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CHEMISTRY & BIOLOGY 2010年第4期17卷 311-312页

作者： McCarthy, Alice Main Text “In June 2003 the scientific and medical communities at MIT Harvard University and its affiliated hospitals and the Whitehead Institute banded together as collaborating partners to form the Eli and Edythe L. Broad Institute based in Cambridge MA. The Broad Institute established with initial funding from a $100 million philanthropic donation from the Los Angeles-based Broad family was primarily viewed as a marriage between the Whitehead Institute's Center for Genome Research (WICGR) and the Harvard Institute of Chemistry and Cell Biology (ICCB). Eli Broad founder and chairman of AIG SunAmerica Inc. explained “the purpose of the Broad Institute is to create a new type of research institute to build on the accomplishments of the human genome project and to move to clinical applications to both prevent and cure diseases.” Every Thursday morning we meet with perhaps 20 faculty members and 100 other researchers to discuss what we're all doing and should be doing next. -David Altschuler This paragraph was written five years ago when the Broad Institute was in its very earliest days as a life science research community (McCarthy 2005). Since that time “the Broad” as it's known has kept true to Eli Broad's vision having attracted a talented group of researchers faculty trainees and professional staff. This 1600 person research community known internally as “Broadies” includes faculty staff and students from throughout the MIT and Harvard biomedical research communities and beyond with collaborations spanning over a hundred private and public institutions in more than 40 countries worldwide. “What is special about the Broad is that we have people from Harvard MIT and the Harvard hospitals come together and work on problems of shared interest that could not be solved in their own individuals labs” explains David Altshuler M.D. Ph.D. Deputy Director and one of the Broad's six core faculty members. “These problems require expertise beyond any one principal investigator and in

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An agent framework to support sensor networks' setup and adaptation

An agent framework to support sensor networks' setup and ada...

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International Multiconference on Computer science and Information Technology, IMCSIT

作者： Edison Pignaton de Freitas Flávio Rech Wagner Tales Heimfarth Carlos Eduardo Pereira Armando Morado Ferreira Tony Larsson IDE - Halmstad University Sweden Computer Science Department UFLA Lavras Brazil Institute of Informatics UFRGS Porto Alegre Brazil Defense Engineering Graduate Program Military Institute of Engineering Rio de Janeiro Brazil IDE - Halmstad University Halmstad Sweden

Sensor networks are being used in several emerging applications not even imagined some years ago due to advances in sensing, computing, and communication techniques. However, these advances also pose various challenges that must be faced. One important challenge is related to the autonomous capability needed to setup and adapt the networks, which decentralizes the control of the network, saving communication and energy resources. Middleware technology helps in addressing this kind of problem, but there is still a need for additional solutions, particularly considering dynamic changes in users' requirements and operation conditions. This paper presents an agent-based framework acting as an integral part of a middleware to support autonomous setup and adaptation of sensor networks. It adds interoperability among heterogeneous nodes in the network, by means of autonomous behavior and reasoning. These features also address the needs for system setup and adaptations in the network, reducing the communication overhead and decentralizing the decision making mechanism. Additionally, preliminary results are also presented.

关键词： Middleware Image sensors Computer networks Communication system control Energy resources Decision making

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An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules

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BMC Systems Biology 2009年第1期3卷 1-20页

作者： Qin, Huaxia Chan, Michael W.Y. Liyanarachchi, Sandya Balch, Curtis Potter, Dustin Souriraj, Irene J. Cheng, Alfred S.L. Agosto-Perez, Francisco J. Nikonova, Elena V. Yan, Pearlly S. Lin, Huey-Jen Nephew, Kenneth P. Saltz, Joel H. Showe, Louise C. Huang, Tim H.M. Davuluri, Ramana V. Human Cancer Genetics Program Department of Molecular Virology Immunology and Medical Genetics The Ohio State University Columbus OH 43210 United States Division of Medical Technology School of Allied Medical Professions The Ohio State University Columbus OH 43210 United States Department of Biomedical Informatics The Ohio State University Columbus OH 43210 United States Department of Medical Sciences Indiana University School of Medicine Bloomington IN 47405 United States Department of Life Science Institute of Molecular Biology National Chung Cheng University Min-Hsiung Chia-Yi 621 Taiwan Institute of Digestive Disease The Chinese University of Hong Kong Hong Kong Hong Kong Center for Systems and Computational Biology Molecular and Cellular Oncogenesis Program The Wistar Institute Philadelphia PA United States

