VictorJuiz/thesis huggingface dataset:
Use of Phospho-flow Cytometry to Define Influence of High-Risk Genetic Abnormalities on Cytokine-responsiveness in Human B-cell Leukemia

B-cell acute lymphoblastic leukemia (B-ALL) represents a collection of diseases that are categorized into subtypes based on the presence of recurrent cytogenetic abnormalities. These abnormalities often result in the expression of oncogenic drivers that denote a standard- or high-risk for relapse. Currently, survival rates boarder 40% for adult patients and relapses are often observed in patients lacking high-risk markers. Thus, there is an unmet need for biomarkers that can identify all high-risk leukemia, and development of novel therapies based on a better understanding of the molecular drivers of B-ALL. To address this need, I designed a multi-parameter phospho-flow cytometry platform and characterized basal and cytokine-potentiated signaling in adult B-ALL samples. I identified patterns of cytokine-responsiveness across B-ALL patients that correlated with the presence of high-risk oncogenic drivers. Furthermore, I demonstrated that small-molecule inhibitors could abrogate cytokine-induced signaling in high-risk patients suggesting these inhibitors may compliment current chemotherapeutic protocols.

Keywords: Leukemia
Signaling
B cell
Cytokine
CRLF2
Advisor: Danska, Jayne
Guidos, Cynthia J.
A Call for Sentencing Enforcement Reform In Ontario Securities Regulation: Restorative Justice, Pyramids and Ladders

This paper is intended, first, to look at the deterrence versus compliance debate, and the various punishment principles that exist in securities regulation. Secondly, a brief overview of the experiences and complexities of securities regulation and sanctioning in Ontario and Canada will be presented. Third, I introduce and apply the “Responsive Regulation” model and the “enforcement pyramid” as posited by Ian Ayres and John Braithwaite to securities enforcement. I advocate for adoption of a three stage enforcement reform process that incorporates restorative justice through an enforcement pyramid and an “enforcement priority ladder”. The expert reports and statistics are used to develop the argument that the OSC is hindered in its enforcement mandate, ultimately, from a lack of sound enforcement guidelines. The end goal is to provide useful recommendations to the OSC and other Canadian securities regulators in achieving a more self-sustaining and investor focused securities regulatory environment.

Keywords: securities regulation
securities
enforcement
restorative justice
provincial regulation
punishment
compliance
deterrence
Advisor: Anand, Anita
A High-performance Architecture for Training Viola-Jones Object Detectors

The object detection framework developed by Viola and Jones has become very popular due to its high quality and detection speed. However, the complexity of the computation required to train a detector makes it difficult to develop and test potential improvements to this algorithm or train detectors in the field. In this thesis, a configurable, high-performance FPGA architecture is presented to accelerate this training process. The architecture, structured as a systolic array of pipelined compute engines, is constructed to provide high throughput and make efficient use of the available external memory bandwidth. Extensions to the Viola-Jones detection framework are implemented to demonstrate the flexibility of the architecture. The design is implemented on a Xilinx ML605 development platform running at 200~MHz and obtains a 15-fold speed-up over a multi-threaded OpenCV implementation running on a high-end processor.

Keywords: FPGA
Object Detection
Reconfigurable Architecture
Advisor: Chow, Paul
Acute Effects of Navy Bean Powder, Lentil Powder and Chickpea Powder on Postprandial Glycaemic Response and Subjective Appetite in Healthy Young Men

In order to examine the effects of industry processed pulse powder (navy bean, lentil and chickpea) on postprandial glycaemic response (BG) and subjective appetite (App) before and after a subsequent meal, three randomized, within-subject experiments on healthy young men were conducted. In experiment 1, all navy bean treatments reduced BG at 30 min and navy bean powder suppressed pre-meal App compared to whole wheat flour. In experiment 2, all lentil treatments reduced pre-meal BG compared to whole wheat flour. However, no App differences were observed. In experiment 3, all chickpea treatments reduced pre-meal BG compared to whole wheat flour. However, no App differences were observed. Therefore, navy bean powder, lentil powder and chickpea powder maintain their low GI and satiating effects, regardless of processing. Pulse powder can be used as a value-added food ingredient to moderate glycaemic response and increase satiety.

