VictorJuiz/thesis huggingface dataset:
Two Methods for Robust Robotiocs Perception: Visual Measurement Integrity Monitoring for Localization and Confidence Guided Stereo 3D Object Detection

Safe autonomous robot operations require robust localization and accurate 3D object detection. This thesis covers two methods to improve the robustness in these two tasks. The first half of this thesis introduces an approach to monitor the integrity of the state estimation in UAV localization by calculating the protection level of the localization solution, i.e. the largest possible translational error. The protection level is validated using the EuRoC dataset and is demonstrated to provide a more reliable bound than the commonly used 3$\sigma$ method. The second half of this thesis proposes a novel stereo-based object Safe autonomous robot operations require robust localization and accurate 3D object detection. This thesis covers two methods to improve the robustness in these two tasks. The first half of this thesis introduces an approach to monitor the integrity of the state estimation in UAV localization by calculating the protection level of the localization solution, i.e. the largest possible translational error. The protection level is validated using the EuRoC dataset and is demonstrated to provide a more reliable bound than the commonly used 3? method. The second half of this thesis proposes a novel stereobased object detection network named CG-Stereo. This pipeline uses separate decoders for foreground and background depth estimation and leverages the confidence estimation from the depth estimation network in the detection phase. The proposed method outperforms all the existing stereo-based 3D object detection methods on the challenging KITTI benchmark in all categories for all classes.

Keywords: Computer vision
Deep learning
Object detection
Robotics
Advisor: Waslander, Steven L
Clinical Validation of Neuronal Pentraxin Receptor as a Candidate Biomarker for Alzheimer’s Disease

Alzheimer’s disease (AD) is an age-associated neurodegenerative disease characterized by progressive cognitive decline and loss of independence. Disruption of cerebrospinal fluid (CSF) biomarkers, depressed amyloid and elevated tau, confers an AD-like pathological profile. Novel biomarkers are needed to capture disease onset at earlier stages, categorize patients, and monitor progression. Previously, targeted proteomics has identified CSF neuronal pentraxin receptor (NPTXR) as depressed in AD patients. The aim of this dissertation is to verify CSF NPTXR as an AD biomarker in independent cohorts. NPTXR levels were measured in CSF using enzyme-linked immunosorbent assays in three cohorts with participants of: 1) various dementia severities; 2) normal cognition, mild cognitive impairment and AD monitored over a 24-month period; 3) preclinical and early AD. NPTXR negatively correlated with disease severity and cognitive function and was associated with core AD biomarkers. Future functional and molecular studies are needed to determine NPTXR’s contribution to AD pathology.

Keywords: Alzheimer's disease
Biomarker
Cerebrospinal fluid
Diagnosis
Neuronal pentraxin receptor
NPTXR
Advisor: Diamandis, Eleftherios P
Diamandis, Phedias
Investigation of Soil Gas Geochemistry at Thorn North Forest Ring

Forest rings are big circular features of low tree density. Studies conducted on Northern Ontario forest rings found CO2 enrichments compared to atmospheric levels in the soil gas at the ring edge. Previous researchers attributed such enrichments to microbial respiration. In this study, shallow and deep samples were obtained from colleagues at the Ontario Geological Survey and were analyzed for their gas composition and stable carbon isotope analysis of CO2 at Stable Isotope Laboratory. The average O2, N2, and CO2 concentrations were 20.79%, 79.00%, and 0.12% respectively. Values of δ13C(CO2) ranged from -11.5‰ to -22.2‰ with the most depleted δ13C(CO2) values associated with the highest CO2 concentrations, and was observed most clearly in the shallow samples, suggesting a larger contribution of microbially-derived CO2. The explanation for this is not yet completely understood, but likely related to greater microbial presence, root respiration, and organic matter decomposition at shallow depths.

Keywords: Forest Ring
Geochemistry
Soil gas
Advisor: Sherwood Lollar, Barbara
Advisement and Transtions in the Trades: A Process of Fustration in Ontario

Ontario, the most populous province in Canada, has the lowest apprenticeship completion rates compared to other provinces. This study seeks to understand the factors that contribute to these poor outcomes by researching policy and practices based on transition systems in Canada which work against the trades. The research focuses on the electrical trades in Ontario and utilizes interviews as its method. Interviews were undertaken with apprentices, electricians, union/association representatives and educators. Given the lack of policy and research about Ontario’s vocational dilemma, whereby poor organization affects access, qualitative methods based on constructivist theory are used to establish exploratory findings. The study seeks to understand how young people were able to enter the electrical trades, the nature of the transitions which supported or undermined these processes, including the kind of student advisement that they received.

