VictorJuiz/thesis huggingface dataset:
Compensation for Bioelectric Signal Changes in Chronic Selective Nerve Cuff Recordings: A Simulation Study
Keywords: Computational Modeling
Convolutional Neural Network (CNN)
Machine Learning
Neural Engineering
Peripheral Nerve Interface
Selective Recording

Peripheral nerve interfaces (PNIs) allow us to extract motor, sensory, and autonomic information from the nervous system and use it as control signals in neuroprosthetic and neuromodulation systems. Recently, the recording selectivity of PNIs has been improved using spatiotemporal patterns from multi-contact nerve cuff electrodes as input to a convolutional neural network (CNN). The performance of this approach during chronic implantations is not known. In this simulation study, approaches were evaluated for maintaining the selective recording performance in the presence of chronic implantation challenges (encapsulation tissue, electrode movements, and contact failures). This study demonstrated that a selective recording algorithm trained at baseline will fail over time due to changes in signal characteristics resulting from the chronic challenges. Results further showed that periodically recalibrating the selective recording algorithm can maintain its performance over time, and that machine learning techniques have the potential to reduce the frequency of recalibration.
Characterizing the Genome-wide Associations of Somatic Mutations and Chromatin Accessibility in Cancer
Keywords: Cancer Genomics
Epigenomics
Machine Learning
Mutational Processes

Somatic mutation rates in cancer genomes are associated with chromatin state and informative of tumor tissue of origin. However, earlier studies considered the chromatin states of cell lines and normal tissues, while those of primary tumors remain uncharacterized. We used a machine-learning approach to evaluate tumor-specific chromatin accessibility profiles as predictors of mutation rates in 2,500 whole cancer genomes with 23 million SNVs. Mutation rates were more accurately predicted by chromatin accessibility derived from tumours than healthy cells, suggesting that somatic mutagenesis is largely associated with the chromatin state of tumour cells rather than normal cells. Interestingly, melanoma mutations were better predicted by normal melanocyte chromatin accessibility, suggesting earlier mutational timing. Furthermore, chromatin state was an accurate predictor of carcinogen-induced mutation rates while the mutations of endogenous mutational processes were only weakly statistically associated. Integrative analysis of mutations and chromatin state provides us insight into tumour evolution and heterogeneity.
"What Happens Beyond the Talking": A Critical Policy Analysis of Sport and Recreation Equity Policies in Higher Education
Keywords: critical policy analysis
critical race theory
discourse
equity
social justice
sport and recreation

This thesis is a critical policy analysis of a Canadian urban university sport and recreation department’s equity policies. Through a documentary analysis and interviews, this research reveals the connection between what equity policies claim to achieve and the (in)equity experienced by students. Findings demonstrate that the policies advance discourses that evince neoliberal values of competition, commodification, and elitism. They also further notions of institutional excellence in equity, while simultaneously lacking a plan to achieve such equity. The study concludes with recommendations for policies rooted in anti-oppression principles that address the needs of marginalized students through structural change, including a measurable action plan. Equity policies should also name publicly histories of oppression and exclusion in Canada as the rationale for institutional commitments to supporting Muslim, transgender, queer, Indigenous, Black, and racialized students who do not identify with Eurocentric cultures of masculine and competitive athletics, or fitness routines revolving around normative bodies.
The Impact of an Informational Website on Behavioural Intentions and Attitudes about Patient Engagement in Research: A Mixed Methods Evaluation
Keywords: patient engagement in research
Social Learning Theory
Theory of Planned Behavior
website evaluation

