VictorJuiz/thesis huggingface dataset:
AutoVM: Accelerating Convolutional Neural Network Training with Actively Managed GPU Virtual Memory
Keywords: CUDA
GPU
High performance computing
Machine Learning
Memory management

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.
The Impact of Radiofrequency Ablation on the Quality of Healthy and Metastatically Involved Bone
Keywords: Bone Metastasis
Bone Quality
Image Analysis
Material Characterization
Radiofrequency Ablation
Rodent Model

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.
An Ecological Approach to Engaging Refugee Language Learners in the ESL Classroom
Keywords: Ecological approach
Engagement
ESL
Mental health
Practical action research case study
Refugee

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.
Adaptation to Climate in Space and Time
Keywords: adaptation
climate change
clines
introduced species
temperature
Trifolium repens

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.
The Effect of Simulated Human Salivary Enzymes and Matrix Metalloproteinase (MMP) Inhibition on the Degradation of the Total-etched Resin-dentin Interface
Keywords: Esterases
Fractography
Interfacial fracture toughness
Matrix metalloproteinases (MMPs)
Resin-dentin interface
Total-etch adhesive

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.
Influence of Baseline Global Longitudinal Strain Measurements on Left Ventricular Functional Outcomes in Children Treated with Anthracycline Chemotherapy
Keywords: Anthracycline
Cardiac Biomarker
Clinical Epidemiology
Echocardiography
Global Longitudinal Strain
Pediatric Oncology

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.
Primary Care use during, and Wait Times to Receiving, Adjuvant Breast Cancer Chemotherapy: A Population-based Retrospective Cohort Study using CanIMPACT Data
Keywords: Adjuvant chemotherapy
Breast cancer
Primary health care
Time to treatment

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.
Preclinical Validation and Clinical Translation of Transrectal Diffuse Optical Tomography for Monitoring Prostate Cancer Photothermal Therapy
Keywords: Diffuse Optical Tomography
Image Reconstruction
Optical Property
Photothermal Therapy
Prostate Cancer
Transrectal

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).
High Performance Fiber Optic Gyroscope-based Attitude Determination and Control System for Autonomous Terrestrial Target Tracking using Small Satellites
Keywords: Fiber Optic Gyroscopes
Kalman Filter
Satellites
Space Exploration
Spacecraft Dynamics and Control
State Estimation

This thesis provides an engineering framework for designing an advanced Attitude Determination and Control Subsystem (ADCS) for small satellite-enabled autonomous target tracking applications from low-Earth orbit requiring a pointing accuracy of ±0.1° (2-σ) and stability of ±0.05 °/s or better. Current Earth-observation satellites designed and built at the University of Toronto Space Flight Laboratory (SFL) are capable of constraining the satellite's fine-pointing accuracy to ±0.3° (2-σ) during terrestrial-target tracking maneuvers. Leveraging high-grade miniaturized and commercially-accessible fiber optic gyroscopes (FOGs), an advanced ADCS compatible with SFL's Next-generation Earth Monitoring and Observation (NEMO) bus and similar micro-satellite platforms, is being developed at the Space Flight Laboratory. High-frequency gyro measurements are used to augment lower-cadence star tracker solutions in an extended Kalman filter, providing superior attitude and rate estimates. To assess the absolute pointing performance of this FOG-based control system, high-fidelity ground-based target tracking simulations were conducted for fixed and moving targets.
Closing the Gap: Comparing Reconciliation and Indigenismo Policies in Higher Education
Keywords: access and success
canada
higher education
indigenous students
mexico
policy

Education is a critical human right, yet Indigenous groups globally face a crisis in higher education (HE) systems. Colonial processes have intentionally and systematically used HE for assimilation which has disrupted cultural connection and economic benefits to Indigenous communities. Drawing on Postcolonial Theory (Loomba, 2002) and the Theory of Justice (Fraser, 2003), this policy review explores factors that have contributed to the pattern of HE exclusion and comparatively poorer outcomes for Indigenous groups in Canada and Mexico. These frameworks will be used to evaluate a range of policies that aim to remedy these gaps. The results indicate that there was a considerable attempt to adopt the principles of Reconciliation and Indigenismo when responding to the needs of Indigenous students. However, the policies do little to redress the racist constructs that are inherent to colonial education, impacting chances for transformative change for Indigenous students.
Investigating the Role of alx-3 in Neuronal Specification in the Freshwater Planarian Schmidtea mediterranea
Keywords: neurogenesis
planarian
regeneration
stem cells

