VictorJuiz/thesis huggingface dataset:
Re-engaging students with nature: Using local settings as a context for learning
Keywords: environmental education
environmental literacy
experiential learning
outdoor learning
place-based education
student engagement

The aim of this case study was to determine how place-based learning in a natural environment impacted disengaged students. Intermediate students at a large suburban high school were provided with an opportunity to engage in a field study that investigated a local creek. Participating students shared their knowledge with a class from a local elementary school and engaged in action that created a greater awareness of environmental issues. The results of this study indicate that place-based learning in a local forest coupled with mentoring opportunities had a positive impact on student perceptions of school and learning. In addition, findings suggest that students developed more of an understanding of ecological principles and gained a greater awareness of local environmental issues.
Serologically Active Clinically Quiescent Systemic Lupus Erythematosus: Clinical and Immunological Correlates
Keywords: Biomarkers
Epidemiology
Remission
Systemic lupus erythematosus

Aim: Some remitted systemic lupus erythematosus (SLE) patients are serologically active (by elevated anti-double-stranded DNA antibodies and/or hypocomplementemia) despite longstanding clinical quiescence ("SACQ"), thus presenting a management dilemma. We described the SACQ period and its patients, and sought biomarkers heralding disease flare in them. Methods: Patients with a prolonged SACQ period were followed prospectively, with clinical and laboratory data collected at each visit. Serologically and clinically active (SACA) and serologically and clinically quiescent (SQCQ) patients served as positive and negative controls, respectively. Descriptive statistics and logistic regression analyses were utilized.Results: SACQ patients were phenotypically unique prior to remission onset, and did not accrue subclinical organ damage over the quiescent period. Fluctuation in immunoglobulin isotype did not predict flare. The SACQ interferon and cytokine/chemokine profiles mirror SQCQ patients.Conclusions: SACQ patients' active serology should not guide treatment decisions, and these patients are best managed conservatively. Alternate biomarkers must be sought.
Modeling the Gynecologic Oncology Workforce Using System Dynamics
Keywords: Forecasting
Gynecologic oncology
Health human resource planning
Surgical oncology
System dynamics
Workforce planning

This research seeks to better understand the workforce needs within gynecologic oncology using health human resource planning and system dynamics modeling. Historical cancer surgeries were obtained from CIHI for 2004-2011 and forecasted for 2012-2032 using double exponential smoothing. A system dynamics model consisting of the fellowship population, aging provider population, and patient need population was developed. The model predicted that 94 new FTEs will need to be hired during 2012-2032. We assumed that in the current environment, the enrolment rate changes based on the workforce shortage or surplus, which results in an oscillating effect between these variables. Therefore, predetermining the fellowship enrolment rate should be undertaken to reduce the oscillation. Transferring follow-up appointments to nurse practitioners proved effective for reducing the workforce shortage, but more research is required into implementation. A similar approach could be used to model the workforce in other medical specialties.
Oxidative Stress in Bipolar Disorder: a Meta-analysis of Oxidative Stress Markers and an Investigation of the Hippocampus
Keywords: 5-hydroxymethylcytosine
Bipolar disorder
Hippocampus
Lipid peroxidation
Oxidative stress
Schizophrenia

Bipolar disorder is a prevalent and debilitating disease, however, its pathophysiology remains unknown. There is substantial evidence of oxidative damage in bipolar disorder from both peripheral and post-mortem samples, especially in the prefrontal cortex. It is the objective of this study to consolidate research measuring oxidative stress biomarkers in bipolar disorder through a meta-analysis and to determine if the hippocampus region is a specific target of oxidative damage through a biochemical study using post-mortem samples. Results from this study further confirm the presence of oxidative damage in bipolar disorder, but suggest that the hippocampus is not a target. We have also shown a global increase of 5-hydroxymethylcytosine in the hippocampus of patients with schizophrenia, suggesting a possible alteration in the demethylation pathway. Determining the exact targets of oxidative stress in bipolar disorder may lead to biomarker development, better treatment and diagnostic options, and ultimately, a better quality of life for patients.
Volitional Modulation of Cortical Neuronal Activity to Control a Closed-Loop Brain-Machine Interface
Keywords: Animal model
Brain-machine interface
Closed-loop control
Neuroplasticity
Single neuron control

