Graduate Theses & Dissertations


Cloud Versus Bare Metal
A comparison of two high performance computing clusters running on AWS and Sharcnet was done to determine which scenarios yield the best performance. Algorithm complexity ranged from O (n) to O (n3). Data sizes ranged from 195 KB to 2 GB. The Sharcnet hardware consisted of Intel E5-2683 and Intel E7-4850 processors with memory sizes ranging from 256 GB to 3072 GB. On AWS, C4.8xlarge instances were used, which run on Intel Xeon E5-2666 processors with 60 GB per instance. AWS was able to launch jobs immediately regardless of job size. The only limiting factors on AWS were algorithm complexity and memory usage, suggesting a memory bottleneck. Sharcnet had the best performance but could be hampered by the job scheduler. In conclusion, Sharcnet is best used when the algorithm is complex and has high memory usage. AWS is best used when immediate processing is required. Author Keywords: AWS, cloud, HPC, parallelism, Sharcnet
Automated Grading of UML Class Diagrams
Learning how to model the structural properties of a problem domain or an object-oriented design in form of a class diagram is an essential learning task in many software engineering courses. Since grading UML assignments is a cumbersome and time-consuming task, there is a need for an automated grading approach that can assist the instructors by speeding up the grading process, as well as ensuring consistency and fairness for large classrooms. This thesis presents an approach for automated grading of UML class diagrams. A metamodel is proposed to establish mappings between the instructor solution and all the solutions for a class, which allows the instructor to easily adjust the grading scheme. The approach uses a grading algorithm that uses syntactic, semantic and structural matching to match a student's solutions with the instructor's solution. The efficiency of this automated grading approach has been empirically evaluated when applied in two real world settings: a beginner undergraduate class of 103 students required to create a object-oriented design model, and an advanced undergraduate class of 89 students elaborating a domain model. The experiment result shows that the grading approach should be configurable so that the grading approach can adapt the grading strategy and strictness to the level of the students and the grading styles of the different instructors. Also it is important to considering multiple solution variants in the grading process. The grading algorithm and tool are proposed and validated experimentally. Author Keywords: automated grading, class diagrams, model comparison
Groundwater Recharge in a Managed Forest on the Oak Ridges Moraine, Southern Ontario
Groundwater recharge was estimated and compared in two open grasslands, three mixed deciduous forest stands (100+ years in age), three young red pine plantations (27 ¨C 29 years in age) and two old red pine plantations (62 ¨C 63 years in age) on the Oak Ridges Moraine, southern Ontario, Canada. Recharge was estimated using a 1-d water balance with measured precipitation, throughfall, stemflow, snowpack water equivalent and soil water storage, and modelled evapotranspiration. Throughfall distribution beneath red pine canopies showed no consistent variation with distance from the tree boles. Old red pines were not major stemflow producers and although the young red pines showed a slight tendency to focus stemflow (focussing ratio > 1), the inclusion of focussed stemflow when calculating recharge at the stand scale made little difference. Conversely, sugar maple (the predominant species in the mixed deciduous stands) showed a strong tendency to focus throughfall proximal to tree boles and produce large quantities of stemflow, resulting in relatively high soil moisture contents and enhanced opportunities for recharge within ~ 0.5 m of tree boles. Inclusion of these focussed inputs resulted in a ~ 11 ¨C 18 % increase in stand scale recharge estimates. The interpretation of land cover control on recharge was complicated by variations in soil texture between sites. Soil texture and its influence on soil water storage capacity resulted in temporal variations in recharge, with sites exhibiting large storage capacities producing less recharge in the fall and greater recharge in the spring than sites with limited storage capacities. Recharge estimates for the entire study period or seasonal values for sites grouped on the basis of soil water storage capacities showed a general trend of increasing recharge in the order: old red pine ¡Ö young red pine ¡ú mixed deciduous forest ¡Ö open grasslands. The disparity between the red pine plantations and the other sites was driven in large part by greater modelled evapotranspiration in the red pine plantations. The similarity in recharge between mixed deciduous forests and open grasslands was the result of focused inputs and less soil evaporation and transpiration in the mixed deciduous forests compared to the open grasslands. The results of this study suggest planting red pine on grasslands on the Oak Ridges Moraine will initially decrease recharge and this decrease will continue as the red pines mature. However, as the red pine plantations are succeeded by mixed hardwood stands recharge will recover to that of the initial grasslands. Author Keywords: Groundwater Recharge, Land Cover Type, Oak Ridges Moraine, Stemflow, Throughfall, Water Balance
