VictorJuiz/thesis huggingface dataset:
Targeting Tumour Metabolism through HIF-1 Inhibition Enhances Radiation Response in Cervix and Head and Neck Xenograft Tumours

Increased glucose metabolism may occur in malignant tumours due to altered gene expression or a response to hypoxia. It has been shown that tumours with high levels of glycolysis, indicated by elevated lactate, are less responsive to radiotherapy. It is not clear whether this effect is caused by lactate itself or rather that high lactate is a surrogate for a radioresistant property such as hypoxia. Furthermore, we are not aware of studies that examine the manipulation of lactate production in tumours to alter radiation response. We propose a novel approach of metabolic targeting of HIF-1 to address these issues. HIF-1 is a major regulator of glycolysis and its inhibition would decrease malignant cell metabolism and could lead to a decrease in lactate production. The goal of this pre-clinical study was to evaluate metabolic targeting as a strategy of enhancing radiation response by inhibiting the HIF-1 transcription factor.

Keywords: cancer
radiation
hypoxia
metabolism
HIF-1
lactate
Advisor: Hill, Richard
Wilson, Brian Campbell
An International Approach to Environmental Protection in the Northwest Passage

This paper evaluates the current international environmental regime governing shipping through the Northwest Passage. Significant literature now exists claiming that the sole means by which to afford adequate protection for the Arctic marine environment is through a Canadian assertion of sovereignty. Historically, there have been strong challenges to Canada’s assertion of sovereignty over the waters of the Arctic Archipelago. Further, a focus on sovereignty could in fact be detrimental to the Canadian position, since it distracts from the practical issues involved in protecting the Arctic environment. Based on three primary sources of international law, namely the UN Law of the Sea Convention, the IMO Guidelines for Ships Navigating in Ice-Covered Waters and the activities of the Arctic Council, this paper argues that the current international regime provides a strong and adequate basis on which to pursue protection for the Arctic environment.

Advisor: Brunnee, Jutta
Simulated Shrub Encroachment Impacts Function of Arctic Spider Communities

The projected increase of shrubs across the Arctic is expected to alter patterns of snow cover, which may affect the phenology and survival of arthropods such as spiders. In this study, we simulated shrub encroachment on a series of tundra plots and examined the effects on the spider assemblages during the following growing season. Our simulated shrub treatment did not affect the abundance or composition of spider communities over the season; however, adults from the dominant genus Pardosa (Lycosidae) had significantly higher body mass on treatment plots. This difference in mass was observed following snow melt and persisted until halfway through the growing season. Given the importance of spiders as arthropod predators and as food sources for breeding birds, such a change in summer body mass could represent a shift in spiders’ functional contributions to Arctic ecosystems.

Keywords: spiders
Arctic
shrub encroachment
ecosystem functioning
arthropods
phenology
snow cover
snow fences
overwintering
Advisor: Weis, Arthur
Insight into the Cargo Recognition Mechanism of Kinesin Light Chain 1

Kinesin-1 transports various cargos along the axon, while the light chain subunits play a role in selecting the types of cargos to transport. However, the mechanisms of cargo recognition and interaction have yet to be characterized. Both c-Jun kinase-interacting protein-1 (JIP1) and alcadein-1 (ALC1) are kinesin-1 cargos and compete with each other for the axonal transport machinery. I identified two polar patches of KLC1 that play a role in the interactions with JIP1 and ALC1, respectively. The main components of these two polar patches are asparagine “clamps” surrounded by positively charged lysines. Consistent with this finding, negatively charged residues of JIP1 and ALC1 are required to interact with KLC1. By structural modeling, I narrowed down the possible key residues of KLC1 that are required for interaction with c-Jun kinase interacting protein-3 (JIP3). Together, these findings reveal the versatility of KLC in the mode of interaction with many different cargos.

