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

作者： Johnson, Daniel Wang, Kun Cramer, Carole L. Huang, Xiuzhen Molecular Bioscience PhD Program Arkansas State University Jonesboro AR United States Department of Computer Science Arkansas State University P.O. Box 9 Jonesboro AR United States Arkansas Bioscience Institute Dept. of Biology Arkansas State University Jonesboro AR United States

ISBN: (纸本)9781450307963

With the tremendous large data sets from next-generation sequencing technology, there is the big challenging task of how to transform the large amount of sequencing data to information meaningful for biologists and life scientists. The initial step is to align these data sets to the known reference genomes, which is essential for further data analysis. However next-generation sequencing read alignment is very time consuming. To address this challenge, we developed a general framework to build genome-wide unique gene markers. This framework includes a novel graph theoretical model for extracting robust gene markers and effective methods for evaluating the sets of gene markers. The genome-wide unique gene markers will help accelerating the next-generation sequencing read alignment process. We use the E. Coli genome as a model genome to illustrate our approach and demonstrate its significance in time saving for read alignment. Further testing on using the sets of gene markers for read coverage analysis is being conducted. Copyright © 2011 ACM.

关键词： Genes

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Simultaneous identification for synergistic transcription factors and their transcription factor binding sites

Simultaneous identification for synergistic transcription fa...

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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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Simultaneous Identification for Synergistic Transcription Factors and their Transcription Factor Binding Sites

Simultaneous Identification for Synergistic Transcription Fa...

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International Conference on Complex, Intelligent and Software Intensive Systems, CISIS

作者： Zing Tsung-Yeh Tsai Grace Tzu-Wei Huang Huai-Kuang Tsai Institute of Information Science Academia Sinica Taipei 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 USA Computer Science and Engineering National Taiwan Ocean University Keelung Taiwan

关键词： Bioinformatics Analysis of variance DNA Databases Gene expression Proteins Stress

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Learning by collaboration in intelligent autonomous systems

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作者： Ierache, Jorge García-Martínez, Ramón De Giusti, Armando Computer Science PhD Program La Plata National University Buenos Aires University Argentina

ISBN: (纸本)3642152856

Very few learning systems applied to problem solving have focused on learning operator definitions from the interaction with a completely unknown environment. Autonomous Intelligent Systems (AIS) deal with that issue by means of architectures where learning is achieved by establishing plans, executing those plans in the environment, analyzing the results of the execution, and combining new evidence with prior evidence. This paper proposes a selective mechanism of learning allowing an AIS to learn new operators by receiving them from another AIS in a higher stage in the Learning Life Cycle (LLC) with more cycles of interaction in the environment. The proposed collaboration mechanism also considers how to deal with theory ponderation (operators ponderation) and how to include the new operators (provided for) in the set of theories of the receiver AIS. The experimental results show how using collaboration-based learning among AIS provides a better percentage of successful plans, plus an improved convergence rate, than the individual AIS alone. © 2010 IFIP.

关键词： Problem solving

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Bioanalysis Young Investigator: Halil Tekin

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Bioanalysis 2011年第16期3卷 1815-1816页

作者： Halil Tekin Ali Khademhosseini Robert S Langer a Position PhD CandidatePhD Electrical Engineering and Computer Science – Bio-Electrical Engineering AreaResearch area Tissue engineering stimuli-responsive platforms and high-throughput screening systemsDepartment of Electrical Engineering & Computer Science of MIT 65 Landsdowne Street Rm. 252 Cambridge MA02139 USA. halil@mit.edu b Harvard-MIT Health Sciences & Technology Department of Medicine Harvard Medical School Brigham & Women’s Hospital Wyss Institute for Biologically Inspired Engineering 65 Landsdowne Street Rm 252 Cambridge MA02139 USA. alik@rics.bwh.harvard.edu c David H Koch Institute of Integrative Cancer Research at MIT Departments of Chemical Engineering & Biological Engineering of MIT Harvard-MIT Health Sciences & Technology 77 Massachusetts Avenue Rm 76-661 MA USA. rlanger@mit.edu

