VictorJuiz/thesis huggingface dataset:
Patient-Specific and Program Outcome Evaluation of a Novel Pediatric Exercise Medicine Program
Keywords: high-risk pediatric patients
lifestyle behavior change
lifestyle medicine
pediatric exercise medicine program
program evaluation

Pediatric patients with high-risk medical conditions present with obesity-related lifestyle risk factors and are at greater risk of developing cardiovascular complications later in life. Recent trials of lifestyle modification programs have demonstrated potential benefits; however, translating these findings into practise remains under-explored. This thesis project aimed to evaluate outcomes of a novel pediatric Exercise Medicine Program -- a home-based physical exercise and lifestyle medicine program for children with high-risk medical conditions. We found that patients referred to the program had a clustering of unhealthy lifestyle behaviors, and that these factors were associated with the risk of being overweight or obese and reduced exercise capacity. Short-term outcomes for cardiac patients participating in the program showed stabilization of body weight and exercise capacity, improved health-related quality of life outcomes, and improved muscular strength. These findings provided evidence from a clinical practice of a lifestyle medicine program for children with high-risk medical conditions.
Timing of Introduction to Solid Food, Growth and Nutrition Risk in Later Childhood
Keywords: BMI
Complementary Feeding
Feeding behaviour
Growth
Height
Obesity

It is recommended in Canada to introduce solid food at 6 months of age in keeping with the recommendations from the World Health Organization. The European Society for Paediatric Nutrition recommends solid food be introduced between 4 and 6 months of age. Few studies have differentiated between this period. In this thesis I aimed to evaluate the relationship between the timing of introduction to infant cereal as the first solid food between 4 and 6 months and growth and nutrition risk. Through a longitudinal study of healthy children participating in the TARGet Kids! cohort, introduction to infant cereal at 4 months, compared to 6 months, was associated with higher body mass index z-score and higher odds of obesity through 10 years of age, worse eating behaviour between 18 months and 5 years and minimal differences in height. These findings support guidelines for introducing solid food around 6 months of age.
Multistage Stochastic Programming Combined with Deep Learning-based Time series Forecasting: New Methodologies and Applications
Keywords: Deep learning
Healthcare
Interpretability
Radiotherapy
Stochastic programming
Time series

We study topics related to both multistage stochastic programming (MSP) and deep learning-based time series forecasts. In terms of MSP, we study the cases where the stochastic process associated with MSP models is either stagewise independent or dependent. In terms of stagewise independent stochastic process, we propose a novel MSP framework for the fractionated intensity modulated radiation therapy problem. We solve a sample average approximation of the problem via stochastic dual dynamic programming. In terms of stagewise dependent stochastic processes, we study the impact time series forecasting methodologies, autoregressive moving average-based models, and DeepAR, on deterministic and two-stage MSP policies. We propose a novel interpretable neural network architecture for probabilistic time series forecasting. Our model computes contributions of features for both mean and standard deviation forecasts. Unlike the existing models which only identify the positive importance score of features, our model identifies both positive and negative contributions.
Life Cycle Greenhouse Gas Emissions of Conventional and Alternative Heavy-duty Trucks: Literature Review and Harmonization
Keywords: Greenhouse gas emissions
Harmonization
Heavy-duty truck
Life cycle assessment
Literature review

Globally, heavy-duty trucks (HDTs) contribute an increasing share of greenhouse gas (GHG) emissions. Switching to alternative HDTs has the potential to mitigate HDT GHG emissions. Studies have evaluated the decarbonization potential of alternative HDTs through life cycle assessments (LCAs). However, these studies used varying study design parameters and assumptions and obtained inconsistent results, making it challenging to generalize findings. In this thesis, I conducted a literature review to examine the results and assumptions in 28 HDT LCAs and identify inconsistencies and best practices for future studies; moreover, I conducted HDT LCA harmonization to evaluate GHG impacts for alternative HDTs and identify sources of variations in HDT GHG emissions reported in the LCAs. An HDT LCA data inventory and a harmonization framework were developed, further, recommendations for future HDT LCAs and policies for HDT decarbonization were provided. The results are expected to facilitate the evaluation and reduction of HDT GHG emissions.
Biomechanics of Medial Opening-wedge High Tibial Osteotomy in Healthy and Arthritic Knees
Keywords: Biomechanics
Knee
Malalignment
Orthopaedics
Osteoarthritis
Surgery