Keywords: Kinesin
Mechanism of Interaction
KLC
JNK-interacting protein (JIP)
Alcadein
Axonal Transport
Advisor: Park, Hee-Won
Mitchell, Jane A.
Stochastic Modelling of a Collection of Correlated Sparse Signals and its Recovery via Belief Propagation Methods

The field of compressive sensing deals with the recovery of a sparse signal from a small set of measurements or linear projections of the signal. In this thesis, we introduce a stochastic framework that allows a collection of correlated sparse signals to be recovered by exploiting both intra and inter signal correlation. Our approach differs from others by not assuming that the collection of sparse signals have a common support or a common component; in some cases, this assumption does not hold true. Imagine a simplified cognitive radio problem, where users can send a single tone (sine-wave) in a finite number of frequencies; it is desired to find the used frequencies over a large area (creation of a radio map). This is a sparse problem; however, as we move spatially, the occuppied frequencies change, thus voiding the assumption of a common support/component. Our solution to multi sparse signal recovery addresses this problem, where signals that are close geographically are highly correlated and their support gradually changes as the distance between signals grow. Our approach consists of the creation of a probabilistic model that accounts for inter and intra signal correlation and then using belief propagation to calculate the posterior distribution of the signals and perform recovery.

Keywords: Compressive Sensing
Belief Propagation
Advisor: Valaee, Shahrokh
High Dynamic Range Image Compression of Color Filter Array Data for the Digital Camera Pipeline

Typical consumer digital cameras capture the scene by generating a mosaic-like grayscale image, known as a color filter array (CFA) image. One obvious challenge in digital photography is the storage of image, which requires the development of an efficient compression solution. This issue has become more significant due to a growing demand for high dynamic range (HDR) imaging technology, which requires increased bandwidth to allow realistic presentation of visual scene. This thesis proposes two digital camera pipelines, efficiently encoding CFA image data represented in HDR format. Firstly, a lossless compression scheme exploiting a predictive coding followed by a JPEG XR encoding module is introduced. It achieves efficient data reduction without loss of quality. Secondly, a lossy compression scheme that consists of a series of processing operations and a JPEG XR encoding module is introduced. Performance evaluation indicates that the proposed method delivers high quality images at low computational costs.

Keywords: high dynamic range imaging
color filter array
compression
lossy
lossless
digital camera
Advisor: Plataniotis, Konstantinos N.
Satellite and In Situ Measurement of NO2

A novel method was developed for producing high-resolution (∼ 11km) maps of surface NO2 concentrations by combining satellite retrieved NO2 columns from OMI with in situ measurements made by permanent monitoring networks. Field data from the BAQS-met field campaign in the Windsor area during 2007 was used to validate this method and explore the uncertainties and biases in the inferred values. Good correlation with the network of passive monitors was found (R = 0.69). Interference of NOz in traditional NO2 measurements was found to be small (0.9 ppb) when considered for 24-hr averages. The inference method was extended to qualitatively analyze long-term trends in Windsor. Comparison against a land-use regression model in Toronto showed similar overall trends, but the downtown core was underestimated considerably by the OMI-inferred map. While the presented inference method can simplify and increase the utility of OMI NO2 data, limitations remain as to the spatial and temporal resolution achievable.

Keywords: no2
atmospheric chemistry
atmospheric physics
remote sensing
Advisor: Evans, Greg J.
Brook, Jeffrey R.
Correlative Fiduciary Liability

The ultimate aim of this thesis is to demonstrate that the effect of applying a corrective structure to fiduciary obligations is edifying. Corrective justice is a bipolar relationship where each of the poles refers to individuals conceptually linked through the legal relationship between them. Because corrective justice is bipolar, the upshot of such an approach ought to result in the promise of greater integrity and clarity flowing from a renewed interest in the relationship between fiduciary and principal. Underlying this polishing of the fiduciary relationship is the long-held ambition for the fiduciary relationship not to suffer from ambiguity as a symptom of its expansion beyond the sphere of trusts.

Keywords: Private Law
Fiduciary
Advisor: Weinrib, Ernest
Effects of Very Preterm Birth on Brain Structure in Mid-childhood

Children born prematurely exhibit a broad range of neuroanatomical abnormalities. The aim of this study was to investigate the long-term effects of very preterm birth on brain volume (cortical and subcortical), cortical thickness and surface area. The participants were 25 children born very preterm (<32 weeks gestational age) without significant post-natal medical sequelae and 32 term-born children between 7 and 10 years of age. Neuroanatomical measures were derived from an automated pipeline. The results suggest a pattern of decreased brain volume, surface area and cortical thickness for children born preterm and the relation between subcortical gray volume and total brain volume differed between groups. The cortex was significantly thinner for children born preterm than term-born children in focal regions of the parietal and temporal lobes. Therefore, even without significant postnatal medical sequelae, very preterm children still exhibit structural differences that persist into middle childhood.

