Stroke is a common multi factorial cerebrovascular disorder with a large impact on global health. It is a disorder primarily associated with old age but environmental factors, lifestyle choices and medical history are all important for the risk of developing the disorder. It is also known that heritability is important for predisposition to the disorder. The aim of this work has been to identify genetic variations that increase the risk of being affected by stroke in the population of northern Sweden, a population well apt for genetic studies due to well kept church and medical records together with limited genetic diversity. In the first paper we used linkage analysis in families with early onset of stroke. By this approach we identified a region on chromosome 5q to be linked to an increased risk of developing stroke, a region previously identified as a susceptibility locus for stroke in the Icelandic population. In the second study we used genealogy to identify common ancestry and thereby identify common susceptibility to stroke. The seven families we connected showed significant linkage to the chromosome 9q31-33 region and four of the families shared a common haplotype over 2.1 megabases. In the third manuscript we investigated sequence variation of two candidate genes, TNFSF15 and TLR4. Sequencing of the TLR4 gene revealed previously identified variations in affected individuals from two of the families. Further SNP analysis showed five separate haplotypes among the investigated families and four haplotypes for TNFSF15. However none of these co-segregated with stroke among the investigated families. In the final paper we used a case-control stroke cohort to ascertain association for genetic variation in five genes and genetic regions previously suggested to be linked with stroke. Initial analyses showed association for the 9p21 chromosomal region and a variant in Factor 5 that showed protection against stroke, but after adjustments for common risk factors for stroke, the findings were no longer significant. In conclusion, by studying selected families we have been able to show linkage to two chromosomal regions, 5q and 9q31-33, that indicate genetic predisposition for developing stroke. Further we have shown that family based studies are still an important tool in deciphering the underlying mechanisms for complex disease.

Prostate cancer is a major health burden throughout the world, yet the etiology of prostate cancer is poorly understood. Evidence has accumulated supporting the existence of a hereditary form of this disease. Improved understanding of the genetic mechanisms underlying the development and progression of prostate cancer would be a major advance for improved prevention, detection and treatment strategies. This thesis evaluates different aspects of the genetic epidemiology of prostate cancer. In a genomic scan two chromosomal regions with evidence for linkage was observed. The strongest support was found on chromosome 19p with an allele sharing LOD score of 2.91 (genome-wide P = 0.032). The second region, showing suggestive evidence of linkage, was observed in the centromeric region of chromosome 5. Linkage analyses of densely spaced markers on chromosome 8p22-23 confirmed (P = 0.03) previously reported linkage to this region. A systematic evaluation of the possible impact that the RNASEL gene have on prostate cancer was performed. Overall, limited evidence for association with prostate cancer risk was found. The results provide strong evidence against a role of RNASEL in prostate cancer etiology in Sweden. In a comprehensive evaluation of occurrence of other malignancies in HPC families, previously reported association between gastric and prostate carcinoma was confirmed. The increased risk was of the same magnitude in early and late onset HPC families and confined to only male relatives. A genome-wide linkage analysis, stratified by occurrence of gastric carcinoma, identified a novel susceptibility locus on chromosome Xp21. In summary, chromosome 5q and 19p represents the regions most likely to harbor susceptibility genes predisposing to prostate cancer in the Swedish population. A common genetic basis for both gastric and prostate cancer has been confirmed and a novel susceptibility locus on chromosome Xp21 has been identified.

The last century, humans have been altering almost all natural environments at an accelerating rate, including the Baltic Sea that has highly eutrophicated areas and many coastal industries such as Pulp-mills. For animals living in a habitat that changes there are basically two alternatives, either to cope with the change or become locally extinct. This thesis aims to investigate if recent anthropogenic disturbance in the Baltic Sea can affect natural populations on a genetic level through natural selection. First, we found a fine-scale genetic structure in three-spine sticklebacks (Gasterosteus aculeatus) populations along the Swedish coast (paper I), indicating limited gene-flow between populations in geographic proximity. Different genetic markers, specifically Amplified Fragment Lenght Polymorpism (AFLP, and microsatellites,  gave different results, highlighting the heterogeneous character of genomes which demonstrates that it is important to choose a genetic marker that is relevant for the question at hand. With a population genomic approach, and a multilocus genetic marker (AFLP), we detected convergent evolution in genotype composition in stickleback populations living in environments affected by pulp-mill effluent (paper II) and in highly eutrophicated environments (paper III), compared to adjacent reference populations. We found loci, in both studies (paper II, III), that were different from a neutral distribution and thus probably under divergent selection for the habitat differences investigated. The selective effect from pulp-mill effluents were more pronounced, but the two different habitats had mutual characters (AFLP loci). In paper IV, we converted five anonymous AFLP loci to sequenced markers and aligned them to the stickleback genome. Four out of five loci aligned within, or close to, coding regions on chromosome I, chromosome VIII, chromosome XIX and chromosome XX. One of the loci, located on chromosome VIII and identified as under divergent selection in both paper II and III, has been identified in other studies as to be under selection for fresh water adaptation, including Baltic Sea stickleback populations. In conclusion, anthropogenic alterations of natural environments can have evolutionary consequences, probably adaptive, for the animals living there and the evolutionary response exhibited by natural populations can be very fast. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 3: Manuscript. Paper 4: Manuscript.</p>