The freshwater planarian Schmidtea mediterranea is capable of producing new neurons to regenerate the brain following loss or injury. This amazing feat of neurogenesis transpiring in an adult organism is in stark contrast to the devastating impact and minimal recovery occurring following damage to the human brain. This thesis aimed to investigate mechanisms governing the specification of stem cells towards a neuronal identity. Here I investigated the expression and function of the paired-like homeobox transcription factor alx-3, whose expression is enriched in planarian stem cells with neuronal character. My results provide support to the hypothesis that alx-3 functions to commit stem cells towards the neural lineage.
Similar Patterns of Spatial Learning as a Result of Individual Differences In Navigational Strategy and Map Use Attributed to The Role of Scene-independent Relational Processing
Keywords: Hippocampus
Individual Differences
Map
Memory
Spatial Learning
Spatial Navigation

Background: Map study (MS) and perspective-taking (PT) can result in differences in scene-independent (SI) or scene-dependent (SD) knowledge, and a tendency to rely on either SI or SD relations can result in more rapid learning or more accurate knowledge, respectively. This work studies effects of strategy on spatial learning, comparing effects of map display design. Method: Part 1 comprised a MS task and Part 2, a PT task in virtual reality. In Part 2, participants assigned to one of three map display conditions viewed the MS objects from Part 1, learning the locations of two new objects. Study blocks were followed by judgements of relative direction and map drawing from memory. Conclusions: Findings suggest that differences in strategy determined by the Navigational Strategies Questionnaire can predict differences in spatial learning, and that PT with a track-up map results in a similar learning trend as MS when using a SI strategy.
Does Pre-cessation Physical Activity Impact Smoking Treatment Outcomes? A Longitudinal Study of Treatment-seeking Smokers in the General Population
Keywords: Exercise
Nicotine Replacement Therapy
Physical Activity
Smoking Cessation

Objectives: This study determines whether pre-cessation physical activity behavior is associated with either smoking cessation or tobacco harm reduction. Methods: Data were collected from a longitudinal study of treatment-seeking smokers making a quit attempt after distributing cost-free nicotine replacement therapy. Logistic regression analyses were used to determine the association between pre-cessation physical activity behavior and smoking treatment outcomes. Results: There was no association between pre-cessation physical activity and smoking abstinence. However, smokers that engaged in physical activity for ≥ 3 days were associated with significantly greater odds for achieving significant smoking reduction at 3 months (AOR = 1.48, 95% CI [1.102 – 1.989], p = 0.009), 6-months (AOR = 1.62, 95% CI [1.195 – 2.187], p = 0.002) and 12-months (AOR = 1.76, 95% CI [1.290 – 2.411], p
Development, Testing and Optimization of a Pico Hydro Turbine for Pressure Regulation and Energy Harvesting
Keywords: Computational Fluid Dynamics
Design of Experiments
Energy Harvesting
Guide Vanes
Pico Turbine
Pressure Regulation

Pressure control valves (PCVs) are conventional devices used to regulate the downstream pressure of a hydraulic process. However, 34% of the pumped energy is typically lost when the flow is throttled by the PCVs. An Energy Harvester consisting of a pico-scale (
The Role of Type VIII Collagen in Atherosclerotic Plaque Stability
Keywords: Atherosclerosis
Calcification
Cardiovascular
Inflammation
Type VIII Collagen

Type VIII collagen (Col8) expression is significantly elevated in atherosclerosis. To study the role of Col8 in atherosclerosis, plaques from Col8+/+ ;ApoE-/- and Col8-/- ;ApoE-/- mice fed a high fat diet for 24-26 weeks were analyzed. Compared to Col8+/+ ;ApoE-/- mice, brachiocephalic plaques from Col8-/- ;ApoE-/- mice had increased features of plaque vulnerability with a significant increase in intraplaque hemorrhage and trends towards reductions in fibrous cap thickness and increased elastin breaks. Col8-/- ;ApoE-/- brachiocephalic plaques had significantly increased macrophage content and MMP expression. Col8-/- ;ApoE-/- mice had significantly increased circulating monocytes, and monocyte bead-labelling experiments suggest a trend towards increased monocyte recruitment to Col8-/- ;ApoE-/- plaques. This study identified a role for Col8 in vascular calcification. Lesser curvature plaques in Col8-/- ;ApoE-/- mice had significantly reduced calcification and markers of osteochondrogenesis, including type II collagen, BMP-2 and osteopontin. Altogether, this data suggests Col8 is essential to promoting plaque stability.
Exploring the Urban Forest: Evidence of Tree Condition Change across Toronto’s Environmental Gradient
Keywords: Canopy condition
Ecosystem services
Exotic species
Land cover
Urban gradient
Urban tree

