Graduate Theses & Dissertations


Time Series Algorithms in Machine Learning - A Graph Approach to Multivariate Forecasting
Forecasting future values of time series has long been a field with many and varied applications, from climate and weather forecasting to stock prediction and economic planning to the control of industrial processes. Many of these problems involve not only a single time series but many simultaneous series which may influence each other. This thesis provides methods based on machine learning of handling such problems. We first consider single time series with both single and multiple features. We review the algorithms and unique challenges involved in applying machine learning to time series. Many machine learning algorithms when used for regression are designed to produce a single output value for each timestamp of interest with no measure of confidence; however, evaluating the uncertainty of the predictions is an important component for practical forecasting. We therefore discuss methods of constructing uncertainty estimates in the form of prediction intervals for each prediction. Stability over long time horizons is also a concern for these algorithms as recursion is a common method used to generate predictions over long time intervals. To address this, we present methods of maintaining stability in the forecast even over large time horizons. These methods are applied to an electricity forecasting problem where we demonstrate the effectiveness for support vector machines, neural networks and gradient boosted trees. We next consider spatiotemporal problems, which consist of multiple interlinked time series, each of which may contain multiple features. We represent these problems using graphs, allowing us to learn relationships using graph neural networks. Existing methods of doing this generally make use of separate time and spatial (graph) layers, or simply replace operations in temporal layers with graph operations. We show that these approaches have difficulty learning relationships that contain time lags of several time steps. To address this, we propose a new layer inspired by the long-short term memory (LSTM) recurrent neural network which adds a distinct memory state dedicated to learning graph relationships while keeping the original memory state. This allows the model to consider temporally distant events at other nodes without affecting its ability to model long-term relationships at a single node. We show that this model is capable of learning the long-term patterns that existing models struggle with. We then apply this model to a number of real-world bike-share and traffic datasets where we observe improved performance when compared to other models with similar numbers of parameters. Author Keywords: forecasting, graph neural network, LSTM, machine learning, neural network, time series
Electrochemical Biosensors for Neurodegenerative Disease Biomarkers
The onset of neurodegenerative diseases such as Alzheimer’s disease (AD) and amyotrophic lateral sclerosis (ALS) are typically characterised by the aggregation of protein biomarkers into cytotoxic fibrils. Novel means of analysing these biomarkers are needed to expand the literature toward earlier diagnosis of these conditions. Electrochemical sensors could offer the sensitivity and selectivity needed for specialised analysis, including potential point-of-care applications. The AD biomarker Tau, and ALS biomarker TDP-43 proteins are explored here by using a label-free electrochemical sensors. Tau protein was covalently bound to gold electrode surface to study the in vitro mechanisms of aggregation for this protein. An immunosensor to TDP-43 was developed by covalently binding primary TDP-43 antibodies (Abs) on gold electrode surface. A novel direct ELISA sensor for TDP-43 with visual detection and electrochemical quantification was also developed. The results validated the experimental designs toward specialised and selective analysis of these biomarkers and their aggregation mechanisms. Author Keywords: ALS, Alzheimer's, Biosensors, Electrochemistry, Tau, TDP-43
Archaeology and Reconciliation in the Williams Treaties Territory
This thesis examines the history of Indigenous inclusion in the discipline of archaeology and how archaeologists can provide reconciliation when working with Indigenous peoples in their territory. This thesis focuses on the territory of the Williams Treaties with a particular focus on the location of Nogojiwanong (Peterborough). My data consists of in-depth interviews from ten informants and studying three case studies that happened in the area. I take my informants’ suggestions and apply them to my case studies, to show practical examples of how we can provide reconciliation in the field of archaeology. Author Keywords: Decolonization , Heritage Management , Indigenous, Reconciliation
