VictorJuiz/thesis huggingface dataset:
Modeling and Control of a Co-axial Helicopter

This thesis lays the foundations for the development of a small autonomous coaxial helicopter. This is an helicopter with two propellers mounted on the same axis and revolving in opposite directions. To steer the helicopter, this thesis proposes a mechanism that moves the helicopter’s centre of mass. Although such a mechanism has already been investigated experimentally in the literature, it has never been rigorously modeled, and a theoretical analysis has never been performed. This thesis, for the first time, presents an accurate mathematical model of the coaxial helicopter which takes into account the gyroscopic effects of the rotors, the reaction forces and torques exerted by the moving mass actuator on the helicopter body, and the fact that the inertia of the helicopter is time-varying. A nonlinear controller is rigorously derived which makes the helicopter hover at desired positions in three-space. A number of physical prototypes are discussed. None of them is capable of autonomous flight yet, but the experimental and simulation results provide reassurances that the proposed methodology is viable.

Keywords: Co-Axial
Control
Advisor: Maggiore, Manfredi
The Effect of Low Temperature on the Binding of External Chlorides

Designing durable concrete structures is becoming increasingly important with emphasis being placed on extending service life. This project focuses on the effect of low temperatures on chloride binding, chloride binding capacity and ion-binder interactions with respect to hydroxyl ions and pH. Three supplementary cementitious materials were used as well as two w/b ratios, and four curing times. The effect of temperature cycling on chloride binding, binding capacity and ion-binder interaction were also investigated. With temperatures decreasing from 23°C to -15°C, there is a decrease in bound chloride and chloride binding capacity, with GGBFS>GU>MK>SF being the order of binding. When temperature cycling was performed, the binding capacity changed depending on the exposure temperature, with warmer temperatures associated with higher binding capacities. When service life estimates were conducted using Life-365 software, it was found chloride binding capacities determined at 23°C may not be conservative when estimating service life in colder climates.

Keywords: Chloride Binding
Cement
Advisor: Panesar, Daman
A Medicago Sativa Draft Genome using Next Generation Sequencing Reads from Reduced Representation Libraries

Medicago sativa (Alfalfa) is an important agricultural plant for animal forage and nitrogen fixation, and has potential value in ligno-cellulosic energy production. In the quest to understand the plant, I generated a draft genome sequence of M. sativa via two reduced representation sequencing approaches: methylation-dependent filtration, and high CoT filtration. Libraries created from each approach were sequenced on an Illumina next-generation sequencing platform yielding approximately 2.5Gb of raw data. A combination of reference-based genome assembly approaches using the closely related species, Medicago truncatula as a reference, and de novo genome assembly approaches were performed to assemble the draft genome. The reference-based assembly generated 312,011 contigs with weighted median contig length (N50) of 247 bases, whereas de novo assembly produced 547,304 contigs with N50 of 275 bases. The creation of the M. sativa draft genome is vital for downstream functional analyses such as genome wide gene mining and gene expression profiling.

Keywords: Genomic
Bioinformatic
Reduced Representation Library
Advisor: Guttman, David S.
Valve Interstitial Cell Activation and Proliferation are Associated with Changes in Beta-catenin

Heart valve interstitial cells (VICs) undergo activation and proliferation in repair and disease, but the mechanisms are not fully understood. We hypothesize that the establishment of N-cadherin/β-catenin cell-cell contacts may decrease VIC activation, and that Wnt3a/β-catenin signaling may increase VIC proliferation. VIC cultures of different densities are stained for α-SMA, cofilin, TGF-β, pSmad2/3, N-cadherin and β-catenin, and probed for phospho-β-catenin by Western blot. Low density VIC cultures are treated with exogenous Wnt3a and measured for cell number, proliferation, apoptosis, α-SMA, β-catenin, and β-catenin-mediated transcription. β-Catenin siRNA knockdown is used to assess β-catenin specificity. Increased staining of α-SMA, cofilin, TGF-β, pSmad2/3, nuclear β-catenin, and increased phospho-β-catenin are associated with few cell-cell contacts. Wnt3a increased VIC cell number, proliferation, nuclear β-catenin and β-catenin-mediated transcription without affecting activation and apoptosis, and proliferation is abolished by β-catenin siRNA. Thus, N-cadherin/β-catenin cell-cell contacts may inhibit VIC activation and Wnt3a/β-catenin signaling may increase VIC proliferation.

