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A Novel Method for Prediction of Protein Domain Using Distance-Based Maximal Entropy

Journal of Bionic engineering 2008年第3期5卷 215-223页

作者： Shu-xue Zou Yan-xin Huang Yan Wang Chun-guang Zhou Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education College of Computer Science and Technology Jilin University Changchun 130012 P. R. China

Detecting the boundaries of protein domains is an important and challenging task in both experimental and computational structural biology. In this paper, a promising method for detecting the domain structure of a protein from sequence information alone is presented. The method is based on analyzing multiple sequence alignments derived from a database search. Multiple measures are defined to quantify the domain information content of each position along the sequence. Then they are combined into a single predictor using support vector machine. What is more important, the domain detection is first taken as an imbal- anced data learning problem. A novel undersampling method is proposed on distance-based maximal entropy in the feature space of Support Vector Machine （SVM）. The overall precision is about 80%. simulation results demonstrate that the method can help not only in predicting the complete 3D structure of a protein but also in the machine learning system on general im- balanced datasets.

关键词： protein domain boundary SVM imbalanced data learning distance-based maximal entropy

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Adsorption mechanisms of cadmium on crosslinked chitosan templated under microwave irradiation

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Gaofenzi Cailiao Kexue Yu Gongcheng/Polymeric Materials science and engineering 2009年第1期25卷 75-78页

作者： Hao, Hong-Ying Shao, Zi-Qiang He, Meng-Chang State Key Joint Laboratory of Environmental Simulation and Pollution Control School of Environment Beijing Normal University Beijing 100875 China School of Material Science and Engineering Beijing Institute of Technology Beijing 100081 China

X-ray photoelectron spectroscopy, IR and chemical analysis were employe to study the adsorption mechanisms of crosslinked chitosan (CCTSCd) on cadmium. According to IR, it showed that -NH2 groups of chitosan were protected by template method and others -NH2 groups which didn't complex with cadmium ions took part in crosslinking reaction. Investigating the changes of element binding energy of O1s, C1s, N1s and Cd3d of XPS, there were chemical shifts of both N1s and Cd3d5/2 and Cd3d3/2 of the sample of adsorption comparing with unadsorption, but O1s and C1s hadn't. At the same time, N1s peak had a shoulder peak. The results indicate that -NH2 groups on CCTSCd complexes with cadmium ions by N1s fit spectra. The adsorption is a chemical adsorption and the experimental data fits Freundlich adsorption isotherm. The sorbent has selectivity and memory to metal ions.

关键词： Microwave irradiation

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Substituent Effect on Infrared Spectra and Thermodynamic Properties of Polynitroamino Substituted Cyclopentane and Cyclohexane

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Chinese Journal of Chemical Physics 2008年第6期21卷 526-534页

作者： Ling Qiu Xue-dong Gong He-ming Xiao Institute for Computation in Molecular and Material Science School of Chemical Engineering Nanfing University of Science and Technology Nanjing 210094 China Key Laboratory of Nuclear Medicine Ministry of Health Jiangsu Institute of Nuclear Medicine Wuxi 214063 China

Density functional theory method was employed to study the effect of the nitroamino group as a substituent in cyclopentane and cyclohexane, which usually construct polycyclic or caged nitramines. Based on the optimized molecular structures of two groups of monocyclic nitramines at the B3LYP/6-31G^＊＊ level, the infrared （IR） spectra were obtained and assigned by harmonic vibrational analysis. The calculated results agree reasonably with the available experimental data. According to the principles of statistic thermodynamics, thermodynamic properties were derived from the IR spectra, which were linearly correlated with the number of nitroamino groups as well as the temperature. The contributions of nitroamino groups to thermodynamic properties are in accord with the group additivity.

关键词： Density functional theory Substituent effect Monocyclic nitramine Infrared spectrum Thermodynamic property

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Method to improve speed and accuracy of transfer path analysis

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Jilin Daxue Xuebao (Gongxueban)/Journal of Jilin University (engineering and Technology Edition) 2009年第SUPPL. 1期39卷 78-82页

作者： Long, Yan Fan, Rang-Lin Shi, Wen-Ku Zhou, Zhou Li, Wei State Key Laboratory of Automobile Dynamical Simulation Jilin University Changchun 130022 China Department of Automobile and Equipment Engineering University of Science and Technology Beijing 100083 China Automobile Engineering Institute Chang'an Automobile Co. Ltd. Chongqing 401120 China

The past progress in transfer path analysis (TPA) and its limitations were reviewed. A innovative unbiased estimative methodology of transfer functionis was introduced and applied. The measurement method of transfer function was improved. Then TPA using the data of easy measurement in operational condition of vehicle can be put in practice. Accuracy of transfer function was improved, the process of measurement was predigested, and time was decreased. A data postprocessing program of measurement was written by MatLab. Finally, the improvement of TPA was validated through idling vibration of engine transmitting to compartment.

