VictorJuiz/thesis huggingface dataset:
Cooperative UAV Search and Intercept

In this thesis, a solution to the multi-Unmanned Aerial Vehicle (UAV) search and intercept problem for a moving target is presented. For the search phase, an adapted diffusion-based algorithm is used to manage the target uncertainty while individual UAVs are controlled with a hybrid receding horizon / potential method. The coordinated search is made possible by an uncertainty weighting process. The team intercept phase algorithm is a behavioural approach based on the analytical solution of Isaac's Single-Pursuer/Single-Evader (SPSE) homicidal chau ffeur problem. In this formulation, the intercepting control is taken to be a linear combination of the individual SPSE controls that would exist for each of the evader/pursuer pairs. A particle swarm optimizer is applied to find approximate optimal weighting coefficients for discretized intervals of the game time. Simulations for the team search, team intercept and combined search and intercept problem are presented.

Keywords: Unmanned Aerial Vehicle
Multi-Agent
Cooperation
Coordination
Diffusion
Search
UAV
Intercept
Pursuit
Evasion
Advisor: Liu, Hugh
An In Vivo Neurophysiological Model of Cortical Ischemia in the Rat

Spontaneous and evoked potentials (EPs) were recorded with cross-cortical microelectrode arrays following partial occlusion of the MCA and ACA in urethane-anaesthetised rats. The control group received no occlusion, while the treatment group was injected with anti-stroke peptide Tat-NR2B9c 5min before ischemia. Spontaneous EEG power significantly decreased in the stroke-only group when compared to controls (p<0.001). A greater loss of EEG power was observed on anterior electrodes closer to the occluded area versus posterior contacts in stroke-only rats (p<0.05). The Tat-NR2B9c+stroke group lost significantly less power when compared to stroke-only animals (p<0.05). EP amplitude in the stroke-only group was significantly reduced following ischemia when compared to control and Tat-NR2B9c+stroke animals (p<0.001). Epileptiform discharges were observed in 8/10 untreated stroke rats and 3/5 stroke rats treated with Tat-NR2B9c. The characteristic features of spontaneous and evoked potentials validate this rat focal stroke model for in vivo testing of pharmacological agents.

Keywords: Ischemia
In vivo
Rat
Cortex
Tat-NR2B9c
Microelectrodes
Potentials
Advisor: Hutchison, William D.
Aarts, Michelle
Behavioral and Electrographic Abnormalities due to Repeated Hypoglycemic Episodes in Mice

Severe hypoglycemia poses the greatest challenge to glycemic control in diabetic patients, especially children with type 1 diabetes mellitus. Although in vivo animal models exist for investigating the effects of hypoglycemia, few studies examine repeated hypoglycemia and none investigate within the context of a juvenile animal model. The main objective of this thesis was to examine electroencephalographic (EEG) and behavioral abnormalities manifesting as a result of repeated hypoglycemia in juvenile diabetic and non-diabetic mouse models. Using a novel implantation technique, the hippocampal and cortical EEG were recorded during repeated insulin-induced hypoglycemia. It was discovered that repeated hypoglycemia exacerbated behavioral convulsion severity and promoted epileptiform EEG activity within the hippocampus and cortex of both diabetic and non-diabetic animals. Furthermore, sustained hypoglycemia caused a significant decrease in hippocampal EEG activity in diabetic animals compared with non-diabetics. These results suggest recurrent hypoglycemia may promote and worsen seizures associated with hypoglycemia in diabetic children.

Keywords: Hypoglycemia
Physiology
Electroencephalography
Diabetes
Advisor: Carlen, Peter Louis
Understanding the Biochemical Basis of Drosophila Fat Function

Drosophila Fat is a large atypical cadherin molecule. Genetic assays show that Fat has multiple function, however, the mechanism of Fat function is poorly understood. Hence, I undertook a biochemical approach to determine the mechanistic function of Fat. Previous data indicated that Fat might be processed; I further confirmed the precursor-product relationships between these proteins. I then looked at sub cellular localization of Fat. My preliminary data suggests that the smaller 110 kDa forms of Ft goes to the nucleus. To characterize the interaction between Fat and Atro, only known binding partner of Fat, I conducted pull-down assays that indicate Fat has multiple binding sites for Atro. However, the interaction is weak, and different experimental conditions will be needed to characterize the interaction. The only known downstream target of both Fat and Atro in PCP is four-jointed. I provided evidence that fjlacZ1.2kb is regulated by the Ecdysone receptor.

