VictorJuiz/thesis huggingface dataset:
Using Thermal Profiles of Cemented Paste Backfill to Predict Strength

Measurement of the strength development of Cemented Paste Backfill in laboratory cast cylinders does not replicate the in situ strengths of CPB in mine stopes. The mass of CPB in a filled stope is large and temperature rises due to the heat of hydration of the cementing materials, thus accelerating the gain in strength, relative to laboratory specimens stored at ambient temperature. The purpose of this study was to determine the impact on strength development when CPB test cylinders were subjected to a temperature profile mimicking that in a large mass, such as a mine stope. Also, maturity (the integral of time and temperature during hydration of the CPB) was compared to actual strengths, and the maturity – strength concept used in concrete technology was applied. It was found that the strength- maturity relationship was applicable to CPB once the base line or datum temperature was adjusted.

Keywords: Cemented Paste Backfill
Thermal Aspect
Maturity
Advisor: Hooton, Robert Douglas
Grabinsky, Murray
A Microfluidic System for Mouse Embryonic Stem Cell Culture and Microenvironment Control

The embryonic stem cell (ESC) microenvironment contains various localized physical and biochemical cues to direct cell fate. Current approaches for microenvironmental regulation rely on restricting cell behaviour to control endogenous signals such as secreted ligands. This report presents a microfluidic device that can directly manipulate the removal of autoregulatory ligands from culture and control the activation of Signal Transducer and Activator of Transcription-3 (Stat3) in ESCs. Specifically, the response of Stat3 was measured under diffusive and convective mass transfer regimes. A Brownian dynamics algorithm was also developed to simulate ligand transport and predict cellular response under these conditions. Stat3 activation under perfusion culture was found to depend on flow rate and axial distance in the flow direction. Long-term perfusion also allowed for the formation of a sustained gradient of Stat3 activation that led to selective loss of ESC pluripotency. These results demonstrate the utility of microfluidic culture for stem cell bioengineering applications.

Keywords: stem cells
mathematical modelling
microfluidics
mESC self-renewal
autocrine signalling
stochastic receptor-ligand interaction dynamics
Advisor: Zandstra, Peter W.
Guenther, Axel
Growth Factor Dependent Co-receptor Function of Neuropilins in Breast Carcinoma

Neuropilin (Nrp) overexpression is correlated with increased invasion and metastasis in many epithelial carcinomas including breast cancer. The exact molecular mechanism of how Nrp promotes cancer cell tumourigenicity is unknown. Nrp is a coreceptor for VEGF, hepatocyte growth factor (HGF), and also shown to activate TGF-beta on tumour cells. We hypothesize that binding of Nrp potentiates growth factor (GF) signalling and results in GF-dependent aggressive phenotype in breast cancer. In the current study, Nrp was shown to potentiate HGF signalling in vitro in MCF-7 cells by increasing phosphorylation of the MET receptor. However MDA-MB-231 cell line failed to show any differences after Nrp knockdown, due to constitutively activated MET. Nrp is also shown to increase the number and size of cancer stem cell (CSC) enriched mammospheres through NF-kB pathway activation. These results suggest a novel function of Nrp in CSCs and identify it as a potential target for effective cancer therapy.

Keywords: breast cancer
cancer stem cells
Neuropilin
Growth factors
Advisor: Prud'homme, Gerald
Clinical Translation of Neuro-regenerative Medicine in India: A Study on Barriers and Strategies

The prevalence of neurodegenerative disease in India is rising. Regenerative medicine (RM) is being developed to treat these conditions. However, despite advances in RM application for neurological disorders (NeuroRM), there is a lack of research on clinical translation of NeuroRM technologies in developing countries. Given that India is one of the first nations to translate in this field, much can be learned on challenges and solutions arising during translation. This study identifies stakeholders involved in such translation and outlines roles of each; it describes India’s regulatory environment concerning NeuroRM translation; and discusses the impact of collaboration in clinical translation. Twenty-three face-to-face interviews with clinicians, researchers and policy-makers within India were undertaken and transcripts subjected to thematic analysis. The study demonstrates that clinical translation of NeuroRM within India is taking place robustly, it identifies barriers and good practices being adopted, and provides recommendations based on participants’ experiences.

