Koi Herpesvirus (KHV), a species-specific DNA virus of the family Herpesviridae, is responsible for mass mortalities of common carp (Cyprinus carpio carpio L.) throughout the world. KHV’s broad geographical distribution and relatively high mortality rate among infected fish, creates significant disposal issues when die-offs occur, especially taking into account the body burden of contaminants in the fish. In locales where adequate disposal facilities are unavailable, or are unable to accommodate additional loadings of contaminated fish carcasses, concerns regarding human and environmental health are raised. During the summer of 2008, residents of the Lake Simcoe Region of southern Ontario, Canada, were faced with a massive die-off of carp, infected with KHV. Carp within the Great Lakes and much of the world are known to bioaccumulate (and biomagnify) contaminants, such as, polychlorinated biphenyls (PCBs), pesticides (e.g., dichlorodiphenyltrichloroethane, DDT, and toxic metals (e.g., mercury). These contaminants have been associated with numerous adverse effects on both human and environmental health, and are thus of important considerations when planning for large-scale carcass disposal, following fish die-offs. Although suites of microbiological tests and water quality assessments are frequently conducted to identify causative factors during extensive fish-kills - assessments of relative contaminant burdens in the carcasses, which should dictate the most appropriate method of carcass disposal - are rarely performed. A case study on Snake Island, Lake Simcoe, Ontario was conducted to further examine the implications of this policy. Soil samples from two known disposal sites and three presumed control locations were sampled on Snake Island and sent to the Analytical Services Unit of Queen’s University for chemical analysis. Although none of the soil samples exceeded any legal guidelines in the present study, there is still concern as future die-offs of other fish species or piscivorous birds and the disposal of large numbers of carcasses may be an issue.

Although complete understanding of the mechanisms of rare genetic variants in disease continues to elude us, Next Generation Sequencing (NGS) has facilitated significant gene discoveries across the disease spectrum. However, the cost of NGS hinders its use for identifying rare variants in common diseases that require large samples. To circumvent the need for larger samples, designing efficient sampling studies is crucial in order to detect potential associations. This research therefore evaluates sampling designs for rare variant - quantitative trait association studies and assesses the effect on power that freely available public cohort data can have in the design. Performing simulations and evaluating common and unconventional sampling schemes results in several noteworthy findings. Specifically, the extreme-trait design is the most powerful design for analyzing quantitative traits. This research also shows that sampling more individuals from the extreme of clinical interest does not increase power. Variant filtering has served as a "proof-of-concept" approach for the discovery of disease-causing genes in Mendelian traits and formal statistical methods have been lacking in this area. However, combining variant filtering schemes with existing rare variant association tests is a practical alternative. Thus, this thesis also compares the robustness of six burden-based rare variant association tests for Mendelian traits after a variant filtering step in the presence of genetic heterogeneity and genotyping errors. This research shows that with low locus heterogeneity, these tests are powerful for testing association. With the exception of the weighted sum statistic (WSS), the remaining tests were very conservative in preserving the type I error when the number of affected and unaffected individuals was unequal. The WSS, on the other hand, had inflated type I error as the number of unaffected individuals increased. The framework presented can serve as a catalyst to improve sampling design and to develop robust statistical methods for association testing.

Related problems of string indexing and sequence analysis have been widely studied for a long time. Recently, researchers turn to consider extended versions of these problems, which provides more realistic applications. In this dissertation, we focus on three problems of recent interest, which are (1)the indexing problem for scaled strings, (2)the merged longest common subsequence problem and its variant with blocks, and (3)the sequence alignment problem with weighted constraints. The indexing problem for scaled strings asks one to preprocess a text string T, so that the matched positions of a pattern string P in T, with some scales £\ applied to P, can be reported efficiently. In this dissertation, we propose efficient algorithms for indexing real scaled strings, discretely scaled strings, and proportionally scaled strings. Our indexing algorithms achieve either significant improvements to previous results, or the best known results. The merged longest common subsequence (merged LCS) problem aims to detect the interleaving relationship between sequences, which has important applications to genomic and signal comparison. In this dissertation, we propose improved algorithms for finding the merged LCS. Our algorithms for finding the merged LCS are also more efficient than the previous results, especially for large alphabets. Finally, the sequence alignment problem with weighted constraints is a newly proposed problem in this dissertation. For this new problem, we first propose an efficient solution, and then show that the concept of weighted constraints can be further used to solve many constraint-related problems on sequences. Therefore, our results in this dissertation have significant contributions to the field of string indexing and sequence analysis.