Medial opening-wedge high tibial osteotomy (MOW-HTO) is a well-established treatment option for patients with medial knee osteoarthritis. This thesis aimed to investigate the difference between healthy and arthritic knees in response to MOW-HTO alignment correction. Additionally, we aimed to investigate the effect of partial and complete superficial medial collateral ligament (sMCL) release across a range of clinically relevant alignment corrections. Cadaver knees were tested under axial loading while measuring tibiofemoral compartment pressure. Arthritic knees did not differ from healthy knees in response to alignment corrections. Compared to constitutional alignment, medial pressure decreased at post-operative mechanical axes crossing the tibial plateau at 50–55% of its width, while sMCL release did not impact medial pressure. This work shows that arthritic status was not a significant factor in MOW-HTO biomechanics and that significant unloading occurs after correcting the mechanical axis to 50–55% of the tibial plateau width, irrespective of sMCL release.
Investigating the Contributions of Physiological Arousal and Emotion Regulation to Anxiety in Autism Spectrum Disorder
Keywords: anxiety
autism
emotion regulation
physiological arousal

Up to 84% of children with autism spectrum disorder (ASD) experience clinically significant anxiety, negatively impacting their academic achievement, employment outcomes, and health. Despite its significance, few evidence-based interventions exist for anxiety in ASD. A key challenge is that underlying factors remain largely unknown. Two mechanisms suggested to underlie anxiety in ASD are difficulties with emotion regulation (ER) and atypical physiological arousal.I investigate physiological arousal, indexing overall arousal and parasympathetic nervous system activity, during resting state and emotionally-arousing tasks in a sample of children with ASD as well as a typically developing (TD) sample. I then explore associations between arousal and ER in these samples. Finally, I test potential relational models explaining associations between arousal, ER, and anxiety. Results display differences in arousal within the ASD sample, associations between arousal and ER, as well as initial support for the proposed models explaining anxiety in ASD.
Non-invasive Measurement of Intravascular Temperature in the Mouse Brain
Keywords: bioheat exchange
magnetic resonance imaging
thermometry
TmDOTMA

Brain temperature is an important physiological parameter that both reflects and modulates brain activity. Regulation of brain temperature is found in healthy conditions and perturbed in certain diseased conditions. Presently, the available methods for measuring in vivo temperature are invasive and impractical for use in small animals. Here, we present a methodology to measure common carotid artery and brain temperature in anesthetized mice by magnetic resonance imaging (MRI) using the temperature-sensitive agent TmDOTMA. Agreement between left and right carotid artery temperature measurements demonstrated self-consistency of this method. A temperature gradient in the brain, increasing from superficial to core regions, was also observed. Additionally, comparison of core brain and arterial temperature showed that the anesthetized mouse brain is warmed by incoming arterial blood. This work provided important insight into the bioheat exchange in mice which can inform our understanding of brain temperature regulation in health.
Investigating Molecular Signatures of GABAergic Neuron Populations in the Developing Cerebellum
Keywords: Cerebellum
Golgi cells
Igfbp5
scRNA-seq
smFISH

The cerebellar GABAergic lineage is comprised of a diverse population of neurons that arise from a common Ptf1-a progenitor. They are generated in a precise spatiotemporal schedule with the help of environmental cues. However, it is unclear what molecular signatures distinguish GABAergic populations during development. The aims of my thesis were to analyze gene expression profiles of developing GABAergic cells from cerebellar single-cell RNA sequencing data, and to identify and validate new markers for interneuron subpopulations. Through dimensionality reduction and pseudotemporal ordering methods, I identified known and novel transcriptional GABAergic lineage markers. To validate my single-cell profiling findings, I developed a script to create oligonucleotide probes for single molecule in situ hybridization (smFISH). I characterized Igfbp5 expression in murine cerebellar tissue and revealed that Igfbp5 is expressed in Golgi cells during embryonic development and downregulated at maturity. My findings provide insight into our understanding of cerebellar neuron diversity.
Upper Small Intestinal Taurochenodeoxycholic acid-FXR Axis Alters Local Oleic Acid Sensing Glucoregulatory Pathways in Rats
Keywords: Farnesoid X Receptor
Glucose Homeostasis
Nutrient Sensing
Taurochenodeoxycholic acid
Type 2 Diabetes
Upper Small Intestine

