VictorJuiz/thesis huggingface dataset:
Cross Validation of the Structure of a Transiently Formed and Low Populated FF Domain Folding Intermediate Determined by Relaxation Dispersion NMR and CS-Rosetta

The atomic resolution structure of a low populated and transiently formed on-pathway folding intermediate of the FF domain from human HYPA/FBP11 has recently been reported[1]. The structure was determined on the basis of backbone chemical shift and bond vector orientation restraints measured on the ‘invisible’ intermediate state using relaxation dispersion nuclear magnetic resonance (NMR) spectroscopy that were subsequently input into the data-base structure determination program CS-Rosetta. This thesis focuses on the cross-validation of the structure so produced. We present here the solution NMR structure of a mimic of the folding intermediate that is highly populated in solution, obtained from the wild-type domain by protein mutagenesis. The ensemble of structures generated of the mimic are within 2Å of the relaxation dispersion/CS-Rosetta structures of the intermediate, with the non-native interactions in the intermediate also observed in the mimic. The results presented in this thesis strongly confirm the structure of the FF domain folding intermediate, in particular, and validate the use of relaxation dispersion derived restraints in structural studies of invisible excited states, in general.

Keywords: Protein Folding
Folding Intermediate
Nuclear Magnetic Resonance (NMR) Spectroscopy
FF domain
Protein Structure
CPMG Relaxation Dispersion NMR
Advisor: Kay, Lewis E.
Forman-Kay, Julie Deborah
Exploring Perceptions of Cultural Difference in IRB Family Sponsorship Decisions

This thesis analyzes the Canadian Immigration and Refugee Board (IRB)’s treatment of culture in recent family sponsorship decisions. Drawing upon theories of cultural difference, identity construction, and Critical Race Theory, it examines IRB decision-makers’ assessments of cultural factors and their influence on the evaluation of parties’ credibility. This thesis argues that appellants and applicants before the Immigration Appeal Division often had to demonstrate that their family class relationships were “performed” in accordance with the norms of their culture. Many IRB Members relied on essentialist conceptions of culture, and thus generated problematic images of both cultural minorities and Canadian society. Further, the identity of parties was often constructed in terms of defined categories such as ethnic background, religion, marital status, age, and disability. In conclusion, this thesis offers reflections on how issues of cultural identity can be more fairly and sensitively addressed by administrative tribunals such as the IRB.

Keywords: law
immigration
Canada
Immigration and Refugee Board (IRB)
cultural difference
Critical Race Theory
family sponsorship
identity construction
Immigration Appeal Division
Advisor: Shachar, Ayelet
Multi-sensor Data Fusion for Traffic Speed and Travel Time Estimation

In this thesis, seven multi-sensor data fusion based estimation techniques are investigated. All methods are compared in terms of their ability to fuse data from loop detectors and Bluetooth tracked probe vehicles to accurately estimate freeway traffic speed. In the first case study, data generated from a microsimulation model are used to assess how data fusion might perform with present day conditions, having few probe vehicles, and what sort of improvement might result from an increased proportion of vehicles carrying Bluetooth-enabled devices in the future. In the second case study, data collected from the real-world Bluetooth traffic monitoring system are fused with corresponding loop detector data and the results are compared against GPS collected probe vehicle data, demonstrating the feasibility of implementing data fusion for real-time traffic monitoring today. This research constitutes the most comprehensive evaluation of data fusion techniques for traffic speed estimation known to the author.

Keywords: Data Fusion
Traffic Speed
Estimation
ITS
Advisor: Abdulhai, Baher
Roorda, Matthew J.
The Use of Endothelial Progenitor Cells to Promote Bone Healing in a Defect Model in the Rat Femur

The objective of this project was to evaluate the effects of local endothelial progenitor cell (EPC) therapy on bone regeneration in a segmental defect in the rat femur. Animals from the EPC-treated (N=28) and control (N=28) groups were sacrificed at 1, 2, 3, and 10 weeks post-operatively. Bone healing was evaluated with radiographic, histological, and micro computed tomography (micro-CT) scans. Radiographically; mean scores of the EPC group at 1, 2, and 3 weeks were significantly higher compared to control group. At 10 weeks, all the animals in the EPC group had complete union (7/7), but in the control group none achieved union (0/7). Histologically, specimens from EPC-treated animals had abundant new bone formation compared to controls. Micro-CT assessment showed significantly improved parameters of bone healing for the EPC group compared to control group. In conclusion, local EPC therapy significantly enhanced bone regeneration in a segmental bone defect in rat femur.

