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Analysis of tandem repeats in the genome of chinese shrimp Fenneropenaeus chinensis

chinese Science Bulletin 2005年第14期50卷 1462-1469页

作者： KONG Jie1 & GAO Huan2.3 1. Key Laboratory for Sustainable Utilization of Marine Fisheries Re- sources, Ministry of Agriculture, Yellow Sea Fisheris Research Insti- tute, chinese academy of Fishery {2., Qingdao 2.6071, china 2. Institute of Oceanology, chinese academy of {2., Qingdao 2.6071, china 3. The Graduate school of the chinese academy of {2.,{12., china Key Laboratory for Sustainable Utilization of Marine Fisheries Resources Ministry of Agriculture Yellow Sea Fisheris Research Institute Chinese Academy of Fishery Sciences Qingdao China Institute of Oceanology Chinese Academy of Sciences Qingdao China The Graduate school of the chinese {2. of sciences Beijing China

Through random sequencing, we found a total of 884000 base-pairs (bp) of random genomic sequences in the genome of chinese shrimp (Fenneropenaeus chinensis). Using bio-soft Tandem Repeat Finder (TRF) software, 2.59 tandem repeats were found, in which there were 1714 mi- crosatellites and 445 minisatellites, accounting for 79.4% and 2..6% of repeat sequences, respectively. The cumulative length of repeat sequences was found to be 116685 bp, ac- counting for 13.2. of the total DNA sequence; the cumula- tive length of microsatellites occupied 9.78% of the total DNA sequence, and that of minisatellites occupied 3.42.. In decreasing order, the 2. most abundant repeat sequence classes were as follows: AT (557), AC (471), AG (2.4), AAT (92., A (56), AAG (2.), ATC (2.), ATAG (2.), AGG (18), ACT (15), C (11), AAC (11), ACAT (11), CAGA (10), AGAA (9), AGGG (7), CAAA (7), CGCA (6), ATAA (6), AGAGAA (6). Dinucleotide repeats, not only in the aspect of the number, but also in cumulative length, were the preponderant repeat type. There were few classes and low copy numbers of repeat units of the pentanucleotide repeat type, which included only three classes: AGAGA, GAGGC and AAAGA. The classes and copy numbers of heptanucleotide, eleven-nucleotide and thirteen-nucleotide primer-number-composed repeats were distinctly less than that of repeat types beside them.

关键词：虾遗传特性遗传基因 DNA

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Modeling and verifying Web services driven by requirements:An ontology-based approach

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Science in china(Series F) 2006年第6期49卷 792-820页

作者： HOU Lishan1,3,JIN ZHi1,2.& WU Budan1,4 1. academy of Mathematics and Systems Science, chinese academy of sciences, beijing 100080, china 2. Institute of Computing Technology, chinese academy of sciences, beijing 100080, china 3. Institute of Software, chinese academy of sciences, beijing 100080, china 4. Graduate University of chinese academy of sciences, beijing 100049, china academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing China Institute of Software Chinese Academy of Sciences Beijing China Institute of Computing Technology Chinese Academy of Sciences Bejing China Graduate University of chinese academy of {2. Beijing China

Automatic discovery and composition of Web services is an important research area in Web service technology, in which the specification of Web services is a key issue. This paper presents a Web service capability description framework based on the environment ontology. This framework depicts Web services capability in two aspects： the operable environment and the environment changes resulting from behaviors of the Web service. On the basis of the framework, a requirement-driven Web service composition model has been constructed. This paper brings forward the formalization of Web service interactions with π calculus. And an automatic mechanism converting conceptual capability description to the formal process expression has been built. This kind of formal specification assists in verifying whether the composite Web service model matches the requirement.

关键词： Web service environment ontology automatic composition π calculus formal verification.

