Graduate Theses & Dissertations


Exploring the Scalability of Deep Learning on GPU Clusters
In recent years, we have observed an unprecedented rise in popularity of AI-powered systems. They have become ubiquitous in modern life, being used by countless people every day. Many of these AI systems are powered, entirely or partially, by deep learning models. From language translation to image recognition, deep learning models are being used to build systems with unprecedented accuracy. The primary downside, is the significant time required to train the models. Fortunately, the time needed for training the models is reduced through the use of GPUs rather than CPUs. However, with model complexity ever increasing, training times even with GPUs are on the rise. One possible solution to ever-increasing training times is to use parallelization to enable the distributed training of models on GPU clusters. This thesis investigates how to utilise clusters of GPU-accelerated nodes to achieve the best scalability possible, thus minimising model training times. Author Keywords: Compute Canada, Deep Learning, Distributed Computing, Horovod, Parallel Computing, TensorFlow
Expression and characterization of cytochrome b5 from Giardia lamblia
Giardia lamblia is an intestinal parasite found globally in freshwater systems that is responsible for endemic outbreaks of infectious diarrhea. As a unicellular parasite that lacks mitochondria, a respiratory chain and lives in the anaerobic environment of its host's intestine, Giardia was assumed for decades to lack heme proteins. However, its genome encodes several putative heme proteins, including three with sequence similarity to the cytochrome b5 family, referred to as Giardia cytochromes b5 (gCYTb5). Recombinant expression of one of these genes (gCYTb5-I), results in a protein (17-kDa) that is isolated with noncovalently bound heme. Resonance Raman and UV-visible spectra of gCYTb5-I in oxidized and reduced states resemble those of microsomal cytochrome b5, while sequence alignment and homology modelling supports a structure in which a pair of invariant histidine residues act as axial ligands to the heme iron. The reduction potential of gCYTb5-I measured by cyclic voltammetry is -165 mV vs the standard hydrogen electrode and is relatively low compared to those of other family members. The amino- and carboxy-terminal sequences that flank the central heme-binding core of the gCYTb5 are highly charged and do not occur in other family members. An 11-kDa core gCYTb5-I variant lacking these flanking sequences was also able to bind heme; however, we observe very poor expression of this truncated protein as compared to the full-length protein. Author Keywords: b-type cytochrome, cytochrome b5, electron transfer protein, Giardia intestinalis, heme/heam protein, spectroelectrochemistry
Expression of Giardia intestinalis flavoenzyme GiOR-1 and characterization of its electron transfer properties
Giardia intestinalis possesses four isotypes of cytochrome b5 (gCYTB-I-IV) that differ from their mammalian counterparts, suggesting different functions in this protozoan parasite. Although the recently discovered Giardia flavoenzyme, GiOR-1, reduces these cytochromes, its properties have not been thoroughly studied, owing to the difficulty in its expression. Here I describe successful conditions for expression of GiOR-1 using autoinduction. GiOR-1 is obtained with flavins bound as indicated by its UV-visible spectrum. Its ability to catalyze electron transfer from donors (NADH, NADPH) to acceptors (oxygen, ferricyanide, cytochrome c, gCYTB5-III) were studied in spectrophotometric rate assays. NADPH is the preferred electron donor, while cytochromes are the preferred electron acceptors. Interestingly, the His-tag used to purify gCYTB5-III decreases its reaction rate with GiOR-1, as an untagged version has slightly faster rates. These findings establish the appropriate conditions for further studies on GiOR-1, including the identification of endogenous electron acceptors. Author Keywords: Autoinduction, Cytochrome b5, Cytochrome P450 oxidoreductase, Giardia intestinalis, GiOR-1, Polyhistidine tag
Expression optimization and NMR spectroscopy of Giardia intestinalis cytochrome b5 isotype III
The parasitic protist Giardia intestinalis does not synthesize heme and lacks many common eukaryotic heme proteins, yet it expresses four cytochrome b5 (gCYTB5) isotypes of unknown function. These have low reduction potentials and distinct subcellular locations that are consistent with structural features and biological functions that differ from their mammalian counterparts. Isotype III (gCYTB5-III) is particularly fascinating for its unusual location in the nuclei of Giardia. This thesis reports the optimization of recombinant gCYTB5-III overexpression for structural studies by NMR spectroscopy. Vital optimization factors for isotope labelling were first identified, finding that auto-induction promotes the optimization of many other conditions, such as colony selection, starter cultures, media components, temperature, pH and aeration. Optimized conditions were then applied to the expression and NMR spectroscopy of isotope-labelled gCYTB5-III and bovine cytochrome b5 as a control. These results can be extended to other heme proteins and will expand our biochemical knowledge of Giardia. Author Keywords: Auto-induction, Cytochrome b5, Giardia intestinalis, Isotope Labelling, Nuclear Magnetic Resonance Spectroscopy, Recombinant Protein