Increasing urbanization creates environmental impacts on flora, fauna, and human populations. Urban trees provide mitigating services that may be maximized by understanding environmental stressors that impact tree health. I explored the relationship between tree condition and urban landcover as evidence of urban stressors. Tree morphology, canopy condition, and insect abundance were expected to vary across an urban land cover gradient, at different spatial scales, and between native/exotic species. These responses were explored in Tilia americana, Tilia cordata, Acer platanoides and Acer saccharnium in Toronto, Ontario, Canada. Specific spatial scales and environmental variables better explained changes in tree response variables. My results suggest Tilia species were more tolerant of urban conditions. Differences between species were described by genera suggesting species trait similarity may determine environmental suitability. Maximizing service provision requires interspecific stress expression consideration. Further research will explore soil conditions, socio-economic factors, and environmental remote sensing in urban tree condition modelling.
Electrochemical Impedance Spectroscopy Based Power-mix Control Strategy for Improved Second-life Battery Performance
Keywords: Battery
Electric Vehicle
Electrochemical Impedance Spectroscopy
Lithium-Ion
Off-Grid
Second-Life

Providing degraded Electric Vehicle (EV) batteries with a second-life when they no longer meet vehicle energy and power requirements has the potential to increase the value of the battery and reduce the total cost of ownership for the EV owner. This thesis focuses on increasing the value that can be extracted from second-life lithium-ion EV batteries used in off-grid stationary-storage applications. Battery modeling is performed using impedance data measured using Electrochemical Impedance Spectroscopy (EIS), and a method to perform EIS measurements online is demonstrated. A control strategy is presented to control the power flow between battery modules at different States-ofHealth (SOH) in an off-grid application in order to reduce the total battery degradation rate. Simulations of the off-grid system show that, on average, the proposed strategy results in a 56% increase in battery system lifetime. Operation of the control strategy is demonstrated experimentally using two custom 3.85kWh battery modules.
Renewable Monomers for 4D Printing
Keywords: 3D Printing
additive manufacturing
furfural
furfuryl alcohol
lignin
renewable

In the automotive industry, 3D printing has the potential to build low volume parts. Glass fiber reinforced phenolic composites are suitable for electric vehicle battery enclosures, but condensation resins have not been adapted to 3D printing. Step growth condensation polymerization is not compatible with popular photo-curing 3D printing techniques. This research presents a novel lignin-furfural-furfuryl alcohol blend developed specifically for two-component, acid-catalyzed, thermoset gel extrusion 3D printing, which utilizes exothermic heat of crosslinking as the 4th controllable dimension. This material was studied as a bio-based replacement for phenolic resin in the application of battery enclosures. A thermoset with high zero-shear viscosity and shear thinning ability resists sag upon deposition while remaining pumpable and extrudable. Stroke cure and isoconversional kinetics were applied to set the hardening time and calculate printing temperature and rate. Tall structures (>50 layers) can be printed with high viscosity resins (>1000 Pa*s) at low applied temperature (~50°C).
Identification and Functional Analysis of Novel Genes Associated with Inherited Bone Marrow Failure Syndromes
Keywords: Bone Marrow Failure
DNAJC21
Genetics
SDS

Inherited bone marrow failure syndromes are multisystem-disorders that affect development of hematopoietic system. One of IBMFSs is Shwachman-Diamond-syndrome and about 80-90% of patients have mutations in the Shwachman-Bodian-Diamond-Syndrome gene. To unravel the genetic cause of the disease in the remaining 10-20% of patients, we performed WES as well as SNP-genotyping in families with SDS-phenotype and no mutations in SBDS. The results showed a region of homozygosity in chromosome 5p-arm DNAJC21 is in this region. Western blotting revealed reduced/null protein in patient. DNAJC21-homolog in yeast has been shown facilitating the release of the Arx1/Alb1 heterodimer from pre-60S.To investigate the cellular functions of DNAJC21 we knocked-down it in HEK293T-cells. We observed a high-level of ROS, which led to reduced cell proliferation. Our data indicate that mutations in DNAJC21 contribute to SDS. We hypothesize that DNAJC21 related ribosomal defects lead to increased levels of ROS therefore altering development and maturation of hematopoietic cells.