Keywords: Advisement
Electricians in Ontario
Ontario Trades education
Ontario Vocational Education
Social Justice
Transition Systems
Advisor: Wheelahan, Leesa
Impact of Language Complexity on Typing Speeds of School-aged Children: A Pilot Study

The present pilot study explored the impact of language complexity on students’ typing speeds, measured in net characters per minute (CPM), and the relationship of typing speed to other academic skills. Students (N =28) in grades two through four were shown three standardized passages in succession and were given two minutes to copy each passage accurately. Each student was shown a passage at the grade one level, their previous grade level, and their current grade level. Passage difficulty only impacted net CPM produced by grade two students such that they typed more characters within the time limit when copying the grade one passage relative to the higher grades. A hierarchical regression demonstrated that typing performance was largely dependent on age, such that older students typed more than younger students. These findings will aid in the selection of appropriate text passages to include in a standardized measurement tool for typing fluency.

Keywords: children
keyboarding
school
typing
Advisor: Cunningham, Todd
Effects of Fuel Doping and Fuel Chemistry on Soot Formation in Co-flow laminar Diffusion Flames at Elevated Pressures

Effects of fuel doping and fuel chemistry on soot formation were studied in laminar diffusion flames at elevated pressures. Soot spectral emission is used to obtain radial temperature, soot volume fraction, and soot yield profiles. This thesis first investigated addition of 0%-40% ethanol in ethylene flames at 3-10 bar. 10% ethanol-doped flames didn’t exhibit measurable soot synergy, whereas 20%-40% ethanol displayed lower soot yields. Secondly, 7.5% of benzene, cyclo-hexane and n-hexane was added into methane flames at 1.4-10 bar. Pressure dependence of sooting propensity is lowest for benzene. Thirdly, 3% of m-xylene and n-octane was mixed with methane at 1.4-10 bar. m-Xylene doped methane flames produced highest soot yields but lowest pressure dependency in soot yields. Results indicate that pressure dependence of highly sooting aromatics weakens compared to that of less sooting n-alkanes at high pressures.

Advisor: Gülder, Ömer L.
Sex Differences in the Effects of Osteocalcin and Exercise on Cognition and Behaviour in a High-fat Diet Model of Type 2 Diabetes

Osteocalcin is a protein produced in bone and found both in the bone matrix and circulation. Mouse studies have demonstrated anti-diabetic and anti-aging effects of osteocalcin. Osteocalcin research in mice has almost exclusively been conducted in only one sex and could not account for sex as a biological variable. We hypothesized that osteocalcin and exercise would improve behavioural outcomes and aimed to record any difference in response between sexes. We compared the effects of diet, exercise, osteocalcin treatment, or the combination of both, in male and female mice on a high-fat diet-induced model of type 2 diabetes. Osteocalcin decreased depressive-like behaviours and improved problem-solving in both sexes, and exercise decreased depression in both sexes. The effects of osteocalcin were similar in male and female mice; however, exercise increased anxiety-like behaviours only in males and improved problem-solving only in females. Osteocalcin and exercise affected behaviour similarly but not identically.

Keywords: Behaviour
Bone metabolism
Diabetes
Exercise
Osteocalcin
Sex
Advisor: Mitchell, Jane
Swardfager, Walter
Exploring the Saskatchewan Grasslands: An Investigation of Crown Land and Appropriate Use

Canadian crown lands are a collection of landscapes which allow for a diversity of actors to interact with. These areas provide platforms for connections between users based on intra-societal values surrounding preservation and extraction. Understanding how actors use crown lands uncovers society’s value of public spaces; and how society influences and is influenced by socio-ecologic connections. Accompanying this is the intimate knowledge constructed through engagements with spaces and local communities. This thesis examines a Saskatchewan case study that focuses on divested crown land from the Prairie Farm Rehabilitation Agency (PFRA) and performs analysis based on interviews surrounding reactions to the divesture. The analysis of citizens and environmental NGO’s (ENGOs) suggests that historic management of PFRA lands was overwhelmingly positive and important on many scales due to their socio-economic and ecologic valuations. Further, this thesis showcases management strategies which could provide similar benefits through administration of crown lands.

