VictorJuiz/thesis huggingface dataset:
Resting-state fMRI and DTI Analysis of Prolonged Recovery following Mild Traumatic Brain Injury
Keywords: DTI
fMRI
functional connectivity
hyperconnectivity
mild traumatic brain injury
persistent symptoms

Currently there is an incomplete picture of the changes in brain physiology associated with prolonged recovery following mild traumatic brain injury (mTBI), with the majority of previous studies focusing on the short-term changes or a single aspect of pathophysiology. This study combined resting-state functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI) to examine both functional and structural alterations in brain physiology, including their association with clinical measures. Compared to healthy controls, mTBI patients with persistent symptoms showed significant alterations in cortical connectivity and white matter integrity, that were associated with symptom severity and performance on neurocognitive tests. The present study suggests that hyperconnectivity is an adaptive compensation to enhance neural function, whereas glial scarring is associated with unresolved symptoms.
Research Gaps in the Study of Microplastics: Method Development for Raman Automation, and Examining Relationships between Ecological Traits and Anthropogenic Particle Ingestion in a Deep-sea Food Web
Keywords: bioaccumulation
food web ecology
microplastics
Monterey Bay
raman spectroscopy
trophic transfer

Microplastics and other anthropogenic microparticles are an emerging class of contaminants in marine ecosystems. I explore two research gaps within the field of microparticle pollution: one related to improving efficiency and accuracy of microparticle quantification, and another related to the fate of microparticles in food webs. First, I validated the use of a non-polymeric adhesive to improve automated spectroscopy methods, as well as tested subsampling strategies to improve quantification efficiency. Second, I characterized the amount and diversity of microparticles ingested by species from a deep-sea food web of Monterey Bay, California. I assessed differences in particle ingestion in the context of ecological traits including habitat, diet, feeding strategy, and body size. I determined that species who occupied the lower-mesopelagic and bathypelagic zones were associated with a less diverse assemblage of particle morphologies compared to epipelagic and upper-mesopelagic species suggesting that where an animal lives in the water column influences exposure.
Thermal Control of a Novel Microsatellite Bus with Deployable Components
Keywords: Deployable
Microsatellite
Spacecraft
Thermal Control

With the emerging need for ever more capable microsatellites, the development of a novel microsatellite bus with deployable components was undertaken by Space Flight Laboratory. This platform, called DEFIANT, will provide a strong foundation for the next generation of microsatellites that will enable satellite constellations. As this is a new novel platform, there is a need for the development of a thermal control subsystem for the DEFIANT platform. This work presents an overview of heat transfer principles and orbital mechanics as is relevant for developing thermal control subsystems. The primary methods of thermal control for small spacecraft are introduced. A lumped mass network model is constructed and the impact of deployable structures predicted using a transient orbital analysis. A finite element model for the DEFIANT microsatellite platform is developed, the development philosophy is discussed, and the thermal control design is analyzed under simulation.
Effects of Mix Design and Curing on Resistance of Mortar and Concrete to Physical Sulfate Attack
Keywords: Concrete
Curing
Durability
Physical Sulfate Attack
Sodium Sulfate
Sulfate Attack

Physical sulfate attack (PSA) is a serious mechanism of concrete deterioration spurred by temperature and humidity changes. Current standard tests assessing sulfate attack measure length change whereas PSA manifests in mass loss. A preliminary test using mass loss as an indicator was developed previously and used to evaluate the influence of mix design on mortar resistance against PSA. This study extended this research by: further assessing the viability of this test method, evaluating different wet curing durations, and extending the research to concretes. Prisms were stored in 30% by volume (24.5% by mass) sodium sulfate solution and cycled for 100 thermal cycles between 5 and 30 °C. Lowering the water-to-cementitious materials ratio and adding slag cement were found to increase resistance against PSA for mortars and concretes. The effect of wet curing is less conclusive due to interference from differential sulfate exposure occurring during initial cycling using this test method.
Energy Injection for Mechanical Systems through the Method of Virtual Nonholonomic Constraints
Keywords: energy injection
virtual nonholonomic constraints