Patient engagement in research (PER) is a rapidly emerging practice and resources are needed to prepare patients and researchers for collaboration. This study asked: What are the perceptions of patients and researchers about an informational website about PER, and how did it impact intentions and attitudes toward PER? A mixed methods approach was used, entailing pre-post surveys, focus groups, and web analytics. 49 patients and researchers participated. The findings revealed 1) intentions and attitudes toward PER decreased after viewing the website, however participants reported that the website did not impact, or positively impacted, their attitudes and intentions, and 2) overall satisfaction with the website, with variation in preferences for design, and a desire for more PER guidance, easily accessible information, and detail regarding diversity in engagement and compensation for participants. These findings reveal considerations for the development of online resources about PER and understanding divergent findings within mixed methods research.
Location and Size of Preterm Cerebellar Hemorrhage and Childhood Development
Keywords: Brain development
Cerebellum
Hemorrhage
MRI
Neurodevelopment
Preterm

Cerebellar hemorrhage (CBH) is a common complication of preterm birth but has never been quantitatively mapped. This thesis aimed to (1) measure and spatially define CBH and (2) examine the association between CBH size and location and neurodevelopmental outcomes, hypothesizing that larger anterior CBH would be associated with neuromotor dysfunction whereas posterior CBH would be associated with cognitive and behaviour problems. The MRIs of 221 very preterm neonates were segmented for CBH. CBH occurred mostly in the inferior posterior cerebellar lobes and CBH volume was associated with motor, visuomotor, and externalizing behavioural outcomes at 4.5 years independent of supratentorial brain injury. Moreover, CBH extending deeper into the cerebellum predicted adverse motor, visuomotor, and behavioural outcomes. Therefore, in preterm neonates, CBH size and location were associated with reduced neurodevelopmental function in a dose- and location-dependent fashion. The volumetric quantification and localisation of CBH may promote improved preterm outcomes via targeted intervention.
HiCSR: A Hi-C Super-resolution Framework for Producing Highly Realistic Contact Maps
Keywords: 3D genome
contact maps
Hi-C
HiCSR
Super-resolution

Hi-C data has enabled the genome-wide study of chromatin folding, and has led to important discoveries in the structure and function of chromatin conformation. Here, high resolution data plays a particularly important role as many chromatin substructures such as Topologically Associating Domains (TADs) and chromatin loops cannot be adequately studied with low resolution contact maps. However, the high sequencing costs associated with the generation of high resolution Hi-C data has become an experimental barrier. By carefully examining the properties of Hi-C maps and integrating various recent advances in deep learning, we developed a Hi-C Super-Resolution (HiCSR) framework capable of accurately recovering the fine details, textures, and substructures found in high resolution contact maps. The resulting framework can generate enhanced Hi-C maps more visually similar to the original high resolution maps, and also excels on a suite of reproducibility metrics produced by members of the ENCODE Consortium compared to existing approaches.
The Effect of an Anticipated Perturbation on Gait Variability and Stability during Treadmill Walking in Young, Healthy Adults
Keywords: Gait
Perturbation
Stability
Treadmill
Variability

Increased movement variability in quiet standing correlates with improved standing stability following a balance perturbation. It is unknown if this translates to gait. This study aimed to determine if increasing gait variability is a strategy to improve stability. We hypothesized that 1) spatio-temporal gait features will be more variable prior to an expected perturbation than during unperturbed walking, and 2) increased spatio-temporal gait variability pre-perturbation will correlate with improved stability post-perturbation. Sixteen healthy young adults completed 15 treadmill-walking trials under two conditions (unperturbed and an expected perturbation). Short- and long-term variability of step length, width, and time were calculated. Stability was defined as the number of steps to restabilization post-perturbation. Long-term step width variability was significantly higher pre-perturbation compared to unperturbed walking. There was no significant relationship between pre-perturbation variability and post-perturbation restabilization. These findings suggest that participants increased movement variability as an exploratory strategy in anticipation of a perturbation.
Fast Eye-in-hand 3D Scanner-robot Calibration for Low Stitching Errors
Keywords: Data stitching
Industrial metrology
Kinematic model
Manufacturing automation
Robot sensing systems
Structured light measurement

