VictorJuiz/thesis huggingface dataset:
Goal-oriented Model Reduction for Time-dependent Nonlinear Parametrized Partial Differential Equations

This thesis presents a goal-oriented projection-based model reduction framework for parameterized time-dependent nonlinear PDEs. The framework builds on the following ingredients: reduced basis spaces, which provide rapidly convergent approximations of the parameterized time-dependent solutions; the empirical quadrature procedure, which provides hyperreduction of nonlinear PDEs; and the dual weighted residual (DWR) method, which provides a posteriori error estimates for quantities of interest. In the offline stage, the method constructs reduced models that meet the user-prescribed output error tolerance using an automated and efficient training procedure. The online stage is rapid and reliable, meaning that the method provides rapid approximation of time-dependent outputs coupled with online-efficient error estimates that make the method reliable by indicating how much error is committed by the reduced model. We demonstrate the framework for an unsteady nonlinear reaction-diffusion equation and an unsteady lid-driven cavity flow.

Keywords: computational fluid dynamics
error estimation
hyperreduction
model reduction
numerical methods
partial differential equation
Advisor: Yano, Masayuki
Characterization of Lung Allograft-derived Extracellular Vesicles and their Role in Graft Injury

Post-transplant acute lung injuries result in part from injuries sustained in the donor. Extracellular vesicles (EVs) are membrane-bound particles released by most cell types. They contain protein and RNA molecules which may play diagnostic and functional roles. We propose that pre-transplantation EVs released by donor lungs reflect the condition of the lung. Here, we report that that fluid recovered after perfusion of donor lungs contain EVs with canonical EV protein markers like CD9, CD81 and CD63. In lungs declined for transplantation, EV-associated CD63 and CD31, an endothelial adhesion marker, were found to be elevated, with an accompanying decrease in CD9. Though inconclusive, these markers may also reflect the degree of acute lung injury in transplant recipients. Next, we aim to characterize the RNA cargo of perfusate EVs in relation to the presence and degree of lung injury after transplantation. Thus, these findings will provide an insight to the potential diagnostic and functional role of EVs in post-transplant lung allograft injury.

Keywords: Ex vivo lung perfusion
Extracellular vesicles
Lung transplantation
Primary graft dysfunction
Advisor: Juvet, Stephen C
Investigating the Validity of the Fitbit ChargeHRTM for Measuring Physical Activity in Children and Youth with Mobility-related Disabilities

Wearable technology, such as Fitbit®, has become widely used as a device-based measure of physical activity (PA). However, little is known about the validity of the Fitbit® in childhood disability populations. The objective of this study was to explore whether the Fitbit ChargeHRTM can accurately capture measures of PA (heart rate [HR], step count) in children and youth with mobility-related disabilities (N = 10, ages 9-21). Intraclass correlation coefficients (ICCs) and Bland-Altman plots were conducted to examine inter-device reliability and absolute agreement. The Fitbit ChargeHRTM underestimated HR and overestimated step count against the criterion measures PolarHRTM monitor and Actigraph GT3X+TM accelerometer, respectively. Individual- level HR findings revealed strongest device agreement for participants with major gait deviations, but step count was consistently underestimated. The Fitbit ChargeHRTM did not demonstrate validity in the given sample. Further research should examine the validity of the Fitbit ChargeHRTM in a larger sample with homogeneous functioning.

Keywords: disability
mobility
mobility challenges
physical activity
wearables
youth
Advisor: Arbour-Nicitopoulos, Kelly
Maternal and Perinatal Outcomes in Female Survivors of Childhood, Adolescent, and Young Adult Cancer

Childhood, adolescent and young adult cancer survivors may develop long-term health issues. Data are lacking on reproductive complications. Using health administrative data, an Ontario provincial cohort of 3,486 survivors and 17,428 matched cancer-free individuals was assembled. Outcomes included recognized pregnancies, maternal and perinatal complications. Overall, survivors were significantly less likely to have a pregnancy compared to cancer-free individuals [Hazard Ratio 0.79,95%CI 0.73-0.86], especially those who received hematopoietic stem cell transplantation (HSCT),and cranial radiation. Survivors had a significant relative risk (RR) for severe maternal morbidity (SMM) (RR 2.31,95%CI 1.49-3.59) and cardiac morbidity (RR 3.23,95%CI 1.58-6.60). Among survivors, SMM predictors included CNS tumour and pre-existing kidney disease. Newborns of survivors were at risk for preterm birth (RR 1.56,95%CI 1.23-1.98). Predictors of preterm birth included alkylating agent chemotherapy and HSCT. This study suggests that survivors are less likely to have a pregnancy and are at risk for SMM, cardiac morbidity, and preterm birth.

