VictorJuiz/thesis huggingface dataset:
Ultrasound Image-guided, High-intensity Focused Ultrasound for Remote Controlled Modification of Polylactic Acid Films

The intrinsic degradation times of biodegradable polymers are not ideal for many temporary implants. Here, ultrasound-guided, high-intensity focused ultrasound (USgHIFU) was investigated as a remote and precise means to modify the mechanical properties of biodegradable polylactic acid (PLA) films to induce stent failure. USgHIFU delivered for 120 seconds, at a power of 150 watts and 100% duty cycle reduced tensile strength and strain at break of PLA films by 21 ± 9% and 98 ± 55%, respectively. Consistent large strain at break reductions in particular support the potential for stent material failure to be achieved. This reduction was likely due to the creation of defects in PLA films at the target from localized HIFU effects. These results support further investigation of USgHIFU to modify mechanical properties of biodegradable polymer-based structures such that future implants can be removed at time points tailored to meet the requirements of their end applications.

Keywords: High-intensity focused ultrasound
Polylactic acid
Ultrasound
Advisor: Matsuura, Naomi
Novel CAD techniques for Reconfigurable Architectures

Reconfigurable architectures, such as field-programmable gate arrays (FPGAs) and coarse-grained reconfigurable arrays (CGRAs), are popular platforms for realizing application-specific accelerators, where the hardware is tailored to an application’s needs, yielding higher performance and energy efficiency. This thesis presents new CAD techniques for FPGAs and CGRAs, with the aim of reducing circuit cost and reducing CAD tool run-time. The proposed techniques leverage recent advances in machine learning and graph algorithms. The first contribution applied reinforcement learning (RL) to logic synthesis for FPGAs in a bid to reduce area. We demonstrated conclusive signs of learning across a suite of benchmark circuits, as well as the ability to generalize learning following training on a circuit set, followed by inference on a different validation circuit set. The second contribution applies a recently published heuristic algorithm for finding graph minors to the CGRA CAD problem. Results show orders of magnitude speedup in run-time vs. existing CGRA mappers.

Advisor: Anderson, Jason
Active Catheter Tracking Error Characterization for MR-guided Cardiac Interventions

Magnetic resonance imaging is a promising imaging modality for guiding minimally invasive cardiac interventions via tracking of catheters containing active elements. Recent work has shown that a targeting accuracy of <5 mm is desired for effective delivery of cardiac regenerative therapies, and so there is a need to characterize the positional error associated with tracking such devices. This thesis features two experiments, through which comparisons were performed between two different pulse sequences employed to track catheters that were either fixed in place or subject to specific motion profiles. In both studies, the 5 mm error constraint was achieved when using a Hadamard multiplexed active tracking pulse sequence in conjunction with the novel “Joint Peak-Normed Gaussian” localization algorithm. Future work will focus on improving tracking accuracy through pulse sequence and localization algorithm modifications, and performing in vivo error characterization, all for facilitating clinical translation of cardiac interventions requiring MR-guided delivery.

Keywords: Cardiac Regenerative Medicine
Catheters
MRI
Myocardial Infarction
Tracking Error
Advisor: Wright, Graham A.
Elucidating Cell Types Associated with Case-control Differences in Cortical Thickness in Neuropsychiatric Disorders

Case-control differences in cortical thickness are hallmarks of numerous neuropsychiatric disorders; however, the cortical cell types that underlie these differences remain largely unknown. Virtual histology methods aim to identify such cell types through correlating interregional profiles of thickness differences to healthy gene expression. We propose a new method, case-control virtual histology (CCVH), that leverages multi-region, case-control gene expression to find cell types that are differentially abundant in regions with largest differences in cortical thickness. In AD, CCVH found that in such regions, excitatory and inhibitory neurons were relatively less abundant, and astrocytes, oligodendrocytes, oligodendrocyte precursor cells and endothelial cells relatively more abundant in cases relative to controls. Traditional virtual histology indicated that healthy control excitatory neuron abundance was associated with thinner cortex in AD, but inhibitory neuron abundance was not. Our findings imply that CCVH might better identify cell types that are directly responsible for case-control differences in cortical thickness.

