Les cytochromes P450s (CYPs) sont des hémoprotéines intervenant dans la fonction de détoxication cellulaire. Le site actif des CYPs est enfoui dans la protéine, mais accessible aux ligands par des canaux. A l'aide d'une méthode récente basée sur la triangulation de Delaunay de la protéine, et implémentée dans le logiciel CCCPP, nous avons modélisé géométriquement ces canaux pour plusieurs isoformes humaines, dont le 3A4, présent au niveau du foie humain et responsable de la métabolisation d'un nombre important de médicaments, afin de constituer un filtre stérique destiné au criblage virtuel rapide de chimiothèques. Cette approche nous a permis d'obtenir des informations sur les mécanismes d'ouverture et de fermeture des canaux, permettant d'expliquer comment des ligands volumineux peuvent accéder au site actif. Ces résultats confirment et étendent ceux de la littérature, et peuvent contribuer à l'élaboration de médicaments nouveaux ou ayant moins d'effets secondaires. / The cytochromes P450s (CYPs) are hemoproteins involved in the cellular detoxification function. The CYPs active site is buried inside the protein, but it can be accessed by the ligands through channels. With a recent method based upon the Delaunay triangulation of the protein, and implemented in the CCCPP software, we modelized geometrically these channels for several human isoforms, including the 3A4, located in the human liver and responsible of the metabolization of an important number of drugs, in order to build a sterical filter devoted to high throughput virtual screening of chemical libraries. This approach let us to get information on mechanisms of opening and closing of the channels, allowing to explain how large ligands can access to the active site. These results are in agreement and extend those found in the literature, and can contribute to the design of new drugs or of drugs having less side effects.

The methods presented in this study are aimed at the identification of subpopulations (clones) of genetically similar cells within tissue samples through measurement of loci-specific Fluorescence in-situ hybridization (FISH) spot signals for each nucleus and analyzing cell spatial distributions by way of Voronoi tessellation and Delaunay triangulation to robustly define cell neighbourhoods. The motivation for the system is to examine lung cancer patient for subpopulations of Non-Small Cell Lung Cancer (NSCLC) cells with biologically meaningful gene copy-number profiles: patterns of genetic alterations statistically associated with resistance to cis-platinum/vinorelbine doublet chemotherapy treatment. Current technologies for gene-copy number profiling rely on large amount of cellular material, which is not always available and suffers from limited sensitivity to only the most dominant clone in often heterogeneous samples. Thus, through the use of FISH, the detection of gene copy-numbers is possible in unprocessed tissues, allowing identification of specific tumour clones with biologically relevant patterns of genetic aberrations. The tissue-wide characterization of multiplexed loci-specific FISH signals, described herein, is achieved through a fully automated, multicolour fluorescence imaging microscope and object segmentation algorithms to identify cell nuclei and FISH spots within. Related tumour clones are identified through analysis of robustly defined cell neighbourhoods and cell-to-cell connections for regions of cells with homogenous and highly interconnected FISH spot signal characteristics. This study presents experiments which demonstrate the system’s ability to accurately quantify FISH spot signals in various tumour tissues and in up to 5 colours simultaneously or more through multiple rounds of FISH staining. Furthermore, the system’s FISH-based cell classification performance is evaluated at a sensitivity of 84% and specificity 81% and clonal identification algorithm results are determined to be comparable to clone delineation by a human-observer. Additionally, guidelines and procedures to perform anticipated, routine analysis experiments are established. / Science, Faculty of / Physics and Astronomy, Department of / Graduate

