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Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis (vol 69, pg 298, 2007)

CHEMICAL BIOLOGY & DRUG DESIGN 2007年第6期69卷 455-455页

作者： Chellappan, S. Center for Advanced Research in Biotechnology University of Maryland Biotechnology Institute 9600 Gudelsky Drive Rockville MD 20850 USA Chemical Biology Program Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester MA 01605 USA Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester MA 01605 USA Department of Chemistry Massachusetts Institute of Technology Cambridge MA 02139 USA Biological Engineering Division Department of Electrical Engineering & Computer Science Massachusetts Institute of Technology Cambridge MA 02139 USA *Correspondence: Michael K. Gilson *Correspondence: * Michael K. Gilson gilson@umbi.umd.edu http://gilsonlab.umbi.umd.edu[?][?]These authors contributed equally to this study.

There is a clinical need for HIV protease inhibitors that can evade resistance mutations. One possible approach to designing such inhibitors relies upon the crystallographic observation that the substrates of HIV protease occupy a rather constant region within the binding site. In particular, it has been hypothesized that inhibitors which lie within this region will tend to resist clinically relevant mutations. The present study offers the first prospective evaluation of this hypothesis, via computational design of inhibitors predicted to conform to the substrate envelope, followed by synthesis and evaluation against wild-type and mutant proteases, as well as structural studies of complexes of the designed inhibitors with HIV protease. The results support the utility of the substrate envelope hypothesis as a guide to the design of robust protease inhibitors.

关键词： AIDS crystal drug design inhibitor protease

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Contribution of engineering management and systems engineering concepts to engineering design

Contribution of engineering management and systems engineeri...

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114th Annual ASEE Conference and Exposition, 2007

作者： Sireli, Yesim Conrad, James Kane, Martin Skinner, Frank University of North Carolina Charlotte United States Engineering Management Program University of North Carolina Charlotte United States ASEE IEEE Engineering Management Society Decision Sciences Institute United States ASEM Korea Republic of Marketing Science Institute United States Honor Society of Phi Kappa Phi United States IEEE Eta Kappa Nu United States Project Management Institute United States IEEE Computer Society Department of Civil and Environmental Engineering University of North-Carolina Charlotte United States Eno ASCE ITE Sigma Xi United States Chi Epsilon Industrial Solutions Department of Mechanical Engineering and Engineering Science University of North Carolina Charlotte United States Robo-Tech. Systems Inc. GE Advanced Products Corp.

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Decision Fusion of Circulating Markers for Breast Cancer Detection in Premenopausal Women

Decision Fusion of Circulating Markers for Breast Cancer Det...

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IEEE Symposium on Bioinformatics and Bioengineering (BIBE)

作者： Jonathan L. Jesneck Sayan Mukherjee Loren W. Nolte Anna E. Lokshin Jeffrey R. Marks Joseph Lo Duke Advanced Imaging Labs Institute for Genome Sciences and Policy Department of Computer Science Duke University USA Department of Electrical and Computer Engineering Division of Hematology/Oncology University of Pittsburgh School of Medicine Pittsburgh PA USA Division of Hematology/Oncology University of Pittsburgh Cancer Institute Pittsburgh PA USA Division of Hematology/Oncology University of Pittsburgh Cancer Institute Pittsburgh PA Institute for Genome Sciences and Policy Department of Experimental Surgery Medical Center Duke University USA Department of Experimental Surgery Duke University Medical Center Medical Physics Graduate Program Duke University Durham NC USA

Current mammographic screening for breast cancer is less effective for younger women. To complement mammography for premenopausal women, we investigated the feasibility screening test using 98 blood serum proteins. Because the data set was very noisy and contained only weak features, we used a classifier designed for noisy data: decision fusion. Decision fusion outperformed both a support vector machine (SVM) and linear regression with forward stepwise feature selection on all three two-class classification tasks: normal tissue vs. cancer, normal tissue vs. benign lesions, and benign lesions vs. cancer. Decision fusion detected cancer moderately well (AUC=0.84 on normal vs. cancer), demonstrating promise as a screening tool. Decision fusion also detected benign lesions similarly well (AUC=0.83 on normal vs. benign lesions) and was the only classifier to achieve any success in separating benign from malignant lesions (AUC=0.64 on benign vs. cancer). The classification results suggest that the assayed proteins are more indicative of a secondary effect, such as immune response, rather than specific for breast cancer. In conclusion, the decision fusion classifier demonstrated some promise in detecting breast lesions and outperformed other classifiers, especially for the very noisy classification problem of distinguishing benign from malignant lesions.

