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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, beijing 100101, {2. 2.1} Genomics Institute, the chinese academy of sciences, beijing 101300, {2. 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

Improving the accuracy of image-based forest fire recognition and spatial positioning

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Science china(Technological sciences) 2010年第S1期53卷 184-190页

作者： JIANG LiLi 1,QI QingWen 1,ZHANG An 1,GUO ChaoHui 2.& CHENG Xi 1,3 1 Institute of Geographical sciences and Natural Resources Research,chinese academy of sciences,{2. 100101,china 2.china Center for Resources Satellite Data and Applications,{2. 100094,china 3Graduate University of chinese academy of sciences,beijing 100049,china chinese Acad Sci Inst Geog Sci & Nat Resources Res Beijing 100101 Peoples R China china Ctr Resources Satellite Data & Applicat Beijing 100094 Peoples R China chinese Acad Sci Grad Univ Beijing 100049 Peoples R China

Forest fires are frequent natural *** is necessary to explore advanced means to monitor,recognize and locate forest fires so as to establish a scientific system for the early detection,real-time positioning and quick fighting of forest *** paper mainly expounds methods and algorithms for improving accuracy and removing uncertainty in image-based forest fire recognition and spatial ***,we discuss a method of forest fire recognition in visible-light *** are four aspects to improve accuracy and remove uncertainty in fire recognition:(1)eliminating factors of interference such as road and sky with high brightness,red leaves,other colored objects and objects that are lit up at night,(2.excluding imaging for specific periods and azimuth angles for which interference phenomena repeatedly occur,(3)improving the thresholding method for determining the flame border in image processing by adjusting the threshold to the season,weather and region,and (4)integrating the visible-light image method with infrared image ***,we examine infrared-image-based methods and approaches of improving the accuracy of forest fire recognition by combining the spectrum threshold with an object feature value such as the normalized difference vegetation index and excluding factors of disturbance such as interference signals,extreme weather and high-temperature ***,a method of visible analysis to enhance the accuracy of forest fire positioning is examined and realized;the method includes decreasing the visual angle,selecting central points,selecting the largest spots,and judging the selection of fire spots according to the central *** studies are examined and the results are found to be satisfactory.

关键词： forest fire monitoring spatial positioning accuracy improvement

Ashkin-Teller Formalism for Elastic Response of DNA Molecule to External Force and Torque

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Communications in Theoretical Physics 2008年第2期49卷 525-528页

作者： CHANG Zhe~1 WANG Ping~(1,2. ZHENG Ying-Hong~(1,2. 1 Institute of High Energy Physics,the chinese academy of sciences,P.O.Box 918(4),beijing 100049,{2. 2.Graduate School,the chinese academy of sciences,beijing 100049,{2. Institute of High Energy Physics the Chinese Academy of Sciences P.O. Box 918(4) Beijing 100049 China Graduate School the Chinese Academy of Sciences Beijing 100049 China

We propose an Ashkin Teller-like model for elastic response of DNA molecule to external force and *** base-stacking interaction is described in a simple and uniform *** obtain the phase diagram of dsDNA,andin particular,the transition from B form to the S state induced by stretching and *** elastic response of thessDNA is presented also in a unified *** close relation of dsDNA molecule structure with elastic response isshown *** calculated folding angle of the dsDNA molecule is 59.2..

关键词： dsDNA elastic property

A mixed method for measuring low-frequency acoustic properties of macromolecular materials

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Science china(Physics,Mechanics & Astronomy) 2006年第6期49卷 729-739页

作者： LIU Hongwei1,YAO Lei1,3,ZHAO Hong1,3,ZHANG Jichuan2.3 & XUE Zhaohong2.1. National Key Laboratory of Acoustics,Institute of Acoustics,chinese academy of sciences,{2. 100080,{2. 2. Institute of Chemistry,chinese academy of sciences,{2. 100080,{2. 3. Graduate University of chinese academy of sciences,beijing 100049,{2. National Key Laboratory of Acoustics Institute of Acoustics Chinese Academy of Sciences Beijing 100080 China Institute of Chemistry Chinese Academy of Sciences Beijing 100080 China Graduate University of chinese academy of sciences Beijing 100049 China

A mixed method for measuring low-frequency acoustic properties of macro-molecular materials is presented. The dynamic mechanical parameters of materials are first measured by using Dynamic Mechanical Thermal Apparatus(DMTA) at low frequen-cies,usually less than 100 Hz; then based on the Principles of Time-Temperature Super-position (TTS),these parameters are extended to the frequency range that acousticians are concerned about,usually from hundreds to thousands of hertz; finally the extended dynamic mechanical parameters are transformed into acoustic parameters with the help of acoustic measurement and inverse analysis. To test the feasibility and accuracy,we measure a kind of rubber sample in DMTA and acquire the basic acoustic parameters of the sample by using this method. While applying the basic parameters to calculating characteristics of the sample in acoustic pipe,a reasonable agreement of sound absorp-tion coefficients is obtained between the calculations and measurements in the acoustic pipe.

