VictorJuiz/thesis huggingface dataset:
The Anchored Separated Representation for High Dimensional Problems
Keywords: Curse of Dimensionality
Function Decomposition
High Dimensional Problems
Sparse Approximation

Although topics in science and engineering that involve dimensions beyond x-y-z appear obscure, in truth numerous examples abound. For instance, uncertainty quantification requires approximating and integrating functions with many inputs, while the study of non-linear random vibrations involve PDEs whose dimensionality scales with the system's degrees of freedom. Such problems are numerically difficult since the application of classical mesh based techniques incur computational demands that scale exponentially with the dimension; this is the curse of dimensionality. In this thesis we formulate two tractable numerical methods that circumvent this curse by assuming sparsity in the model representation. The first method, the anchored separated representation, is a provably minimal decomposition for functions that are sparse in a multiplicative sense. The second method is an iterative extension for approximating functions that are sparse in rank. We illustrate with numerical examples the application of both methods to a broad class of high dimensional problems.
Bread or Circuses? Parsing Representative and Representational Democratic Discourse on U.S. Political Blogs
Keywords: blogs
democracy
discourse
identity
pragmatism
psychoanalysis

This thesis finds empirical support for Jodi Dean's theory of declining symbolic efficiency through a qualitative content analysis of discourse concerning the 2013 U.S. government shutdown on political blogs. Themes of this thesis explore reflexivity, decontextualization, and an erosion of meaning brought about by changing media technologies and practices. Humanistic analyses of media and politics by scholars such as Benkler (2006) and McChesney (1999) are contrasted with works by Gitlin (1980), Postman (1985), and Dean (2010), who see media systems operating outside human control. This study's methodology relies upon Knight and Johnson's (2011) pragmatic justification for democratic institutions. The analysis uses a system of categories to describe statements about political strategy along four dimensions: operant; method of action; operand; and the consequence of the strategy. This study identifies important distinctions between textual descriptions of nominal and instrumental strategy; it is argued that nominal discourse represents the influence of symbolic inefficiency.
A Spatial Analysis of Pedestrian Injury in the City of Toronto
Keywords: Age
Pedestrian safety
Spatial Analysis

The City of Toronto experienced a ten-year high in pedestrian fatalities last year and has the highest pedestrian collision rate of Canadian cities. Understanding the geography of pedestrian motor vehicle collisions (PMVCs) can provide evidence to inform policy and planning targeting increased walking while reducing pedestrian injury risk. This thesis explores spatial patterns of PMVCs in the City of Toronto, with a specific focus on two particularly vulnerable road users; children and seniors. Distinct spatial patterns of PMVCs and injuries by type and age are found. This finding is further investigated by exploring the relationship between an attempt to measure equity across neighbourhoods in Toronto and pedestrian injury risk. The results suggest age- based differences in the relationship between neighbourhood equity indicators and PMVCs. A higher PMVC and injury risk for children was observed in neighbourhoods with poorer equity outcomes, while no significant relationship with equity outcomes was observed for seniors.
Evaluation of the Shaping Characteristics of ProTaper Gold, ProTaper NEXT and ProTaper Universal Systems in Curved Canals and the Analysis of Torsional Profiles of New and Used Instruments
Keywords: canal transportation
micro-computed tomographic imaging
nickel-titanium instruments
root canal preparation
rotary instruments
torsional failure

Shaping characteristics and torsional profiles of the ProTaper Gold system (PTG) were compared with that of ProTaper NEXT (PTN) and ProTaper Universal (PTU) systems. Twenty-four mandibular first molars with 2 separate mesial canals were matched anatomically by micro-CT and prepared with rotary systems (n =16) to F2 or X2 instruments, respectively. Co-registered images were evaluated for 2- and 3-dimensional morphometric measurements. Maximum torque and angle of deflection were determined for 30 new or used PTG, PTN and PTU X2 or F2 instruments. Data was statistically compared using Kruskal-Wallis or Bonferroni/Dunn tests for post hoc and 1-way ANOVA tests (α=5%). PTG and PTN produced less transportation and % decrease in dentin thickness than PTU. PTN had less canal wall contact than PTG and PTU. PTN demonstrated the lowest maximum torque and angle of deflection at fracture and overall mean torque and angle of rotation at fracture decreased after use.
Re-evaluating Secondary Disinfectants as Sentinels of Contamination and Using a Systems Vulnerability Model
Keywords: Distribution System
Drinking Water
Secondary Disinfectants
Secondary Disinfection

