VictorJuiz/thesis huggingface dataset:
Development of a Patient-derived Hepatitis C Viral Pseudo-particles Library

The evaluation of neutralization potency for the Hepatitis C (HCV) targeting antibodies and infectivity of the virus remains a difficult task because HCV is highly genetically variable. There is an urgent need to develop an efficient in vitro system consisting of a library of heterogeneous HCV cDNA clones, representative of the real viral variants. In our lab, we developed a HCV pseudo-particles (HCVpps) library derived from 120 infected HCV patients. The aim of this study is to investigate whether these HCVpps can mimic in vivo viral interaction in Huh-7 cell culture. My findings have indicated that anti-E2 antibody was highly specific for its E2 antigen and it did not neutralize other variants of virus. In addition, the sequence analysis data has indicated that our HCV cDNA clones have sequences that are highly distinct from each other and they can be used to build upconstitute the cDNA library representing different HCV variants.

Keywords: HCV cDNA library for real viral variants
HCV pseudo-particles-luciferase
Hepatitis C
Neutralization mediated by antibodies
Purification of viral derivatives (HCVpps VLPs)
Viral entry processes
Advisor: AbouHaidar, Mounir G.
Feld, Jordan
Protection from Endoplasmic Reticulum Stress and Apoptosis via PPARδ and Bcl-2 in Breast Cancer

Estrogen receptor positive breast cancer accounts for the majority of breast cancer cases. Anti-estrogens, such as tamoxifen, are used to prevent the growth and survival of these cancer cells. However, patients often develop resistance to this drug due to dysregulated apoptosis. The overexpression of either Bcl-2, an anti-apoptotic protein, or PPARδ, a nuclear receptor protein, allows cancer cells to evade endoplasmic reticulum stress and survive. MCF-7 cells were used to investigate how dysregulated apoptosis contributes to tamoxifen resistance. Synergistic protection was observed in cells that overexpressed both PPARδ and Bcl-2, suggesting that the proteins work through different pathways. This implies that patients would require different treatments depending on the expression levels of Bcl-2 and or PPARδ in their tumours. In addition, the Bcl-2 inhibitor, ABT-199, was unable to sensitize cells that overexpressed Bcl-2 to drug treatments that elicit endoplasmic reticulum stress, revealing a novel BH3-independent mechanism of resistance through Bcl-2.

Keywords: ABT-199
Apoptosis
Breast Cancer
Endocrine Therapy
ER stress
Tamoxifen
Advisor: Andrews, David W
Traffic Jam is Required during Ovary Development and at the Adult Stage to Maintain a Functional Drosophila Ovarian Stem Cell Niche

Cap cells, escort cells, and terminal filament (TF) cells form the germline stem cell (GSC) niche in the Drosophila ovary. The transcription factor Traffic Jam (Tj) is expressed in cap and escort cells, but not in TF cells. Tj regulates the formation and number of GSCs by controlling the fate and spatial organization of cap cells. I provide further evidence indicating that Tj is required in cap and escort cells for the establishment/maintenance of GSCs during ovary development. Importantly, my data show that Tj is required to maintain GSCs and facilitate germ cell differentiation after the GSC niche has formed. Together, these data indicate that Tj has an important function in controlling somatic cell arrangement during ovary development and in maintaining GSCs and facilitating germ cell differentiation during the adult stage.

Advisor: Godt, Dorothea
Aerodynamic Focusing of an Abrasive Air Jet

In order to decrease the size of the eroded footprint resulting from abrasive jet machining, the aerodynamic focusing of an abrasive particle jet was investigated. For an abrasive jet from a slot nozzle, the best focusing employed a pair of bounding air jets tilted 60° to the abrasive jet, and impinging it approximately 10% of the standoff distance from the workpiece. An optimum bounding jet pressure existed to achieve the maximum focusing, resulting in a machined channel width reduction of up to 16 % with a corresponding depth increase of 84%. A novel apparatus was constructed to generate an annular bounding jet impinging a central abrasive jet formed from a round nozzle. However, aerodynamic focusing in this case could not be achieved due to the large stagnation zone that formed near where the annular jet impinged. Computational fluid dynamics simulations were used to understand the mechanics of particle focusing.