Keywords: Fracture Healing
Endothelial Progenitor Cells (EPC)
Advisor: Schemitsch, Emil H.
Understanding the Adsorption of Polycyclic Aromatic Hydrocarbons from Aqueous Phase onto Activated Carbon

Non-competitive adsorption of polycyclic aromatic hydrocarbons (PAHs) from water onto activated carbon was studied alongside the performance of CO2-activated petroleum coke as a low-cost adsorbent. PAH adsorption was a two-stage process: a short, fast initial period followed by a long, slow period corresponding to the intra-particle diffusion of PAH molecules in macropores and micropores. The adsorption capacity was determined by total surface area accessible to PAH and the availability of active surface chemical groups. The positive dependence of adsorption capacity on surface oxygen groups and temperature was observed, suggesting a chemical nature of PAH adsorption. The interaction between PAH-activated carbon was however, weak and energetically similar to that of hydrogen bonds. Overall, PAH adsorption was an exothermic process that combined physisorption and chemisorption. CO2-activated petroleum coke had a greater SSA-normalized capacity than coal-derived commercial activated carbon (0.26 vs. 0.19 mg/m2). The capacity was significantly increased by post-oxidation to 0.62 mg/m2.

Keywords: polycyclic aromatic hydrocarbons
adsorption
activated carbon
kinetics
equilibrium
mechanism
Advisor: Jia, Charles Q.
Chinese Influence on the African “Resource Curse”

This thesis explores the impact that Chinese aid and investment has on the political economy of resource-rich African countries. In particular, it examines the effects of Chinese resource-for-infrastructure agreements on the political economy of the resource curse. Using Ghana as a case study, this thesis highlights the peculiar obstacles that countries face with regard to managing their resources. In turn, it argues that general prescriptions against the resource curse, such as resource revenue transparency initiatives, like the Extractive Industries Transparency Initiative, are insufficient. As a result, African recipients of Chinese aid require specific institutional arrangements that accurately reflect the specific “rules of the game” that exist under their respective political economies. In the case of Ghana, this thesis argues that vetting Chinese resource-for-infrastructure agreements through the Public Procurement Act serves that need.

Keywords: Mining
Institutions
Advisor: Trebilcock, Michael
A Time-varying Feedback Approach to Reach Control on a Simplex

This thesis studies the Reach Control Problem (RCP) for affine systems defined on simplices. The thesis focuses on cases when it is known that the problem is not solvable by continuous state feedback. Previous work has proposed (discontinuous) piecewise affine feedback to resolve the gap between solvability by open-loop controls and solvability by feedbacks. The first results on solvability by time-varying feedback are presented. Time-varying feedback has the advantage to be more robust to measurement errors circumventing problems of discontinuous controllers. The results are theoretically appealing in light of the strong analogies with the theory of stabilization for linear control systems. The method is shown to solve RCP for all cases in the literature where continuous state feedback fails, provided it is solvable by open loop control. Textbook examples are provided. The motivation for studying RCP and its relevance to complex control specifications is illustrated using a material transfer system.

Keywords: control
feedback
affine
reach control
simplex
flow
invariance condition
equilibria
M-matrix
Advisor: Broucke, Mireille E.
The Effects of Memory Remoteness on Recall and Recognition: Development of a Novel Measure of Naturalistic Memory

The current study introduced a new measure for the study of naturalistic memory, which involved the use of a homogeneous, controlled event for all participants. We tested participants’ memory for this so-called staged event with both the Autobiographical Interview (AI) and our novel receiver operating characteristic (ROC) task. Statistical analyses indicated that scores on the AI and on our new ROC measure showed time sensitivity consistent with the literature. These data were difficult to interpret, however, because of a confound of age. We will need to age-match our groups before drawing any major conclusions. That said, we found a significant positive correlation between measures of recollection on both the AI and ROC task, which was a promising finding in terms of validating the new measure against an established procedure. Overall, our results suggest that assessing recall and recognition for a staged event is a viable method for studying naturalistic memory.