Anthropogenic particles and microplastics in headwater lake catchments in Muskoka-Haliburton, Canada
Microplastics, plastic particles less than 5 mm in diameter, are ubiquitous in the environment. This study estimated the abundance of microplastics (MP) in atmospheric deposition from four background monitoring stations in Muskoka-Haliburton, south-central Ontario, Canada and quantified the fate of microplastics to three background headwater lake catchments in Muskoka-Haliburton. Microplastics were observed across all sample media with polyethylene terephthalate and polyamide being predominant. The average atmospheric deposition of anthropogenic particles was 57 particles/m2/day with a plastic deposition rate of 7 MP/m2/day. Atmospheric deposition represented the highest daily microplastic flux rate to the three headwater lake catchments compared, 1.5 to 4 times greater than the flux rate for the inflow streams suggesting that atmospheric deposition can account for all the inflowing microplastics. A large fraction of the microplastics from atmospheric deposition (41 – 73%) were retained in the terrestrial catchment and there was a high retention of microplastics in each of the study lakes (1.44 – 7.39 million MP/day; 30 – 45%) suggesting that a large fraction of the terrestrial catchment export is retained by the lakes and that lakes are a reservoir for microplastics. Author Keywords: Atmospheric deposition, Microplastics, Ontario, Plastic pollution, Sinks, Sources
evolutionary ecology of Alaska's mountain goats with management implications
The integration of genetic and environmental information can help wildlife managers better understand the factors affecting a species’ population structure and their response to disturbance. This thesis uses genetic techniques to assess the broad and fine scale population structure of mountain goats in Alaska. The first chapter aims to determine the number of genetically distinct subpopulations and model the demographic history of mountain goats in Alaska. The second chapter investigates the population structure and demographic history of mountain goats in Glacier Bay National Park and examines the impact that climate change will have on these mountain goats. My results indicate that Alaska has eight subpopulations which diverged during the Wisconsin glaciation. In Glacier Bay, population structure is reflective of the landscape during colonization, and mountain goat population density and movement corridors are likely to decline due to future climate change. Author Keywords: Alaska, biogeography, gene flow, landscape genetics, mountain goat, population genetic structure
Forging Masks Through Perceptions of the Maskless in Benjamin Britten’s 'Peter Grimes'
This thesis proposes that Benjamin Britten’s 'Peter Grimes' leads its audience toward actively constructing an attitude toward its maskless protagonist. Grimes’s tragedy results from the social construction of his character from ambiguous and unseen actions. Utilizing the theories of Hannah Arendt and Carl Jung, this thesis proposes that Grimes may have resisted tragedy by constructing a public persona for himself. This thesis analyses the opera’s music and narrative according to the difference between Grimes’s lack of a public persona and the Borough- members’ construction of a mask for him. A central contention of the thesis is that as another element of Britten’s persona, Peter Grimes permitted the composer’s entrance into the public sphere, despite his private inclinations and illegal sexuality. Like the opera’s drama, the opera’s “Sea Interludes” reveals the tragedy resulting from the failure to construct an attitude toward the public world. These “Sea Interludes” work alongside the opera’s drama to induce the audience into a common perception of the opera’s whole. Through ironic relation to the opera’s musical and narrative parts, Benjamin Britten induces his audience’s construction of personae, thereby bringing himself and them into a shared public realm. Author Keywords: Benjamin Britten, E. M. Forster, English Opera, Montagu Slater, Peter Grimes, W. H. Auden
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
Experiencing buhts’an qu’inal from sHachel jwohc’ a’tel through sna'el ya'beyel stuc te bin ay ma'yuc
