VictorJuiz/thesis huggingface dataset:
Application of Gaussian Moment Closure Methods to Three-Dimensional Micro-Scale Flows

A parallel, block-based, three-dimensional, hexahedral finite-volume scheme with adaptive mesh refinement has been developed for the solution of the 10-moment Gaussian closure for the modelling of fully three-dimensional micro-scale, non-equilibrium flows. The Gaussian closure has been shown to be a more effective tool for modelling rarefied flows lying within the transition regime than the Navier-Stokes equations, which encounter mathematical difficulties approaching free-molecular flows, and is computationally less expensive than particle-based methods for flows approaching the continuum limit. The hyperbolic nature of the moment equations is computationally attractive and the generalized transport equations can be solved in an accurate and efficient manner using Godunov-type finite-volume schemes as considered here. Details are given of the Gaussian closure, along with extensions for diatomic gases and slip-flow boundaries. Numerical results for several canonical flows demonstrate the potential of these moment closures and the parallel solution scheme for accurately predicting fully three-dimensional non-equilibrium flow behaviour.

Keywords: CFD
Micro-scale
Advisor: Groth, Clinton P. T.
The Effects of Helium on Deuterium Retention in Tungsten Under Simultaneous Irradiation

The trapping behavior of deuterium and helium in polycrystalline tungsten (PCW) under D+-only, He+-only, sequential and simultaneous irradiation was studied as a function of incident ion fluences and irradiation temperature. Deuterium implanted at 300 and 500 K gets trapped at surface adsorption sites, vacancy-related traps, or extended defects. No deuterium was trapped for 700 K implantations. Results were affected by tungsten-carbide impurities in PCW specimens. It is suggested that He trapping occurs via the formation of He clusters, at impurity sites, or as part of He-vacancy complexes. For sequential implantations, D and He were found to de-trap each other, with He impeding the trapping of D when implanted first at 300 K. Under simultaneous irradiation a decrease in D inventories was observed for all cases, and a re-distribution of He to higher energy traps (associated with He-vacancy complex formation) was observed for higher fluences and temperatures.

Keywords: Fusion
Tungsten
Deuterium
Helium
Plasma Surface Interactions
Simultaneous irradiation
Advisor: Haasz, Anthony A.
Davis, James W.
Effect of Selective/Non-selective COX Inhibition on Rosuvastatin-Mediated Protection from Ischemia-reperfusion Induced Endothelial Dysfunction in the Human Forearm Vasculature

Statins can act as preconditioning agents against ischemia reperfusion (IR)-injury through a mechanism involving cyclooxygenase (COX)-2 and the upregulation of prostaglandin synthesis. The following study investigated the effect of selective and non-selective COX inhibition on rosuvastatin-mediated protection against IR-induced endothelial dysfunction in the human forearm vasculature. Healthy volunteers were randomized to drugs with different COX-inhibiting properties: 81mg aspirin (OD), 325mg aspirin (OD), 400mg ibuprofen (QID), 200mg celecoxib (BID) or placebo. A single dose of 40mg rosuvastatin was also administered 24-hours prior to IR. Endothelial function before and after IR was assessed by measuring flow-mediated dilation of the radial artery. Our results show that 81mg and 325mg aspirin (more COX-1 selective), 400mg ibuprofen (similar selectivity for COX-1/2) and 200mg celecoxib (COX-2 selective) all effectively abolished statin-mediated protection against IR-induced endothelial dysfunction in the forearm (2-way ANOVA, p<0.05). These findings indicate that even partial COX-2 inhibition is sufficient to attenuate statin-induced preconditioning.

Keywords: statin
ischemia reperfusion injury
preconditioning
cox
Advisor: Parker, John
Acoustic Streaming Pump for Microfluidic Applications

A prototype acoustic streaming pump for microfluidic applications was developed. A novel integration scheme was devised based on the acoustic reflector concept. Numerical simulations were conducted to predict the flow patterns around the transducer. Ultrasound transducers using P(VDF-TrFE) as the piezoelectric element were fabricated using lithography-based microfabrication technology. Silicon channels were fabricated using anisotropic etching. A heat-press bonding technique was adopted to bond the transducers with the silicon chips using CYTOP fluoropolymer as the adhesive. The piezoelectric transducers were characterized to have a resonance frequency of 82 MHz. Micro-PIV experiments were performed in the near and far-fields of the ultrasonic transducer/pump. The near field experiments showed complex flow patterns that could enhance mixing. Estimates of the pumping pressure were obtained using transient flow velocities in the far-field. Conservative estimates indicate the total back pressure the micropump can pump against is 39 Pa. Future research directions were suggested.

