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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 20043., china shanghai {3. for Bioinformation 1 Technology, shanghai 20023., china School of Life sciences, Fudan University, shanghai 20043., china Bioinformation {3. of shanghai Institutes for Biological sciences, the chinese academy of sciences,{13., china Department of Computing and Information Technology Fudan University Shanghai 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

Study on growth and properties of novel γ-LiAlO_2 substrate

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Science china(Technological sciences) 2006年第2期49卷 188-193页

作者： ZOU Jun1,2, ZHOU Shengming1, XU Jun1 & ZHANG Rong3.1. shanghai Institute of Optics and Fine Mechanics, chinese academy of sciences, shanghai 201800,{3. 2. Graduate School of chinese academy of sciences, Beijing 10003.,{3. 3. Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093.{3. 1. shanghai Institute of Optics and Fine Mechanics Chinese Academy of Sciences Shanghai 201800 China 2. Graduate School of chinese academy of sciences Beijing 100039 China 3. Laboratory of Solid State Microstructures and Department of Physics Nanjing University Nanjing 210093 China

Transparent γ-LiAlO2 single crystal has been grown by Temperature Gradient technique. The surface of the wafer annealed in O2-atmosphere at 1100°C for 70 h became opaque and Li-poor phase (LiAl5O8); while, that annealed in Li-rich atmosphere kept transparent and smooth. The full-width at half maximum value dropped to 3. arcsecs when the wafer was annealed in Li-rich atmosphere. That annealed in O2-atmosphere increased to 78 arcsec. Compared with absorption spectra, we can conclude that the 196 nm absorption peak was caused by Li vacancies and the 73. nm peak was caused by O vacancies.

关键词： γ-LiAlO2 crystal, scanning electron micrograph (SEM), absorption spectra.

An H_2O flare in GGD25

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chinese Science Bulletin 2001年第1期46卷 35-39页

作者： XU Ye, ZHENG Xingwu JIANG Dongrong, ZHANG Fujun& YU Zhiyao1. shanghai astronomical Observatory, chinese academy of sciences,{3., china 2. chinese National Observatories, chinese academy of sciences, Beijing 100080, china 3. Department of astronomy, Nanjing University, Nanjing 210093. china shanghai astronomical Observatory Chinese Academy of Sciences Shanghai China chinese National Observatories Chinese Academy of Sciences Beijing China Department of astronomy Nanjing University 210093 China

We report the observing results of a short time scale monitoring of the 22 GHz water maser emission in GGD25. A rapid water maser outburst with the time scales of 4 d has been detected, and the variations are accompanied by some changes in the line width. The time variations were probably caused by a collision pump which led to changes in the pump input.

关键词： interstellar masers (ISM) individual GGD25 masers.

Waiting time in block fading MIMO systems with dynamic-depth interleaving

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Science china(Information sciences) 2010年第8期53卷 1622-1627页

作者： GUO HaiYou 1,2 , HU HongLin 1,2 & ZHANG Yan 3.1 Key Laboratory of Wireless Sensor Network & Communication, shanghai Institute of Microsystem and Information Technology, chinese academy of sciences, shanghai 200050,{3. 2 shanghai research center for Wireless Communications, shanghai 2003.5,{3. 3.Simula research Laboratory, Lysaka 13.5, Norway 1. Key Laboratory of Wireless Sensor Network & Communication Shanghai Institute of Microsystem and Information Technology Chinese Academy of Sciences Shanghai 200050 China2. Shanghai Research Center for Wireless Communications Shanghai 200335 China3. Simula Research Laboratory Lysaka 1325 Norway

Interleaving is an efficient measure to resolve the bursty errors in a block fading multiple-inputs multiple-outputs (MIMO) system. For the metrics of network layer, interleaving exerts two conflicting effects on the ultimate delay performance. Specifically, interleaving can advantageously reduce data transmit time. On the other hand, it comes at a cost, entailing an undesired delay penalty resulting from interleaving depth. Here, we exploit a unified model to accommodate these two conflicting effects, and derive the average waiting time in block fading MIMO systems with dynamic-depth interleaving. Such a unified model is developed with a combined method of both information theory and queueing theory. Therefore, the model is capable of characterizing the randomness of data arrival process, hence the nature of dynamic-depth interleaving. The methodology and the results are applicable to designing, evaluating, and tuning the practical interleaving systems.