This thesis develops a theoretical foundation for the framework of virtual nonholonomicconstraints, which are relations between the generalized coordinates and generalized momenta of a mechanical system that can be enforced via feedback control. The theory is applied towards energy injection for two standard underactuated systems: the variablelength pendulum and the acrobot. Virtual nonholonomic constraints are designed for each system by examining human motion, and energy injection properties of these constraints are proven rigorously. The acrobot constraint is tested on a real-world acrobot, demonstrating highly effective energy-injection properties and robustness to a variety of external disturbances.
High Dispersion Planar Antennas for Frequency Beam Scanning
Keywords: antenna
frequency-scanning
leaky-wave

Leaky-wave antennas scan their main beam through space as frequency is modulated and are useful for many applications. Planar, loaded transmission-line antennas are a type of leaky-wave antenna that can be easily fabricated with commercial PCB facilities. In this work the scanning sensitivity, or relation between scan angle and frequency, is investigated for planar loaded transmission line leaky-wave antennas. Methods are developed to realize unit cells with a desired scan dispersion, which can be used to design antennas that scan through large areas of space within a small bandwidth. Examples are designed and fabricated in the Ka-band and tested to validate the methods used. One design has a measured scan sensitivity of 10.5 degrees-per-percent-bandwidth, the highest of any known work of this type. Another design exhibits a smaller beamwidth and larger gain, illustrating some trade-offs inherent to antennas with enhanced scan sensitivity.
Functional Characterization of Actin-interacting Protein 1 in the Drosophila Follicular Epithelium
Keywords: Actin
Actin-interacting protein 1
AIP1
Drosophila
Epithelium
F-actin

Actin filaments (F-actin) are essential for many cellular functions. Their dynamic remodeling allows various processes, including cell division, cell adhesion, cell polarization, and formation of stress fibres and cellular protrusions. One factor contributing to actin remodeling is Actin-interacting protein 1 (AIP1), a cofactor for cofilin in F-actin depolymerization. I used the Drosophila follicular epithelium to investigate the function of AIP1 in regulating the actin cytoskeleton and associated structures. AIP1 depletion caused an increase in F-actin amounts in the apical cytocortex and ectopic globular F-actin aggregates. Additionally, it resulted in microvilli of altered length, extended basal stress fibres, and defects in the distribution of adherens junction components and the spectrin cytoskeleton. Moreover, AIP1 reduction led to nuclear enlargement and multi-nucleation in follicle cells, suggesting defects during cytokinesis. These findings suggest that AIP1-mediated actin turnover is critical for normal actin organization, which is important for cellular protrusions, cell adhesion, and cell division.
Investigating a Question Prompt List to Support Patient-Centred Care for Women with Hypertensive Disorders of Pregnancy at Risk for Cardiovascular Disease
Keywords: Cardiovascular Disease
Hypertensive Disorders of Pregnancy
Implementation Science
Patient-Centred Care
Question Prompt Tool
Women's Health

Introduction: Hypertensive disorders of pregnancy (HDP) lead to increased cardiovascular disease (CVD) risk. Clinicians, and consequently women, are unaware of this link. Question prompt lists (QPL) may improve patient-centred care (PCC) by supporting discussions about HDP and CVD risk.Methods: This thesis included a scoping review to identify the characteristics of effective QPLs; and qualitative interviews to understand how a QPL might support PCC for women with HDP. Results: The scoping review included 53 studies. QPLs were most commonly 1 page long and had 38 questions. Interviews included 22 women with HDP. All women said a QPL would improve PCC, by raising awareness about HDP and CVD risk, helping them avoid clinician dismissal, and helping them prepare for consultations. Conclusions: This thesis contributes to a greater understanding of QPLs, and PCC for women with HDP, which may ultimately lead to improved PCC and equality in the healthcare system.
Exploring the Impacts of Motion-based Technology on Balance, Movement Confidence, and Cognitive Function Among People with Dementia and Mild Cognitive Impairment
Keywords: Balance
Cognition
Dementia
Exercise
Motion-based technology
Movement