To build a framework in which secondary disinfectants can be quantitatively evaluated, three tasks were performed: (1) A sampling campaign was conducted at a community using an alternative secondary disinfectant (HuwaSan peroxide) to evaluate various water quality parameters; (2) bench-scale experiments examined the efficacy of different disinfectants as sentinels of contamination; and (3) a systems vulnerability assessment was performed (EPANET-MSX). The results show that: (1) HuwaSan, can limit DBP formation while maintaining acceptable water quality in terms of the parameters measured; (2) chlorine was observed to be the most appropriate sentinel of intrusion under the tested conditions; and (3) under modeled conditions, E. coli propagation was controlled by all tested disinfectants. For Giardia intrusions, Cl2, ClO2, and HSP achieved 3-log inactivation between 30-150 minutes, although an assumed inactivation rate for HSP was used. The same inactivation required chloramines and H2O2 between 330-1180 and 170-910 minutes, respectively.
Examining the Function of β-catenin at Adherens Junctions during Dorsal Closure and the Formation of the Ventral Epidermis in Drosophila
Keywords: Adherens junctions
Armadillo
Cadherin-catenin complex
Dorsal closure

Adherens junctions (AJs) consist of Cadherin-Catenin Complexes (CCCs); each CCC contains DE-cadherin, p120catenin, β-catenin (Armadillo in Drosophila) and α-Catenin. The question addressed here was whether β-catenin functions primarily to physically link DE-cadherin to α-Catenin or it has additional regulatory function in AJ stability. Dorsal closure (DC) defects in cadherin-deficient embryos are partially rescued by fusion proteins that directly link DE-cadherin to α-Catenin without recruiting Armadillo/β-catenin to AJs. This suggests that Armadillo at AJs is important for DC apart from being a linker. However, ventral defects were completely rescued by the same chimeras, indicating that Armadillo/β-catenin has no essential regulatory function at AJs in the ventral epidermis. Lastly, DC defects in Armadillo/β-catenin-deficient embryos were only partially rescued by the expression of DE-cadherin α-Catenin chimeras perhaps due to compromised Wnt signalling. Therefore, Armadillo/β-catenin has a general essential function in linking DE-cadherin to α-Catenin but a tissue-specific role in controlling AJ dynamics.
The Formulation of a Comprehensive Strategy for Computed Tomography Radiation Dose Optimization in Ontario
Keywords: Computed tomography (CT)
policy development
policy evaluation
radiation dose management
radiation dose optimization

As the awareness for the cancer risks associated with diagnostic computed tomography (CT) exams rise, countries and institutions have begun to prioritize dose optimization. Currently, Ontario’s only regulation for CT operation does not address dose management. This study aimed to develop an achievable and comprehensive model for CT dose management regulations in Ontario. A relationship analysis of evaluation results from the Regulatory Assessment for CT (RACT 2) and dose level comparisons was performed to elicit factors that are predictive of highly effective regulations. Qualitative interviews with jurisdictional representatives, radiologists and medical physicists extracted the facilitators and barriers to uptake of CT regulations. Ontario’s model contained minimum requirements to initiate dose management efforts, and four possible dose optimization specific approaches, which are diagnostic reference levels, compliance monitoring, peer-review process and radiation protection committee. It is recommended that at least one specific approach be adopted by Ontario’s new CT dose management regulations.
A Spiking Circuit Model of Sequence Learning
Keywords: model
plasticity
process memory
sequence learning
spiking
STDP