Common sunflower is a competitive annual native dicot found in disturbed areas, on roadsides, dry prairies, and in row crops. Common sunflower is a competitive weed, but little data exist on interference, economic impacts, and competition in field corn. Field studies were conducted in 2006 and 2007 to 1) define the density-dependent effects of common sunflower competition with corn; 2) define the necessary weed-free periods of common sunflower in corn; 3) evaluate common sunflower control with herbicides; 4) and define the economic impact of common sunflower interference with corn. Corn grain yield was significantly reduced when common sunflower densities reached 1 plant/m of row and potentitially damaging common sunflower densities occurred if allowed to compete for more than 2 to 4 wk after planting for maximum corn yield. No significant corn yield reduction occurred if common sunflowers emerged 8 wk after planting. Growing degree day (GDD) heat units for corn showed that the critical point for control of common sunflower was approximately 300 GDD. Atrazine applied PRE, atrazine followed by (fb) glyphosate or halosulfuron POST, glyphosate POST, halosulfuron POST, and halosulfuron plus nicosulfuron POST controlled >87% of common sunflower. Atrazine applied PRE in a 30-cm band, nicosulfuron POST, and atrazine broadcast plus S-metolachlor PRE showed significantly lower common sunflower control and corn grain yield, when compared to atrazine PRE fb glyphosate POST. Economic impact of one sunflower/6 m of crop row caused a yield loss of 293 kg/ha. Various corn planting densities showed that corn yield can be reduced 1990 kg/ha with common sunflower competition. Corn planting densities of 49400 and 59300 plants/ha provided the greatest net returns with or without the presence of common sunflower competition. The highest net returns occurred with no common sunflower competition in 2006 and 2007, at $3,046/ha and $2,687/ha, respectively, when net corn prices were $0.24/kg ($6.00/bu). Potential control costs of various herbicide treatments revealed net returns of $1,156 to $1,910/ha in 2006 and $1,158 to $1,943/ha in 2007. Determining the economic impact of common sunflower interference in field corn allows producers to estimate the overall net return based upon density and duration of common sunflower interference, while considering varying net corn prices, crop planting density, and herbicide application costs.

The currently used DSL splitters or filters are designed for ADSL band up to 1104 KHz and ADSL2+ band up to 2208 KHz. To meet faster internet access, DSL technology has evolved from ADSL into VDSL2 with an operating band up to 30 MHz. However, the splitters in VDSL2 band have some design difficulties in longitudinal conversion loss and isolation. The main purpose of this thesis is to find some solutions to overcome these design difficulties for splitters operating in VDSL2 band. The proposed solutions include the use of common-mode choke and compensation circuit. The final testing results of the splitters can validate the proposed solutions.

Various approaches have been proposed for finding the longest common subsequence (LCS) of two sequences. The time complexities of these algorithms are usually $O(n^2)$ in the worst case, where $n$ is the length of input sequences. However, these algorithms would become infeasible when the input length, $n$, is very long. Recently, the $k$-LCS $(k ≥ 2)$ problem has become more attractive. Some algorithms have been proposed for solving the problem, but the execution time required for solving the $k$-LCS problem is still too long to be practical. In this thesis, we propose a genetic algorithm for solving the $k$-LCS problem with time complexity $O(Gpk(n + |P_j|))$, which $G$ is the number of generations, $p$ is the number of template patterns, $k$ is the number of input sequences, $n$ and $|P_j|$ are the length of input sequences and the length of template patterns, respectively. As our experimental results show, when $k$ is 20 and $n$ is 1000, the performance ratio ($|CS|/|LCS|$) of our algorithm is greater than 0.8, where $|CS|$ denotes the length of the solution we find, and $|LCS|$ represents the length of the real (optimal) LCS. Comparing the performance ratios with Expansion Algorithm and BNMAS Algorithm, our algorithm is much better than them when the number of input sequences varies from 2 to 20 and the length of the input sequences varies from 100 to 2000.

Thesis (Ph. D.)--University of Rhode Island, 2002. / Typescript. Includes bibliographical references (leaves 96-102).

published_or_final_version / Politics and Public Administration / Master / Master of Philosophy

Populations in fragmented habitat patches may show ecological differentiation, which has implications for metapopulation viability. In this study we used a common garden with two watering treatments to contrast mean differences in ecophysiological traits and the relationships between traits and performance among seven populations of three alvar species. These species differ in their alvar specialization in Ontario, from almost endemic (Solidago ptarmicoides) to highly confined (Dasiphora fruticosa) to a widespread generalist (Hypericum perforatum). Populations of all species exhibited mean differences in at least one trait: photosynthesis (Amax), growth rate and specific leaf area. More surprisingly, the relationship between functional traits and performance was significantly different among populations in all species, suggesting different strategies for maximizing growth in different environments. The ecological differentiation observed affected all species regardless of distribution and is likely genetically based. This differentiation may destabilize metapopulation dynamics and reduce rates of spread if colonization is negatively impacted.

Populations in fragmented habitat patches may show ecological differentiation, which has implications for metapopulation viability. In this study we used a common garden with two watering treatments to contrast mean differences in ecophysiological traits and the relationships between traits and performance among seven populations of three alvar species. These species differ in their alvar specialization in Ontario, from almost endemic (Solidago ptarmicoides) to highly confined (Dasiphora fruticosa) to a widespread generalist (Hypericum perforatum). Populations of all species exhibited mean differences in at least one trait: photosynthesis (Amax), growth rate and specific leaf area. More surprisingly, the relationship between functional traits and performance was significantly different among populations in all species, suggesting different strategies for maximizing growth in different environments. The ecological differentiation observed affected all species regardless of distribution and is likely genetically based. This differentiation may destabilize metapopulation dynamics and reduce rates of spread if colonization is negatively impacted.