Advisor: Tripathy, Shreejoy
Examining the Association Between Mild Behavioral Impairment and Oxidative Stress in Mild Vascular Cognitive Impairment

Mild behavioral impairments (MBI) are neuropsychiatric symptoms that present in a pre-dementia state, such as mild vascular cognitive impairment (mVCI). mVCI is defined by the presence of early cognitive deficits and vascular dysfunction. MBI is a major risk factor for dementia. It has shown association with oxidative stress (OS)-related damage in early stages of cognitive impairment, however, this relationship has never been explored in mVCI, where OS may be more pronounced. This thesis showed that in 28 mVCI participants, anterior cingulate cortex glutathione levels showed no association with MBI-Checklist (MBI-C) scores. However, 12 weeks of exercise, a known antioxidant, significantly decreased MBI-C scores in 32 mVCI participants [t(31)=2.44,p=0.02,d=0.56]; specifically improving apathy, mood and anxiety. Future longitudinal studies with larger sample size and higher MBI-C scores can further explore OS and other neurotrophic and axonal damage markers to better explain exercise’s effects on MBI and learn about MBI’s role in dementia.

Advisor: Lanctôt, Krista KL
Swartz, Rick RS
Health Service Delivery in the Humanitarian-Development-Peace Nexus: Envisioning the Role of International Organizations in Rebuilding Fragmented Health Systems in the Post-conflict Peacebuilding Process

The delivery of health services in conflict-affected states has significant implications for the health and security of communities. However, little evidence regarding the process of rebuilding health systems in the humanitarian context exists. This novel review of the reconstruction process at the Humanitarian-Development-Peace Nexus presents two chapters analyzing the theory and practice of health service delivery in the post-conflict transition. First, a narrative review finds the international community’s process shifts donor-funded health services to state-planned health systems as state institutions stabilize through novel financing and governing mechanisms. Second, a scoping review of post-conflict Essential Packages of Health Services (EPHS) interventions finds significant variations in benefit packages, financing schemes, and government control over contracting mechanisms. Cross-sectoral priorities identified for delivering EPHS interventions post-conflict include stabilizing security from attacks, improving access to financial resources, and mitigating gender disparities. Recommendations call for additional evaluations of EPHS to build evidence supporting peace-responsive health systems.

Keywords: conflict
global health
health services
humanitarian
international organization
peacebuilding
Advisor: Di Ruggiero, Erica
Supporting Grade 9 Students in Destreamed Mathematics Classrooms

This study investigates teachers’ perceptions of the new destreamed Ontario Grade 9 mathematics curriculum. The Ten Dimensions of Mathematics Education serves as a framework through which this case study of four teachers was conducted. Teacher practices and challenges in the implementation of the new curriculum are discussed. The key findings include the need for differentiation in order to accommodate a diverse group of learners, the importance of an open and inclusive classroom environment, and the need for teacher professional development in order to successfully administer the program. Recommendations for further research are also discussed.

Keywords: Case
Destreamed
Differentiation
Grade 9
Mathematics
Teachers
Advisor: McDougall, Doug
The Differential Effect of Early-life Threat and Deprivation on Child and Adolescent Emotional Attention Bias: A Systematic Review

I evaluate differences in the association between experiences of threat and deprivation with attentional biases. In a systematic review of 44 studies, associations with the discrete dimensions of both threat and deprivation with attentional biases were reported. Consistent with hypotheses of the Dimensional Model of Adversity and Psychopathology, threat but not deprivation was generally associated with attentional biases for angry/threatening faces. In contrast, we found that early life adversity seems to be somewhat more consistently associated with a bias away from, rather than towards, angry/threatening faces. Evidence is comprehensively synthesized from studies which utilized the dot-probe task, the emotional Stroop task, the emotional Go-No/Go task, the visual search task, the emotional oddball task, the modified Posner task, as well as tasks that used eye-tracking methods. Results from this review may inform ways to offset mechanistic pathways towards the expression of psychopathology in children and adolescents.

