VictorJuiz/thesis huggingface dataset:
Biochar for Restoration in the Boreal Forest of Northwestern Ontario, Canada

Pyrolyzed organic material, or biochar, has been proposed as an effective soil amendment for reforestation and mine reclamation due to its capacity to retain soil nutrients and water, immobilize toxic metals, and its recalcitrance to mineralization. Potential sources of biochar in remote northern sites are high-carbon wood ash from wood waste gasification, and natural charcoals generated by wildfire. My thesis examines the effects of biochar application on boreal species growth and establishment in three study systems: (1) the effects of a poplar wood biochar and a mixed-feedstock high-carbon wood ash biochar on soil and vegetation in a 3-year field experiment in NW Ontario, Canada; (2) the effects of a ‘natural’ biochar and mixed-feedstock high-carbon wood ash biochar on mine tailings reclamation in a 2-year field experiment at a gold mine in northern Ontario, Canada; and, (3) the potential for biochars to sorb allelochemicals and mitigate allelopathic effects on seed germination and early seedling development in three common invasive plants in Canada, garlic mustard (Alliaria petiolata), tree of heaven (Ailanthus altissima) and yellow sweetgrass (Melilotus officinalis). I found that biochars improved soil conditions and enhanced growth of native plant species, resulting in large increases in substrate C, reduced substrate bulk density, and up to a 4.5-fold increase in planted native grass biomass. Biochar additions also enhanced availability of the plant nutrients P, K, Mg, and Zn; high-carbon wood ash biochar increased spot measurements of soil moisture, but also increased levels of Cu, Mn, and Pb. Natural biochar and mixed-feedstock high-carbon wood ash biochar reduced cover of Melilotus spp., an abundant invasive and allelopathic taxon. Amendments had large effects on plant community composition, generally favoring native species. Addition of high-carbon wood ash resulted in declines in growth performance of planted white spruce (Picea glauca); a path analysis suggests this was due to effects of toxic elements rather than indirect effects of competition with non-tree vegetation. I conclude that while there are large differences in plant species responses to biochars, and potential for toxicity effects and indirect effects mediated by plant competition, overall, results suggest some benefits of biochars, including high-carbon wood ash biochars, for forest regeneration and mine reclamation in northern environments.

Keywords: Amendment
Biochar
Boreal
Reclamation
Restoration
Advisor: Thomas, Sean C.
Topology Optimization of Thin-Coated Structures

Thin coatings of relatively stiff material on relatively lightweight and compliant substrates, such as a metal coating deposited on a polymer, can produce high performance-to-weight ratio structures for engineering applications dominated by bending and torsion. Additive manufacturing techniques combined with electrodeposition enable manufacturing of structures with complex geometries and very thin coatings relative to the bulk thickness. Topology optimization is an attractive tool for designing such structures, as it does not require intuition about the optimal topology beforehand. While topology optimization methods have been developed for coated structures, their use of ersatz material methods makes them unsuited to very thin coatings, such as those produced by electrodeposition. A mixed-dimensional finite element model is developed in this thesis to model very thin coatings, involving the development of a transition finite element. This model is incorporated into a level set topology optimization algorithm, which requires the development of a heuristic-based discrete topology change step. Numerical studies are presented for MBB-beam and L-beam problems for a variety of initial geometries. The mixed-dimensional algorithm is shown to produce results similar to a reference solution for an MBB beam with a relatively thick coating, and results are also shown for more realistic material properties and dimensions. Converged solutions exhibit multimodality and unintuitive features resulting from the algorithm falling into local minima. The type of topology optimization algorithm developed in this thesis is a step forward in the optimization of thin-coated structures, but development of additional heuristics and post-processing methods is required for practical use.