The random deployment of Wireless Sensor and Actuator Network (WSAN) nodes in areas often inaccessible, results in so-called coverage holes – i.e. areas in the network that are not adequately covered by nodes to suit the requirements of the network. Various coverage protocol algorithms have been designed to reduce or eliminate coverage holes within WSANs by indicating how to move the nodes. The effectiveness of such coverage protocols could be jeopardised by inaccuracy in the initial node location data that is broadcast by the respective nodes. This study examines the effects of location inaccuracies on five sensor deployment and reconfiguration algorithms – They include two algorithms which assume that mobile nodes are deployed (referred to as the VEC and VOR algorithms); two that assume static nodes are deployed (referred to as the CNPSS and OGDC algorithms); and a single algorithm (based on a bidding protocol) that assumes a hybrid scenario in which both static and mobile nodes are deployed. Two variations of this latter algorithm are studied. A location simulation tool was built using the GE Smallworld GIS application and the Magik programming language. The simulation results are based on three above-mentioned deployment scenarios; mobile, hybrid and static. The simulation results suggest the VOR algorithm is reasonably robust if the location inaccuracies are somewhat lower than the sensing distance and also if a high degree of inaccuracy is limited to a relatively small percentage of the nodes. The VEC algorithm is considerably less robust, but prevents nodes from drifting beyond the boundaries in the case of large inaccuracies. The bidding protocol used by the hybrid algorithm appears to be robust only when the static nodes are accurate and there is a low degree of inaccuracy within the mobile nodes. Finally the static algorithms are shown to be the most robust; the CPNSS algorithm appears to be immune to location inaccuracies whilst the OGDC algorithm was shown to reduce the number of active nodes in the network to a better extent than that of the CPNSS algorithm. Copyright / Dissertation (MSc)--University of Pretoria, 2010. / Computer Science / unrestricted

The Oseberg ship is known as one of the finest surviving artifacts from the Viking age, with origins dated back to the 800s. The ship has been displayed in the Viking ship museum in Oslo since 1926. The nearly 100 years on museum display along with the over 1000 years it was buried has weakened the structure of the ship. To slow down the deterioration, several research projects has been initiated, among them the project ''Saving Oseberg''. A part of ''Saving Oseberg'' is contributing to the planning of a new museum for the ship. As a basis for the planning, the ship has been monitored with photogrammetry. This is intended as a way to visualise the deformation and displacements of the ship due to seasonal changes in indoor temperature and humidity. In this thesis the photogrammetry data from the hull of the ship was used to make a finite element model, and through this model calculate the average strain on each element. The method was based on a previous research project conducted on the Swedish warship Vasa by a research group at the Division of Applied Mechanics at Uppsala University. The measurements of the ship was formed into a hull by Delaunay triangulation. The strain was approximated as a Green strain and evaluated using isoparametric mapping of the elements. Through the nodal displacements, the strain was evaluated by approximating the elements as tetrahedrons and calculating the average strain from these elements between the measurements. The result showed an oscillating behavior of the displacements, proving the proposal of seasonal depending displacements. The measured principal strains also matched to the corresponding relative humidity fluctuation during the year. The strain magnitude was relatively even throughout the ship, mostly varying between ±0.4% but certain areas were more subjected than others. A few elements on the starboard side showed very large strains through most of the measurements, this seemed very unusual and was probably the result of inaccuracies or errors in the data. Though the ship is subjected to relative small strains and permanent displacements after annual cycles, the mechano-sorptive strains may lead to accumulated deformation and eventually failure in the weak parts of the wood or at the high stress concentraion parts. In addition, the cyclic strain even in elastic range may cause fatigue failure in any material which could pose a large threat for the future conservation of the ship.

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Today taxpayers (those who pay for services) and clients (those who receive services) wish the best use for the money that they invest. The public is not as accepting of generalities, observations or intuitive success measures of social agencies' performance. Emotional problems are costly. Often they can lead to loss of employment, inefficiency, break-up of marriages, retarding the emotional development of children and use of monies invested by other agencies, i.e., welfare, juvenile courts, etc. Social agencies, in response to the general public, are raising issues around what are appropriate measures tor evaluating treatment outcome. The instant study is one such response on the part of Delaunay Institute for Mental Health. The study. attempts to ascertain treatment outcome in the Delaunay program and at the same time test out the PARS (Personal Adjustment and Role Skill) as an evaluative instrument in making treatment assessment.

