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Predicting helix-helix interactions from residue contacts in membrane proteins

Bioinformatics 2009年第8期25卷 996-1003页

作者： Lo, Allan Chiu, Yi-Yuan Rødland, Einar Andreas Lyu, Ping-Chiang Sung, Ting-Yi Hsu, Wen-Lian Bioinformatics Program Taiwan International Graduate Program Academia Sinica Taipei Taiwan Institute of Bioinformatics and Structural Biology Department of Life Sciences National Tsing Hua University Hsinchu Taiwan Bioinformatics Laboratory Institute of Information Science Academia Sinica Taipei Taiwan Centre for Cancer Biomedicine University of Oslo NO-0027 Oslo Norway SAMBA Norwegian Computing Center Blindern NO-0314 Oslo P.O. Box 114 Norway

Motivation: Helix-helix interactions play a critical role in the structure assembly, stability and function of membrane proteins. On the molecular level, the interactions are mediated by one or more residue contacts. Although previous studies focused on helix-packing patterns and sequence motifs, few of them developed methods specifically for contact prediction. Results: We present a new hierarchical framework for contact prediction, with an application in membrane proteins. The hierarchical scheme consists of two levels: in the first level, contact residues are predicted from the sequence and their pairing relationships are further predicted in the second level. Statistical analyses on contact propensities are combined with other sequence and structural information for training the support vector machine classifiers. Evaluated on 52 protein chains using leave-one-out cross validation (LOOCV) and an independent test set of 14 protein chains, the two-level approach consistently improves the conventional direct approach in prediction accuracy, with 80% reduction of input for prediction. Furthermore, the predicted contacts are then used to infer interactions between pairs of helices. When at least three predicted contacts are required for an inferred interaction, the accuracy, sensitivity and specificity are 56%, 40% and 89%, respectively. Our results demonstrate that a hierarchical framework can be applied to eliminate false positives (FP) while reducing computational complexity in predicting contacts. Together with the estimated contact propensities, this method can be used to gain insights into helix-packing in membrane proteins. © 2009 The Author(s).

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AAAI 2008 workshop reports

AAAI 2008 workshop reports

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作者： Anand, Sarabjot Singh Bunescu, Razvan Carvcdho, Vitor Chomicki, Jan Conitzer, Vincent Cox, Michael T. Dignum, Virginia Dodds, Zachary Dredze, Mark Furcy, David Gabrilovich, Evgeniy Göker, Mehmet H. Guesgen, Hans Hirsh, Haym Jannach, Dietmar Junker, Ulrich Ketter, Wolfgang Kobsa, Alfred Koenig, Sven Lau, Tessa Lewis, Lundy Matson, Eric Metzler, Ted Mihalcea, Rada Mobasher, Bamshad Pineau, Joelle Poupart, Pascal Raja, Anita Ruml, Wheeler Sadeh, Norman Shani, Guy Shapiro, Daniel Smith, Trey Taylor, Matthew E. Wagstaff, Kiri Walsh, William Zhou, Rong Department of Computer Science University of Warwick United Kingdom School of Electrical Engineering and Computer Science Ohio University United States Microsoft Live Labs United States computer science and engineering University at Buffalo United States Computer science and economics Duke University United States Intelligent Computing group of BBN Technologies Utrecht University Netherlands Department of Computer science Harvey Mudd College United States University of Pennsylvania United States University of Wisconsin United States Yahoo Research PricewaterhouseCoopers Center for Advanced Research United States Department of Computer science School of Engineering and Advanced Technology Massey University New Zealand Departent of Computer science Rutgers University United States Department of Computer Science Dortmund University of Technology. Germany ILOG Rotterdam School of Management Erasmus University Netherlands Donald Bren School of Information and Computer Sciences University of California Irvine United States Depatrment of Computer science University of Southern California United States IBM Almaden Research Center United States Department of Computer Information Technology Southern New Hampshire University United States Computer and Information Technology Program College of Technology Purdue University United States Hughes Program for Religion and Science Dialogue Oklahoma City University United States Department of Computer Science and Engineering University of North Texas United States School of Computing DePaul University United States Department of Computer Science McGill University Canada School of Computer Science University of Waterloo Canada Department of Software and Information Systems University of North Carolina Charlotte United States University of New Hampshire United States Microsoft Research Institute for the Study of Learning and Expertise Applied Reactivity Inc. United States NASA Ames Research Center Carnegie Mellon University West