As the capabilities of autonomous vehicles increase, their use in situations that are dangerous or dull for humans is becoming more popular. Autonomous systems are currently being used in several military and civilian domains, including search and rescue operations, disaster relief coordination, infrastructure inspection and surveillance missions. In order to perform high level mission autonomy tasks, a method is required for the vehicle to localize itself, as well as generate a map of the environment. Algorithms which allow the vehicle to concurrently localize and create a map of its surroundings are known as solutions to the Simultaneous Localization and Mapping (SLAM) problem. Certain high level tasks, such as drivability analysis and obstacle avoidance, benefit from the use of a dense map of the environment, and are typically generated with the use of point cloud data. The point cloud data is incorporated into SLAM algorithms with scan registration techniques, which determine the relative transformation between two sufficiently overlapping point clouds. The Normal Distributions Transform (NDT) algorithm is a promising method for scan registration, however many issues with the NDT approach exist, including a poor convergence basin, discontinuities in the NDT cost function, and unreliable pose estimation in sparse, outdoor environments. This thesis presents methods to overcome the shortcomings of the NDT algorithm, in both 2D and 3D scenarios. To improve the convergence basin of NDT for 2D scan registration, the Multi-Scale k-Means NDT (MSKM-NDT) algorithm is presented, which divides a 2D point cloud using k-means clustering and performs the scan registration optimization over multiple scales of clustering. The k-means clustering approach generates fewer Gaussian distributions when compared to the standard NDT algorithm, allowing for evaluation of the cost function across all Gaussian clusters. Cost evaluation across all the clusters guarantees that the optimization will converge, as it resolves the issue of discontinuities in the cost function found in the standard NDT algorithm. Experiments demonstrate that the MSKM-NDT approach can be used to register partially overlapping scans with large initial transformation error, and that the convergence basin of MSKM-NDT is superior to NDT for the same test data. As k-means clustering does not scale well to 3D, the Segmented Greedy Cluster NDT (SGC-NDT) method is proposed as an alternative approach to improve and guarantee convergence using 3D point clouds that contain points corresponding to the ground of the environment. The SGC-NDT algorithm segments the ground points using a Gaussian Process (GP) regression model and performs clustering of the non ground points using a greedy method. The greedy clustering extracts natural features in the environment and generates Gaussian clusters to be used within the NDT framework for scan registration. Segmentation of the ground plane and generation of the Gaussian distributions using natural features results in fewer Gaussian distributions when compared to the standard NDT algorithm. Similar to MSKM-NDT, the cost function can be evaluated across all the clusters in the scan, resulting in a smooth and continuous cost function that guarantees convergence of the optimization. Experiments demonstrate that the SGC-NDT algorithm results in scan registrations with higher accuracy and better convergence properties than other state-of-the-art methods for both urban and forested environments.

We present a geometrical and mathematical solution to a problem faced in the glass industry in this work. Volume measurement of the glass gob is vital in making glassware. Geometric models were used to represent the glass gob. A line scan camera system takes the images of the glass gob and the volume information of the glass gob is obtained by the image processing in the industry. This work is carried out to implement a simulator which estimates the change in the volume measurement of glass gob through line scan when it is rotated or when its shape is changed. A mixture of graphical and mathematical approaches is used to carry out this study. Geometric models have been used to represent the different gob models. Geometric models facilitate the manipulation of volumetric data.A simple and effective technique is used in this work. The problem is divided into steps. Volume measurement through a line scan technique is simulated. An easy to use graphical user interface (GUI) is designed to interact with the gob model and check the results of volume measurements.We present a geometrical and mathematical solution to a problem faced in the glass industry in this work. Volume measurement of the glass gob is vital in making glassware. Geometric models were used to represent the glass gob.A line scan camera system takes the images of the glass gob and the volume information of the glass gob is obtained by the image processing in the industry.This work is carried out to implement a simulator which estimates the change in the volume measurement of glass gob through line scan when it is rotated or when its shape is changed. A mixture of graphical and mathematical approaches is used to carry out this study. Geometric models have been used to represent the different gob models. Geometric models facilitate the manipulation of volumetric data. A simple and effective technique is used in this work. The problem is divided into steps. Volume measurement through a line scan technique is simulated. An easy to use graphical user interface (GUI) is designed to interact with the gob model and check the results of volume measurements.