Brain-machine interfaces transform neural activity from the brain into output commands. Current BMI technology employs extensive computational neuronal modeling to extract relevant information pertinent to motor output or motor imagery. We developed an invasive closed-loop BMI system that uses simple transforms from single neurons in the cortex of rats to control one degree of freedom. The BMI task consisted in up-regulation of the neural activity and we trained one rat to modulate 5 different neurons during 7 sessions. We found that the brain can learn to control the BMI system by modifying the tuning properties of individual neurons in the cortex through neuroplasticity, a process that can take place within single training sessions and produce movement of a mechanical object that does not emulate a physical output. This volitional control can potentially feel naturalistic to the user, ultimately assisting individuals with severe disabilities to facilitate their activities of daily living.
High-Order CENO Reconstruction Scheme For Three-Dimensional Unstructured Mesh
Keywords: aerospace
ceno
engineering

Research and development of high-order methods in the past decade have focused on obtaining more accurate solutions with the additional advantage of decreasing overall computational cost and memory requirements. The present research focuses on implementation of the CENO reconstruction scheme for three-dimensional unstructured meshes. The CENO reconstruction scheme makes use of a hybrid reconstruction technique based on a fixed single central stencil which is particularly advantageous for unstructured meshes. A smoothness indicator facilitates the switching from a k-exact reconstruction in smooth regions of the solution to a limited piecewise linear reconstruction in unresolved or discontinuous regions. This scheme has been implemented to reconstruct both continuous and discontinuous functions on three-dimensional unstructured tetrahedral meshes.
Concurrent Markov Decision Processes for Robust Robot Team Learning under Uncertainty
Keywords: L-Alliance
Markov Decision Process
Multi-agent Learning
Q-Learning
Robotics

For robots to become a more common fixture in private and public industries, they must exhibit compliant individual and social learning. To achieve social compliance, while maintaining individual performance, robots must represent knowledge accurately in both certain and uncertain environments. Robots also need to quantify effective decision making both when isolated and when teamed with peer robots and humans. Thus, this thesis considers improvements to the Concurrent Individual and Social Learning (CISL) approach [30, 31], and addresses all of the above problems by exploring three subjects: learning problem representation using Markov Decision Processes (MDPs) [17], state uncertainty and state estimation [18], and advice sharing from both robot and human advisors [17, 19].
Robust Synchronization in Networks of Compartmental Systems
Keywords: compartmental models
control theory
coupled harmonic oscillators
robustness
synchronization
systems biology

This thesis studies robust synchronization in networks of compartmental systems motivated by cellular networks. These networks consist of compartments each of which is composed by interconnected subunits. We investigate conditions on the dynamics of the subunits and on the interconnection topology that guarantee robust synchronization in the presence of external disturbances and possibly nonlinear perturbations on the network. The results are illustrated with several examples, including a network of genetic oscillators.
Numerical Investigation of Sooting Propensity of Ethanol at Elevated Pressures
Keywords: Combustion
Computational Fluid Dynamics

The effects of pressure on the combustion properties of ethanol were investigated. One-dimensional analysis was employed to evaluate the fundamental combustion properties of ethanol as a function of equivalence ratio and pressure. Two mechanisms were used in the one-dimensional simulation. The predicted results displayed good agreement with experimental data. Further, a state of the art computational framework was used to simulate the two-dimensional, axisymmetric, co-flow laminar diffusion flames of ethanol. The framework is a highly-scalable combustion modelling tool designed specifically for use on large multi-processor parallel computer systems. The flame structure predictions were obtained for ethanol. The soot volume fraction had an annular structure and maximum concentrations occured in the annular region. In agreement with the past theoretical and numerical measurements for other gaseous fuels, the current work showed a constant flame height and an increasing trend of soot yield with increasing pressure.
Image-based Characterization of the Mechanical Behaviour of Healthy and Metastatically-involved Vertebrae
Keywords: Biomechanics
Finite element analysis
Image registration
Metastasis
Micro CT imaging
Microdamage