Keywords: Abrasive Air Jet
Aerodynamic Focusing
Computational Fluid Dynamics
Micro-Machining
Advisor: Spelt, Jan K
Papini, Marcello
Development of a Real-time Vision Framework for Autonomous Mobile Robots in Human-centered Environments

Autonomous mobile robots typically have limited computational power and memory available on-board, and often require information in real-time to make real-time deci- sions. Thus, a vision framework for such robots must provide information about the robots surroundings in real-time while being computationally efficient and memory con- scious. This thesis presents the development of a novel real-time vision framework that incorporates direction invariant person detection and recognition, and object detection and state recognition using deep learning and computer vision algorithms. The framework was integrated into two mobile robot architectures and was validated using real-world experiments on interactive mobile robots.

Keywords: Computer Vision
Deep Learning
Machine Learning
Mobile Robotics
Social Robotics
Advisor: Nejat, Goldie
On the Bacterial Endosymbionts of Placobdella (Annelida: Hirudinea: Glossiphoniidae)

The objective of this project was to survey the diversity of bacterial endosymbionts of the genus Reichenowia inhabiting the esophageal organs of the blood feeding leech genus Placobdella. I aimed to (1) place these symbionts in a phylogeny among other bacterial phyla, (2) compare the evolutionary histories of these symbionts with those of their hosts, and (3) to explore the mode of transmission between parent and offspring to shed light on the vertical transmission of the bacteria inside of the leeches. I confirmed the presence of bacteria in ten previously untested Placobdella species by recovering bacterial DNA from bacteriome tissues and used TEMs to capture bacterial morphology and their location within their host. Lastly, phylogenetic analyses based on 16S and 23S rRNA found Reichenowia to be a monphyletic group of bacteria placing within the alphaproteobacterial family Rhizobiaceae and found no evidence of expected cospeciation between hosts and symbionts.

Keywords: bacteria
cophylogeny
endosymbiont
leeches
phylogeny
symbiosis
Advisor: Kvist, Sebastian
Evaluating the Field Performance of a Thermally-retrofitted Historic Masonry Home Using a Nested Thermal Envelope Design

In 2013, the Gemini home in Toronto was retrofitted to create the first Nested Thermal Envelope Design building. A one-year monitoring study of the building was conducted. The monitoring data were analyzed to evaluate the heating season performance of the design. In this study, energy models were developed and calibrated. When the entire Gemini home was heated (i.e., Standard Operating Mode), 25% less heating energy was required compared to an equivalent Ontario Building Code (OBC)-compliant home. Heating demand curves were developed to estimate the home’s energy use in other operating modes. In Lower-Energy Operating Mode, the Gemini home uses 63% less heating energy than the OBC model. Using the observed temperature data, a ratio, known as the Operating Ratio (O.R.), was developed to guide the operation of the interzonal heat pump. The O.R. can be used as a tool to determine the minimum operating setpoint temperatures in the Perimeter zone.

Keywords: building monitoring study
energy modeling
historic home
Nested Thermal Envelope Design
Ontario Building Code
retrofit
Advisor: Pressnail, Kim
McCabe, Brenda
Role of Free-water Loss on Residual Strain and Fracture Predilection in Root Dentin: A Three-dimensional Digital Image Correlation Analysis

Free-water loss induced residual strain, with and without axial loading, and the mechanical effect of cyclic loading in fully hydrated and partially dehydrated root dentin were evaluated using 3D-Digital Image Correlation and Micro CT imaging. 2 hours of free-water loss resulted in the formation of residual compressive strain with areas of tensile strain localized to root canal and outer dentin. More residual compressive strain was observed in the apical dentin compared to the cervical dentin. More residual shear strain was observed in the outer dentin compared to the inner dentin. Axial loading resulted in an increase in the load-induced compressive strain in the direction perpendicular to dentinal tubules. Fully hydrated samples displayed a higher mean number of cycles to fracture with micro-cracks characteristic of toughness when compared to partially dehydrated samples. Free-water loss occurring in endodontically treated teeth may play a significant role in their predisposition to vertical root fractures.

