VictorJuiz/thesis huggingface dataset:
Mechanisms of 4-hydroxytamoxifen-induced Apoptosis in Rhabdomyosarcoma Cells

Rhabdomyosarcoma (RMS) is a malignant soft-tissue sarcoma in children, accounting for about 40% of pediatric soft-tissue tumours. Five-year survival for metastatic RMS is only about 25%. Furthermore, there has been no significant improvement in RMS survival since 1975, pointing to a need for improved therapy. Previous work in our lab has shown that 4-hydroxytamoxifen (4OHT) leads to increased apoptosis and decreased viability in RMS cells. Expanding on this work, the current project aims to elucidate the mechanisms behind 4OHT-induced apoptosis in RMS cells, focusing on the roles of estrogen receptors (ER) and MAP kinases (MAPK). We found that: 1) 4OHT-induced apoptotic signaling was associated with increased MAPK phosphorylation, 2) Inhibition of MAPK protected cells against 4OHT, 3) Inhibition of ER also protected against 4OHT, and 4) ER inhibition blocked 4OHT-associated MAPK phosphorylation.

Keywords: rhabdomyosarcoma
tamoxifen
4-hydroxytamoxifen
estrogen
estrogen receptor
apoptosis
JNK
p38
ERK
Advisor: Malkin, David
Development of a Comprehensive Mathematical Model and Physical Interface for Manual Wheelchair Simulation

The aim of this project is to provide a manual wheelchair simulator for advanced wheelchair research within Toronto Rehabilitation Institute‘s Challenging Environment Assessment Laboratory (CEAL). To achieve this, a comprehensive mathematical model of the wheelchair/user system and a fully adjustable physical interface (which mimics various wheelchair configurations) have been developed. The mathematical model is unique in its ability to predict complex motions such as wheelies, and is able to update the wheelchair‘s position in a virtual environment, and calculate the force-feedback required for simulating various slopes and surfaces. The physical interface is used to measure the inputs required by the mathematical model (hand-rim input torques, hand and torso positions, and user centre-of-mass position), and utilizes servo motors to provide force-feedback at the wheelchair‘s hand-rims. Preliminary results comparing real-world wheelchair motion data to the mathematical model‘s predictions are presented, along with the physical interface design and mathematical model development.

Keywords: wheelchair
manual wheelchair simulator
simulation
mathematical model
Toronto Rehab
CEAL
virtual reality
Advisor: Fernie, Geoff
In Search of Interaction Partners for the Saccharomyces cerevisiae Magnesium Channel Alr1p

Magnesium, the second most abundant cation in the cell, is involved in a diverse range of biochemical activities. This project focuses on the mechanism of magnesium import into the cell through the action of Alr1p. Alr1p resides in the plasma membrane of yeast and belongs to the CorA-Alr1p-Mrs2p family of magnesium channels. Potential regulators of CorA were found through genetic screening and yeast two-hybrid screens have pulled out interactors of Alr1p. Interactors that influence Alr1p and its conformation will, with very high probability, also change the channel’s ability for magnesium import. Membrane proteins are not easily amenable to traditional yeast two-hybrid screens due to their hydrophobic nature. The goal of this thesis is to identify interactors of Alr1p using iMYTH, a modified yeast two-hybrid method. Of the eighteen Alr1p interactors identified, Vma3p and Vma11p, which are both subunits of the V-ATPase, showed the most promise for further Alr1p interaction characterizations.

Keywords: protein interaction
magnesium channel
Advisor: Pai, Emil F.
Design and Evaluation of Dual-ended Detectors for PET Mammography

Current positron emission mammography (PEM) depth of interaction (DOI) enabling detectors have low scintillator to photodetector encoding ratios, RE causing high system complexity and cost. The modularized dual-ended readout block (DERB) detector combines the Anger logic block detector with dual-ended readout to increase RE while measuring DOI. To investigate the trade-off between RE and spatial resolution, scalable DERB detectors with varying RE and light guide thickness were modelled with Monte- Carlo. Simulation showed RE can increase up to six-fold compared to the dual-ended readout design without significantly degrading spatial resolution. Experimental characterization of a RE = 9 : 8 DERB detector was found to achieve super-resolution <0.5 mm for resolving crystal indices, DOI resolution of ~5 mm FWHM, and mean energy resolution of 20% without recovering photons lost to neighbouring detector modules. The model was validated by agreement of simulation results adjusted for detector quantum efficiency with experimental results.