Keywords: Finite element method
Level set method
Topology optimization
Advisor: Steeves, Craig A
Mental Health And Health Care Provision

The modern health care system encounters new challenges, among which is fast-rising mental health problems. Evidence points to the increase in mental health conditions being driven not only by growing awareness, but also a substantial rise in the underlying prevalence. As a result, deft responses from the health care system are imperative. To address the growing burden from conditions that require early interventions and long-term management, such as mental health disorders, the system requires innovative solutions in health care delivery and provider payment. This thesis presents three chapters discussing various aspects of health care reforms, from the social change propelling rising mental health needs to the innovative team-based care delivery model, and concerns in the existing provider payment models, in particular relating to the physician gender pay gap. Chapter 1 investigates the extent to which social media are harmful for teenagers, leveraging rich administrative data from the Canadian province of British Columbia and quasi-experimental variation related to the introduction of wireless internet there. I find that high-speed wireless internet significantly increased teen girls’ severe mental health diagnoses – by 90% – relative to teen boys over the period when visual social media became dominant in teenage internet use. Chapter 2 assesses the efficacy of Ontario’s team-based care policy Family Health Teams. I find FHTs improved overall primary care quality, significantly reducing emergency room. I find evidence of an adjustment in mental health care provision: while early-wave FHTs substituted social workers for physicians, yielding no change in quality, later-wave FHTs saw significant quality improvements, with physicians and social workers collaborating. Chapter 3 explores the roles of selection and practice style in driving the well documented physician gender pay gap. I leverage rich administrative health care data from Ontario along with a quasi-experiment that randomly assigns physicians in emergency departments based on exogenous physician availabilities. I find that selection of female physicians to lower-paying shifts leads to a 5% gap in male and female physicians’ per-visit pay. Female physicians also spend around 10% more time on each visit, resulting in lower hourly wages.

Keywords: Empirical Microeconomics
Health Economics
Health Services Research
Mental Health
Public Economics
Advisor: McMillan, Robert
Updating and Developing Risk Prediction Models for Incident Cardiovascular Disease in Ontario, Canada

The Framingham Risk Score and Pooled Cohort Equations are used to predict cardiovascular disease risk and select individuals for preventative therapy. Studies have suggested these scores overestimate risk, may be underutilized because they are time consuming, and may predict narrower outcomes that may not be the most relevant endpoint for primary prevention. The objectives of this dissertation were: (1) recalibrate and validate the Framingham Risk Score and Pooled Cohort Equations; (2) develop and validate new sex-specific models for atherosclerotic cardiovascular disease using common serum laboratory tests; and (3) estimate the rate of nine cardiovascular disease manifestations in a contemporary primary prevention population.In the first study, the Framingham Risk Score was recalibrated in 6,938,971 individuals and validated in 71,450 primary care patients. Recalibration reduced overestimation in women (109% to 49%) and men (131% to 32%). However, recalibration of the Pooled Cohort Equations did not improve risk estimates. These results suggest recalibration is feasible but dependent on the model used. In the second study, sex-specific laboratory models were developed and internally validated for atherosclerotic cardiovascular disease in 3,995,218 individuals. The C-statistic was 0.77 in women and 0.72 in men with less than 2% relative difference between mean predicted and observed risks. External validation in 31,707 primary care patients demonstrated C-statistics of 0.72 in both sexes and less than 15% relative difference between mean predicted and observed risks. This suggests cardiovascular risk can be predicted without clinical risk factors which may simplify risk estimation in routine clinical practice. In the final study, among 7,496,165 individuals followed for 11 years, the rate of incident atherosclerotic cardiovascular disease defined by a myocardial infarction, stroke, or circulatory death event was 3.95 per 1000 person-years. When including unstable angina, transient ischemic attack, heart failure, peripheral arterial disease, coronary revascularization, and out-of-hospital cardiac arrest events, the rate was almost doubled at 6.67 per 1000 person-years. The most common additional manifestations were heart failure (12.0%) and coronary revascularization (12.7%). Therefore, atherosclerotic cardiovascular disease accounts for just over half of all incident cardiovascular disease manifestations. This suggests broader endpoints may enhance risk-discussions with patients and improve informed decision-making.

