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A novel model-free approach for reconstruction of time-delayed gene regulatory networks

中国科学：生命科学英文版 2006年第2期49卷 190-200页

作者： JIANG Wei1,2, LI Xia1,2,3,4, GUO Zheng1,2,3, LI Chuanxing1, WANG Lihong1 & RAO Shaoqi1,5 1. Department of Bioinformatics, Harbin Medical University, Harbin 150086, China 2. Department of Computer science, Harbin institute of technology, Harbin 150080, China 3. School of Life science and technology, Tongji University, Shanghai 200092, China 4. Biomedical Engineering institute, Capital University of Medical sciences, Beijing 100054, China 5. Departments of Cardiovascular Medicine and molecular Cardiology, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA Department of Bioinformatics Harbin Medical University Harbin China Department of Computer science Harbin Institute of Technology Harbin China School of Life science and technology Tongji University Shanghai China Departments of Cardiovascular Medicine and molecular Cardiology Cleveland Clinic Foundation Cleveland USA

Reconstruction of genetic networks is one of the key scientific challenges in functional genomics. This paper describes a novel approach for addressing the regulatory dependencies be-tween genes whose activities can be delayed by multiple units of time. The aim of the proposed ap-proach termed TdGRN (time-delayed gene regulatory networking) is to reversely engineer the dy-namic mechanisms of gene regulations, which is realized by identifying the time-delayed gene regu-lations through supervised decision-tree analysis of the newly designed time-delayed gene expres-sion matrix, derived from the original time-series microarray data. A permutation technique is used to determine the statistical classification threshold of a tree, from which a gene regulatory rule(s) is ex-tracted. The proposed TdGRN is a model-free approach that attempts to learn the underlying regula-tory rules without relying on any model assumptions. Compared with model-based approaches, it has several significant advantages: it requires neither any arbitrary threshold for discretization of gene transcriptional values nor the definition of the number of regulators (k). We have applied this novel method to the publicly available data for budding yeast cell cycling. The numerical results demonstrate that most of the identified time-delayed gene regulations have current biological knowledge supports.

关键词： gene regulatory networks, time delayed, decision tree.

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Spatial and Temporal Variability of N, P and K Balances for Agroecosystems in China

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Pedosphere 2005年第3期15卷 347-355页

作者： SHENRun-Ping SUNBo ZHAOQi-Guo instituteofSoilscience ChineseAcademyofSciencesNanjing210008（China）／／DepartmentofSpatialInformationScienceNanjingUniversityofInformationScienceandTechnologyNanjing210044（China） instituteofSoilscience ChineseAcademyofSciencesNanjing210008（China）

Nitrogen, phosphorus, and potassium balances for agroecosystems in China from 1993 to 2001 were calculated at national and provincial levels using statistical data and related parameters, and their spatial and temporal variabilities were analyzed with GIS to estimate the potential impacts of nutrient N, P and K surpluses or deficits to soil, water and air. At the national scale, the N and P balances from 1993 to 2001 showed a surplus, with the nitrogen surplus remaining relatively stable from 1997—2001. Although during this period the P surplus pattern was similar to N, it had smaller values and kept increasing as the use of phosphate fertilizer increased year by year. However, K was deficient from 1993 to 2001 even though from 1999 to 2001 the K deficit decreased. The spatial analysis revealed higher N surpluses in the more developed southeastern provinces and lowest in the western and northern provinces where there was less chemical fertilizer input. The serious K deficit mainly occurred in Shanghai and Beijing municipalities, Jiangsu, Zhejiang and Hubei provinces, and Xinjiang autonomous regions. For the years 1992, 1996 and 2001, N surpluses and K deficits had significant positive spatial correlations with per capita gross domestic product (GDP), per capita gross industrial output value, and per capita net income of rural households. This showed that the level of economic development played an important role on nutrient balances in the agroecosystems.

关键词： China economic factors NPK balance spatial and temporal variability

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Suppressing the multimodal size distribution of InAs/GaAs quantum dots through flattening the surface fluctuation

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science China(Physics,Mechanics & Astronomy) 2010年第5期53卷 788-792页

作者： WANG Lu1,2,LI MeiCheng1,WANG WenXin2,GAO HanChao2,TIAN HaiTao2,XIONG Min1 & ZHAO LianCheng1 1 School of Material science and technology,Harbin institute of technology,Harbin 150001,China 2 national Laboratory for Condensed Matter Physics,institute of Physics,Chinese Academy of sciences,Beijing 100190,China School of Material science and technology Harbin Institute of Technology Harbin China national Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of Sciences Beijing China

A method of suppressing the multimodal size distribution of InAs/GaAs quantum dots(QDs) using molecular beam epitaxy through flattening the substrate surface is reported in this *** is found that the surface roughness plays an important role in the growth of QDs through continuous surface evolution(SEQDs).SEQDs are the main components of small QD ensemble in QDs with multimodal size *** is suggested that most of the SEQDs are very likely to nucleate during the growth interruption rather than during the *** growth of QDs on a smoother surface has largely reduced the density of *** photoluminescence line width of uniform QDs is found to be only 17 meV at a low temperature.