This thesis proposes a new eye-in-hand 3D scanner-robot calibration approach to realize low data stitching/registration errors during long-term continuous measurement of industrial parts. Eye-in-hand systems are commonly used for complete measurement of an object under test (OUT) from multiple fields of view (FOVs). To align the multiple FOVs into a single coordinate system, marker-free stitching assisted by robot’s positioning is attractive since it bypasses the cumbersome traditional fiducial marker-based method. Based on capturing calibration images from a 2D calibration target, scanner’s and robot kinematic model’s parameters are optimized. The challenges overcome include, (1) compensating for the center-detection error in scanner calibration; (2) avoiding the dependency of hand-eye calibration on DH parameters; and (3) calculating an accurate world-to-robot transformation. In the experiments, the mean stitching error was effectively maintained to be
Badiou, Freire, and the Pedagogy of Concentration
Keywords: Badiou
Dialectics
Freire
Marxism
Pedagogy

The renowned pedagogical theorist Paulo Freire made political subjectivity one of his core concerns, and he opposed approaches to subjectivity which considered the latter in terms of classical transparency and approaches which understand subjectivity in a deterministic fashion. I argue that Freire’s approach is an example of “concentration”, a concept I borrow from Alain Badiou’s Theory of the Subject. I use Badiou’s dialectical concepts in order to argue that Freire’s famous Pedagogy of the Oppressed is a Marxist text, but one that engages in constructing an anti-deterministic approach to subjectivity. I make this argument via a consideration of the problems of subjectivity and objectivity in the classical Marxist canon in order to show how Freire and Badiou depart from this canon while building upon it. This analysis is intended to pose in new terms the relationship between Freire and Marxism, and between Badiou and education.
Big Data Insights into MRI Demand and Wait Time
Keywords: Big data
Healthcare
Magnetic resonance imaging
Population-based study
Retrospective study
Statistics

The demand for Magnetic Resonance Imaging (MRI) in Ontario has been increasing annually, resulting in longer wait times for patients. This big data study links multiple administrative data sets to characterize and explore drivers of growth in MRI imaging in Ontario between 2008 and 2017. Our retrospective population-based big data study shows an increasing trend in the use of MRI scans, outpacing capacity. Demand increased the greatest amongst family physicians, and there were also wide variations in MRI referral rates among this group. Subgroup analysis demonstrates that family physicians practicing sports medicine ordered more extremities and spine MRIs. Multiple physician characteristics, including years of practice and physician demographics, also impacted the use of MRIs. Overall, 8% family physicians were consistent higher testers, who contributed to nearly 25% of extremities, spine, and brain MRI tests. These findings may help better target interventions to reduce variations in care and overuse.
Data-driven Parameter Learning without Groundtruth for Improving Robotic State Estimation
Keywords: Localization
Parameter Learning
Sensor Fusion
State Estimation

Probabilistic state estimation for robotics is a field that has greatly matured in recent years. Yet the performance of modern estimators is still heavily dependent on robot model parameters that can be difficult to determine from first principles. While it may be sufficient to hand tune these parameters, this is often time consuming or impossible due to the sheer number of unknown parameters. In this thesis, we investigate methods for learning parameters based on data, to come up with the parameter values most suitable for the particular robot and sensor. We first develop a novel continuous-time motion prior trained with data to improve an existing continuous-time estimation framework. We then provide a detailed investigation into parameter learning within a Gaussian variational inference setting using Expectation Maximization. We validate our work on various trajectory estimation problems using a 36 km long vehicle dataset collected as part of this work.
Generalizable Approaches for Tracking, Estimating, Optimizing, and Quantifying Uncertainty of Fuel Use in Earthworks Operations
Keywords: Construction
Discrete Event Simulation
Earthworks
Fuel use tracking
Greenhouse Gas Emissions