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Lithospheric seismic fabrics of Sulu ultrahigh-pressure metamorphic belt

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Science china Earth sciences 2005年第5期48卷 585-600页

作者： YANG Wencai 1 , YANG Wuyang 1 , JIN Zhenmin 2.& CHENG Zhenyan 1 1. Institute of Geology, chinese academy of Geological {2., beijing 10003., china 2. china University of Geo{2., Wuhan 430074, china chinese academy of Geological {2. Institute of Geology Beijing China china University of Geosciences Wuhan China

Calibration of seismic reflectors appearing in the crust of the chinese continent sci- entific drilling site can be completed through the correlation studies between direct evidences, such as the drill cores, and geophysical signatures; therefore the interpretation of geophysical data could produce reliable results of crustal structure and composition. On the other hand, there are two Cenozoic volcanoes close to the scientific drilling site; analyzing composition of xenoliths existent in the volcanoes and evaluating their seismic velocities can also offer information about the mantle and lower crust. After the calibration via cores and well-logging data, the seismic re- flectors appearing in the UHP belt can be caused by lithological changes within the UHP rock slice, ductile shearing rock-suites, and later fracture zones. Among these sources, ductile shearing resulted in displacement and detachment of original rock-sheets, producing some rock-interbeds of several hundred meters thick that are named the ductile shearing rock-suites. A suite consists of mylonized gneiss and eclogite slices that underwent shearing, becoming the major mechanism responsible to generate regional strong reflections. The UHP rock-slice is characterized by complicated structures and high density, high seismic velocity and high electri- cal resistivity, its thickness is usually less than 11 km. Velocity and density of the gneiss-layer beneath gradually tend to normal with increasing depth. Based on the xenoliths we can infer that the middle crust contains a lot of gneisses, and the lower crust consists of different granulites. The lithospheric mantle has multi-layer structures and consists mainly of spinal lherzolite and harzburgite, implying late Mesozoic lithospheric thinning. The seismic fabrics with different ori- gins were possible products of different geodynamic processes. For instance, the UHP rock-slice was produced by the UHP metamorphic process and the exhumation of subducted supe

关键词： deep seismic reflection, ultrahigh-pressure belt, Sulu china, calibration of reflectors, lithospheric fabrics.

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Teleconnection between the Indian summer monsoon onset and the Meiyu over the Yangtze River Valley

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Science china Earth sciences 2008年第7期51卷 1021-1035页

作者： LIU YunYun1,2.3 & DING YiHui2.1 chinese academy of Meteorological {2., beijing 100081, china 2.National Climate Center, beijing 100081, china 3 Graduate University of chinese academy of {2., beijing 100049, china chinese academy of Meteorological {2. Beijing China National Climate Center Beijing China Graduate University of chinese academy of {2. Beijing China

Based on the Indian and chinese precipitation data and the NCEP-NCAR reanalysis circulation data, the relationship between the Indian summer monsoon (ISM) onset and the Meiyu over the Yangtze River Valley has been discussed by the methods of correlation analysis and composite analysis. The results show that the date of ISM onset over Kerala in the southwestern coast of the Indian Peninsula is about two weeks earlier than the beginning of the Meiyu over the Yangtze River Valley. After the outbreak of ISM, the teleconnection mode sets up from the western coast of India via the Bay of Bengal (BOB) to the Yangtze River Valley and southern Japan. It is different both in time and space from the telecon- nection mode which is from the northwest of India via the Tibetan Plateau to northern china. The for- mer mode is defined as the "south" teleconnection of the Asian summer monsoon, forming in the pe- riod of ISM onset; while the latter mode is called the "north" teleconnection, mainly occurring in the Asian monsoon culminant period. During the process of the "south" teleconnection’s formation, the Asian monsoon circulation has experienced a series of important changes: ISM onset, the northward movement of the south Asia high (SAH), the onset vortex occurrence, the eastward extension of the stronger tropical westerly belt, and the northeastward jump of the western Pacific subtropical high (WPSH), etc. Consequently, since ISM sets up over Kerala, the whole Asian continent is covered by the upper SAH after about two weeks, while in the mid- and lower troposphere, a strong wind belt forms from the Arabian Sea via the southern India, BOB and the South china Sea (SCS), then along the western flank of WPSH, to the Yangtze River Valley and southern Japan. With the northward moving of the subtropical jet streams, the upper westerly jet stream and the low level jet have been coupled ver- tically over east Asia, while the Yangtze River Valley happens to locate in the ascending motion