Keywords: Naturalistic memory
Recognition memory
Advisor: Levine, Brian
The Role of CD40L and CD40 in the Pathogenesis of Kawasaki Disease

Kawasaki Disease (KD) is a childhood disease leading to coronary arteritis. Elevated numbers of CD40L+ platelets in circulation is correlated with risk of heart damage. CD40L is a tumor necrosis family member that binds to CD40 and αIIbβ3, receptors which are also expressed on platelets. A single injection of Lactobacillus casei Cell Wall Extract (LCWE) induces a disease similar to KD in mice, where LCWE superantigen (SAg) reactive T-cells persist in the coronary artery. This phenotype is inconsistent with the fate of SAg-stimulated cells and is likely mediated by co-stimulation. This work shows that stimulation with a SAg induces platelet activation and CD40L expression in vitro. Furthermore, enhanced survival of SAg-reactive T-cells is demonstrated following antibody-mediated CD40L cross-linking. This effect is mediated via inhibition of the extrinsic apoptosis pathway. In addition, CD40 cross-linking is also reported to enhance SAg-reactive T-cell survival by enhancing CD86 expression on APCs and CD28 co-stimulation.

Keywords: Kawasaki Disease
CD154
CD40L
Platelet
CD40
Superantigen
Advisor: Yeung, Rae S. M.
Characterization of Executive Dysfunction in Real World Tasks: Analysis of Behaviours Performed during Completion of the Multiple Errands Test

This study furthers our understanding of the impact of executive dysfunction on everyday activities in stroke survivors. A classification system was developed to analyze a wide range of behaviours performed by 14 stroke survivors and 12 matched controls on the Baycrest Multiple Errands Test, a task requiring participants to buy specific items and collect certain information on the main floor of the hospital. The event recorder was used to code the occurrences and frequencies of behaviours performed by participants. Results demonstrated that participants with stroke performed significantly more task specific relevant inefficient behaviours (p < .05) and non-task specific irrelevant behaviours (p < .10) compared to controls. This study indicates the importance of performing a detailed analysis of behaviours performed to better understand the impact of ED in everyday life.

Keywords: Rehabilitation
Stroke
Multiple Errands Test
Assessment
Executive Dysfunction
Event Recording
Advisor: Dawson, Deirdre R.
High Speed Clock and Data Recovery Techniques

This thesis presents two contributions in the area of high speed clock and data recovery systems. These contributions are focused on the fast phase recovery and adaptive equalization techniques. The first contribution of this thesis is an adaptive engine for a 2x blind sampling receiver. The proposed adaptation engine is able to find the phase-dependent DFE coefficients of the receiver on the fly. The second contribution is a burst-mode clock and data recovery architecture which uses an analog phase interpolator. The proposed burst-mode CDR is capable of locking to the first data transition it receives. The phase interpolator uses the inherent timing information in the data transition to rotate the phase of a reference clock and align it with the incoming data edge. The feasibility of the concept is demonstrated through fabrication and measurements.

Keywords: CDR
Burst-Mode receiver
equalization
adaptation
ADC-based Receiver
Blind Sampling
CMOS
PON
Advisor: Sheikholeslami, Ali
The Effects of Hyperbaric Oxygen Therapy on Bone Distant from Site of Surgery

Background: Hyperbaric Oxygen Therapy (HBOT) is used to promote soft and hard tissue repair at sites of injury or disease. It is not known whether it has any effect on uninjured tissues. Objective: To evaluate the effect of HBO on vertebral bones distant from a calvarial surgical site. Materials and Methods: 22 male New Zealand white rabbits were divided into two groups (n=11). All animals underwent surgery to produce bilateral calvarial critical sized defects. Group 1 received HBOT while Group 2 served as controls breathing room air (NBO). The Marx HBO protocol was used (90min, 100% oxygen at 2.4 ATA, 5 days a week for 4 weeks). Subjects were sacrificed at 6 weeks. The vertebrae were analyzed by micro-CT (μCT) and histology. Results: There were no statistical significant differences between the two groups. Conclusion: we concluded that there were no harmful effects of HBOT on non-injured vertebrae at 6 weeks.

