VictorJuiz/thesis huggingface dataset:
The Effect of Diet, Exercise and Metformin on the Progression of Prostate Cancer

Prior research has suggested that life style factors, such as diet and physical activity, influence prostate cancer (PCa) progression. Metformin intake has been shown to be associated with decreased cancer risk in type II diabetic patients. We hypothesize that a low carbohydrate diet, prolonged aerobic exercise and metformin treatment can all independently slow prostate tumor development and a combination regimen will have an additive benefit. We used LNCaP xenografts to test this hypothesis. Results revealed that a diet low in carbohydrate reduced food consumption and a combination with exercise significantly reduced animal body weights. Ten weeks of metformin did not significantly alter tumor growth rate compared to control animals. Ten weeks of exercise significantly inhibited tumor growth. Out results suggest that dietary carbohydrate alteration or the administration of metformin alone cannot significantly influence prostate tumor progression. A suitable sustained exercise regimen may offer a more protective effect against PCa progression.

Keywords: Prostate Cancer
Exercise
Diet
Metformin
Advisor: Venkateswaran, Vasundara
Intraspecific Trait Plasticity in Coffee Agroforestry Systems of Costa Rica

Although a common plant response to environmental gradients, leaf trait plasticity is often uncharted in agroforestry systems. The objective of this study was to examine the effect of a i) local-scale gradient (light, nutrients) induced by shade tree diversity and ii) large-scale gradient (climato-edaphic) induced by altitude on coffee plant response on multiple agroforestry research farms in Costa Rica. Results show large variability of coffee traits: leaf photosynthetic rates, specific leaf area (SLA) and number of fruiting nodes deviate along both gradients. Mean SLA increased with increasing shade tree diversity. However, with increasing altitude, full sun coffee photosynthesized at higher rates than shaded coffee. Concurrently, other coffee leaf physiological and morphological traits differentiated between full sun and shaded coffee with increasing altitude. Results suggest soil moisture and light availability dominate environmental correlates to intraspecific coffee trait plasticity, providing insight to sources of coffee performance variability in monoculture and agroforestry systems.

Keywords: agroforestry
coffee
trait plasticity
Costa Rica
biodiversity
climate
shade grown coffee
intraspecific
edaphic
CATIE
trait variability
landscape scale
local scale
altitude
photosynthesis
yield
shade tree
leaf physiology
leaf morphology
plant interactions
plant response
phenotypic plasticity
Advisor: Isaac, Marney
Development and Evaluation of an Objective Assessment of Dynamic Balance Post-stroke

There are limited tools available for clinicians to affordably and objectively assess balance control to prescribe treatments and measure progress post-stroke. The objectives of this thesis were to: 1) develop a toolkit to quantitatively measure dynamic balance control and determine the repeatability of outcomes within and between-sessions in healthy adults; and 2) determine the repeatability of the tasks and the association between outcomes of an advanced clinical model of care in a post-stroke population. In study 1 a wireless balance assessment toolkit was developed using a grid of four Nintendo Wii Balance boards and custom software and repeatability of the outcomes were established in healthy adults. Study 2 revealed the measures to be repeatable in a sub-acute stroke population while further evidence is required to validate the toolkit, as it did not associate with outcomes from an advanced clinical model of care.

Keywords: balance
assessment
stroke
rehabilitation
Advisor: McIlroy, William
A New Architecture of the Public Sphere: Online Deliberation at the Liberal Party of Canada’s 2011 Extraordinary Convention

This thesis examines the quality and effectiveness of online political deliberation, within the framework of Jurgen Habermas’ public sphere and discourse theories. The thesis analyzes a deliberative process that took place online, in June 2011, as part of the Liberal Party of Canada’s Extraordinary Convention, specifically through content and discourse analysis of data from online discussion platforms. The analysis sought to ascertain whether the objectives of the convention were met, measured the quality of discourse and identified insights to support the creation of more effective spaces for political deliberation online. Analysis of the results revealed a difference in the discourse quality for each platform, attributed to the synchronicity or asynchronicity of the platform. The thesis concludes with suggestions for a design that makes use of both the synchronous and asynchronous features of the online discussion platforms in order to more specifically target the objectives of the political process.