Unstructured simplicial mesh is an integral and critical part of many computational electromagnetics methods (CEM) such as the finite element method (FEM) and the boundary element method (BEM). Mesh quality and robustness have direct impact on the success of these CEM methods. A combined quadtree/Delunay 2D mesh generator, based on the early work of Schroeder (1991, PhD), is presented. The method produces a triangulation that approximates the original geometric model but is also topologically consistent. The key advantages of the method are: (a) its robustness, (b) ability to create a-priori graded meshes, and (c) its guaranteed mesh quality. The method starts by recursively refining the grid and using a 2:1 balanced quadtree data structure to index each cell. Once the quadtree grid is refined at a user-defined level associated with each geometrical model topological entity, each cell in the grid is successively triangulated using the Delaunay method. Finally, the method handles some modeling errors by merging vertices and allowing overlapped faces.

Delaunay refinement is a mesh triangulation method with the goal of generating well-shaped triangles to obtain a valid Delaunay triangulation. In this thesis, an approach of using this method for meshing continuous height field terrains is presented using Perlin noise as the height field. The Delaunay approach is compared to grid-based meshing to verify that the theoretical time complexity O(n log n) holds and how accurately and deterministically the Delaunay approach can represent the height field. However, even though grid-based mesh generation is faster due to an O(n) time complexity, the focus of the report is to find out if Delaunay refinement can be used to generate meshes quick enough for real-time applications. As the available memory for rendering the meshes is limited, a solution for providing a cohesive mesh surface is presented using a hole filling algorithm since the Delaunay approach ends up leaving gaps in the mesh when a chunk division is used to limit the total mesh count present in the application. The methods were implemented in the programming language C++ using the open source library libnoise to generate the Perlin noise and the off-the-shelf solution CGALmesh provided a Delaunay refinement implementation. The video game engine Unity was used to render the output meshes created by the Delaunay and grid approach by interfacing with C++ via a Windows DLL. The time complexity of Delaunay refinement was verified to hold, although it was not possible to draw any conclusions regarding the Delaunay refinement's impact on the mesh's accuracy due to the test parameters used. It was also found that the CGALmesh implementation failed to provide a deterministic generation which is a significant drawback compared to the grid-based approach. Disregarding this, the Delaunay approach was found to be suitable for real-time applications as the generation time took less than 1 second, and is promising for volumetric terrain mesh generation. / Delaunay-raffinemang är en trianguleringsmetod med målet att generera reguljära trianglar för att uppnå en giltig Delaunay-triangulering. I denna avhandling presenteras en metod användandes Delaunay-raffinemang för att skapa polygonytor av kontinuerliga höjdfältsterränger, där Perlin noise används som höjdfält. Delaunay-metoden jämförs med en rutnätsbaserad metod för att verifiera att tidskomplexiteten O(n log n) gäller och hur exakt och deterministiskt som Delaunay-metoden förhåller sig till att representera höjdfältet. Även fast rutnätsmetoden är snabbare på grund av en O(n) tidskomplexitet är rapportens fokus att ta reda på om Delaunay-raffinemang är snabb nog för att användas i realtidsapplikationer för att generera polygonytor. Eftersom det tillgängliga minnet för att rendera polygonytorna är begränsat presenteras en lösning för att få sammanhängande ytor genom en hålutfyllningsalgoritm då Delaunaymetoden lämnar hål i ytan när chunk-uppdelning används för att begränsa det totala antalet polygonytor i applikationen. Metoderna implementerades i programmeringsspråket C++ användades biblioteket libnoise för att generera Perlin noise och den färdiga lösningen CGALmesh användes som implementation av Delaunay-raffinemang. Datorspelsmotorn Unity användes för att rendera polygonytorna som skapades av Delaunay- och rutnätsmetoden genom ett C++-gränssnitt via en Windows DLL. Tidskomplexiteten av Delaunay-raffinemang gällde, men det var inte möjligt att dra några slutsatser gällande hur exakt metoden förhållde sig till höjdfältet på grund av testparametrarna som användes. Ytterligare visade det sig att CGALmesh-implementationen var oförmögen att deterministiskt generera ytorna vilket är en stor nackdel jämfört med rutnätsmetoden. Bortsett från detta så visade sig Delaunay-metoden användbar för realtidsapplikationer då generingstiden tog mindre än 1 sekund, och metoden har dessutom potential för volymetrisk terränggenerering.

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