Keywords: Digital Image Correlation
Free-water
Residual Strain
Advisor: Kishen, Anil
Software Development and Environmental Testing for New Frontier Microspace Missions

This thesis presents contributions to the Vector Gravimeter for Asteroids (VEGA) and a microsatellite formation flying mission developed at the Space Flight Laboratory (SFL). Due to growing interest in space mining, SFL is helping to develop VEGA, an instrument to enable early prospecting of rich metal asteroids. The first focus of this thesis is software development hardware acceptance for the VEGA Power Board. In addition, constellations of multiple small spacecraft are an effective tool for reducing cost and risk while increasing mission flexibility. The ability for spacecraft to perform formation flight allows for sophisticated and lucrative applications of constellations such as geolocation of radio frequency signals. The second focus of this thesis is development of automated testing software for a three-spacecraft formation flying mission based on the improved SFL NEMO platform and system level environmental testing of all spacecraft prior to launch in the fall of 2018.

Keywords: aerospace
embedded software
environmental testing
formation flying
microsatellite
small satellite
Advisor: Zee, Robert E
Investigating Iron Status and Infant Feeding Practices Across a Multi-ethnic Cohort

Background: There is limited research on iron deficiency (ID) and infant feeding practices considered known risk factors for ID (breastfeeding >12 months, cow’s milk consumption >2 cups per day, bottle use >15 months and current infant formula use) across ethnic groups. Methods: Multivariable logistic regression was used to test the association between maternal ethnicity and ID. We used mediation analyses to test whether infant feeding practices mediated this association among children 1-3 years of age. Results: ID was more prevalent among South Asian children compared with non-South Asian children (20.1% vs. 11.4%; RR 1.76 95% CI 1.27, 2.45). While there was an increased risk for bottle use >15 months and cow’s milk consumption >2 cups per day among South Asian children than non-South Asian children, none of the four infant feeding practices were mediators. Conclusion: South Asian children are at increased risk for ID. Other factors may mediate this association.

Advisor: Borkhoff, Cornelia M.
Parkin, Patricia C
Human Automation Coordination: Supporting Driver Takeover during Predictable and Unpredictable Automation Failures

Today’s vehicles are becoming highly automated, changing the driver’s task from one of purely driving to one of monitoring the automation. Drivers may fail to monitor the automation, and therefore when drivers are forced to react to unexpected automation failures, they exhibit worse performance than manual driving. Through a driving simulator experiment, this thesis aims to 1)understand how different types of automation failure events, whether predictable or unpredictable, impact the driver’s takeover performance, and 2)compare driver takeover performance when using different displays, specifically the Takeover Request (TOR) and the reliability display. Findings show that drivers put their hands on the wheel sooner and have greater situation awareness for predictable failures; drivers appear to takeover sooner and have a better takeover quality during predictable failures when the reliability display is present than when TOR is present. As compared to no display, both displays provide a benefit to the driver’s takeover performance.

Keywords: Automated Vehicles
Driving Simulator
Lateral Automation
Reliability Display
Takeover Request
Advisor: Donmez, Birsen
Upscaling Micromechanical Indentation Properties to Mesoscale Behaviour in Geomaterials

The limited sampling volume in indentation analyses is both a strength and a weakness. While the testing method can be used to investigate specific grain scale mechanics in geomaterials, it is not easily translated to mesoscale behaviour. This work demonstrates the use of large indentation grid programs in addition to numerical modelling to investigate the mesoscopic behaviour of geomaterials. Using various facies from the lower Triassic Montney formation, a series of indentation grids of varying scales are used to demonstrate the variability in indentation modulus and fracture toughness due to bioclastic content. Alternatively, when explicitly defining the heterogeneity in a cementitious material, the indentation results from each constituent can inform and calibrate numerical models. A detailed mesoscale model is then calibrated for unconfined compressive strength, split tensile, and triaxial testing with the aid of indentation moduli from an exhaustive indentation program to form the basis for future field scale modelling.