关键词： dynamic-depth interleaving multiple-inputs multiple-outputs (MIMO) queueing analysis waiting time

Synthesis and Characteristics of an Aspartame Analogue,L-Asparaginyl L-3.Phenyllactic Acid Methyl Ester

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Acta Biochimica et Biophysica Sinica 2004年第6期36卷 385-389页

作者： Hu TAO1, Da-Fu CUI1, and You-Shang ZHANG1,2* 1Institute of Biochemistry and Cell Biology, shanghai Institutes for Biological sciences, chinese academy of sciences, Graduate School of the chinese academy of sciences, shanghai 2.003., china Institute of Protein research, Tongji University, shanghai 2.003., china Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of SciencesShanghai 200031 China Institute of Protein research Tongji UniversityShanghai 200031 China

An aspartame analogue, L-asparaginyl L-3.phenyllactic acid methyl ester was synthesized with aspartic acid replaced by asparagine and peptide bond replaced by ester bond. The aspartic acid of aspartame could be replaced by asparagine as reported in the literature. In this analogue, the hydrogen of amide group could still form a hydrogen bond with the oxygen of ester bond and the ester bond was isosteric with peptide bond. However, the product was not sweet, showing that the peptide bond could not be replaced by ester bond. The peptide C-N bond behaves as a double bond that is not free to rotate and the C, O, N and H atoms are in the same plane. The replacement of peptide bond by ester bond destroyed the unique conformation of peptide bond, resulting in the loss of sweet taste.

关键词： artificial sweetener aspartame derivative peptide bond

Regular behaviors in SU(2) Yang-Mills classical mechanics

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Nuclear Science and Techniques 1997年第3期8卷 139-143页

作者： Xu Xiao Ming (shanghai Institute of Nuclear research, the chinese academy of sciences, shanghai 201800) shanghaiInstituteofNuclearresearch theChineseAcademyofSciencesShanghai201800

ＲｅｇｕｌａｒｂｅｈａｖｉｏｒｓｉｎＳＵ（２）ＹａｎｇＭｉｌｓｃｌａｓｉｃａｌｍｅｃｈａｎｉｃｓＸｕＸｉａｏＭｉｎｇ（ＳｈａｎｇｈａｉＩｎｓｔｉｔｕｔｅｏｆＮｕｃｌｅａｒＲｅｓｅａｒｃｈ，ｔｈｅＣｈｉｎｅｓｅＡ... 详细信息

ＲｅｇｕｌａｒｂｅｈａｖｉｏｒｓｉｎＳＵ（２）ＹａｎｇＭｉｌｓｃｌａｓｉｃａｌｍｅｃｈａｎｉｃｓＸｕＸｉａｏＭｉｎｇ（ＳｈａｎｇｈａｉＩｎｓｔｉｔｕｔｅｏｆＮｕｃｌｅａｒＲｅｓｅａｒｃｈ，ｔｈｅＣｈｉｎｅｓｅＡｃａｄｅｍｙｏｆＳｃｉｅｎｃｅｓ，...

关键词： SU(2) 杨-Mills经典力学正则行为

Serine racemase expression in mouse cerebral cortex after permanent focal cerebral ischemia

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Acta Pharmacologica Sinica 2004年第4期25卷 38-43页

作者： Li-zhenWANG, Xing-zu ZHU2 Department of Pharmacology, shanghai Institute of Materia Medica, shanghai Institutes for Biological sciences,{3., shanghai 201203. china Department of Pharmacology Shanghai Institute of Materia MedicaShanghai Institutes for Biological Sciences Chinese Academy of Sciences

