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High Throughput SNP Genotyping with Two Mini-sequencing Assays

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Acta Biochimica et Biophysica Sinica 2004年第6期36卷 379-384页

作者： Chunqing LUO1,2., Libin DENG1#, and Changqing ZENG1,2. The Institute of Genetic and Developmental Biology, the Chinese academy of sciences, {2. 100101, china 2.2. Genomics Institute, the Chinese academy of sciences, {2. 101300, china The Institute of Genetic and Developmental Biology the Chinese Academy of SciencesBeijing 100101 China beijing Genomics Institute the Chinese Academy of SciencesBeijing 101300 China

Two mini-sequencing methods, FP-TDI (template-directed dye-terminator incorporation with fluorescence-polarization) and MassArray (matrix assisted laser desorption ionization time of flight detection mass spectrometry), were optimized. A numeric standard was introduced to evaluate the SNP scoring quality of FP-TDI assay, thus made the optimization work easier. At the same time, using multi-PCR technology, 8-plex genotyping of MassArray assay was successfully carried out, some softwares were developed and the data process of MassArray was highly automated. Then these two methods were applied to high throughput SNP genotyping, the accuracy, efficiency and robustness were compared. The result shows FP-TDI is more sensitive to the concentration of SNPprimer and PCR product, as well as extension cycles, the SNPprimer length of FP-TDI should be 2.–30 bp long, whereas MassArray assay prefers to be as short as only 16 *** 6440 SNP sites of human chromosome 3 were genotyped in a sample of 90 individuals, 4792.sites by FP-TDI assay and 1648 sites by MassArray assay, the success rates of FP-TDI and MassArray were 67.7% and 93.6% respectively. The throughput of MassArray was higher than FP-TDI, and the cost of MassArray was lower, MassArray was more suitable for high throughput SNP genotyping.

关键词： SNP genotyping FP-TDI MassArray high throughput

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 china, Hefei 2.002., china 2. Chinese academy of meteorological sciences, beijing 1.0081. china 1. School of Earth and Space sciences University of Science and Technology of China Hefei 230026 China 2. Chinese academy of meteorological {2. Beijing 100081 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.

A comparative analysis on two solar proton events

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Chinese Science Bulletin 2007年第1期52卷 47-51页

作者： LE GuiMing1,2.3,4, HAN YanBen2.& ZHANG YiJun3 1 Key Laboratory of Radiometric Calibration and Validation for Environmental Satellites, china meteorological Administration,{2. 2.National Astronomical Observatories, Chinese academy of sciences, beijing 100012. china 3 Chinese academy of meteorological sciences, china meteorological Administration,{2. 4 National Center for Space Weather, china meteorological Administration,{2. Key Laboratory of Radiometric Calibration and Validation for EnvironmentalSatellites China Meteorological Administration Beijing 100081 China

This paper presents a comparative analysis on the two Solar Proton Events (SPE), which occurred on 14 July 2.00 (Bastille Day) and 2. October 2.03 (2.OCT03) respectively. It is found that although the peak flux of the latter seemed to be greater than that of the former based on geostationary observations, the maximum intensities of the energetic protons (>10 MeV and 30 MeV) during the Bastille Day event were all higher than those of the 2.OCT03 event according to the interplanetary observations. Further analysis indicated that the quantity of the seed particles, which could be accelerated to the energies exceeding 10 and 30 MeV by the Coronal Mass Ejection (CME)-driven shock on 14 July 2.00, was far larger than that of the 2.OCT03 event. In the Bastille Day case, when the CME approached to the height around 14 R⊙, the CME-driven shock would reach its maximum capacity in accelerating the solar en- ergetic protons (>100 MeV). In contrast, on 2. October 2.03, when CME approached to the height about 58R⊙, the CME-driven shock reached its highest potential in accelerating the solar energetic protons of the same category. At this moment, the peak flux (>100 MeV) was about 155 pfu, which was much lower than 355 pfu measured on 14 July 2.00. This demonstrated that in the Bastille Day event, the quantity of the seed particles, which could be accelerated to the energy beyond 100 MeV, was significantly larger than its counterpart in the 2.OCT03 case. Therefore, the peak flux of an SPE event depends not only on the interplanetary intensity of the solar energetic particles, but also on the velocity of the associated CME-driven shock, and the quantity of the seed particles as well as on the interplanetary magnetic en- vironment. This paper also reveals that the magnetic sheath associated with ICME on 2. October 2.03 captured a large number of solar energetic protons, including those having energy greater than 100 MeV.