Keywords: Fat, Cadherins, Drosophila, PCP
Advisor: McNeill, Helen
Surface Modification for Digital Microfluidic Devices

Digital Microfluidics (DMF) is a new field of science and technology that introduces movement of nanoliter to microliter size droplets on patterned electrodes. Droplets can be moved, dispensed, merged, and split on devices. Sequential chemical reaction, and DNA extraction are examples of biological applications of DMF. In this thesis, sol-gel technology has been used as a coating method for thin film fabrication. Sol-gel is suitable for coating thin films with flexible shapes. BaTiO3 was used as a dielectric material for coating the insulator layer of the device. The material was spin coated on glass substrates. Devices were coated spinning at 500 rpm for 45 s, and annealed at 600 °C for 2hrs. The ceramic layer obtained, had a thickness of ~1 µm and average roughness of 60 nm. Nanoliter size droplets of water of ~400 nl were moved on the surface of the devices applying minimum voltage of 30 Volts.

Keywords: Digital Microfluidics
Sol-Gel
Advisor: Mostaghimi, Javad
Wheeler, Aaron
Hybrid Magnetic Attitude Controller for Low Earth Orbit Satellites using the Time-varying Linear Quadratic Regulator

The following is a study of an attitude control system (ACS) for a low earth orbit nanosatellite. Control actuation is applied using three reaction wheels and three mutually orthogonal current-driven magnetorquers which produce torques by interacting with the earth’s magnetic field. Control torques are distributed amongst the actuators allowing them to work together in concert. This type of control is referred to as hybrid magnetic attitude control. To account for the nearly periodic behavior of the earth’s magnetic field, control torques are assigned using periodic and optimal control theory. The primary focus is to apply the time-varying Linear Quadratic Regulator controller to test the stability and energy consumption of the ACS when reaction wheels are removed from the control law, or are simulated to be missing. Other situations studied include the effects of control saturation, introducing uncertainty in the orbital inclination, and observing performance as the number of magnetic coils is increased.

Keywords: Attitude Control
LQR
Advisor: Damaren, Christopher John
Dopaminergic Control of Trigeminal Motor Outflow to Upper Airway Muscles in Anaesthetized Rats

The role of dopamine in directly modulating somatic motoneuron excitability and hence muscle tone is unknown. We investigated whether dopamine influences the trigeminal motor pool (MoV) that innervates the masseter and tensor palatini muscles, both of which function to maintain upper airway patency. We hypothesized that dopamine facilitates motor outflow at the MoV. We focally applied apomorphine (nonspecific dopamine receptor agonist) at the MoV in anaesthetized rats. We also applied receptor-specific agonists and antagonists to determine the receptor subtype mediating dopaminergic mechanisms of action. We demonstrated that dopaminergic transmission at the MoV potently increased motor outflow via the D1-like receptor and facilitated masseter and tensor palatini muscle tone. It is unknown whether endogenous dopamine release on to airway motoneurons influences their activity to regulate muscle tone in natural sleep-wake behaviours. This issue warrants investigation because the neurochemical basis of upper airway motor dysfunction (e.g. obstructive sleep apnea) remains poorly characterized.

Keywords: dopamine
trigeminal motor nucleus
tensor palatini
obstructive sleep apnea
upper airway patency
Advisor: Peever, John H.
Inhibition of Beta2 Integrin-mediated Leukocyte Adhesion Attenuates the Inflammatory Response and is Neuroprotective Following Global Cerebral Ischemia

Leukocyte adhesion to cerebral endothelial cells plays a critical role in the inflammatory response following transient global cerebral ischemia but its contribution to delayed neuronal cell death is not completely understood. We compared ischemic mice treated with a monoclonal antibody to β2-integrin adhesion receptors (anti-CD18) or a non-binding control antibody following ischemia. Inflammation was characterized by increased CD18 expression on leukocytes and inflammatory mediators in the peripheral blood and brain tissue. Notably, interleukin-1β, which has been shown to mediate cell death in neurons, was elevated in the blood and brain. Anti-CD18 blocked leukocyte adhesion as well as the inflammatory responses, including interleukin-1β expression in neurons. Blocking leukocyte adhesion protected the structural integrity of the hippocampus, cerebral cortex and thalamus, and preserved spatial. Leukocytes adhesion to endothelial cells plays an important role in the evolution of neurological deficit in global cerebral ischemia despite the lack of transmigration of leukocytes across blood-brain-barrier.