AIM: To study the alterations of the expressions of serine racemase in C57BL/6 mouse brain after permanent focal cerebral ischemia. METHODS: The mRNA level and the protein level of serine racemase were assayed by semiquantitative reverse transcription polymerase chain reaction (RT-PCR) and Western blot, respectively. The amount of D-serine and L-serine were measured by HPLC. RESULTS: High levels of serine racemase were constitutively expressed in the normal cortex of mouse. At early stage after middle cerebral artery occlusion (MCAO), no significant change in expression of serine racemase was observed in temporoparietal cortex in ipsila- teral hemisphere. However, delayed transient decreases of serine racemase in both mRNA and protein levels were detected from d 6 to d 10 after ischemia. Correspondingly, D-serine concentration also declined in the ipsilateral cortex during this period when compared with the D-serine level in the contralateral cortex. CONCLUSION: Delayed decreases in serine racemase expression and D-serine level occurred in the temporoparietal cortex at the late stage after focal cerebral ischemia.

关键词： D-serine L-serine serine racemase inbred C57BL mice brain ischemia

Functional Analysis of Multiple Transcription Factor Sites in a Regulatory Element of Human ε-Globin Gene

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Acta Biochimica et Biophysica Sinica 2004年第10期36卷 673-680页

作者： Chun-Hui HOU, Jian HUANG, and Ruo-Lan QIAN* State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, shanghai Institutes for Biological sciences, chinese academy of sciences, Graduate School of the chinese academy of sciences, shanghai 2.003., china State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of Sciences

The developmental control of the human ε-globin gene expression is mediated by transcrip- tional regulatory elements in the 5’ flanking DNA of this gene. A previously identified negative regulatory element (–3.28 to –2902 bp, termed ε-NRAII) was analyzed and one putative NF-κB site and two GATA sites locate at –3.04 bp, –2975 bp and –2948 bp were characterized. Electrophoresis mobility shift assay (EMSA) showed that the putative NF-κB site was specifically bound by nuclear proteins of K562 cells. Data obtained from transient transfection showed that the expression of reporter gene could be upregulated about 50% or 100% respectively when ε-NRAII was inserted upstream of the SV40 promoter or ε-globin gene proximal promoter (–177 bp to +1 bp), suggesting that ε-NRAII might not be a classic silencer. Mutation in the putative NF-κB site or in the GATA site (at –2975 bp) slightly reduced the expression of reporter gene driven by SV40 promoter or ε-globin gene proximal promoter. However, the mutation of GATA site at –2948 bp remarkably reduced the reporter gene activity driven by SV40 promoter, but not by ε-globin gene proximal promoter. Further mutation analysis showed that the negative effect of mutation in GATA site at –2948 bp on SV40 promoter was not affected by the mutation of the putative NF-κB site, whereas it could be abolished by the mutation of GATA site at –2975 bp. Furthermore, the mutation of both GATA sites could synergistically reduce the reporter gene activity driven by ε-globin gene proximal promoter. Those results suggested that ε- NRAII might function differently on the SV40 promoter and ε-globin gene proximal promoter.

关键词： ε-globin gene regulatory element NF-κB GATA

Some developments of hot accretion flow theory in the past ten years

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Science china(Physics,Mechanics & astronomy) 2010年第S1期53卷 24-30页

作者： YUAN Feng Key Laboratory for research in Galaxies and Cosmology,shanghai astronomical Observatory,{3. academy of sciences,shanghai 2.003.,china 1. Key Laboratory for research in Galaxies and Cosmology Shanghai Astronomical Observatory Chinese Academy of Sciences Shanghai 200030 China

The hot accretion flow model was re-discovered in 1994 by Narayan and *** theoretical works have been conducted and significant progresses have been *** this paper,we review several developments in the past ten *** mainly includes the finding of outflow and convection and its dynamical effect on inflow;the direct electron heating by viscous dissipation;the effect of large scale toroidal magnetic fields in the inner region of the accretion flow;and the effect of global Compton *** observational applications are also introduced very briefly.

关键词： flow Some developments of hot accretion flow theory in the past ten years