Short-term high-fat feeding increases upper intestinal taurochenodeoxycholic acid (TCDCA) and impairs upper intestinal oleic acid sensing glucoregulation. Transplantation of chow-fed microbiome into the upper tract of high-fat fed rats restores upper intestinal oleic acid sensing glucoregulation and reduces TCDCA levels. TCDCA is a Farnesoid X receptor (FXR) agonist and gut FXR inhibition improves metabolic dysfunction. It remains unknown whether high-fat induces the TCDCA-FXR axis in the upper tract to alter oleic acid sensing glucoregulation. Intravenous glucose tolerance test with mechanistic gain/loss-of-function studies targeting TCDCA-FXR axis in the upper tract were performed. Transplantation of chow-fed upper intestinal microbiome into the upper tract of high-fat fed rats inhibited FXR by reducing gut TCDCA levels. Inhibition of upper intestinal FXR enhanced oleic acid sensing glucoregulation in high-fat fed rats. In summary, we revealed a microbiome regulated TCDCA-FXR axis in the upper small intestine governing oleic acid sensing glucoregulatory pathways in rats.
Developing Language-specific Screening Tools: Assessing Phonological Awareness Skills in Urdu-English Bilingual Children
Keywords: Bilingualism
Assessment tools
Child language development
Heritage language
Literacy precursors
Phonological awareness

Childhood literacy is a major contributor to future academic and socio-economic success. It is therefore important to provide early reading intervention, via literacy precursor screening tools that can detect potential reading difficulties. Our systematic review and meta-analysis highlighted phonological awareness and vocabulary as commonly assessed literacy precursors that are consistently associated with (and in many cases predict) reading abilities in bilinguals (Chapter 2). To address the English-language assessment bias evident in our review, I developed an age- and linguistically-appropriate Urdu phonological awareness test (Chapter 3). I assessed 95 typically-developing Urdu-English simultaneous bilinguals, in Grades 1-2, across Canada and Pakistan on Urdu and English phonological awareness, expressive vocabulary and word/non-word reading measures. Simple and multiple linear regression analyses indicated significant within-language associations between the novel Urdu phonological awareness test and word/non-word reading, thereby demonstrating criterion-based validity. The developed Urdu phonological awareness test will facilitate early literacy screening in Urdu and linguistically-related languages.
Using the Global Positioning System for Relative Navigation of Mobile Robots
Keywords: GPS
localization
navigation
odometry
relative
robotics

Mobile robots rely on many sensors including the Global Positioning System (GPS) for navigation. It is important to consider the particulars of the application when determining how best to incorporate GPS observables into a state estimation pipeline. In this thesis, we show how GPS can be fit into a relative navigation paradigm. We begin by developing a single-receiver GPS odometry pipeline that achieves a relative drift rate of 0.6%. We then combine GPS with visual localization and obtain few-centimetre-level path-tracking accuracy on a joint indoor-outdoor route with large appearance change. Finally, we implement GPS odometry as an alternative to visual odometry (VO) in Visual Teach Repeat 3 providing robust navigation in the case of sensor failure. Our methods were validated through both offline evaluations on datasets we collected and live closed-loop robot experiments.
Quantification of Exercise Burden in Recreational Masters Endurance Athletes
Keywords: Athletes
Cardiac Burden
Endurance Exercise
Excessive Exercise
Exercise Burden