关键词： quantum dots multimodal surface fluctuation

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Recognition of amino acids and anions by a Zn(Ⅱ)-methylazacalix[4]pyridine complex

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science China Chemistry 2009年第10期52卷 1639-1645页

作者： GONG HanYuan, WANG DeXian, HUANG ZhiTang & WANG MeiXiang Beijing national Laboratory for molecular sciences, CAS Laboratory of molecular Recognition and Function, institute of Chemistry, Chinese Academy of sciences, Beijing 100190, China Beijing national Laboratory for molecular sciences CAS Laboratory of Molecular Recognition and Function Institute of Chemistry Chinese Academy of Sciences Beijing China

As a powerful macrocyclic host molecule with unique conformation and cavity structure that are fine-tuned by the bridging nitrogen atoms, methylazacalix[4]pyridine (MACP-4) has been shown to selectively recognize Zn2+ and form stable Zn(Ⅱ)-MACP-4 complexes both in solid state and solution with an association constant up to 5.97 (logKs). The molecular recognition of Zn(Ⅱ)-MACP-4 complexes towards various amino acids and anions with different geometry was investigated by using the spectral titration methods and X-ray analysis. The Zn(Ⅱ)-MACP-4 complex was found to recognize the 17 amino acids tested with the association constant up to 3.97 (logKs). On the other hand, the Zn(Ⅱ)-MACP-4 complex selectively interacted with anions and the maximum association constant of 3.9 (logKs) was obtained.

关键词： Zn(Ⅱ)-MACP-4 complex amino acids anions recognition

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INFLUENCE OF TRACES OF WATER ON THE SYNTHESIS AND ELECTROLUMINESCENCE PROPERTIES OF POLY(2-METHOXY, 5- (2' -ETHYLHEXYL OXY)- 1, 4-PHENYLENE VINYLENE)

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Chinese Journal of Polymer science 2002年第5期20卷 461-465页

作者： Yue-qi Mo Jian Huang Jia-xin Jiang Xian-yu Deng Yu-hua Niu Yong Cao institute of Optoelectronic Materials & Devices Colleg of Material science and Engineering South China University of technology,Guangzhou 510640,China institute of Optoelectronic Materials & Devices College of Material Science and Engineering South China University of Technology Guangzhou 510640

It was found that traces of water in the reaction medium would result in a great increase of gel and a decrease of molecular weight of the poly(2-methoxy,5-(2'-ethylhexyloxy)-1,4-phenylene vinylene) during the polymerization, which ultimately led to inferior film qualities and device properties. The device (ITO/PEDOT/MEH-PPV/Ba/Al) with MEH-PPV prepared under dry conditions has an external quantum efficiency of above 2.0%.

关键词： poly(phenylene vinylene) light-emitting diodes

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Fluorescence dynamics of interactions between polyamide PyPyPyβDp and DNA

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science China Chemistry 2006年第1期49卷 75-80页

作者： ZHANG Huijuan1,2, WANG Jin3, WU Yishi1, YUAN Gu3, AI Xicheng1, WANG Li4 & ZHANG Jianping1 1. State Key Laboratory for Structural Chemistry of Unstable and Stable Species, institute of Chemistry, Chinese Academy of sciences, Beijing 100080, China 2. School of Life science and technology, Beijing institute of technology, Beijing 100081, China 3. College of Chemistry and molecular Engineering, Peking University, Beijing 100080, China 4. Center for Condensed Matter Physics, institute of Physics, Chinese Academy of sciences, Beijing 100080, China Correspondence should be addressed to Ai Xicheng and Zhang Jianping State Key Laboratory for Structural Chemistry of Unstable and Stable Species Institute of Chemistry Chinese Academy of Sciences Beijing China School of Life science and technology Beijing Institute of Technology Beijing China College of Chemistry and molecular Engineering Peking University Beijing China Center for Condensed Matter Physics Institute of Physics Chinese Academy of Sciences Beijing China

The photophysical properties of the polyamide PyPyPyβDp (PPP) were investigated by means of steady-state absorption and fluorescence spectroscopies, as well as time-resolved fluo-rescence spectroscopy. It was found that the excited-state properties of PPP are very sensitive to solvents. In TKMC buffer PPP exhibited weak fluorescence with a decay time constant of 16 ps, while with the decrease of the solvent polarity PPP showed the blue-shifted peak position, increased inten-sity and lengthened life-time for its fluorescence behavior. In the presence of calf thymus DNA, it was observed that the fluorescence intensity was enhanced and the fluorescence lifetime increased from 16 to 32 ps for PPP, which verified that PPP bound into the minor groove of DNA duplex.

关键词： polyamide (PPP), calf thymus DNA (ctDNA), time-resolved fluorescence spectroscopy, recognition dynamics.