Keywords: regenerative medicine
qualitative research methods
global health
neuroscience
Advisor: Abdallah, Daar
A High Capacity Reversible Multiple Watermarking Scheme - applications to Images, Medical Data, and Biometrics

Modern technologies have eased the way for adversaries to bypass the conventional identity authentication and identification processes; hence security systems have been developed to a great extent for protection of privacy and security of identities in different applications. The focus of this thesis is digital watermarking, security and privacy, as well as the ability to employ electrocardiogram as a method to enhance the security and privacy level. A high capacity reversible multiple watermarking scheme is introduced to mainly target the medical images. Furthermore, the use of ECG biometric signals in the form of the embedded watermark is studied. Experimental results indicate that the reversible data hiding scheme outperforms other approaches in the literature in terms of payload capacity and marked image quality. Results from the ECG mark embedding also show that no major degradation in performance is noticeable compared to the case where no watermarking is needed.

Keywords: Reversible watermarking
integer wavelet transform watermarking
Advisor: Hatzinakos, Dimitrios
Clonal Expansion of B and T lymphocytes Defines a Spectrum of Monoclonal Lymphocytosis

Monoclonal B lymphocytosis (MBL) has been recognized as a novel diagnostic condition. This study aims at the identification of clonal lymphocytosis in the patients with asymptomatic lymphocytosis. A total of 203 patients were evaluated for clonal B and T lymphocytosis by using flow cytometry and multiplex-PCR. Among them clonal B- or T-cells were detected in 54.2% of the cases, of which 38.4% were clonal B-cells and 15.8% were clonal T-cells cases. By immunophenotype, MBL was classified into the chronic lymphocytic leukemia (CLL) type (21.7%) and non-CLL-type (7.4%). Flow cytometry analysis and cell counts were used to determine the size of clonal population, and the data indicate that MBL and CLL are present in a continuous spectrum of clonal expansion. The findings may contribute to the current understanding of MBL and evaluation of incidental lymphocytosis. Further studies are required to evaluate clonal progression as a precursor stage of lymphoid malignancy.

Keywords: Clonal lymphocytosis
Monoclonal B lymphocytosis (MBL)
Chronic Lymphocytic Leukemia
Clonal T-cell lymphocytosis
Lymphocytosis
Advisor: Wang, Chen
Development of a High-order Finite-volume Method for Unstructured Meshes

The development of high-order solution methods remain a very active field of research in Computational Fluid Dynamics (CFD). These types of schemes have the potential to reduce the computational cost necessary to compute solutions to a desired level of accuracy. The goal of this thesis has been to develop a high-order Central Essentially Non Oscillatory (CENO) finite volume scheme for multi-block unstructured meshes. In particular, solutions to the compressible, inviscid Euler equations are considered. The CENO method achieves a high-order spatial reconstruction based on the k-exact method, combined with hybrid switching to limited piecewise linear reconstruction in non-smooth regions to maintain monotonicity. Additionally, fourth-order Runge-Kutta time marching is applied. The solver described has been validated through a combination of high-order function reconstructions, and solutions to the Euler equations. Cases have been selected to demonstrate high-orders of convergence, the application of the hybrid switching method, and the multi-block techniques which has been implemented.

Keywords: Computational Fluid Dynamics
High-Order
Central Essentially Non-Oscillatory
Unstructured Mesh
Fluid Dynamics
Advisor: Groth, Clinton P. T.
Exploring the Role of the Foraging Gene on Egg-laying Preferences in Drosophila melanogaster

Egg-laying decisions can have significant fitness consequences. In female Drosophila melanogaster, egg-laying involves foraging-like behaviour. Natural allelic variation in foraging (for) underlies the rover/sitter foraging behaviour polymorphism found in D. melanogaster. for encodes a cGMP-dependent protein kinase (PKG) where rovers have higher for-PKG transcript levels and PKG activity than sitters. Interestingly, the orthologue of for in nematodes (egl-4) affects both egg-laying and foraging behaviours. When given a choice between low- and high-nutrient patches, rovers preferentially lay more eggs on the low-nutrient patches while sitters and a sitter mutant prefer high-nutrient patches. Using the neuronal driver elav-GAL4, rover-like preferences were rescued in sitter flies. Compared to sitters, rovers have higher fitness on a sub-optimal substrate which may explain the observed egg-laying preferences. By studying the link from genes to behaviour, this study provides insight to the evolutionary basis and maintenance of behaviour.