关键词： Breast cancer Cancer detection Lesions Proteins Support vector machines Support vector machine classification Mammography Testing Blood Linear regression

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Three-dimensional visualization of lymph node morphology using OCT

Three-dimensional visualization of lymph node morphology usi...

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Biomedical Topical Meeting, BIO 2006

作者： Nguyen, Freddy T. Luo, Wei Zysk, Adam M. Ralston, Tyler S. Chaney, Eric J. Marks, Daniel L. Oldenburg, Amy L. Brockenbrough, John Boppart, Stephen A. Department of Chemistry Medical Scholars Program College of Medicine Beckman Institute for Advanced Science and Technology United States Department of Electrical and Computer Engineering Beckman Institute for Advanced Science and Technology United States Carle Foundation Hospital College of Medicine United States 405 North Mathews Avenue Urbana Illinois 61801 United States

We report the first demonstration of OCT for the three-dimensional visualization of lymph node morphology and microarchitecture from human and carcinogen-induced rat mammary tumor specimens. © 2006 Optical Societ... 详细信息

ISBN: (纸本)1557528071

关键词： Body fluids

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Aircraft maintenance technology education: Integrating asynchronous technology & virtual reality

Aircraft maintenance technology education: Integrating async...

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113th Annual ASEE Conference and Exposition, 2006

作者： Sadasivan, Sajay Vembar, Deepak Stringfellow, Paris Washburn, Carl Duchowski, Andrew Gramopadhye, Anand Cemson University Department of Industrial Engineering Clemson University SC United States Department of Computer Science Clemson University SC United States Greenville Tech United States Aircraft Maintenance Program Greenville Technical College United States Department of Computer Science Clemson University United States Industrial Engineering Department Advanced Technology Systems Laboratory Clemson University SC United States

This paper describes a research program with an objective to develop and implement an interactive virtual reality (VR) model of the aircraft inspection maintenance process for asynchronous delivery. Existing approaches have not been able to mimic accurately the complexity of the aircraft maintenance process, reporting limited transfer capabilities and student preparedness for the workplace. This use of virtual reality technology will enable educators to create and students to experience the complex aircraft maintenance environment in an educational classroom, a setting where it has not yet been successfully created using traditional multimedia-based technologies. This model will emphasize the curriculum development and workplace preparedness needed by modern aircraft maintenance technology for local, state and national audiences. The primary objectives of this research are curriculum enhancement and assessment of VR as a pedagogical tool. This innovative approach is the first effort to extend tested VR technology to the aircraft maintenance technology curriculum in a two-year college. The outcome of this research will lead to the following: an innovative, high-impact model for curriculum application in aircraft maintenance technology for college students and industry employees;an increased workplace pool of aircraft maintenance technicians prepared for the transition from learning to workforce;a program providing the use of VR technology as a pedagogical tool. The successful completion of this effort will fill a state and national need for well-prepared students entering the aircraft maintenance industry and will provide a better understanding of the use of VR as a pedagogical tool. © American Society for Engineering Education, 2006.

关键词： Aircraft

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Global academy'-remote network applications connecting Japan and Chile over GEMnet2 and R&E networks

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NTT Technical Review 2006年第5期4卷 28-38页

作者： Uose, Hisao Oinuma, Morihide Noguchi, Kazuto Sakai, Yoshihisa Tatematsu, Ken'ichi Vera, Eduardo S. Baloian, Nelson Pulgar, Hernán Ramos, Manuel Mujica, Luis Felipe NTT Advanced Technology Corporation Musashino-shi 180-858 Japan NTT Service Integration Laboratories NTT Photonics Laboratories of Japan IEEE IEICE ALMA-J Project Office National Astronomical Observatory of Japan Nagova University Nobeyama Radio Observatory University of Texas Austin Electrical Engineering and Computer Science Departments University of Chile AccessNova Program University of Tokyo Computer Science Department University of Chile Waseda University Japan Astronomy Department University of Chile ALMA Project Office Santiago Mining Section Andina Division CODELCO Andina Division Photonics Network Project IM2 Chile IM2

This article describes two demonstrations at the NTT Group Communication EXPO held at the Tokyo International Forum in December 2005. These showed visitors two of our trials on the feasibility of remotely operating instruments in Chile from Japan: an optical telescope and rock hammers in an underground copper mine. These applications use a relatively high bandwidth of around 100 Mbit/s and require short delay times for smooth interactive operation. To satisfy these requirements we used NTT's experimental research network GEMnet2 in collaboration with partner R&E (research and education) networks in North and South America. The demonstrations showed that Internet-based networks can handle interactive network applications with sufficient quality between two sites separated by almost the maximum possible distance on the Earth as long as the bandwidth and the route are carefully managed.