The ability to integrate information over time is fundamental to cognition. Any sensory experience, from object recognition to speech comprehension, utilizes this ability. Contrary to traditional models in which memory and perception are supported by separate circuits, recent work has demonstrated perceptual circuits can integrate information over time, as their response to an input at one moment may depend on what happened seconds earlier. We implemented a spiking model utilizing spike-timing dependent synaptic plasticity in a localized visual cortical circuit to investigate how sensory circuits are able to integrate information over time. We demonstrate that a lengthening circuit memory develops as a result of repeated exposure to a stimulus and that repeated exposure also leads to stronger synapses between neurons processing the input as well as associating sequential stimuli.
Characterization of Novel Glucagon Receptor Interactors that Modify Receptor Activity
Keywords: Glucagon receptor
Glucose production
Hepatocytes
Interactome
Membrane proteins

Glucagon helps maintain blood glucose homeostasis by stimulating gluconeogenesis and glycogenolysis. Elevated glucagon levels have been reported in type 2 diabetics, and may be in part responsible for their abnormally high blood glucose. A comprehensive understanding of glucagon receptor regulators is currently unavailable. Members of my lab performed a mass spectrometry screen to detect glucagon receptor interactors, 5 of which were validated to be true interactors by co-immunoprecipitation and Western blotting. The project outlined in this thesis began with the functional characterization of these interactors. Two interactors, low-density lipoprotein receptor (LDLR) and transmembrane emp24 domain trafficking protein 2 (TMED2) significantly enhanced glucagon stimulated glucose production, while tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta (YWHAB) lowered glucagon stimulated glucose production in primary hepatocytes. Because of YWHAB’s ability to lower glucose production, the underlying mechanism was explored and evidence suggests YWHAB enhances endocytosis of the glucagon receptor into the cell following glucagon stimulation.
The Anatomic Connectome and Functional Dissection of the Caenorhabditis elegans First-stage Larvae (L1) Motor Circuit
Keywords: calcium imaging
c elegans
development
locomotion

During development, neural networks exhibits anatomic and functional modifications yet the activity patterns change remains poorly understood. The neural circuit controlling locomotion of C. elegans undergoes major reconstructions at the end of first-larval (L1) stage. In adults, the ventral/dorsal body wall muscles are symmetrically innervated by cholinergic and GABAergic motor neurons (MNs). Cholinergic MNs innervating ventral muscles are not derived during early L1 stage, yet the animals can still generate undulation. This study addressed how L1 C. elegans produces undulation and the mechanism underlying muscle innervations. We demonstrated that the activities of dorsal cholinergic MNs are required for both dorsal and ventral muscle contraction, and the GABAergic MNs mediate only ventral muscle relaxation. This indicated a differential synaptic wiring between MNs and muscles in L1 to permit undulation. Through this comparative analysis between juvenile and adult locomotion, we hope to provide insights on principles of behavioral adaptation during sensorimotor development.
Polyelectrolyte Multilayers: an Investigation into their Assembly and Behavior with Diffraction Based Sensing
Keywords: diffraction
diffraction sensing
polyelectrolyte multilayer

A diffraction based sensing set-up was evaluated for use in monitoring the assembly of polyelectrolyte multilayers (PEMs). PEMs are thin films assembled via the layer-by-layer method, which consists of exposing a substrate to polyanions and polycations in sequence. Understanding the fundamental behavior of PEMs is instrumental to designing their properties to fulfill unique functions. In this work, diffraction based sensing is explored as a method to monitor the build-up of multilayers. The initial polymer layer is printed as a diffraction grating pattern and the PEM is assembled on top resulting in a change in height of the grating. This change in height can be monitored by the change in intensity of the diffracted spots. To demonstrate diffraction sensing is sensitive to PEM assembly, experiments testing its response to salt concentration, polymer concentration, and post assembly processing were carried out.
Characterization of the Immune Basis for Reduced IFN-α in Serologically Active Clinically Quiescent SLE Patients
Keywords: Interferon
SACQ
SLE