AAAI was pleased to present the AAAI-08 Workshop program, held Sunday and Monday, July 13-14, in Chicago, Illinois, USA. The program included the following 15 workshops: Advancements in POMDP Solvers;AI Education Workshop Colloquium;Coordination, Organizations, Institutions, and Norms in Agent Systems, Enhanced Messaging;Human Implications of Human-Robot Interaction;Intelligent Techniques for Web Personalization and Recommender Systems;Metareasoning: Thinking about Thinking;Multidisciplinary Workshop on Advances in Preference Handling;Search in Artificial Intelligence and Robotics;Spatial and Temporal Reasoning;Trading Agent Design and Analysis;Transfer Learning for Complex Tasks;What Went Wrong and Why: Lessons from AI Research and Applications;and Wikipedia and Artificial Intelligence: An Evolving Synergy. Copyright © 2009, Association for the Advancement of Artificial Intelligence. All rights reserved.

关键词： Human robot interaction

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Achieving compelling student comprehension of complex information structures for both on-site and on-line courses

Achieving compelling student comprehension of complex inform...

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2008 ASEE Annual Conference and Exposition

作者： Uhlig, Ronald Farahani, Alireza Viswanathan, Shekar Evans, Howard Sotelo, Mark National University Department of Computer Science and Information Systems School of Engineering and Technology National University Wireless Communications for the Master ot Science in Wireless Communications Program International Telecommunications Academy School of Engineering and Technology Department of Applied Engineering Lead Faculty for Engineering Management and Homeland Security and Safety Engineering Academic Computing for National University

Teaching engineering and technology subjects involves conveying understanding of abstract information structures and processes such as complex telecommunications protocols, complex mathematical concepts, and data structures. These are multidimensional and can be difficult to grasp quickly. Supported by a Hewlett-Packard (HP) Technology for Teaching grant, the School of Engineering and Technology at National University has embarked on a project to enable students to grasp these complex concepts more quickly and easily, using continuous dialog among students and instructors as the structures are first introduced and then examined from multiple perspectives through real-time interaction among students, small groups, and instructors. HP Wireless Tablet PCs are used to discuss and experiment with diagrams and processes in realtime. This allows combining lectures and problem-solving sessions into a single class session. Our hypothesis is that: 1) an in-depth learning of theory is accomplished, and 2) student engagement is enhanced. Presentation of theory by the instructor is integrated with application while the theory is still in the student's short-term memory. Students no longer have to wait for a separate session such as a recitation session to apply the concepts. This approach often takes less time. In addition to accelerating the learning process, expert instructors find this approach more rewarding as students grasp new concepts more quickly. Analysis of data captured from both students and instructors are presented to support our hypotheses, and our results are compared with similar research carried out by other universities. In addition, the level of interaction enabled by the use of HP Tablets in on-line classes is discussed. The best teaching tools available in existing on-line teaching platforms are compared with the additional tools available in on-site courses when every student has a wireless Tablet PC and specific recommendations are made to on-line teachi

关键词： Students

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DLM: A distributed Large Memory System using remote memory swapping over cluster nodes

DLM: A distributed Large Memory System using remote memory s...