Keywords: Atherosclerotic Cardiovascular Disease
Primary Prevention
Risk Prediction
Statins
Advisor: Ko, Dennis T
Quantum State and Unitary Complexity

Many natural problems in quantum computing involve constructing a quantum state or implementing a unitary transformation. However, relatively little is known about the computational complexity of these problems compared to that of computing boolean functions. In this thesis we do the following:• We prove upper bounds on the complexity of constructing arbitrary states and implementing arbitrary unitaries with the help of a classical oracle. • We prove bounds on the complexity of computing parity in QAC0, a quantum analogue of AC0, by way of a reduction to the task of constructing a certain type of state. • We prove upper bounds on the circuit size and depth required to construct arbitrary states and implement arbitrary unitaries, in various quantum circuit models. Many of these bounds are tight. • We define models of interactive proofs for constructing states and implementing unitaries with the help of an untrusted prover. We prove a quantum state analogue of the inclusion PSPACE ⊆ QIP, and obtain somewhat analogous results for unitaries and with multiple entangled provers. • We present barriers to improving several of the above results.

Keywords: circuit complexity
interactive proofs
quantum complexity
quantum state
query complexity
unitary transformation
Advisor: Rossman, Benjamin
Yuen, Henry
Device Placement Optimization with Deep Reinforcement Learning

With the proliferation of machine learning, deep neural networks (DNNs) have become ubiquitous in various real-world applications, and their sizes have become increasingly massive. In order to train DNNs with hundreds of millions of parameters, it is customary to employ a cluster of accelerators, such as GPUs and TPUs, to expedite the training process. As such, there is a pressing need to coordinate the accelerators for efficient DNN training, which gives rise to the device placement problem. Recently, deep reinforcement learning (DRL) has been proposed as an approach to fully automated and effective device placement optimization. In this dissertation, we examine critical research problems concerning the utilization of DRL for discovering optimal device placements for training complex and large DNNs. We begin by reviewing some key concepts, unique properties, and principles of distributed machine learning and DRL. Then we present EAGLE to generate device placement for large deep neural networks. Specifically, EAGLE is an end-to-end framework that groups and places the operations of a deep neural network via two jointly trained policy networks. An advanced DRL algorithm proximal policy optimization (PPO) is applied to achieve better sample efficiency. In addition to EAGLE, we propose Mars, to further improve the granularity and generalizability of the DRL agent. Mars pre-trains a graph neural network with contrastive learning, to generate comprehensive embeddings for each operation. Then, the placer can easily decide the placement for each operation based on its embedding. Lastly, we study the device placement problem in a pipeline parallelism setting, where model parallelism and data parallelism are combined to speed up the DNN training. Specifically, we carefully redesigned the action space of the DRL agent for pipelined device placement, especially for the placement of multi-branching DNNs. We conducted extensive experiments on different DNN training workloads, and our experimental results demonstrated that our approach effectively achieves the highest speedup for various DNN training workloads.

Keywords: Deep Reinforcament Learning
Distributed Machine Learning
Advisor: Li, Baochun
Leaving Long-Term Care during a Global Pandemic: Decision-Making and Experiences of Residents, Care Partners, and Health Professionals in Ontario