Supervisor’s supporting commentsI am very pleased to nominate Halil Tekin for theBioanalysisYoung Investigator award. Halil has proven himself to be an excellent researcher, a very bright laboratory member and a strong leader since joining my laboratory. He has excelled at all of the skills required of a phd candidate at MIT with his research focusing primarily on future advances in drug development, drug discovery and medicine with high-throughput drug toxicity screening. His efforts have focused on developing novel biomimetic tissue constructs by microengineering methods to further advance the applications of implantable tissues and drug toxicity screening devices. Halil has demonstrated an unprecedented ability not only to learn new material quickly, but more importantly to synthesize new information and ask the important questions needed to move science forward. I am constantly impressed with Halil’s ability, drive and determination in learning, and contributing to the research conducted in my laboratory. Halil’s unique combination of a strong electrical engineering background and his current knowledge and experience in tissue engineering has enabled him to look at fundamental challanges in a novel and insightful way, which resulted in very interesting *** is an exceptional phd student conducting outstanding research in tissue engineering which can bring novel applications in human health care. Halil published a paper in a top journal in the field of microtechnology,Lab on a Chip, describing a new way of making cell aggregates and then retrieving them from the microwells in a controllable manner for further experimentation and analysis. He also published a paper inLangmuir, introducing a novel method to fabricate conformally coated thermo-responsive microgrooves to form stripe tissues and harvest them in a temperature-dependent manner. These responsive microstructures can be scalable into high-throughput systems and potentially be useful in tissue

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A proposal for consistency checking in dynamic software product line models using OCL

A proposal for consistency checking in dynamic software prod...

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International Conference on Software Engineering (ICSE)

作者： Fabiana G. Marinho Master and PhD Program in Computer Science Federal University of Ceará Fortaleza Ceara Brazil

Ubiquitous applications use context information to provide services and relevant information for their users. On the other hand, in Software Product Line approaches, commonality and variability of a system family should be identified and documented through variability modeling. Thus, one of the challenges to build Context-Aware Product Lines, called Dynamic Software Product Lines, is the consistent representation of context information that influences the variability model. This work proposes the use of UML profiles and OCL to formalize and represent variability and context concepts in a consistent manner.

关键词： Unified modeling language Context modeling Context Software Adaptation models Computational modeling Prototypes

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Sliding-mode Controller for Four-Wheel-Steering Vehicle: Trajectory-Tracking Problem

Sliding-mode Controller for Four-Wheel-Steering Vehicle: Tra...

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The 8th World Congress on Intelligent Control and Automation(第八届智能控制与自动化世界大会 WCICA 2010)

作者： Adrian Filipescu Razvan Solea Silviu Filipescu Bogdan Dumitrascu Department of Automation and Industrial Informatics University “Dunarea de Jos” of Galati Domneasca Master student in Intelligent Control Systems at the Faculty of Computer Science PhD student in Control Systems at the Faculty of Computer Science

A solution to trajectory-tracking control problem for a four-wheel-steering vehicle (4WS) is proposed using sliding-mode approach. The advantage of this controller over current control procedure is that it is applicable to a large class of vehicles with single or double steering and to a tracking velocity that is not necessarily constant. The sliding-mode approach make the solutions robust with respect to errors and disturbances, as demonstrated by the simulation results.