Keywords: Oviposition
Drosophila
Advisor: Fitzpatrick, Mark
Developing Methods for Studying the Fate and Transport of Contaminants in Snow and Ice

Snow and ice can significantly affect the environmental fate of contaminants. This thesis presents a laboratory technique for measuring mercury in metamorphosing snow, and a computer model for organic contaminants in a seasonally ice covered ocean. The laboratory method to study the fate of mercury in snow was developed using laboratory-made snow of controlled composition made in a cold room, aged and melted, with mercury quantified in air, snow, and dissolved and particulate fractions of the melt water. It was found that the method gave a mass balance for mercury, and can be used to look at mercury fate in snow representative of different environments. The fugacity based fate and transport model for organic contaminants in a seasonally ice-covered ocean was parameterized to Barrow Strait, and tested against environmentally derived net air to sea water fluxes. It was found that the model could reproduce these environmental data.

Keywords: mercury
snow
multimedia fate and transport model
environmental chemistry
environmental chemistry
Advisor: Wania, Frank
Characterizing the Pyocin Activity of Diverse Pseudomonas aeruginosa Isolates

Pseudomonas aeruginosa is a versatile Gram-negative pathogen that can infect a diversity of immunocompromised patients. Interest in alternatives to traditional antibiotics has inspired our investigation of R- and F-type pyocins as novel therapeutics. These phage tail-like bacteriocins are produced by P. aeruginosa to kill competing strains via pore formation in target cells. We aimed to characterize the diversity of pyocins and bacteriophages generated by diverse P. aeruginosa strains so as to identify pyocins of therapeutic value. Strategies to delineate pyocin and phage activities included physical methods, the modulation of pyocin regulation, and antibody-based detection of tail-like pyocins. We have identified the dominance of R- and F-type pyocins in impacting P. aeruginosa populations and revealed a small number of strains producing particularly potent pyocins. In addition, the co-regulation of phages and pyocins, the dependence of pyocins on pili for activity, and the striking diversity of pyocin susceptibility have all been recognized.

Keywords: Pseudomonas
Bacteriophage
Phage therapy
Pyocin
Advisor: Davidson, Alan R.
Transgenerational Effects of Early Exposure to Soy Isoflavones on Reproductive Health and Bone Development in CD-1 Mice

Previous studies showed that early exposure to soy isoflavones resulted in improved bone mineral density (BMD) and bone quality that resulted in stronger bones in CD-1 mice. This study investigated whether the benefits to bone health are transferred to second generation (F2) females and if there are any adverse effects on reproductive health. First generation (F1) female CD-1 mice received subcutaneous injections of the isoflavones daidzein (DAI) and genistein (GEN) or corn oil from postnatal day (PND) 1 to 10 or 21. F1 and F2 treated-females experienced earlier pubertal onset and lengthened anogenital distance but only F1 had reduced fertility, histological abnormalities in the uterus and ovaries, and altered estrous cycling. F2 had higher BMD and stronger bones at 4 months of age. In conclusion, early life exposure to soy isoflavones compromise reproductive function but confer a transgenerational benefit to bone development in CD-1 mice.

Keywords: soy isoflavones, early development, CD-1 mice
Advisor: Ward, Wendy
Cracking Behaviour of Steel Fibre Reinforced Concrete Containing Conventional Steel Reinforcement

It is well known that crack spacings and widths can be reduced with the addition of steel fibres to a concrete mix. However, test data for the tensile behaviour of steel fibre reinforced concrete members containing conventional steel reinforcement (R/FRC members) are scarce relative to those of reinforced concrete (RC) specimens and fibre reinforced concrete (FRC) specimens without reinforcing bars. In this research program, uniaxial tension tests were conducted on 12 RC and 48 R/FRC specimens in order to observe cracking and tension stiffening behaviour. The parameters under observation were fibre volumetric content, fibre length and aspect ratio, conventional reinforcement ratio and steel reinforcing bar diameter. ‘Dog-bone’ tension tests and bending tests were also performed in order to determine tensile material properties. It was discovered that currently available crack spacing formulae significantly overestimate the average stabilized crack spacing for R/FRC; therefore, an improved crack spacing model was developed and proposed.