Domestication is the process by which animals become adapted to the environment provided by humans. The process of domestication has let to a number of correlated behavioural, morphological and physiological changes among many domesticated animal species. An example is the changes of plumage colour in the chicken. Plumage colour is one of the most readily observable traits that make distinction between breeds as well as between strains within a breed. Understanding the genetic architecture of pigmentation traits or indeed any trait is always a great challenge in evolutionary biology. The main aim of this study was to map quantitative trait loci (QTLs) affecting the red and metallic green coloration in the chicken plumage. In this study, a total of 572 F8 intercross chickens between Red Junglefowl and White Leghorn were used. Phenotypic measurements were done using a combination of digital photography and photography manipulating software. Moreover, all birds were genotyped with 657 molecular markers, covering 30 autosomes. The total map distance covered was 11228 cM and the average interval distance was 17 cM. In this analysis, a total of six QTLs (4 for red and 2 for metallic green colour) were detected on four different chromosomes: 2, 3 11 and 14. For red colour, the most significant QTL was detected on chromosome 2 at 165 cM. An additional QTL was also detected on the same chromosome at 540 cM. Two more QTLs were detected on chromosomes 11 and 14 at 24 and 203 cM respectively. Additionally, two epistatic pairs of QTLs were also detected. The identified four QTLs together can explain approximately 36% of the phenotypic variance in this trait. In addition, for metallic green colour, one significant and one suggestive QTLs were detected on chromosomes 2 and 3 at 399 and 247 cM respectively. Moreover, significant epistatic interactions between these two QTLs were detected. Furthermore, these two QTLs together can explain approximately 24% of the phenotypic variance in this trait. These findings suggest that the expression of pigmentation in the chicken plumage is highly influenced by both the epistatic actions and pleiotropic effects of different QTLs located on different chromosomes.

The understanding of behavioral patterns in different species is an important part of the proper management and conservation of wild populations of animals. This study aims to contribute to the understanding of behavioral patterns in the samango monkey (Cercopithecus albogularis erythrarcus) of northern South Africa. Using the scan- sampling procedure, the behaviors of an isolated population of free-ranging samango monkeys in the Soutpansberg, Limpopo Province, were recorded during 16 days in the summer of 2010. The day was divided into the intervals: morning, midday and afternoon, and the behaviors social, resting, movement, and feeding were recorded and analyzed. The results showed a behavioral pattern in which the relative frequency of occurrence of social behaviors and movement were significantly different depending of the time of day, whereas the behaviors resting and feeding were not. During midday, social behaviors increased, while movement decreased. The groups’ degree of arboreality was also recorded and analyzed. The group spent significantly more time on the ground during midday compared to morning and afternoon. The amount of time this group spent on the ground is not entirely consistent with what has been described in the literature, where the samango has been described as strictly arboreal. A longer study including more environmental parameters, and using focal animal sampling together with the scan sampling method would be valuable for the further understanding of the behavior of the samango monkey.

<p>In this thesis, we explore techniques in statistics and persistent homology, which detect features among data sets such as graphs, triangulations and point cloud. We accompany our theorems with algorithms and experiments, to demonstrate their effectiveness in practice.</p><p></p><p>We start with the derivation of graph scan statistics, a measure useful to assess the statistical significance of a subgraph in terms of edge density. We cluster graphs into densely-connected subgraphs based on this measure. We give algorithms for finding such clusterings and experiment on real-world data.</p><p></p><p>We next study statistics on persistence, for piecewise-linear functions defined on the triangulations of topological spaces. We derive persistence pairing probabilities among vertices in the triangulation. We also provide upper bounds for total persistence in expectation. </p><p></p><p>We continue by examining the elevation function defined on the triangulation of a surface. Its local maxima obtained by persistence pairing are useful in describing features of the triangulations of protein surfaces. We describe an algorithm to compute these local maxima, with a run-time ten-thousand times faster in practice than previous method. We connect such improvement with the total Gaussian curvature of the surfaces.</p><p></p><p>Finally, we study a stratification learning problem: given a point cloud sampled from a stratified space, which points belong to the same strata, at a given scale level? We assess the local structure of a point in relation to its neighbors using kernel and cokernel persistent homology. We prove the effectiveness of such assessment through several inference theorems, under the assumption of dense sample. The topological inference theorem relates the sample density with the homological feature size. The probabilistic inference theorem provides sample estimates to assess the local structure with confidence. We describe an algorithm that computes the kernel and cokernel persistence diagrams and prove its correctness. We further experiment on simple synthetic data.</p> / Dissertation