关键词： Wheels Trajectory Kinematics Mobile robots Bicycles

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Did you cook your lesson based on right recipe? (Accommodating the Students Preferences in Class)

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Procedia - Social and Behavioral sciences 2010年第2期2卷 383-387页

作者： Zahra Naimie Saedah Siraj Rana Ahmed Abuzaid Reihaneh Shagholi PhD student University of Malaya Faculty of Education50603 Kuala LumpurMalaysia Dean Faculty of EducationUniversity of Malaya50603 Kuala LumpurMalaysia PhD student University of Malaya Faculty of Computer Science and Information Technology 50603 Kuala LumpurMalaysia

The purpose of this study is to identify how accommodating the teacher behaves toward congruency and in congruency in the classroom. The major approach in this study was qualitative. The data were collected through observation and interviews. The participants were two lecturers and 100 students in an English major program in Iran. The findings from this study imply that it is crucial for teachers to have knowledge about learner preferences in their classes to consider in their teaching design. The students show a positive response and higher achievement when their learning preferences and needs are accommodated by their lecturers.

关键词： Accommodating students need learning styles

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Investigation of transient cavitating flow in viscoelastic pipes

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IOP Conference Series: Earth and Environmental science 2010年第1期12卷

作者： A Keramat A S Tijsseling A Ahmadi PhD student Department of Civil Engineering Shahrood University of Technology Iran Department of Mathematics and Computer Science Eindhoven University of Technology PO Box 513 5600 MB Eindhoven The Netherlands Department of Civil Engineering Shahrood University of Technology Iran Post Code: *** University Boulevard Shahrood Iran presently Department of Mathematics and Computer Science Eindhoven University of Technology The Netherlands

A study on water hammer in viscoelastic pipes when the fluid pressure drops to liquid vapour pressure is performed. Two important concepts including column separation and the effects of retarded strains in the pipe wall on the fluid response have been investigated separately in recent works, but there is some curiosity as to how the results for pressure and discharge are when column separation occurs in a viscoelastic pipe. For pipes made of plastic such as polyethylene (PE) and polyvinyl chloride (PVC), viscoelasticity is a crucial mechanical property which changes the hydraulic and structural transient responses. Based on previous developments in the analysis of water hammer, a model which is capable of analysing column separation in viscoelastic pipes is presented and used for solving the selected case studies. For the column-separation modelling the Discrete Vapour Cavity Model (DVCM) is utilised and the viscoelasticity property of the pipe wall is modelled by Kelvin-Voigt elements. The effects of viscoelasticity play an important role in the column separation phenomenon because it changes the water hammer fundamental frequency and so affects the time of opening or collapse of the cavities. Verification of the implemented computer code is performed for the effects of viscoelasticity and column separation – separately and simultaneously – using experimental results from the literature. In the provided examples the focus is placed on the simultaneous effect of viscoelasticity and column separation on the hydraulic transient response. The final conclusions drawn are that if rectangular grids are utilised the DVCM gives acceptable predictions of the phenomenon and that the pipe wall material's retarded behaviour strongly dampens the pressure spikes caused by column separation.

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Numerical simulation of continuous casting process of bloom by fifite point method

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TMS 2009 Annual Meeting and Exhibition

作者： Jenabali-Jahromi, Seyed Ahmad Alizadeh, Mostafa Nasihatkon, Sayyed Behrouz Professor Department of materials science and engineering Shiraz University Shiraz Iran PhD student Department of materials science and engineering Shiraz University Shiraz Iran M.S. student Department of computer engineering Shiraz University Shiraz Iran

ISBN: (纸本)9780873397353

In this paper a meshless method called Finite Point Method (FPM) is developed to simulate the solidification process of continuously cast bloom steel in both primary and secondary cooling region. The method is based on the use of a weighted least-square interpolation procedure. A transverse slice of bloom as it moves with casting speed is considered as computational domain. The two dimensional heat transfer equation together with temperature dependent thermophysical properties is solved in the computational domain. The present work is verified in the mold region by the comparison of the surface temperature simulated by FPM and finite volume method (FVM) and also comparison of solidified shell thickness simulated by FPM and measured on a breakout bloom. For secondary cooling region the validation is done by comparison of the surface temperature simulated by FPM, FVM and thermovision measurements.

关键词： Continuous casting

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