The COVID-19 pandemic exposed pre-existing vulnerabilities in long-term care (LTC) sectors globally, prompting a change in the decision-making and care trajectories of many residents. In Ontario, some care partners responded to the crisis in LTC by moving residents home with them for the duration or a portion of the pandemic. This type of care transition, from LTC to home care, was previously uncommon and complex to arrange due to the multiple stakeholders involved. This thesis aims to explore the nature of individual and group decision-making during periods of crisis and change. The research comprises a scoping review and an exploratory qualitative study. Findings are presented across three interconnected papers. Paper 1 is a scoping review that synthesizes existing knowledge on institutional care transition planning from the perspectives of the care triad (i.e., older adults, care partners and health professionals). 39 articles were included and stakeholders’ perspectives on, and involvement in, care transition planning is discussed. Seven factors appeared to guide decision-making: (a) institutional priorities and requirements; (b) resources; (c) knowledge; (d) risk; (e) group structure and dynamic; (f) health and support needs; and (g) personality, preferences and beliefs. Papers 2 and 3 present a qualitative description of the care triad’s transition decision-making in Ontario’s LTC settings during the COVID-19 pandemic. Interviews were conducted with 3 residents, 18 care partners, and 11 health professionals. Paper 2 discusses stakeholder involvement in care transition planning during the pandemic and the factors that guided their decision-making. Decisions to move a resident out of LTC during the pandemic were largely made by care partners, and stakeholders considered each of the seven factors identified in Paper 1. Paper 3 analyzes stakeholders’ decision-making through the lens of Crisis Decision Theory. Individual and group differences in how participants assessed the severity of the crisis and evaluated response options were identified. Overall, this thesis demonstrates the complexity of care transition planning from multiple perspectives. The findings provide insights towards individual and group decision-making in crisis situations, and can be used to better support Ontarians through LTC to community transitions, particularly in event of future pandemics.

Keywords: Aging
Care Transition
COVID-19
Crisis
Decision-Making
Long-Term Care
Advisor: Kuluski, Kerry
Aberrant Synaptic Function in Mouse Models of Disease-associated GRIN1 Genetic Variants of the NMDA Receptor

N-methyl-D-aspartate receptors (NMDARs) are tetrameric ligand-gated ion channels that participate in excitatory synaptic transmission by allowing Na+, K+, and Ca2+ to permeate through their channel. NMDARs are composed of two obligatory GluN1 subunits and two GluN2 (A-D) subunits. Therefore, mutations in the obligate GluN1 subunit can manifest as a wide-range of neurodevelopmental phenotypes, emphasizing the importance to investigate the underlying pathophysiology. Genetic variants in GRIN1, the gene encoding the GluN1 subunit, have been identified in a considerable number of individuals affected with GRIN variants through whole exome sequencing. Two such de novo missense variants in GRIN1, c.1858G>C/A and 2479G>C/A, result in the substitution of a glycine to an arginine at amino acid positions 620th (G620R) and 827th (G827R) of GluN1, respectively. Although functional analysis using recombinant systems has demonstrated deficits in NMDAR function, the impact of both variants on synaptic function in a native physiological context remains unknown. In this thesis, electrophysiological recordings – both extracellular field potential and whole-cell patch clamp – were made in acute hippocampal slices prepared from adult (8-12 weeks) transgenic mice mimicking the G620R and G827R missense variants found in patients in order to assess the physiological consequences of these Grin1 variants on NMDARs and synaptic functions. The Grin1-G620R variant significantly impaired NMDAR-mediated synaptic transmission and plasticity without affecting circuit formation or basal synaptic transmission in the CA1 hippocampus. Reduced NMDAR transmission caused by the Grin1-G620R variant was accompanied by reduced GluN2B activity and altered channel kinetics. However, Grin1-G620R did not affect NMDAR expression at the synapse or voltage-dependent magnesium block. The Grin1-G827R variant also significantly diminished NMDAR function. This phenotype was resulted from a reduced synaptic NMDAR expression, suggesting that GluN1-G827R containing NMDARs fail to assemble or traffic to the synapse. Interestingly, NMDAR dysfunction in Grin1-G827R variant mice was accompanied by an enhancement of presynaptic release probability.