关键词： Indian summer monsoon (ISM) the Meiyu over the Yangtze River Valley teleconnection mode

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Statistical distribution of nonlinear random wave height

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Science china Earth sciences 2006年第4期49卷 443-448页

作者： HOU Yijun1, GUO Peifang1,2. SONG Guiting1,2. SONG Jinbao1, YIN Baoshu1 & ZHAO Xixi1,2.1. Institute of Oceanology, chinese academy of {2., Qingdao 2.6071, china 2. Graduate University of the chinese academy of {2., beijing 10003., china Institute of Oceanology Chinese Academy of Sciences Qingdao China Graduate University of the chinese academy of {2. Beijing China

A statistical model of random wave is developed using Stokes wave theory of water wave dynamics. A new nonlinear probability distribution function of wave height is presented. The results indicate that wave steepness not only could be a parameter of the distribution function of wave height but also could reflect the degree of wave height distribution deviation from the Rayleigh distribution. The new wave height distribution overcomes the problem of Rayleigh distribution that the prediction of big wave is overestimated and the general wave is underestimated. The prediction of small probability wave height value of new distribution is also smaller than that of Rayleigh distribution. Wave height data taken from East china Normal University are used to verify the new distribution. The results in- dicate that the new distribution fits the measurements much better than the Rayleigh distribution.

关键词： Random ocean wave, nonlinearity, wave height distribution.

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Kinetics and reaction mechanism of phenol hydroxylation catalyzed by La-Cu_4FeAlCO_3

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Science china Chemistry 2005年第6期48卷 530-537页

作者： CHEN Chunxia1,2. XU Chenghua1, FENG Liangrong1, SUO Jishuan1 & QIU Fali1 1. Chengdu Institute of Organic Chemistry, chinese academy of {2., Chengdu 610041, china 2. Graduate school of the chinese academy of {2., beijing 10003., china Chengdu Institute of Organic Chemistry Chinese Academy of Sciences Chengdu China Graduate school of the chinese {2. of sciences Beijing China

The present work synthesizes La-Cu4FeAlCO3 catalyst under microwave irradiation and characterizes its structure using XRD and IR techniques. The results show that the obtained La-Cu4FeAlCO3 has a hydrotalcite structure. In the phenol hydroxylation with H2.2.catalyzed by La-Cu4FeAlCO3, the effects of reaction time and phenol/H2.2.molar ratio on the phenol hy-droxylation, and relationships between the initial hydroxylation rate with concentration of the catalyst, phenol, H2.2.and reaction temperature are also investigated in details. It is shown the phenol conversion can reach 50.09% (mol percent) in the phenol hydroxylation catalyzed by La-Cu4FeAlCO3, under the reaction conditions of the molar ratio of phenol/H2.2.1/2. the amount ratio of phenol/catalyst 2., reaction temperature 343 K, reaction time 12. min, 10 mL distilled water as solvent. Moreover, a kinetic equation of v = k[La ? Cu 4 FeAlCO 3 ][C 6 H 5 OH][H 2.O 2.. and the activation energy of Ea=58.37 kJ/mol are obtained according to the kinetic studies. Due to the fact that the HO-Cu+-OH species are detected in La-Cu4FeAlCO3/H2.2.system by XPS, the new mechanism about the generation of hydroxyl free radicals in the phenol hydroxylation is pro-posed, which is supposed that HO-Cu+-OH species are transition state in this reaction.

关键词： rare earth, hydrotalcite, microwave irradiation, phenol hydroxylation, kinetics, reaction mechanism.