Keywords: Glycaemic Response
Appetite
Pulse Powders
Pulse
Advisor: Anderson, G. Harvey
A Generic Bed Planning Model

In April 2008, the Ontario government announced its top two healthcare priorities for the next 4 years, one of which is reducing wait time in emergency rooms. To study the wait time in emergency rooms or any other departments in a hospital, one must investigate resource planning, scheduling, and utilization within the hospital. This thesis provides hospitals with a set of simulation and optimization tools to help identify areas of improvement, particularly when there are a number of alternatives under consideration. A simulation tool (a Monte Carlo simulation model) estimates patient demand for beds in a hospital during a typical week. Two optimization tools (an integer programming mathematical model and a heuristics model) demonstrate opportunities for smoothing the patient demand for beds by adjusting the operating room schedule.

Keywords: simulation
bed management
health care
bed management
bed planning
operating room schedule
mixed integer programming
generic
Advisor: Carter, Michael W.
Employing Olympism as an Educational Tool: An Examination and Evaluation of the School-based Olympic Education Programs in the Beijing 2008 Olympic Games

This thesis examines the school-based Olympic education (OE) programs implemented in the Beijing Olympic Games from both top-down and bottom-up perspectives. The research employs a three-pronged methodology for data collection, using textual analysis, semi-structured interviews with five key informants, and storytelling with six student participants. Findings suggest that OE in China was primarily government-led, with BOCOG, academic experts and numerous volunteers providing expertise and assistance. The students’ narratives shed light on how OE was conceptualized and experienced by its recipients as well as the useful role it served in revitalizing the traditional education system. To strengthen OE during future Games, the thesis recommends that future organizers and host governments embed programs of OE in the ongoing state school systems, set clear learning objectives in advance and monitor and evaluate implementation continually. It also recommends that future researchers continue this students’ focus on the student voice.

Keywords: Olympic Education
Beijing Olympic Games
Advisor: Kidd, Bruce
FMRI of a Visual Patterns N-back Task in Typical Development

The term working memory (WM) refers to a set of cognitive processes that allows for the temporary storage and manipulation of information. Neural correlates of the N- back task, a well-established WM measure used in neuroimaging, have been studied extensively in adults but less so in developmental populations. This thesis determines the effect of age on brain activations that mediate cognitive processes for remembering non- verbal/visual stimuli. Block-design fMRI was used to record activity in 84 subjects (6-35 years) during a visual-patterns 0- and 1-back task. Regions activated during the 1-back condition were largely common to all age groups, with adults displaying the largest extent of activations. Children and adolescents showed similar 0-back activations (distinct from 1-back) while adults engaged an analogous 1-back activation pattern during 0-back, suggesting that brain mechanisms underlying memory and attentional processes required for this task in children and adolescents are not yet mature and that strategy usage is still developing.

Keywords: Neuroimaging
Typical Development
Working memory
Developmental cognitive neuroscience
Advisor: Taylor, Margot
Adaptation of a Dechlorinating Culture, KB-1, to Acidic Environments

KB-1 is an anaerobic Dehalococcoides-containing microbial culture used industrially to bioremediate sites impacted with chlorinated solvents. The culture is typically grown at pH 7. However, lower pH is often encountered and therefore the effect of pH was investigated. Both sudden and stepwise decreases in pH from 7 to 6 and 5.5 were investigated over a period of 450 days. An electron balance was also calculated to look at the flow of electrons for dechlorination. More than 95% of the reducing equivalents went towards methanogenesis and acetogenesis. Select microorganisms were compared by quantitative Polymerase Chain Reaction. It was found that lower rates of dechlorination correspond to low Dehalococcoides numbers and that different methanogens were enriched on different electron donors.