Keywords: heart valve interstitial cell
beta-catenin
activation
proliferation
Advisor: Gotlieb, Avrum I.
Slow Flow of a Viscoelastic Fluid Past a Circular Cylinder

Flow around a cylinder is important in the motion of microorganisms found in biological viscoelastic fluids that propel themselves by flagella. Flow around a cylinder experiments are difficult to perform because of the influence of the walls and ends. An approach was developed to measure the drag on a cylinder by correcting for wall and end effects. Cylinders were vertically dipped into fluids in an annular shaped tank, which was rotated to generate a flow. The force acting on a cylinder was measured using a custom force transducer. This method was used for a Newtonian fluid and two Boger fluids. The drag of the Boger fluids was several times that of an equivalent Newtonian fluid. A cavity was observed to develop behind the cylinders once the flow surpassed a critical velocity. Streakline images taken during the experiment confirmed the presence of a wake region behind the cylinders.

Keywords: Fluid Mechanics
Rheology
Advisor: James, David F.
Structural Determinants of T Wave Alternans in Patients with Cardiomyopathy

Structural barriers can promote discordant action potential (AP) duration alternans, T wave alternans (TWA) and tachyarrhythmia in animal hearts and simulation studies. We hypothesized that heterogeneous scar (gray zone) and dense midwall scar (midwall core) would promote TWA in patients with cardiomyopathy by slowing conduction and uncoupling transmural APs, respectively. Scar core and gray zone were quantified in 40 cardiomyopathy patients using late gadolinium enhanced cardiac magnetic resonance imaging and related to the results of a clinically validated TWA test. The percentages of gray zone, epicardial core and midwall core were greater in the +TWA group, correlated with TWA magnitude and related to a lower heart rate onset for TWA. These specific scar patterns contribute to the genesis and severity of TWA in cardiomyopathy. Greater knowledge of the substrates that promote TWA in cardiomyopathy patients is valuable in determining those at risk of lethal ventricular arrhythmias.

Keywords: cardiac
electrophysiology
T wave alternans
myocardial scar
tachyarrhythmia
sudden death
LGE CMR
cardiomyopathy
Advisor: Chauhan, Vijay
Effect of Yellow Pea Protein and Fibre on Short-term Food Intake, Subjective Appetite and Glycemic Response in Healthy Young Men

In order to elucidate the component(s) of yellow peas responsible for their health benefits, the effects of 10 or 20 g of isolated yellow pea protein (P10 and P20) or fibre (F10 and F20) on food intake (FI) at an ad libitum pizza meal served at 30 min (experiment 1) or 120 min (experiment 2), blood glucose (BG) and appetite in young healthy males (20-30 y) were investigated. In experiment 1, P20 suppressed FI compared to all other treatments and lowered cumulative FI (pizza meal kcal + treatment kcal) compared to F10. Protein treatments suppressed pre-meal (0-30 min) BG compared to control, whereas only P20 suppressed post-meal (50-120 min) BG. In experiment 2, there was no effect of treatment on any outcome measures. Thus, protein is the component responsible for the short-term effects of yellow peas on glycaemia and FI, but its second-meal effects diminish by 2 hours post-consumption.

Keywords: Pulses
Yellow peas
Glycemia
Blood glucose
Protein
Fibre
Fiber
Appetite
Food Intake
Advisor: Anderson, G. Harvey
Microglia Podosomes: Characterization, Ca2+ Regulation and Potential Role in Migration

Microglia, immune cells of the central nervous system, activate in response to pathophysiological stimuli. One of their reactive phenotypes is to migrate to site of injury where they could have either beneficial or detrimental effects. However, little is known regarding the mechanisms underlying microglial migration and how they traverse the unique extracellular environment in brain tissue to reach their destination. Our laboratory first discovered that microglia express structures called podosomes, which can adhere to as well as degrade extracellular matrix. In this study, I further characterize microglial podosomes, and show that they associate with Iba1, Orai1 and calmodulin, proteins not yet observed in podosomes of other cell types. I also present evidence that podosome formation depends on Ca2+ and its entry through store-operated Ca2+ channels. The findings in this thesis contribute to a better understanding of podosome dynamics and their probable roles in microglia migration.

