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5th International Conference on Complex, Intelligent and Software Intensive Systems, CISIS 2011

作者： Tsai, Zing Tsung-Yeh Huang, Grace Tzu-Wei Tsai, Huai-Kuang Institute of Information Science Academia Sinica Taipei 115 Taiwan Bioinformatics Program Taiwan International Graduate Program Taiwan Institute of Biomedical Informatics National Yang-Ming University Taiwan Joint CMU-Pitt PhD Program in Computational Biology University of Pittsburgh Carnegie Mellon University Pittsburgh PA United States Research Center for Information Technology Innovation Taipei 115 Taiwan Computer Science and Engineering National Taiwan Ocean University Keelung 202 Taiwan

ISBN: (纸本)9780769543734

Identifying transcription factor binding sites (TFBSs) is crucial for understanding the mechanism of transcriptional regulation. It is known that transcription factors (TFs) often cooperate to regulate genes. While traditional approaches can be used to discover binding motifs of a group of co-regulated genes, they often fail to accurately assign motifs to the corresponding TFs. Here, we consider two TFs together to infer their TFBSs and their synergistic relationship simultaneously. The basic idea is that if two TFs interact, their TFBSs, if distinct, would be conserved across species and coincided in the promoter regions of the genes they co-regulated. Applying our method to Saccharomyces cerevisiae chromatin immunoprecipitation data, we predicted 110 TF pairs with statistically significant motif assignments. A majority of these TF pairs have literature support to be synergistic, and the designated motifs to TFs match well with their known consensus. We further examined the synergism of predicted TF pairs in seven experimental conditions using ANOVA, and identified significant interactions. © 2011 IEEE.

关键词： Yeast

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Generating Activity Streams from Events occurring in company-internal IT infrastructures

Generating Activity Streams from Events occurring in company...

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2011 IEEE 13th International Conference on Communication Technology(ICCT 2011)

作者： Eng.S.M.Khaled Reza S.M.Mohsin Reza Masters Program in Computational Engineering (Distributed Systems Engineering) Faculty of Computer Science Dresden University of Technology Dresden Germany Masters Program in Information Technology (Embedded Systems Engineering) Faculty of Computer Science Electrical Engineering and Information Technology University of Stuttgart Germany

In the current era of technology,the Internet and web technologies become the center source of *** to the huge amount of contents,one of the main challenges of modern information technology is aimed at how to reduce and manage information in a structured way with mobilizing users to the similar kind of relevant ***,any intelligent system should be able to understand people's interest about a particular type of information and automatically mobilize him to the similar kind of available information *** idea of high level Activity Streams along with its standardized format can play a vital role to solve this problem in the broader *** paper introduces a novel system called CoASGen (Consolidation and Activity Streams Generator) which is able to automatically generate high level Activity Streams after aggregating and consolidating from different independent systems (*** a software company context:version management system,wikis,bug trackers etc.).It retrieves life time information as heterogeneous web feed by sensing user activities from those independent systems and then it transforms several similar types of atomic activities into high level Activity Streams using semantic technologies along with its specific standardized ***,it shows these high level Activity Streams to the user interface which is able to automatically motivate users to find relevant information easily without either missing any data or losing valuable *** system solves the problem "data silos" by reducing and managing information in a structured way.

关键词： Activity Streams,Atomic Activity,High Level Activity Stream,CoASGen System

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Generalized Enhanced Multivariance Product Representation for Data Partitioning: Constancy Level

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AIP Conference Proceedings 2011年第1期1389卷 1152-1155页

作者： M. Alper Tunga Metin Demiralp aBahçeşehir University Faculty of Engineering Software Engineering Department Beşiktaş 34349 İstanbul Turkey bİstanbul Technical University Informatics Institute Computational Science and Engineering Program Maslak 34469 İstanbul Turkey

Enhanced Multivariance Product Representation (EMPR) method is used to represent multivariate functions in terms of less‐variate structures. The EMPR method extends the HDMR expansion by inserting some additional support functions to increase the quality of the approximants obtained for dominantly or purely multiplicative analytical structures. This work aims to develop the generalized form of the EMPR method to be used in multivariate data partitioning approaches. For this purpose, the Generalized HDMR philosophy is taken into consideration to construct the details of the Generalized EMPR at constancy level as the introductory steps and encouraging results are obtained in data partitioning problems by using our new method. In addition, to examine this performance, a number of numerical implementations with concluding remarks are given at the end of this paper.