关键词： low-frequency acoustic properties,dynamic mechanical properties,Principles of Time-Temperature Superposition,acoustic pipe,sound absorption coefficient.

Evaluation of Sustainable Land Management and Diagnosis of Obstacle at County Scale in Sichuan Basin:Taking Lezhi County as Example

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Wuhan University Journal of Natural sciences 2006年第4期11卷 1046-1051页

作者： CHEN Guangjian 1, 2. 3 , LIU Qing 1 1. Chengdu Institute of Biology, chinese academy of sciences, Chengdu 610041, Sichuan,china 2. Graduate University of chinese academy of sciences, beijing 100049, china 3. academy of Land Reconnaissance and Layout of Sichuan Province , Chengdu 610031, Sichuan, china Chengdu Institute of Biology Chinese Academy of Sciences Chengdu Sichuan China Graduate University of chinese academy of sciences Beijing China academy of Land Reconnaissance and Layout of Sichuan Province Chengdu Sichuan China

This paper established sustainable land resources evaluating indicators fit for hilly area in Sichuan Basin, Southwest of china, and evaluated the case of sustainable land management of Lezhi County from 1990 to 2.01. The result showed that the land resource sustainable utilization ability in Lezhi County is belong to Second level （better sustainable）. Secondly, this paper diagnosed some years obstacles of sustainable land management of Lezhi County from base period to goal period and compared the obstacles factors in the indicators system. There were 16 indexes orderly become major affect factor to land sustainable utilization of Lezhi county in indicator system, of which there are 8 obstacles indexes exist both in 1990 and 2.01. The value of obstacles degree of five indicators exceeded 5 in 1990, but in 2.01, only two indicators＇ values were more than 5.

关键词： land resources sustainable land management assessment indicators diagnosis of obstacle

Relationship between surface subsidence factor and mining depth of strip pillar mining

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中国有色金属学会会刊：英文版 2011年第S3期21卷 594-598页

作者： GUO Wen-bing1, 2. HOU Quan-lin 1, zou You-feng2.1. College of Earth Science, Graduate University of chinese academy of sciences, {2., {2. 2. School of Energy Science and Engineering, Henan Polytechnic University, Jiaozuo 454000, {2. chinese Acad Sci Coll Earth Sci Grad Univ Beijing 100049 Peoples R China Henan Polytech Univ Sch Energy Sci & Engn Jiaozuo 454000 Peoples R China

Strip pillar mining is one of the most important technical measures to control mining subsidence in china. Mining depth is one of the most important factors that can affect the mining subsidence in strip pillar mining. Six numerical simulation models were set up to simulate the surface subsidence of strip pillar mining in different mining depths. The mining depth in these six models ranges from 300 to 800 m. The simulated results were compared and analyzed. The formula was established based on the simulated results. It demonstrated that the subsidence of strip pillar mining method is related to mining depth. While the other conditions are the same, the subsidence of strip pillar mining increases with the increase of mining depth by logarithmic relationship.

关键词： subsidence factor strip pillar mining mining depth numerical simulation

Optimization of mathematical models for thematic maps

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Science china(Technological sciences) 2010年第S1期53卷 15-24页

作者： QI QingWen1,ZHANG An1,JIANG LiLi1,zou XiuPing2.XU Li3 & CHENG Xi1,4 1 Institute of Geographical sciences and Natural Resources Research,{2.,{2. 100101,china 2.Institute of Policy and Management,{2.,{2. 100080,china 3 Taishan University,Taian 2.102.,china 4 Graduate University of {2.,beijing 100049,china chinese Acad Sci Inst Geog Sci & Nat Resources Res Beijing 100101 Peoples R China chinese Acad Sci Inst Policy & Management Beijing 100080 Peoples R China Taishan Univ Tai An 271021 Shandong Peoples R China chinese Acad Sci Grad Univ Beijing 100049 Peoples R China

The thematic map is a major class of maps designed to demonstrate particular features or concepts,functioning as an indispensable tool in geographical *** process of thematic mapping is one into which geographical research goes deeply and *** key activity and course of thematic map production is the use of mathematical models to create thematic data ***,the selection and optimization of mathematical models is in the forefront of thematic map *** theoretical foundations,mechanisms and methods of mathematical model optimization are expounded in this paper,including two approaches,the phase by phase mode and the multi-aim scheme balance *** studies in eco-environment mapping and emergency mapping are described and analyzed,with a hierarchical analysis method being used in the model optimization for eco-environment fragility and sensitivity assessment mapping in Beibuwan (Guangxi) District,the dynamic system (DS) method being used in the model optimization for ecological security adjustment mapping in Xishuang Banna,Yunnan province,and the multi-phase mode being used in the models for forest fire and infectious diseases mapping.