Keywords: Hyperbaric
Bone
Advisor: Peel, Sean
Validation of Road Safety Surrogate Measures as a Predictor of Crash Frequency Rates on a Large-scale Microsimulation Network

A study was done to explore the suitability of intersection and arterial collision prediction models based on traffic conflicts, generated using the Paramics microsimulation suite and the Surrogate Safety Assessment Model (SSAM). A linear regression model and a generalized linear model with a negative binomial error structure were explored to correlate conflicts to crash rates, as well as the conflict-based models suggested by SSAM. The model predictions were compared to volume-based predictions and historical data from Toronto, Ontario, Canada. The volume- based predictions were calculated using a negative binomial generalized linear model, fitted to the same arterial and intersection sets used to fit the conflict-based models. The results show the predictions generated by a conflict-based model were comparable for intersections, but poor for arterials.

Keywords: traffic conflict
microsimulation
crash frequency
road safety
SSAM
Advisor: Shalaby, Amer Saïd
Persaud, Bhagwant
Optimization of Aggregate Gradation Combinations to Improve Concrete Sustainability

By optimizing the packing of the combined aggregate gradations, the cement paste content needed to make concrete can be reduced, improving sustainability, cost, performance, durability, and workability. Optimization can be achieved using theoretical and empirical techniques, or waste concrete material as an intermediate size fraction. However, the potential for improvement is currently limited by prescriptive grading specifications that require meeting individual requirements for fine and coarse aggregates. From this study, using various optimization techniques, it was found that by inclusion of an intermediate sized aggregate material, a reduction in cement paste up to 16% is possible for 35 MPa and 50 MPa mix designs typically used in Ontario bridge decks. The aggregate materials used were a natural sand, and two crushed limestones of 19.0 mm and 6.7 mm maximum size. From these findings, recommendations are made for improving the current Ontario Provincial Standard Specification (OPSS) 1002 used for concrete aggregates.

Advisor: Hooton, Robert Douglas
Kuwait and Bahrain’s Anti-terrorism Laws in Comparative and International Perspective

Counter terrorism is one of the contemporary issues that concerns both the international community and Arab states. A problematic issue in this regard is the lack of a definition, which allows states to criminalize “terrorism” based on the best interest of each individual state. This thesis examines the laws that deal with terrorism in Kuwait, which rely on Kuwait’s broad national security laws. Problems with these laws include the lack of the rule of law and violation of human rights. This thesis highlights Bahrain’s experience with counter terrorism and the human right violation during the February 2011 revolution. The thesis emphasises the importance of having an appropriate definition that coincides with the rule of law and human rights, by adhering to the international guidance provided by the 1999 ‘International Convention on Suppression of Terrorism Financing’ and the UN Security Council Resolution 1566 (2004) as a first serious step in combating terrorism.

Keywords: Anti-terrorism
Advisor: Roach, Kent
Role of Acculturation, Social Capital and Oral Health Literacy on Access to Dental Care among Preschool Children of Arabic-speaking Immigrants in Toronto, Canada

Objectives: To determine access to dental care among preschool children of Arabic-speaking immigrant families; to investigate the influence of social and cultural factors on access to dental care; and to measure preschool children’s oral health as reported by their parents. Methods: This survey used a semi-structured questionnaire to interview 100 Arabic-speaking parents of children under the age of 5 who were identified from community centres. Five scales were used to measure acculturation, social capital, oral health literacy, oral health knowledge, and health literacy. Results: Only 34% of families had visited the dentist to obtain dental care for their preschool children. Nineteen-percent of Arabic parents in our sample rated their children’s oral health as being fair or poor. None of the scales used in this study had a significant impact on access to dental care; however, higher scores on these scales tended to be associated with better access to dental care.

