VictorJuiz/thesis huggingface dataset:
Unsettling White Settler Subjectivity in Social Justice Education: Towards a Pedagogy of Risk

This thesis explores the co-constitutive connections between colonial violence and white settler subjectivity in order to highlight the responsibilities that white settlers have in addressing the death, disappearance, and usurpation of Indigenous land and/or life. The three chapters are guided by the assertion that the “issue” at the heart of Indigenous-Settler relations in Canada is not simply settler ignorance or a lack of empathy but access to land and resources. Operating from this perspective, the thesis proposes that white settler subjects are not simply implicated in settler colonialism but also created by it. As such, the thesis rejects a rationalist approach to improving intersubjective relations through “knowing the other” and instead proposes a political and/or educational approach that invites learners to, in a sense, risk themselves and their power by unsettling their psycho-affective investment in the settler colonial project and white settler subjectivity itself.

Keywords: Education
Philosophy
Race
Settler Colonialism
Social Justice Education
Subjectivity
Advisor: Cannon, Martin J
FPGA Logic Block Architectures for Efficient Deep Learning Inference

Reducing the precision of deep neural networks can yield large efficiency gains with little or no accuracy degradation compared to single-precision floating-point representation. A wide range of precisions fall on the pareto-optimal curve of hardware efficiency vs. accuracy with no single precision dominating, making the variable precision capabilities of field-programmable gate arrays (FPGAs) very valuable. This thesis proposes six FPGA logic block architectures that improve the area efficiency of multiplications and additions implemented in the soft fabric. Increasing the look-up table fracturability and adding two adders to the adaptive logic module leads to a 1.5x area reduction for machine learning (ML) kernels and increases their speed, while simultaneously reducing the area of general applications by 6%. On the other hand, adding a 9-bit shadow multiplier to logic blocks reduces ML kernels' area by 2.4x and critical path delay by 1.4x, but increases the area of general applications by 15%.

Keywords: deep learning
deep neural networks
field-programmable gate arrays
inference
logic blocks
low-precision
Advisor: Betz, Vaughn
Late Interventions in SNX Rats Reveal a Disconnect between GFR and Proteinuria

Many animal studies investigate therapies in the prevention setting and report proteinuria as the primary efficacy outcome, while the late intervention setting is more representative of human therapy and glomerular filtration rate (GFR) is more important than proteinuria. In this study, we used the subtotal nephrectomy (SNX) model, one of the few models that exhibits progressive GFR decline along with proteinuria, hypertension, glomerulosclerosis and tubulointerstitial fibrosis. To allow for development of kidney disease, we intervened six weeks after surgery with therapies known to be effective in the prevention setting. Both ACE inhibition (enalapril) and SIRT1 activation (SRT3025) reduced proteinuria, but only ACE inhibition reduced structural damage and neither improved GFR contrary to their effects in the prevention setting. These results demonstrate the difference in therapeutic efficacy in prevention versus late intervention, and show that in the SNX model, GFR, proteinuria, and structural damage are not inextricably linked.

Keywords: ACE inhibitor
Chronic Kidney Disease
Glomerular Filtration Rate
Proteinuria
SIRT1
Subtotal nephrectomy
Advisor: Gilbert, Richard E
The ATCUN Motif as a Paramagnetic Beacon in Fragment-based Drug Discovery

G-protein coupled receptors (GPCRs) constitute a large family of 7-transmembrane domain proteins that transduce extracellular signals to a cell’s interior. Approximately 35% of all FDA-approved drugs target a disproportionally small part of this family. As our understanding of these receptors continues to evolve, developments in drug discovery focus on facilitating the identification of novel orthosteric and allosteric druggable sites. In this work, an attempt was made to employ fragment-based drug discovery (FBDD) for the adenosine 2A receptor (A2AR), expressed in P. pastoris, via electron paramagnetic resonance (EPR). This technique uses unpaired electrons to provide information on conformation, local topology, and dynamics. In this study, spin labeled A2AR ligands were synthesized, in order to observe ligand binding to A2AR and develop a competition assay to observe drug binding. To enhance the magnitude of EPR spectral changes, an amino-terminal copper and nickel binding (ATCUN) motif was installed at the N-terminus of A2AR.