Keywords: AYA
Childhood Cancer
Late-effects
Obstetrical
Perinatal
Survivorship
Advisor: Nathan, Paul C
Canadian General Dentists’ Perceptions about their Relationship with Specialists

Fostering inter-professional relationships is crucial to improving clinical collaboration, patient experience, and patient health. General dentists’ perceptions of specialists (and vice versa) plays an important role in the relationship between them. An internet-based survey of a nationally representative sample of Canadian general dentists was conducted to assess perceptions about their relationship with specialists. A 47-item questionnaire collected socio- demographic, practitioner-related and practice-related information. A ‘strained’ relationship was defined as a general dentist who did not perceive specialists as ‘completely collegial’ and perceived medium/large competitive pressure from specialists. The response rate was 11.7%. The number of practices worked in, location of the primary practice, practice ownership, specialists in close proximity, and practicing with a General Practice Residency/Advanced Education in General Dentistry were strongly associated with general dentists perceiving a ‘strained’ relationship. This was the first exploration of the nature of the general dentist–specialist relationship in the context of Canadian dentistry and dentistry elsewhere.

Advisor: Quiñonez, Carlos
Investigating Operative and Non-operative Treatments for Patella Fractures in Elderly, Low-demand Patients

Management protocols for displaced patella fractures in older (≥65 years) patients are lacking. While surgery is recommended for displaced fractures and non-operative management is suggested for non/minimally-displaced fractures in young/active patients, it is unclear if this algorithm is applicable to older, low-demand patients. The purpose of this thesis was to evaluate outcomes following operative and non-operative patella fracture management in older patients. Through an orthopaedic surgeon survey, we found that there remains a lack of consensus on the degree of displacement warranting operative management. Through a database study of 6258 patients, we found that re-operation rates are high, and emergency department readmissions are common but generally unrelated to patella fracture diagnosis. These results suggest that managing fractures in older patients is complex, and complications are prominent. Future studies comparing both interventions are needed. Protocols for a multicenter retrospective study and prospective randomised trial to address these questions are also presented.

Keywords: Orthopaedic Surgery
Patella Fractures
Advisor: Nauth, Aaron
Metabarcoding Approach to Identifying Early Life Stages of Great Lakes Fishes

Accurately identifying fishes in their early life stages using morphology is challenging, time-consuming, and requires taxonomic expertise. Metabarcoding is a method that can be used to identify species in batch samples (Cruaud et al. 2017). Detection of early life stages of fishes is important for understanding life history patterns and critical spawning habitat. In this study, metabarcoding is used as an identification tool to identify 1119 egg and larva batch samples from Sydenham River and Rondeau Bay. I identified 34 species from Sydenham River and 8 species from Rondeau Bay and the spawning months of these species based on date of capture. I determined the materials and supplies cost of metabarcoding in this study to be $6597.33, compared to $62289.09 for individual-based barcoding. This study shows the potential of metabarcoding as a broad-scale detection and identification method for early life stages of Great Lake fishes.