关键词： Transfer functions

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Theoretical Studies on Thermolysis Mechanism and Stability of trans-1,4,5,8-Tetranitro-1,4,5,8-tetraazadecalin Isomers

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中国化学(英文版) 2008年第12期26卷 2165-2172页

作者： QIU,Ling GONG,Xue-Dong XIAO,He-Ming Institute for Computation in Molecular and Material Science School of Chemical EngineeringNanjing University of Science and TechnologyNanjingJiangsu 210094China Key Laboratory of Nuclear Medicine (Ministry of Health) Jiangsu Institute of Nuclear Medic Institute for Computation in Molecular and Material Science School of Chemical EngineeringNanjing University of Science and TechnologyNanjingJiangsu 210094China

A systematic study on the thermolysis mechanism and stability of a series of energetic cyclic nitramines, trans-1,4,5,8-tetranitro-1,4,5,8-tetraazadecalin isomers, was performed by density functional theory (DFT) and semiempirical molecular orbital (MO) calculations. Bond dissociation energies (BDE) and activation energies (Ea) of the thermolysis processes were computed at the B3LYP/6-31G** and PM3 levels, respectively. The effect of ni-troamino groups on the thermal stability and pyrolysis mechanism of the title compounds was evaluated by the BDE and Ea. The correlations among BDE, Ea, bond overlap populations, energies of the frontier orbitals, and energy gaps were examined in detail. The results indicate that thermal stabilities and decomposition mechanisms of the title compounds derived from the BDE, Ea and static electronic parameters are basically consistent. Homolysis of the N-NO2 bond is the initial step in the thermolysis of the title compounds, the meta-isomers are more stable than the para-isomers, and the ortho-isomers are the most sensitive.

关键词： trans-1 4 5 8-tetranitro-1 4 5 8-tetraazadecalin isomer density functional theory (DFT) thermolysis mechanism thermal stability bond dissociation energy (BDE) activation energy (Ea)

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Canonical Huffman code based full-text index

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Progress in Natural science:Materials International 2008年第3期18卷 325-330页

作者： Yi Zhang a,b, Zhili Pei a, Jinhui Yanga, Yanchun Liang a, a College of Computer science and Technology, Jilin University, key laboratory of Symbol computation and Knowledge engineering of the Ministry of Education, Changchun 130012, China b Department of Computer science, Jilin Technology and Business College, Changchun 130062, China College of Computer Science and Technology Jilin University Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education Changchun 130012 China Department of Computer Science Jilin Technology and Business College Changchun 130062 China

Full-text indices are data structures that can be used to find any substring of a given string. Many full-text indices require space larger than the original string. In this paper, we introduce the canonical Huffman code to the wavelet tree of a string T[1. . .n]. Compared with Huffman code based wavelet tree, the memory space used to represent the shape of wavelet tree is not needed. In case of large alphabet, this part of memory is not negligible. The operations of wavelet tree are also simpler and more efficient due to the canonical Huffman code. Based on the resulting structure, the multi-key rank and select functions can be performed using at most nH0 + jRj(lglgn + lgn lgjRj)+O(nH0) bits and in O(H0) time for average cases, where H0 is the zeroth order empirical entropy of T. In the end, we present an efficient construction algorithm for this index, which is on-line and linear.

关键词： Full-text index Su?x automaton Canonical Hu?man code

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Novel trusted authentication and evaluation framework in VANET

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Tongxin Xuebao/Journal on Communications 2009年第1 A期30卷 107-113页

作者： Wu, Jing Liu, Yan-Heng Wang, Jian Li, Wei-Ping College of Computer Science and Technology Jilin University Changchun 130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun 130012 China Changchun Jilin University Information Technologies Co. Ltd. Changchun 130012 China

Vehicular ad hoc networks (VANET) have many new characteristics unlike tranditional network, such as centriclessness, mobility and multi-hop transmission, which invalidate conventional key managements. The fast development and successful application of trusted computing technology provide a potential solution to achieve effective authentication and trust evaluation. According to the VANET with self-organization, a new authentication and trust evaluation framework was proposed based on trusted computing technology, the concepts of "trusted attribute" and "trusted grade" were introduced, and the key management architecture as well as authentication process of mobile node were explained in detail. Moreover, the potential real application of the presented framework was discussed, and the trust evaluation method and its argumentation in the presented framework were given.