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Kinematics and dynamics of the Mesozoic orogeny and late-orogenic extensional collapse in the Sino-Mongolian border areas

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Science china Earth sciences 2005年第7期48卷 849-862页

作者： ZHENG Yadong 1 & WANG Tao2.1. Key Laboratory of Orogenic Belts and Crustal Evolution (Peking University), Ministry of Education, beijing 100871, china 2. Institute of Geology, {2. academy of Geological sciences, beijing 10003., china Key Laboratory of Orogenic Belts and Crustal Evolution (Peking University) Ministry of Education Beijing 100871 China Institute of Geology Chinese Academy of Geological Sciences Beijinq 100037 China

The Sino-Mongolian border areas underwent two important tectonic events during Mesozoic time after late Paleozoic orogeny: a late Triassic to earlier Jurassic contractional event that resulted in a large-scale south-vergent thrust during the orogeny and a late Jurassic-earlier Cretaceous extensional event in a north-south direction that formed a metamorphic core complex. The kinematic and dynamic analyses show that the thrust sheet moved southwards with a kinematic vorticity number of ca. -0.10 and sub-horizontal maximum compressive stress axis that belongs to a contraction-thickening shear. The upper plate of the late-orogenic detachment relatively moved in a 165°direction. The average kinematic vorticity in its earlier stage was 0.74 that belongs to simple shear dominated shearing and related to the maximum compressive stress axes dipping at ～66°, while the later average kinematic vorticity was ～0.55°that belongs to pure shear dominated shearing with sub-vertical maximum compressive stress axes. This suggests that the thrusting led to the crust thickened and the lower plate rocks that were originally located in the upper crust depressed through a brittle-ductile transition zone into the lower crust and became warmer. The heated rocks trended to uplift since their increasing volume and decreasing density while the loading of the upper-plate rocks increased due to the structural thickening. Under the combined effect of the loading and the thermal-uplifting, the ductile shear zone in between increased in its component of vertical pure shear. Once its pure-shear component exceeded its simple-shear one the ductile shear zone became an extension-thinned shear zone. This progressive transitional process reflects internal and essential temporal and spatial relationships: the extensional factor nucleated during the crust thickening by thrusting and increase of the extensional factor finally led to late-orogenic collapse.

关键词： Mesozoic thrusting,late-orogenic collapse,kinematic vorticity number,stress state.

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Genetic structure and phylogeography of a relict tree fern,Sphaeropteris brunoniana (Cyatheaceae) from china and Laos inferred from cpDNA sequence variations:Implications for conservation

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Journal of Systematics and Evolution 2011年第1期49卷 72-79页

作者： 1,2.Zi-Juan WANG 1 Kai-Yun GUAN 1 (Kunming Institute of Botany, chinese academy of {2., Kunming 6502.4, china) 2.(Graduate University of chinese academy of {2., beijing 100049, china) (Kunming Institute of Botany Chinese Academy of Sciences Kunming 650204 China) (Graduate University of chinese academy of {2. Beijing 100049 China)

In this study, we analyzed the genetic structure and phylogeography of Sphaeropteris brunoniana from china and Laos. Combining cpDNA trnL-trnF and atpB-rbcL sequence variations, five haplotypes were identi- fied from the 10 investigated populations. Moderate haplotype diversity (h = 0.66580) and low nucleotide diver- sity (π = 0.2. × 10 ?3 ) were detected. The S. brunoniana in Yunnan region had much higher genetic diversity (h = 0.60195, π = 0.35 × 10 ?3 ) than that of Hainan–Laos (h = 0.00000, π = 0.00). A high level of genetic differentiation (94.74%) between the two regions was revealed by AMOVA. Nested clade analysis identified two major clusters of the five haplotypes, one clade in the Yunnan region and the other in Hainan–Laos. The analysis indicated that restricted gene flow with isolation by distance and allopatric fragmentation were likely the major processes that shaped the spatial distribution of the haplotypes. The isolated distribution of clades implied the emergence of independent refugia of this species in each region during Quaternary glaciations. The Yunnan populations frequently contained an ancestral haplotype, and most of them harbored other descendent haplotypes. Based on the distribution pattern of haplotypes and the nested clade analysis results, the Yunnan region potentially had several refugia of this species during glacial periods, whereas the Hainan populations were probable new colonizations.