Keywords: Cementitious modelling
Finite-Discrete Element Modelling
Instrumented Indentation
Numerical Modelling
Unconventional Reservoir
Upscaling
Advisor: Grasselli, Giovanni
Peterson, Karl
Application-specific Fixed-point Design of the Alternating Direction Method of Multipliers for Linear Program Decoding

We consider the design of linear-programming (LP) decoding in hardware of low-density parity-check (LDPC) codes. Previous work has shown that the alternating direction method of multipliers can be applied to solve LP decoding in a message passing manner amenable to hardware. Wasson et al demonstrated the feasibility of a hardware implementation in a field-programmable gate array. However, the area footprint and message bit-width of the implementation was not competitive with classic alternatives such as min-sum decoding. We leverage recent work by Jiao et al on implementing the central computational primitive of ADMM-LP decoding via look-up tables. In this thesis, we use the work of Jiao et al to develop a modified version of Wasson’s ADMM-LP decoding algorithm, realizing a bit-width reduction of about 50%.

Advisor: Draper, Stark
Plasmonic Sensor using Double-layered Stimuli-responsive Polymer Microgel for Multiplexed Detection

Herein we present a sensor that uses surface plasmon resonance (SPR) and plasmonic waveguide resonance (PWR) modes to probe the behavior of two layers of stimuli-responsive polymers, called microgels, deposited on a gold film. These microgels can be molecularly imprinted, resulting in a high-loading-capacity synthetic receptor. In response to external stimuli, such as molecular binding events, their refractive index and thickness vary. Fabrication and testing demonstrated that changes in the SPR mode correspond to changes in the lower layer’s refractive index and thickness with p-values below 0.03, whereas changes in the PWR mode correspond to changes in the upper layer’s refractive index and thickness with p-values

Keywords: Biosensor
Microgel
Mycotoxin
Plasmonic
Sensing
Waveguide
Advisor: Aitchison, James Stewart
Geoarchaeology: Analyzing the Relationships Between Fluvial Environments, Fluvial Processes, and the Presence of Archaic/Woodland Occupation Sites in Southern Ontario

The Ausable, Saugeen, and Thames river floodplains are analyzed in terms of archaeological and geomorphic data to examine the relationships that might exist between fluvial environments, fluvial processes, and Archaic/Woodland archaeological occupation sites in southern Ontario. A large-scale spatial analysis is conducted using data from the Ontario Archaeological Sites Database (OASD) in order to create a matrix of variables that may illuminate how rivers and occupation sites relate to each other. The Davidson site on the lower Ausable River is used as a case study due to the wide scope of archaeological and geomorphic research that has been conducted there. The OASD is found to be a useful tool in terms of data volume, quality, and accessibility for research projects of this scale. Indications of relationships between the location and preservation of archaeological sites and variables such as distance from river, elevation, and stream power are present in the results.

Keywords: Archaeological
archaeology
floodplain
fluvial
ontario
river
Advisor: Desloges, Joseph R.
Creating Useful Road Mortality Models: Identifying Drivers of Road Mortality at Different Resolutions in the Greater Toronto Area

Road propagation has led to landscape level threats due to habitat destruction, pollution, and mortality. Road mortality risk prediction converges on three drivers: habitat availability, landscape connectivity, and traffic volume. This study assessed the relative importance of mortality drivers in a peri-urban landscape at different taxonomic levels. Road mortality data and land cover data were provided by Toronto and Region Conservation Authority, and traffic data from governmental sources were used. I modelled landscape connectivity using circuit theory algorithms. Driver significance was assessed using univariate multiple regression models and multivariate redundancy analyses, using total road mortality, taxa-based road mortality, and species level road mortality for American toads and grey treefrogs. Local scale drivers such as wetland patchiness and amount had the greatest effects on road mortality. Greater divergence occurred at the species scale, though conserved patterns were seen across multiple taxonomic levels.

Keywords: American Toad Anaxyrus americanus
Amphibian
Conservation Management
Grey Treefrog Hyla versicolor
Road Ecology
Urban Ecology
Advisor: Fortin, Marie-Josée
Self-reported Oral Health Status and Diabetes Outcomes in a Cohort of Diabetics in Ontario, Canada

Objectives: To determine the difference in complications among diabetics reporting oral health. Methods: A cohort study was undertaken of diabetics from the CCHS (2003; 2007-8). Self-reported oral health (SROH) was linked to health records for participants aged > 40 years (N=5,183). A series of hazards and logistic regressions were constructed to determine the risk and odds of acute/chronic complications. Participants without complications were censored at death or at March 31/ 2016. Models were adjusted for age, sex, social and behavioural factors. Results: Those reporting “poor-fair” oral health had a 30% hazard of a complication (HR 1.29 95%CI 1.03, 1.61), and a 10% odds of acute (OR 1.10 95%CI 0.81, 1.51) and 34% odds of chronic complications (OR 1.34 95%CI 1.11, 1.61), greater than those reporting “good-excellent” oral health Conclusion: Oral health status is associated with diabetes complication; this study is the first to explore the oral health-diabetes link in Ontario.