Fuel use in earthworks processes are responsible for a considerable portion of global anthropogenic greenhouse gas (GHG) emissions and are directly tied to operation costs. Environmental and financial interests are therefore tied to the mitigation of fuel use. There is limited research devoted to understanding how to estimate, and ultimately minimize fuel use in earthwork processes, prompting a detailed analysis into how factors related to equipment, operations, and worksite influence the consumption of fuel. These factors were investigated in a comprehensive review of literature related to earthwork emissions and fuel use. In seeking to address these inconsistencies found in reviewed fuel use tracking efforts, a set of recommendations for tracking influencing factors during earthworks fuel use studies was developed and outlined in detail. Additionally, a modelling approach was developed to accurately estimate fuel use, GHG emissions, activity duration, and cost in a variety of earthwork contexts.
Research Perspectives on the Marginalization of Core French Teachers: A Qualitative Meta-analysis and Research Agenda for Elementary-level Ontario Core French Education
Keywords: Core French
Education
Elementary Education
FSL
Ontario
Second Language

French as a Second Language (FSL) education is mandatory in Ontario. Research on elementary Core French education in Ontario has shown that its teachers are marginalized in practice. How this marginalization is positioned by researchers and what researchers recommend to end it are key foci of this thesis. Using a hybrid framework of complexity theory, critical theory, and language as right, the research perspective on the marginalization of Core French teachers is examined in order to form an agenda for future research. Dichotomy and variability in researchers’ positioning of the issue as well as in their recommendations are uncovered. A move toward grassroots-level activist research is highlighted, with a salient theme of agency and empowerment. A major implication of this research is the need to address the place of Core French within national bilingualism. Suggestions for future research include larger sample sizes, quantitative investigations, and interventionist research. L'enseignement du français langue seconde (FLS) est obligatoire en Ontario. La recherche sur l'enseignement du français de base au niveau primaire en Ontario ont montré que les enseignant.es sont marginalisé.es. Comment cette marginalisation est positionnée par les chercheurs et ce que les chercheurs recommandent pour y mettre fin sont les axes clés de cette thèse. En utilisant un cadre hybride de théorie de la complexité, de théorie critique, et de langage comme juste (Language-as-Right), les perspectives de la recherche sur la marginalisation des enseignants de français de base est examinée afin de former un agenda pour les recherches futures. La dichotomie et la variabilité du positionnement des chercheurs sur la question et aditionellement dans leurs recommandations sont découvertes. Un mouvement vers la recherche militante au niveau local est souligné, avec un thème saillant de l'agence et de l'autonomisation. Une implication majeure de cette recherche est la nécessité d'envisager la place du français de base dans le bilinguisme officiel du Canada. Les suggestions de recherche future comprennent des échantillons plus grands, des enquêtes quantitatives, et de recherche interventionniste.
Telemedicine use Amongst Homeopaths and Naturopaths in Ontario, Canada
Keywords: Complementary and Alternative Medicine
Health Services
Telemedicine

Telemedicine, in the form of online video consultations, holds great potential for the delivery of medical care. This research aims to investigate the extent of, rationale for, and the motivations for telemedicine use by homeopaths and naturopaths. State-regulated homeopaths and naturopaths in Ontario were surveyed. Survey questions captured telemedicine use, demographic and socio-economic data, and opinions regarding respondents’ motivations behind telemedicine use. The survey, conducted between October 2018-January 2019, had 183 homeopath and 366 naturopath respondents. Telemedicine consultations were performed by 65.6% of homeopaths and 32.5% of naturopaths in the previous 6 months. There were no significant differences between telemedicine users and non-users for gender, geographical location, and age. The best fit regression model of motivational factors comprised of attitude towards telemedicine and perceived ability to use telemedicine (Nagelkerke R-squared=.281). Telemedicine is used substantially by Ontario homeopaths. Attitude and perceived ability to use telemedicine were associated with telemedicine use.
A Computational Wind Engineering Framework for Studying Climate Change on High-rise Buildings in Dense Urban Areas
Keywords: climate change
Computational Fluid Dynamics (CFD)
k-ω turbulence model
Wind load