Motion-based technologies can encourage exercise, but the impacts of motion-based technologies for people with dementia and Mild Cognitive Impairment (MCI) are underexplored. This study examined the impacts of a motion-based technology intervention on balance, movement confidence, and cognition among people with dementia and MCI. Twenty-eight participants took part in a group motion-based technology intervention twice weekly for 10 weeks. Participants completed the Mini Balance Evaluation Systems Test and the Montreal Cognitive Assessment at pre- and post-intervention. Intervention video recordings were captured during weeks one, five, and 10 to examine movement confidence. Data were analyzed using related-samples Wilcoxon signed rank tests. While participants experienced substantial cognitive, balance, and mobility impairments, their movement confidence was relatively high at baseline. Among participants who completed the study, there were no significant changes in balance, movement confidence, or cognition. The study highlights a need for physical rehabilitation for this population, alongside interventions for their cognition.
Multifunctional Bio-based Chitin Materials: Fabrication, Characterization and Applications
Keywords: aerogel
chitin
ionic liquids
nanowhiskers
thermosets

Chitin is the second most abundant biopolymers in the world owning outstanding mechanical strength, biocompatibility, and potential of functionalization. The development of various functional chitin materials aims for the high performance as well as the sustainability in different applications. This thesis reviews the current progress of chitin processing and multifunctional chitin materials, addressing two concerns in terms of the dispersion of chitin nanowhiskers in epoxy nanocomposites and development of a non-toxic chemical crosslinker for chitin aerogels. The first study developed an ionic liquid-chitin-epoxy composite with high chitin nanowhisker loading by incorporating ionic liquids. The samples have been characterized for structure-property relationship, demonstrating the reinforcing effect of chitin nanowhisker and dispersing role of ionic liquids. The second study developed a double crosslinked chitin aerogel via etherification with high porosity, low density, and improved mechanical properties. EGDE has been demonstrated an effective crosslinker and excessive of which causes emulsion and macroporous structure.
A Big Data Approach to Accounting Fraud Detection Using Data Envelopment Analysis and One Class Support Vector Machine
Keywords: Anomaly Detection
Data Envelopment Analysis
One Class Support Vector Machine

This thesis investigates a method to use Data Envelopment Analysis (DEA) in the context of big data to improve data analysis for the volume and velocity aspects of big data. First, DEA is used to identify fraud indicators in a large dataset. One class support vector machine (OC-SVM) is then used to identify outliers in the same dataset to evaluate the performance of the proposed DEA model. A second DEA model is proposed as a variable selection tool to enhance the performance of an OC-SVM model. The results show that although the proposed DEA model on its own is not as effective in detecting anomalies as OC-SVM, there is potential to use DEA as a variable selection tool to enhance the training and prediction process for anomaly detection using OC-SVM. The parameters and methods examined in this thesis are not exhaustive, but it does provide a baseline for future work.
Model Extraction in the Context of Audio Classifiers
Keywords: Adversarial Machine Learning
Audio Processing
Computer Security
Machine Learning
Model Extraction