Abstract The interpretation and identification of information from the side-scan sonar imagery are mainly depended on visual observation and personal experiences. Recent studies tended to increase the identification efficiency by using numerical analysis methods. This can reduce the error that cause by the differences of observer¡¦s experience as well as by extended time observation. The position around the center line of the slant range corrected side-scan sonar imagery might result in the degradation of the ability of numerical methods to successfully detect artificial objects. Theoretically, this problem could be solved by using a specific characteristic function to identify the existence of concrete reefs, and then filtering the noise of the central line area with a threshold value. This study was intended to develop fully automatic sonar imagery processing system for the identification of cubic concrete and cross-type protective artificial reefs in Taiwan offshore area. The procedures of the automatic sonar imagery processing system are as follows: (1) Image Acquisition¡G500kHz with slant range of 75m. (2) Feature Extraction¡Ggrey level co-occurrence matrix (i.e., Entropy, Homogeneity and Mean) (3) Classification¡Gunsupervised Bayesian classifier. (4) Object Identification¡Gby characteristic feature (i.e., Entropy). (5) Object¡¦s Status Analysis¡Gobject¡¦s circumference¡Barea¡Bcenter of mass and quantity. This study used the sonar images collected at Chey-Ding artificial reef site in Kaohsiung City as a case study, aiming to verify the automatic sonar imagery processing system and find out the optimum window size. The image characteristic functions include one set of first order parameter (i.e., mean) and two sets of second order parameter (i.e., entropy and homogeneity). Eight(8) sonar images with 1-8 sets of cubic concrete and cross-type protective artificial reefs where used in this step. The identification efficiency of the system, in terms of the produce¡¦s accuracy, is 79.41%. The results illustrated that there were 16~28 sets of artificial reefs being detected in this case which is comparable with the actual amount of 17 sets. Based on this investigation, the optimum window size was concluded to be 12¡Ñ12 pixels with sliding size of 4 pixel. Imagery collected at Fang-Liau artificial reef site of Pingtung County was tested. For the purpose of applicability, the original imagery (2048¡Ñ2800 pixels) was divided into 8 consecutive smaller sized imagery frames(2048¡Ñ350 pixels). The influence of using a two-fold classification procedure and a central filtering method to reduce the noise that caused by slant range correction were discussed. The results showed that central line filtering method is applicable. The results of object¡¦s status analysis showed that there are 156-236 sets of reefs existed. Automatic determination of the target using the characteristic function of entropy is feasible. If the value is larger than 1.45, it represents positive identification of concrete artificial reefs. It can be classified as muddy sand seabed type if the value is smaller than 1.35. If the value is between 1.35~1.45, it illustrates the existence of a transition zone where objects of smaller in dimensions might exist. To achieve the purpose of automatic operation, firstly, we have to identify the existence of the concrete reefs by using the specific characteristic function. Based on the result of existing concrete reefs, suture line filtering method will hence be used to filter the noise from the image information. For that all of the procedures are automatically operated without human intervention. Key word: side-scan sonar ; characteristic function ; gray level co-occurrence matrix ; Bayesian classification ;entropy ; homogeneity ; mean

Polymer liquid crystal possesses advantages of polymer in chemical industry and liquid crystal in display industry,so it is attracted more attention in science and technology. Diacrylate is a polymer liquid crystal with photosensitive property, so ,it can be applied to optical storage . He-Ne laser induced polymerization in diacrylate mesogen RM257 and RM82 had been verified in previous study. Furthermore, holography pattern can be recorded in RM257 and RM82 by controlling both the temperature of sample and the time of exposing. In this study, we consider the study of nonlinear optical properties of diacrylate using Z-SCAN techeique.¡¨Z-SCAN¡¨ is a simply yet highly sensitive single-beam experimential technique ,it can be used to measure both nonlinear absorption and nonlinear refraction.In this study ,we measured effect of absorption of diacrylate in irradiation of He-Ne laser using Z-SCAN technique.To investigate the reason that He-Ne laser induced polymerization in both RM257 and RM82.