Keywords: Deliberative democracy
Public sphere
Political parties
Online deliberation
Advisor: Lyons, Kelly
Zirconium and Palladium Catalyzed Telescopic Synthesis of (E)-alkenes

Alkenes are remarkably versatile motifs as they can be further functionalized by a vast array of addition, reduction, and oxidation reactions. Thus their efficient synthesis is highly desired. Over the past 35 years, the Suzuki-Miyaura cross-coupling reaction has emerged as a powerful synthetic tool for the formation of carbon-carbon bonds. Herein is described the development of a one-pot two-step protocol for the synthesis of (E)-alkenes comprising palladium-catalyzed Suzuki-Miyaura cross-coupling of aryl or heteroaryl halides, including chlorides, with alkenyl pinacolboronates, prepared in situ via solvent-free zirconium-catalyzed hydroboration of terminal alkynes. Avoiding isolation of intermediates saves time and reduces waste. The regio- and stereochemistry of the alkene is set by initial hydrozirconation of the alkyne. Addition of water to the second step deactivates the zirconocene catalyst, which is otherwise deleterious to cross-coupling. Thus this sequence exploits the water tolerance of the Suzuki-Miyaura reaction.

Keywords: alkenes
domino
telescopic
bimetallic
catalyzed
Suzuki
hydroboration
zirconium
palladium
one-pot
Advisor: Lautens, Mark
Ecological Differentiation Among Populations of Three Alvar Plant Species: Linking Traits to Growth in a Common Garden

Populations in fragmented habitat patches may show ecological differentiation, which has implications for metapopulation viability. In this study we used a common garden with two watering treatments to contrast mean differences in ecophysiological traits and the relationships between traits and performance among seven populations of three alvar species. These species differ in their alvar specialization in Ontario, from almost endemic (Solidago ptarmicoides) to highly confined (Dasiphora fruticosa) to a widespread generalist (Hypericum perforatum). Populations of all species exhibited mean differences in at least one trait: photosynthesis (Amax), growth rate and specific leaf area. More surprisingly, the relationship between functional traits and performance was significantly different among populations in all species, suggesting different strategies for maximizing growth in different environments. The ecological differentiation observed affected all species regardless of distribution and is likely genetically based. This differentiation may destabilize metapopulation dynamics and reduce rates of spread if colonization is negatively impacted.

Keywords: Alvar
Common Garden
Functional Traits
Advisor: Gilbert, Benjamin
Scalable Routing for Networks of Dynamic Substrates

The ever-increasing number of devices capable of, not only connecting to existing communication networks, but also, independently creating new ones is defining a new communication network, in which the Internet is only one of the substrate networks pro- viding connectivity between diverse devices. This is a network with many interconnected mobile devices connecting to infrastructure networks and creating their own dynamic substrate networks. We present a novel routing scheme for diverse collections of substrate networks with a mix of mobile and static nodes. A key element of the routing scheme is to utilize the exiting routing paths in substrate networks, and set up routing paths between substrate networks. We use sets of nodes as landmarks and define locators that describe node position in the network relative to landmarks. This allows our routing scheme to scale to a large number of nodes, as only information about landmarks needs to be propagated throughout the network.

Keywords: routing
multi substrate
reachability domain
Advisor: Liebeherr, Jorg
Mechanical Aspects of Design, Analysis and Testing of the Nanosatellite for Earth Monitoring and Observation – Aerosol Monitor (NEMO-AM)

A next generation nanosatellite bus is under development at the University of Toronto’s Space Flight Laboratory (SFL), and is being used for the first time in an ambitious Earth observation mission to identify and monitor atmospheric aerosol species. The spacecraft system brings together novel advanced designs that expand the capability envelope of nanosatellites, with heritage SFL technology that is presently defining the state-of-the-art in microspace applications. The work presented in this thesis pertains primarily to the development of the structural subsystem of the Nanosatellite for Earth Monitoring and Observation – Aerosol Monitor (NEMO-AM). Described extensively are the design and analysis efforts made by the author to validate and finalize the structural design in order to bring it to a manufacturing-ready stage. Subsequent work to meet the mechanical requirements of ground operations during the assembly and testing of the spacecraft is also presented.