Serologically active clinically quiescent (SACQ) patients with systemic lupus erythematosus (SLE) are clinically quiescent despite the presence of autoantibodies. SACQ patients differ from serologically active clinically active (SACA) patients in terms of decreased levels of IFN-α and IFN signature. Given the role of IFN-α in SLE, we sought to determine the mechanisms underlying the lack of type I IFN elevation in SACQ patients. In assays containing peripheral blood mononuclear cells and nuclear extracts, SACQ serum induced decreased levels of IFN-α compared to SACA serum. Mixing experiments revealed that there are factors in SACQ serum that inhibit IFN-α production. The presence of anti-IFN-α antibodies was found in a small proportion of SLE patients and correlated with the ability to block IFN-α in-vitro but not with a decreased IFN signature in-vivo or clinical activity. These results suggest that SACQ patients have multiple mechanisms that lead to their decreased type I IFN production.
Deficiency of Myelin Proteins during Brain Development in Fragile X Mice
Keywords: Autism
Epidermal growth factor
Epidermal growth factor receptor
Fragile X Syndrome
Myelination
Myelin basic protein

Fragile X syndrome (FXS) is the most common inherited form of mental impairment and the leading genetic cause of autism. Our laboratory has previously reported that myelination is delayed in the cerebellum of a mouse model of FXS. In my study, I assessed the spatial and temporal aspects of this myelination defect and found that the defect occurs throughout the brain in the early developing fragile X mouse. Additionally, I also examined the levels of epidermal growth factor receptor (EGFR) and two of its ligands but found little to no deficiencies in the fragile X brain. However, epidermal growth factor (EGF) levels in the plasma and thyroid of adult fragile X mouse were found to be significantly reduced. Lastly, the fragile X mice were treated with intranasal heparin binding EGF-like growth factor (HB-EGF) in an attempt to rescue the myelination defect but the treatment did not promote early postnatal myelination.
Driving under Involuntary and Voluntary Distraction: Individual Differences and Effects on Driving Performance
Keywords: Driver Distraction
Driving Simulator
Human Factors
Involuntary Distraction
Load Theory
Voluntary Distraction

Distracted driving compromises safety. Distractions stem from intentional engagement in secondary tasks (voluntary) or an inability to supress non-driving related information (involuntary). This thesis aims to understand, through two driving simulator experiments, how involuntary and voluntary distraction affect drivers and individual differences in susceptibility to either type of distraction. Findings show involuntary and voluntary distraction degrade driving performance. Drivers appear more cognisant of voluntary distractions compared to involuntary distraction. They compensate for their accelerator release delays in response to lead vehicle braking by transitioning more quickly to the brake pedal under voluntary distraction, but not under involuntary distraction. Drivers self-reporting frequent distraction engagement in real-world driving glanced more frequently at the voluntary distraction task used in the experiments and drivers self-reporting greater everyday distractibility had longer glances toward involuntary distraction stimuli. Involuntary distraction engagement was not related to the manipulated environmental visual complexity nor inhibition ability measured through cognitive tasks.
Measuring the Young's Moduli of Sugar Cross-linked Native Type I Collagen Fibrils
Keywords: Atomic force microscopy
Collagen
Cross-link
Fibril
Nanoindentation
Sugar

Collagen is the most important structural protein in the human body, providing tissues with increased structural rigidity and elasticity. Through ageing, collagen-containing tissues such as the myocardium stiffen. This gradual loss in tissue elasticity can lead to pathogenesis, and can further be expedited through diabetes mellitus. This stiffening may be attributed to collagen cross-linking initiated through prolonged exposure to reducing sugars in blood. Atomic force microscopy (AFM) was employed to image native collagen fibrils, and measure their reduced Young’s moduli via nanoindentation, to quantify the impact of sugar-induced cross- linking. Comparing control and D-ribose-incubated (sample) fibrils revealed a statistically significant difference between their average reduced moduli, which was observed in collagen fibrils exposed to glutaraldehyde, a standard biological cross-linker. D-ribose-induced cross-linking was verified by sample fibrils displaying resistance to acid degradation via monitoring their turbidity. These experimental findings revealed an increase in collagen fibril stiffness due to D-ribose-induced cross-linking.
Risk Factors for High-risk, Oncogenic Human Papillomavirus (HPV) anal Infection in HIV-positive and HIV-negative Men who have Sex with Men (MSM)
Keywords: Anal cancer screening
Human immunodeficiency virus
Human papillomavirus
Men who have sex with men
Sexually transmitted infections