Keywords: dechlorination
anaerobic
KB-1
pH
chlorinated ethene
bioremediation
Advisor: Edwards, Elizabeth A.
Oxidation Resistance and Nanoscale Oxidation Mechanisms in Model Binary and Ternary Alloys Exposed to Supercritical Water

The oxidation behavior of model binary and ternary alloys in supercritical water (SCW) was examined. Binary alloys contained 9 or 14 at% Cr. Ternary alloys had 1.5 at% of one of the following elements: Si, Al, V, Mn or Ti. Samples with different surface finishes were exposed to SCW for up to 500 hours. The oxidized samples were characterized using gravimetry, SEM, HRTEM and EDX. After exposure, a uniform double layer oxide with outwardly grown magnetite inwardly grown Fe-Cr mixed oxide was detected on most of samples. Alloys contains 14 at% Cr or/and 1.5 at% Si showed a mixed oxidation mode, where relatively thick double layer oxides coexisted with thin protective oxide. The coverage with the thin oxide increased with the increase of deformation and/or Cr and/or Si content. A 20 nm thick Si-enriched layer was detected at such alloy/oxide interfaces. This behavior is very similar to “third element effect”.

Keywords: Supercritical water
Oxidation
Fe-Cr alloys
Third element effect
Advisor: Newman, Roger C.
Structural Studies of the Klebsiella Pneumoniae Pantothenate Kinase in Complex with Pantothenamide Substrate Analogues

N-substituted pantothenamides are analogues of pantothenate, the precursor of the essential metabolic cofactor coenzyme A (CoA). These compounds are substrates of pantothenate kinase (PanK) in the first step of CoA biosynthesis, possessing antimicrobial activity against multiple pathogenic bacteria. This enzyme is an attractive target for drug discovery due to low sequence homology between bacterial and human PanKs. In this study, the crystal structure of the PanK from the multidrug-resistant bacterium Klebsiella pneumoniae (KpPanK) was first solved in complex with N-pentylpantothenamide (N5-Pan). The structure reveals that the N5-Pan pentyl tail is located within a highly aromatic pocket, suggesting that an aromatic substituent may enhance binding affinity to the enzyme. This finding led to the design of N-pyridin-3-ylmethylpantothenamide (Np-Pan) and its co-crystal structure with KpPanK was solved. The structure reveals that the pyridine ring adopts alternative conformations in the aromatic pocket, providing the structural basis for further improvement of pantothenamide-binding to KpPanK.

Keywords: pantothenate kinase
X-ray crystallography
vitamin B5 analogues
enzyme-substrate complex
antimicrobial drug design
structural biology
Advisor: Park, Hee-Won
McPherson, John Peter
Relationships between Changes in Coping Strategies and Community Integration Status at 6 and 12 Months after Traumatic Brain Injury

The purpose of this prospective cohort study was to determine the relationships between changes in coping strategies and community integration at 6 and 12 months post traumatic brain injury (TBI). Seventy-one participants were adult significant others (SOs) (family members/friends) of people with TBI. SOs, proxies for TBI patients, completed coping and community integration questionnaire to describe TBI patients’pre-injury status immediately post-injury as baseline information. Followed-up interviewed were completed at 6 and 12 months. Results showed that increased emotional preoccupation coping from baseline to 6 months were significantly associated with decreased productive activities and decreased social integration at 6 months and 12 months and modestly associated with decreased home integration at 12 months. Multivariable regressions showed that changes in emotional preoccupation coping from baseline to 6 months contributed significantly to social integration and productive activities above and beyond demographic factors and injury severity. Implications for cognitive rehabilitation are discussed.

Keywords: Coping strategies
Brain Injury
Community Integration Status
Productive Activities
Advisor: Dawson, Deirdre R.
Software for the Canadian Advanced Nanospace eXperiment-4/5

The CanX-4 and CanX-5 mission currently under development at The University of Toronto Institute for Aerospace Studies Space Flight Laboratory UTIAS/SFL is a challenging formation flying technology demonstration. Its requirements of sub-metre control accuracy have yet to be realized with nanosatellites. Many large technical challenges must be addressed in order to ensure the success of the CanX-4/5 mission. This includes the development of software for an intersatellite communication system, integration and optimization of key formation flying algorithms onto the Payload On-Board Computer as well as the development of a Hardware-In-The-Loop simulator for full on-orbit mission simulations. This thesis will provide background knowledge of the Space Flight Laboratory and its activities, the CanX-4/5 mission, and nally highlight the authors contributions to overcoming each of these technical challenges and ensuring the success of the CanX-4 and CanX-5 mission.

