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Jackknife and Bootstrap Tests of the Composition Vector Trees

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Genomics, Proteomics & Bioinformatics 2010年第4期8卷 262-267页

作者： Guanghong Zuo1,2, Zhao Xu1,3, Hongjie Yu1,4, and Bailin Hao1,5,6 1T-Life Research Center & Department of Physics, Fudan University, Shanghai 200433, china 2Shanghai institute of Applied Physics, chinese Acadamy of sciences, Shanghai 201800, china 3Applied Biosystems, Inc., beijing 10002., china 4Fudan-VARI Center for Genetic Epidemiology, Fudan University, Shanghai 200433, china 5institute of Theoretical Physics, chinese Acadamy of sciences, beijing 100190, china 6Santa Fe institute, Santa Fe, NM 87505, USA. [a] T-Life Research Center & Department of Physics Fudan University Shanghai 200433 china [b] Shanghai institute of Applied Physics chinese Acadamy of sciences Shanghai 201800 china [c] Applied Biosystems Inc. beijing 10002. china [d] Fudan-VARI Center for Genetic Epidemiology Fudan University Shanghai 200433 china [e] institute of Theoretical Physics chinese Acadamy of sciences beijing 100190 china [f] Santa Fe institute Santa Fe NM 87505 USA

Composition vector trees （CVTrees） are inferred from whole-genome data by an alignment-free and parameter-free method. The agreement of these trees with the corresponding taxonomy provides an objective justification of the inferred phylogeny. In this work, we show the stability and self-consistency of CVTrees by performing bootstrap and jackknife re-sampling tests adapted to this alignment-free approach. Our ultimate goal is to advocate the viewpoint that time-consuming statistical re-sampling tests can be avoided at all in using this alignment-free approach. Agreement with taxonomy should be taken as a major criterion to estimate prokaryotic phylogenetic trees.

关键词： composition vector phylogeny topological distance bootstrap jackknife CVTree

Biochemical characterization of the protein encoded by rice osRACD gene

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Progress in Natural Science:Materials International 2004年第4期 46-51页

作者： XU Yunzhe, MI Zhiyong, QU Hong, YOU Ruilin and WU Naihu (1. institute of Genetics and Developmental Biology, chinese academy of sciences, beijing 100080, china 2. College of Life sciences, Peking University, beijing 100871, china) instituteofGeneticsandDevelopmentalBiology ChineseAcademyofSciencesBeijing100080China CollegeofLifesciences PekingUniversityBeijing100871China

A recombinant plasmid pE,T-racd was first constructed by cloning osRACD, the development-regulating gene that controls photoperiod fertility transformation in the photoperiod sensitive genie male sterile rice Nongken 58S, into a prokaryote expression vector pET28a( + ). It was then transformed into E. coli BL-21. Cutting with thrombin of the fusion protein extracted from transformants and PAGE separation yielded pure osRACD protein, which was further concentrated using ultrafiltration and renatured using glutathione oxidation/reduction refolding system for later functional study. As demonstrated by in vitro functional assay, the osRACD protein expressed in E . coli B-21 shows remarkable activity in binding GTP specifically and hydrolyzing it.

关键词： rice (Oryza saliva L.) expression of osRACD gene photoperiod fertility transformation small molecular weight GTP-binding protein.

Embryonic stem cells generated by nuclear transfer of human somatic nuclei into rabbit oocytes

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Cell Research 2003年第4期13卷 251-263页