Keywords: Global Cerebral Ischemia
Integrins
Cytokines
Neuroprotection
Advisor: Kavanagh, Brian
Reconfiguration and Recovery of Formation Flying Spacecraft in Eccentric Orbits

The problem of reference trajectory reconfiguration and long-term uncontrolled recovery of a formation of spacecraft is considered in an eccentric orbit under the influence of the J2 perturbation. Reference trajectories considered are the Projected Circular Orbit, Along-Track Orbit, and their eccentric modifications. Reconfiguration is accomplished using two, finite-pulse thrusts, modeled as impulses. The state transition matrix (STM) is calculated by four methods: (i) analytically from the Hill-Clohessy-Wiltshire equations, (ii) numerical integration using a fourth-order Runge-Kutta method, (iii) from the fundamental matrix of the linearized equations of motion, and (iv) computing the STM for the relative mean orbital elements, the geometric method. Only the geometric method takes into account J2, and it is shown to perform the transfers most accurately of all the methods. The methods are also applied to the reconfiguration maneuvers of the University of Toronto's CanX 4/5 formation flying mission.

Keywords: formation flying
state transition matrix
canx
geometric method
Advisor: Damaren, Christopher John
"Collingwood" Strata in South-central Ontario - A Petrophysical Chemostratigraphic Approach to Comparison and Correlation Using Geophysical Borehole Logs

A petrophysical chemostratigraphic comparison and correlation of “Collingwood” strata across central Ontario was conducted using geophysical borehole log data and core produced by the Ontario Oil Shale Assessment Project (OSAP). Outcrop sections were also measured, sampled and described. The resultant geophysical correlation was compared to sections in the Michigan Peninsula. Microfacies analyses and a biostratigraphic review were also conducted. The dark organic rich rocks collectively referred to as the “Collingwood Member, Lindsay Formation”, in Ontario were deposited during the progressive drowning of a mid to late Ordovician carbonate ramp. Due to variability in ramp palaeotopography, condensation intensity (sedimentation stress) varied across the region during drowning. This variability resulted in regional differences in Collingwood section thickness and facies. Less condensed carbonate rich “Collingwood” sections are associated with palaeotopographic highs such as the Algonquin Arch in Ontario and grade upwards and outwards (off-arch) from predominantly deep-shelf carbonates (microfacies type SMF 9, FZ 2 – open sea shelf –deep undatherm below wave base) to more condensed deeper water shale rich strata (microfacies type SMF 3, FZ1- basin fondotherm below oxygen level) – that contain abundant graptolites and Triarthrus trilobites.

Keywords: Geology
Advisor: Miall, Andrew
Responses of Astrocytes Exposed to Elevated Hydrostatic Pressure and Hypoxia

Several research groups have applied elevated hydrostatic pressure to ONH astrocytes cultured on a rigid substrate as an in vitro model for glaucoma. These studies have shown significant biological effects and this hydrostatic pressure model is now becoming generally accepted in the ophthalmic community. However, since the applied pressures were modest the finding of significant biological effects due to pressure alone is surprising. We hypothesized that the application of hydrostatic pressure as described in these studies also altered gas tensions in the culture media. Our goal was to design equipment and carry out experiments to separate the biologic effects of pressure from those of hypoxia on cultured astrocytes. We designed equipment and carried out experiments to subject cultures of DITNC1 astrocytes to the four combinations of two levels of each parameter. We explored the morphology and migration rates of astrocytes, but observed no significant change in any of these properties.

Keywords: Astrocyte
Hypoxia
Elevated Hydrostatic Pressure
Migration
Optic Nerve Head
Advisor: Ethier, C. Ross
Simmons, Craig Alexander
Mental Workload Measurement Using the Intersaccadic Interval

Mental workload is commonly defined as the proportion of a person's total mental capacity in use at a given moment. A measure of mental workload would have utility in a number of rehabilitation medicine applications, but no method has been adequately examined for these purposes. A candidate measure is the intersaccadic interval (ISI), which is the duration between two successive saccades. Previous studies indicate that ISI length may be linked to mental workload, but this link is poorly understood for tasks that are not primarily visual. Therefore, the current study was an investigation of ISI and workload intensity in three non-visual tasks: mental arithmetic, verbal fluency, and audio perception. Workload was manipulated through changes in task difficulty as well as study participant motivation level. An analysis of eye movements and other experimental workload measures indicated a significant association between audio perceptual workload and ISI length.

