VictorJuiz/thesis huggingface dataset:
Volitional Modulation of Cortical Neuronal Activity to Control a Closed-Loop Brain-Machine Interface

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.

Keywords: Animal model
Brain-machine interface
Closed-loop control
Neuroplasticity
Single neuron control
Advisor: Popovic, R. Milos
High-Order CENO Reconstruction Scheme For Three-Dimensional Unstructured Mesh

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.

Keywords: aerospace
ceno
engineering
Advisor: Groth, P. T. Clinton
Goal-oriented Know-how Mapping: Mapping process, prototype, and empirical studies

We elaborate and evaluate a goal-oriented modelling approach for mapping the means-ends knowledge in technology domains. The means-ends relationship connects a solution to a problem, capturing "know-how" of a domain that can be made explicit. Means-ends knowledge from publications is codified and used to create a know-how map in order to organize domain knowledge in terms of problems and their solutions. Domain researchers as well as newcomers, can use the map to search for problems and solutions, and to evaluate the strengths and weaknesses of alternative solutions. A know-how map is expected to facilitate discovery of knowledge gaps, thus promoting new research and innovation. This work further explores goal modelling approach to know-how. The process of creating and using goal-oriented know-how maps is documented. The user evaluation conducted in this work gathered empirical data about the performance of know-how maps in comparison to a written review of the domain.

Advisor: Yu, Eric
Concurrent Markov Decision Processes for Robust Robot Team Learning under Uncertainty

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].

Keywords: L-Alliance
Markov Decision Process
Multi-agent Learning
Q-Learning
Robotics
Advisor: Emami, Mohammed Reza
Robust Synchronization in Networks of Compartmental Systems

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.

Keywords: compartmental models
control theory
coupled harmonic oscillators
robustness
synchronization
systems biology
Advisor: Scardovi, Luca
Numerical Investigation of Sooting Propensity of Ethanol at Elevated Pressures

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.

Keywords: Combustion
Computational Fluid Dynamics
Advisor: Groth, P.T. Clinton
Image-based Characterization of the Mechanical Behaviour of Healthy and Metastatically-involved Vertebrae

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.

Keywords: Biomechanics
Finite element analysis
Image registration
Metastasis
Micro CT imaging
Microdamage
Advisor: Whyne, Cari
Cone Photoreceptor Structure and Function in Adolescents and Young Adults with 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

Keywords: Adaptive optics retinal imaging
Cone photoreceptors
Electrophysiology
Type 1 diabetes
Advisor: Westall, Carol
Analysis of Force Distribution on Upper Body Limbs during Ambulation with Crutches

Crutches provide support for various mobility impairments as well as aid during recovery of lower limbs. Resultant forces on upper limbs can cause pain and conditions such as carpal tunnel syndrome. This study aims to develop a system to accurately measure forces present on the interaction points between the upper limb and crutch, to determine if there are differences between crutch manufacturing options (spring dampening component), as well as between the environments in which crutches are used, such as up and down hills or on a rocky surfaces. Overall, it was seen that the forces at the interface are highest over the carpal tunnel region. The spring was shown to reduce the maximum rate of loading. The largest environmental effect was seen by the rocks, which increased the maximum rate of loading. Gait over rocks was also seen to increase the maximum forces seen at the interfaces, though not significantly.

Advisor: Andrysek, Jan
Enhancing the Efficiency of the Polynomial Chaos Expansion Finite-difference Time-domain Method

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.

Keywords: Finite-difference time-domain
polynomial chaos
uncertainty quantification
Advisor: Sarris, D Costas
Evaluation of Liquid Fuel Spray Models for Hybrid RANS/LES and DLES Prediction of Turbulent Reactive Flows

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.

Keywords: Atomization
CFD
Spray
Advisor: Groth, P.T Clinton
Evidence for the Fast Exercise Drive to Breathe During Sinusoidal Cycle Ergometry

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.