Model extraction is the process of reverse-engineering the parameters of a machine learning model exposed through a query interface. Prior work on this class of attacks focuses on the vision domain for the most part. We demonstrate that subtle, yet crucial, distinctions between learning from audio and vision preclude us from directly applying existing model extraction attacks to audio. A key example is that the discriminative features learned by raw audio models appear to be more task-dependent. To extract audio models we thus need to carefully query the victim model to expose these task-specific or difficult-to-learn representations. To this end, we propose a simple task-dependent extraction approach using generative models to synthesize a diverse pool of candidate queries. Our experimentation shows this approach makes it possible to extract a victim model trained on LibriSpeech using a surrogate dataset, Voxceleb with a test accuracy of 76.51% given a budget of 3M queries. L'extraction de modèles correspond au processus visant à reconstruire par rétro-ingénierie les paramètres d'un modèle d'apprentissage automatique accessible via une interface de requête. Les travaux antérieurs menés sur cette classe d'attaques se sont concentrés pour la plupart sur le domaine de la vision. Nous démontrons l'existence de différences subtiles mais cruciales entre les domaines de l'audio et de la vision qui empêchent l'application des techniques existantes dans le cadre de l'audio. Un exemple marquant nous est donné par le fait que les caractéristiques discriminantes apprises par les modèles travaillant sur des données audio brutes semblent plus dépendantes de la tâche à résoudre qu'en vision. L'extraction de modèles d'audio nécessite ainsi l'utilisation de requêtes bien choisies qui exposent les représentations apprises. Dans ce but, nous proposons une approche d'extraction simple et dépendante de la tâche à résoudre qui utilise des modèles génératifs afin de synthétiser un ensemble divers de signaux candidats pour les requêtes. Nos expériences montrent que notre approche permet d'extraire un modèle cible entraîné sur LibriSpeech à l'aide d'un jeu de données de substitution, Voxceleb, avec une précision de 76,51 % et un budget de 3 millions de requêtes.
Enabling Skeletal Muscle Repair and Functional Recovery following Denervation-induced Injury Using Ultrasound Mediated Gene Delivery (UMGD)
Keywords: denervation
FAPs
gene therapy
micro bubbles
skeletal muscle
ultrasound

Skeletal muscle is essential for mobility and its health relies upon innervation. Peripheral nerve injury denervates target skeletal muscle, causing immediate loss of function, atrophy, and development of fibrosis. Delayed re-innervation can result in permanent functional loss, leading to a myriad of physical, financial, social, and psychological burdens on affected individuals. Ultrasound-mediated Gene Delivery (UMGD) is a relatively novel technique that has been shown to provide localized and effective gene therapy in vivo. We hypothesize that UMGD of myogenic genes IGF-1, VEGF, and Ang-1 would sustain the mass and regenerative potential of denervated muscle awaiting reinnervation. After two weeks, UMGD of these genes mildly increased gross muscle weight, Type II fibre CSA, and vascularization compared to denervated muscle given no transgene. We have shown that UMGD is a viable model for targeted gene delivery to skeletal muscle through partial prevention of the atrophy and vascular loss induced by denervation injury.
Uncovering the Molecular Mechanism of Cholesterol Uptake in Class B Scavenger Receptor LIMP-2
Keywords: Computational biology
Molecular dynamics simulations

Class B scavenger receptor proteins fulfill a variety of functions in immunity and homeostasis, including key roles in preventing heart disease, currently the leading cause of death worldwide. Recent evidence indicates that one class B receptor, LIMP-2, facilitates the uptake of cholesterol from bound lipoproteins to the lysosomal membrane and may therefore play a role in regulating cholesterol homeostasis. I hypothesize that uptake occurs through the large, predominantly hydrophobic cavity that spans the LIMP-2 ectodomain. To test this hypothesis, I perform extensive atomistic molecular dynamics simulations of cholesterol and LIMP-2 successively in solution, in a membrane mimetic, and using a novel reverse micelle approach to model a membrane and lipoprotein bound state. I demonstrate that cholesterol has an orientational preference in the LIMP-2 cavity and propose a novel ‘reversase’ mechanism of cholesterol uptake that I then sample using an enhanced-sampling algorithm. Our results indicate that the putative pathway includes a large side pocket which may enable cholesterol to flip within the protein, thereby facilitating its insertion into lipid membranes. Overall, our findings support the reversase mechanism of cholesterol uptake through LIMP-2 and raise the possibility that similar pathways for lipid uptake exist in other class B scavenger receptors, expanding our understanding of the molecular processes that mitigate heart disease risk.
Being Academically At-risk and Building Capacity for Self-regulated Learning in University
Keywords: academic failure
academically at-risk
educational psychology
higher education
self-regulated learning
university