Keywords: Barcoding
Great Lakes
Icthyoplankton
Metabarcoding
Rondeau Bay
Sydenham River
Advisor: Lovejoy, Nathan R
Mandrak, Nicholas E
Evaluation of a Novel Anabolic Bone Drug with Synthetic Bone Graft Biomaterials in a Rat Jaw Bone Defect

Several graft materials have been investigated and used for treating large bone defects in oral and maxillofacial surgery as alternatives to autogenous grafts. This thesis combines a non-degradable and a degradable graft material, commercially available bovine bone (i.e. BioOss®) and monetite respectively, with two novel drug conjugates (C3 and C6) which are made of an anabolic agent (EP4-receptor agonist) linked to a bone targeting molecule (inactive alendronate). The rationale is that when carrying these conjugates locally to bone defects, the anabolic agent will promote bone formation without the side effects associated with systemic administration. The in vivo efficacy of C3 and C6 conjugates with BioOss® and monetite was investigated by using an established rat mandibular bone defect model. Results showed that loading the bone grafts with C3 and C6 conjugates increased bone formation in the defect area, and the C6 loaded materials had higher bone formation than the C3 counterparts.

Keywords: Bone grafts
Bone regeneration
Calcium phosphates
deproteinized bovine bone mineral
Drug Targeting
Advisor: Grynpas, Marc D
Glogauer, Michael
Kinetic and Isotopic Investigation on Hydrogenation of Aliphatic Aldehydes over Dispersed Ru Nanoparticle Catalysts

Kinetic assessment and isotopic studies establish a kinetic model that describes the behavior of vapor phase hydrogenation of aliphatic aldehydes over Ru/SiO2 catalysts. CO formed from decarbonylation is the most abundant surface species, which inhibits hydrogenation turnovers. Water promotes hydrogenation through a dynamic mechanistic transition in surface H-addition sequences. Without water, aldehyde hydrogenation turnovers increase linearly with butanal and H2 pressures, and shows fast C-H/C-D exchange rates, suggesting the Alkoxy pathway, initiated by quasi-equilibrated C-H bond formation before a kinetically relevant O-H bond formation. In the presence of water, rate of the first hydrogen attack is not affected, while the second hydrogen attack is greatly promoted. Theoretical calculations and kinetic isotope effects indicate the stabilization of transition state through hydrogen bonding. This work provides significant understanding in the reaction pathway of carbonyl hydrogenation under different conditions, which links and extends understanding from previous studies in the gas and liquid phase.

Keywords: aldehyde
hydrogenation
reaction mechanism
Ru catalyst
water effects
Advisor: Chin, Cathy (Ya-Huei)
Circadian Anticipation of Significant Events in Mice

Circadian clocks allow organisms to anticipate the recurrence of significant events on a daily basis. This thesis reviews the clock-based circadian anticipatory ability of organisms, the mammalian time-keeping mechanisms, and the daily anticipation of ephemeral arousing events at matching contexts through formation of time memory with a context-entrainable oscillator (CEO). We investigated CEO’s capacity to register circadian information and gate context-dependent anticipation by conducting conditioned place avoidance (CPA) and preference (CPP) on C57BL/6 mice with moderately aversive and appetitive stimuli. We found that the circadian-gating of anticipation could not be obtained with the current CPP paradigm. The results suggest that either (a) the visual difference between contexts was not distinct; or (b) the high stimulus strength produced generalization in the temporal dimension. We propose an improved mice CPP/CPA paradigm by strengthening visual cues and adjusting the appetitive stimulus. Future multiple time memory (MTM) experiment plans are also proposed.

Keywords: Behaviour
Circadian Clock
Conditioned Place Learning
Mice
Time Memory
Advisor: Ralph, Martin R
Assessing Impact of Donor Heterogeneity in Optimizing Culture Parameters for Bone Marrow-derived Mesenchymal Stromal Cells

Understanding donor heterogeneity and optimizing mesenchymal stromal cells (MSC) manufacturing process based on their anti-inflammatory, immunomodulatory and angiogenic properties is key for successful MSC clinical trials. This study was focused on using a statistical modeling tool to optimize culture conditions that maximize cell potency, using markers that predict therapeutic efficacy, and understanding whether this optimization needs to be donor-specific or not. The results demonstrated that parameter optimization was donor-specific only where oxygen concentration (O2) was important, such as MSC therapeutic use in angiogenic conditions or hypoxic conditions because of the non-obvious interactions between donor and O2, but less important otherwise such as MSC therapeutic use in inflammatory and immunomodulatory conditions. Characterizing donors into putative groups based on a clinical trial predicted their response to O2. Cells exposed to serum-free medium had lower gene expression than serum-containing medium. This study will open up avenues for potentially predicting MSC potency on a donor-to-donor basis.