Evidence for hybrid breakdown in the cattail (Typha) hybrid swarm in southern Ontario
Heterosis, expressed as phenotypic superiority over parental species, typically peaks in first generation hybrids (F1s), while later generations (F2 +) exhibit lower fitness. The decrease in hybrid fitness is called hybrid breakdown. The overall incidence of hybrid breakdown in invasive hybrid zones remains poorly understood. The Laurentian Great Lakes (LGL) region contains a hybrid zone comprised of: native Typha latifolia, Typha angustifolia, and hybrid Typha × glauca. F1 T. × glauca display heterosis and are invasive, while later generation hybrids are relatively rare. To investigate possible hybrid breakdown, I compared seed germination and plant growth of backcrossed and advanced-generation (F2) hybrids to F1s and T. latifolia. I found evidence for hybrid breakdown in F2s and backcrossed hybrids, expressed as reduced growth and germination rates. Expression of hybrid breakdown in F2s and backcrosses may explain their relative rarity in the LGL hybrid zone. Author Keywords: Advanced-generation hybrids, Backcrossed hybrids, Hybridization, introgression, Invasive species, plant competition
Sex-Specific Graphs
Sex-specific genetic structure is a commonly observed pattern among vertebrate species. Facing differential selective pressures, individuals may adopt sex-specific life historical traits that ultimately shape genetic variation among populations. Although differential dispersal dynamics are commonly detected in the literature, few studies have investigated the potential effect of sex-specific functional connectivity on genetic structure. The recent uses of Graph Theory in landscape genetics have demonstrated network capacities to describe complex system behaviors where network topology intuitively represents genetic interaction among sub-units. By implementing a sex-specific network approach, our results suggest that Sex-Specific Graphs (SSG) are sensitive to differential male and female dispersal dynamics of a fisher (Martes pennanti) metapopulation in southern Ontario. Our analyses based on SSG topologies supported the hypothesis of male-biased dispersal. Furthermore, we demonstrated that the effect of the landscape, identified at the population-level, could be partitioned among sex-specific strata. We found that female connectivity was negatively affected by snow depth, while being neutral for males. Our findings underlined the potential of conducting sex-specific analysis by identifying landscape elements that promotes or impedes functional connectivity of wildlife populations, which sometimes remains cryptic when studied at the population level. We propose that SSG approach would be applicable to other vagile species where differential sex-specific processes are expected to occur. Author Keywords: genetic structure, Landscape Genetics, Martes pennanti, Population Graph, sex-biased dispersal, Sex-Specific Graphs
Habitat Preferences and Feeding Ecology of Blackfin Cisco (Coregonus nigripinnis) in Northern Algonquin Provincial Park
Blackfin Cisco (Coregonus nigripinnis), a deepwater cisco species once endemic to the Laurentian Great Lakes, was discovered in Algonquin Provincial Park in four lakes situated within a drainage outflow of glacial Lake Algonquin. Blackfin habitat preference was examined by analyzing which covariates best described their depth distribution using hurdle models in a multi-model approach. Although depth best described their distribution, the nearly isothermal hypolimnion in which Blackfin reside indicated a preference for cold-water habitat. Feeding structure differentiation separated Blackfin from other coregonines, with Blackfin possessing the most numerous (50-66) gill rakers, and, via allometric regression, the longest gill rakers and lower gill arches. Selection for feeding efficiency may be a result of Mysis diluviana affecting planktonic size structure in lakes containing Blackfin Cisco, an effect also discovered in Lake Whitefish (Coregonus clupeaformis). This thesis provides insight into the habitat preferences and feeding ecology of Blackfin and provides a basis for future study. Author Keywords: allometric regression, blackfin cisco, habitat, hurdle models, lake whitefish, mysis