关键词：太阳质子 CME 太阳耀斑太阳系

Experimental investigation and numerical simulation on the effect of fissure water pressure in vertical sliding surface

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Science china(Technological sciences) 2005年第z1期48卷 53-64页

作者： ZHANG Lei1,2. LI Shihai1, LIAN Zhenzhong1,2.& WANG Yuannian1 1. Institute of Mechanics, Chinese academy of sciences, {2. 100080, china 2. Graduate School, Chinese academy of sciences, {2. 100060, china 1. Institute of Mechanics Chinese Academy of Sciences 100080 Beijing China 2. Graduate School Chinese Academy of Sciences 100060 Beijing China

This paper studies the effect of fissure water pressure in different fractures on the critical angle of landslide by laboratory investigation and numerical simulation in order to understand the mechanisms of fissure water pressure on landslide stability. Laboratory observations show that the effect of fissure water pressure on the critical angle of landslide is little when the distance between water-holding fracture and slope toe is three times greater than the depth of fissure water. These experimental results are also simulated by a three-dimensional face-to-face contact discrete element method. This method has included the fissure water pressure and can accurately calculate the critical angle of jointed slope when fissure water pressure in vertical sliding surface exists. Numerical results are in good agreement with experimental observations. It is revealed that the location of water-holding structural surface is important to landslide stability. The ratio of the distance between water-holding fissure and slope toe to the depth of fissure water is a key parameter to justify the effect of fissure water pressure on the critical angle of landslide.

关键词： jointed rock slope, discrete element method, fracture in vertical sliding surface, model experiment,fissure water pressure.

Assessing the Carrying Capacity of Tourist Resorts: An Application of Tourists’ Spatial Behavior Simulator Based on GIS and Multi-Agent System

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Wuhan University Journal of Natural sciences 2005年第4期10卷 779-784页

作者： ZHANG Ren-jun 1,2.1. Institute of Mountain Hazards and Environment, Chinese academy of sciences, Chengdu 610041, Sichuan, {2. 2. Graduated School of the Chinese academy of sciences, beijing 100039, {2. Chinese academy of sciences Institute of Mountain Hazards and Environment Chengdu Sichuan China (GRID:grid.9227.e) (ISNI:***) Graduated School of the Chinese academy of sciences Beijing China (GRID:grid.9227.e) (ISNI:***)

Based on the study of visitors' individual spatial behaviors, a tourists'spatial behavior simulator (TSBS) to assess the carrying capacity of tourist resorts was developed,TSBS employs GIS (Geographic Information System) to manage the spatial data,and Multi-Agent systemto simulate the actions of individual visitors. By utilizing TSBS, visitors' travel patterns such aslocation, cost, and state can be analyzed and predicted. Based on this analysis and prediction, themodel of assessing the carrying capacity of resorts is built. Our results show that TSBS will be aneffective tool to accurately assess the carrying capacity of tourist resorts.

关键词： tourist resort carrying capacity TSBS GIS Multi-Agent simulator

Variations of δ^(18)O in precipitation from the Muztagata Glacier, East Pamirs

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Science china Earth sciences 2006年第1期49卷 36-42页

作者： LI Zhen1, YAO Tandong1,2. TIAN Lide1,2. XU Baiqing1,2.& Wu Guangjian2.1. Key Laboratory of Cryosphere and Environment, Jointly Established by Cold and Arid Regions Environmental and Engi-neering Research Institute and Institute of Tibetan Plateau Research, Chinese academy of sciences and Chinese academy of meteorological sciences, china meteorological Administration, CAS, Lanzhou 730000, china 2. Laboratory of Environment and Process on Tibetan Plateau, Institute of Tibetan Plateau Research, Chinese academy of sciences, beijing 100085, china 1. Key Laboratory of Cryosphere and Environment Jointly Established by Cold and Arid Regions Environmental and Engineering Research Institute and Institute of Tibetan Plateau Research Chinese Academy of Sciences and Chinese Academy of Meteorological Sciences China Meteorological Administration Lanzhou 730000 China 2. Laboratory of Environment and Process on Tibetan Plateau Institute of Tibetan Plateau Research Chinese Academy of Sciences Beijing 100085 China

Expeditions to Muztagata (in the eastern Pamirs) during the summer seasons of2.02.and 2.03 collected precipitation samples and measured their oxygen isotopes. The δ^(18)O inprecipitation displays a wide range, varying from -17.40per thousand to +1.33per thousand inJune—September 2.02.and from -2..31per thousand to +4.59per thousand in May—August 2.03. Theδ^(18)O in precipitation correlates with the initial temperature of precipitation during theobserving periods. The positive correlation between δ^(18)O and temperature suggests that δ^(18)Ocan be used as an indicator of temperature in this region. The δ^(18)O values in fresh-snow samplescollected from two snow events at different elevations on the Muztagata Glacier show a strong''altitude effect'', with a ratio of nearly -0.40per thousand per 100 m from 5500 m to 7450 m.

关键词： Muztagata, δ18O, temperature, altitude effect.