The quantification of exercise burden in ageing endurance athletes (EA) is important given the evidence suggesting a threshold of cumulative vigorous exercise may elicit adverse cardiac outcomes despite limited objective data or methods to quantify training volume. This study quantified exercise burden using objective and subjective measures during a typical cycling training session (42 km) in 40 recreational masters EA (≥40 years old) with extensive long-distance cycling histories. Serial and post-ride measures of perceived exertion were gathered by questionnaire and continuous measures of power (watts) and heart rate. The results indicate that reliance on subjective reports of exercise intensity alone may yield highly inaccurate estimates of exercise burden defined by metabolic equivalents (METs). In addition, discordance between metabolic and cardiac burden was observed, as less fit individuals may accrue a greater cardiac burden for a given training session than fitter individuals, despite exerting a similar relative intensity.
Eulerian-based Moment Closures for the Modelling of Polydisperse Polykinetic Sprays
Keywords: CFD
Coupled Moments
High Order
Maximum Entropy
Moment Methods
Sprays

In this thesis, multiple Eulerian-based maximum entropy spray models for higher order velocity space are extended to allow the modelling of sprays with different sized droplets. The moment space considered includes 14 moments for fully three-dimensional physical space. Eulerian-based moment methods are possibly less expensive than Lagrangian-based particle tracking methods and yet can provide statistical information on computational grids of infinitesimal size. In particular, the 5-,10-, and 14- moment maximum entropy velocity moment closures are applied witha corresponding 5-moment maximum entropy size model coupled using the CoupledSize Velocity Moment (CSVM) method. The resulting method is applied to one-dimensional closures producing 11 coupled size and velocity moments. The numerical implementations of so-called “partially” polydisperse versions of these spray models, whereby only bulk velocity depends on droplet size, are presented along with results for canonical particle trajectory crossing problems which demonstrate the predictive capabilities of each model.
Combining Hyperspectral Imagery and Real-time Kinematic GPS Data to Classify Mixed-wood Forest and Detect Emerald Ash Borer Infestation
Keywords: Emerald ash borer
Hyperspectral
Image classification
Precise point positioning
Real-time kinematic GPS
Remote sensing

The invasive Emerald Ash Borer (EAB) has devastated native ash tree populations in North America. The rapid expansion of its range requires effective monitoring techniques such as remote sensing to understand the severity of these impacts over large geographic areas. I used a real-time kinematic GPS to collect coordinates of individual trees and analyzed sources of error in an EAB-infested old-growth forest. Individual tree locations were collected with sub-decimeter accuracy. Hyperspectral image-derived datasets, including full spectra, derivative, principal components, narrowband multispectral, and textural information, were evaluated in classifying ash from non-ash trees and identifying stages of ash decline. Overall, hyperspectral data differentiated ash and non-ash trees with high accuracy, and narrowband multispectral data provided highest overall accuracy in distinguishing EAB-related ash tree decline. This work highlights challenges and opportunities associated with using high-spatial and spectral resolution data for disturbance detection and improves workflow mapping the severity of forest insect infestations.
A Methodological Comparison of Utilizing Different Mobile Monitoring Techniques to Predict the Spatial Variation of Ambient Air Pollution in Southern Ontario, Canada
Keywords: Air Pollution
Land Use Regression
Machine Learning
Mobile Monitoring

This thesis has two main objectives: examine if generating models based on linear representations of air pollution observations could help account for the sampling distance travelled during mobile monitoring and produce better performing models; second, investigate the difference in model performance when utilizing different mobile monitoring platforms within the same study with replicated routes to predict air pollution concentrations in an urban environment. Objective one was achieved by comparing the performance of models generated with a traditional point based methodology and a contemporary line based methodology. Results demonstrated that despite the benefit of incorporating sampling distance travelled, the line based approach produced models with similar performance as the point based models. Objective two was achieved by comparing models from two different monitoring modes; bicycles with air pollution sensors and a motor vehicle with research-grade instruments. Results indicated that the motor vehicle-based models outperformed the bicycle-based models for all assessment cases.
Eroticizing Egypt: Voyeurism and Commodification at the Petrie Museum of Egyptian Archaeology
Keywords: Colonialism
Commodification
Egyptology
Erotohistoriography
Ethnopornography
Petrie Museum