Keywords: Adverse childhood experiences
Attention bias
Child maltreatment
Dimensional Model of Adversity and Psychopathology
Early life adversity
Socioemotional
Advisor: Wade, Mark
Thermal Design and Analysis of a Microsatellite Constellation

In order to address the growing demand of microsatellite constellations, the Space Flight Laboratory has aimed to create repeatable, modular spacecraft designs that can be produced with lower costs and shorter timelines. DEFIANT is a spacecraft platform developed at the Space Flight Laboratory that has been adapted for a constellation mission. Microsatellite constellations present unique thermal challenges calling for innovative thermal design solutions. The thermal design for this mission is one of the many design aspects that has been tuned for a constellation. The thesis will present the thermal design and temperature predictions for spacecraft using either a field-emission electric propulsion system or a water-based resistojet, validated through on-orbit correlations. In addition, a novel thermal modeling approach was proposed to optimize the thermal design for any orbit within an altitude range. With this work, the DEFIANT satellite thermal design has been improved and streamlined, thus enabling the rapid production of future spacecraft to complete this growing microsatellite constellation.

Keywords: Constellation
Heat Transfer
Microsatellite
Spacecraft
Thermal
Advisor: Zee, Robert E
Mulheres, Get on your Bikes!: Critical Consciousness Building and Women’s Cycling Mobility Spaces in Brazil

Over the past decade, cycling groups, collectives, and social projects specifically dedicated to improving the everyday cycling mobility experiences of women have emerged across Brazil. My research categorizes these cycling groups, collectives, and social projects as women’s Cycling Mobility Spaces (CMSs). Women’s CMSs use collective practices to address the gender, race, and class relations that have contributed to the underrepresentation of women cyclists in Brazil. For example, in Niterói, the Brazilian city with the highest share of women cyclists, women only represent 12 per cent of the cyclists (Franco 2014). My research draws from interview data with women across 10 different cities and 14 different CMSs to answer the following question: why and how do women use cycling as a method for social transformation? I argue that the collective practices of women’s CMSs reflect the process of critical consciousness-building. The critical consciousness-building activities of women’s CMSs in Brazil highlight the significance of non-physical cycling infrastructure in mobilizing cycling mobility justice in the Latin American context.

Keywords: critical consciousness
cycling
Latin America
mobility
sustainability
transportation
Advisor: Bunce, Susannah
Analysis of the T Cell Composition of Clinically Stable ISHLT Grade A1 Rejection Lesions

CD4+FOXP3+ Regulatory T cells (Tregs) may modulate acute cellular rejection (ACR)-associated immune responses and the progression of ACR to Chronic Lung Allograft Dysfunction (CLAD) following lung transplantation (LTx). Treg stability is enhanced by demethylation of the Treg-specific demethylated region (TSDR) in the FOXP3 locus. Grade A1 ACR is not treated in clinically stable patients in the Toronto Lung Transplant Program, affording the opportunity to study its natural history in relation to its cellular composition. Our hypothesis was that a greater Treg content in first, clinically stable, grade A1 transbronchial biopsies is associated with a lower risk of CLAD. Results demonstrated that patients who developed CLAD within 2 years of LTx showed greater CD8+ T cell infiltration compared to stable patients, but no significant difference in Tregs. These results suggest that in asymptomatic patients with a first episode of A1 rejection, greater CD8+ T cell content may be indicative of a poorer long-term outlook.

Keywords: Acute Rejection
Chronic Lung Allograft Dysfunction
Cytotoxic T Cells
Lung Transplant
Regulatory T Cells
Rejection
Advisor: Juvet, Stephen C
Fluorine-19 MRI of Perfluoropolyether-labeled Stem Cell-derived Alveolar-like Macrophages

This thesis demonstrates the feasibility of in vitro detection of alveolar-like macrophages (ALMs) labeled with perfluropolyether (PFPE) in rat lungs using fluorine-19 (19F) magnetic resonance imaging (MRI) at 3T. ALMs present therapeutic potential in treating chronic lung diseases, as they augment resident alveolar macrophage’s immunological functions. Understanding the biodistribution of ALMs in lungs with MRI could provide important information for optimizing cell delivery. Through in vitro cell experiments, the labeling and viability of PFPE-labeled ALMs were assessed. Based on the results from in vitro imaging, the MRI detection threshold of ALMs in suspension was determined to be 666,000 cells/voxel. Instillation of PFPE-labeled ALMs in rat lungs was performed. Placement was confirmed using two-photon tomography, though the cells were not detectable by 19F-MRI. ALM tracking in vivo may be possible through improvements in MRI. Cellular imaging using 19F-MRI shows potential to advance clinical translation of cellular therapy for lung disease.