Keywords: Microfluidics
MEMS
Ultrasound
Piezoelectric
Advisor: Guenther, Axel
Sinclair, Anthony
Quantifying the Influence of Crown Size on Mechanical Wood Properties in White Spruce (Picea Glauca)

Conceptual models of wood formation suggest that trees with large crowns produce low quality wood, but few studies have explicitly examined the relationship between crown size and wood quality. In this study, I examine how crown size influences the strength and stiffness of wood, as measured by Modulus of Elasticity (MOE) and Modulus of Rupture (MOR), using 42- and 72-old year plantation white spruce (Picea glauca) from Ontario, Canada. Mechanical properties were determined from 10x10x140 mm mini-clear samples (n=657), selected from a radial gradient at three heights within the stems. Non-linear mixed-effects models showed that strength and stiffness significantly decreased with crown size, and that MOE and MOR were best predicted by cambial age and crown ratio. The results suggest that the models could be used in conjunction with remotely sensed data to identify high quality timber prior to harvest.

Keywords: Wood Quality
Crown Size
White Spruce
Forestry
Advisor: Caspersen, John
Patterns of Post-zygotic Isolation among Genetically Diverse Strains of Caenorhabditis briggsae and Caenorhabditis sp. 9

The study of speciation is key to understanding the origins of biodiversity. Model organisms, with a host of genetic and molecular tools, are crucial to dissecting the genetics of speciation. Crosses between the recently-discovered Caenorhabditis sp. 9 and the well-known C. briggsae produce fertile F1 hybrid females, opening the door to genetic studies of speciation for the first time within the genus. I crossed eight different isogenic strains of C. briggsae reciprocally with six inbred lines of C. sp. 9 to investigate: Haldane’s rule, systematic asymmetries in hybrid viability, and whether genetic variation for hybrid viability segregates within each species. Results of these crosses confirm Haldane’s rule and demonstrate strong asymmetric parent-of-origin effects. Furthermore, I observed genotype-dependent differences in the number of F1 hybrid progeny. This provides evidence for genetic variation for hybrid viability within both species, allowing insights into the genetic forces driving the evolution of incompatibility loci.

Keywords: evolution
speciation
Caenorhabditis
Haldane's rule
Darwin's corollary to Haldane's rule
DMI
intraspecific variation
Caenorhabditis briggsae
Caenorhabditis sp. 9
Advisor: Cutter, Asher
ASPIRE: Adaptive Service Provider Infrastructure for VANETs

User desire for ubiquitous applications on-board a vehicle motivates the necessity for Network Mobility (NEMO) solutions for Vehicular Ad-Hoc Networks (VANETs). Due to the dynamic topology of VANETs, this approach incurs excessive infrastructure cost to maintain stable connectivity and support these applications. Our solution to this problem is focused on a novel NEMO-based Network Architecture where vehicles are the main network infrastructure. Within this Architecture, we present a Network Criticality-based clustering algorithm, which adapts to mobility changes to form stable self-organizing clusters of vehicles and dynamically builds on vehicle clusters to form more stable Mobile Networks. Simulation results show that the proposed method provides more stable clusters, lower handoffs and better connectivity compared to popular density-based vehicle clustering methods. In addition, they confirm the validity of the proposed Network Architecture. The proposed method is also robust to channel error and exhibits better performance when the heterogeneity of vehicles is exploited.

