Ryanodine receptors (RyR) are intracellular channels that are intricately involved in Ca2+ release. These channels large membrane proteins~2.26MDa in size. In this multi-goal project firstly we successfully studied the gating mechanics of the RyR1 in the presence of Mg2+. We used single particle reconstruction and image processing techniques to obtain the 3D structure of the RyR1 with Mg2+. The 3D structure in the presence of Mg2+ and an ATP analog is the closest representation of human physiological conditions. The open and closed state structures of RyR1 are known. However, the physiologically closed state has not been studied before. Understanding this structure will help in the understanding of protein interactions. Our second goal was the validation of this 3D structure under different levels of noise. Validation under different noise levels analyzed the problem of noise bias is present in the field of cryo-EM and single particle reconstruction in select cases.

Each year in the United States over a million people experience a myocardial infarction. The majority of these attacks are caused by coronary artery plaque cap rupture with subsequent thrombus formation. Because rupture is a mechanical event and the tendency of a plaque to rupture is due in part to increases in the mechanical stresses in the fibrous cap, mechanical analyses are important to understanding plaque stability. Histology is the only method capable of identifying plaque features that are associated with vulnerability. Therefore, minimally distorted histologic sections should serve as a basis for constructing the models used in mechanical analyses. Further, because substantial longitudinal variations in geometry and mechanical properties often exist, models should be three-dimensional (3-D). Finally, given the complex geometries of atherosclerotic plaques and the fact that they are composed of different materials, the finite element (FE) method should be used to determine the distribution of stress under physiological loading. Until now, a critical need has existed to determine the distribution of stress in 3-D FE models of human coronary atherosclerotic plaques based on minimally distorted histologic sections. In this research study, a method to measure and correct for distortions caused by acrylic histologic processing was first created. The devised strain-based method yields a limited set of parameters needed for a first order correction. Thus, corrections can be easily implemented using FE methods. Next, a methodology to create 3-D finite FE models of human coronary atherosclerotic plaques based on stable acrylic histologic sections was developed. Models of plaques, ranging in disease severity, were generated using the developed methodology. Lastly, the distributions of stress in these models were obtained and the effects of some plaque features on stresses were determined. Results from this study confirm that morphological description of a plaque is not sufficient to predict plaque rupture. The findings suggest that in many cases the 3-D stress field within a plaque must be known in order to assess plaque stability. Finally, the results show that patient specific models must be developed if the 3-D stress field within a plaque is to be determined.

In order to predict the behavior of bubbly flows, it is necessary to know the three dimensional profiles of the bubbles present in the flow. With advancements in the field of flow visualization, accurate reconstruction of the bubble shape has become necessary. The PIV and the SIV techniques, used to acquire images of particles and bubbles, have been found to be extremely useful in this regard. The study, development, implementation, applications and limitations of a unique reconstruction technique applied to various regular and irregular bubble shapes, using the two orthogonal projections of the three-dimensional bubble profiles as captured by the SIV cameras are presented here. The technique is a blend of neural networks, combinatorial optimization and advanced computer aided design methods. The technique involves the robustness and ruggedness of the neural network approach and the flexibility and reliability of advanced computer aided design methods. The technique uses a well-known problem in neural networks and combinatorial optimization known as the Traveling Salesman Problem approach to identify the bubble boundaries on the images. An optimization solution technique known as the Simulated Annealing technique is employed to solve the Traveling Salesman Problem and obtain the bubble profiles. These results are employed to reconstruct bubble shapes using NURBS computer aided design software. Two main applications of this technique are demonstrated and the results are found to be promising. The first application included the calculation of the void fraction at a particular depth of the channel/ pipe and at a particular radius of the channel. The second application was Lagrangian tracking of bubbles, wherein the centroids of the bubbles were tracked between image frames to determine the linear and transverse velocities of the bubbles. This technique has shown scope for development including the development as integrated bubble surface reconstruction software and advanced modifications at various levels for efficient and accurate reconstruction.