Keywords: adenosine 2A receptor
ATCUN motif
electron paramagnetic resonance
fragment-based drug discovery
G-protein coupled receptor
Advisor: Prosser, Scott
A CFD Study of the Effects of Rings on Flow and Temperature in Lime Kilns

Rotary lime kilns, used in the kraft chemical recovery process to convert lime mud into lime, suffer from the formation of ring-shaped deposits called rings. Prior research has led to better understanding of ring growth, although it is still not fully understood, since the process is concealed within the kiln. For this reason, a steady state, 2D axisymmetric lime kiln, ring, and virtual bed heat sink model has been developed in this work, and was validated by predicting the shell temperature of a real kiln with good accuracy. Various ring configurations were then simulated in a typical lime kiln in order to study their effects on flow and temperature. The results show that ring-related jets and recirculation zones form in the gas, temperature deviations occur upstream and downstream of the rings, and, recarbonation, causing ring hardening, occurs over a wide range of ring thickness for both front-end and mid-kiln rings.

Keywords: CFD
Lime Kilns
Pulp and Paper
Ringing
Advisor: Bussmann, Markus
Tran, Honghi N
Policy-aware Model Learning for Policy Gradient Methods

This thesis studies the problem of learning a model in Model-Based Reinforcement Learning (MBRL). We consider model classes that do not contain a perfect model of the underlying environment, and suggest that model learning should be closely related to how the model will be used. We examine how the planning module of an MBRL algorithm uses the model, and propose that the model learning module should incorporate the way the planner is going to use the model. This is in contrast to conventional model learning approaches that learn a predictive model of the environment without explicitly considering the interaction of the model and the planner. We focus on policy gradient planning algorithms and derive new loss functions for model learning which we call Policy-Aware Model Learning (PAML). We theoretically analyze a generic model-based policy gradient algorithm and empirically evaluate our proposed method on some benchmark problems.

Keywords: Decision-aware
Maximum Likelihood
MDP
Policy-aware
Policy-gradient
Reinforcement Learning
Advisor: Frey, Brendan J
Using Context to Verify Human Intent

We show that all defenses for operating system-level user impersonation attack (OS-UImp) fall preyto a new class of user interface(UI) attacks — Context Forgery (CF). It can be executed by the sameattacker as OS-UImp and cause the same consequence: unintended requests are accepted and executedby services. We design and build AINT to protect users from deceptive UI and capture human intent. AINTcaptures a video recording of the display which contains the rendering and user interactions. Therendering is validated against specifications from the service to ensure UI integrity. To extract humanintent, AINT relies on a non-malicious user to validates her inputs is displayed properly on the screen— a process we call Implicit Confirmation (IC). This allows AINT to extract user inputs from the videorecording and use that as the human intent.

Advisor: Lie, David
A Study of the Role of Organic Acids in Monel Tube Corrosion in Nuclear Industry Steam Generators

Monel 400 tubes in OPG’s Pickering Unit 4 steam generators were found to have undergone dealloying. S, Pb and Cl were not found by Analytical Transmission Electron Microscopy and were hence not causal. Since carbon and associated oxygen were detected near metal-oxide interfaces, the degradation is suspected to be from the build-up of organic acids, due to thermal decomposition of morpholine (added for secondary side cooling water chemistry control). In this thesis, dealloying of Monel was studied in the presence of organic acids and sulfate. Most of the work was done at or near the Cu equilibrium potential, with Cu2+ in solution. Electrochemical tests were conducted on Monel samples in acetic acid, sulfate and formic acid. Cross-sectional SEM-EDX studies showed dealloying and intergranular attack on Monel. It was found that formic acid was the most aggressive, followed by sulfate and acetic acid.