关键词： Remote control

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Modeling resource management by agents interaction

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WSEAS Transactions on Information science and Applications 2005年第1期2卷 48-54页

作者： Suesaowaluk, Poonphon Sadananda, Ramakoti Computer Science and Information Management Program School of Advanced Technologies Asian Institute of Technology Patumthani 12120 Thailand

A scenario is envisaged in which agents have tasks to perform and are in a position to exchange tasks to improve their performance, and thus perhaps affect the overall performance of the system. Our model uses two computing machines with their usual resources, and with random initial jobs to be processed. Their performance is dependent not only on absolute total load but also on how much of each machine's resources are in demand, thus giving scope for the beneficial exchange of jobs. This paper describes the development of a negotiation mechanism for job exchange between machines and measurement of system performance. The concept may be extended to multiple machines that act as agents exchanging resources and tasks.

关键词： Intelligent agents

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An agent interaction model for performance enhancement of network system

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WSEAS Transactions on computers 2005年第5期4卷 440-448页

作者： Suesaowaluk, Poonphon Sadananda, Ramakoti Computer Science and Information Management Program School of Advanced Technologies Asian Institute of Technology Patumthani 12120 Thailand

We envisage a scenario where a system of network computer initially with random loads, exchange jobs to balance load among themselves to enhance their individual performance and to provide augmented quality of service (QoS) to the user community. We model the individual machines as agents interacting with one another. The agents have beliefs and aspirations. The aspiration of an agent is seek load from other, when it did not have enough to begin with, and sheds the same of it finds itself excessively loaded. This paper develops the concept with a design of a utility function to reflect the agent aspiration. We also propose a measure of load imbalance between networked machines. Negotiation mechanism is developed for exchange of jobs between agents. We report our result of the simulation with two machines and extend the same for three machines. The extension of the idea to a large number of machines entail coming to term with complexity in form of administrative overloads. We discuss the "small word" concept in the content of a simulation massively large number of machines interconnected.

关键词： Software agents

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Emotional design II: Affective information behavior research with adult and child populations

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

作者： Diane Nahl Dania Bilal Allison Druin Karen Fisher Library and Information Science Program Department of Information and Computer Sciences University of Hawaii 1680 East-West Road Honolulu HI 9682 University of Tennessee Knoxville College of Communication & Information School of Information Sciences 444 Communications Bldg. Knoxville TN 37996-0341 University of Maryland College of Information Studies Institute for Advanced Computer Studies Room 4121H Hornbake College Park MD 20742-4345 University of Washington The Information School Box 352840 Seattle WA 98195-2840

“;Emotions, we now know, change the way the human mind solves problems—the emotional system changes how the cognitive system operates.” (Norman, 2004: 18). Affective variables drive cognitive information behavior through a person's interests, motivation, feelings, and persistence. Recent research suggests that uncertainty contributes to cognitive load and negatively affects success, while optimism positively affects it (Nahl, 2004; 2005). Therefore, a focus on the interaction of affect and cognition, particularly studies examining the varieties of affect that arise in different situations and their impact on cognition, is necessary to understanding the information behavior of various groups. The research presented includes international data, both child and adult populations, and a variety of information settings. The research domains of the presenters include affective load in information tasks (Nahl), emotion in international children's use of cross-cultural interfaces (Bilal), emotional metadata of children (Druin), and information behavior in everyday life (Fisher). The panelists present findings from their current research on affective information behavior (AIB) that illustrates its determining effect on thinking and action, and provide a review of research in the affective domain from related fields.

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Germanium hut nanostressors on free-standing ultrathin SOI

Germanium hut nanostressors on free-standing ultrathin SOI

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207th ECS Meeting

作者： Roberts, Michelle Tinberg, Daniel Evans, Paul Lagally, Max Lee, Chung-Hoon Lal, Amit Xiao, Yanan Lai, Barry Cai, Zhongbou Materials Science Program Department of Materials Science and Engineering University of Wisconsin Madison WI 53706 Electrical and Computer Engineering Cornell University Ithaca NY 14853 Advanced Photon Source Argonne National Laboratory Argonne IL 60431

Heteroepitaxial growth of SiGe on thin Si membranes leads to the sharing of the epitaxial strain between the Si template layer and the deposited thin film. At high Ge concentrations, at which Ge forms dislocation-free hut nanostructures, there can be significant bending underneath self-assembled Ge huts. We have fabricated undercut mesas to approximate a freestanding Si membrane and produced Ge hut structures using molecular beam epitaxy. Using synchrotron x-ray microdiffraction to probe the strain and bending of the template layer directly, we compare strain sharing in conventional blanket film structures with the strain induced by Ge hut structures.

关键词： Silicon on insulator technology

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