歯科基礎医学会, 金子 知生 = Tomoo Kaneko, 歯に矯正力を加えた際の圧迫側歯周組織の三次元的様相について = Three-dimensional situation of periodontal tissue at pressure side incident to orthodontic tooth movement, 歯科基礎医学会雑誌, 36(2), APR 1994, pp.170-186 / Hokkaido University (北海道大学) / 博士 / 歯学

Cyro-EM and three-dimensional reconstruction have become important research tools for virus structure. These techniques have benefit of fast and keep samples in native folding. Simulated prefer orientation images of DGNNV, PaV and TBSV were reconstructed by SPIDER or PurdueEM, with projection matching with. SPIDER prefers 3-fold and 5-fold view fields, and PurdueEM prefers 2-fold view fields. SPIDER could reconstruction images which have more noise than PurdueEM can successfully reconstruct. Reconstruction of RNA-cages has some relationship with the symmetry of capsid protein. Prefer orientation, noise and RNA-cages are the factors that can effect reconstruction.

京都大学 / 0048 / 新制・論文博士 / 博士(人間健康科学) / 乙第13143号 / 論人健博第4号 / 新制||人健||4(附属図書館) / (主査)教授 精山 明敏, 教授 澤本 伸克, 教授 伊佐 正 / 学位規則第4条第2項該当 / Doctor of Human Health Sciences / Kyoto University / DFAM

A realistic visualization that enhances a virtually authentic experience is the ambition of any visualization system in a simulator environment. But calibrating and maintaining a high quality visualization system entail large costs, resources and time. Hence, a soft- ware has been developed to facilitate the measuring of three useful metrics that lay the foundation for automatic calibration of visual projector systems. The software and associ- ated method conducts relevant measurements which are compatible with arbitrary surface shapes and can be utilized as an assurance of quality measurement tool. The measure- ments include absolute surface shape, absolute geometry and projector blending zone con- tributions. The implementation decrease manual complexity for users, adds environmen- tal flexibility, increase density of measurement points and is more cost and time efficient then existing methods. / <p>Examensarbetet är utfört vid Institutionen för teknik och naturvetenskap (ITN) vid Tekniska fakulteten, Linköpings universitet</p>

Made available in DSpace on 2014-06-11T19:24:47Z (GMT). No. of bitstreams: 0 Previous issue date: 2008-06-27Bitstream added on 2014-06-13T19:31:50Z : No. of bitstreams: 1 joiafilho_p_me_bauru.pdf: 1705037 bytes, checksum: e438b4083e3b354705865523aa6eb7a4 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Uma das primeiras fases da análise estrutural por elementos finitos é a criação do modelo geométrico. Este modelo deve representar fielmente a estrutura no que diz respeito a ângulos, dimensões e forma. Quando os objetos de estudo são estruturas biomecânicas, a dificuldade na realização das análises aumenta, primeiro porque os modelos considerados apresentam geometria quase sempre irregular, segundo pela dificuldade na realização de experimentos desta natureza, já que envolvem, em geral, organismos e tecidos vivos. Inserida, portanto, no contexto de Modelagem Científica Computacional, esta pesquisa procurou aplicar a computação a outras áreas do conhecimento, com o objetivo de criar modelos computacionais para situações em que é inviável testar ou medir as diversas soluções possíveis para um fenômeno a partir de modelos experimentais, neste caso, regiões ósseas. Para atingir este objetivo um programa computacional foi desenvolvido: o bioMeshCreate. O bioMeshCreate é uma aplicação final, independente, multi-plataforma, orientado a objeto, implementado em C++ com o auxílio de um toolkit de visualização científica, o VTK (The Visualization Toolkit), e seu objetivo principal é reconstruir estruturas ósseas tridimensionais a partir de seções planas, normalmente imagens médicas digitais obtidas por exames de tomografia computadorizada ou ressonância magnética. A aplicação também permite visualizar as fatias planas, gerar a malha sobre a superfície reconstruída, aplicar filtros de redução de elementos e suavização de superfícies e integrar o volume obtido com softwares de análise por elementos finitos, a fim de completar a análise sobre a estrutura. Ainda é possível exportar dados em formatos compatíveis com processos de prototipagem rápida e gerar modelos de realidade virtual, os quais podem ser distribuídos e visualizados em um browser... / One of the first phases of the structural analysis by finite elements is to create a geometric model. This model must faithfully represent the structure in what is related to angles, dimensions and form. When the study objects are biomechanical structures, the level of difficulty in the accomplishment of the analyses increases, first because the considered models present geometry almost always irregular, second for the difficulty for the accomplishment of experiments of this nature, as they involve, in general, organisms and live tissues. Inserted, therefore, in the context of Scientific Computational Modeling, this research tried to apply the computation to other areas of knowledge, with the objective of creating computational models for situations in which testing or measuring the several possible solutions for a phenomenon starting from experimental models isn’t viable, in this case, bone areas. To reach this purpose, a computational program was developed: the bioMeshCreate. The bioMeshCreate is a final application, independent, multi-platform, object-oriented, developed in C++ with the support of a toolkit for scientific visualization, the VTK (The Visualization Toolkit), and its main objective is to rebuild three-dimensional bone structures starting from plane sections, usually digital medical images obtained by exams of computed tomography or magnetic resonance. The application allows the visualization plane slices, to generate the mesh on the rebuilt surface, to apply filters of elements reduction and mesh smoothing and to integrate the volume obtained with finite elements analysis softwares, in order to complete the analysis on the structure. It is still possible to export data in compatible formats with rapid prototyping processes, and to generate virtual reality models, which can be distributed and visualized in a browser. Tests with patients' real data were accomplished... (Complete abstract click elctronic access below)