Keywords: preterm
brain structure
MRI
cortical thickness
Advisor: Taylor, Margot
Nonrigid Registration of Dynamic Contrast-enhanced MRI Data using Motion Informed Intensity Corrections

Effective early detection and monitoring of patient response to cancer therapy is important for improved patient outcomes, avoiding unnecessary procedures and their associated toxicities, as well as the development of new therapies. Dynamic contrast-enhanced magnetic resonance imaging shows promise as a way to evaluate tumour vasculature and assess the efficacy of new anti-angiogenic drugs. However, unavoidable patient motion can decrease the accuracy of subsequent analyses rendering the data unusable. Motion correction algorithms are challenging to develop for contrast-enhanced data since intensity changes due to contrast-enhancement and patient motion must somehow be differentiated from one another. A novel method is presented that employs a motion-informed intensity correction in order to facilitate the registration of contrast enhanced data. The intensity correction simulates the presence or absence of contrast agent in the image volumes to be registered in an attempt to emulate the level of contrast-enhancement present in a single reference image volume.

Keywords: image registration
contrast-enhanced imaging
DCE-MRI
kidney
Advisor: Martel, Anne L.
Rhodium-catalyzed Addition of Arylboronic Acids to Nitriles: Application in the Synthesis of Unsymmetrical Polysubstituted Pyridines

Investigations pertaining to the rhodium(I)-catalyzed addition of arylboronic acids to (arylsulfonyl)acetonitriles were undertaken. The resulting carbon-carbon bond forming reaction has led to the efficient synthesis of novel stereoselective (Z)-β-sulfonylvinylamines, which upon acidic hydrolysis, afford useful β-keto sulfones possessing a diverse range of aryl and sulfonyl substituents. The synthetic utility of these (Z)-β-sulfonylvinylamines was subsequently explored by generating the corresponding 1-aza-allyl anion equivalents under basic conditions. This interesting anionic intermediate was then introduced to various α,β-unsaturated systems to produce a diverse array of functionalized pyridine derivatives including unsymmetrical polysubstituted pyridines.

Keywords: rhodium
nitrile
pyridine
unsymmetrical
1-aza-allyl anion
β-keto sulfone
β-sulfonylvinylamine
Advisor: Lautens, Mark
Visual Odometry Aided by a Sun Sensor and an Inclinometer

Due to the absence of any satellite-based global positioning system on Mars, the Mars Exploration Rovers commonly track position changes of the vehicle using a technique called visual odometry (VO), where updated rover poses are determined by tracking keypoints between stereo image pairs. Unfortunately, the error of VO grows super-linearly with the distance traveled, primarily due to the contribution of orientation error. This thesis outlines a novel approach incorporating sun sensor and inclinometer measurements directly into the VO pipeline, utilizing absolute orientation information to reduce the error growth of the motion estimate. These additional measurements have very low computation, power, and mass requirements, providing a localization improvement at nearly negligible cost. The mathematical formulation of this approach is described in detail, and extensive results are presented from experimental trials utilizing data collected during a 10 kilometre traversal of a Mars analogue site on Devon Island in the Canadian High Arctic.

Keywords: Aerospace
Robotics
Visual Odometry
Sun Sensor
Advisor: Barfoot, Timothy D.
Online Music Knowledge: The Case of the Non-musician

Five cases of ‘non-musicians’ learning how to make music were used to explore the information practice of users in the domain of music to support the design of music information systems and platforms. In all five cases, the use of online music knowledge was situated within a larger process of self-directed learning, as well as the larger socio-musical world of the non-musicians. Effective access to and use of available resources is paradoxically predicated on a non-musician’s ability to articulate their information needs using terms with which they are not yet familiar. The findings articulate the information practice of non-musicians as being characterized by the emergent nature of their information needs and the exploratory nature of their information practice. In particular, the user’s socio-musical world, learning or knowledge trajectories, as well as their modes of learning offer an innovative approach to understanding and anticipating music information needs.

