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

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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.

SEMIPARAMETRIC MODEL SELECTION IN LARGE SAMPLES

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Journal of Systems Science & Complexity 2001年第4期14卷 378-387页

作者： SHI Peide, WANG Haiyan, ZHENG Zhongguo (Department of Probability and Statistics, Peking university, beijing 100871, china) 北京大学北京 100871

For semiparametric regression model selection, based on a model selection criterion there is no finite order (or number of parameters) of the nonparametric part to be estimated consistently, but there is a finite order (or number of predictor variables) of the linear part to be estimated consistently. The models selected by using AIC and AICC are not consistent estimates of linear part of the true model. In this paper, we study the consistency in model selection by investigating the asymptotic properties of AIC* and AICC*, the modified versions of AIC and AICC respectively, which were proposed by a referee of the reference Shi and Tsai. Under some regular conditions, we prove that the parametric models of the semiparametric regression selected with AIC* and AICC* converge to the true model in probability. In addition, in terms of the mean integrated squared error plus a penalty, these two criteria can also provide an asymptotically efficient selection.

关键词： AIC AICC model selection information criterion.

Genetic variability of half-smooth tongue sole Cynoglossus semilaevis populations using microsatellite markers

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Acta Oceanologica Sinica 2011年第3期30卷 76-83页

作者： LIU Yunguo GUO Yinghui LIU Shuaishuai LI Junfeng YE Naihao Inspection ＆ Quarantine Technology Center Shandong Entry-Exit Inspection ＆ Quarantine Bureau Qingdao 266002 China Ocean university of china Qingdao 266003 China College of Basic Medical Sciences Shandong University of Traditional Chinese Medicine Jinan 250355 China Yellow Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Qingdao 266071 China College of Chemical Engineering Qingdao University of Science ＆ Technology Qingdao 266042 China

Ten highly variable microsatellite loci were performed in order to evaluate the genetic variability of wild and hatchery samples of half-smooth tongue sole Cynoglossu＇s semilaevis. A group of 200 genotypes belonging to four wild samples, Laizhou （LZ）, Weihai （WH）, Qingdao （QD）, Rizhao （RZ） and one hatchery sample, Mingbo （MB）, were screened. All of the： ten microsatellite loci screened in this study showed marked polymorphism. A total of 70 different alleles were observed over all loci. The number of alleles per locus ranged from 4.2 to 1006 the average of expected and observed heterozygosity ranged from 0.67 to 0.82, and from 0：77 to0.87 respectively. A total of 10, 16, 10, 11 and 5 unique alleles each were found in LZ, WH~ QD：RZ and MB populations. The effective number of alleles varied from 2.87 for HSTS_7 to 6.83 for HSTS_h. The number of average genotypes ranged from 6.0 for HSTS a to 15.4 for HSTS_h： As compared with the wild populations, the hatchery population, MB, showed significant genetic changes such as fewer alleles per locus （P〈0.05）, a smaller number of low frequency alleles （P〈0.05）, a small number of unique alleles and a small number of genotypes （P〈0.05）, all indicative of a reduction in genetic diversity.

关键词： Cynoglossus semilaevis microsatellite marker population genetic variability

Icosahedral quasicrystalline phase in an as-cast Mg-Zn-Er alloy

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Rare Metals 2009年第3期28卷 297-301页

作者： LI Jianhui DU Wenbo LI Shubo WANG Zhaohui School of Materials Science and Engineering Beijing University of Technology Beijing 100124 China

The microstructure of an as-cast Mg-Zn-Er alloy was investigated through scanning electron microscopy （SEM） and transmission electron microscopy （TEM） equipped with energy dispersive spectroscopy （EDS）. The results indicate that two different second phases, one with eutectoid-lamellar morphology and the other with granular shape, distribute in the α-Mg matrix. The coexistence of the face-centered icosahedral quasicrystalline phase （I-phase） and W-phase with the face-centered cubic structure is found in the as-cast alloy. The coexistence of I-phase and W-phase in the Mg-Zn-Er alloy is because the W-phase is the primary phase and the I-phase forms by peritectic reaction during solidification.

关键词： magnesium alloy microstructure quasicrystal erbium

Multi-carbazole derivatives for two-photon absorption data storage:Synthesis,optical properties and theoretical calculation

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Science china Chemistry 2010年第4期53卷 884-890页