University students who experience academic failure are at risk of becoming curbed by a pattern of failure in the absence of adequate self-regulatory processes. Repeated academic failures can result in academic probation or suspension, and the student is labeled academically at-risk (AAR). Adapted from Pintrich and Zusho’s (2007) model for student motivation and self-regulated learning (SRL) in the postsecondary classroom, this study proposes a model specific to the AAR student experience. Using existing literature on academically struggling student SRL and motivation, and psychometric analyses of an academic intervention’s assessment of the study habits and attitudes of AAR undergraduate students, this research investigates SRL within the AAR student experience, expands on the original model’s areas of SRL (cognition, behaviour, motivation and affect, and context), and demonstrates the intervention’s effect on AAR students’ SRL capacity. Future directions for AAR-specific SRL research, refinements to the model and assessments, and other implications are discussed.
Investigating the Role of Onecut1 in Establishment of Cell- type-specific Enhancers during Mouse Motor Neuron Differentiation
Keywords: ChIP-seq
Differentiation
Embryonic Stem cells
Genome wide
Spinal motor neurons
Transcription factors

Spinal motor neuron identity is established by three programming transcription factors (TFs): Ngn2, Isl1 and Lhx3. Isl1 and Lhx3 TFs bind to enhancers in nascent motor neurons regulating expression of many effector genes. In maturing motor neurons, Lhx3 downregulation results in relocation of Isl1 to Onecut1 TF bound enhancers. I characterized the role of Onecut1 in spinal motor neuron differentiation using CRISPR-Cas9 system to generate a Onecut1 mutant mouse embryonic stem (ES) cell line, followed by in-vitro differentiation of these ES cells into spinal motor neurons. Analysis for global gene expression changes revealed attenuated expression of a subset of motor neuron genes. Whereas, chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) showed global redistribution of Isl1 binding and changes in enhancer activity in absence of Onecut1. Together, my analyses revealed association of Onecut1 with expression of a subset of neuronal genes via protein-protein interaction with Isl1 at motor neuron enhancers.
Whole-genome Sequencing Approach to Characterize the Population Structure of Bacillus cereus at a Human Milk Bank
Keywords: Bacillus cereus
Bioinformatics
Milk banking
Pangenome
Phylogenetics

Stringent milk handling protocols including pasteurization are used at human milk banks serving critically-ill, preterm neonates. However, up to 30% of donated human milk is lost to contamination with the potentially neonatal pathogen Bacillus cereus, whose spores can resist pasteurization. Here, we used genomics to evaluate the population structure of a collection of B. cereus organisms recovered from pre- and post-pasteurized human milk donated to a human milk bank, from patients seeking care at that facility and from the hospital environment. Pangenome analysis revealed an unexpectedly high level of genetic diversity within the milk bank/hospital strain population. Phylogenetic analyses using core-genome polymorphisms did not permit identification of sources of human milk contamination by B. cereus. Genome-wide association studies revealed that variants of genes involved in sporulation are overrepresented among organisms recovered from post-pasteurized milk. The results may be used to improve milk banking protocols and research around the world.
VOCs in Toronto During the 2020 COVID-19 Lockdown and Potential Anthropogenic Isoprene and Monoterpenes
Keywords: air quality
atmospheric chemistry
environmental chemistry
monoterpenes
PTR-MS
VOC

Volatile organic compounds can have either anthropogenic or biogenic sources. With the compositional shift of anthropogenic emissions towards volatile consumer products, it is becoming increasingly important to better understand the sources of VOCs in urban settings. In this work, the trends of VOCs in Toronto and various other Canadian locations are explored. Outdoor ambient VOC data were collected from the months of March to June in 2020 during the COVID-19 lockdown. Traffic-related data were analyzed to determine if there were changes in mixing ratios brought about by the change lockdown. Evidence for potential anthropogenic sources of isoprene and monoterpenes in Toronto is also explored. It was found that the lockdown brought about lower than normal mixing ratios of benzene and toluene. As well, from analysis of National Air Pollution Surveillance (NAPS) data, there is evidence to show that there are non-biogenic sources of monoterpenes in Toronto.