Keywords: self-directed learning
music information retrieval
information practice
user study
music knowledge
system design
music library
digital library
Advisor: Ratto, Matthew
Predicting Kinase Substrates using Conservation of Local Motif Density

Short linear motifs (SLM) play critical roles in cell signaling and are associated with important biochemical events such as phosphorylation, glycosylation, and other post translational modifications. The primary aim of this thesis is to develop a new computational method (“ConDens”) to predict kinase substrates by assessing the evolution of phosphorylation SLM’s in a novel manner. This method could predict yeast Cdc28 kinase substrates that were not confidently detected by several other prediction methods published in literature and was demonstrated to be generalizable to other kinases. Genome-wide predictions experiments with this method also revealed potentially interesting novel substrates of Mec1, Prk1, PKA, and CKII.

Keywords: phosphorylation
cdk1
Advisor: Moses, Alan
Aerodynamic Shape Optimization of a Blended-wing-body Aircraft Configuration

Increasing environmental concerns and fuel prices motivate the study of alternative, unconventional aircraft configurations. One such example is the blended-wing-body configuration, which has been shown to have several advantages over the conventional tube-and-wing aircraft configuration. In this thesis, a blended-wing-body aircraft is studied and optimized aerodynamically using a high-fidelity Euler-based flow solver, integrated geometry parameterization and mesh movement, adjoint-based gradient evaluation, and a sequential quadratic programming algorithm. Specifically, the aircraft is optimized at transonic conditions to minimize the sum of induced and wave drag. These optimizations are carried out with both fixed and varying airfoil sections. With varying airfoil sections and increased freedom, up to 52% drag reduction relative to the baseline geometry was achieved: at the target lift coefficient of 0.357, a drag coefficient of 0.01313 and an inviscid lift-to-drag ratio of 27.2 were obtained.

Keywords: aerodynamic shape optimization
blended-wing-body
computational fluid dynamics
computational aerodynamics
aerodynamics
Advisor: Zingg, David W.
Criminalization of Marital Rape in Kenya

Marital rape is not a criminal offence in Kenya. This thesis argues that criminalization of marital rape in Kenya is a necessary but insufficient means of addressing marital rape. I shall analyze the Kenyan legal framework and the international framework. The analysis of the international framework shall be focused on the Convention on the Elimination of all forms of Discrimination against Women (CEDAW). I shall undertake a comparative analysis of how South Africa and Zimbabwe have addressed marital rape. I will examine the benefits and limitations of criminal law in addressing marital rape. I will argue that an examination of the wrongful gender stereotypes of married women is essential to create effective and holistic remedies; that wrongful gender stereotypes of married women violate their rights to equality and non-discrimination and the right to be free from violence.

Keywords: Marital Rape
Kenya
Criminalization
Advisor: Cook, Rebecca J.
Oral Health-related Quality of Life in an Aging Canadian Population

The purpose of the study is to describe the impact of oral health-related quality of life (OHRQoL) on the lives of pre-seniors and seniors living in Nova Scotia, Canada. This cross-sectional study involved 1461 participants, grouped by age (pre-seniors [45-64] and seniors [65+]) and residential status (long-term care facility [LTC] or community). OHRQoL was measured using the 14-item Oral Health Impact Profile questionnaire. Approximately one in four pre-seniors and seniors reported at least one OHRQoL impact ‘fairly/very often’. Of those residing in the community, pre-seniors (28.8%) reported significantly more impacts than seniors (22.0%). Logistic regression revealed that for the community dwelling sample, those who were dissatisfied with their teeth or dentures were 5.16 times more likely to report an impact ‘fairly/very often’, which was the strongest indicator. Among the LTC sample, those who have poor perceived mouth health were 9.87 times more likely to report an impact.