Keywords: microglia
podosomes
migration
Ca2+
Advisor: Schlichter, Lyanne
A Novel Approach to Identify Candidate Imprinted Genes in Humans

Many imprinted genes are necessary for normal human development. Approximately 70 imprinted genes have been identified in humans. I developed a novel approach to identify candidate imprinted genes in humans using the premise that imprinted genes are often associated with nearby parent-of-origin-specific DNA differentially methylated regions (DMRs). I identified parent-of-origin-specific DMRs using sodium bisulfite-based DNA (CpG) methylation profiling of uniparental tissues, mature cystic ovarian teratoma (MCT) and androgenetic complete hydatidiform mole (AnCHM), and biparental tissues, blood and placenta. In support of this approach, the CpG methylation profiling led to the identification of parent-of-origin-specific differentially methylated CpG sites (DMCpGs) in known parent-of-origin-specific DMRs. I found new DMRs for known imprinted genes NAP1L5 and ZNF597. Most importantly, I discovered many new DMCpGs, which were associated with nearby genes, i.e., candidate imprinted genes. Allelic expression analyses of one candidate imprinted gene, AXL, suggested polymorphic imprinting of AXL in human blood.

Keywords: Allele
Allele-specific DNA Methylation
Allele-specific Gene Expression
Allele-specific Expression
Allele-specific Methylation
AnCHM
Androgenetic
Androgenetic Mole
Mole
Complete Mole
Hydatidiform Mole
Complete Hydatidiform Mole
Androgenetic Hydatidiform Mole
Androgenetic Complete Hydatidiform Mole
Biparental Tissue
Bisulfite
Bisulphite
Blood
Blood DNA
Computational Biology
DNA Methylation
DNA Methylation Profiling
Epigenetic
Epi-genetic
Epigenomic
Epi-genomic
Expression
Expression Regulation
Gene Expression
Gene Expression Regulation
Genetic
Genetic Imprint
Genetic Imprinting
Genomic
Genomic DNA
Genomic Imprint
Genomic Imprinting
Human
Imprint
Imprinting
Teratoma
Ovarian Teratoma
Cystic Teratoma
Mature Teratoma
Mature Cystic Teratoma
Mature Ovarian Teratoma
Cystic Ovarian Teratoma
Mature Cystic Ovarian Teratoma
MCT
Methylation
Cytosine Methylation
Microarray
Neoplasm
Ovarian Neoplasm
Placenta
Profiling
Promoter
Promoter Region
Sodium Bisulfite
Sodium Bisulphite
Uniparental Tissue
WB
WBC
Imprinted Gene
Polymorphic Imprinting
Parent-of-origin
Parent-of-origin-specific DNA Methylation
Parent-of-origin-specific Methylation
Parent-of-origin-specific Gene Expression
Parent-of-origin-specific Expression
Advisor: Weksberg, Rosanna
FormWorks-Plus: Improved Pre-processor for VecTor Analysis Software

VecTor© is a suite of computer programs developed for nonlinear finite element analysis of reinforced concrete. A graphics-based pre-processor (FormWorks) was developed for 2D concrete membrane structures, greatly contributing to the software’s utility and success. However, modeling other types of structures is a time consuming process, requiring manual definition of the finite element mesh, loads and analysis parameters in standard text files. A user-friendly pre-processor is required for the entire suite of programs if they are to be of greater use to design engineers. The purpose of this study is to develop an updated version of FormWorks, FormWorks 3.5, which is more user-friendly and compatible with the improvements made in VecTor2 over the past ten years. In addition, an extended version of FormWorks, FormWorks-Plus, will be created for the remaining VecTor programs with a wide range of viewing features, and facilities for specification of node coordinates, elements, loads and material properties.

Keywords: FormWorks
VecTor
Pre-processor
Advisor: Vecchio, Frank J.
Trends in Access to Dental Care among Middle-class Canadians

Objective: To explore the changes in the accessibility of dental services among middle-class Canadians in response to recent changes in the labour market and the increasing costs of dental plans. Methods: Secondary analyses of all Canadian surveys that collected information on dental insurance, utilization and out-of-pocket expenditures were conducted. Descriptive analyses were used to identify and compare trends among middle-class against the Canadian average. Results: Since 1996, the number of insured middle-class grew from 43% to 48%, with the number perceiving cost-barriers to dental care increasing by 2.7 times. In 2009, 30% of middle-class visited a dentist only when emergency happened. Since 1978, fewer middle-income households spent out-of-pocket on dental care, while per capita costs per household spending increased. Compared to national average, middle-class trends implied to poorer access. Conclusions: Access to dental care issues might be ascending from lower income sectors to involve middle-income earners as well.