Keywords: Crown Lands
Natural Resource Management
Advisor: Olive, Andrea
PostGUI: A Modern Web Application for Sharing Biological Big Data

Life science research has traditionally been a data-centric research field. Advancements in high- throughput instrumentation and next generation sequencing technology has made it easier than ever to generate biological data. The low-cost and large-volume nature of the high-throughput technologies allow even the research laboratories with a limited budget to produce enormous volumes of biological data. This focus on producing and analysing large amounts of data has elevated life science research into the “big data” realm. Here we provide a web-based platform that solves data sharing and data management needs of life science researchers. Our platform features three components: a database system (PostgreSQL), an automatic API tool (PostgREST), and a web application (PostGUI). This platform ensures long-term data integrity of research data by using proven technologies to manage and share biological big data for collaborative research hypothesis generation. This is a data agnostic platform that automatically adapts to any tabular data sets.

Keywords: big data
data access
data management
data sharing
postgresql
web application
Advisor: Guttman, David S
Provart, Nicholas J
Complement Receptor-mediated Phagocytosis is more Pro-inflammatory than Fcγ Receptor-mediated Phagocytosis in Murine Macrophages

Macrophages are immune cells capable of recognizing and removing foreign organisms through phagocytosis. It is widely believed that Fc receptor (FcR)-mediated phagocytosis is pro-inflammatory while complement receptor (CR)-mediated phagocytosis is not. Our work involved examining cytokine and chemokine levels, post-phagocytosis of opsonized sheep red blood cells (sRBCs), as a means of determining the murine macrophage’s inflammatory response. Interestingly, our cytokine array and ELISA data showed that CR-mediated phagocytosis is more pro-inflammatory than FcR-mediated phagocytosis in bone marrow-derived murine macrophages. We further explored the use of a physiologically relevant alternative CR activator, GM-CSF. We also determined that unbound sRBC decay does not stimulate cytokine production. Additionally, inhibitors of NF-κB, calpain and phagocytosis were used to determine their roles in the pro-inflammatory response that we observed in macrophages. Our data reveals that CR-mediated phagocytosis is more pro-inflammatory than FcR-mediated phagocytosis for opsonized sRBCs and is potentially mediated by calpain activation of NF-κB.

Keywords: Complement
Cytokine
Fc
Macrophage
Murine
Phagocytosis
Advisor: Harrison, Rene E.
Association of Dietary Protein Intake with Skeletal Muscle Mass in 4-year-old Children in Dhaka, Bangladesh

Skeletal muscle mass (SMM) is a key determinant of metabolic health in children and adults; yet, despite its importance, there has been a lack of research on the determinants of SMM development, particularly in low-resource settings with emerging concerns related to the ‘double burden’ of malnutrition. In a cross-sectional study of 4-year-old children in Dhaka, Bangladesh, we measured appendicular lean mass (ALM) using dual-energy x-ray absorptiometry, dietary protein intake using repeated 24-hour recall, hand-grip strength, and anthropometry. Multivariable-adjusted linear regression models showed that there was no association between dietary protein intake and ALM (n=93). In a secondary analysis of an extended cohort of children (n=566), a 1 kg increase in ALM was associated with a 1.04 kg increase in muscle strength (hand-grip test) (p

Keywords: children
low or middle income countries
Protein
Skeletal muscle mass
Advisor: Roth, Daniel E
The Percy Papers

The Indian Residential School era took its toll on the health and wellbeing of the entire Indigenous population in Canada. How does one rehabilitate after suffering tremendous loss of culture, language, voice, and self? My father, Percy James Bird, spent 15 years in an Indian Residential School. He then worked nineteen years with the federal government. After retirement, he took a creative writing course, producing 21 stories. A critical read of the stories, using Indigenous story telling methods, begins the process of tearing down a negative colonized version of Percy. As a silent survivor, his stories diffuse much of the violence from his past. The objective of this rehabilitation science inquiry is to use an Indigenous storywork research approach to explore patterns of healing and examine how Percy’s personal healing led to his later aspirations to create systems of healing for his people.