Keywords: satellite
finite element modeling
satellite structure
finite element analysis
FEM
FEA
Earth observation
aerosol
nanosatellite
mechanical design
ground support equipment
microsatellite
Advisor: Zee, Robert
Generic Wind Turbine Generator Model Comparison Based on Optimal Parameter Fitting

Parameter tting will facilitate model validation of the generic dynamic model for type-3 WTGs. In this thesis, a test system including a single 1.5 MW DFIG has been built and tested in the PSCAD/EMTDC environment for dynamic responses. The data generated during these tests have been used as measurements for the parameter tting which is carried out using the unscented Kalman lter. Two variations of the generic type-3 WTG model (the detailed model and the simpli ed model) have been compared and used for parameter estimation. The detailed model is able to capture the dynamics caused by the converter and thus has been used for parameter tting when inputs are from a fault scenario. On the other hand, the simpli ed model works well for parameter tting when a wind speed disturbance is of interest. Given measurements from PSCAD, the estimated parameters using both models are indeed improvements compared to the original belief of the parameters in terms of prediction error.

Keywords: Generic Wind Turbine Generator Model
Parameter Estimation
Advisor: Tate, Joseph Euzebe (Zeb)
Development of an Improved Bedside Methodology for Measurement of Cerebrovascular Reactivity

Changes in cerebrovascular reactivity (CVR) to carbon dioxide (CO2) are reported in many neurological conditions. My aim was to validate a method for computerized prospective targeting of CO2 levels (RespiractTM) as a bedside tool for impaired CVR. I hypothesized that 1) The RespiractTM and TCD method can be used to detect impairment of CVR after SAH and that 2) CVR is impaired in SAH patients. In 18 SAH patients and 26 controls CVR index was calculated dividing the percentage change in middle cerebral artery blood flow velocity (MCAv) by the change in PETCO2. The absolute MCAv values were similar in both groups, but CVR was significantly different (hypercapnia: 0.044 ± 0.076 - controls; 0.014 ± 0.037 - SAH; p=0.0007). I showed that impaired CVR can be detected at the bedside using TCD and CO2 challenge with the RespiractTM, control of CO2 is precise and minimal changes are required.

Keywords: cerebral blood flow
cerebrovascular reactivity
carbon dioxide challenge
Transcranial Doppler
Advisor: Michael, Tymianski
Perception-response Time to Emergency Roadway Hazards and the Effect of Cognitive Distraction

A critical part of traffic safety is a driver’s ability to detect and respond to emergency roadway hazards. This thesis uses eye movements and motor responses to divide driver perception-response time in three stages: perception, inspection, and movement time. The effects of cognitive distraction and repeated exposure on each stage were investigated for three distinct hazards (left-turning vehicle, pedestrian, right-incursion vehicle). In general, there were varying effects of cognitive distraction observed depending on the hazard being responded to. Cognitive distraction resulted in a significant increase in perception times for the pedestrian and right-incursion vehicle hazards, whereas cognitive distraction resulted in significantly longer inspection times for the left-turning vehicle hazard. When considering the effect of repeated scenario exposure, perception times were the most greatly affected. Perception times were significantly shorter during the second exposure to the left-turning vehicle hazard in the baseline condition, and for all hazards in the distraction condition.