Keywords: bioprocess parameters
design of experiments
donor heterogeneity
hypoxia
mesenchymal stromal cells
statistical modeling
Advisor: Audet, Julie
Viswanathan, Sowmya
Edge Detection in 3D Point Clouds for Industrial Applications

3D point clouds are a commonly used medium to represent and analyze object shapes. Edge detection is important for 3D point cloud processing since it provides geometrical clues for analyzing point clouds, serving as the foundation for point cloud processing tasks and industrial applications. Existing geometry-based edge detectors use angle-dependent geometrical quantities to detect edges. Since the quantities are affected by edge angles and are similar near edges, they suffer from missed detections and redundant detections and require fine-tuned thresholds for every point clouds. This work proposes a novel edge detector to solve these problems. A new two half-planes model (THP) is proposed to estimate geometric quantities that are not affected by edge angles. We developed adapted non-maximum suppression (ANMS) by applying directional constraints on point cloud neighborhood for suppressing redundant detections. Experimental results show that the proposed detector can improve the detection result without the need to fine-tune thresholds.

Advisor: Sun, Yu
The Aim versus the Action: Race, Intention, and Moral Judgment

Intent is often studied as a binary (intentional vs. unintentional). The Proximal Intent / Distal Intent model of lay theories of intent breaks this binary by parsing intention into the orthogonal categories of proximal and distal intent. Constructs such as psychological distance and lay theories of cognitive control have been demonstrated to vary independently in observers minds at the levels of proximal and distal intent. However, former studies have manipulated the observer, not the target. This exploratory study measures observer’s moral evaluations of black and white actors proximal and distal intent. Analysis reveals that predominantly white observers rate black actors as more morally culpable when the actors display distal intent, but not proximal intent. Additionally, when proximal and distal intent are either both present or both absent in the actors minds, observers rating of actor’s did not differ significantly across race. Implications for these findings are discussed within.

Keywords: Decision making
Intention
Moral Judgment
Moral psychology
Race
Advisor: Plaks, Jason
The Development of Green Building Standards in Canada

This research looks to understand where green building standards exist in Canada and what factors motivate the uptake of this type of sustainability practice. Although literature has highlighted the use of standards, there is a lack of research done in Canada. A mixed-method approach is used to answer these questions and includes geographical information system mapping of green certified buildings across Canada and the analysis of policy, demographics, and economic variables to evaluate when and where standards have been used. The findings show a concentration of green building standards in Canadian cities. Median income, number of buildings, and population density are also shown to have a positive and statistically significant relationship with green building standard use. Further, the findings highlight that policy is a driving factor for the increase in overall standard use and building type certified and that economics is a motivating factor for the type of standard used.

Keywords: BOMA
Energy Star
green building
green building standards
LEED
sustainability
Advisor: Besco, Laurel
Downscaling the Maximum Carboxylation Rate (Vcmax) Derived from Satellite Sun-induced Chlorophyll Fluorescence Data Using High-resolution Remote Sensing Products

The maximum carboxylation rate (Vcmax) influences the magnitude of gross primary productivity (GPP). Currently, reliable global Vcmax products derived from satellite sun-induced chlorophyll fluorescence (SIF) data are at coarse resolutions, which cannot meet the demand of global ecological research. In this thesis, the Vcmax25 (Vcmax normalized to 25°C) dataset derived from satellite SIF at a coarse resolution (0.1°, ~11 km) is downscaled to a higher resolution (1 km) through a downscaling scheme using photochemical reflectance index (PRI) and spatial scaling algorithms based on leaf chlorophyll content (LCC) and normalized difference vegetation index (NDVI). The Boreal Ecosystem Productivity Simulator (BEPS) is used to evaluate the downscaled Vcmax25 using tower flux data. The results show that the LCC-downscaled Vcmax25 data appreciatively improve GPP simulations at the tower sites, indicating LCC as a feasible way for downscaling the Vcmax25 dataset. GPP estimations at the 0.1° resolution decrease by 2-7% after Vcmax25 downscaling.