Keywords: VANET
Clustering
Network Architecture
NEMO
Criticality
vehicular network
Mobile Network
network mobility
Service Provider
vehicle communication
Advisor: Leon-Garcia, Alberto
The Fanconi Anaemia Protein FANCJ is Involved in the Alternative Lengthening of Telomeres (ALT) Mechanism in Human Cells

Approximately 15% of human cancers utilize a recombination-based mechanism termed Alternative Lengthening of Telomeres (ALT) to maintain the lengths of their telomeres. The Fanconi anaemia protein FANCJ localizes to telomeric foci in human ALT cells, but not in telomerase-positive or primary cells. Telomere-associated FANCJ frequently localizes with FANCD2 and BRCA1, and primarily localizes to ALT-associated PML nuclear bodies. Depletion of FANCJ in human ALT cells causes the loss of BRCA1 at telomeric foci and a decrease in telomeric repeat DNA content primarily as a result of the loss of the brightest telomeric repeat DNA foci. In contrast, depletion of the FANCD2 results in increased telomeric repeat DNA synthesis and this is suppressed upon the codepletion of FANCJ. Together, data from this study suggest that FANCJ is required for telomeric repeat DNA synthesis in human ALT cells, which may or may not be dependent on BRCA1, and FANCD2 restrains this synthesis.

Keywords: Fanconi anaemia
Telomeres
Cancer
FANCJ
Advisor: Meyn, M. Stephen
Development and Characterization of a Controlled Expression System for Osteogenic Genes

Current treatment methods for non-union bone defects present problems. The objective of this study was to genetically engineer primary and immortalized cell types to express osteogenic molecules BMP2, RUNX2, OSX, or VEGF in a doxycycline dose-dependent manner for tissue regeneration. Coding cDNA sequences for all four factors were sub-cloned into the pRTS-1 expression plasmid and transfected into HUCPVCs, RBMCs, ROS cells. Electroporation was the most effective method of transfection for all cells but stably transfected cells could only be established for RBMCs and ROS cells. Cells achieved maximum expression within 72hours of induction and returned to basal levels after 18 days. Enhanced osteogenic bioactivity was only observed upon activation of BMP-2. The tight regulation of the pRTS-1 system allowed for a controlled gene expression. Future transplantation experiments using these engineered RBMC and ROS cells in vivo will evaluate the usefulness of the dox-inducible gene expression system in bone defects.

Keywords: BMP-2
Controlled Expression
pRTS-1
Transfection
Advisor: Ganss, Bernhard
Davies, John Edward
An Analysis and Recommendations for Improvements to the Oakville Trafalgar Memorial Hospital Emergency Department

In an attempt to improve patient care and compensate for growing demands, new tools and strategies are under constant review and development for improvements and analyses. Advances in technology, analyses of the use of public funding, acquiring additional capital, and adapting practical tools and resources from other industries are commonly considered to improve the situation. This work provides a series of recommendations and analyses of solutions for emergency healthcare developed with Oakville Trafalgar Memorial Hospital (OTMH) in mind that can be scaled and adapted for all hospitals and emergency departments. Solutions applied were analyzed for their effect on patient care and health care providers. Recommendations for future improvements and work have been made and numerous concepts were drawn from previous studies and applications in other industries, and adapted for OTMH. It is concluded that the solutions had a positive effect on both the staff experience as well as patient throughput.

Keywords: health care
management
Advisor: Paradi, Joseph C.
Controlling Iron Defeciency Anemia and Preventing Calcium Deficiency in Bangladesh Children: A Novel Approach Using a Multi-micronutrient Powder (MNP) Formulation

Iron deficiency anemia (IDA) and calcium deficiency affect millions of children globally. Sprinkles is a multi-micronutrient powder (MNP) that has successfully treated anemic infants and can be modified to include additional micronutrients. The efficacy for treating IDA and preventing calcium deficiency requires evaluation due to potential nutrient interactions. We assessed the efficacy of Sprinkles MNP including iron with and without calcium on hemoglobin (Hb) response in 100 anemic rural Bangladeshi infants for 2 months. Sprinkles MNP with and without calcium resulted in a significantly higher Hb concentrations in both groups (P<0.0001 and P<0.0001). However, infants who received Sprinkles MNP without calcium had a significantly higher change in Hb concentration (P=0.024) and rate of recovery from anemia (P=0.008). No differences in socio-demographic or dietary characteristics were documented between groups. Although both groups had an improvement in Hb status, the antagonistic interaction between iron and calcium requires further study.

