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京都大学 / 新制・課程博士 / 博士(理学) / 甲第25150号 / 理博第5057号 / 新制||理||1721(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)准教授 大石 高生, 教授 中村 克樹, 教授 明里 宏文 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

Topology-related issues are becoming increasingly important in Computer Graphics. This research examines the use of topological analysis for solving two important problems in 3D Graphics: surface parameterization, and vector field design on surfaces. Many applications, such as high-quality and interactive image synthesis, benefit from the solutions to these problems. Surface parameterization refers to segmenting a 3D surface into a number of patches and unfolding them onto a plane. A surface parameterization allows surface properties to be sampled and stored in a texture map for high-quality and interactive display. One of the most important quality measurements for surface parameterization is stretch, which causes an uneven sampling rate across the surface and needs to be avoided whenever possible. In this thesis, I present an automatic parameterization technique that segments the surface according to the handles and large protrusions in the surface. This results in a small number of large patches that can be unfolded with relatively little stretch. To locate the handles and large protrusions, I make use of topological analysis of a distance-based function on the surface. Vector field design refers to creating continuous vector fields on 3D surfaces with control over vector field topology, such as the number and location of the singularities. Many graphics applications make use of an input vector field. The singularities in the input vector field often cause visual artifacts for these applications, such as texture synthesis and non-photorealistic rendering. In this thesis, I describe a vector field design system for both planar domains and 3D mesh surfaces. The system provides topological editing operations that allow the user to control the number and location of the singularities in the vector field. For the system to work for 3D meshes surface, I present a novel piecewise interpolating scheme that produces a continuous vector field based on the vector values defined at the vertices of the mesh. I demonstrate the effectiveness of the system through several graphics applications: painterly rendering of still images, pencil-sketches of surfaces, and texture synthesis.

This work aims to investigate some applications of the conjugate duality for scalar and vector optimization problems to the construction of gap functions for variational inequalities and equilibrium problems. The basic idea of the approach is to reformulate variational inequalities and equilibrium problems into optimization problems depending on a fixed variable, which allows us to apply duality results from optimization problems. Based on some perturbations, first we consider the conjugate duality for scalar optimization. As applications, duality investigations for the convex partially separable optimization problem are discussed. Afterwards, we concentrate our attention on some applications of conjugate duality for convex optimization problems in finite and infinite-dimensional spaces to the construction of a gap function for variational inequalities and equilibrium problems. To verify the properties in the definition of a gap function weak and strong duality are used. The remainder of this thesis deals with the extension of this approach to vector variational inequalities and vector equilibrium problems. By using the perturbation functions in analogy to the scalar case, different dual problems for vector optimization and duality assertions for these problems are derived. This study allows us to propose some set-valued gap functions for the vector variational inequality. Finally, by applying the Fenchel duality on the basis of weak orderings, some variational principles for vector equilibrium problems are investigated.

Submitted by Franciele Moreira (francielemoreyra@gmail.com) on 2017-12-27T14:12:36Z No. of bitstreams: 2 Tese - Ubirajara José Gama de Castro - 2017.pdf: 14188106 bytes, checksum: 942882692cd259cae5e8d267f6ac1188 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2017-12-28T09:43:26Z (GMT) No. of bitstreams: 2 Tese - Ubirajara José Gama de Castro - 2017.pdf: 14188106 bytes, checksum: 942882692cd259cae5e8d267f6ac1188 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2017-12-28T09:43:26Z (GMT). No. of bitstreams: 2 Tese - Ubirajara José Gama de Castro - 2017.pdf: 14188106 bytes, checksum: 942882692cd259cae5e8d267f6ac1188 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-11-28 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / In this work we study reversible vector fields in two zones and equivariant vector fields in two zones. Our main result is the classification of the symmetric singularities of codimensions 0,1 and 2 of such vector fields. More precisely, in the reversible case in R3, where the dimension of the fixed points variety of the involution associated to the vector field is 2, we present all bifurcation diagram of the codimensions 1 and 2 singularities, describing the changes in the behavior of the symmetric singularities and tangents of the vector field with the transition manifold, S, according to the variation of the bifucartion parameter. We also show the existence of invariant cylinders and, in this case, doing small perturbations we determine invariant manifolds that persisted and we determine the number of limit cycles that were born. When the vector field defined on two zones is equivariant, the dynamic is enriched with the emergence of the sliding vector field and we also do a local study and the classification of singularities (and pseudo-singularities) of codimensions 0,1 and 2. We show the existence of homoclinic sliding orbit and that it is a codimension one phenomenon. Moreover, provided the symmetry we get a double Shilnikov sliding orbit. / Neste trabalho, estudamos campos vetoriais em duas zonas reversíveis e campos vetoriais em duas zonas equivariantes. Nosso resultado principal é a classificação das singularidades simétricas de codimensões 0, 1 e 2 de tais campos vetoriais. Mais precisamente, no caso reversível em R3, onde a dimensão da variedade de pontos fixos da involução associada ao campo vetorial é 2, apresentamos todos os diagramas de bifurcação das singularidades de codimensão 1 e 2, descrevendo as mudanças no comportamento das singularidades simétricas e das tangências do campo vetorial com a variedade de transição S, de acordo com a variação do parâmetro de bifurcação. Mostramos também a existência de cilindros invariantes e, nesse caso, fazendo pequenas perturbações determinamos variedades invariantes que persistiram e determinamos o número de ciclos limites que surgiram. Quando o campo vetorial definido em duas zonas é equivariante, a dinâmica é enriquecida com o surgimento do campo vetorial deslizante e também fazemos um estudo local e a classificação das singularidades (e pseudossingularidades) de codimensões 0, 1 e 2. Mostramos a existência de órbitas homoclínicas deslizantes e que esse é um fenômeno de codimensão 1 e devido à simetria do campo vetorial equivariante, teremos um duplo Shilnikov deslizante.