Structures in the built environment that are safe and serviceable under current wind loading conditions may experience problems in the coming decades as wind load characteristics get affected by rapidly changing climate. Given the high uncertainty in predicting future wind environment conditions, there is a need to formulate flexible adaptation strategies that mitigate climate change effects in urban regions. The present work proposes a multi-disciplinary framework to investigate and address the impact of climate change and the associated wind load effects on the built environment. As an example application of this framework, computational fluid dynamics (CFD) simulations are performed on a building located in downtown Toronto, under current and projected wind conditions to evaluate its response. The framework seeks to translate the range of predicted effects of climate change into actionable knowledge useful in the area of urban building design.
Investigating Mitochondrial Dysfunction in Bipolar Disorder: From Peripheral Biomarkers to Patient-Derived Induced Pluripotent Stem Cells
Keywords: Bipolar Disorder
Induced Pluripotent Stem Cells
Lactate
Mitochondria

Bipolar disorder (BD) is a neuropsychiatric illness characterized by cycles of high and low mood states. The pathophysiology of BD is not fully understood but studies show mitochondrial dysfunction may play a role. Our objective is to interrogate the link between mitochondrial dysfunction and BD using patient blood samples. We observe an increase in serum lactate and a positive correlation between lactate and circulating cell-free mitochondrial DNA (ccf-mtDNA) in BD. Our meta-analysis found elevated ccf-mtDNA in patients with psychiatric conditions, suggesting evidence of mitochondrial stress. We reprogram patient blood cells into induced pluripotent stem cells (iPSC) that are capable in differentiating into neural progenitor cells and we show exploratory work differentiating these into cortical neurons that will be used to investigate the role of mitochondrial dysfunction in BD. We highlight our findings in support of mitochondrial dysfunction in BD and a future direction in understanding BD using these iPSCs.
Quantification of Event-related Desynchronization under anAction-observation Prompting Paradigm
Keywords: Action Observation
Brain-Computer Interface
Electroencephalography
Event-Related Desynchronization
Rehabilitation

Brain-computer interface (BCI)-based rehabilitation techniques have recently shown promisefor restoring motor function in stroke survivors. BCIs detect the intent to move in brain signalsby identifying a pattern of neural activity called event-related desynchronization (ERD), andthen triggering the intended movement by some external modality, such as robotics. BCI-basedtherapy may be improved by enhancing the ability to detect ERD. This study examined theeffect of prompting various motor tasks with action observation (AO) as a paradigm for en-hancement of ERD. The magnitude, duration, and latency of ERD as well as the ability of aBCI to detect ERD were compared across several tasks with and without AO-prompting. Itwas found that AO-prompting reliably produced ERD in motor regions of the brain, but AO-prompted tasks were shorter in duration and smaller in magnitude than alternatively-promptedtasks used for comparison.
Characterizing a Novel Mutation in MECP2 using an hiPSC Model of Rett Syndrome
Keywords: dendrite complexity
iPSC
MEPC2
neurodevelopmental
rett syndrome
stem cell

Rett Syndrome (RTT) is a neurodevelopmental disorder in girls with mutations in the X-linked gene that encodes methyl-CpG-binding protein 2 (MECP2). Using neurons differentiated from patient-derived induced pluripotent stem cells (iPSC), I analyzed the MECP2 RNA levels, MECP2 protein levels, morphology, and extracellular electrophysiology of a novel L124W MECP2 mutation. My results show that L124W exhibits no change in RNA, protein, dendrite length, soma size, or electrophysiology but does show a subtle significant change in dendrite order and dendrite complexity. This is the first in vitro iPSC characterization of a mild RTT case. While developing a CRISPR/Cas9 protocol that will eventually genetically rescue the L124W mutation, I also generated the first iPSC knock-out lines for NEDD4L, a downstream target of MECP2. Overall, this work can be used to further elucidate MECP2 pathways and eventually identify treatments for RTT.