作者： LI Lin1, YANG JiaXiang1,2, WANG CaiXia1, HU ZhangJun1, TIAN YuPeng1,2, LI Jing3, WANG ChuanKui3, LI Ming4, CHENG GuangHua4, TANG HuoHong5, HUANG WenHao5, TAO XuTang2 & JIANG MinHua2 1Department of Chemistry, Anhui university, Hefei 230039, china 2State Key Laboratory of Crystal Materials, Institute of Crystal Materials of Shandong university, Jinan 250100, china 3Department of Physics, Shandong Normal university, Jinan 250014, china 4State Key Laboratory of Transient Optics and Photonics, Xi’an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi’an 710119, china 5Department of Precision Machinery and Precision Instrumentation, university of Science and Technology of china, Hefei 230026, china Department of Chemistry Anhui University Hefei China State Key Laboratory of Crystal Materials Institute of Crystal Materials of Shandong University Jinan China Department of Physics Shandong Normal University Jinan China State Key Laboratory of Transient Optics and Photonics Xi’an Institute of Optics and Precision Mechanics Chinese Academy of Sciences Xi’an China Department of Precision Machinery and Precision Instrumentation University of Science and Technology of China Hefei China

Two novel quadrupolar organic compounds, 3-(4-((E)-2-(9-butyl-9H-carbazol-6-yl) vinyl)styryl)-9-propyl-9H-carbazole (BCSPC) and 3-(3-(3-((1E)-2-(4-((E)-2-(3-(3,5-bis(9-butyl-9H-carbazol-6-yl)phenyl)-9-butyl-9H-carbazol-6-yl)vinyl)phenyl) vinyl)-9-butyl-9H-carbazol-6-yl)-5-(9-butyl-9H-carbazol-6-yl)phenyl)-9-butyl-9H-carbazole (BCPBC), with different conjugated arms, have been designed and synthesized. Their one-and two-photon absorption (TPA) and excited fluorescence properties have been experimentally investigated. The two-photon absorption cross-sections of two compounds were estimated by two-photon excited fluorescence technique using 200 fs, 76 MHz, Ti:sapphire laser, which are 22 and 154 GM for BCSPC and BCPBC, respectively. The optimal excitation wavelengths are 780 nm for both BCSPC and BCPBC. A data recording experiment proved the potential application of the materials.

关键词： initiator optical data storage fluorescence two-photon absorption theoretical calculation

STRONG CONSISTENCY OF M-ESTIMATES OF MULTIPLE REGRESSION COEFFICIENTS

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Systems Science and Mathematical Sciences 1995年第1期8卷 82-87页

作者： CHEN Xiru (Graduate School of the Chinese Academy of Sciences, beijing 100039, china)ZHAO Lincheng (Department of Mathematics, university of Science and Technology of china, Hefei 230026, china)

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关键词： Linear regression M-estimate strong consistency.

INITIAL-BOUNDARY VALUE PROBLEM FOR THE UNSATURATED LANDAU-LIFSHITZ SYSTEM

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Chinese Annals of Mathematics,Series B 2000年第3期21卷 389-402页

作者： DINGSHIJIN GUOBOLING DeuartmentofMathematics SouthChinaNormalUniversityGuangzhou510630China. CenterforNonlinearStudies InstituteofAppliedPhysicsandComputationalMathematicsP.O.Box8009Beijing：100088China.

The existence, partial regularity and uniqueness of weak solution to the initial boundary value problem for the unsaturated Landau-Lifschitz systems are given.

关键词：边值问题不饱和兰道-利普希茨系统弱解唯一性偏正则性存在性

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Editor’s note

Science china(Information Sciences) 2011年第5期54卷 913-914页

作者： HUANG Ru, Guest Editor Peking university beijing 100871, china ZHAO Bin, Guest Editor Fairchild Semiconductor 32 Discovery, Irvine, CA 92618, USA WANG RunSheng, Guest Editor Assistant CAI YiMao, Guest Editor Assistant Peking university beijing 100871, china Peking university Beijing China Fairchild Semiconductor Irvine USA

In recent years, driven by ever-increasing market demand in computing, communication, and multimedia applications, the microelectronics industry has undergone rapid development. Because of technical innovation and advances in almost all aspects of materials, processes, equipment, devices, circuits and systems, siliconbased logic and memory IC technologies using nano-scaling continue to be the industry’s major R&D focus. This maintains microelectronics industry adherence to the traditional "Moore’s Law", increasing the function

关键词： than s note Editor

A New Wavelength Selective Photoreceiver

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Chinese Journal of Lasers 2000年第5期9卷 51-55页

作者： LIU Kai HUANG Yongqing REN Xiaomin LI Jianxin GUO Wei (Optical Communication Center, beijing university of Posts and Telecommunications, beijing 100876, china)MA Xiaoyu KANG Xuejun LIAO Qiwei (Institute of Semiconductor, The Chinese Academy of 北京邮电大学北京中科院半导体所北京

A new kind of wavelength selective photoreceiver is proposed. It was constructed by a Fabry Perot (F P) etalon filter and a resonant cavity enhanced (RCE) photodetector. The photoreceiver′s spectral response is determined by the F P etalon filter with a FWHM of less than 4 nm. Moreover, with such a photoreceiver, the transmission loss of the F P etalon filter can be compensated to some extent. And this will benefit its applications.

关键词： wavelength selection photodetector WDM and optoelectronics device