Skeletal metastasis leads to changes in bone architecture, quality and strength, including microdamage accumulation. This dissertation aims to combine image-based computational and experimental techniques to study trabecular bone microdamage in healthy and metastatic whole bones. Deformable image registration was used to demonstrate proof of concept that post-euthanasia strain analysis of µCT images represents in vivo quasi static mechanical behavior of whole rat vertebrae. The ability to concurrently identify microdamage in whole vertebrae using histologic techniques (calcein and fuschin) and contrast enhanced BaSO4 µCT imaging was demonstrated and compared to stresses and strains calculated through micro finite element analysis. Significantly higher stresses and strains were found in regions of trabecular microdamage compared to undamaged regions, and in metastatic compared to healthy vertebrae. The techniques and knowledge developed through this work improve understanding of trabecular bone microdamage and form a solid platform for modeling the material and structural behaviour of skeletal tissue.
Cone Photoreceptor Structure and Function in Adolescents and Young Adults with Type 1 Diabetes
Keywords: Adaptive optics retinal imaging
Cone photoreceptors
Electrophysiology
Type 1 diabetes

This cross-sectional study assessed properties of cone photoreceptors in patients with type 1 diabetes, as potential biomarkers of sub-clinical retinopathy. Patients with no vascular signs of retinopathy (ages 12-25) exhibited abnormal neuroretinal structure and function of the cone photoreceptor layer as compared to age-similar controls. White flash electroretinogram a-waves, demonstrating L- and M-cone function, were significantly less steep in patients than in controls (by 1.3 mV/ms, 95% CI: -0.3, -2.3, p=0.01). Red flash electroretinograms did not differ between groups. Adaptive optics retinal imaging was used to visualize L- and M-cones in vivo. At 7.1
Enhancing the Efficiency of the Polynomial Chaos Expansion Finite-difference Time-domain Method
Keywords: Finite-difference time-domain
polynomial chaos
uncertainty quantification

The polynomial chaos based finite-difference time-domain (PCE-FDTD) method is a promising technique for quantifying the impact of parameter variability on the performance metrics of electromagnetic structures. With the aim to improve the versatility and computational efficiency of the PCE-FDTD method, this thesis presents two novel formulations of the PCE-FDTD. First, a formulation and systematic study of the convolutional perfectly matched layer for terminating simulation domain constituting random media is presented, and demonstrates excellent efficiency for the study of microwave structures with substrate permittivity uncertainties. Second, a hybrid Monte Carlo / PCE-FDTD method based on the control variate is developed to mitigate the large computation cost associated with multi-parametric uncertainty analysis using PCE-FDTD. This method is applied to a Bragg reflector structure with uncertain slab permittivities and leads to a considerable reduction in computation time over conventional PCE-FDTD method.
Evaluation of Liquid Fuel Spray Models for Hybrid RANS/LES and DLES Prediction of Turbulent Reactive Flows
Keywords: Atomization
CFD
Spray

An evaluation of Lagrangian-based, discrete-phase models for multi-component liquid sprays encountered in the combustors of gas turbine engines is considered. In particular, the spray modeling capabilities of the commercial software, ANSYS Fluent, was evaluated. Spray modeling was performed for various cold flow validation cases. These validation cases include a liquid jet in a cross-flow, an airblast atomizer, and a high shear fuel nozzle. Droplet properties including velocity and diameter were investigated and compared with previous experimental and numerical results. Different primary and secondary breakup models were evaluated in this thesis. The secondary breakup models investigated include the Taylor analogy breakup (TAB) model, the wave model, the Kelvin-Helmholtz Rayleigh-Taylor model (KHRT), and the Stochastic secondary droplet (SSD) approach. The modeling of fuel sprays requires a proper treatment for the turbulence. Reynolds-averaged Navier-Stokes (RANS), large eddy simulation (LES), hybrid RANS/LES, and dynamic LES (DLES) were also considered for the turbulent flows involving sprays. The spray and turbulence models were evaluated using the available benchmark experimental data.
Evidence for the Fast Exercise Drive to Breathe During Sinusoidal Cycle Ergometry
Keywords: afferent feedback
breathing
Exercise hyperpnoea