作者： YING CHEN, ZHI Xu HE, AILIAN LIU, KAI WANG, WEN WEI MAO, JIAN XIN CHU, YONG LU, ZHENG Fu FANG, YING TANG SHI, QING ZHANG YANG, DA YUAN CHEN, MIN RANG WANG, JIN SONG LI, SHAO LIANG HUANG, XIANG YIN KONG, YAO ZHOU SHI, Zm QIANG WANG, JIA HuI XIA, ZHI GAO LONG, ZHI GANG XUE, WEN XIANG DING, HuI ZHEN SHENG Center for Developmental Biology, Shanghai Second Medical University, Shanghai 200092, china Laboratory of Stem Cell Biology, institute of Biochemistry and Cell Biology, Shanghai institutes for Biological sciences, chinese academy of sciences, 1665 Kong Jiang Road, Shanghai 200092, china Center for Stem Cell Research, the Second Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510120,china State Key Laboratory of Reproductive Biology, institute of Zoology, chinese academy of sciences, 19 Zhong-guan Cun Road, Haidian District, beijing 100080, china Health Science Center, Shanghai institutes of Biological sciences, chinese academy of sciences and Shanghai Second Medical University, Shanghai 200025, china National Laboratory of Medical Genetics, Central South University, 88 Xiangya Road, Changsha 410078, china Xinhua Hospital, Shanghai Second Medical University, 1665 Kong Jiang Road, Shanghai 200092, china 2Laboratory of Stem Cell Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 1665 Kong Jiang Road Shanghai 200092 China. 3Center for Stem Cell Research the Second Affiliated Hospital Sun Yat-Sen University Guangzhou 510120 China. 2Laboratory of Stem Cell Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 1665 Kong Jiang Road Shanghai 200092 China. 2Laboratory of Stem Cell Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 1665 Kong Jiang Road Shanghai 200092 China. 2Laboratory of Stem Cell Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 1665 Kong Jiang Road Shanghai 200092 China. 2Laboratory of Stem Cell Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 1665 Kong Jiang Road Shanghai 200092 China. 2Laboratory of Stem Cell Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 1665 Kong Jiang Road Shanghai 200092 China. 2Laboratory of Stem Cell Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 1665 Kong Jiang Road Shanghai 200092 China. 2Laboratory of Stem Cell Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 1665 Kong Jiang Road Shanghai 200092 China. 2Laboratory of Stem Cell Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 1665 Kong Jiang Road Shanghai 200092 China. 4State Key Laboratory of Reproductive Biology Institute of Zoology Chinese Academy of Sciences 19 Zhong-guan Cun Road Haidian District Beijing 10008

To solve the problem of immune incompatibility, nuclear transplantation has been envisaged as a means to produce cells or tissues for human autologous transplantation. Here we have derived embryonic stem cells by the transfer of human somatic nuclei into rabbit oocytes. The number of blastocysts that developed from the fused nuclear transfer was comparable among nuclear donors at ages of 5, 42, 52 and 60 years, and nuclear transfer (NT) embryonic stem cells (ntES cells) were subsequently derived from each of the four age groups. These results suggest that human somatic nuclei can form ntES cells independent of the age of the donor. The derived ntES cells are human based on karyotype, isogenicity, in situ hybridization, PCR and immunocytochemistry with probes that distinguish between the various species. The ntES cells maintain the capability of sustained growth in an undifferentiated state, and form embryoid bodies, which, on further induction, give rise to cell types such as neuron and muscle, as well

关键词： nuclear transfer (NT) somatic cell nuclear transfer (SCNT) embryonic stem cells (ES cell) therapeutic cloning rabbit oocyte.

Construction and Physical Properties of a Single Molecular Device

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Construction and Physical Properties of a Single Molecular D...

Numerical modeling of geothermal groundwater flow in karst aquifer system in eastern Weibei,Shaanxi Province,china

中国化学会第26届学术年会纳米化学分会场

作者： Hongjun Gao beijing National Laboratory of Condensed Matter Physics & institute of Physics, chinese academy of sciences, PO Box 603, beijing 100190, china

＜正＞Constructing single molecular devices of functionalities has stimulated a great interest in the past decades. One of the challenges in this field is to make the single molecule stably connected to a single metal atom on metal surfaces, and further to make the molecule create electric energy and optical/electro radiation by rotating the molecule.

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Numerical modeling of geothermal groundwater flow in karst a...