Stoichiometric food quality affects responses of Daphnia to predator-derived chemical cues
While both resource quality and predator-derived chemical cues can each have profound effects on zooplankton populations and their function in ecosystems, the strength and nature of their interactive effects remain unclear. We conducted laboratory experiments to evaluate how stoichiometric food quality (i.e., algal carbon (C):phosphorus (P) ratios) affects responses of the water flea, Daphnia pulicaria, to predator-derived chemical cues. We compared growth rates, body elemental content, metabolic rates, life history shifts, and survival of differentially P-nourished Daphnia in the presence and absence of chemical cues derived from fish predators. We found effects of predator cues and/or stoichiometric food quality on all measured traits of Daphnia. Exposure to fish cues led to reduced growth and increased metabolic rates, but had little effect on the elemental content of Daphnia. Elevated algal C:P ratios reduced growth and body %P, increased respiration, and increased body %C. Most of the effects of predator cues and algal C:P ratios of Daphnia were non-interactive. In contrast, the declines in daphnid survival and related population growth rates that arose because of poor food quality were amplified in the presence of predator-derived cues. Our results demonstrate that stoichiometric food quality interacts with anti-predator responses of Daphnia, but these effects are trait-dependent and appear connected to animal life-history evolution. Author Keywords: Daphnia, ecological stoichiometry, indirect predator effects, life history, phosphorus, predator-prey relationships
Self-Organizing Maps and Galaxy Evolution
Artificial Neural Networks (ANN) have been applied to many areas of research. These techniques use a series of object attributes and can be trained to recognize different classes of objects. The Self-Organizing Map (SOM) is an unsupervised machine learning technique which has been shown to be successful in the mapping of high-dimensional data into a 2D representation referred to as a map. These maps are easier to interpret and aid in the classification of data. In this work, the existing algorithms for the SOM have been extended to generate 3D maps. The higher dimensionality of the map provides for more information to be made available to the interpretation of classifications. The effectiveness of the implementation was verified using three separate standard datasets. Results from these investigations supported the expectation that a 3D SOM would result in a more effective classifier. The 3D SOM algorithm was then applied to an analysis of galaxy morphology classifications. It is postulated that the morphology of a galaxy relates directly to how it will evolve over time. In this work, the Spectral Energy Distribution (SED) will be used as a source for galaxy attributes. The SED data was extracted from the NASA Extragalactic Database (NED). The data was grouped into sample sets of matching frequencies and the 3D SOM application was applied as a morphological classifier. It was shown that the SOMs created were effective as an unsupervised machine learning technique to classify galaxies based solely on their SED. Morphological predictions for a number of galaxies were shown to be in agreement with classifications obtained from new observations in NED. Author Keywords: Galaxy Morphology, Multi-wavelength, parallel, Self-Organizing Maps
Comparing Two Tablet-Based Visuomotor Tasks to Standard Laboratory Versions
The assessment of visuomotor function can provide important information about neurological status. Several visuomotor tasks exist for testing in the laboratory, although attempts to make these tests portable to allow quick and reliable assessment have been limited. We developed an assessment tool using two laboratory visuomotor tests as a tablet application: the double-step task, and an interception task. Performance was assessed by measuring the participants’ ability to reach toward unpredictably moving targets in each task. Response patterns were compared across equipment types to determine if participants were responding similarly to the moving targets in the standard laboratory and the tablet version of the tasks. On the double-step task, participants adjusted to the displaced target adequately in both the lab and tablet versions. On the interception task, participants intercepted non-accelerating targets, and performed worse on accelerating targets in both versions of the task. These findings suggest that the tablet version of these tasks assesses similar visuomotor processing as the respective laboratory version. Author Keywords: concussion assessment, double-step task, interception task, visuomotor processing, visuomotor system