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IEEE International Conference on Cluster computing

作者： Hiroko Midorikawa Motoyoshi Kurokawa Ryutaro Himeno Mitsuhisa Sato Department of Computer and Information Science Seikei University Musashino Tokyo Japan Graduate School of Systems and Information Engineering University of Tsukuba Tennodai Tsukuba Ibaraki Japan Advanced Center of Computing and Communication Wako Saitama Japan Research Program for Computational Science RIKEN Wako Saitama Japan

Emerging 64 bitOSpsilas supply a huge amount of memory address space that is essential for new applications using very large data. It is expected that the memory in connected nodes can be used to store swapped pages efficiently, especially in a dedicated cluster which has a high-speed network such as 10 GbE and Infiniband. In this paper, we propose the distributed large memory system (DLM), which provides very large virtual memory by using remote memory distributed over the nodes in a cluster. The performance of DLM programs using remote memory is compared to ordinary programs using local memory. The results of STREAM, NPB and Himeno benchmarks show that the DLM achieves better performance than other remote paging schemes using a block swap device to access remote memory. In addition to performance, DLM offers the advantages of easy availability and high portability, because it is a user-level software without the need for special hardware. To obtain high performance, the DLM can tune its parameters independently from kernel swap parameters. We also found that DLMpsilas independence of kernel swapping provides more stable behavior.

关键词： Kernel Arrays Memory management Servers Bandwidth Performance evaluation Benchmark testing

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Overcoming Bandwidth and Satellite Communications Limitations to Accelerate Applications of Remote Sensing and High Performance computing for Sustainable African Development: Contributions from Egypt, Nigeria and South Africa

Overcoming Bandwidth and Satellite Communications Limitation...

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IEEE International Symposium on Geoscience and Remote Sensing (IGARSS)

作者： Gilbert L. Rochon Magdy Wahab Gamal El Afandi Ado Dan-Isa Happy Sithole Khomotso Kganyago Souleymane Fall Joseph Quansah Akilah Martin Bereket Araya Chetan Maringanti Cliff Robinson Kaiem L. Frink Jean Pierre Antelo Rosen Center for Advanced Computing Purdue Terrestrial Observatory Purdue University-Information Technology IN USA Department of Astronomy & Meteorology Faculty of Science Cairo University Cairo Egypt Department of Meteorology & Astronomy Al-Azhar University Cairo Egypt Department of Computer Engineering Bayero University Kano Nigeria Center for High Performance Computing CHCP-CSIRO Cape Town South Africa Department of Agricultural & Biological Engineering Purdue University West Lafayette IN USA School for New Learning De Paul University Chicago IL USA Purdue Research Opportunities Program West Lafayette IN USA

Sixty-two years after the first photos of earth taken by a camera aboard a V-2 rocket in October, 1946, and forty-eight years since the first CORONA satellite images were captured, the status of remote sensing research and applications within the African continent has made dramatic progress. Many African countries now have remote sensing research centers, within government agencies, research institutes and universities. Some countries in Africa currently have earth observing and/or telecommunications satellites in orbit and/or have such assets in various planning stages. The authors document such progress, in addition to the constraints to further applications of remote sensing for sustainable development in Africa, with special reference to data distribution constraints. Moreover, the authors address the urgency for bandwidth improvements within the African continent, so as to enable sustainable development initiatives to benefit from advances in high performance computing, required for ab initio near-real-time analysis of satellite-data. Such capabilities, it is argued, are propaedeutic for time-critical initiatives, such as vulnerability assessment, disaster preparedness and mitigation, emergency response, humanitarian assistance and post-calamity reconstruction, associated with a wide array of biogenic and anthropogenic disasters. Case studies of advances in infrastructure for satellite remote sensing and high performance computing, with implications for sustainable development in Africa, are provided from Egypt, Nigeria and South Africa.

关键词： Bandwidth Satellite communication Acceleration Remote sensing High performance computing Africa Sustainable development Earth Continents Cameras

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A deliberate integration of information technology into the classroom

A deliberate integration of information technology into the ...