Keywords: PET
Positron Emission Tomography
Positron Emission Mammography
Scintillators
Arrays
Block Detector
Photonics
Pixel
Spatial Resolution
Dual-ended readout
Depth of interaction
DOI
Monte Carlo
DETECT2000
Gamma Detector
Detector design
Advisor: Rowlands, John A.
Laser-induced Incandescence of Soot for High Pressure Combustion Diagnostics

Accurate determination of soot emissions from combustion is of interest in both fundamental research and industries that rely on combustion. Laser-induced incandescence of soot particles is a young technique that allows unobtrusive measurements of both soot volume fraction and particulate size. An apparatus utilizing this technique has been brought to function for both atmospheric and high pressure measurements. Proof of concept measurements of an atmospheric ethylene-air laminar diffusion flame at 35, 42, and 47 mm above the burner exit correlate well with literature findings. Profile trends of a methane-air diffusion flame at 10, 20, and 40 atm at 6 mm above the burner are similar to reports in literature and are compared to trends from spectral soot emission measurements. Particle size is found to be roughly proportional to pressure. Discussion on the errors of laser-induced incandescence as well as recommendations for improving the apparatus are herein.

Keywords: Laser-Induced Incandescence
LII
Soot
High Pressure
Combustion
Diagnostics
Advisor: Gulder, Omer L.
Utility Assessment of Health-related Quality of Life (HRQOL) in Colorectal Cancer Patients: A Mixed Methodology Study

Background: Variation exists in quality of life (i.e., utility) estimates depending on the utility elicitation method utilized. Using the EQ-5D, VAS, and HUI-III, the aim of this thesis was to determine whether these measures adequately capture HRQOL in a CRC population and assess the relationship between utility estimates generated. Methods: A mixed methods study design was employed to collect health status scores and interview data from a sample of 50 CRC patients in Toronto, Ontario. Results: Mean utility scores between the EQ-5D and HUI-III were identical at 0.76 (95% CI), with an overall VAS score of 0.72 (95% CI). Conclusion: The fact that the EQ-5D and HUI-III resulted in identical mean utility scores provides assurance for future studies using these tools in CRC. However, many factors that CRC patients identify as important to their HRQOL are not captured by these instruments. These findings have implications for informing economic evaluations.

Keywords: health services research
economic evaluation
colorectal cancer
quality adjusted life year (QALY)
qualitative
utility
Advisor: Hoch, Jeffrey
An Investigation of the Hydration of Steam-cured Ternary and Quaternary Cement Blends

The influence of supplementary materials such as slag, metakaolin and limestone in steam-cured ternary and quaternary cement blends on physical and chemical hydration mechanisms was studied by analyzing the evolution of non-evaporable water content, hydration products and compressive strength. The role of limestone in hydration reactions of cement was also investigated. These properties were studied through the use of differential thermal and thermogravimetric analyses, as well as the loss-on-ignition, X-ray diffraction and compressive strength tests at 1, 3, 7, and 28 days. Research findings revealed that it is possible to replace up to 40% cement with other materials and still achieve compressive strengths similar to mixtures with a 25% cement replacement at 0.34 w/b ratio. Additionally, ternary limestone mixtures exhibited superior mechanical properties to ternary metakaolin mixtures. Lastly, limestone powder was determined to behave as inert filler, accelerating hydration at early ages through heterogeneous nucleation.