The collecting of “erotic” artifacts in 19th century Egyptology reveals the ways in which museums constructed knowledge around sex and grappled with sexual content in relation to the perceived value of artifacts. By looking at two types of artifacts, those with an overt sexual nature or meaning, and those which have been transformed to have an erotic intention in the context of a museum collection, this thesis explores how the commodification of museum objects impact perceptions and treatment of ancient Egyptian “erotic” material culture. This thesis uses the Petrie Museum of Egyptian Archaeology in London, England as a case study for synthesizing an erotohistoriographic analysis into the biography of an object due to its unique context of colonial intervention, Victorian sexual mores, collecting habits and motivations of its founders, Amelia Edwards and Sir W.M Flinders Petrie, at a moment in Egyptology’s infancy as a “scientific” field. Centering pleasure in the study of erotic artifacts reveals new epistemological potential in both Egyptology and Museology.
Development of Cell4D, a Spatial Stochastic Cell Simulator, and Applications towards CEACAM1 Pathway Modelling
Keywords: Calmodulin
CEACAM1
Cell4D
Computational modeling
Spatial stochastic simulation
T cell

Carcinoembryonic antigen-related cell adhesion molecules (CEACAMs) are known to be involved in biological functions such as metabolism, apoptosis, receptor signaling, and tumorigenesis. However, some mechanisms of CEACAM1 activation are still poorly understood from a systemic point of view, partially due to the complexity of the pathway. Here I present Cell4D, a graphical stochastic spatial cell simulator that I have developed to simulate hypothetical CEACAM1 pathways. Cell4D is more robust and complex than other publicly available meso-scale simulators with similar capabilities. I applied Cell4D to create computational models of CEACAM1 signaling systems and made functional predictions about the system through model perturbations. The simulation models predict that clustering increases the effective concentration of CEACAM1, and these clusters can self-propagate upon reaching a critical concentration threshold. In summary, the aim of this thesis is to further investigate mechanisms of CEACAM1 signalling in the context of T cells through computational modelling.
Using Micro-ultrasound to Investigate the Effectiveness of Short-term Rehabilitation following Focal Ischemic Stroke
Keywords: Imaging
Rehabilitation
Stroke
Ultrasound

Ischemic stroke leaves 40% of survivors with moderate to severe impairment. Understanding how rehabilitation affects brain structure and function will be critical in its effective application to individual patients and in its combination with promising new interventions. In this work we investigated the impact of two weeks of skilled reaching rehabilitation on motor function, cerebrovascular tortuosity, cerebral blood flow and neuronal activity on a rodent model. Micro-ultrasound, intracerebral array electrophysiology and Montoya staircase testing were used to characterize changes in the brain and motor function following stroke. Perilesional vessels were significantly more tortuous than vessels in the contralesional cortex with a further abolishment of hypercapnia-elicited homogenization of microbubble velocities in perilesional arterioles. Rehabilitation significantly improved skilled reaching and elevated neuronal power ratios. This current project highlights functional motor recovery and neuronal plasticity in the subacute stage following stroke in the absence of cerebrovascular changes using a dual imaging modality setup.
Fabrication of Multi-chamber Graphene Liquid Cell and Characterization of Liquid
Keywords: anodic aluminum oxide
bubble evolution
graphene liquid cell
liquid droplet
liquid phase TEM
two-stage evolution

In this study, a graphene/anodic aluminum oxide (AAO)/graphene liquid cell was fabricated. Five nanometer gold nanoparticles dispersed in trisodium citrate buffer were used as a test system to prove the quality of the liquid cell. The liquid was observed and characterized using a Hitachi HT7700 TEM. A two-stage liquid dynamical process was discovered when the liquid was irradiated by the electron beam, and the first stage is dependent on the amount of liquid. Besides, liquid droplets were observed in the liquid cell which could be explained by the surface effect of AAO membrane and graphene. The sandwiched nanopore liquid cell showed a self-closing effect and a good sealing quality of liquid sample, which would possibly enable a true single particle imaging and reconstruction in the future.