Keywords: Alveolar-like macrophage
Cell tracking
Detection threshold
Imaging
MRI
Advisor: Santyr, Giles
Effects of Long-chain Branching and Molecular Weight on the Foamability of Polypropylene in Foam Injection Molding

Polypropylene (PP) typically produces foams with poor cell morphology and limited expansion due to low melt strength and a lack of strain hardening – causing cell coalescence. Research to improve PP foamability has focused on low-melt flow rate (MFR) resins, whereas methods such as foam injection molding (FIM) require high-MFR resins for easy processability. This thesis evaluates the use of high-MFR, high molecular weight (Mw) PP resins for use in FIM processes. In linear PP, high Mw correlated to higher expansion capabilities due to higher crystallization temperatures and improved extensional rheology. However, low Mw correlated to increased cell nucleation, which is attributed to decreased interfacial tension. Relative to linear counterparts, long-chain branching was found to further increase crystallization temperatures and exhibited strain hardening, resulting in improved high-temperature foaming. These findings provide insights into the mechanisms governing expansion and cell nucleation in high-MFR PP resins, which can guide application-based resin selection.

Keywords: branching
foaming
Injection molding
molecular weight
polypropylene
Advisor: Lee, Patrick C
Two Calcium Imaging Analysis Workflows for Identifying Coordinated Networks underlying C. elegans Locomotion

Though previous research has elucidated the Central Pattern Generator (CPG) networks governing backward and forward crawling in the C. elegans body below the neck, an undiscovered CPG controlling the head likely exists. Calcium imaging constitutes an effective means for visualising neuronal activity, useful for identifying candidate CPGs and neuronal assemblies. I developed SNCI_track, an autotracker wrapper and interface for proofreading of small-number calcium imaging (SNCI) experiments. SNCI_track incurs few autotracking errors and enables fast proofreading, improving the time-until-results of an SNCI workflow. Toward identifying candidate oscillators and neuronal assemblies in the head, I implemented a collaborator-authored pan-neuronal calcium imaging (PNCI) workflow on a single unc-13(s69); unc-2(hp647); hpIs675 whole-brain recording of 135 neurons. Qualitative appraisal identifies 12 neuronal assemblies in the recording, two of which may be oscillators. This thesis demonstrates use of two calcium imaging analysis workflows and preliminary results that may elucidate new features of the C. elegans head locomotory network.

Keywords: autotracking
C. elegans
calcium imaging
functional imaging
locomotion
neuroscience
Advisor: Zhen, Mei
The Impact of a Remotely-delivered Yoga Intervention on Cognitive Function in Breast Cancer Survivors: A Feasibility Study

Cancer-related cognitive impairment (CRCI) is a common quality of life complaint among breast cancer survivors (BCS). Evidence suggests that exercise may be able to improve CRCI. The purpose of this study was to explore the feasibility of an 8-week, remotely-delivered yoga intervention and examine its impact on cognitive function, fatigue, and exercise levels in BCS using a concurrent mixed-methods design. Participants (N=18) completed measures of self-reported and objective cognitive function, fatigue, and exercise levels pre- and post-intervention. Qualitative interviews were conducted to understand participants’ experiences with the intervention/study. The intervention surpassed a priori feasibility indicators (adherence rate = 83.7%, attrition rate = 5.4%, no adverse events) and qualitative themes indicated that it was enjoyable and beneficial. Participants had improvements in memory, fatigue, and weekly minutes of moderate-to-vigorous physical activity post-intervention. Future randomized controlled trials examining the impact of virtually-supervised, remotely-delivered yoga interventions on cognitive function in BCS are warranted.