Keywords: access to dental care
immigrants
acculturation
social capital
oral health literacy
oral health knowledge
Advisor: Lawrence, Herenia P.
The Role of 4-1BB in Kawasaki Disease

Kawasaki disease (KD) is a multisystem vasculitis with predilection for the coronary arteries. Although the cause of KD remains elusive, there is evidence to suggest a superantigenic trigger. When T-cells are activated by a superantigen (SAg) they undergo massive proliferation but eventually apoptose; however, in KD, we hypothesize that these T-cells persist and infiltrate the coronary arteries. Previous studies have shown that enhanced costimulation through CD28 or 4-1BB rescues T-cells from apoptosis and exacerbates disease in a mouse model of KD. Our results suggest that this signal needs to be initiated close in timing to that of the SAg. In addition, the two molecules can act independently of one another, but are not additive. Also, stimulation of the 4-1BB pathway in the presence of a SAg elicits a Th1 phenotype. Lastly, TRAF1 regulates this enhanced survival downstream of 4-1BB. Thus, these results provide new insights into the effects of costimulation in SAg-mediated disease, and suggest that these pathways need to be targeted early to abrogate the enhanced survival of SAg-activated T-cells.

Keywords: Kawasaki Disease
superantigen
T-cell
costimulation
Advisor: Yeung, Rae S. M.
Information and Decision-making Processes Leading to Corporate Failure: Enron and Red Flags

Enron is examined as a critical case study to understand the role of information in the Enron’s Board’s decision-making processes. Three major events in the Enron failure were analyzed in detail using thematic analysis. Three themes were identified regarding the communication and use of information in Enron: interdependency of authority relationships, information control, and decision protocol and policies that shaped the information that management sent to the Board during the approval process. The Board was dependent on advisors to provide approvals first, prior to Board approval. The relationships between advisors and management influenced the information sent to the Board and affected controls used to monitor deals. The Board maintained that they were unaware of red flags, such as warnings related to incomplete disclosures and conflict of interest issues. The Board received information for arrangements which required Board approval but it had limited access to information regarding Enron’s operations.

Keywords: information processes
decision-making processes
Advisor: Choo, Chun Wei
Changes in Extreme Temperature Trends in the Greater Toronto Area from 1971 to 2000

The impacts of extreme temperatures on human health and morbidity have been well documented in many studies. In literature, changes in the trends of extreme temperatures have been studied using percentiles, indicators and climate modeling. The aim of this study is to determine if the trend exhibited in the literature of statistically significant increases in extreme minimum temperatures, is also exhibited in the Greater Toronto Area during the 1971 to 2000 timeframe. A methodological approach using counts is the basis for the analysis. Statistical significance is determined through the use of Spearman’s Rank, Kendal-Tau and T-tests. A total of five stations are analysed, three being urban and two representing the surrounding suburban areas. The results indicate that statistically significant decline in extreme minimum temperature counts have occurred. In agreement with the literature, statistically significant increases in extreme maximum temperature counts can not be determined.

Keywords: Extreme
Temperature
Advisor: Gough, William A.
Identification of Novel Genes Critical for CNS Regeneration in L. stagnalis

Neuronal regeneration in the mammalian central nervous system (CNS) is severely compromised due to the presence of extrinsic inhibitory signals and a reduced intrinsic regenerative capacity. Understanding the cellular and molecular processes underlying injury and regeneration in the CNS is necessary for the development of effective therapeutic strategies. Lymnaea stagnalis, a freshwater pond snail, has proven to be a powerful model for studying the fundamental mechanisms underlying neurite outgrowth and regeneration. In this study I designed the first custom L. stagnalis microarray gene chip and carried out microarray analysis to profile gene expression changes following CNS injury. From a pool of significantly regulated genes, I provided the first evidence that C/EBP, a transcription factor, plays an integral role in regeneration by maintaining the viability of the distal neurite. We also proposed a novel signaling network and demonstrated that BCL 7 regulates neurite regeneration, an effect that may be mediated through Ca2+-dependent growth cone formation.

Keywords: Invertebrate
Regeneration
Advisor: Zhong-Ping, Feng