The aim of the thesis was to characterize chosen expression vectors used in biotechnologically important bacterial species, Corynebacterium glutamicum, and to test their use in studies of promoter activity control by sigma factors of RNA polymerase. Different properties of these vectors (level of expression of the cloned gene, leaky expression without inducer, dependence of expression level on inducer concentration and cell population homogeneity) were found by determination of expression level of the model gfpuv gene by fluorescence intensity assay of the produced protein and by gfpuv-expressing C. glutamicum cell population analysis using flow cytometry. The vector pEC-XT99A was chosen for testing the bi-plasmid system for assignment of a sigma factor to the chosen promoter. Although the level of expression provided by pEC-XT99A was not high, the vector showed no leaky expression, expression from the vector was comparable for a wide range of IPTG concentrations and the cell population was homogenous concerning the gene expression. Using pEC-XT99A from which individual stress sig genes were expressed, the σD factor was clearly assigned to the up-to-now unknown Pcg0420 promoter. Another vector for isolation and purification of C. glutamicum proteins was used to express the C. glutamicum sigM gene and to...

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Master of Science / Department of Anatomy and Physiology / Jishu Shi / The development of reverse genetics systems for the manipulation of viral and bacterial genomes has provided platforms for identifying virulence genes, studying pathogenesis and developing vaccines. Replication-competent vaccines (e.g., modified live virus (MLV) vaccines and replicating viral/bacterial vectors) are considered the most efficacious approach for vaccine development. We constructed replication-competent candidate vaccines for two viral diseases in pigs via reverse genetics. The first vaccine we designed is to protect against highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV). HP-PRRSV can cause high mortality in pigs of all ages. Vaccines to protect pigs from HP-PRRSV are not commercially available in the US. According to previous studies, the non-structural protein (NSP) coding region of HP-PRRSV is closely related to the high mortality rate and the structural protein (SP) coding region contributes to the induction of broadly protective neutralizing antibodies. We created a chimeric PRRSV, of which the SP coding region was derived from HP-PRRSV and NSP coding region was derived from a low-pathogenic strain. This chimeric PRRSV caused similar CPE in cells as parental viruses, but had slower growth kinetics. We hypothesize that this chimeric virus will have a low pathogenicity and could serve as a candidate vaccine that can provide protection against HP-PRRV. The second vaccine vector is a modified Listeria innocua (L.inn), a non-pathogenic strain of Listeria. Genetically related Listeria monocytogenes (L.m) is a well-known intracellular pathogen that encodes specialized virulent determinants facilitating its intracellular growth and spread. Our goal is to make L.inn a vaccine vector that can deliver classical swine fever (CSF) viral antigen into intracellular environments by complementation of L.inn with selected L.m virulence genes necessary for intracellular survival and induction of a robust immune response. In this study, we constructed a shuttle vector pHT-E2 that can express CSFV antigen E2 in L.inn. We cloned the plcA-prfA operon of L.m virulence gene cluster (vgc) into pHT-E2, which enhanced the expression of E2 in L.inn. In future studies, we plan to clone additional L.m virulence genes into the shuttle vector to increase immunogenicity of this recombinant L.inn and test its ability to protect pigs from CSFV.