Keywords: concrete
fibre
steel
reinforced
sfrc
frc
crack
cracking
tension
tension stiffening
experimental
model
rebar
r/frc
uniaxial
Advisor: Vecchio, Frank J.
Bullying, Ethnic Discrimination or Both? A Phenomenological Study of the Experiences of Immigrant Adolescents

The present study explored the experiences of victimization and immigration among immigrant youth in the Peel region in Ontario, Canada. Victimization included the experiences of bullying and ethnic discrimination in the school environment. The study utilized a phenomenological approach to investigate how immigrant youth interpreted their experiences and whether they identified victimization as bullying, ethnic discrimination or both. The effects of victimization on adaptation and acculturation were also explored. Results from individual interviews of six youth (ages 16 or 17) indicated that immigrant youth viewed bullying and discrimination as separate constructs. Themes that emerged from the interviews included the importance of language proficiency; the role of peer affiliations; and factors associated with resiliency. It was evident through their descriptions that immigrant youth face unique challenges, which include adjusting to a new culture and country of residence, establishing a new social circle, and gaining comfort in utilizing the English language.

Keywords: bullying
discrimination
immigrant
adolescents
Advisor: Mishna, Faye
Accelerated Cytotoxicity Mechanism Screening of 4-Aminobiphenyl in an in vitro Hepatocyte Inflammation Model

4-Aminobiphenyl is an aromatic amine compound that is present in cigarette smoke, diesel exhaust, cooking oil fumes and dye intermediates. It is a well-known human bladder carcinogen and liver carcinogen in experimental animals that is metabolically activated by liver CYP1A1/2. We have used the “Accelerated Cytotoxicity Mechanism Screening” (ACMS) techniques to analyze the molecular cytotoxic mechanisms of 4-aminobiphenyl. Hepatocyte exposure to an inflammatory system significantly increased hepatocyte susceptibility to 4-aminobiphenyl. 4-Aminobiphenyl- induced cytotoxicity and lipid peroxidation were both prevented by altering cellular redox status and with the addition of antioxidants. Toxicity was increased with the depletion of hepatocyte GSH levels and by inhibiting N-acetyltransferase. These results will provide more insight into the cytotoxic and genotoxic mechanisms of 4-aminobiphenyl and also suggest that inflammation may be responsible for an increase in arylamine carcinogenesis.

Keywords: Cytotoxicity
Aromatic Amine
Advisor: O'Brien, Peter J.
Alternative Test Methods for Evaluating Fly Ash for use in Concrete

Fly Ash was tested in relation to its ability to mitigate alkali-silica reaction, its contribution to strength, electrical resistance and heat release with the aim of recommending improvements to fly ash specifications. ASTM C 1567 accelerated mortar bar test results were in agreement with an expansion limit of 0.10 % at 14 days. A non-standard alkali leaching test showed that with high alkali fly ashes as replacement level increases the amount of alkalis leached increases while prism expansions decrease. Measures of pozzolanic activity can be improved by measuring against non-pozzolanic fillers, This requires high replacement levels to reduce statistical variability. Isothermal calorimetry tests showed that high calcium fly ashes can lead to delays in hydration, these delays can be reduced by calcium hydroxide additions. Calcium sulphate additions can also improve hydration.

Keywords: fly Ash
concrete
alkali-silica reaction
ASR
Advisor: Hooton, Robert Douglas
Biophysical Studies of the First Nucleotide Binding Domain of SUR2A

ATP-sensitive potassium (KATP) channels have crucial roles in several biological processes. KATP channels possess four regulatory sulfonylurea receptors. The SUR proteins are members of the ubiquitous ATP-binding cassette (ABC) superfamily. However, unlike most ABC proteins, SURs do not transport substrates but function strictly as regulators of KATP channel activity. Currently, studies into the molecular basis by which various mutations in SUR2A cause disease are highly limited. This is primarily a consequence of poor solubility of isolated SUR2A NBDs, as is typical for many eukaryotic NBDs. By employing structure-based sequence alignments and biophysical studies, we determined domain boundaries for SUR2A NBD1 that enabled, for the first time, NMR studies of NBD1. Our biophysical studies demonstrate that the isolated SUR2A NBD1 is folded and exhibits differential dynamics upon ATP binding activity. Additional studies are now possible to examine the effects of disease-causing mutations on structure, dynamics, and interactions of NBD1.