Human experimentation investigating the role of limb movement frequency on the fast exercise drive to breathe has not reached agreement on the mechanism that produces this response. To investigate the role of limb movement frequency and endurance exercise training on the fast exercise drive to breathe, two sinusoidal exercise protocols were employed in these experiments: one at constant workload with sinusoidal pedaling cadence, and a second with sinusoidal workload at constant cadence. Metabolic rate (Vo2) was matched between experiments. The ventilation response was significantly faster when limb movement speed was varied, compared to when pedal loading was varied. Ventilation response amplitudes were higher during pedal cadence variation versus pedal loading variation. Similar findings were obtained for athletes, but with significantly attenuated ventilation responses to exercise. Therefore, fast changes in limb movement frequency are a potent stimulus to ventilation at submaximal workloads, and this response is susceptible to attenuation through training.
Scalable Approach for Extrusion and Perfusion of Tubular, Heterotypic Biomaterials
Keywords: 3D Bioprinting
Hydrogels
Perfusable Materials
Tubular Structures

Soft material tubes are critical in the vasculature of mammalian tissues, forming networks of blood vessels and airways. Homogeneous and heterogeneous hydrogel tubes were extruded in a one-step process using a three layer microfluidic device. Co-axial cylindrical flow of crosslinking solutions and an alginate matrix is generated by a radial arrangement of microfluidic channels at the device's vertical extrusion outlet. The flow is confined and begins a sol-gel transition immediately as it extrudes at velocities upwards of 4 mm/s. This approach allows for predictive control over the dimensions of the rapidly formed tubular structures for outer diameters from 600 µm to 3 mm. A second microfluidic device hosts tube segments for controlled perfusion and pressurization using a reversible vacuum seal. On-chip tube deflection is observed and modeled as a measure of material compliance and circumferential elasticity. I anticipate applications of these devices for perfusion cell culture of cell-laden hydrogel tubes.
Protocol Parameter Optimization and Characterization of Superconducting Nanowire Single Photon Detector
Keywords: decoy state
quantum cryptography
quantum information
quantum key distribution
quantum physics
superconducting detector

The unconditional security of QKD is based on quantum physics. However, unconditional security, which relies on reasonable assumptions, is not the same as absolute security, which make no assumptions, and QC protocols can be breached by means of side channels. Recently, Measurement Device Independent QKD (MDI-QKD) has been proposed to remove the side channels.In parallel to improving performance by optimization, superconducting Nanowire Single Photon Detector (SNSPD) has emerged among others as a promising technology. In this thesis, we present a characterization procedure of SNSPD, and we report the important finding of the phenomenon of afterpulse", which is a clustered detection event at 180ns after a first event in a chain. Then, we postulate that the origin of this afterpulse is from the limited bandwidth of the amplifier. By replacing the amplifiers with those with a larger bandwidth, the phenomenon of afterpulse disappears.
Indoor Simulation of Wildfire Detection and Monitoring using UAV
Keywords: Navigation
Quadrotor
Tracking
UAV
Wildfire

Wildfires have been a major source of environmental and economical damage for Canada. Wildfire detection and monitoring using UAVs have garnered great interest. This thesis project investigates the use of colour-based vision feedback for tracking a dynamically expanding wildfire simulated in a fully coloured environment. A custom Indoor Simulation Platform is developed to test and debug various navigation algorithms using a physical quadrotor. The proposed fire perimeter tracking navigation algorithm has been tested in both computational simulation and on the Indoor Simulation Platform, and could be used in an outdoor mission with high confidence of success.
Anti-diabetic Glucagon-like peptide-1 induces Formation of New Elastic Fibers in Human Cardiac Fibroblasts after Cross-activation of IGF-1R
Keywords: Cardiac Fibroblasts
Cardioprotection
Elastin
GLP-1
IGF-1R

