In this thesis, we study the Euclidean Steiner tree problem (ESTP) which arises in the field of combinatorial optimization. The ESTP asks for a network of minimal total edge length spanning a set of given terminal points in Rd with the ability to add auxiliary connecting points (Steiner points) to decrease the overall length of the network. The graph theory literature contains extensive studies of exact, approximation, and heuristic algorithms for ESTP in the plane, but less is known in higher dimensions. The contributions of this thesis include a heuristic algorithm and enhancements to an exact algorithm for solving the ESTP. We present a local search heuristic for the ESTP in Rd for d ≥ 2. The algorithm utilizes the Delaunay triangulation to generate candidate Steiner points for insertion, the minimum spanning tree to create a network on the inserted points, and second order cone programming to optimize the locations of Steiner points. Unlike other ESTP heuristics relying on the Delaunay triangulation, the algorithm inserts Steiner points probabilistically into Delaunay triangles to achieve different subtrees on subsets of terminal points. The algorithm extends effectively into higher dimensions, and we present computational results on benchmark test problems in Rd for 2 ≤ d ≤ 5. We develop new geometric conditions derived from properties of Steiner trees which bound below the number of Steiner points on paths between terminals in the Steiner minimal tree. We describe conditions for trees with a Steiner topology and show how these conditions relate to the Voronoi diagram. We describe more restrictive conditions for trees with a full Steiner topology and their implementation into the algorithm of Smith (1992). We present computational results on benchmark test problems in Rd for 2 ≤ d ≤ 5.

The fabrication and characterization of surface-anchored hydrogel microstructures are described. The hydrogel structures are constructed from poly(N-isopropylacrylamide), or poly(NIPAAm), which is a well-known thermoresponsive polymer that swells and contracts with changes in temperature. When patterned on a surface, these structures can experience a variety of shape changes induced by nonuniform swelling. Depending on the aspect ratio, patterns can, for instance buckle upon swelling and form wave-like patterns. Such structural changes replicate oscillatory motion of the smooth muscle cells and can be used to transport objects in microfluidics. The work, herein, investigates methods of pattern production and introduces a new technique for characterizing local swelling in the patterns. In order to achieve the latter, fluorescent microspheres were embedded in hydrogel patterns and their positions were mapped in three-dimensions using confocal microscopy. The measurements permit, for the first time, swelling maps of the structures based on relative movements of the microspheres. This information will ultimately aid in understanding how swollen macroscopic structures are related to gradients in localized swelling.

Ad-Hoc Wireless routing has become an important area of research in the last few years due to the massive increase in wireless devices. Computational Geometry is relevant in attempts to build stable, low power routing schemes. It is only recently, however, that models have been expanded to consider devices with a non-uniform broadcast range, and few properties are known. In particular, we find, via both theoretical and experimental methods, extremal properties for the Localized Delaunay Triangulation over the Mutual Inclusion Graph. We also provide a distributed, sub-quadratic algorithm for the generation of the structure.

Ad-Hoc Wireless routing has become an important area of research in the last few years due to the massive increase in wireless devices. Computational Geometry is relevant in attempts to build stable, low power routing schemes. It is only recently, however, that models have been expanded to consider devices with a non-uniform broadcast range, and few properties are known. In particular, we find, via both theoretical and experimental methods, extremal properties for the Localized Delaunay Triangulation over the Mutual Inclusion Graph. We also provide a distributed, sub-quadratic algorithm for the generation of the structure.

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.

HIV/AIDS is widely spread and ranks as the sixth biggest killer all over the world. Moreover, due to the rapid replication rate and the lack of proofreading mechanism of HIV virus, drug resistance is commonly found and is one of the reasons causing the failure of the treatment. Even though the drug resistance tests are provided to the patients and help choose more efficient drugs, such experiments may take up to two weeks to finish and are expensive. Because of the fast development of the computer, drug resistance prediction using machine learning is feasible. In order to accurately predict the HIV drug resistance, two main tasks need to be solved: how to encode the protein structure, extracting the more useful information and feeding it into the machine learning tools; and which kinds of machine learning tools to choose. In our research, we first proposed a new protein encoding algorithm, which could convert various sizes of proteins into a fixed size vector. This algorithm enables feeding the protein structure information to most state of the art machine learning algorithms. In the next step, we also proposed a new classification algorithm based on sparse representation. Following that, mean shift and quantile regression were included to help extract the feature information from the data. Our results show that encoding protein structure using our newly proposed method is very efficient, and has consistently higher accuracy regardless of type of machine learning tools. Furthermore, our new classification algorithm based on sparse representation is the first application of sparse representation performed on biological data, and the result is comparable to other state of the art classification algorithms, for example ANN, SVM and multiple regression. Following that, the mean shift and quantile regression provided us with the potentially most important drug resistant mutants, and such results might help biologists/chemists to determine which mutants are the most representative candidates for further research.

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.

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 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.

No description available.