Background: The TGF-β/SMAD pathway is part of a broader signaling network in which crosstalk between pathways occurs. While the molecular mechanisms of TGF-β/SMAD signaling pathway have been studied in detail, the global networks downstream of SMAD remain largely unknown. The regulatory effect of SMAD complex likely depends on transcriptional modules, in which the SMAD binding elements and partner transcription factor binding sites (SMAD modules) are present in specific context. Results: To address this question and develop a computational model for SMAD modules, we simultaneously performed chromatin immunoprecipitation followed by microarray analysis (ChIP-chip) and mRNA expression profiling to identify TGF-β/SMAD regulated and synchronously coexpressed gene sets in ovarian surface epithelium. Intersecting the ChIP-chip and gene expression data yielded 150 direct targets, of which 141 were grouped into 3 co-expressed gene sets (sustained up-regulated, transient up-regulated and down-regulated), based on their temporal changes in expression after TGF-β activation. We developed a data-mining method driven by the Random Forest algorithm to model SMAD transcriptional modules in the target sequences. The predicted SMAD modules contain SMAD binding element and up to 2 of 7 other transcription factor binding sites (E2F, P53, LEF1, ELK1, COUPTF, PAX4 and DR1). Conclusion: Together, the computational results further the understanding of the interactions between SMAD and other transcription factors at specific target promoters, and provide the basis for more targeted experimental verification of the co-regulatory modules. © 2009 Qin et al;licensee BioMed Central Ltd.

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Novel Low-Temperature Behavior in Classical Many-Particle Systems

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Physical Review Letters 2009年第5期103卷 050602-050602页

作者： Robert D. Batten Frank H. Stillinger Salvatore Torquato Department of Chemical Engineering Princeton University Princeton New Jersey 08544 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Princeton Materials Institute Program in Applied and Computational Mathematics Princeton Center for Theoretical Science Princeton University Princeton New Jersey 08544 USA School of Natural Sciences Institute for Advanced Study Princeton New Jersey 08544 USA

We show that classical many-particle systems interacting with certain soft pair interactions in two dimensions exhibit novel low-temperature behaviors. Ground states span from disordered to crystalline. At some densities, a large fraction of normal-mode frequencies vanish. Lattice ground-state configurations have more vanishing frequencies than disordered ground states at the same density and exhibit vanishing shear moduli. For the melting transition from a crystal, the thermal expansion coefficient is negative. These unusual results are attributed to the topography of the energy landscape.

关键词： Ground state

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The policy, structure and evaluation of long-term care networks: The differentiated requirements referred to the example of integrated long-term care in Austria

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International Journal of Networking and Virtual Organisations 2009年第3期6卷 270-302页

作者： Ostermann, Herwig Staudinger, Bettina Staudinger, Oskar Kern, Katharina Them, Christa Staudinger, Roland Institute for Applied Systems Research and Development University for Health Sciences Medical Informatics and Technology EWZ 1 A-6060 Hall/Tyrol Austria S2-engineering Im Stadtgut A1 A.-4407 Steyr-Gleink Austria Institute for Nursing University for Health Sciences Medical Informatics and Technology EWZ 1 A-6060 Hall/Tyrol Austria Institute for Applied Systems Research and Development Austria S2-engineering Austria Health Care Management Program UMIT Hall/Tyrol Austria Institute for Nursing Science UMIT Austria

Long-term care facilities are currently exposed to powerful forces demanding organisational change based on synergy and cooperation. The adoption of network structures is frequently regarded as an appropriate solution to this challenge by health politics. Focusing on the concrete example of the integrated long-term care network for the elderly in the Austrian land of Tyrol, the article aims (1) to explore which criteria the lawgiver formulated for the nursing cooperation structures, (2) to examine which targets and functional requirements the managers of the nursing institutions involved theoretically demand from a network structure in long-term care and (3) to investigate the functionality of the network by means of an empirical study focusing on the processes at interorganisational interfaces. Merging the major findings of the legal, theoretical and empirical enquiry, structural and functional efficiency criteria are derived, which are suggested as a framework for the evaluation of integrative nursing networks. Copyright © 2009 Inderscience Enterprises Ltd.

关键词： Nursing

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Conditional IMS Learning Design Generation Using User Modeling and Planning Techniques

Conditional IMS Learning Design Generation Using User Modeli...