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114th Annual ASEE Conference and Exposition, 2007

作者： Fairfax, Duane Huggins, Kevin Goda, Bryan USMA United States Computer Science Program US Military Academy United States IEEE Department of Electrical Engineering and Computer Science US Military Academy at West Point United States Association for Computing Machinery Institute of Electrical and Electronic Engineers Information Technology Program US Military Academy United States

The information Age has revolutionized the way students learn in the classroom. The United States Military Academy (USMA) emphasizes the importance of information Technology (IT) through an academy-wide IT specific goal. This goal supports the USMA's mission of producing Army Officers who can respond effectively to technological changes in the defense of our nation. Courses augmented with IT can be daunting for cadets who lack the experience and confidence level to succeed in the course. As a result, these types of courses are avoided by cadets if at all possible. This is not an option for an aspiring officer who will lead the soldiers of tomorrow on a digitized battlefield. Since 1990, cadets have been issued a computer which has played a central role in bringing the power of IT to all graduates of the Military Academy. Integration of IT in the curriculum begins early with every cadet receiving a laptop computer. An integrated software package is included to support any course of instruction. Cadets receive two courses in IT, one in their freshman year and one in their junior year. The freshman course teaches the cadet the basic functionality of the laptop, a basic programming language, and creating a basic website. The junior course builds on the freshman course by teaching the cadets to create an advanced website, design and build a network, manage a database, and create an information system. IT plays a central role in several overlap courses between engineering and the humanities in such areas as information warfare, terrorism, and the legal aspects of intellectual property rights. What makes this approach unique is the methodical diffusion of IT into course design which removes the barrier between learning and the implementation of IT as an academic multiplier. An academy-wide committee consisting of 12 members is responsible for examining collected data to see how well the Military Academy is meeting its LT goal. This data comes from a variety of sources such

关键词： information technology

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Middleware Vertical Handoff Manager: A Neural Network-Based Solution

Middleware Vertical Handoff Manager: A Neural Network-Based ...

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IEEE International Conference on Communications (ICC)

作者： N. Nasser S. Guizani E. Al-Masri Department of Computing & Information Science University of Guelph Guelph ONT Canada Foundation Program Unit Qatar University Doha Qatar

Major research challenges in the next generation of wireless networks include the provisioning of worldwide seamless mobility across heterogeneous wireless networks, the improvement of end-to-end quality of service (QoS), supporting high data rates over wide area and enabling users to specify their personal preferences. The integration and interoperability of this multitude of available networks will lead to the emergence of the fourth generation (4G) of wireless technologies. 4G wireless technologies have the potential to provide these features and many more, which at the end will change the way we use mobile devices and provide a wide variety of new applications. However, such technology does not come without its challenges. One of these challenges is the user's ability to control and manage handoffs across heterogeneous wireless networks. This paper proposes a solution to this problem using artificial neural networks (ANNs). The proposed method is capable of distinguishing the best existing wireless network that matches predefined user preferences set on a mobile device when performing a vertical handoff. The overall performance of the proposed method shows 87.0 % success rate in finding the best available wireless network. To test for the robustness and effectiveness of the neural network algorithm, some of the features were removed from the training set and results showed a significant impact on the overall performance of the system. Hence, managing vertical handoffs through user preferences can be significantly affected with the selection of features used to provide the closest match of the available wireless networks.

关键词： Middleware Neural networks Wireless networks Quality of service Roaming Communications Society Computer network management Quality management Computer networks information science

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Remote internetworking laboratory

Remote internetworking laboratory

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113th Annual ASEE Conference and Exposition, 2006

作者： Jabbour, Imad Haydamous, Linda Kazan, Wissam Hayek, Amine Massachusetts Institute of Technology United States Information Technology Program MIT United States MIT's Center for Educational Computing Initiatives IEEE New Jersey Institute of Technology United States Engineering Management Program New Jersey Institute of Technology United States Operations Research Stanford University United States Computer Science Program Stanford University United States

Remote experimentation is the process of conducting real lab experiments without being physically in contact with lab devices. Recently, the development of Internet technologies fostered the spread of online laboratories, and significant benefits helped establish remote experimentation as a potential substitute to real experimentation. Internetworking lab experiments usually involve very expensive hardware;and providing remote access to this type of laboratories is highly desired, especially when a large number of students must share a limited set of devices. Very few remote internetworking laboratories have previously been implemented, and they had several drawbacks. In this paper, we discuss our design of a Remote Internetworking Laboratory which provided access to the internetworking lab at the American University of Beirut (AUB). The uniqueness of our approach is that it uses VLANs (Virtual LANs) to build network topologies, a technique that separates network subnets into different broadcast domains before allowing users to configure each lab device. The proposed scheme overcomes the limitations of other designs, and allows users to build any desired network topology and configure the lab devices in real-time. Many technical and educational features were integrated into the system, and possible enhancements were suggested based on several evaluation criteria. © American Society for Engineering Education, 2006.