Keywords: Corrosion
Dealloying
Electrochemistry
Monel
Nuclear
Organic acids
Advisor: Newman, Roger Charles
Influence of Chrna5 on Habenulopeduncular Neurotransmission

The habenulopeduncular pathway is known to modulate aversion behaviours, which are tightly associated with Chrna5 gene expression. Chrna5 encodes the α5 nicotinic receptor subunit, which is highly expressed in the interpeduncular nucleus but remains pharmacologically intractable. Here we investigate the impact of this subunit using wild-type and Chrna5-deleted mice. We optogenetically activated the habenulopeduncular pathway; thought to co-release acetylcholine and glutamate, to probe the electrophysiological role of α5 in interpeduncular neurons in acute brain slice. Optogenetic stimulation of this pathway yielded heterogenous responses in wild-type and Chrna5 deleted mice. Unexpectedly, the absence of the Chrna5 gene led to stronger light-evoked glutamatergic and GABAergic neurotransmission. These light-evoked glutamatergic responses were acutely attenuated by nicotinic antagonists in Chrna5 deleted mice. Intriguingly, our optogenetic experiments did not evoke a distinct cholinergic current in either genotype. This work provides insight into the action of Chrna5 on habenulopeduncular circuitry and raises new mechanistic questions.

Keywords: alpha 5 nicotinic receptor subunit
Chrna5
habenula
interpeduncular nucleus
nicotinic receptors
Advisor: Lambe, Evelyn K
AutoVM: Accelerating Convolutional Neural Network Training with Actively Managed GPU Virtual Memory

The size of neural networks a GPU can train is limited by the GPU’s memory capacity. Although GPU virtual memory enables training arbitrarily large neural networks, such trainings are often accompanied by severe performance penalties. Furthermore, popular frameworks for constructing machine learning applications, like TensorFlow, have disabled using GPU virtual memory by default. We propose AutoVM, a software layer that can better manage GPU virtual memory in neural network training by incorporating our understandings of neural networks. AutoVM schedules data transfers between GPU and CPU memory to relieve the memory pressure on GPU; and in turn optimizes training speed. We have integrated AutoVM into TensorFlow such that existing machine learning applications can benefit from AutoVM with minimal effort. Our tests suggest that training VGG-19 using AutoVM can be at most 2.5× faster compared to using default Nvidia virtual memory.

Keywords: CUDA
GPU
High performance computing
Machine Learning
Memory management
Advisor: Stumm, Michael
The Impact of Radiofrequency Ablation on the Quality of Healthy and Metastatically Involved Bone

Bone is third most frequent diagnosed site for cancer metastasis. Bone remodeling is dysregulated in the presence of metastases, resulting in regions exhibiting excess bone-formation (osteoblastic), excess bone-resorption (osteolytic) or a mixed involvement of osteolytic and osteoblastic disease. While previous study has characterized the impact of osteolytic and mixed disease on bone quality, considering both the mineral and organic phases of bone, establishing a purely osteoblastic preclinical animal model is necessary to quantify the effect of osteoblastic disease on bone quality. These models of bone metastasis also provide a foundation upon which to study the impact of cancer treatments on bone quality. Image-based methodologies and analytical approaches are utilized in this work to quantify the impact of osteoblastic disease on bone quality in a preclinical rodent model. Further work quantifies the impact of radiofrequency ablation on bone quality in healthy and metastatically involved femora. Overall, this work contributes to a foundation of knowledge from which the relative impact of metastatic disease and its treatments on bone quality will be considered in directing the utilization of systemic and local minimally invasive therapeutic approaches alone or in combination for the treatment of skeletal metastases.

Keywords: Bone Metastasis
Bone Quality
Image Analysis
Material Characterization
Radiofrequency Ablation
Rodent Model
Advisor: Akens, Margarete K.
Zipper Codes: High-rate Spatially-coupled Codes with Algebraic Component Codes

Zipper codes, a new framework for describing spatially-coupled product-like codes, are introduced. This framework encompasses many types of codes such as staircase codes and braided block codes. New types of codes such as tiled and delayed diagonal zipper codes are also introduced. Simulation results show that these new type of codes achieve comparable performance to staircase codes while requiring less memory. This thesis also analyzes the types of stall patterns that can arise in zipper codes and how they affect the error floor. Finally, the impact of error-and-erasure decoding in zipper codes is also studied. Software simulation results show that adding erasure symbols improves the coding gain by around 0.1 dB with only a small increase in memory overhead and decoding complexity.