Facilitating Self-Regulation through Physical Activity
Self-regulation skills have been connected to positive school success and increased academic achievement (McClelland, Acock, & Morrison, 2006). One recently explored method to aid students in their ability to self-regulate is physical activity (Becker, et al., 2011). The purpose of this study was to explore the facilitation of self- regulation through physical activity via access to an exercise bicycle within an elementary and secondary school setting. Student bicycle usage was explored via student documentation to determine frequency and duration of use. Teacher observations were collected via email correspondence were analyzed via thematic content analysis and reflections made by the teachers at a follow-up debriefing session were summarized. Overall, a novelty effect was apparent with the bicycle, where it was used extensively in the first month of the study and then use sharply declined thereafter. Teachers felt that the bicycle appeared to provide some students with support, however there were challenges with integrating the exercise bicycle into the classroom. As well, teachers stated that factors such as bicycle placement and engagement levels must be explored further in order to understand the impact an exercise bicycle could possibly have on a student’s ability to self-regulate. Author Keywords: exercise bicycle, physical activity, self-regulation
Factors Controlling Peat Chemistry and Vegetation Composition in Sudbury Peatlands after 30 Years of Emission Reductions
Peatlands are prevalent in the Sudbury, Ontario region. Compared with the well documented devastation to the terrestrial and aquatic ecosystems in this region, relatively little work has been conducted on the peatlands. The objective of this research was to assess factors controlling peat and plant chemistry, and vegetation composition in 18 peatlands in Sudbury after over 30 years of emission reductions. Peatland chemistry and the degree of humification varies considerably, but sites closer to the main smelter had more humified peat and the surface horizons were enriched in copper (Cu) and nickel (Ni). Copper and Ni concentrations in peat were significantly correlated with Cu and Ni in the plant tissue of leatherleaf, although the increased foliar metal content did not obviously impact secondary chemistry stress indicators. The pH and mineral content of peat were the strongest determining factors for species richness, diversity and community composition. The bryophyte communities appear to be acid and metal tolerant, although Sphagnum mosses are showing limited recovery. Author Keywords: anthropogenic emissions, bryophytes, community comspoition, heavy metals, peatlands, wetland vegetation
Factors affecting road mortality of reptiles and amphibians on the Bruce Peninsula
Road mortality is one of the leading causes of global population declines in reptiles and amphibians. Stemming losses from reptile and amphibian road mortality is a conservation priority and mitigation is a key recovery measure. I developed a model of road mortalities relative to non-­‐mortalities, based on predictors varying across space (road surface type, traffic volume, speed limit, distance to wetland) and time (weather conditions, traffic volume). Herpetofauna road mortalities were recorded during daily bicycle and vehicle surveys to investigate the impact of roads on reptiles and amphibians within the Bruce Peninsula, Ontario in 2012 and 2013. A total of 2541 observations of herpetofauna on roads were recorded, 79% of which were dead. The major factor influencing turtle road mortality was proximity to the nearest wetland and dates early in the season (spring). For the Massasauga, high daily temperatures and low daily precipitation were associated with road mortality. The major factors driving colubrid snake mortality were also high daily temperature, low daily precipitation, as well as low speeds and paved roads. Frog and toad mortality was driven by proximity to wetland and late summer dates. These models will increase our understanding of factors affecting road losses of herpetofauna and serve as a basis for planned, experimental mitigation within the Bruce Peninsula. Author Keywords: amphibians, hotspot, mitigation, reptiles, road ecology, road mortality
Fall Migratory Behaviour and Cross-seasonal Interactions in Semipalmated Plovers (Charadrius semipalmatus) Breeding in the Hudson Bay Lowlands, Canada