Numerical simulation of Meiyu front and the diagnosis of moist vorticity vector

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Progress in Natural Science:Materials International 2007年第11期17卷 1341-1347页

作者： Ping Fan1,2.and Luo Zhexian2.1. Institute of Atmospheric Physics, Chinese academy of sciences, {2. 10002., china 2. Nanjing University of Information sciences & Technology, Nanjing 2.0044, china) Institute of Atmospheric Physics Chinese Academy of Sciences Beijing 100029 China Nanjing University of Information sciences & Technology Nanjing 210044 China

Moist vorticity vector is introduced to study the development and evolution of mesoscale convective vortex (MCV) in the Meiyu front precipitation with the Advanced Regional Predication System (ARPS). In this study, the heavy rainfall is simulated to investigate the genesis, development and dissipation of middle scale convective vortex, which occurred from 0000 UTC 3 July to 12.0 UTC 5 July over the Jianghuai River valley. Moist vorticity vector (MVV) has zonal, radial and vertical components in its 3D spatial distribution. The simulation shows that the vertical component of moist vorticity vector well demonstrates the spatial distribution characteristics of middle scale convective vortex, especially in the process of Meiyu front precipitation. Diagnosis upon zonal, radial averaged and mass-integrated quantities of MVV shows that its vertical component and the surface precipitating ratio are in phase with a correlation coefficient of 0.68, indicating that the vertical component of MVV is closely associated with the Meiyu front precipitation. In addition, the tendency of the vertical component of MVV is mainly determined by the interaction between the vorticity and the zonal and radial gradient of condensational or depositional heating.

关键词： moist vorticity vector mesoscale convective vortex Meiyu front precipitation

Zonal propagation of kinetic energy and convection in the South china Sea and Indian monsoon regions in boreal summer

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Science china Earth sciences 2004年第12期47卷 1076-1084页

作者： CHEN Longxun 1 ,GAO Hui 2.,HE Jinhai 2.,TAO Shiyan 3 & JIN Zuhui 3 1.Chinese academy of meteorological {2.,beijing 1.0081.china 2.Nanjing Institute of Meteorology,Nanjing 2.0044,china 3.Institute of Atmospheric Physics,Chinese academy of {2.,beijing 10002.,china 1. Chinese academy of meteorological {2. 100081 Beijing China 2. Nanjing Institute of Meteorology 210044 Nanjing China 3. Chinese academy of sciences Institute of Atmospheric Physics 100029 Beijing China

Zonal propagation of kinetic energy (KE) and convection in the South china Sea (SCS) and Indian summer monsoon areas are examined in present study. Results suggest that the SCS and Indian summer monsoon prevailed regions (5 —15°N) are dominated by the southwesterly wind, however, the disturbances of KE at 850 hPa and convection are observed mainly coming from the western Pacific Ocean (140—150°E), after passing through the SCS, and westward propagated into the Bay of Bengal (90—100°E). In the Indian summer monsoon domain, where the disturbances of KE are found mainly coming from the Arabian Sea (AS) and eastward propagated into the Bay of Bengal. Therefore, the SCS and the Indian summer mon- soon are quite different in zonal propagation of KE and convection. The SCS summer monsoon is mainly affected by the KE and convection coming from the tropical western Pacific. The Indian summer monsoon, however, can be partly influenced by the AS and the SCS summer monsoon. The analysis also suggests that the interaction region between the SCS and the Indian summer monsoon is around 90—95°E, rather than 105°E as proposed by earlier studies.

关键词： zonal propagation of KE and convection, East Asian monsoon, Indian monsoon.

Parentage determination of an isolated Yangtze finless porpoise population Neophocaena phocaenoides asiaeorientalis in the Yangtze Tian-e-Zhou Baiji National Natural Reserve based on molecular data

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Progress in Natural Science:Materials International 2005年第2期15卷 54-61页

作者： XIA Junhong 1,2. ZHENG Jinsong 1,2. XU Limei 1,2.and WANG Ding1*(1. Institute of Hydrobiology, Chinese academy of sciences, Wuhan 430072. {2. 2. Graduate School of the Chinese academy of sciences, beijing 100039, {2.) Institute of Hydrobiology Chinese Academy of Sciences Wuhan 430072 China. Graduate School of the Chinese academy of sciences Beijing 100039 China

Reproductive behaviors are poorly known for the Yangtze finless porpoise Neophocaena phocaenoides asiaeorientalis. In this study, the parentage of an isolated Yangtze finless porpoise population inhabiting the Yangtze Tian-e-Zhou Baiji National Natural Reserve is determined by analysis of microsatellite loci and mitochondrial DNA (mtDNA) control region sequences, and the porpoise's reproductive behaviors are studied. Overall 4 full parentage assignments and additional 3 single parentage assignments were determined for the population of 2. individuals. The analysis shows that their estimated reproductive cycle is shorter than that reported previously and there probably exists an overlapping between gestation and lactation period. The study also shows that the female does not show fidelity to a particular male for breeding and vice versa, the oldest males did not monopolize mating and the dominance rank could not be so strict for the porpoise society. Moreover, the porpoise's mating pattern and relatedness among candidate parents are discussed here. These results provide important information for making guidelines of management and conservation for this protected population.

关键词： Yangtze finless porpoise isolated population reproductive behavior parentage