Advisor: Kschischang, Frank R
An Ecological Approach to Engaging Refugee Language Learners in the ESL Classroom

In this case study, the principles of Miller and Rasco’s (2004) ecological approach to supporting the mental health of refugees formed the basis of an intervention which was implemented in an ESL course for adult refugee English language learners (ELLs). Using action research methodology, the study investigated learners’ perceptions of the effect of the intervention on their engagement. Activities that attended to learners’ needs, were personally relevant, equipped them with tools for learning, and promoted relatedness to others were among the facets of the intervention that participants perceived as most supportive of their engagement. The findings confirm the compatibility of the ecological model with the recommendations in the literature on supporting refugee ELLs, and its suitability in providing a strengths-based, trauma-sensitive framework for supporting their engagement. The study concludes by calling for structural changes which would facilitate a more holistic approach to accommodating refugee learners in the Canadian ESL classroom.

Keywords: Ecological approach
Engagement
ESL
Mental health
Practical action research case study
Refugee
Advisor: Kerekes, Julie
Le Pichon-Vorstman, Emmanuelle
Adaptation to Climate in Space and Time

Many species evolve adaptive clines in response to climatic gradients. This thesis investigated adaptation to climate across environmental gradients through time using cyanogenesis (release of HCN upon tissue lysis) in Trifolium repens as a model. First, adaptive responses to recent and rapid climate change were tested. No clear evidence of adaptation to climate change through time was found. Second, the continued evolution of cyanogenesis in T. repens’ introduced range was tested. Although the strength of cyanogenic clines did not increase through time, some evidence of continued adaptation was detected but not as predicted. Finally, the importance of herbivory in maintaining the cyanogenic polymorphism was tested. Higher frequencies of cyanogenesis in lower latitude populations appear to decrease herbivory in these populations in T. repens’ native range. Together these results provide information about the pace at which adaptation in this system is proceeding and the importance of cyanogenesis as an antiherbivore defense.

Keywords: adaptation
climate change
clines
introduced species
temperature
Trifolium repens
Advisor: Johnson, Marc TJ
The Effect of Simulated Human Salivary Enzymes and Matrix Metalloproteinase (MMP) Inhibition on the Degradation of the Total-etched Resin-dentin Interface

Background: Oral esterases and dentinal matrix metalloproteinases (MMPs) contribute to interfacial degradation of composite restorations, compromising structural integrity, and longevity. Hypothesis: MMP inhibition modulates simulated human salivary esterase (SHSE) degradation of mechanical performance parameters for composite-dentin bonds with total-etched adhesives. Objective: Assess effect of SHSE and MMP inhibition on biostability, interfacial fracture toughness (FT), and failure mode (FM) for total-etched resin-dentin interfaces. Methods: FT and FM analyses were performed on mini short-rod FT specimens (N=10/group), prepared with Scotchbond MP, with/without MMP inhibition (galardin), after incubation for up to 180 days in phosphate buffered saline (PBS) or SHSE. Results: The amount of a resin degradation biomarker, Bis-hydroxypropoxyphenylpropane (BisHPPP), was higher for SHSE vs. PBS incubated specimens. FT after 180-days in SHSE, with/without galardin, were significantly lower (0.71±0.2 MPa√m) than non-inhibited 0-day specimens (1.06±0.4 MPa√m). Galardin slowed down the trend of change in fracture mode from composite/adhesive into hybrid layer over time.

Keywords: Esterases
Fractography
Interfacial fracture toughness
Matrix metalloproteinases (MMPs)
Resin-dentin interface
Total-etch adhesive
Advisor: Finer, Yoav
Influence of Baseline Global Longitudinal Strain Measurements on Left Ventricular Functional Outcomes in Children Treated with Anthracycline Chemotherapy

Pediatric cancer patients who receive anthracycline chemotherapy are at risk for developing cardiac dysfunction during and after treatment. Global longitudinal strain (GLS) has been proposed as a sensitive marker of early myocardial changes in adults. We examined the significance of a lower baseline GLS in children with cancer. Echocardiograms were performed at baseline, before each subsequent dose of anthracycline, and 12 months after treatment completion. A total of 176 pediatric cancer patients were included in our analyses. Patients who presented with a lower baseline GLS (17.2 ± 1.5%) had improved GLS at 12-months post- treatment (19.6 ± 2.6%), p=0.004. Overall, no difference in left ventricular systolic function was observed during and after anthracycline treatment between patients with a lower baseline GLS compared with age- and cancer diagnosis-matched patients who had higher baseline GLS. These suggest that lower baseline GLS values should not preclude pediatric cancer patients from receiving anthracycline chemotherapy.