Keywords: afferent feedback
breathing
Exercise hyperpnoea
Advisor: Wells, D Greg
Scalable Approach for Extrusion and Perfusion of Tubular, Heterotypic Biomaterials

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.

Keywords: 3D Bioprinting
Hydrogels
Perfusable Materials
Tubular Structures
Advisor: Guenther, Axel
Protocol Parameter Optimization and Characterization of Superconducting Nanowire Single Photon 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.

Keywords: decoy state
quantum cryptography
quantum information
quantum key distribution
quantum physics
superconducting detector
Advisor: Lo, Hoi-Kwong
Investigation of the Epigenetic Landscape at Disease-causing Polymorphic Repeat Loci

There are over 40 genetic diseases caused by repeat locus-specific instability. The causes of repeat instability are poorly understood and a mechanism that explains their occurrence in full has yet to be identified. Numerous studies have shown epigenetic modifiers and cis-elements to play a role in repeat instability. Here, ENCODE datasets (histone modifications, DNA methylation, CTCF binding, DNase I hypersensitivity, and CpG sites) were analyzed at disease-causing repeat loci, control non-disease causing repeat loci, mono- and dinucleotide repeat loci, short interspersed nuclear element loci, long interspersed nuclear element loci, telomeric repeat loci, and classical satellite I, II, and III loci. Loci were assessed in hippocampus, skeletal muscle, liver and kidney. We identified epigenetic mark patterns at these loci. A striking symmetric distribution pattern centrally localized around specific tandem repeats showing epigenetic enrichment or depletion of marks was observed indicating a possible nucleosome positioning effect. Tissue-specific patterns were also identified.

Advisor: Pearson, E Christopher
Indoor Simulation of Wildfire Detection and Monitoring using UAV

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.

Keywords: Navigation
Quadrotor
Tracking
UAV
Wildfire
Advisor: Liu, H.T. Hugh
Anti-diabetic Glucagon-like peptide-1 induces Formation of New Elastic Fibers in Human Cardiac Fibroblasts after Cross-activation of 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.

Keywords: Cardiac Fibroblasts
Cardioprotection
Elastin
GLP-1
IGF-1R
Advisor: Hinek, Aleksander
Chemical Kinetic and Thermal Numerical Simulation of Coking Process of Jet Fuels in Thin Nozzle Sections within Autoxidation Temperature Regime

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.

Keywords: autoxidation
coking
injector nozzle
jet fuel
numerical simulation
thermal stability
Advisor: Gulder, L Omer
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

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.

Keywords: Mariner-like elements
Plant Genome
Tc1-like element
Tc1/Mariner
Tranposition acitivity
Transposable elements
Advisor: Yang, Guojun
Biomechanical Optimization of the Angle and Position for Surgical Implantation of a Straight Short Stem Hip Implant

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.

Keywords: Biomechanics
Conservative Hip Implants
Design of Experiments
Finite Element Modelling
Orthopaedic Surgery
Total Hip Arthroplasty
Advisor: Schemitsch, Emil H
Along the Highway: Landscapes of National Mourning in Canada

Between 2002 and 2011, 158 Canadian Forces soldiers died while serving in Afghanistan and were repatriated via Canadian Forces Base Trenton to the Office of the Chief Coroner of Ontario in Toronto for autopsy. The repatriation route took their bodies along Highway 401 in central Ontario, where thousands assembled on bridges above the highway to pay their respects. In this thesis, I detail the memorial landscape that developed around what came to be known as the Highway of Heroes, and I use this conception of the highway as a landscape to demonstrate the ways in which it participates in the ongoing remilitarization of Canada. Following the work of Judith Butler, I argue that the Highway of Heroes contributes to the production of a hierarchy of grievable subjects, and the act of memorializing soldiers is implicated in the erasure of other victims of state violence, including missing and murdered Indigenous women.

Keywords: Canadian Forces
highway
landscape
memorialization
military
mourning
Advisor: Cowen, Deborah
Farish, Matthew