Keywords: Steam-curing
Cement blends
Ground granulated Blast Furnace Slag
Metakaolin
Limestone
Hydration
Advisor: Panesar, Daman
Big Gay Library: An Ethnography of the Pride Library at the University of Western Ontario

Officially founded in 1997, the Pride Library is a pioneering Lesbian, Gay, Bisexual, Trans and Queer (LGBTQ) Canadian information-based organization. Although located within D.B. Weldon Library at the University of Western Ontario, the library maintains a primarily grassroots framework. The Pride Library case study reflects a tradition within LGBTQ communities towards preserving and disseminating information otherwise marginalized by larger society. Operating outside of conventional professional informed and institutionally-dominated models, LGBTQ communities create unique grassroots information organizational contexts. In order to develop a deeper understanding of LGBTQ information organizations, an ethnographic study of the Pride Library was developed. The thesis addresses the library’s use patterns, and approaches to space, materials and labour relations. Findings demonstrate that the Pride Library is not only valued for providing LGBTQ-specific information resources, but also for creating a symbolically significant, socially-oriented and community-based LGBTQ environment.

Keywords: LGBTQ
queer
ethnography
library
archive
Pride Library
University of Western Ontario
Advisor: Hartel, Jenna
Colour Standardization: Its Past and a Possible Future

In this thesis, I address the problem and promise of decentralization, in the context of standard-setting for physical systems. I explore how the process of the decentralization of power works in the context of physical information, in three subsets:the relationship between existing standards and the decentralized control of physical information; how hands-on experimentation helps to shed light on the decentralized control of physical information; and how existing Free/Libre Open Source Software culture addresses the decentralized control of physical information.

Keywords: standards
open source
Advisor: Ratto, Matthew
An Exploratory Study of the Fundamental Characteristics Influencing the Analysis and Communication Activities of Health Care Incident Reporting Systems

Incident reporting systems offer rich opportunities for learning from errors in health care. However, little attention has been given to understanding how the implementation of reporting system characteristics impact analysis and communication activities. This research explored the characteristics of reporting systems that promote analysis and communication activities. Ten characteristics were identified through a comprehensive literature review. Two reporting systems were then compared to assess how differences in the implementation of the characteristics impact the contents of the database. The results demonstrated that differences in the characteristics’ implementation have an effect on the ability to extract information essential to analysis activities. Next, the reporting processes of the two systems were mapped onto a hierarchical framework to highlight how the characteristics influence the communication of incident information across the health care system. The presented work furthers the understanding of characteristics needed to design reporting systems more effective at promoting learning.

Keywords: Heath care
incident reporting
Advisor: Easty, Anthony
Trbovich, Patricia
Strategies for Protecting Group Free Glycosidation

The synthesis of glycoconjugates is of interest in biological and medicinal research. There are numerous approaches to the synthesis of glycosides involving protecting group free methods. This thesis outlines what has been achieved in the field and two novel approaches for O-glycosidation. The first approach involves the use of a toluenesulfonohydrazide glycoside with a purification handle designed for simple glycoside purifications. The butyl 3-O-octyl-D-glucopryanoside was successfully synthesized but did not have the desired property of yielding simple-to-purify glycosides as products. The second approach uses a thiouronium glycosyl donor; a variety of glycosidations using this donor were investigated. The glucosyl thiouronium salt donor was shown to undergo glycosidation effectively with simple alcohols.

Keywords: glycosidation
organic chemistry
carbohydrate chemistry
organic synthesis
Advisor: Nitz, Mark
Staufen Regulates Eye Development

Despite their undisputed importance to embryonic growth, the role of mRNA transport proteins in the developing visual system has been widely uncharacterized. Through RNA interference, this study aims to discover the function of Staufen 2 (Stau2), an mRNA transport protein, in chick eye development. When Stau2-miRNA was electroporated into the E1.5 primary optic vesicle, two days later they exhibited a reduction of eye size by 47%, whereas control miRNA did not significantly change eye size. TUNEL, β-III tubulin and BrdU staining were used to analyze the retinal apoptotic, differentiation and proliferative levels respectively, in response to Stau2 knockdown. These data suggest that the small eye is a result of a decrease in proliferation, and not cell death or pre-mature differentiation. Rescue experiments were done with each of the three Stau2 isoforms and confirmed both the direct effect of Stau2-miRNA and the involvement of these isoforms in eye development.