Keywords: Iron Deficiency Anemia
Calcium Deficiency
Nutrient-Nutrient Interaction
Micronutrient Powder
Advisor: Zlotkin, Stanley H.
Role of TAp73 in the Transformation of Mouse Ovarian Surface Epithelium

Tumour suppressor 73 (Trp73) gene shares structural and functional homology with p53. Trp73 encodes multiple isoforms with opposing effects. The TAp73 isoform is a transcription factor and is classified as a tumour suppressor where as the DNp73 isoform is a putative oncogene. Imbalance of the two opposing isoforms has been reported in human malignancies including ovarian cancer. TAp73 deficiency results in a dramatic increase in the DNp73 isoform, mimicking the altered isoform balance observed in human ovarian cancer. The effects of TAp73 deficiency in mouse OSE cells were assessed. TAp73 deficiency is not sufficient to induce ovarian cancer in mice. However, TAp73 deficiency compromises cellular proliferation in OSE cell lines. Furthermore, expression of p73 isoforms and epithelial markers is altered in TAp73 deficient cell line. Further studies are needed to determine if TAp73 deficiency in conjunction with other molecular alterations can mediate transformation of OSE cells leading to ovarian cancer.

Keywords: p73
OSE
ovarian cancer
Advisor: Jurisicova, Andrea
Synthesis of Cyclic α,β-unsaturated Ketones via a Divergent Aldehyde Allylation and Ring-closing Metathesis Method

Montmorillonite-catalyzed allylation of aldehydes with potassium allyltrifluoroborate is a convenient method for the synthesis of homoallylic alcohols. This chemistry was applied to various unsaturated aldehydes, and the homoallylic alcohols produced were used as common intermediates for two separate but related synthetic routes to α,β-unsaturated ketones. In the first route, oxidation of the alcohol to the ketone was followed by base-catalyzed isomerization of the olefin to the α,β-unsaturated ketone. This was subjected to ring closing metathesis conditions to afford the cyclic enone of ring size n. In the other route, ring-closing metathesis was performed first, followed by oxidation of the alcohol and isomerization of the olefin to the cyclic enone of ring size n+1.

Advisor: Batey, Robert A.
Structural Studies of the Inhibitory Role of Tctex-1 for the Microtubule-associated RhoGEF Lfc

Lfc is a guanine nucleotide exchange factor (GEF) for RhoA and is negatively regulated by its association with the microtubule array. Tctex-1, a light chain subunit of the dynein motor complex, was identified as an Lfc-interacting protein in a yeast two-hybrid screen. In mouse embryonic fibroblast (MEF) cells, over-expression of Tctex-1 represses Lfc-induced actin stress fiber and focal adhesion complex formation. Here, we present biochemical evidence obtained from a real-time, nuclear magnetic resonance (NMR)-based assay indicating that the microtubule exerts its inhibitory effect on Lfc through a mechanism that is dependent on the presence of Tctex-1. We also present NMR structure data showing that Lfc and the dynein intermediate chain (DIC) bind to different surfaces of Tctex-1. The biochemical and structural data together support a model in which Lfc is recruited to the microtubules through the dynein cargo adaptor function of Tctex-1, resulting in inhibition of Lfc function.

Keywords: biochemistry
structural biology
molecular biology
nuclear magnetic resonance
protein-protein interaction
small GTPases
guanine nucleotide exchange factors
dynein motor complex
Advisor: Ikura, Mitsuhiko
Rottapel, Robert
Engineering the (S)-3-O-Geranylgeranylglyceryl Phosphate Synthase (GGGPS) Monomer from its Dimer

(S)-3-O-Geranylgeranylglyceryl Phosphate Synthase (GGGPS) is a TIM (βα)8 barrel protein found in Archaea and the enzyme catalyzing the first step in the biosynthesis of archaeal membrane lipids. The TIM (βα)8 barrel protein fold is thought to have evolved by duplication and fusion of (βα)4 half barrels. We propose that the GGGPS has also evolved from (βα)4 half barrels. One way to test this hypothesis is to generate putative half-barrels experimentally. GGGPS from Archaeaglobus fulgidus, is a dimer of (βα)8 barrels. Thus, before constructing half barrels, a stable monomer is needed to be engineered. Introducing three substitutions into the dimer interface formed the GGGPS monomer. AUC showed ~50 % of the protein is in the monomeric state. CD experiments confirmed that the engineered protein was properly folded but had decreased thermal stability. In an enzymatic assay, the monomeric GGGPS protein proved as active as the WT protein on a subunit basis.