Keywords: Acute complication
Chronic complication
Diabetes
Oral health
Population health
Advisor: Quiñonez, Carlos R
Rosella, Laura C
A Critical Exploration of the Educational Trajectories of Six Hungarian Refugee Roma in Canada: Navigating Whiteness and Ethnic Identity

Moving away from bleak statistics on Roma and educational attainment, this paper looks to explore the life narratives of six Hungarian Roma refugee individuals who have migrated to Canada and have pursued non-obligatory education. The findings show three common experiences amongst the participants; (a) consistent parental messaging about the value of education (b) mostly positive experiences in earlier school years and (c) positive external influences. However, participants explained their positionality including their proximity to whiteness and Romungro identification as also playing a salient role in their positive experiences. This paper utilizes Critical Race Theory to explore these factors as they contribute to internal and external aspects of their lives and their educational trajectories.

Keywords: Canada
Critical Race Theory
Ethnicity
Hungary
Roma
Roma Education
Advisor: Waterman, Stephanie
Automatic Accelerator Selection for the LegUp ARM Hybrid Flow

Devices combining a general purpose processor and reconfigurable FPGA fabric in the same package have recently become popular. Many tools exist to help simplify implementing designs on these devices. In particular, High Level Synthesis (HLS) tools are capable of taking code, written in languages such as C, as input and producing hybrid processor-accelerator systems. These systems include a software portion running on the processor and a custom hardware portion implemented in the FPGA fabric. However, given an application, it is often unclear how to distribute the workload between the reconfigurable logic and the processor. This thesis presents two approaches to estimate the performance of hybrid processor-accelerator systems generated with the open-source LegUp HLS tool. An accurate estimate can be used either to automatically generate the fastest hybrid system for an application, or to speed up the design of hardware accelerators and systems.

Keywords: Accelerator
ARM
FPGA
HLS
Profiling
Advisor: Brown, Stephen
Characterizing the Association between Brain Morphology and Behavioural Symptomatology in Autism Spectrum Disorder and Attention Deficit Hyperactivity Disorder

Autism spectrum disorder (ASD) and attention decit/hyperactivity disorder (ADHD) are prevalent and highly co-occurring neurodevelopmental disorders. The brain correlates of these disorders remain mostly unknown. This is partly due to the limitations of existing analytic methods in coping with the large within disorder variability and overlap between disorders. To address this challenges, we propose a new method called Bagged-Regression clustering for data-driven discovery of diagnosis-agnostic subgroups that may share brain-behaviour associations. This approach clusters the sample data into K groups, each with its own linear regression function. Using both simulated data and a real-dataset of brain-behaviour associations in ASD and ADHD, we show that the proposed method is able to recover multiple regression lines in the data.

Keywords: attention deficit/hyperactivity disorder
autism spectrum disorder
clusterwise regression
regression clustering
social communication
Advisor: Kushki, Azadeh
Capacity Considerations for Data Storage in Memristor Arrays

Memristor arrays are a promising memory technology that store information in a crossbar array of two-terminal devices that can be programmed to patterns of high or low resistance. While extremely compact, this technology suffers from the ``sneak-path'' problem: certain information patterns cannot be recovered, as multiple low resistances in parallel make a high resistance seem low. In this thesis we review the current state of memristor technology, including proposed solutions to the sneak-path issue. We extend this discussion by proposing some variations on existing encoding schemes involving one-hot encoding that improve reliability and ease of access, taking into account the scaling of peripheral hardware. We also extend the scope of the discussion by deriving the information capacity of models of multi-layer memristor devices, which is higher than that of the same number of single-layer devices stacked.

Keywords: Combinatorics
Memristor array
Multi-layer memristor array
Resistive memory
Sneak-path
Advisor: Kschischang, Frank R