The dinoflagellate cyst Subtilisphaera from the Eocene of the Qaidam Basin,northwest china,and its implications for hydrocarbon exploration

中国科学院地质与地球物理研究所2007学术年会

作者： LI Ming~(1+),LI GuoMin~1,YANG Liao~2,DANG XueYa~3,ZHAO ChunHu~1,HOU GuangCai~3 & ZHANG MaoSheng~3 1 State Key Laboratory of Lithospheric Evolution,institute of geology and geophysics,chinese academy of sciences,beijing 10002.,china 2 Xinjiang institute of Ecology and Geography,chinese academy of sciences,(U|¨)r(u|¨)mqi 830011,china 3 Xi’an institute of geology and Mineral Resources,Xi’an 710054,china

The quantitative assessment of geothermal water resources is important to the exploitation and utilization of geothermal *** the geothermal water systems the density of groundwater changes with the temperature,therefore the variations in hydraulic heads and temperatures are very complicated. A three-dimensional density-dependent model coupling the groundwater flow and heat transport is established and used to simulate the geothermal water flow in the karst aquifers in eastern Weibei, Shaanxi Province,*** multilayered karst aquifer system in the study area is cut by some major faults which control the regional groundwater *** order to calibrate and simulate the effect of the major faults,each fault is discretized as a belt of elements with special hydrological parameters in the numerical *** groundwater dating data are used to be integrated with the groundwater flow pattern and calibrate the *** results show that the calculated hydraulic heads and tem- perature fit with the observed data well.

关键词： geothermal water numerical modeling fault karst aquifer system Weibei of Shaanxi Province

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The dinoflagellate cyst Subtilisphaera from the Eocene of th...

DETERMINATION OF VOLATILE PHENOLS IN chinese LIQUORS BY GC-MS

中国科学院地质与地球物理研究所第11届（2011年度）学术年会

作者： Liming Ji~(a,b,c*),Fanwei Meng~d,Kui Yan~d,Zhiguang Song~c ~aKey Laboratory of Petroleum Resources Research,institute of geology and geophysics,chinese academy of sciences,Lanzhou 730000,china ~bBureau of Economic geology,Jackson School of Geosciences,The University of Texas at Austin,Austin,TX 78713,USA ~cState Key Laboratory of Organic Geochemistry,Guangzhou institute of Geochemistry,chinese academy of sciences,Guangzhou 510640,china ~dState Key Laboratory of Palaeobiology and Stratigraphy,Nanjing institute of geology and Palaeontology,chinese academy of sciences,Nanjing 210008,china

Although an abundance of 4-methyl-sterane and dinosterane thought to derive from dinoflagellates,has been detected in the Palaeogene source rocks and crude oils in the Qaidam Basin,china,no unequivocal dinoflagellate cysts have been found previously in Cretaceous-Palaeogene terrestrial deposits in this basin, including the Xiaganchaigou *** study reports on a new discovery using detailed analysis of a dinoflagellate cyst assemblage,composed solely of Subtilisphaera,from the Xiaganchaigou Formation on the north margin of the Qaidam *** biomarkers 4-methylsterane and dinosterane in the corresponding fossil-bearing beds have also been detected,further validating the dependability of dinoflagellate *** fossils provide direct evidence of the dinoflagellate contribution to Palaeogene crude oil in the Qaidam Basin and fill a long-existing gap in oil-source correlation.

关键词： Subtilisphaera Dinosterane source rock Xiaganchaigou Formation Qaidam Basin

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chinese Chemical Letters 1990年第2期1卷 187-190页

作者： Chun Sheng LIU Jia Rui GUAN Mao Sun LU Chang Tai YAN institute of Materia Medica,chinese academy of Medical sciences,beijing,china 100050 Chemistry Department,Shandong University,Jinan,china 250100 Chemistry Department,Qingdao University,Qingdao,china 266071

A new method for determining volatile phenols in chinese liquors is proposed. Phenols are sorbed on a macroporous anion-exchange resin after the liquors were brought to a pH value of 12.5,then eluted with HCl-acetone,extracted with methylene dichloride and concentrated to a suitable concentration for derivatization with pentafluorobenzyl bromide (PFB).The PFB derivatives of phenols were successfully separated by gas chromatography on a 30 m SE-54 elastic glass capillary column and detected with Ni-63 electron capture detec- *** characteristics of this method are:high sensitivity,low interference and 95% average recovery of *** method was used successfully in the determination of vola- tile phenols in eight kinds of chinese liquors.

