80 research outputs found

    Bounds on the Complexity of Halfspace Intersections when the Bounded Faces have Small Dimension

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    We study the combinatorial complexity of D-dimensional polyhedra defined as the intersection of n halfspaces, with the property that the highest dimension of any bounded face is much smaller than D. We show that, if d is the maximum dimension of a bounded face, then the number of vertices of the polyhedron is O(n^d) and the total number of bounded faces of the polyhedron is O(n^d^2). For inputs in general position the number of bounded faces is O(n^d). For any fixed d, we show how to compute the set of all vertices, how to determine the maximum dimension of a bounded face of the polyhedron, and how to compute the set of bounded faces in polynomial time, by solving a polynomial number of linear programs

    Investigating the validity of current network analysis on static conglomerate networks by protein network stratification

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    <p>Abstract</p> <p>Background</p> <p>A molecular network perspective forms the foundation of systems biology. A common practice in analyzing protein-protein interaction (PPI) networks is to perform network analysis on a conglomerate network that is an assembly of all available binary interactions in a given organism from diverse data sources. Recent studies on network dynamics suggested that this approach might have ignored the dynamic nature of context-dependent molecular systems.</p> <p>Results</p> <p>In this study, we employed a network stratification strategy to investigate the validity of the current network analysis on conglomerate PPI networks. Using the genome-scale tissue- and condition-specific proteomics data in <it>Arabidopsis thaliana</it>, we present here the first systematic investigation into this question. We stratified a conglomerate <it>A. thaliana </it>PPI network into three levels of context-dependent subnetworks. We then focused on three types of most commonly conducted network analyses, i.e., topological, functional and modular analyses, and compared the results from these network analyses on the conglomerate network and five stratified context-dependent subnetworks corresponding to specific tissues.</p> <p>Conclusions</p> <p>We found that the results based on the conglomerate PPI network are often significantly different from those of context-dependent subnetworks corresponding to specific tissues or conditions. This conclusion depends neither on relatively arbitrary cutoffs (such as those defining network hubs or bottlenecks), nor on specific network clustering algorithms for module extraction, nor on the possible high false positive rates of binary interactions in PPI networks. We also found that our conclusions are likely to be valid in human PPI networks. Furthermore, network stratification may help resolve many controversies in current research of systems biology.</p

    Jet energy measurement and its systematic uncertainty in proton–proton collisions at √s=7 TeV with the ATLAS detector

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    The jet energy scale (JES) and its systematic uncertainty are determined for jets measured with the ATLAS detector using proton–proton collision data with a centre-of-mass energy of √s=7 TeV corresponding to an integrated luminosity of 4.7 fb −1. Jets are reconstructed from energy deposits forming topological clusters of calorimeter cells using the anti-kt algorithm with distance parameters R=0.4 or R=0.6, and are calibrated using MC simulations. A residual JES correction is applied to account for differences between data and MC simulations. This correction and its systematic uncertainty are estimated using a combination of in situ techniques exploiting the transverse momentum balance between a jet and a reference object such as a photon or a Z boson, for 20≤pTjet1 TeV. The calibration of forward jets is derived from dijet pT balance measurements. The resulting uncertainty reaches its largest value of 6 % for low-pT jets at |η|=4.5. Additional JES uncertainties due to specific event topologies, such as close-by jets or selections of event samples with an enhanced content of jets originating from light quarks or gluons, are also discussed. The magnitude of these uncertainties depends on the event sample used in a given physics analysis, but typically amounts to 0.5–3 %

    Distributed path planning for building evacuation guidance

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    Zone Planning in Public Transportation Systems

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    k-Best constrained bases of a matroid

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