This thesis shows and emphasizes the importance of Indigenous Knowledge (IK) in informing collaborative efforts that promote sustainable economic development in Indigenous communities. It tells the story of a participative research study undertaken with six Tseltal communities located in the Region Selva of Chiapas, Mexico, in the context of the Covid19 pandemic of 2020 and early 2021. In this study, the research participants reflect on their endeavours pursuing projects focused on the economic self-sufficiency of their communities. Their initiatives, which are deeply grounded in Tseltal practices while accompanied by the local non-profit organization IXIM AC, focus on developing economically self-sustaining enterprises in self-organized groups led by local Indigenous women. The findings offer a deep immersion into two aspects that emerge from Tseltal knowledge: The Nucleus of Tseltal community wellbeing and the Four Elements of Buhts’an qu’inal (Tseltal community wellbeing). The study’s results show that these two IK grounded aspects guide the participants’ endeavours in developing sHachel jwohc’ a’tel (Tseltal initiatives of entrepreneurship) while also enabling opportunities for gender transformative collaborative work and sustained engagement in local initiatives of sna'el ya'beyel stuc te bin ay ma'yuc (Tseltal economic development oriented to community wellbeing). Author Keywords: Community Wellbeing, Indigenous Entrepreneurship, Indigenous Knowledges, Indigenous Women, Participative Action Research, Sustainable Development
Frequency-time and polarization considerations in spectral-focusing-based CARS microscopy
Spectral-focusing-based coherent anti-Stokes Raman scattering (SF-CARS) microscopy is a powerful imaging technique that involves temporally and spectrally stretching ultrashort laser pulses and controlling their frequency-time characteristics. However, a broader and more detailed understanding of the frequency-time characteristics of the laser pulses and signals involved, how they are related, and how they influence important aspects such as the spectral resolution is needed to understand the full potential of SF-CARS systems. In this work, I elucidate these relationships and discuss how they can be exploited to optimize SF-CARS microscopy setups. I present a theoretical analysis of the relationships between the spectral resolution, the degree of chirp-matching, and pulse bandwidth in SF-CARS. I find that, despite allowing better ultimate spectral resolution when chirp-matching is attained, the use of the broadest bandwidth pulses can significantly worsen the spectral resolution if the pulses are not chirp-matched. I demonstrate that the bandwidth of the detected anti-Stokes signal is minimized when the pump is twice as chirped as the Stokes, meaning that (perhaps counter-intuitively) a narrow anti-Stokes bandwidth does not imply good spectral resolution. I present approximate expressions that relate the bandwidths of the pump, Stokes, and anti-Stokes pulses to the degree of chirp-matching and outline how these could be used to estimate the amount of glass needed to attain chirp-matching. I develop a spectral-focusing-based polarization-resolved (SFP-CARS) setup, by modifying our existing system, to explore the merits of integrating polarization-dependent detection as an add-on to existing SF-CARS setups. By using the system to study polarization-dependent features in the CARS spectrum of benzonitrile, I assess its capabilities and demonstrate its ability to accurately determine Raman depolarization ratios. Ultimately, the detected anti-Stokes signals are more elliptically polarized than desired, hindering a complete suppression of the non-resonant background. Nevertheless, I find that the SFP-CARS setup is a useful tool for studying polarization-dependent features in the CARS spectra of various samples and is worthy of further investigation. This work clarifies several technical aspects of SF-CARS microscopy and provides researchers with valuable information to consider when working with SF-CARS microscopy systems. Author Keywords: coherent anti-Stokes Raman scattering, nonlinear microscopy, polarization, spectral focusing, spectroscopy
Assessing the environmental correlates of a lethal amphibian pathogen, Batrachochytrium dendrobatidis, in Ontario wetlands
Many emerging infectious diseases are caused by pathogens that possess free-living life stages, in which they interact with the environment directly rather than through the mediation of a host. These diseases represent major impediments to wildlife conservation; however, the dynamics of their interaction with the environment are poorly studied, often due to the difficulty of detecting these microscopic pathogens in environmental samples. One of these pathogens is Batrachochytrium dendrobatidis (Bd), a fungus that has been linked to declines in many amphibian species. In this thesis I use an emerging technique, environmental DNA detection (eDNA), to detect and quantify Bd in the water of southern Ontario (Canada) wetlands and