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Experiment of Flow Control Using Laser Energy Deposition Around High Speed Propulsion System

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AIP Conference Proceedings 2011年第1期1402卷 416-423页

作者： HyoungJin Lee InSeuck Jeung SangHun Lee Seihwan Kim aDepartment of Mechanical and Aerospace Engineering & Institute of Advanced Aerospace Technology Seoul Nation University Seoul Korea bInterdisciplinary Program in Computational Science and Technology Seoul National University Seoul Korea

An experimental investigation was conducted to examine the effect of a pulsed Nd:YAG laser energy deposition on the shock structures in supersonic/hypersonic flow and quiescent air. The effect of the laser energy and pressure in the blast wave generation were also investigated. As a result, the strength of plasma and blast wave becomes stronger as pressure or laser energy increase. And the breakdown threshold of air by laser energy deposition is 0.015 bar at 508 mJ laser energy, the blast wave threshold generation in air by laser energy deposition is 0.100 bar at same laser energy. As qualitative analysis, schlieren images are also obtained. After the series of experiments, the effect of laser energy deposition (LED) on high speed flow around the shock—shock interaction created by a wedge and blunt body. By LED, the structure of shock—shock interaction was collapsed momentary and the pressure of the stagnation point was fluctuated while interference of wave.

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Basic Issues in Vector High Dimensional Model Representation

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AIP Conference Proceedings 2011年第1期1389卷 1143-1146页

作者： Burcu Tunga Metin Demiralp aIstanbul Technical University Faculty of Computer and Informatics Maslak 34469 Istanbul Turkey bIstanbul Technical University Informatics Institute Computational Science and Engineering Program Maslak 34469 Istanbul Turkey

A multivariate modelling may involve a set of multivariate functions. A vector valued function structure can be used to mathematically express the given problem and each multivariate function can be considered as an element of this vector. This work aims to construct a new approach representing the elements of this vector structure in terms of less‐variate functions to reduce the computational complexity. For this purpose, a new method based on the plain High Dimensional Model Representation (HDMR) philosophy is developed. The basic concepts of this method and several illustrative numerical implementations are given here.

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Compaction and Tensile Forces Determine the Accuracy of Folding Landscape Parameters from Single Molecule Pulling Experiments

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Physical Review Letters 2011年第13期106卷 138102-138102页

作者： Greg Morrison Changbong Hyeon Michael Hinczewski D. Thirumalai School of Engineering and Applied Science Harvard University Cambridge Massachusetts 02138 USA Biophysics Program Institute For Physical Science and Technology University of Maryland College Park Maryland 20742 USA School of Computational Sciences Korea Institute for Advanced Study Seoul 130-722 Republic of Korea

We establish a framework for assessing whether the transition state location of a biopolymer, which can be inferred from single molecule pulling experiments, corresponds to the ensemble of structures that have equal probability of reaching either the folded or unfolded states (Pfold=0.5). Using results for the forced unfolding of a RNA hairpin, an exactly soluble model, and an analytic theory, we show that Pfold is solely determined by s, an experimentally measurable molecular tensegrity parameter, which is a ratio of the tensile force and a compaction force that stabilizes the folded state. Applications to folding landscapes of DNA hairpins and a leucine zipper with two barriers provide a structural interpretation of single molecule experimental data. Our theory can be used to assess whether molecular extension is a good reaction coordinate using measured free energy profiles.

关键词： Free energy

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RTM process simulation by using XFEM and level set method

RTM process simulation by using XFEM and level set method

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18th International Conference on Composites Materials, ICCM 2011

作者： Jung, Yeonhee Han, Woo-Suck Vautrin, Alain Kim, Seung Jo LCG/UMR 5148 Centre SMS Ecole Nationale Supérieure des Mines de Saint-Etienne 42023 Saint-Etienne France Interdisciplinary Program in Computational Science and Technology Seoul National University Seoul 151-742 Korea Republic of School of Mechanical and Aerospace Engineering Seoul National University Seoul 151-742 Korea Republic of

A numerical simulation program for Resin Transfer Molding (RTM) manufacturing process is developed using eXtended Finite Element Method (XFEM) combined with the level set method. The level set method is used to track the resin flow front at each time step. XFEM allows to obtaining better accuracy of the resin pressure field in the flow front region than the classical FEM. The enriched shape functions of XFEM are derived by using the level set values of the front region. Finally, the level set values are calculated by an implicit characteristic Galerkin method. The numerical fill time is compared with the analytical solution to validate this program.