Keywords: CanX
Embedded Systems
Software
Protocol Stack
Satellite Communications
On-board Computers
Software Optimizations
Nanosatellites
Advisor: Zee, Robert E.
Tailoring the Acoustic Properties of Truss-Core Sandwich Structure

Undesirable cabin noise has an adverse physiological effect on passengers and crews in an aircraft. In order to reduce the noise level, a passive approach using a truss-core sandwich (TCS) panel as a sound insulator is proposed. Design guidelines and analysis methodologies were developed in order to explore the vibro-acoustic characteristics of TCS structure. Its sound isolation properties can be thereby assessed. Theoretical analyses show that the transmission-loss and sound radiation properties of a TCS structure can be represented by the root-mean-square velocity of its surface, and a beam structure analysis is sufficient to reveal many of the important aspects of TCS panel design. Using finite element analysis, a sensitivity study was performed to create design guidelines for TCS structures. Transmission-loss experiments show that the analytical and numerical analyses correctly predict the trend of TCS structure’s vibro-acoustic performance.

Keywords: acoustics
Truss-Core Sandwich
composite
multifunctional
cabin noise
Advisor: Steeves, Craig A.
Survivin Gene Therapy using Ultrasound-targeted Microbubble Destruction in a Rat Model of Doxorubicin-induced Cardiomyopathy

With the recent advent of gene therapy, anti-apoptotic therapy has been receiving spotlight as a potential modality to inhibit the deterioration of pump function in the failing heart. We hypothesized that anti-apoptotic therapy using survivin gene delivery will 1) salvage H9c2 cells exposed to doxorubicin toxicity, and 2) ameliorate the progressive decline in left ventricular function in a rat model of doxorubicin-induced cardiomyopathy. The in vitro data suggested that survivin successfully prevented cell death under doxorubicin stress by both direct and indirect/paracrine mechanisms. Doxorubicin-treated animals developed progressive left ventricular dysfunction as evident by echocardiography and invasive pressure-volume loop analysis, which was prevented by ultrasound-mediated survivin plasmid delivery, but not empty plasmid delivery. Post-mortem analysis of myocardial tissue indicated a lowered apoptotic index in survivin-treated hearts, with evidence of decrease in interstitial fibrosis. In conclusion, survivin gene therapy was shown to ameliorate doxorubicin-induced cardiomyopathy, by decreasing apoptosis and preventing adverse remodeling.

Keywords: Heart Failure
Apoptosis
Gene Therapy
Ultrasound
UTMD
Cardiomyopathy
Rat
Doxorubicin
Microbbuble
cardiomyocyte
Advisor: Leong-Poi, Howard
How Environmental Tribunals Contribute to Important Advances in Environmental Laws

This article offers an analysis of how environmental tribunals contribute to important advances in environmental laws. The article compares the legislative and adjudicative administrative processes and examines decisions from environmental tribunals and courts in Canada. The author also reviews developments in environmental protection legislation since the 1970s. Consideration is also given to whether environmental laws are better framed on a model of comprehensive rationality or an incrementalist approach. The article concludes such tribunals make significant contributions to environmental laws by articulating emerging principles of environmental law. In doing so, the author examines the legislative underpinning and characteristics of tribunals which enable them to articulate such principles, namely that the statute express as its purpose protection of the environment. Also, the tribunal should have expertise in environmental matters, permit participation by third parties in the proceedings, be independent and be accountable through providing written reasons and the mechanism of judicial review.