Keywords: Downscaling
Global Carbon Cycle
Maximum Carboxylation Rate
Spatial Heterogeneity
Vcmax25
Advisor: Chen, Jing M
Mechanism and Significance of the BMRF1-NuRD Interaction

BMRF1 has known roles as the EBV DNA polymerase processivity factor and in activating the transcription of EBV genes. However, its roles in manipulating cellular processes have not been previously examined. AP-MS experiment showed that all 14 subunits of the NuRD complex co-purified with BMRF1. Interactions between NuRD and some cellular proteins are mediated by an RKKQxxP motif. We have identified this motif on BMRF1 and confirmed that mutations in this motif abrogate the BMRF1-NuRD interaction. BMRF1 NuRD-binding mutant did not activate transcription from EBV promoters and failed to recruit NuRD to these promoters. Similarly, mutations in the motif abrogated the inhibition of ubiquitylation at DSBs and induction of cellular SUMOylation by BMRF1. In keeping with this finding, silencing of NuRD subunits resulted in induction of SUMOylation, mimicking the effect of BMRF1. Together, our findings indicate that BMRF1 modulates the DDR, SUMOylation, and EBV gene expressions through interactions with NuRD.

Advisor: Frappier, Lori
Exploring Counter-space Adult Literacy Practices in Kingston Galloway Orton Park

Classifying adult literacy as an essential skill for the job market in Canada perpetuates capitalistic and elite structures. Through policy changes and shifts, adult literacy programs have been structured as a pathway to employability. However, only 5 to 10 percent of adults who require literacy and upgrading ever enroll in a program, and many of those who do, drop out (Pound, 2006). This research employs Henri Lefebvre's philosophies on the counter-space theory which focuses on the rejection of dominant structures and emphasizes the importance of creating spaces of resistance. The Kingston Galloway Orton Park Adult Literacy Program (KGO ALP) located in Toronto, Canada is an example of a program which uses counter-space literacy practices. The program operates on the assumption that adult literacy learning is a process of self-development. Using a case study design, I found KGO ALP’s counter-space practices reveal learner-centered and progressive practices that allow for more creative, flexible, and innovative solutions.

Keywords: Adult education
Adult literacy
Community
Counter-space
Literacy
Scarborough
Advisor: Mirchandani, Kiran
An Exploration of Predictors of Adoption and Use of In-vehicle Voice Control Systems

In-vehicle voice control systems (VCS) have the potential to reduce driver distraction and thereby, increase road safety. However, little is known about factors that influence their adoption and use. This thesis examines VCS usage patterns and uses the Technology Acceptance Model framework to explore predictors of VCS use. A survey study (N = 198), which was informed by the findings of a focus group study (N = 9), was conducted and structural equal modelling was used to build predictive models. While multiple constructs predicted drivers’ attitude toward VCS, which in turn projected their use, the strongest predictors were perceived ease-of-use and perceived usefulness toward accomplishing tasks when compared to visual-manual interactions. A driving simulator study was designed to examine the role of context and impact of reliability notifications on VCS acceptance and driving performance, in the presence of background noise, but was not carried out due to the COVID-19 pandemic.

Keywords: adoption
technology acceptance model
vehicle
voice control systems
voice interface
Advisor: Donmez, Birsen
A Cost-Utility Analysis of First-Line Systemic Therapy for Patients with Metastatic Renal Cell Carcinoma

The systemic therapy landscape for first-line treatment of metastatic renal cell carcinoma (mRCC) has seen a dramatic increase in efficacious therapies over the last decade. The substantial costs associated with these treatments necessitate evaluation of cost-effectiveness, to facilitate prioritization of therapies that offer best value-for-money. Our objective was to conduct a cost-utility analysis (CUA) of contemporary first-line systemic therapies for patients with mRCC, inclusive of standard-dose sunitinib, dose-individualized sunitinib, pazopanib, cabozantinib, nivolumab-ipilimumab and pembrolizumab-axitinib. This CUA found pazopanib to be the most cost-effective option at cost-effectiveness thresholds (CET)

Advisor: Chan, Kelvin KW
Sander, Beate