Aeolian Impact Ripples in Sand Beds of Varied Texture
A wind tunnel study was conducted to investigate aeolian impact ripples in sand beds of varied texture from coarsely skewed to bimodal. Experimental data is lacking for aeolian megaripples, particularly in considering the influence of wind speed on ripple morphometrics. Additionally, the modelling community requires experimental data for model validation and calibration. Eighteen combinations of wind speed and proportion of coarse mode particles by mass were analysed for both morphometrics and optical indices of spatial segregation. Wind tunnel conditions emulated those found at aeolian megaripple field sites, specifically a unimodal wind regime and particle transport mode segregation. Remote sensing style image classification was applied to investigate the spatial segregation of the two differently coloured size populations. Ripple morphometrics show strong dependency on wind speed. Conversely, morphometric indices are inversely correlated to the proportion of the distribution that was comprised of coarse mode particles. Spatial segregation is highly correlated to wind speed in a positive manner and negatively correlated to the proportion of the distribution that was comprised of coarse mode particles. Results reveal that the degree of spatial segregation within an impact ripple bedform can be higher than previously reported in the literature. Author Keywords: Aeolian, Impact Ripples, Megaripple, Self-organization, Wind Tunnel
We investigated whether hand-proximity effects arise from the recruitment of visual-tactile bimodal cells. In Experiment 1, we executed right-hand open-loop reaching movements to targets, presented either near or far from the resting left-hand, and after applying repetitive transcranial magnetic stimulation (rTMS) to suppress neuronal activity in the PMd and AIP, in Experiment 2. Results from Experiment 1, indicated that near-hand targets improved accuracy and reduced variability. In Experiment 2, suppressing PMd showed similar near-hand effects as above. In contrast, applying rTMS to AIP disrupted the representation of target location, indicating less accuracy and greater error. Near-hand proximity effects possibly arise from the recruitment of visual-tactile bimodal cells within the human AIP. Author Keywords: anterior intraparietal sulcus, peripersonal space, repetitive transcranial magnetic stimulation (rTMS), , rTMS, anterior intraparietal sulcus, AIP., visual-tactile bimodal neurons
Interactome study of the Giardia intestinalis nuclear localized cytochrome b5
Giardia intestinalis is a waterborne enteric parasite that lacks mitochondria and the capacity for heme biosynthesis. Despite this, Giardia encodes several heme proteins, including four cytochrome b5 isotypes (gCYTB5-I – IV) of unknown function. The aim of this thesis is to gain insight into the function of the Giardia cytochrome b5 isotype III (gCYTB5-III) that is found in the nucleus, as first reported by our laboratory using immunofluorescence microscopy experiments with an isotype-III specific antibody. Nuclear localization of isotype-III is supported by two of my experiments: i) immunoblot analysis of crude cytoplasmic and nuclear enriched fractions of Giardia trophozoites; ii) association of gCYTB5-III with the insoluble fraction of Giardia lysates crosslinked with formaldehyde is reversed by DNase I treatment. To gain an understanding of the possible roles of gCYTB5-III, I performed immunoprecipitation (IP) experiments on lysates from Giardia trophozoites to identify its protein partners. Mass spectroscopy analysis of the immunoprecipitate identified proteins localized to the nucleus (RNA polymerase, DNA topoisomerase, histones, and histone modifying enzymes). Intriguingly, over 40% of the known mitosomal proteome, which functions in iron-sulfur (Fe-S) cluster assembly was also associated with gCYTB5-III. One of these proteins, the flavoenzyme GiOR-1, has been shown to mediate electron transfer from NADPH to recombinant gCYTB5-III. These IP results provide evidence that GiOR-1 and gCYTB5-III interact in vivo, and furthermore, suggest that some proteins in the mitosome could interact with those in the nucleus. I also found that DNA stress, caused by low concentrations of formaldehyde (0.1 – 0.2%) resulted in the increased expression of gCYTB5-III. Collectively these findings suggest a role of gCYTB5-III in Giardia's response to DNA stress and perhaps the formation of Fe/S clusters. Author Keywords: cluster, cytochrome, heme, iron, mitosome, nuclear


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