Orientador: Edson Antonio Capello Sousa / Banca: Sérgio Scheer / Banca: José Eduardo Cogo Castanho / Resumo: Uma das primeiras fases da análise estrutural por elementos finitos é a criação do modelo geométrico. Este modelo deve representar fielmente a estrutura no que diz respeito a ângulos, dimensões e forma. Quando os objetos de estudo são estruturas biomecânicas, a dificuldade na realização das análises aumenta, primeiro porque os modelos considerados apresentam geometria quase sempre irregular, segundo pela dificuldade na realização de experimentos desta natureza, já que envolvem, em geral, organismos e tecidos vivos. Inserida, portanto, no contexto de Modelagem Científica Computacional, esta pesquisa procurou aplicar a computação a outras áreas do conhecimento, com o objetivo de criar modelos computacionais para situações em que é inviável testar ou medir as diversas soluções possíveis para um fenômeno a partir de modelos experimentais, neste caso, regiões ósseas. Para atingir este objetivo um programa computacional foi desenvolvido: o bioMeshCreate. O bioMeshCreate é uma aplicação final, independente, multi-plataforma, orientado a objeto, implementado em C++ com o auxílio de um toolkit de visualização científica, o VTK (The Visualization Toolkit), e seu objetivo principal é reconstruir estruturas ósseas tridimensionais a partir de seções planas, normalmente imagens médicas digitais obtidas por exames de tomografia computadorizada ou ressonância magnética. A aplicação também permite visualizar as fatias planas, gerar a malha sobre a superfície reconstruída, aplicar filtros de redução de elementos e suavização de superfícies e integrar o volume obtido com softwares de análise por elementos finitos, a fim de completar a análise sobre a estrutura. Ainda é possível exportar dados em formatos compatíveis com processos de prototipagem rápida e gerar modelos de realidade virtual, os quais podem ser distribuídos e visualizados em um browser... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: One of the first phases of the structural analysis by finite elements is to create a geometric model. This model must faithfully represent the structure in what is related to angles, dimensions and form. When the study objects are biomechanical structures, the level of difficulty in the accomplishment of the analyses increases, first because the considered models present geometry almost always irregular, second for the difficulty for the accomplishment of experiments of this nature, as they involve, in general, organisms and live tissues. Inserted, therefore, in the context of Scientific Computational Modeling, this research tried to apply the computation to other areas of knowledge, with the objective of creating computational models for situations in which testing or measuring the several possible solutions for a phenomenon starting from experimental models isn't viable, in this case, bone areas. To reach this purpose, a computational program was developed: the bioMeshCreate. The bioMeshCreate is a final application, independent, multi-platform, object-oriented, developed in C++ with the support of a toolkit for scientific visualization, the VTK (The Visualization Toolkit), and its main objective is to rebuild three-dimensional bone structures starting from plane sections, usually digital medical images obtained by exams of computed tomography or magnetic resonance. The application allows the visualization plane slices, to generate the mesh on the rebuilt surface, to apply filters of elements reduction and mesh smoothing and to integrate the volume obtained with finite elements analysis softwares, in order to complete the analysis on the structure. It is still possible to export data in compatible formats with rapid prototyping processes, and to generate virtual reality models, which can be distributed and visualized in a browser. Tests with patients' real data were accomplished... (Complete abstract click elctronic access below) / Mestre