Keywords: oral health-related quality of life
elderly
aging
seniors
Advisor: Lawrence, Herenia P.
Evaluation and Characterisation of the Thermal Grill Apparatus for Spinal Cord Injury Patients

Patients suffering from central neuropathic pain have thermal sensory deficits within the painful area. Prior research proposed that the loss of thermal sensation in regions of central neuropathic pain may reflect similar central nervous system interaction between warm and cold sensory inputs that underlie the Thermal Grill Illusion (TGI) in which burning pain is felt while reduced warm/cold sensations are reported. This work presents a portable and reliable device that was used to systematically evaluate the characteristics of the TGI in healthy individuals. The results suggest that the spatial distribution of the warm and cool stimuli significantly affected the quality of perceived TGI. Additionally, simultaneous tactile and thermal stimulation was shown to be significantly less painful than thermal stimulation alone. A high correlation was also seen in the subject‘s TG intensity scores and their cold pain threshold. These results are useful for future TGI studies for central neuropathic pain.

Keywords: central neuropathic pain
thermal grill
spinal cord injury
Advisor: Popovic, Milos R.
DNA Methylation Changes at Promoters of Endothelial Cell-enriched Genes during in vitro Differentiation

This study examined DNA methylation patterns at promoters of endothelial cell (EC)-enriched genes during differentiation of mouse ES cells towards the EC. We have previously shown that eNOS, CD31, VE-cadherin and vWF, which have an EC-enriched pattern of gene expression are differentially methylated between EC and vascular smooth muscle cells. Given that differential promoter DNA methylation is functionally important we asked when these distinct patterns are established. Using the hanging drop method to differentiate ES cells, followed by FACS, we isolated early (EB-day4 VEGFR2-positive) and late (EB-day7 CD31-positive) endothelial progenitor cells. Though current paradigms suggest that lineage-restricted genes are methylated in ES cells, we show heterogeneous promoter DNA methylation. We show DNA demethylation at the CD31 promoter in EB-day 7 CD31-positive cells. In contrast, the eNOS promoter is still heavily methylated in EB-day 7 CD31 positive cells compared with murine EC where there is no DNA methylation.

Keywords: endothelial cell
epigenetics
DNA methylation
differentiation
Advisor: Marsden, Philip A.
Classification of Ordinary Chondrite NWA 6514 and Pb-Pb Chondrule Chronology

This study presents a petrographic description and a classification of ordinary chondrite NWA 6514 and aims to establish the first high-precision Pb-Pb age of a single ordinary chondrite chondrule. Furthermore, the distribution of different isotopic Pb signatures among chondritic components will be investigated by Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS). This study shows that NWA 6514 can be classified as a highly unequilibrated (subtype 3.10) L or LL chondrite that has experienced moderate terrestrial weathering (W2) and a low degree of shock (S2). The LA-ICP-MS measurements suggest that radiogenic Pb signatures have been locally preserved in chondrules. However, the Pb isotopic compositions of leaches from a large chondrule obtained by thermal ionization mass spectrometry show an anomalous distribution that indicates the presence of an exotic Pb component. The best estimate for the chondrule formation age is a model age of the last leach (4566.8 ± 2.6 Myr).

Keywords: Meteorite classification
Chondrule chronology
Advisor: Davis, Donald W.
Quantification of Vehicle-induced Turbulence on Roadways Using Computational Fluid Dynamics Simulation

Turbulence is a significant factor in near-road air quality, as it affects the initial dilution, dispersion, and the ultimate fate of pollutants. This study used computational fluid dynamics simulations to model the turbulent kinetic energy (TKE) on roadways, focusing on vehicle-induced turbulence. TKE was shown to decay with different power-law exponents depending on vehicle types; vehicle speeds and winds affect TKE; and thermal impacts are negligible. It was found that TKE is superimposed for vehicles in series; TKE does not dissipate far laterally, and the side-by-side interactions are not significant regardless of the directions. Thus, TKE for different traffic compositions may be expressed as a sum of the contribution from each type of vehicle. Insights gained in this study may enable the quantification of TKE for various traffic scenarios based on TKE values of single vehicle of different types, and simplify the TKE estimations in regional air quality models.

Keywords: Computational Fluid Dynamics
Vehicle-induced Turbulence
Advisor: Jia, Charles Q.
Gong, Sunling