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International Conference on Advanced Learning Technologies (ICALT)

作者： Jorge Hernandez Silvia Baldiris Olga C. Santos Ramón Fabregat Jesus G. Boticario System Engineering Program Corporación Universitaria de la Costa Colombia Institute of Informatics and Aplications (IliA) Universidad de Girona Spain ADeNu Research Group Artificial Intelligence Department Computer Science School UNED (Spanish National University of Distance Education) Spain aDeNu Research Group Computer Science School UNED

Active modeling is required in learning settings to cope with the dynamic evolution of the knowledge, since learners competences evolves over time as they participate in the course activities. Moreover, one of the main issues in a competence based eLearning process is to deliver personalized instructional designs adjusted to both 1) intrinsic characteristics of users (i.e. learning styles) and 2) the desired and achieved competences in the learning process (i.e. specific and generic competences). This delivery includes the adaptation of the content and the activities in a learning scenario based on a dynamic user model that evolves according to user interactions. In this paper, an approach to support Conditional Plans Generation (IMS Learning Designs) in the context of a virtual learning environment is presented. The process is supported by a pervasive usage of standards and specifications (IMS family of specifications) in conjunction with an integral user modeling.

关键词： Learning Artificial intelligence Process planning Monitoring Technology planning Design engineering Knowledge engineering Systems engineering and theory informatics Computer science

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Dense packings of polyhedra: Platonic and Archimedean solids

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Physical Review E 2009年第4期80卷 041104-041104页

作者： S. Torquato Y. Jiao Department of Chemistry Princeton University Princeton New Jersey 08544 USA Princeton Center for Theoretical Science Princeton University Princeton New Jersey 08544 USA Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA School of Natural Sciences Institute for Advanced Study Princeton New Jersey 08540 USA Department of Mechanical and Aerospace Engineering Princeton University Princeton New Jersey 08544 USA

Understanding the nature of dense particle packings is a subject of intense research in the physical, mathematical, and biological sciences. The preponderance of previous work has focused on spherical particles and very little is known about dense polyhedral packings. We formulate the problem of generating dense packings of nonoverlapping, nontiling polyhedra within an adaptive fundamental cell subject to periodic boundary conditions as an optimization problem, which we call the adaptive shrinking cell (ASC) scheme. This optimization problem is solved here (using a variety of multiparticle initial configurations) to find the dense packings of each of the Platonic solids in three-dimensional Euclidean space R3, except for the cube, which is the only Platonic solid that tiles space. We find the densest known packings of tetrahedra, icosahedra, dodecahedra, and octahedra with densities 0.823…, 0.836…, 0.904…, and 0.947…, respectively. It is noteworthy that the densest tetrahedral packing possesses no long-range order. Unlike the densest tetrahedral packing, which must not be a Bravais lattice packing, the densest packings of the other nontiling Platonic solids that we obtain are their previously known optimal (Bravais) lattice packings. We also derive a simple upper bound on the maximal density of packings of congruent nonspherical particles and apply it to Platonic solids, Archimedean solids, superballs, and ellipsoids. Provided that what we term the “asphericity” (ratio of the circumradius to inradius) is sufficiently small, the upper bounds are relatively tight and thus close to the corresponding densities of the optimal lattice packings of the centrally symmetric Platonic and Archimedean solids. Our simulation results, rigorous upper bounds, and other theoretical arguments lead us to the conjecture that the densest packings of Platonic and Archimedean solids with central symmetry are given by their corresponding densest lattice packings. This can be regarded to be

关键词： Optimization

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Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop

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Standards in genomic sciences 2010年第3期3卷 259-66页

作者： Carsten Kettner Dawn Field Susanna-Assunta Sansone Chris Taylor Jan Aerts Nigel Binns Andrew Blake Cedrik M Britten Ario de Marco Jennifer Fostel Pascale Gaudet Alejandra González-Beltrán Nigel Hardy Jan Hellemans Henning Hermjakob Nick Juty Jim Leebens-Mack Eamonn Maguire Steffen Neumann Sandra Orchard Helen Parkinson William Piel Shoba Ranganathan Philippe Rocca-Serra Annapaola Santarsiero David Shotton Peter Sterk Andreas Untergasser Patricia L Whetzel Beilstein-Institut Frankfurt am Main Germany Centre for Ecology & Hydrology UK Oxford e-Research Centre University of Oxford UK The European Bioinformatics Institute (EBI) UK Faculty of Engineering - ESAT/SCD Leuven University Leuven-Heverlee Belgium Division of Pathway Medicine University of Edinburgh Medical School Edinburgh UK MRC Harwell UK Medical Department University Medical Center Johannes Gutenberg University-Mainz Mainz Germany Consortium for Genomic Technology Milano Italy University of Nova Gorica Nova Gorica Slovenia NIEHS NIH US National Toxicology Program USA Swiss Institute of Bioinformatics Geneva Switzerland Computational and Systems Medicine and Department of Computer Science University College London London UK Department of Computer Science Aberystwyth University Aberystwyth UK Center for Medical Genetics Ghent University Ghent Belgium Department of Plant Biology University of Georgia Athens USA Department of Stress- and Developmental Biology Institute for Plant Biochemistry Halle Germany Peabody Museum of Natural History Yale University New Haven USA Macquarie University Sydney Australia National University of Singapore Singapore Cancer Pharmacology The Mario Negri Institute for Pharmacological Research Milan Italy Image Bioinformatics Research Group Department of Zoology University of Oxford Oxford UK Wellcome Trust Sanger Institute UK Zentrum für Molekulare Biologie der Universität Heidelberg Heidelberg Germany The National Center for Biomedical Ontology / Stanford Center for Biomedical Informatics Research Stanford University Stanford USA