Keywords: Chick
Retina
Eye
Development
Proliferation
Advisor: Monnier, Philippe
Public Engagement through the Toronto Health Policy Citizens Council: What do Citizens Value in Health Care?

Health policy making is fraught with difficult decisions that result from conflicts between people’s values. Citizens are important stakeholders in this process, and it is through methods of public engagement that they can be involved in developing health policy. Deliberative forms, in particular, have the ability to improve decision quality and promote greater acceptance of decisions. This study used the Toronto Health Policy Citizens Council to examine citizens’ values on 7 specific health policy questions asked over a two-year period. A thematic analysis was performed on the transcript content derived from the audiotaped deliberations from Council meetings. Nineteen values were identified. The results suggest that it may be a combination of factors of the health policy topic discussed that shapes the values elicitation seen in this kind of public engagement. In conclusion, citizens councils appear effective at eliciting citizens’ values, and are a good way to actively educate participants about health care.

Keywords: Public engagement
Health policy
Citizens Councils
Qualitative methods
Advisor: Upshur, Ross
Better the Devil We Know: How Sociology Informs the Debate Over Antidumping Laws

Trade and other governmental policy decisions are frequently made based on neoclassical economic theory, which in turn is based on simplifying assumptions that result in unrealistic predictions. In this thesis, I argue that sociology is an important social science that can help to inform economic theory in policy-making. Understanding how social relations affect market actors and institutions is crucial, as markets are themselves composed of social relationships. I present an example using antidumping regulations. Economic scholars have argued that antidumping laws should be abolished based on pure economic theory. I argue that, from a sociological perspective, antidumping laws serve to provide a necessary stabilizer for markets, resulting in controlled competition and greater trade liberalization. Such laws should therefore be maintained.

Keywords: Antidumping
Sociology
Law
Policy
Advisor: Fadel, Mohammad
Beamforming Based MIMO Processing with Closely Spaced Antennas

When antennas are placed closely spaced together, the mutual coupling and spatial correlation effects undermine the advantages provided by multiple input and multiple output (MIMO) antennas. In this thesis, we compare and analyze the performance of digital beamforming, fixed radio frequency (RF) beamforming and element based patterning with closely spaced antenna systems. In the case where only one RF-chain is available, we have demonstrated performance improvements using RF beamforming-based MIMO processing instead of element-based MIMO processing with closely spaced metamaterial antennas. The result indicates that even without mutual coupling, antenna based MIMO processing is greatly impacted when moving from rich to correlated scattering environments. In the second half of the thesis, we investigate the switch and examine receiver combining (SEC) technique. We derive the switching rate of SEC and show that even though it has the same outage probability as traditional selection combining, it has a significantly lower switching rate.

Keywords: MIMO
Beamforming
RF-Beamforming
closely spaced antennas
Advisor: Adve, Raviraj
Towards the Development of a Quantum Dot based Bioprobe for Intracellular Investigations of Nucleic Acid Hybridization Events using Fluorescence Resonance Energy Transfer

The unique spectroscopic properties of quantum dots (QDs) are of interest for application in intracellular studies of gene expression. QDs derivatized with single-stranded probe oligonucleotides were used to detect complementary target sequences via hybridization and fluorescence resonance energy transfer (FRET). As nucleic acid targets are not labeled within cells, a displacement assay for nucleic acid detection featuring QDs as FRET donors was developed. QDs conjugated with oligonucleotide probes and then pre-hybridized with labeled target yielded efficient FRET in vitro. Studies in vitro confirmed that displacement kinetics of pre-hybridized target was a function of the stability of the initial hybridized complex. Displacement was observed as reduction in FRET intensity coupled with regeneration of QD fluorescence. By engineering the sequence of the labeled target, faster displacement was possible. The QDprobe+target system was successfully delivered into cells via transfection. Although QDs with their cargo remained sequestered in endosomal vesicles, fluorescent properties were retained.