Glucagon-like peptide 1 (GLP-1) is a metabolic hormone that regulates glucose homeostasis by inducing insulin synthesis and secretion. It has been recently reported in a number of studies that GLP-1 also exerts cardioprotective effects and leads to improved functional recovery after myocardial infarction. Particularly, GLP-1 treatment lead to sustained improvement in cardiac function in long-term studies, suggesting the involvement of mechanisms beyond acute metabolic and cytoprotective effects. We hypothesized that GLP-1 contributes to cardiac functional recovery through its interaction with the cardiac fibroblasts responsible for the initial healing and remodeling of the injured myocardium. Here, we report that cultures of human cardiac fibroblasts, treated with GLP-1 peptides, demonstrate a selective up-regulation in elastin gene expression and elastic fibers production, despite the fact that they do not express the classic GLP-1R. Importantly, we provide experimental evidence that the GLP- 1-induced production of this resilient extracellular matrix (ECM) component by cardiac fibroblasts is triggered through the cross-activation of their IGF-1 receptors (IGF-1R). We speculate that this elastogenic effect may contribute to beneficial and functionally compliant remodelling of the heart following prolonged ischemia and infarction.
Chemical Kinetic and Thermal Numerical Simulation of Coking Process of Jet Fuels in Thin Nozzle Sections within Autoxidation Temperature Regime
Keywords: autoxidation
coking
injector nozzle
jet fuel
numerical simulation
thermal stability

The autoxidation and deposition process of air saturated Jet A-1 was simulated for injection nozzle-like test sections with preheated fuel in the range of autoxidation regime. The model also includes a preheating section to represent upstream condition of injection nozzles. 2-D computational fluid dynamics along with a pseudo-detailed chemical kinetics model was used to model deposition. Oxygen consumption is the key to measure the extent of oxidation in the preheating section. Velocity and temperature profiles can significantly influence the chemical reactions. Deposition rate in the test section is dependent on both upstream and local conditions. Higher temperatures in the test section resulted in increased deposition rate. To determine the deposition rate at a certain location, the entire history of the upstream conditions or the exact chemical composition at the location of interest is necessary.
Elucidating Transposable Elements Survival Mechanisms: Invasion and Evasion by Tc1/mariner Superfamily DNA Transposons – Analysis of plant Tc1-like elements horizontal transfers and rice Mariner-like elements autoregulation
Keywords: Mariner-like elements
Plant Genome
Tc1-like element
Tc1/Mariner
Tranposition acitivity
Transposable elements

Transposable elements are mobile DNA elements residing in almost all sequenced genomes. However, the kingdom Plantae has not previously been reported to harbor Tc1-like elements (TLEs). This study reports the characterization of several plant TLEs. It was proposed that the wide distribution of transposons may be partly due to horizontal transmissions, and some cases of highly similar TLEs from distantly related species were found in this study. Once a transposon invades a new genome, it may freely amplify. Being mutagenic in nature, they are under constant scrutiny of host inhibitory mechanisms that often keep transposition activity at a basal level. A potential evasive mechanism by a rice Mariner-like element is described here to auto-regulate activity via a subterminal transposase binding motif.
Biomechanical Optimization of the Angle and Position for Surgical Implantation of a Straight Short Stem Hip Implant
Keywords: Biomechanics
Conservative Hip Implants
Design of Experiments
Finite Element Modelling
Orthopaedic Surgery
Total Hip Arthroplasty

Conservative hip implants preserve healthy bone for revision surgeries and improve physiological loading; however, they have few supporting biomechanical data. This thesis determined the 3D orientation of a straight short stem hip implant within the proximal femur that would yield a stress distribution most similar to an intact femur. Synthetic femurs were implanted with a stem in one of seven maximum angles or positions and axially loaded, with resultant strain values used to validate a finite element model. Design of experiments was used to analyze the range of potential implant orientations under three gait cycle loading conditions. A global optimal orientation of 9.14 valgus, 2.49 anteversion, 0.48mm posterior position, and 0.23mm inferior position yielded optimal stress distributions across the range of the gait cycle. Orthopaedic surgeons should therefore implant straight short stem hip implants in valgus up to 10 with an otherwise neutral position and version for maximal physiological loading.