关键词： Network architecture

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Examining design threads: Issues in Web design across student populations

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Proceedings of the Association for information science and Technology 2006年第1期42卷

作者： Joette Stefl-Mabry Allison Druin Dania Bilal Michael Radlick Thomas Mackey Carol Doll Diane Nahl Department of Information Studies of the College of Computing and Information and School of Education University at Albany State University of New York University of Maryland College of Information Studies and Institute for Advanced Computer Studies School of Information Sciences The University of Tennessee 1345 Circle Park Knoxville TN 37996 The Not for Profit Institute for Research on Learning Technology Visions Department of Information Studies of the College of Computing and Information University at Albany State University of New York Department of Information and Computer Sciences Library and Information Science Program University of Hawai'I at Manoa

This session relates directly to this year's conference theme Sparking Synergies: Bringing Research and Practice Together as it brings together researchers from different disciplines (information science and educational technology) to discuss current issues and trends related to Web usage across student populations. “Complex design problems require more knowledge than any single person possesses” (Arias, Eden, Fischer, Gorman, and Scharff, 2000, p. 84), thus each panelist will contribute highlights of his or her current research regarding the design, information, and pedagogical, needs of specific student populations (K-12 to higher education). After the panelists have presented their findings Diane Nahl will intertwine the threads of the panelists' conversations and, with the audience's assistance, begin to weave a fabric to uncover common usability issues.

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Real-time organ motion tracking and fast image registration system for MRI-guided surgery

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Systems and Computers in Japan 2006年第1期37卷 83-92页

作者： Tokuda, Junichi Hirano, Masaya Tsukamoto, Tetsuji Dohi, Takeyoshi Hata, Nobuhiko Graduate School of Information Science and Technology University of Tokyo Tokyo 113-8656 Japan GE Yokogawa Medical Systems Ltd. Hino 191-8503 Japan International Society for Computer-Aided Surgery Japan Society for Computer-Aided Surgery Japan Society for Magnetic Resonance in Medicine GE Yokogawa Medical Systems Ltd. Imaging Application Tech. Center MR Group R and D Laboratory Technology Center GE Yokogawa Medical Systems Ltd. Society for Magnetic Resonance in Medicine Graduate School of Information Science and Technology Society for Life Support Technology Japan Society for Organ Preservation Biology and Medicine Society for Precision Engineering Society for Medical Image Computing and Computer Assisted Intervention International Union for Physics and Engineering Sciences in Medicine JSMEBE Japan Society for Life Assistance Technology Brigham and Women's Hospital Harvard Medical School MR Therapy Program

The advantage of magnetic resonance imaging (MRI)-guided surgery, in which MR images taken during surgery are used to guide the surgery, has been recognized recently. However, there is a problem, due to long imaging time of MRI, that it is difficult to capture the respiratory organ motion. It is often a constraint that the patient must hold his or her breath, especially in the treatment of the abdominal region. Consequently, this paper proposes a method of eliminating this constraint in MRI-guided surgery by real-time monitoring of the movement of the organ involved in the surgery by means of the signal derived from MRI. Specifically, the navigator echo is extracted in imaging during surgery. The movement of the organ involved in surgery is detected on the basis of the change in the calculated projection profile, and the results are presented to the surgeon. In this study, the procedure is built into a 1.5-T clinical MRI system. The feasibility of the proposed system was examined under clinical conditions by evaluating its accuracy and delay in a phantom experiment, and also in an in vivo experiment on the liver of a volunteer. The results are reported in this paper. © 2005 Wiley Periodicals, Inc.

关键词： Motion estimation

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