This report summarizes the proceedings of the second workshop of the 'Minimum Information for Biological and Biomedical Investigations' (MIBBI) consortium held on Dec 1-2, 2010 in Rüdesheim, Germany through the sponsorship of the Beilstein-institute. MIBBI is an umbrella organization uniting communities developing Minimum Information (MI) checklists to standardize the description of data sets, the workflows by which they were generated and the scientific context for the work. This workshop brought together representatives of more than twenty communities to present the status of their MI checklists and plans for future development. Shared challenges and solutions were identified and the role of MIBBI in MI checklist development was discussed. The meeting featured some thirty presentations, wide-ranging discussions and breakout groups. The top outcomes of the two-day workshop as defined by the participants were: 1) the chance to share best practices and to identify areas of synergy; 2) defining a series of tasks for updating the MIBBI Portal; 3) reemphasizing the need to maintain independent MI checklists for various communities while leveraging common terms and workflow elements contained in multiple checklists; and 4) revision of the concept of the MIBBI Foundry to focus on the creation of a core set of MIBBI modules intended for reuse by individual MI checklist projects while maintaining the integrity of each MI project. Further information about MIBBI and its range of activities can be found at http://***/.

关键词： Minimum Information European Bioinformatics institute Biomedical Ontology Stable Link Breakout Group

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Optimal packings of superballs

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Physical Review E 2009年第4期79卷 041309-041309页

作者： Y. Jiao F. H. Stillinger S. Torquato Department of Mechanical and Aerospace Engineering Princeton University Princeton New Jersey 08544 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA Princeton Center for Theoretical Science Princeton University Princeton New Jersey 08544 USA School of Natural Sciences Institute for Advanced Study Princeton New Jersey 08540 USA

Dense hard-particle packings are intimately related to the structure of low-temperature phases of matter and are useful models of heterogeneous materials and granular media. Most studies of the densest packings in three dimensions have considered spherical shapes, and it is only more recently that nonspherical shapes (e.g., ellipsoids) have been investigated. Superballs (whose shapes are defined by |x1|2p+|x2|2p+|x3|2p≤1) provide a versatile family of convex particles (p≥0.5) with both cubic-like and octahedral-like shapes as well as concave particles (0

关键词： Temperature

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Interactions leading to disordered ground states and unusual low-temperature behavior

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Physical Review E 2009年第3期80卷 031105-031105页

作者： Robert D. Batten Frank H. Stillinger Salvatore Torquato Department of Chemical Engineering Princeton University Princeton New Jersey 08544 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Princeton Materials Institute Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA Princeton Center for Theoretical Science Princeton University Princeton New Jersey 08544 USA School of Natural Sciences Institute for Advanced Study Princeton New Jersey 08544 USA

We have shown that any pair potential function v(r) possessing a Fourier transform V(k) that is positive and has compact support at some finite wave number K yields classical disordered ground states for a broad density range [R. D. Batten, F. H. Stillinger, and S. Torquato, J. Appl. Phys. 104, 033504 (2008)]. By tuning a constraint parameter χ (defined in the text), the ground states can traverse varying degrees of local order from fully disordered to crystalline ground states. Here, we show that in two dimensions, the “k-space overlap potential,” where V(k) is proportional to the intersection area between two disks of diameter K whose centers are separated by k, yields anomalous low-temperature behavior, which we attribute to the topography of the underlying energy landscape. At T=0, for the range of densities considered, we show that there is continuous energy degeneracy among Bravais-lattice configurations. The shear elastic constant of ground-state Bravais-lattice configurations vanishes. In the harmonic regime, a significant fraction of the normal modes for both amorphous and Bravais-lattice ground states have vanishing frequencies, indicating the lack of an internal restoring force. Using molecular-dynamics simulations, we observe negative thermal-expansion behavior at low temperatures, where upon heating at constant pressure, the system goes through a density maximum. For all temperatures, isothermal compression reduces the local structure of the system unlike typical single-component systems.

关键词： Ground state

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