关键词： atpB-rbcL Hainan–Laos phylogeography Sphaeropteris brunoniana trnL-trnF Yunnan.

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Numerical simulations of the bi-level and branched structure of intracloud lightning flashes

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Science china Earth sciences 2006年第6期49卷 661-672页

作者： TAN Yongbo1, TAO Shanchang1, ZHU Baoyou1, MA Ming2.& LU Weitao2.1. school of Earth and Space sciences, University of Science and Technology of{2., Hefei 2.002.,{2. 2. chinese academy of Meteorological sciences, beijing 100081,{2. school of Earth and Space sciences University of Science and Technology of China Hefei China chinese academy of Meteorological {2. Beijing China

Intracloud (IC) lightning flashes have been simulated in fine resolution (12.5 m) by using a bidirectional stochastic lightning parameterization scheme within 2.dimensional domain. The simu-lated results show that the IC flashes have a bilevel channel structure and the altitudes of the hori-zontal channels are at the same heights of potential wells, which are supported by the previous VHF source observations and balloon soundings of electric field profile in the thundercloud. Further con-clusions are: (1) After an IC flash is initiated near the boundary between positve and nagetive charge zone, the negative (or positive) leader tends to propagate into the positive (or negative) charge zone. Both types of positive and negative IC flashes have been reproduced and their polarity depends on the up and down disposition of the positive and negative charge regions. (2. The extension range of leaders is correlative with the cloud charge distribution. The leader is possible to extend through the inverted charge region all over where it is extending, but keeps away from the isolated charge area of the same polarity. (3) The channel structures also depend on the electric potential distributions in the thundercloud. Before propagating into the central area of potential wells, the leader tends to extend along the direction with the maximum of potential gradient. Once extending away from the center of potential wells, the leader tends to extend along the direction with the slowest potential change. (4) The IC flash channels have the fractal feature with fractal dimension 1.45 before leaders pass through the central area of charge regions. The exponent decreases rapidly once leaders extend into the low-density charge regions. (5) The induced charges of opposite polarity are deposited in the leader channels within preexisting positive and negative charge regions during IC flash discharges. This causes a new and complicated charge distribution in the thundercloud, and the potential

关键词： IC, lightning parameterization, branched bilevel structure, fractal feature, propagation tendency.

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Novel Tumor-associated Antigen of Hepatocellular Carcinoma Defined by Monoclonal Antibody E4-65

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Acta Biochimica et Biophysica Sinica 2007年第5期39卷 359-365页

作者： Ke ZOU~(1,2., Jihang JU~(1,2., and Hong XIE~~(1*)1 Institute of Biochemist13, and Cell Biology, Shanghai Institutes for Biological sciences, chinese {2. of sciences, Shanghai 2.0031, china. 2.Graduate school of the chinese {2. of sciences beijing 100049, china Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of SciencesShanghai 200031 China Graduate school of the chinese {2. of sciencesbeijing 100049 China

A monoclonal antibody, E4-65, produced by immunizing mice with SMMC-772. cells, a human hepatocellular carcinoma (HCC) cell line, was used to identify and characterize an unreported HCC-associated antigen. Indirect immunofluorescence studies showed that E4-65 antibody reacted with five out of eight HCC cell lines, but not with 10 non-HCC tumor cell lines or a normal liver cell line. Using immunohistochemical examination, E4-65 antigen was detected on the cell membranes and in the cytoplasm of human liver tumor tissues, but was not found in most other tumors, or normal adult or fetal tissues, except for a weakly positive reaction in tissues of the digestive system. Western blot analysis showed that E4-65 antibody bound to a 45 kDa protein in the human HCC cell line and tissue lysates. Enzyme treatment and lectin blotting did not detect the carbohydrate chain in E4-65 antigen. This HCC-associated protein represents a potentially useful target for diagnoses and immunotherapy of human HCC.

关键词： hepatocellular carcinoma immunohistochemistry monoclonal antibody neoplasm antigen

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