Keywords: ABC Transporters
NMR
Nucleotide Binding Domain
Sulfonylurea Receptor
KATP Channels
ATP
Advisor: Kanelis, Voula
Genetic Modifiers of Caffeine Consumption and Risk of Myocardial Infarction

The variability in caffeine consumption and inconsistencies among studies linking caffeine to heart disease may be explained by genetic variation. Caffeine antagonizes adenosine receptors with downstream effects on dopamine and serotonin. The objectives of this thesis were to determine whether the DRD2 957C>T or HTR2A 102C>T polymorphisms are associated with caffeine consumption or modify the association between coffee consumption and risk of myocardial infarction (MI). DRD2 genotype was associated with caffeine consumption among non-smokers and CYP1A2 -163C allele carriers. HTR2A genotype was associated with caffeine consumption among non-smokers and subjects with the ADORA2A TT genotype. Neither polymorphism modified the association between coffee consumption and risk of MI; however, a significant coffee x HTR2A interaction was seen among subjects with the CYP1A2 -163C allele. The results suggest caffeine’s reinforcing effects may be mediated by the dopamine and serotonin receptors and implicate serotonin in caffeine’s effect on risk of MI.

Keywords: Caffeine
Gene-Environment Interaction
Myocardial Infarction
Coffee
HTR2A
DRD2
Serotonin Receptor 2A
Dopamine D2 Receptor
Polymorphism
Advisor: El-Sohemy, Ahmed
Topics in Designing Low Thermal Expansion Lattices at the Microscale

Microscale bi-material lattices with near zero thermal expansion are designed to create a thermally stable optical surface for applications in a space telescope. To facilitate the design, the thermal expansion of a unit cell with spacers is derived analytically and validated via finite element studies. Predicting the lattice behaviour also requires knowledge of the constituent properties. To this end, molecular dynamics simulations are performed to determine the thermal expansion and recrystallization behaviour of aluminum and titanium thin films, and nanoindentation experiments are conducted to extract their elastic-plastic properties. Unit cell configurations giving near zero thermal expansion are obtained through iterative analysis. The resulting designs are analyzed and validated via finite element simulations and shown to exhibit long term stability.

Keywords: Low Thermal Expansion Lattices
Amorphous Materials
Molecular Dynamics
Nanoindentation
Advisor: Steeves, Craig A.
Investigating the Role of Alternative Oxidase in Nicotiana tabacum during Light Acclimation

Photosynthetic electron transport produces ATP and NADPH which support carbon fixation by the Calvin Cycle. To avoid over-reduction of the electron transport chain, plants must balance absorption and consumption of light energy. Mitochondrial alternative oxidase (AOX) is a non-energy-conserving electron sink, making it an ideal candidate to oxidize excess reductant and regulate chloroplastic redox state. Wild-type (WT) and transgenic Nicotiana tabacum lines with enhanced or suppressed AOX protein levels were grown under low light (LL) and moderate light (ML). LL-grown plants were also shifted to ML. AOX transcript and protein levels were enhanced in WT plants under ML. Chlorophyll fluorescence, gas exchange, and contents of chlorophyll, carbohydrate, and malondialdehyde were measured. Lack of AOX protein decreased Photosystem II (PSII) quantum efficiency and CO2 assimilation rates while enhancing PSII excitation pressure compared to WT. These findings suggest a role for AOX in mediating the chloroplast-mitochondrion relationship during acclimation to higher irradiance.

Keywords: Alternative oxidase
Photosynthesis
Respiration
Nicotiana tabacum
Chloroplast-mitochondrion relationship
Advisor: Vanlerberghe, Greg
Experimental Study of the Microstructural Evolution of Chemical Vapor Deposited (CVD) Nickel upon Annealing

The effect of annealing conditions on the microstructure evolution of CVD nickel was investigated systematically in the present study by differential scanning calorimetry, optical microscopy and transmission electron microscopy (TEM), upon both ex-situ and in-situ annealing. TEM observation revealed the as-deposited CVD nickel possessed a bi-modal grain structure, with large columnar grains embedded in nanocrystalline matrix. Ultrafine and nano growth twins were present as well as multiply twinned grains with five-fold symmetry. Microstructure observation upon annealing showed that grain growth did not occur until annealing at 400ºC. Detwinning was observed at 400ºC and higher temperatures. The ultrafine and nano twins tended to transform into dislocation cell structures and this phenomenon was driven by the excess free energy associated with the high density of grown-in twin boundaries. The five-fold twinned grains were found to be thermally stable up to 600ºC. The hardness was observed to decrease with increasing annealing temperature.

Keywords: CVD nickel
detwinning
five-fold twinned particles
bi-modal grain size distribution
Chemical vapor deposition
Advisor: Wang, Zhirui