Keywords: mental workload
saccade
mental effort
eye movements
Advisor: Fernie, Geoff
Green, Robin
Effects of Genistein Following Fractionated Lung Irradiation in Mice

Radiation therapy for lung cancer and cancers of the upper thorax is limited by side effects to normal tissue of the lung. An understanding of mechanisms leading to radiation induced lung damage is essential to developing protective agents. In this thesis an anti-oxidant and anti-inflammatory agent Genistein was investigated for its potential to affect DNA damage, tissue inflammation, functional deficits and survival. We hypothesized that chronic oxidative stress and the subsequent inflammatory response play a key role in the development of major lung complications, radiation pneumonitis and fibrosis. If side effects of radiation could be reduced, then larger doses could be delivered to the tumor with a better chance of eradicating the disease.

Keywords: genistein
mouse lung
pneumonitis
fibrosis
Advisor: Hill, Richard
An Investigation of Ethylene Laminar Diffusion Flames at Sub-atmospheric Pressures to Simulate Microgravity

Ethylene/Air diffusion flames were studied at sub and super-atmospheric pressures to simulate a microgravity environment at fuel flow rates of 0.482 mg/s and 1.16 mg/s. Flame properties including flame dimensions, soot formation, temperature, and attachment mechanisms were investigated. Overall, luminous flame height decreased with decreasing pressure to the point of visible luminosity disappearance, resulting in blue flames. Flame width increased with decreasing pressure until the flame was almost spherical. Soot formation decreased with decreasing pressure to negligible concentrations in a near vacuum. At 0.482 mg/s, the percentage of carbon converted into soot was between 0.01% and 0.12%, whereas at 1.16 mg/s, this percentage was between 0.5% and 11% at sub-atmospheric pressures. Maximum flame temperatures increased with decreasing pressure. Regardless of fuel flow rate, the diffusion flames remained attached to the exterior of the burner. This attachment point moved further down the burner exterior as pressure decreased until a near vacuum.

Keywords: Microgravity
Combustion
Advisor: Gulder, Omer L.
ICAM-1 as a Novel Binding Partner for LPS to Mediate TLR4-Independent Cell Activation

Introduction: The mechanism of cell activation by LPS in the absence of surface Toll-like receptor 4 (TLR4) is unclear. We hypothesize that ICAM-1 binds LPS on the cell surface, mediating cell activation independent of TLR4. Methods: The interaction between murine ICAM-1 and LPS was measured in a binding assay. Alveolar macrophages (AMs) isolated from TLR4 deficient mice were stimulated with LPS. Cell activation was measured by flow cytometry and cytokine production. The role of ICAM-1 in cell activation was determined by siRNA transfection. Results: Murine ICAM-1 binds LPS. TLR4 deficient AMs respond to LPS stimulation by upregulation of LPS binding sites, ICAM-1 expression and cytokine release. Cell activation is attenuated by treatment with polymyxin B and ICAM-1 gene silencing. Conclusions: ICAM-1 binds LPS and is important in TLR4-independent cell activation. Strategies devised to target ICAM-1 may have the potential to block the excessive inflammatory response seen in gram-negative sepsis.

Keywords: Lipopolysaccharide
ICAM-1
TLR4-Independent
Advisor: Zhang, Haibo
A Cost-effectiveness Analysis of Capecitabine and Folfox for the Adjuvant Treatement of Stage III Colon Cancer: Which is the More Cost-Effective Option in Ontario?

Background: There are a number of treatment options for colon cancer. These regimens have different toxicity profiles and the age of the patient may affect outcomes of care and cost-effectiveness. An economic evaluation was conducted to explore treatment options for stage III colon cancer. Methods: A Markov model was developed to compare the cost-effectiveness of capecitabine with oxaliplatin combined with fluorouracil/leucovorin (FOLFOX) for the adjuvant treatment of stage III colon cancer. Results: At age 70, FOLFOX was the preferred option, costing $25,314 per quality-adjusted life-year gained. However, the difference in effect between the regimens ranged by 6 months and the model was sensitive to a number of variables. At age 80, capecitabine became the preferred option. Conclusion: FOLFOX is the most cost-effective treatment option in Ontario, but above age 80, capecitabine becomes the favoured option. Uncertainty remains in determining the most cost-effective treatment option for stage III colon cancer.