Background: Most anal cancers are caused by high-risk (HR)-HPV, occurring at much higher rates in MSM. There is little evidence on specific risk factors for HR-HPV in this population. Objective: To determine sexual and behavioural risk factors for HR-HPV anal canal infection. Methods: Cross-sectional study recruiting a clinic-based MSM sample. Participants completed a questionnaire, and had HPV/STI testing. Multivariable logistic regression was performed to assess HR-HPV risk factors. Results: 442 MSM were recruited: 267 HR-HPV-positive, 162 HR-HPV-negative. Multivariable analyses revealed risk factors associated with HR-HPV infection: HIV status (OR: 1.86, 95% CI 1.20-2.89); current smoking status (OR: 2.24, 95% CI 1.33-3.79); and >50 lifetime sexual partners (OR: 2.37, 95% CI 1.05-5.35). Conclusions: This study highlights important risk factors for HR-HPV anal infection. On a background of limited evidence for HPV screening modalities, this information may shed light on novel ways to risk stratify MSM to further anal cancer screening interventions.
Tropospheric Ozone Variations over North America
Keywords: Ozone
Ozonesonde
TOST
Trends
Troposphere
Variations

The spatial and temporal variations in tropospheric ozone over North America from the 1970s to 2000s are studied using the newly developed Trajectory-mapped Ozonesonde dataset for the Stratosphere and Troposphere (TOST) and the ozonesonde data. The variations in the lower, middle, and upper troposphere are examined in long-term, by decade and season. Throughout the decades, the highest ozone concentrations generally appeared over central mid-latitudes of North America in the lower and middle troposphere, while in the upper troposphere, high concentrations appeared over the Arctic. The overall ozone trends in the four decades averaged over the North America are positive, increasing with altitude. TOST is compared with the ozonesonde data at selected stations and both datasets correlate closely, stronger in high latitudes. TOST is resolved in latitude, longitude, and altitude so new insights gained from this study on the variations of tropopsheric ozone in these dimensions are particularly valuable.
The Privacy/Security Tradeoff for Multiple Secure Sketch Biometric Authentication Systems
Keywords: Biometrics
Coding Theory
Information Theory
Optimization
Privacy
Security

When designing multiple biometric authentication systems, there is tension between minimizing privacy leakage and maximizing security. This work studies the tradeoff between the two measures for jointly designed "secure sketch" systems. Secure sketch is a biometric system architecture where, as with error-correcting codes, a system is characterized by a parity-check matrix over a finite field. Single systems have been widely researched, but little is known about the privacy and security of joint designs, when leakage of one system can compromise the security of the others. This work introduces worst-case measures of privacy leakage and security for sets of systems and studies the tradeoff between them: First by studying the algebraic structure of the problem, then through a continuous relaxation of the problem (in a restricted case) and performing optimizations. An analytic expression for the tradeoff in that restricted case is proposed which aligns with simulation results.
Measuring Changes in Membrane Structure and Rhodopsin levels in Drosophila Melanogaster Retinas using THG Microscopy
Keywords: Drosophila
Pupal Development
Retina
Rhodopsin
THG microscopy

Third harmonic generation (THG) microscopy is a valuable imaging modality that can be used to reveal structural information in a biological system without staining. THG signal is observed at an interface between refractive indices and is augmented in the presence of conjugated carbon chains. I sought to determine whether THG microscopy could serve as a platform for developmental studies. I used the eye of Drosophila melanogaster as a model for its well-known anatomy and availability of genetic tools. In the first series of observations THG microscopy was shown to be an effective tool for monitoring photoreceptor development. In the second series of experiments, using dietary restrictions or genetic alleles, THG microscopy detected rhabdomere degeneration and reduced rhodopsin expression earlier than fluorescence microscopy. In conclusion, THG microscopy presents itself as a new technique to detect retinal degeneration. Further development of this technology could aid in early detection of human retinal degeneration.