Orientador: Siome Klein Goldenstein / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Computação / Made available in DSpace on 2018-08-13T11:06:36Z (GMT). No. of bitstreams: 1 Hauagge_DanielCabrini_M.pdf: 29273846 bytes, checksum: d697300202f6081a1441b4748b9a711c (MD5) Previous issue date: 2008 / Resumo: Apresentamos nesta dissertação quatro algoritmos voltados para a classicação automatizada de frutas. A subtração de fundo baseada na distância de Mahalanobis. O rastreamento das frutas em uma esteira usando a subtração de fundo, casamento de padrões e fluxo óptico. A reconstrução tridimensional da fruta a partir de imagens dela na esteira, onde recuperamos a posição da câmera com relação a fruta usando fluxo óptico e uma estimativa grosseira do movimento da fruta. A forma da fruta é obtida a partir das silhuetas reprojetadas no espaço tridimensional usando duas abordagens diferentes. Finalmente, a localização do pedúnculo e cálice a partir do eixo de simetria da reconstrução tridimensional. Realizamos testes com os quatro algoritmos. Obtivemos bons resultados com os dois primeiros. Para a reconstrução tridimensional verificamos bons resultados para algumas etapas do processo (fluxo óptico, estimativa inicial e otimização não-linear do movimento de câmera). Resultados fracos foram obtidos para a reprojeção das silhuetas usando os dois métodos. Analisamos as causas dos erros e propomos métodos que poderiam ser usados para melhorá-los. Os resultados da localização do pedúnculo e cálice foram insatisfatórios mas acreditamos que melhorariam se obtivéssemos uma reconstrução mais precisa. Também criamos um sistema de captura que reproduz as condições dentro de um sistema comercial de classificação. Com este aparato construímos quatro grandes bases de dados com aproximadamente 3000 frutas, 35 imagens de cada uma, contendo quatro variedades de maçã. Outras 6 bases menores foram criadas. / Abstract: We present in this dissertation four algorithms targeted at the automated classification of fruits. Background subtraction based on Mahalanobis distance. Fruit tracking on a conveyor belt using background subtraction, pattern matching and optical flow. The 3D reconstruction of the fruit from its images on the conveyor belt, where we recover the camera position, with respect to the fruit, using optical flow and a rough estimate of fruit motion. The fruit's shape is recovered from the silhouette re-projected into 3D space using two different approaches. Finally, the location of the stem and calyx based on the symmetry axis of the 3D reconstruction. We also present the results of tests conducted with the four algorithms. We obtained good results with the first two. For the three-dimensional reconstruction we obtained good results with some of the intermediary steps (optical flow, initial estimate and nonlinear re_nement of camera motion). Poor results were obtained for the re-projection of the silhouette's, using two approaches. We analyze the causes of these difficulties and suggest approaches that could improve them. The localization of stem and calyx was compromised by the poor 3D reconstruction so we believe that it will improve once we address the problems with the reconstruction algorithm. We created an image capturing system that reproduces the conditions inside a commercial grading machine. With this device we acquired four big data sets with approximately 3000 apples, 35 images of each, comprising four varieties. Another 6 smaller data-sets were also created. / Mestrado / Visão Computacional / Mestre em Ciência da Computação