Keywords: access
dental care
middle-class
dental insurance
Advisor: Quiñonez, Carlos
Real-time Correction By Optical Tracking with Integrated Geometric Distortion Correction for Reducing Motion Artifacts in fMRI

Artifacts caused by head motion are a substantial source of error in fMRI that limits its use in neuroscience research and clinical settings. Real-time scan-plane correction by optical tracking has been shown to correct slice misalignment and non-linear spin-history artifacts, however residual artifacts due to dynamic magnetic field non-uniformity may remain in the data. A recently developed correction technique, PLACE, can correct for absolute geometric distortion using the complex image data from two EPI images, with slightly shifted k-space trajectories. We present a correction approach that integrates PLACE into a real-time scan-plane update system by optical tracking, applied to a tissue-equivalent phantom undergoing complex motion and an fMRI finger tapping experiment with overt head motion to induce dynamic field non-uniformity. Experiments suggest that including volume by volume geometric distortion correction by PLACE can suppress dynamic geometric distortion artifacts in a phantom and in vivo and provide more robust activation maps.

Keywords: Functional MRI
Artifact Correction
Advisor: Graham, Simon James
Angiopoietin-1 and -2 in Infectious Diseases associated with Endothelial Cell Dysfunction

Normal endothelial cell function is controlled in part by a tightly regulated balance between angiopoietin-1 and -2 (Ang-1 and Ang-2). Angiopoietin dysregulation (decreased Ang-1 and increased Ang-2) leads to an activated endothelium that is contractile, adhesive, and prothrombotic. Since an activated endothelial phenotype is seen in invasive group A streptococcal infection, E. coli O157:H7-induced hemolytic-uremic syndrome (HUS), and sepsis, we hypothesized that angiopoietin dysregulation might also be present in these syndromes, and to that end, measured angiopoietin levels in several well-characterized patient cohorts. Decreased Ang-1 and/or increased Ang-2 were found in all three syndromes, and were predictive of clinical outcome in HUS and sepsis. The prognostic utility of Ang-2 in sepsis was further enhanced by combination with biomarkers of inflammation. Angiopoietin dysregulation may therefore represent a shared final common pathway to endothelial activation as well as a clinically useful prognostic biomarker in streptococcal toxic shock, HUS, and sepsis.

Keywords: angiopoietin-1
angiopoietin-2
endothelial cell
streptococcal toxic shock
hemolytic-uremic syndrome
sepsis
Advisor: Liles, W. Conrad
Modeling Damage and Damage Evolution in Periodic Cellular Sandwich Panels

Among the light bending structures currently available, truss core panels are one of the most efficient when properly designed. The proper selection of the truss core lattice allows the incorporation of additional functionality. To exploit the multi-functional advantages of truss core sandwich structures, it is crucial to understand how the materials survive in challenging environments. In this research, the strengths of truss core panels have been predicted. Numerical calculations and experiments were carried out to validate the predictions. The effects of damage and damage propagation on the overall strength of the panel were also addressed. The strength and failure surfaces of arrays of partially damaged truss core unit cells were calculated under shear and axial loading. The results highlight the modes and trends of damage propagation in truss core panel, and the estimated damaged strength. Experiments were also performed to validate the damaged strength.

Keywords: multifuctinal structures, truss core, macroscopic strength, failure surface, damaged state
Advisor: Steeves, Craig A.
Endothelial Progenitor Cells (EPCs) for Fracture Healing and Angiogenesis: A Comparison with Mesenchymal Stem Cells (MSCs)

The purpose of this study was to compare the effects of two types of stem/progenitor cells on the healing of critical sized bone defects in a rat model. Endothelial progenitor cells (EPCs), a novel cell type with previously demonstrated effects on both osteogenesis and angiogenesis, were compared to both a control group (no cells), and a treatment group of mesenchymal stem cells (MSCs). The hypothesis was that EPCs would demonstrate both superior bone healing and angiogenesis, when compared to MSCs and controls. EPCs, MSCs, or a control carrier were placed in surgically stabilized bone defects in a rat femur and both bone formation and angiogenesis were assessed. EPC treated defects demonstrated significantly more bone formation and angiogenesis at the bone defect site than MSC or control treated defects. These results strongly suggest that EPCs are more effective than MSCs for therapeutic osteogenesis and angiogenesis in a bone defect model.