Keywords: economic evaluation
Advisor: Hoch, Jeffrey
Barnsley, Janet
Genomic and Transcriptome Profiling of Serous Epithelial Ovarian Cancer

Epithelial ovarian cancer is the leading cause of death by gynaecological malignancy. Elucidation of the driver genes of ovarian cancer will lead to treatment targets and tailored therapy for this disease. The Affymetrix Genome-Wide SNP Array 6.0 was used to study 100 serous ovarian samples and 10 normal ovarian samples to identify loci and driver genes. The ovarian cancer genome was found to have high overall genomic instability across all chromosomes and key known genes in this disease were identified in the dataset. Aberrant regions of copy number gain were located in “blocks” of constant copy number at 1p, 1q, 8q, 12p, 19q and 20q. The range in copy number for gains was 4.2 to 5.1. The “blocks” of genes were located at 8p and 5p for copy number losses. The range for copy number loss was 0.6 to 0.9.

Keywords: ovarian cancer
copy number variation
Advisor: Mak, Tak Wah
Hyper-methylation of the SOCS2 Promoter in AML: An Unexpected Association with the FLT3-ITD Mutation

Haematopoiesis requires strict regulation in order to maintain a balanced production of the various blood cell components. Escape from this regulation contributes to the development of cancers such as leukemia. SOCS2 is a member of the Suppressor of cytokine signalling (SOCS) family, and normally functions as a negative regulator of the JAK/STAT pathway. I examined gene expression and promoter methylation in acute myeloid leukemia (AML) cell lines and patient samples. SOCS2 expression was quite variable in AML patients, and very low in acute promyelocytic leukemia (APL) patients. Promoter hyper-methylation was found in these patients, particularly those with high white blood cell count and a FLT3-ITD. I speculate that SOCS2 interacts with an aspect of the signalling complex to inhibit cell growth in these patients, and silencing SOCS2 is necessary for leukemia progression. Treating these patients with a de-methylating agent, such as decitabine, may show promise in the clinic.

Keywords: Leukemia
Methylation
Advisor: Minden, Mark
Integrating Transit Pass Ownership into Mode Choice Modelling

The relationship between monthly transit pass ownership and home-work trip mode choice in the Greater Toronto Area was explored using a logit formulation. A Nested Logit model was specified with the primary mode (non-motorised, auto, transit, or auto access to transit) in the upper level and the pass ownership in the lower transit nests. Inclusive value parameters confirm the chosen structure, and a range of policy sensitive, statistically significant parameters having expected signs and magnitudes reveal differences between socio-economic characteristics of pass holders and non-pass holders. In particular, pass holders are less likely to possess a driver’s license or automobile than non-pass holders, implying that passes can be thought of as complementary mobility tools. Cost parameters, which include differentiated pricing for pass and non-pass holders, result in plausible in-vehicle values of time of approximately $31/hour, $33/hour and $8/hour for auto, auto access to transit, and transit all way, respectively.

Keywords: Logit Model
Transit Pass
Mode Choice
Advisor: Miller, Eric
Role of Distal Airway Epithelial Glucocorticoid-Glucocorticoid Receptor Signalling in Mouse Lung in Late Gestation

Glucocorticoid (GC) signalling via the GC receptor (GR) regulates many aspects of lung development. To determine the need for epithelial GC-GR signalling, triple transgenic (TT) mice with doxycycline (dox) – inducible suppression of GR exclusively in the distal lung epithelium (DLE) were created. Following exposure to dox, E18.5 TT fetuses showed a reduction in GR mRNA levels and elimination of GR protein expression exclusively in the DLE. Newborn TT pups had decreased viability and TT fetal lungs had increased tissue to airspace ratios, decreased levels of proximal epithelial protein CC10, of all surfactant proteins (ATII cell proteins), of ion conductance channels β and γENaC, of water channel AQP5, and of ATI cell protein T1α. Thus DLE GC-GR signalling is important for neonatal viability and increased mortality of TT pups could be due to impaired epithelial differentiation, leading to decreased surfactant protein expression, delayed fluid clearance and/or increased lung cellularity.

Keywords: Lung
Development
Glucocorticoid Receptor
Advisor: Sweezey, Neil