关键词： SE GC

Seasonal variation of soil respiration under different land use/land cover in arid region

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Science china Earth sciences 2007年第S1期 76-85页

作者： ZHANG LiHua1,2, CHEN YaNing1, LI WeiHong1 & ZHAO RuiFeng1,2 1 Key Laboratory of Oasis Ecology and Desert Environment, Xinjiang institute of Ecology and Geography, chinese academy of sciences, ürümqi 830011, china 2 Graduate University of chinese academy of sciences, beijing 100049, china

Through combining the soil respiration with the main environmental factors under the planting shelterbelt (Populus woodland) and the natural desert vegetation (Tamarix ramosissima+Phragmites communis community and Haloxylon ammodendron community) in the western Junngar Basin, the difference in soil respiration under different land use/land cover types and the responses of soil respiration to temperature and soil moisture were analyzed. Results showed that the rate of soil respiration increased with temperature. During the daytime, the maximum soil respiration rate occurred at 18:00 for the Populus woodland, 12:00 for T. ramosissima+Ph. communis community, and 14:00 for H. ammodendron community, while the minimum rate all occurred at 8:00. The soil respiration, with the maximum rate in June and July and then declining from August, exhibited a similar trend to the near-surface temperature from May to October. During the growing season, the mean soil respiration rates and seasonal variation differed among the land use/land cover types, and followed the order of Populus woodland >T. ramosissima+Ph. communis community > H. ammodendron community. The difference in the soil respiration rate among different land use/land cover types was significant. The soil respiration of Pouplus woodland was significantly correlated with the near-surface temperature and soil temperature at 10 cm depth (P < 0.01) in an exponential manner. The soil respiration of T. ramosissima+Ph. communis and H. ammodendron communities were all linearly correlated with the near-surface temperature and soil surface temperature (P < 0.01). Based on the near-surface tempera-ture, the calculated Q10 of Populus woodland, T. ramosissima+Ph. communis community and H. ammodendron community were 1.48, 1.59 and 1.63, respectively. The integrated soil respiration of the three land use/land cover types showed a significant correlation with the soil moisture at 0―5 cm, 5― 15 cm and 0―15 cm depths (P < 0.01). The quadr

关键词： soil respiration diurnal variation seasonal variation land use/land cover temperature soil moisture

TESTING FOR LONG MEMORY IN THE ASIAN FOREIGN EXCHANGE RATES

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Journal of Systems Science & Complexity 2006年第2期19卷 182-190页

作者： Abdol S. SOOFI Shouyang WANG Yuqin ZHANG Department of Economics University of Wisconsin PlatteviUe WI 53818 USA. institute of Systems Science Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing 100080 China. School of International Trade and Economics University of International Business and Economics Beijing 100029 China.

In this paper, we use the plug-in and Whittle methods that are based on spectral regression analysis to test for the long memory property in 12 Asian/dollar daily exchange rates. The results according to the plug-in method show that with the exception of chinese renminbi all series may have long memory properties. The results based on the Whittle method, on the other hand, show that only Japanese yen and Malaysian ringgit may have long memory properties. It is well known that inference about the differencing parameter, d, in presence of structural break in a series entails considerable difficulties. Therefore, given the financial crisis of 1997-1998 in Asia, further tests for unravelling of the memory property and presence of structural break in the exchange rate series are required.

关键词： Exchange rates long memory plug-in method Whittle method.