Keywords: quantum dot
FRET
hybridization
Advisor: Krull, Ulrich Jorg
The Effect of Salvia hispanica L. (Salba) on Weight Loss in Overweight and Obese Individuals with Type 2 Diabetes Mellitus

Canadian statistics indicate that the incidence of obesity is rising, and that the prevalence of type 2 diabetes mellitus (T2DM) within this group is significantly higher than those of a healthy weight. Preliminary evidence has shown that the oil-rich grain, Salvia hispanica L. (Salba), improves glycemic control, suppresses appetite, and affects additional cardiovascular disease (CVD) risk factors. This study followed a randomized, double-blind, placebo-controlled, parallel design in a sub-set population of twenty individuals who were overweight or obese and had T2DM. Participants received supplements of Salba, or an energy- and fibre-matched control, and followed a hypocaloric diet for 24 weeks. Findings of this study reveal that Salba does not significantly affect weight loss, glycemic control or other CVD risk factors. These findings are preliminary and highlight the complexities of weight loss research. Further investigation into the potential health benefits of Salba is currently being carried out.

Keywords: Weight Loss
Type 2 Diabetes Mellitus
Obesity
Advisor: Vuksan, Vladimir
Global Optimization Algorithms for Aerodynamic Design

This work focuses on an investigation of multi-modality in typical aerodynamic shape optimization problems and development of optimization algorithms that can find a global optimum. First, a classification of problems based on the degree of multi-modality is introduced. Then, two optimization algorithms are described that can find a global optimum in a computationally efficient manner: a gradient-based multi-start Sobol algorithm, and a hybrid optimization algorithm. Two additional algorithms are considered as well: a gradient-based optimizer and a genetic algorithm. Finally, we consider a set of typical aerodynamic shape optimization problems. In each problem, the primary objectives are to classify the problem according to the degree of multi-modality, and to select the preferred optimization algorithm for the problem. We find that typical two-dimensional airfoil shape optimization problems are unimodal. Three-dimensional shape optimization problems may contain local optima. In these problems, the gradient-based multi-start Sobol algorithm is the most efficient algorithm.

Keywords: aerodynamics
CFD
optimization
Advisor: Zingg, David W.
Effects of Proteasome Inhibition on Tau Protein

The ubiquitin-proteasome system is an important proteolytic pathway implicated in the formation of neurofibrillary tangles from hyperphosphorylated tau, a pathological hallmark of tauopathies such as Alzheimer’s disease. We hypothesize that proteasome inhibition will result in tau accumulation, leading to the formation of aggregates. We established a combined pharmacological and genetic model of proteasome inhibition in SHSY-5Y neuroblastoma cells. Through lentiviral infection, we expressed a mutant T1A form of the β5 proteasome subunit to impair the chymotryptic proteolytic activity of the proteasome. Cells were then treated with different pharmacological inhibitors of the proteasome to further exacerbate the effects of mutation-mediated proteasome inhibition and tested for changes in tau expression. Contrary to our hypothesis, chronic proteasome inhibition and exposure to mild oxidative stress concurrently resulted in increased tau degradation. Therefore, although chronic proteasome inhibition was insufficient to induce changes in tau turnover, it rendered cells more vulnerable to oxidative insult.

Keywords: Tau
Proteasome
Advisor: Tandon, Anurag
Facial Feature Point Detection

Facial feature point detection is a key issue in facial image processing. One main challenge of facial feature point detection is the variation of facial structures due to expressions. This thesis aims to explore more accurate and robust facial feature point detection algorithms, which can facilitate the research on facial image processing, in particular the facial expression analysis. This thesis introduces a facial feature point detection system, where the Multilinear Principal Component Analysis is applied to extract the highly descriptive features of facial feature points. In addition, to improve the accuracy and efficiency of the system, a skin color based face detection algorithm is studied. The experiment results have indicated that this system is effective in detecting 20 facial feature points in frontal faces with different expressions. This system has also achieved a higher accuracy during the comparison with the state-of-the-art, BoRMaN.

Keywords: computer vision
biometrics
image processing
Advisor: Plataniotis, Konstantinos N.