关键词： Resin transfer molding

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Continuum model of irradiation-induced spinodal decomposition in the presence of dislocations

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Physical Review B 2011年第17期83卷 174106-174106页

作者： J. J. Hoyt M. Haataja Department of Materials Science and Engineering McMaster University Hamilton Ontario Canada L8S4L7 Department of Mechanical and Aerospace Engineering Princeton Institute for the Science and Technology of Materials (PRISM) Program in Applied and Computational Mathematics (PACM) Princeton University Princeton New Jersey 08544

A model of phase-separation kinetics in systems exposed to energetic particle irradiation has been extended to include the effects of mobile dislocations. It is shown that when dislocations are allowed to participate in the decomposition reaction, phase separation can occur at temperatures above the coherent spinodal, which is in agreement with several experiments on irradiated alloys. A linear stability analysis of the governing kinetic equations is performed and three regimes of microstructural evolution are identified within the parameter space of damage cascade size vs incident flux: complete phase separation, solid-solution behavior, and compositional patterning. In addition, numerical simulations of the evolving dislocation density and composition fields are performed. The numerical results provide the amplitude and wavelength of the stable patterns that can form under irradiation and elucidate the role of misfit dislocations in reducing the coherency strain due to atomic size mismatch.

关键词： PHASE transformations (Physics) THERMODYNAMICS PARTICLES (Nuclear physics) ALLOYS IRRADIATION STRAINS & stresses (Mechanics)

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Improving protein-RNA interface prediction by combining sequence homology based method with a naive bayes classifier: Preliminary results 11

Improving protein-RNA interface prediction by combining sequ...

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2011 ACM Conference on Bioinformatics, computational Biology and Biomedicine, ACM-BCB 2011

作者： Xue, Li C. Walia, Rasna EL-Manzalawy, Yasser Dobbs, Drena Honavar, Vasant Bioinformatics and Computational Biology Program Iowa State University Ames IA 50011 United States Department of Genetics Development and Cell Biology Iowa State University Ames IA 50011 United States Department of Computer Science Iowa State University Ames IA 50011 United States Department of Systems and Computer Engineering Al-Azhar University Cairo Egypt

ISBN: (纸本)9781450307963

Protein-RNA interactions play important roles in cellular processes like protein synthesis, RNA processing, and gene expression regulation. Reliable identification of the interfaces involved in RNA-protein interactions is essential for comprehending the mechanisms and the functional implications of these interactions and provides a valuable guide for rational drug discovery and design. Because the determination of 3D structures of protein-RNA complexes has various technical limitations and is typically costly, reliable in silico interface prediction methods that require only the sequence information are urgently needed. We present HomPRIP, a homologous sequence based method for predicting protein-RNA interfaces, based on our conservation analysis of protein-RNA interfaces. We test Hom-PRIP on a benchmark dataset of 199 proteins and compare it with the state-of-the-art protein-RNA interface prediction methods. Our results show that HomPRIP can reliably identify protein-RNA interface residues in 71% of test proteins with at least one putative sequence homolog passing the similarity thresholds of HomPRIP. Moreover, to facilitate predictions for proteins with no identified homologs, we develop HomPRIP-NB, a method combining the HomPRIP predictor and a Naive Bayes (NB) classifier trained using evolutionary information derived from alignments against the NCBI nr database. Our results suggest that HomPRIP-NB significantly outperforms the state-of-the-art machine learning methods for predicting protein-RNA interface residues. Copyright © 2011 ACM.

关键词： Proteins

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Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces: A preliminary study 11

Ranking docked models of protein-protein complexes using pre...

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2011 ACM Conference on Bioinformatics, computational Biology and Biomedicine, ACM-BCB 2011

作者： Xue, Li C. Jordan, Rafael A. El-Manzalawy, Yasser Dobbs, Drena Honavar, Vasant Bioinformatics and Computational Biology Program Iowa State University Ames IA 50011 United States Department of Genetics Development and Cell Biology Iowa State University Ames 50011 United States Department of Computer Science Iowa State University Ames IA 50011 United States Department of Computer Science Pontificia Universidad Javeriana Cali Colombia Department of Systems and Computer Engineering AI-Azhar University Cairo Egypt

ISBN: (纸本)9781450307963

computational protein-protein docking is a valuable tool for determining the conformation of complexes formed by interacting proteins. Selecting near-native conformations from the large number of possible models generated by docking software presents a significant challenge in practice. We introduce a novel method for ranking docked conformations based on the degree of overlap between the interface residues of a docked conformation formed by a pair of proteins with the set of predicted interface residues between them. Our approach relies on a method, called PS-HomPPI, for reliably predicting proteinprotein interface residues by taking into account information derived from both interacting proteins. PS-HomPPI infers the residues of a query protein that are likely to interact with a partner protein based on known interface residues of the homo-interologs of the query-partner protein pair, i.e., pairs of interacting proteins that are homologous to the query protein and partner protein. Our results on Docking Benchmark 3.0 show that the quality of the ranking of docked conformations using our method is consistently superior to that produced using ClusPro cluster-size-based and energy-based criteria for 61 out of the 64 docking complexes for which PS-HomPPI produces interface predictions. An implementation of our method for ranking docked models is freely available at: http://***/DockRank/. Copyright © 2011 ACM.

关键词： Proteins

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