Keywords: Breast cancer
Cognitive function
Fatigue
Feasibility
Yoga
Advisor: Trinh, Linda
The Effect of Photostimulable Phosphor Plate Artifacts on Dental Caries Diagnosis

Background: Photostimulable phosphor (PSP) plate damage results in grey or white artifacts on radiographic images, which may affect interpretation.Objectives: To objectively quantify PSP plate artifacts and assess these metrics with the accuracy of caries interpretation. Study Design: PSP plate artifacts were assessed using three criteria: surface area, intensity, and location. Plate scan counts were also analyzed. Artifact-free bitewing images were overlaid with the images of damaged PSP plates, and these simulated images were assessed by clinicians for caries. Results: With increasing area of white artifact, logistic regression modeling demonstrated decreased odds ratios for sensitivity, specificity, and accuracy of caries interpretation, lowered clinician’s interpretation confidence and increased odds ratio of clinicians’ decisions to discard a plate. Scan count had no effect. Conclusion: Caries interpretation accuracy decreased as the surface area of white artifacts increased. Interpretation accuracy, clinician confidence, and discard rate were unrelated to the number of times a plate was used.

Keywords: artifacts
computer simulation
photostimulable phosphor
quality assurance
radiology
Advisor: Perschbacher, Susanne E
Lam, Ernest WN
Exploring the Molecular Mechanism of Dentogingival Attachment Mediated by Laminin-332 and the Enamel Protein SCPPPQ1

It has recently been shown that the novel extracellular matrix protein SCPPPQ1, secreted during the late stage of enamel formation and present in a specialized basal lamina of the junctional epithelium (JE), can accelerate and enhance the adhesion of oral epithelial cells to hydroxyapatite when combined with laminin-332 (LAM332). In this study, LAM332/SCPPPQ1 coated superparamagnetic microbeads were incubated with oral epithelial cells to form integrin- based adhesion complexes, which were isolated for biochemical analysis. Mass spectroscopy confirmed the presence of most hemidesmosomal components, and the amount of plectin and integrin β4 appeared to be significantly higher in the adhesion complexes formed with LAM332/SCPPPQ1. This was further confirmed by western blot and immunofluorescence analyses. No novel protein components could be identified. The study suggests that cellular adhesion to LAM332/SCPPPQ1 likely does not involve any novel components or attachment apparatus, but results in an increase of the engagement of known hemidesmosomal components.

Advisor: Ganss, Bernhard
Accelerated PDE-constrained Optimization by Adaptive Reduced Order Modelling and Goal-oriented Hyperreduction

We present a framework to accelerate the solution of optimization problems constrained by nonlinear partial differential equations (PDEs). To reduce the cost of objective function evaluations by several orders of magnitude, we replace the high-fidelity model (HFM) with a reduced order model (ROM). The nonlinearity motivates the use of hyperreduction, for which we use a goal-oriented empirical quadrature procedure. The hyperreduced ROM is trained specifically to preserve zero- and first-order consistency with the HFM, which provides the optimization framework with a convergence guarantee. Several optimization problems are solved using the framework, including a thermal fin problem governed by a nonlinear heat equation, an inverse aerodynamic design problem governed by the Euler equations, and an inverse aerodynamic design problem governed by the Reynolds-averaged Navier-Stokes (RANS) equations. Some speedup is observed for the first two cases, but more research on hyperreduction is necessary before a cost advantage will be seen with RANS.

Keywords: Hyperreduction
Optimization
Partial differential equations
Reduced order modelling
Trust region methods
Advisor: Yano, Masayuki
An Exploratory Study of Functional Brain Activation Underlying Cognitive Control in Major Depressive Disorder and Borderline Personality Disorder

Cognitive control is associated with impulsive and harmful behaviours, such as substance abuse and suicidal behaviours, as well as major depressive disorder (MDD) and borderline personality disorder (BPD). The association between MDD and BPD is partially explained by shared pathological personality traits, which may be underpinned by aspects of cognitive control, such as response inhibition. The neural basis of response inhibition in MDD and BPD is not fully understood and could illuminate factors that differentiate between the disorders and that underlie individual differences in cross-cutting pathological traits. In this study, we measured functional brain activity underlying response inhibition using functional magnetic resonance imaging and compared participants with MDD with and without comorbid BPD, and controls with neither disorder. Whereas response-inhibition-related activation was observed bilaterally in frontoparietal cognitive control regions across groups, there were no group differences in activation or significant associations between activation in regions-of-interest and pathological personality traits.

Keywords: Borderline Personality Disorder
Cognitive Control
Disinhibition
fMRI
Major Depressive Disorder
Response Inhibition
Advisor: Ruocco, Anthony
Lee, Andy