Keywords: Fracture Healing
Stem Cell Therapy
Advisor: Schemitsch, Emil H.
Role of Oxidative Stress in Mediating Elevated Atrial Fibrillation by Tumor Necrosis Factor-alpha

Atrial fibrillation (AF), the most common arrhythmia encountered in clinical practice, is a major source of morbidity and mortality, and is highly associated with inflammation and oxidative stress. In the present study, we show that acute exposure of mice atrial tissue to tumor necrosis factor-α (TNF-α) increases susceptibility to AF. We further show that acute exposure to TNF-α led to increased spontaneous sarcoplasmic reticulum (SR) calcium release and generated triggered activities in isolated mice atrial myocytes. This increase in spontaneous SR calcium activity was found to be due to elevated reactive oxygen species production from mitochondria and NADPH oxidase sources triggered by TNF-α. Hence we concluded that acute exposure to TNF-α leads to elevated oxidative stress that increases spontaneous SR Ca2+ release and triggered activity through which it can lead to AF induction and maintenance

Keywords: Atrial Fibrillation
Oxidative Stress
Reactive Oxygen Species (ROS)
Inflammation
TNF-alpha
Calcium Sparks
Triggered Activity
Mitochondria
NADPH Oxidase
Advisor: Backx, Peter
The Influence of Thermal Barrier Coating Surface Roughness on Spark Ignition Engine Performance and Emissions

The effects on heat transfer of piston crown surface finish and use of a metal based thermal barrier coating (TBC) on the piston crown were studied in an SI engine. Measured engine parameters such as power, fuel consumption, emissions and cylinder pressure were used to identify the effects of the coating and its surface finish. Two piston coatings were tested: a baseline copper coating and a metal TBC. Reducing surface roughness of both coatings increased in-cylinder temperature and pressure as a result of reduced heat transfer through the piston crown. These increases resulted in small improvements in both power and fuel consumption, while also having measurable effect on emissions. Oxides of nitrogen emissions were increased while total hydrocarbon emissions were decreased. Improvements attributed to the TBC were found to be small, but statistically significant. At an equivalent surface finish, the TBC performed better than the baseline copper finish.

Keywords: Thermal Barrier Coating
Surface Roughness
Emissions
Performance
SI Engine
Heat Transfer
Advisor: Wallace, James S.
Utility of Lorenz Curves in Examining Physician Prescribing Practices: Example of Ontario Neurologist Prescribing of Multiple Sclerosis Disease-modifying Therapies in 2009

BACKGROUND: Differences in disease-modifying therapy (DMT) prescribing patterns between different groups of neurologists have not been explored. HYPOTHESIS: MS-specialist neurologists use a broader range of DMTs in contrast to generalist neurologists who preferentially prescribe Avonex. METHODS: Ontario neurologist demographic and geographical characteristics were linked to 2009 DMT prescription data. Lorenz curves and Gini coefficients were constructed to examine prescribing patterns; separating neurologist characteristics dichotomously and separating Avonex from the other DMTs. Gini Coefficients were compared using jack-knife statistical techniques to derive 95% confidence intervals. RESULTS: Prescriptions are highly concentrated with 12% of Ontario neurologists prescribing 80% of DMTs. High-volume prescribers show a broader range of DMT use while low-volume prescribers tend to use a particular DMT. CONCLUSIONS: The majority of DMTs are prescribed by a small subset of neurologists. High-volume prescribers show more variability in DMT use while low-volume prescribers tend to individually focus on a narrower range of DMTs.

Keywords: multiple sclerosis
Lorenz curve
Advisor: O'Connor, Paul
Investigation of the Effects of Aging and Small Vessel Disease on Cardiac Frequency Signal in Cerebral White Matter as Imaged by Echo Planar Imaging using Magnetic Resonance

Cerebral small vessel disease (SVD) is highly prevalent in older adults and is a predictor of stroke, dementia, and death. SVD is also associated with cognitive dysfunction, gait problems, and urinary incontinence. SVD is diagnosed based on white matter hyperintensities on T2 weighted scans. This thesis investigates the cardiac frequency component of resting state functional magnetic resonance imaging data in young healthy adults, older healthy adults, and older adults with pronounced SVD. A cardiac pulsatility metric is defined, and a tissue type contrast is observed between white matter, grey matter, and cerebrospinal fluid. Aging and disease effects are observed on cardiac pulsatility in white matter. The increased pulsatility may reflect the pathology of venous collagenosis and draining vein stenosis. Developing a better understanding of the etiology of SVD is an important step towards treating the disease.

Keywords: magnetic resonance imaging
small vessel disease
MRI
SVD
physiological noise
echo planar imaging
Advisor: MacIntosh, Bradley
Black, Sandra