I used the Motus Wildlife Tracking System to monitor the fall migration behaviour and assess the underlying drivers of migration strategy in a small shorebird, the Semipalmated Plover (Charadrius semipalmatus), breeding at two subarctic sites: Churchill, Manitoba and Burntpoint Creek, Ontario, Canada. Semipalmated Plovers from both sites departed breeding areas between mid-July and early August, with females preceding males and failed breeders preceding successful breeders. Migrants showed between and within-population variation in migration behaviour, though birds from both sites tended to follow interior or coastal routes and congregated in three major stopover regions along the mid-Atlantic coast of North America. I found that later-departing birds had initial flight tracks oriented more toward the south, faster overall ground speeds, were less likely to stopover in North America, and stopped at lower latitudes, suggesting that later-departing individuals use aspects of a time-minimizing strategy on fall migration. My findings emphasize the importance of the mid-Atlantic coast for Semipalmated Plovers and establish connectivity between sites used during breeding and migration. Author Keywords: Breeding, Migration, Motus, Semipalmated Plover, Shorebird, Stopover
Family Experiences in Nature
Children may be spending less time outdoors in nature than in previous generations, with one potential reason being parents in their role as ‘gatekeepers’ to the outdoors. This study investigated how families are spending their time during the COVID-19 pandemic, and how parents may influence children’s outdoor nature experiences. Parents (N = 121) from across Canada completed measures related to their family’s activities as well as their own connection with nature, attitudes about nature, and childhood nature contact. Results suggest that having easy access to nature, a greater connection with nature, believing in the importance of outdoor experiences, and doing outdoor activities in childhood may be associated with more current family time outside in nature. By understanding the reasons behind parental decisions regarding where and how families spend time outside, strategies can be developed to help parents increase their children’s nature time in the future. Author Keywords: children, family, nature, nature-relatedness, outdoors, parents
Fate of Silver Nanoparticles in Lake Mesocosms
The fate of silver nanoparticles (AgNPs) in surface waters determines the ecological risk of this emerging contaminant. In this research, the fate of AgNPs in lake mesocosms was studied using both a continuous (i.e. drip) and one-time (i.e. plug) dosing regime. AgNPs were persistent in the tested lake environment as there was accumulation in the water column over time in drip mesocosms and slow dissipation from the water column (half life of 20 days) in plug mesocosms. In drip mesocosms, AgNPs were found to accumulate in the water column, periphtyon, and sediment according to loading rate; and, AgNP coating (PVP vs. CT) had no effect on agglomeration and dissolution based on filtration analysis. In plug mesocosms, cloud point extraction (CPE), single-particle-inductively coupled mass spectroscopy (spICP-MS), and asymmetrical flow field-flow fractionation (AF4-ICP-MS) confirmed the temporal dissolution of AgNPs into Ag+ over time; however, complexation is expected to reduce the toxicity of Ag+ in natural waters. Author Keywords: AF4-ICP-MS, cloud point extraction, fate, mesocosms, silver nanoparticles, SP-ICP-MS
Fathering Experience of the Transition Into Parenthood
Men who become fathers undergo a transitional period during which they adjust to their new role as the caregiver of a child, a time that is usually viewed as a major life transition (Lamb, 2010). Much of the published literature focuses on fathers with identified issues (e.g., divorced fathers); therefore, there is a need for research that looks at the experiences of more typical fathers in the current Canadian context. To understand how fathers experience this transition, a series of focus groups were conducted with first-time fathers across the Peel Region of Ontario, Canada. Analysis of the focus group transcripts using an interpretative phenomenology framework identified four overarching metathemes: intrapersonal experiences, extrapersonal experiences, father’s role, and supports. Practical implications, theoretical implications, and limitations are discussed. Author Keywords: Fathering, Fathering Experience, First-Time Fathers, Transition Into Parenthood
Finger-Counting Habits and Number Processing in Canadian and Chinese University Students
In the past few years there has been increasing attention paid to the influence of the motor system on numerical cognition. A 2010 study by Domahs, Moeller, Huber, Willmes and Nuerk tested German and Chinese university students. Number processing time was influenced by cross cultural differences in finger counting habits This thesis replicated and elaborated on the aforementioned research design. This consisted of recruiting a sample of from a Chinese university and comparing them to a sample of Canadian university students. This study also compared within culture differences in participants' starting counting hand using additional SNARC analyses. A second experiment evaluated the possibility that asking participants about finger counting habits prior to the experiment may influence later answers. Cross cultural and within culture differences in finger counting habits influenced number processing. Participants also appeared to be more reliable reporters of their finger counting habits if asked at the end of the task rather than at the beginning. Author Keywords: Canadian, Chinese, Cross-cultural, Finger-counting, Magnitude, Number


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