Keywords: environmental
law
tribunal
Advisor: Green, Andrew
Upgrade of Seismically Deficient Steel Frame Structures Built in Canada Between the 1960s and 1980s Using Passive Supplemental Damping

A typical 1960s Type 2 Construction steel MRF hospital structure in Quebec, representative of a prevalent construction philosophy of the time, was investigated and modelled in OpenSees using an advanced strength degradation model. The structure was then subjected to a nonlinear time-history analysis (NLTHA) for Montreal (MTL) and Vancouver (VAN) ground motions and was found to be deficient under the design hazard levels. Retrofits were proposed for the two orthogonal frames at both sites using a performance-based approach. An experimental program determined that the connections had less ductility than expected and began deteriorating around 2.0% interstorey drift. The OpenSees model was updated according to the experimental connection behaviour and the predicted NLTHA performance of the structure worsened. The proposed retrofit designs for both orthogonal frames in both MTL and VAN were updated with the new connection behaviour and final retrofit designs were proposed.

Keywords: steel moment-resisting frames
Type 2 Construction
nonlinear time-history analysis
supplemental damping
performance-based design
Advisor: Christopoulos, Constantin
The Role of Mechanical Stress in Regulating Integrin Recruitment to Latent TGF-β1

Fibrosis is characterized by excessive extracellular matrix (ECM) production and contraction of myofibroblasts that differentiate from fibroblasts under the action of pro-fibrotic cytokine TGF-β1 and mechanical stress. Myofibroblasts liberate active TGF-β1 by integrin-mediated pulling on the latency-associated protein pro-peptide (LAP) which is stored together with the latent TGFβ1-binding protein-1 (LTBP-1) in the ECM. I hypothesized that the binding affinity/strength of LAP binding integrins, in particular of integrin αvβ3, is regulated by the mechanical stress arising from the contractile fibroblast cytoskeleton and the stiff ECM. To test this hypothesis, different methods were employed to investigate mechanically-regulated integrin αvβ3 recruitment to LAP in the physiological context of fibroblasts. The main findings of my thesis work are that (a) fibroblasts use αvβ3 integrin to bind to LAP; (b) αvβ3 integrin is capable of transmitting considerable cell force to LAP; and (c) mechanical stress increases the recruitment of αvβ3 integrin to LAP.

Keywords: Biology
Advisor: Hinz, Boris
A Mathematical Model for Carbothermic Reduction of Dust−carbon Composite Agglomerates

A mathematical model to simulate the reaction kinetics of dust–carbon composite agglomerates in an RHF was developed. Major chemical, thermal and physical phenomena taking place during RHF treatment were formulated and the corresponding equations were solved to yield the trend of solid composition, temperature and gas composition of the agglomerates. The model calculation results indicate that the pellet reduction is accelerated by the reducing gas from high–volatile reductants if the gas is released after the pellet temperature is sufficiently high for reduction. The reduction of zinc oxide can also be represented using the model by implementing its small particle size caused by the inherent vaporization/re–oxidization process that zinc comes through in a melter. It was demonstrated that the proposed model can be used as an engineering tool to determine the optimum operating conditions for the RHF process to promote recycling a wide range of waste materials.

Keywords: dust recycling
carbothermic reduction
rotary hearth furnace (RHF)
mathematical model
Advisor: Barati, Mansoor
Generation of Cell-laden Biopolymer Microgels with Tunable Mechanical Properties for Cancer Cell Studies

This thesis describes the development of a high-throughput approach towards the encapsulation of cancer cells in biopolymer microgels with tunable mechanical properties. In particular, this thesis is focused on: i) the high-throughput generation of biopolymer microgels with tunable mechanical properties ii) the measurement of the mechanical properties of the microgels, and iii) the high-throughput encapsulation of a cancer cell line within biopolymer gels. The microgels will be generated by (i) introducing in a microfluidic device two distinct streams of biopolymer solutions; (ii) mixing the streams; (iii) emulsifying the biopolymer and (iv) using thermosetting to transform the droplets in situ into microgels. By applying a compression force to the hydrogel microbead and measuring its deformation, the Young’s modulus and relaxation time of the microgel can be examined. The properties of cells were examined within the gels using various spectroscopic techniques such as absorption (UV-Vis) and fluorescence microscopy (fluorescent microscopy, confocal microscopy).

Keywords: Biopolymer
Cancer Cell
Cellular Microenvironment
Microfluidics
Atomic Force Microscopy
Elastic Modulus
Mechanical Properties
Microfluidics
Advisor: Walker, Gilbert C.