Keywords: Health
Indian Residential School
Indigenous
Storywork
Advisor: Nixon, Stephanie
Learned Adjustment of Camera Gain and Exposure Time for Improved Visual Feature Detection and Matching

Ensuring that captured images contain useful information is paramount to successful visual navigation. In this thesis, we explore a data-driven approach to account for environmental lighting changes, improving the quality of images for use in visual odometry (VO). We investigate what qualities of an image are desirable for navigation through an empirical analysis of the outputs of the VO front end. Based on this analysis, we build and train a deep convolutional neural network model to predictively adjust camera gain and exposure time parameters such that consecutive images contain a maximal number of matchable features. Our training method leverages several novel datasets consisting of images captured with varied gain and exposure time settings in diverse environments. Through real-world experiments, we demonstrate that our network is able to anticipate and compensate for lighting changes and maintain a higher number of inlier feature matches compared with competing camera parameter control algorithms.

Keywords: Autonomous Vehicles
Cameras
Deep Learning
Robotics
State Estimation
Visual Odometry
Advisor: Kelly, Jonathan S
Development of Small Satellite Platforms for Low Earth Orbit Constellation Missions

With advances in microspace technology, many satellite constellation mission objectives can be realized at affordable costs by launching multiple small satellites. The Space Flight Laboratory is developing new small satellite platforms to extend the capabilities of low Earth orbit constellation missions, adding to their line of versatile platforms. This thesis presents contributions to multiple phases of the spacecraft development cycle for two new platforms: the SPARTAN nanosatellite and the DEFIANT microsatellite. In the design phase, heritage flight components were modified to fit in the compact SPARTAN platform. Analysis and testing of the attitude and structure subsystems were completed to verify system level requirements for both platforms. The first build of the DEFIANT spacecraft in a cleanroom is detailed, with ground support equipment designed to ease assembly, integration, and environmental testing. Finally, launch campaign preparations are discussed for upcoming missions using the DEFIANT microsatellite.

Keywords: Constellation
Engineering
Microsatellite
Nanosatellite
Satellite
Spacecraft
Advisor: Zee, Robert E.
Impact of Genetic Variation in the Endocannabinoid-Degrading Enzyme FAAH on Dopamine D2/3 Receptor Status: Neuroimaging studies in Human and Mice with implications for Addictions

BACKGROUND: The endocannabinoid and dopaminergic systems have independently been implicated in addiction. We investigated a potential interaction between a genetically inherited variation in fatty acid amide hydrolase (FAAH C385A), the enzyme which metabolizes the endocannabinoid anandamide, and dopamine receptor status in brain. METHODS: Brain binding of the dopamine D3-preferring probe [C-11]-(+)-PHNO was measured with positron emission tomography (PET) in 79 healthy participants genotyped for the FAAH C385A polymorphism. Autoradiography with [H-3]-(+)-PHNO and in situ hybridization with a D3-specific S-35 riboprobe were carried out in a FAAH knock-in mouse model replicating the FAAH C385A polymorphism. RESULTS: Humans and knock-in mice with the C385A variant showed reduced FAAH activity demonstrated higher dopamine D3 receptors. CONCLUSIONS: Results may provide a mechanistic link between dopamine and endocannabinoid systems and explain greater risk for addiction with lower FAAH (C385A variant).

Advisor: Boileau, Isabelle
Large-swing DACS for 56+ GBaud Optical Modulator Applications

A new large-swing digital to analog converter is proposed based on series-stacked cascode CMOS inverters for directly driving optical modulators at 56 GBaud and higher symbol rates. A 4.6-Vppd 56-64 GS/s 6-bit digital-to-analog converter (DAC) along with support circuitry was fabricated in a production 22nm (FDSOI) CMOS technology. To the author’s knowledge, this is the first circuit to transform the single input series-stacked cascode power amplifier topology into a large-swing DAC topology with the use of gate-finger segmentation on the input PMOS and NMOS transistors. It achieves the highest symbol rate and efficiency in CMOS to date. Measurements show the DAC achieving 0.4-Vpp per-side 66-Gb/s NRZ, 0.75-Vpp per-side 62-GBaud 3-PAM, 1.1-Vpp per-side 60-GBaud 4-PAM, 2.3-Vpp per-side 52-GBaud 4-PAM, and 1.38-Vpp per-side 56-GBaud 5-PAM eye diagrams. The power consumption of the DAC and all on-chip support circuitry is 450 mW. Alone, the DAC output stage consumes only 168 mW.