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Binding and endocytosis of monoterbium transferrin by K562 cells

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Chinese science Bulletin 2003年第2期48卷 127-130页

作者： ZHAO Chungui1, YANG Binsheng1,2, ZHANG Wei3, BAI Haijing2 & LIU Wen2 1. institute of Biological technology, Shanxi University, Taiyuan 030006, China 2. institute of molecular science, Shanxi University, Taiyuan 030006, China 3. Chinese institute of Radiation Protection, Taiyuan 030006, China Correspondence should be addressed to Yang Binsheng (e-mail: yangbs@***) institute of Biological technology Shanxi University Taiyuan China institute of molecular science Shanxi University Taiyuan China Chinese institute of Radiation Protection Taiyuan China

Using isotopic labeling of human serumapotransferrin, the binding and the endocytosis of monoter-bium transferrin (TbC-apotransferrin, TbC-apotransferrin-FeN) by K562 cells, a human leukemic cell line, have beeninvestigated. There are about (8.58±2.41)×105 binding sites per cell surface at 0℃. The association constant for TbC-apotransferrin binding is 4.1×107 mol-1·L, for TbC-apotransferrin-FeN 2.7×107 mol-1·L at 0℃. At pH 7.4, upon warming cells to 37℃, endocytosis starts. The rate constantsfor the endocytosis are about 0.97 min-1 and 0.31 min-1 and the endocytosis ratio reaches 56% and 80% for TbC-apotransferrin and TbC-apotransferrin-FeN, respectively.

关键词： K562细胞转铁蛋白铽离子结合内噬作用碘125标记

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Accurate prediction of interference minima in linear molecular harmonic spectra by a modified two-center model

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Chinese Physics B 2016年第3期25卷 163-168页

作者：崔鑫张頔玉陈高陈基根曾思良郭福明杨玉军 institute of Atomic and molecular Physics Jilin UniversityChangchun 130012China Jilin Provincial Key Laboratory of Applied Atomic and molecular Spectroscopy Jilin UniversityChangchun 130012China School of science Changchun University of Science and TechnologyChangchun 130022China Department of Physics and Materials Engineering Taizhou UniversityTaizhou 318000China institute of Applied Physics and Computational Mathematics Beijing 100088China

We demonstrate that the interference minima in the linear molecular harmonic spectra can be accurately predicted by a modified two-center model. Based on systematically investigating the interference minima in the linear molecular harmonic spectra by the strong-field approximation （SFA）, it is found that the locations of the harmonic minima are related not only to the nuclear distance between the two main atoms contributing to the harmonic generation, but also to the symmetry of the molecular orbital. Therefore, we modify the initial phase difference between the double wave sources in the two-center model, and predict the harmonic minimum positions consistent with those simulated by SFA.

关键词： high-order harmonic generation molecular harmonics

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Map building for dynamic environments using grid vectors

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Journal of Zhejiang University-science C(Computers and Electronics) 2011年第7期12卷 574-588页

作者： Wen-fei WANG,Rong XIONG ,Jian CHU (State Key Laboratory of industrial Control technology,institute of Cyber-Systems and Control,Zhejiang University,Hangzhou 310027,China) State Key Laboratory of industrial Control technology Institute of Cyber-Systems and Control Zhejiang University Hangzhou China

This paper addresses the problem of creating a geometric map with a mobile robot in a dynamic indoor *** form an accurate model of the environment,we present a novel map representation called the 'grid vector',which combines each vector that represents a directed line segment with a slender occupancy grid map.A modified expectation maximization (EM) based approach is proposed to evaluate the dynamic objects and simultaneously estimate the robot path and the map of the *** probability of each grid vector is evaluated in the expectation step and then used to distinguish the vector into static and dynamic *** robot path and map are estimated in the maximization step with a graph-based simultaneous localization and mapping (SLAM) *** representation we introduce provides advantages on making the SLAM method strictly statistic,reducing memory cost,identifying the dynamic objects,and improving the accuracy of the data *** SLAM algorithm we present is efficient in computation and *** on three different kinds of data sets show that our representation and algorithm can generate an accurate static map in a dynamic indoor environment.

关键词： Grid vector Line Segments Dynamic Simultaneous localization and mapping (SLAM) Expectation maximization (EM)

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Structures and aromaticity of the planar Al_2P_2^(n-) (n=1―4) clusters

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science China Chemistry 2009年第12期52卷 2237-2242页

作者： XU WenGuo,ZHANG YuanChun & ZHAI Lei institute of Chemical Physics,Beijing institute of technology,Beijing 100081,China institute of Chemical Physics Beijing Institute of Technology Beijing China

Clusters Al2P2n-(n = 1―4) were theoretically investigated using density functional theory (DFT) methods at the B3LYP/6-311+G* and B3PW91/6-311+G* levels of theory. The calculated results showed that the planar structure (D2h symmetry) of Al2P2n-(n = 1―4) species was the global minimum. And the negative nucleus-independent chemical shift (NICS) value of Al2P2n-(n = 1―4) species indicated the existence of a ring current in the planar structure (D2h symmetry). A detailed molecular orbital (MO) analysis revealed that the planar structures (D2h symmetry) had π aromaticity,which further exhibited the strongly aromatic character for Al2P2n-(n = 1―4) species.

关键词： DFT calculation geometric structure nucleus-independent chemical shift molecular orbital

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