Keywords: Anthracycline
Cardiac Biomarker
Clinical Epidemiology
Echocardiography
Global Longitudinal Strain
Pediatric Oncology
Advisor: Mertens, Luc
Primary Care use during, and Wait Times to Receiving, Adjuvant Breast Cancer Chemotherapy: A Population-based Retrospective Cohort Study using CanIMPACT Data

OBJECTIVES: To determine how physical and/or mental comorbidities affect primary care physician (PCP) use during adjuvant breast cancer chemotherapy and how PCP continuity affects time to chemotherapy. METHODS: Population-based, retrospective cohort study of 12,781 women diagnosed with stage I-III breast cancer in Ontario who received adjuvant chemotherapy. RESULTS: Six-month PCP visit rate increased during chemotherapy (mean 2.3 baseline visits, 3.4 chemotherapy visits). Low physical/mental comorbidity patients saw larger increases (1.4/1.8 baseline, 2.8/3.0 chemotherapy) versus high physical/mental comorbidity (5.6/3.5 baseline, 5.3/4.1 chemotherapy). Median time to chemotherapy (126 days) was shorter by 3.21 days in symptom-diagnosed patients with low PCP continuity, 17.43 days in screen-diagnosed immigrants with high PCP continuity and 10.68 days in symptom-diagnosed patients with no baseline PCP utilization. CONCLUSIONS: Patients with low physical and/or mental comorbidity showed greater increases in PCP use during adjuvant chemotherapy. Higher PCP continuity was associated with shorter median time to chemotherapy in screen-diagnosed immigrants.

Keywords: Adjuvant chemotherapy
Breast cancer
Primary health care
Time to treatment
Advisor: Lofters, Aisha
Grunfeld, Eva
Predicting Hospital Readmission and Assessing the Cost-Effectiveness of Post-Discharge Intervention Programs

Hospital readmissions are common, costly, and impose a difficult challenge for hospitals to address in the face of increasing costs and budgetary constraints. In this thesis, we develop readmission prediction models for seven clinical programs at the University Health Network using only data available shortly after patient discharge to provide a 30-day unplanned readmission risk prediction. We conduct sensitivity analysis to assess the model performance under varying operational complexity and show improved performance can be achieved using simpler models with a careful selection of predictors. Additionally, we investigate the use of readmission risk predictions in design of cost-effective intervention programs. Specifically, we answer the question of whether a hypothetical intervention program implemented over a period of time in the past with some cost and efficacy level would have been cost-effective or not. Our results demonstrate that cost-effective intervention programs are possible through the use of more targeted intervention strategies using predicted readmission risks.

Advisor: Sarhangian, Vahid
Preclinical Validation and Clinical Translation of Transrectal Diffuse Optical Tomography for Monitoring Prostate Cancer Photothermal Therapy

Continuous-wave diffuse optical tomography in transrectal configuration (TRDOT) has been developed to monitor photocoagulation front progression to achieve tumor ablation while avoiding rectal damage during photothermal therapy of localized prostate cancer. The TRDOT system can reconstruct optical properties of coagulation lesions, namely the absorption and reduced scattering coefficients, in phantoms and canine models in vivo. The TRDOT system is sensitive to porphysome accumulation in the tumor in vivo with approximately a 10-fold increase in absorption property in a canine tumor model. Reconstruction of lesion sizes is mostly within a spatial resolution of 1 mm, which is considered necessary for clinical translation. Clinical safety and technical feasibility of the TRDOT system in prostate cancer patients have been demonstrated for the first time. Further improvements in system performance, particularly to increase the scan speed during treatment, are in progress. This work is supported by the Terry Fox Research Institute (grant #1075).

Keywords: Diffuse Optical Tomography
Image Reconstruction
Optical Property
Photothermal Therapy
Prostate Cancer
Transrectal
Advisor: Wilson, Brian C.
Weersink, Robert A.