Sciences,Chinese Academy of Sci-ences,shanghai 200031,China 2 Graduate University of Chinese Academy of Sciences,shanghai 200031,China 3 shanghai Center for Bioinformation Technology,shanghai 200235,China 4 Key Laboratory of Systems Biology,shanghai Institutes for Biological Sciences,Chinese Academy of Sciences,shanghai 200031,China Bioinformatics Center Key Laboratory of Systems Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China Graduate University of Chinese Academy of Sciences Shanghai China shanghai Center for Bioinformation Technology Shanghai China Key Laboratory of Systems Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China

Schistosomes cause schistosomiasis disease which severely threatens human health. Little is known about the functions of EF-hand domain containing schistosomes tegument proteins other than as an-tigens. More possible functions of these tegument proteins were investigated with in silico analyses including protein-protein functional interaction,site-specific variation and glycosylation modification. The analysis results suggested that schistosomes could actively modulate host immune responses for its own favor through functional interactions with host proteins with immunomodulatory function,and passively regulate host immune responses through sequence variation under positive selection and glycosylating the recognition sites of host immune attack. In addition,the analysis of the C-terminal domain of these tegument proteins indicated that they could assist schistosomes in escaping host immune attacks through inhibiting chemotaxis and non-complement fixing antibody (IgG4) responses. In summary,our results suggested that these tegument antigen proteins could assist schistosomes in escaping and modulating host immune responses for self-protection during the process of host-para-site interaction.

关键词：寄生虫血吸虫皮蛋白质健康

Phylogeographic analysis of human papillomavirus 58

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Science China(Life Sciences) 2009年第12期52卷 1164-1172页

作者： LI YanYun1, LI ZuoFeng2, HE YiFeng1, KANG Yu1, ZHANG XiaoYan1, CHENG MingJun1, ZHONG Yang2, 3· & XU CongJian1· 1 Obstetrics and Gynecology Hospital of Fudan University, shanghai 200011, China 2 shanghai Bioinformation Research Center, shanghai 200235, China 3 School of Life Sciences, Fudan University, shanghai 200433, China Obstetrics and Gynecology Hospital of Fudan University Shanghai China shanghai Bio-information Research Center Shanghai China School of Life Sciences Fudan University Shanghai China

Human papillomavirus 58 (HPV58) is one type of HPV with high risk of causing cervical cancer. Unusually high prevalence of HPV58 has been reported in Asia, Africa and some other areas. However, due to the scattered distribution of global data, in addition to the lack of data of some HPV58 high-incidence nations and regions, like China's Mainland, a comprehensive analysis of the global geographical distribution of HPV58 remains blank so far. In this study, HPV58 from the human cervical cancer tissue was detected in China's Mainland, and 14 new HPV58-E6/L1 gene sequences were obtained. Moreover, phylogeographic analysis has been conducted combining the HPV58 sequences that have been deposited in GenBank since 1985. The study result shows that the sequences detected from the shanghai, Jiangsu and Sichuan areas are homologous with those found in the past from Hong Kong and Xi'an, China, as well as Japan and other Southeast Asian areas. Furthermore, Western Africa is considered to be the "root" source of the HPV58 variant, while China's Mainland and Southeast Asia are "transit points" and the new sources of HPV58 after receiving the isolates from the "root" source; like HPV16 and HPV18, the HPV58 might also be one of the major HPV types associated with the development and spread of cervical cancer.

关键词： human papillomavirus 58 (HPV58) cervical cancer phylogeography molecular evolution