examine its correlation with a variety of aspects of water quality, surrounding habitat, and seasonal timing. My purpose was to inform not only on potential environment-pathogen dynamics for Bd in northern environments, but to provide insight into the use of eDNA as a disease surveillance tool. I found that not only was there high geographic variation in Bd detection and intensity, but also high temporal variation within the same site on time scales as low as two weeks. While Bd prevalence was not strongly correlated with any of the variables tested, intensity showed strong correlation with canopy cover, with greater canopy cover over a waterbody correlating to lower Bd intensity. My results present several promising avenues for further examination of Bd in northern ecosystems, and indicate that, while caution is warranted in its implementation, eDNA may become an important tool in amphibian pathogen surveillance. Author Keywords: amphibian disease, Batrachochytrium dendrobatidis, disease monitoring, environment-pathogen dynamics, environmental DNA, wildlife disease
Demographic history and conservation genomics of caribou (Rangifer tarandus) in Québec
Genetic variation is the raw material and basis for evolutionary changes in nature. The loss of genetic diversity is a challenge many species are facing, with genomics being a potential tool to inform and prioritize decision making. Whole genome analysis can be an asset to conservation biology and the management of species through the generation of more precise and novel metrics. This thesis uses whole genome re-sequencing to characterize the demographic history and quantify genomic metrics relevant to conservation of caribou (Rangifer tarandus) in Québec, Canada. We calculated the ancestral and contemporary patterns of genomic diversity of five representative caribou populations and applied a comparative population genomics framework to assess the interplay between demographic events and genomic diversity. When compared to the census size, NC, the endangered Gaspésie Mountain caribou population had the highest ancestral Ne:NC ratio which is consistent with recent work suggesting high ancestral Ne:NC is of conservation concern. These ratios were highly correlated with genomic signatures (i.e. Tajima’s D) of recent population declines and explicit demographic model parameters. Values of contemporary Ne, estimated from linkage-disequilibrium showed Gaspêsie having among the highest contemporary Ne:NC ratio. Importantly, classic conservation genetics theory would predict this population to be of less concern based off this metric alone. Inbreeding measures suggested nuanced patterns of inbreeding and correlated to the demographic models. This study suggests that while the Québec populations are all under decline, they harbour enough ancestral genetic variation to replenish any lost diversity, if conservation decisions are made in favour of these populations, specifically supporting NC. Author Keywords:
Immunotherapies Targeting the Amyotrophic Lateral Sclerosis-Associated Protein TDP-43
Transactive response (TAR) DNA-binding protein of 43 kDa (TDP-43) pathology, including fibrillar aggregates and mutations, develops in amyotrophic lateral sclerosis (ALS) and is characterized by hyperphosphorylation and aggregation patterns, a mechanism largely understudied. In addition, ALS remains without a cure. Herein, in vitro aggregation of phosphorylated TDP-43 was explored, and the anti-TDP-43 antibodies tested for their inhibitor efficacies. Additionally, in vitro phosphorylation of TDP-43 by protein kinases was conducted to identify which protein kinases catalyze phosphorylation. The aggregation of phosphorylated and unphosphorylated full-length TDP-43 protein (pS410) was monitored by transmission electron microscopy (TEM), turbidity absorbance, and thioflavin (ThT) fluorescence spectroscopy. The protein aggregates were largely insoluble, ThT-positive and characterized with heterogeneous morphologies. Antibodies specific to epitopes within the RNA-recognition motifs and the C-terminal domains reduced the formation of β-sheets and insoluble aggregates, with outcomes highly dependent on the type of antibodies, indicating dual functionality. The only protein kinase able to phosphorylate TDP-43 at S410 was MARK4, indicating its role in the onset of PTMs in the protein. Thus, targeting TDP-43 epitopes for inhibition of aggregation and in vitro phosphorylation represent viable biochemical assays for screening protein kinase inhibitors as potential drugs against ALS. Author Keywords: aggregation, ALS, antibody-based inhibition, phosphorylation, protein kinase, TDP-43


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Format: 2023/10/02