Keywords: CMOS
DAC
FDSOI
High-speed
Optical
PAM
Advisor: Voinigescu, Sorin P
Predicting Open-water Thermal Regimes of Temperate North American Lakes

Temperature affects lakes’ physical, chemical, and biological attributes, and is influenced by several abiotic factors. Lake temperature modelling permits regional estimates of seasonal fish thermal habitat; however, this requires accurate models for large spatial scales. To address this, I fit a semi-mechanistic seasonal temperature-profile model (STM) to 369 North American lakes with data spanning 1971-2016. STM with a fixed-depth thermocline formula accurately modelled lake temperature (median lake-year-specific RMSE: 1.13 ºC). I selected candidate predictors using random forests, then used linear mixed-effects modelling to create empirical equations to predict STM parameters from lake-specific morphometry and climate. I tested the accuracy of my equations with 776 Ontario lakes and found good agreement between predicted and observed temperatures (median lake-year-specific RMSE: 2.28 ºC) and stratification occurrence (91.9%). These findings enhance our understanding of factors that influence lake temperatures and could identify lake types and regions that may be especially susceptible to climate change.

Keywords: Lake
Modelling
Semi-mechanistic
Stratification
Temperature
Thermal habitat
Advisor: Minns, Charles K
Shuter, Brian J
Morbidity, Mortality, and Healthcare Use Among Siblings of Children with Cancer

We investigated the impact of childhood cancer on siblings by characterizing their long-term physical health outcomes. Population-based cohorts of exposed and unexposed siblings were created and linked to health services data. Outcomes compared between the two groups included: 1) physical health conditions (e.g., hypertension, diabetes); 2) acute healthcare use (hospitalizations and emergency department [ED] visits), and; 3) preventive healthcare use (e.g., periodic health checkups and influenza vaccinations). Compared to 30,364 unexposed siblings, 7,591 exposed siblings were at increased risk of hypertension [HR 1.8; 95CI 1.1-2.9; p=0.016]. They also had higher rates of ED visits [RR 1.1; 95CI 1.1-1.2; p

Keywords: Caregiver health
Health services research
Morbidity
Mortality
Pediatric cancer
Siblings
Advisor: Gupta, Sumit
Risk Parity Return Trade-off in Relaxed Risk Parity Portfolio Optimization

This paper formulates a relaxed risk parity optimization model to control the balance of risk parity violation against the total portfolio performance. Risk parity is criticized as being conservative and it is improved by re-introducing the asset expected returns into the model and permitting the portfolio to violate the risk parity condition. The incorporation of an explicit target return goal into a second-order-cone model of a risk parity optimization is proposed. When the target return is greater than risk parity return a violation to risk parity allocations occurs that is controlled using a computational construct to obtain near risk parity portfolios to retain risk parity like traits. This model is used to demonstrate empirically that higher returns can be achieved without the risk contributions deviating dramatically from the risk parity allocations. This study also reveals that the relaxed risk parity model exhibits advantageous traits of robustness to expected returns.

Keywords: asset allocation
portfolio optimization
relaxation
risk parity
risk-based
robust optimization
Advisor: Kwon, Roy H
Slope Stability Analysis of Tasiast Mine using Spatially Conditioned Discrete Fracture Network (DFN) Models

Rock structures play an essential role in jointed rock slope designs for open pit mines, as a primary factor controlling slope stability, in both bench scale and large scale. Discrete Fracture Network (DFN) is a numerical technique for structural complexity modeling of rock mass characteristics. DFNs had been used for modelling the local uncertainties in rock mass fracture systems, however, on a larger scale, these models become potentially unrepresentative, due to the geological heterogeneity at mine scale. Subsequently, rock mass parameters become highly spatially variable and new approaches are needed to account for mine-scale variability. This thesis demonstrates the development and applications of a conditioned DFN modeling approach, where fractures are spatially and geometrically constrained by a 3D geostatistical model of fracture intensity as well as drone-mapped trace data. This thesis aims to present the methodology behind model generation and the improvement in slope stability assessment using conditioned DFN models.

Advisor: Esmaeili, Kamran