Keywords: perception-response time
cognitive distraction
human factors
driving simulator
emergency roadway hazards
repeated hazard exposure
Advisor: Donmez, Birsen
The Regulation of the Inflammatory Response in Tie-2-Expressing Monocytes by Tie-2 Ligands

Tie-2 expressing monocytes (TEMs) were identified to be a subset of monocytes that was potent inducer of tumor angiogenesis in various types of cancer. On the other hand, monocytes and macrophages are crucially involved in the innate immune response, but the function of TEMs in this process is not well understood. Therefore, we studied the role of Tie-2 in regulating the inflammatory response initiated by lipopolysaccharide in murine macrophages. First, we observed that a small percentage of bone marrow-derived macrophages express Tie-2. Furthermore, we observed that Tie-2 ligands were able to induce phosphorylation of signalling proteins in macrophages. However, we found that Tie-2 ligands were not able to regulate pro-inflammatory cytokine secretion, nor were the ligands able to prevent apoptosis induced by lipopolysaccharide in macrophages. These results suggest that contrary to current evidence in the literature, Tie-2 ligands may not play a role in modulating the pro-inflammatory response in TEMs.

Keywords: Signalling
Inflammation
Angiogenesis
Monocytes
Tie-2
Angiopoietins
Advisor: Dumont, Daniel Joseph
Preparing for Simulation-based Education and Training Through Web-Based Learning: The Role of Observational Practice and Educational Networking

Simulation and Web-based Learning (WBL) are both educational approaches that are increasingly applied in medical education. However, little is known about how these two instructional approaches may be integrated to improve learning outcomes. A prospective three-arm experimental study of different WBL preparation materials was conducted. Thirty undergraduate medical students with no prior experience in central venous catheterization (CVC) were randomly assigned to one of three preparatory interventions: tradition reading materials (TM), observational practice (OP), or OP and educational networking (OPEN). Participants then completed a simulation-based training workshop in CVC and a delayed retention test. Performance was assessed by a task-specific checklist, global rating scale (GRS) and by measuring time to competency. Main findings reveal a significant linear trend across the TM, OP and OPEN groups in time to competency. This exploratory study demonstrates the potential utility of Web-based observational practice and collaborative learning for improving the efficiency of simulation-based training.

Keywords: Medical Education
Simulation
Web-based learning
psychomotor
technical skills
observational learning
collaborative learning
CSCL
motor learning
Advisor: Dubrowski, Adam
Assessing Public Perceptions of Cardiopulmonary Resuscitation and Bystander Willingness to Act in Out-of-hospital Cardiac Arrest

Low survival rates following out-of-hospital cardiac arrest (OHCA) remain a serious health concern internationally. Early bystander cardiopulmonary resuscitation (CPR) and rapid defibrillation can increase the chances of survival dramatically. However, the number of OHCA patients who receive these interventions remains low. This study sought to characterize Canadian public knowledge, attitudes and willingness to perform both traditional and chest-compression-only CPR using a two-phase, mixed methods approach. Twenty-one qualitative interviews were conducted, the results of which informed an online, scenario-based, Canada-wide survey. Significant knowledge gaps regarding recognition of cardiac arrest, the precise steps of CPR and perceived survival rate were identified and common to both phases. A larger proportion of survey respondents demonstrated a willingness to perform chest-compression-only CPR compared to traditional CPR in general, and specifically in situations involving strangers and unkempt individuals. Knowledge gaps and misconceptions seem to dominate the public perspective, leading to the recommendation for a tailored knowledge translation solution.

Keywords: out-of-hospital cardiac arrest
cardiopulmonary resuscitation
bystander CPR
Advisor: Morrison, Laurie J
Trigeminal Central Sensitization and Its Modulation in Acute and Chronic Orofacial Pain Models

This study aimed to examine whether trigeminal nerve injury induces chronic nociceptive behaviour and central sensitization (CS) in functionally identified medullary dorsal horn (MDH) nociceptive neurons in mice, and whether CS in acute and chronic orofacial pain models and nociceptive behaviour in the chronic model are affected by systemic administration of pregabalin. Infraorbital nerve injury induced chronic facial mechanical allodynia as well as MDH CS; acute noxious tooth pulp stimulation also induced MDS CS. Systemic administration of pregabalin attenuated the nerve injury-induced allodynia as well as the MDH CS in both the chronic and acute pain models. These findings reveal that MDH CS occurs in mouse models of acute and chronic orofacial pain and that pregabalin may prove useful clinically in acute and chronic orofacial pain states.