Advisor: Collingridge, Graham
Comparing Canada's Antigonish Movement and Farm Radio Forum: Economic, Technological, and Social Factors

The Antigonish movement and Canada’s Farm Radio Forum were two acclaimed adult education initiatives that helped thousands of Canadians address rural problems in the mid-20th century by promoting self-help initiatives such as cooperatives. The Antigonish movement operated through the St. Francis Xavier University Extension Department in Nova Scotia, during the 1930s and 1940s. Farm Radio Forum began broadcasts in 1941 under the joint sponsorship of the Canadian Association for Adult Education, the Canadian Federation of Agriculture, and the Canadian Broadcasting Corporation, and ran until 1965. Typically, literature presents the two movements as similar examples of a critical Canadian adult education tradition. However, scholars have not, to date, compared them, particularly in terms of how they were impacted by economic, technological, and social factors. Considering the postmodern turn taken by some historians of adult education in recent decades, this dissertation takes a more nuanced historical materialist approach that accepts that many factors interact to produce the historical phenomena we study. The study asks: What can a comparison of the and Farm Radio Forum in terms of how they were impacted by economic, technological, and social factors tell us about the similarities—and differences—between these two adult education movements? iii The comparison was carried out by exploring the economic, technological, and social backgrounds of each movement. Archival and secondary source materials were then examined and analyzed to identify reflections of background factors in the education the movements provided. A focus on education about cooperatives was used to set parameters for the study. The research found that economic, technological, and social factors significantly impacted the purposes of each movement, the choice of topics for discussion, and the tone adopted for presenting information. Most telling among the findings was that the Antigonish movement provided answers to discussion questions, but Farm Radio Forum did not, preferring to let participants arrive at their own conclusions. Many of the differences can be traced back to constraints imposed by the Farm Radio Forum three-party sponsorship arrangement and the often conflicting economic, technological, and social perspectives it embodied. More generally, the dissertation demonstrates the value of a materialist approach to understanding historical developments in adult education. The study supports future research into Canadian adult education history that focuses on economic, technological, and social factors to return the field to its critical tradition.

Keywords: adult education in Canada
Antigonish movement
economic factors
Farm Radio Forum
philosophy of education
technological factors
Advisor: Vieta, Marcelo
Refining Prognostication in Resected Colorectal Cancer: The Role of Emerging Clinicopathologic Features

Clinical practice guidelines have been developed to optimize oncologic care and outcomes for patients with colorectal cancer (CRC). Prognostication relies heavily on the universally adopted Tumour-Node-Metastasis (TNM) staging system, which also helps guide clinical decision-making regarding therapeutic modalities. However, the ability of TNM staging to account for patient or tumour heterogeneity remains limited, which may lead to prognostic inaccuracies and inappropriate therapeutic strategies. I hypothesized that refined assessment of other emerging clinical and pathologic features may improve prognostication beyond that provided by TNM staging alone for CRC. To address this, I generated a comprehensive clinicopathologic database of patients who underwent resection of primary CRC at a quaternary care centre during a 20-year period. A subset of included cases further underwent histopathology review by experienced gastrointestinal pathologists. In concordance with established quality-of-care indicators and the evolution of multimodal treatment for CRC, significant changes in the use of neoadjuvant and adjuvant therapies were observed, as well as a striking improvement in lymph node assessment (LNA). Rates of cancer-specific mortality for patients with TNM stage I-III disease were excellent but have not significantly improved over the last few decades, suggesting that the management and outcomes of locoregional CRC have plateaued. In contrast, 5-year disease-specific survival of metastatic CRC has improved from 13% to ~30% over this span, likely owing to advancements in systemic therapeutic options and the use of metastasectomy. Furthermore, TNM staging alone insufficiently discriminated prognosis for specific substages. Generalizability of pathological features emerging as independently prognostic remains limited due to variability in their assessment. I further characterized the roles of powerful prognostic features in CRC, including venous invasion (VI) and tumour budding (TB). The use of elastin staining markedly improved the detection of VI and enabled identification of unique features that impact prognosis. Moreover, we discovered elements of TB assessment can be further optimized to refine the prognostic role of this biological process. These findings endorse the routine consideration of additional histopathologic features, when optimally assessed, to enhance the accuracy of survival and recurrence predictions for CRC patients, and to facilitate more strategic use of adjuvant therapies and surveillance strategies.

Advisor: Swallow, Carol J