关键词： thematic map mathematic model optimization

Input function and simulated distributions of tritium in the North Pacific

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Science china Earth sciences 2010年第3期53卷 441-453页

作者： BA Qi1,2.& XU YongFu1 1 State Key Laboratory of Atmospheric Boundary Layer Physics and Atmospheric Chemistry, Institute of Atmospheric Physics, chinese academy of sciences, beijing 10002., {2. 2.Graduate University of chinese academy of sciences, beijing 100049, {2. 1. State Key Laboratory of Atmospheric Boundary Layer Physics and Atmospheric Chemistry Institute of Atmospheric Physics Chinese Academy of Sciences Beijing 100029 China2. Graduate University of Chinese Academy of Sciences Beijing 100049 China

An ocean general circulation model (OGCM) of the North Pacific with a southern open boundary condition is used to simulate the distribution and transport of tritium in the North Pacific. First, the observed tritium in precipitation dataset of GNIP/ISOHIS is chosen, and used to develop an input function of tritium for the model domain from 1951 to 1997 in terms of the triangulation for interpolation. Then, the input function is used as an upper flux for the tritium model. The OGCM with tritium is integrated for 47 years with the initial condition of zero tritium concentrations. Compared with the observations from GEOSECS and WOCE, the model generates a meridional gradient of surface tritium concentrations and the high tritium concentrations in the subsurface layer, which is consistent with that indicated in the observations. The simulated time series of total tritium fluxes from the atmosphere to the ocean shows a spike in 1963. The total inventory of tritium in the ocean changes slowly with time after 1975. Tritium enters the higher-latitude region, and then is mainly transported by the subsurface process towards the equatorial region, which is well simulated in the model. However, the difference mainly occurs at 30°N–40°N, which can be seen also in the simulation of CFCs. This difference may partly originate from the insufficient description of physical processes in the OGCM. Nevertheless, some uncertainties exist in the development of the tritium input function, which can also influence the simulated results.

关键词： North Pacific basin-wide ocean general circulation model tritium input function tritium distributions

Bio-regeneration of p-complexation desulfurization adsorbents

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Science china Chemistry 2005年第6期48卷 538-544页

作者： LI Wangliang1,2. XING Jianmin1, XIONG Xiaochao1,2. SHAN Guobin1,2.& LIU Huizhou1 1. Laboratory of Separation Science and Engineering, Institute of Process Engineering, chinese academy of sciences, beijing 100080, {2. 2. Graduate School of the chinese academy of sciences,beijing 100039, {2. 1. Laboratory of Separation Science and Engineering Institute of Process Engineering Chinese Academy of Sciences 100080 Beijing China 2. Graduate School of the chinese academy of sciences 100039 Beijing China

The coupling of adsorption desulfurization and biodesulfurization is a new approach to produce clean fuels. Sulfur compounds are firstly adsorbed on adsorbents, and then the ad-sorbents are regenerated by microbial conversion. p-Complexation adsorbent, Cu(I)-Y, was ob-tained by ion exchanging Y-type zeolite with Cu2. and then by auto-reduction in helium at 450℃ for 3 h. Dibenzothiophene (DBT) was used as a model compound. The effects of cell concentra-tion, volume of oil phase, the ratio of aqueous phase to adsorbent on DBT desorption by a bac-terium were studied. The amounts of DBT desorbed and 2.HBP produced can be apparently increased with addition of n-octane. BDS activity can be improved by increasing cell concentra-tion and the ratio of water-to-adsorbent. 89% of DBT desorbed from the adsorbents can be converted to 2.HBP within 6 h and almost 100% within 2. h, when the volume ratio of oil-to-water was 1/5 mL/mL, the cell concentration was 60 g·L?1, and the ratio of adsorbent-to-oil was 0.03 g·mL?1. The amount of 2.HBP produced was strongly dependent on the volume ratio of oil-to- water, cell concentration and amount of adsorbent. Adsorption capacity of the regenerated ad-sorbent is 95% that of the fresh one after being desorbed with Pseudomonas delafieldii R-8, washed with n-octane, dried at 100℃ for 2. h and auto-reduced in He.

关键词： adsorption desulfurization p-complexation adsorbents bio-regeneration Pseudomonas delafieldii desorption.