Keywords: pain
trigeminal
orofacial
chronic
mechanisms
Advisor: Sessle, Barry J
Friedman, Shimon
Vascular Reactivity Response Characteristics to Hypoxia

Oxygen is a necessary part of our everyday lives and is important for normal eye function. Blood flow through the retinal vasculature supplies oxygen to the inner retina. The resistance of the retinal vessels can change, increasing and decreasing blood flow by dilation and constriction of the vessel. The response of retinal hemodynamics to vasoactive stimuli is termed vascular reactivity. To investigate vascular reactivity characteristics, a system that prospectively targets a certain level of oxygen is employed. We characterize how the retinal vessels respond over time to hypoxia as well as define vascular reactivity to different oxygen concentrations in healthy participants. We demonstrate that the vessels increase diameter fully after 6 minutes and flow after 10 minutes. The relationship between retinal hemodynamics and arterial partial pressure of oxygen (PaO2) is demonstrated in healthy humans. Future studies should investigate these changes in diseased models to better understand when the retinal vasculature response may be insufficient.

Keywords: vascular reactivity
hypoxia
hyperoxia
retina
Advisor: Fisher, Joseph
Hudson, Christopher
FullMonte: Fast Biophotonic Simulations

Modeling of light propagation through turbid (highly-scattering) media such as living tissue is important for a number of medical applications including diagnostics and therapeutics. This thesis studies methods of performing such simulations quickly and accurately. It begins with a formal definition of the problem, a review of solution methods, and an overview of the current state of the art in fast simulation methods encompassing both traditional software and more specialized hardware acceleration approaches (GPU, custom logic). It introduces FullMonte, the fastest mesh-based Monte Carlo software model available and highlights its novel optimiza- tions. Additionally, it demonstrates the first fully three-dimensional hardware simulator using Field-Programmable Gate Array (FPGA) custom logic, offering large (40x) power-efficiency and performance (3x) gains. Next, a plan for significant future feature enhancements and performance scale-out is sketched out. Lastly, it proposes applying the simulators developed to a number of problems relevant to current clinical and research practice.

Keywords: Monte Carlo
biophotonics
photodynamic therapy
turbid media
Advisor: Betz, Vaughn
Lilge, Lothar
Blood Velocity and Volumetric Flow Rate Calculated from Dynamic 4D CT Angiography using a Time of Flight Approach

Purpose: A time of flight approach to the analysis of 4D CT angiography is examined to calculate blood flow in arteries. Materials and Methods: Software was written to track contrast bolus TOF along a central vessel axis. Time density curves were analyzed to determine bolus time to peak at successive vessel cross-sections which were plotted against vessel path length. A line of best fit was plotted through the resulting data and 1/slope provided a measurement of velocity. Results: Validation was successful in simulation and in flow phantoms, though quality of results depended strongly on quality of curve fit. In phantoms and in vivo, accuracy and reproducibility of measurements improved with longer path lengths and, in vivo, depended on the avoidance of venous contamination. Conclusions: Quantitative functional intravascular information such as blood velocity and flow rate may be calculated from 4D CT angiography.

Keywords: blood velocity
CT
Advisor: Mikulis, David
Stochastic Mixed-integer Programming for Financial Planning Problems using Network Flow Structure

Portfolio design is one of the central topics in finance. The original attempt dates back to the mean-variance model developed for a single period portfolio selection. To have a more realistic approach, multi-period selections were developed in order to manage uncertainties associated with the financial markets. This thesis presents a multi-period financial model proposed on the basis of the network flow structure with many planning advantages. This approach comprises two main steps, dynamic portfolio selection, and dynamic portfolio monitoring and rebalancing throughout the investment horizon. To build a realistic yet practical model that can capture the real characteristics of a portfolio a set of proper constraints is designed including restrictions on the size of the portfolio as well as the number of transactions, and consequently the management costs. The model is solved for two-stage financial planning problems to demonstrate the main advantages as well as characteristics of the presented approach.

Keywords: Financial engineering
Portfolio optimization
Advisor: Kwon, Roy H.
Melek, William W.