关键词： Authentication

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Substituent effect on the molecular stability,group interaction,detonation performance,and thermolysis mechanism of nitroamino-substituted cyclopentanes and cyclohexanes

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science China Chemistry 2008年第12期51卷 1231-1245页

作者： QIU Ling GONG XueDong JU XueHai XIAO HeMing Institute for Computation in Molecular and Material Science School of Chemical EngineeringNanjing University of Science and TechnologyNanjing 210094China Key Laboratory of Nuclear Medicine Ministry of HealthJiangsu Institute of Nuclear MedicineWuxi 214063China

Density functional theory (DFT) method has been employed to study the effect of nitroamino group as a substituent in cyclopentane and cyclohexane, which usually construct the polycyclic or caged nitra-mines. Molecular structures were investigated at the B3LYP/6-31G** level, and isodesmic reactions were designed for calculating the group interactions. The results show that the group interactions ac-cord with the group additivity, increasing with the increasing number of nitroamino groups. The dis-tance between substituents influences the interactions. Detonation performances were evaluated by the Kamlet-Jacobs equations based on the predicted densities and heats of formation, while thermal stability and pyrolysis mechanism were studied by the computations of bond dissociation energy (BDE). It is found that the contributions of nitroamino groups to the detonation heat, detonation velocity, detonation pressure, and stability all deviate from the group additivity. Only 3a, 3b, and 9a-9c may be novel potential candidates of high energy density materials (HEDMs) according to the quantitative cri-teria of HEDM (ρ≈ 1.9 g/cm3, D ≈ 9.0 km/s, P ≈ 40.0 GPa). Stability decreases with the increasing number of N-NO2 groups, and homolysis of N-NO2 bond is the initial step in the thermolysis of the title com-pounds. Coupled with the demand of thermal stability (BDE > 20 kcal/mol), only 1,2,4-trinitrotriazacy-clohexane and 1,2,4,5-tetranitrotetraazacyclohexane are suggested as feasible energetic materials. These results may provide basic information for the molecular design of HEDMs.

关键词： density functional theory (DFT) substituent effect monocyclic nitramine high energy density material (HEDM) group interaction detonation performance thermal stability bond dissociation energy (BDE)

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Isolation of a Pseudomonas Stutzeri strain that degrades 1,2,4-trichlorobenzene and characterization of its degradative plasmid

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Frontiers of Environmental science & engineering 2008年第1期2卷 69-72页

作者： Lei SONG Hui WANG Hanchang SHI Hongying HU Environmental Simulation and Pollution Control State Key Joint Laboratory Department of Environmental Science and EngineeringTsinghua UniversityBeijing 100084China

The genetic information encoding metabolic pathways for xenobiotic compounds in bacteria often resides on catabolic *** aim of the present work was to know the location of the genes for degrading 1,2,*** this paper a 1,2,4-trichlorobenzene-degrading strain THSL-1 was isolated from the soil of Tianjin Chemical Plant using 1,2,4-trichlorobenzene as the sole carbon *** strain was identified as Pseudomonas stutzeri through morphologic survey and 16S rDNA sequence determination.A plasmid was discovered from strain THSL-1 by using the alkali lysis *** the plasmid was transformed into ***109 by the CaCl2 method,the transformant could grow using 1,2,4-trichlorobenzene as the sole carbon source and had the degradation function of 1,2,***,it could be deemed that the plasmid carried the degradative genes of 1,2,*** average size of the plasmid was finally determined to be 40.2 Kb using selectively three kinds of restricted inscribed enzymes(HindIII,BamHI,and XholI)for single cutting and double cutting the plasmid pTHSL-1,respectively.

关键词： 1,2,4-trichlorobenzene 16S rDNA degradative plasmid Pseudomonas sp.

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Improvement of detection method of Cryptosporidium and Giardia in reclaimed water

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Frontiers of Environmental science & engineering 2008年第3期2卷 380-384页

作者： Tong ZHANG Xing XIE Hongying HU Yudong SONG Qianyuan WU Zusheng ZONG Environmental Simulation and Pollution Control State Key Joint Laboratory Department of Environmental Science and EngineeringTsinghua UniversityBeijing 100084China

Cryptosporidium and Giardia are two typical species of pathogenic protozoans that seriously endanger water *** works indicated that detection of Cryptosporidium and Giardia with modified United States Environmental Protection Agency(USEPA)method-1623 using a membrane filtration-elution for sample concentration attained better recovery and lower cost compared to the USEPA *** improvements of membrane filtration-elution step as well as immunomagnetic separation(IMS)steps were investigated and an optimized method for detection of Cryptosporidium and Giardia in wastewater reclamation system was recommended in this *** experimental results show that an overnight soak of the membrane after scraping and vortex agitation before elution could enhance and stabilize the *** turbidity to 4 NTU by adding kaolin clay before filtration could effectively improve the recovery of low-turbidity *** the concentrate after centrifugation and twice acid dissociation both reduced the impact of water quality to protozoan *** in different water samples were determined by this optimized method,and the recovery of Cryptosporidium and Giardia were above 70% and 80%respectively,much higher than the acceptance of method-1623.

关键词： concentration Cryptosporidium Giardia immunomagnetic separation(IMS) wastewater reuse

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