Keywords: Protein Engineering
TIM Barrel evolution
Archaea
GGGPS
Archaeal Membrane Lipid Synthesis
Advisor: Pai, Emil F.
The Role of the Dopamine D, Receptors in Cue-induced Reinstatement of Nicotine-seeking Behaviour

Dopamine D3 receptors (DRD3) are implicated in relapse to drugs. The current study investigated the role of DRD3 in cue-induced reinstatement of nicotine-seeking in rats. Rats were trained to lever-press for intravenous infusions of nicotine, associated with the illumination of a cue-light, under a fixed-ratio schedule of reinforcement. Following extinction of the behaviour, where lever pressing had no consequences, reinstatement testing was performed by reintroduction of the cues after systemic or local administration (into discrete brain areas) of the DRD3 selective antagonist SB277011-A. Systemic antagonism of DRD3 significantly attenuated cue-induced reinstatement of nicotine-seeking. The same effect was observed upon infusions of SB277011-A into the basolateral amygdala or the lateral habenula, but not the nucleus accumbens. The current findings implicate DRD3 in cue-induced reinstatement of nicotine, delineate some of the neural substrates underlying this role and support a potential for using selective DRD3 antagonists for the prevention of relapse to smoking.

Keywords: dopamine D3 receptors
addiction
brain
drug discovery
motivation
Advisor: Foll, Bernard Le
Le, Anh Dzung
Light Localization in Coupled Optical Waveguides

This thesis analyzes different light localization phenomena in waveguide arrays. We report on the observation of quasi-Bloch oscillations, a new type of dynamic localization in the spatial evolution of light in curved, coupled optical waveguides. The delocalization and final relocalization of an optical beam in a waveguide array is shown by spatially resolving the optical intensity at various propagation distances. Through comparison to different structures, quasi-Bloch oscillations are shown to be robust beyond the nearest-neighbor tight-binding approximation.

Keywords: Waveguide array
Bloch Oscillation
Dynamic Localization
Quasi-Bloch
Curved waveguide
Advisor: Aitchison, J. Stewart
Poon, Joyce
Learning Deficits after Experimental Subarachnoid Hemorrhage (SAH)

Survivors of subarachnoid hemorrhage (SAH) often have learning and memory deficits. This study tested the hypothesis that SAH in rats is associated with similar deficits and that they are due to neuronal injury in the hippocampus. SAH was induced in rats. Behaviour was investigated in the Morris water maze and brain injury by microscopy. Rats with SAH had deficits in spatial learning and working memory and had significantly more fluoro-Jade- and TUNEL-positive neurons in the hippocampus, cerebral cortex and cerebellum. Microthromboemboli in microvessels were more frequent in brains of rats with SAH and deficits there was vasospasm of the anterior and middle cerebral arteries. The amount of cell death in the hippocampus did not appear to be sufficient to cause the observed in the Morris water maze. This suggests that other factors such as dysfunction of neurotransmission or other pathology in hippocampal pathways might contribute to the impairment.

Keywords: SAH
Learning
Stroke
Memory
Biomedical
Neuroscience
Advisor: Macdonald, Robert Loch
The Effect of Temperature on the Chronic Hypoxia-induced Changes to pH/CO2-sensitive Fictive Breathing in the Cane Toad (Bufo marinus)

This study examined the effects of temperature and chronic hypoxia (CH) on pH/CO2- sensitive fictive breathing, and central pH/CO2 chemosensitivity, in cane toads (Bufo marinus). Toads were exposed to CH (10% or 15% O2) or control conditions (21% O2) for 10 days at either room temperature (controls), 10°C or 30°C following which in vitro brainstem-spinal cord preparations were used to examine central pH/CO2-sensitive fictive breathing (i.e., motor output from respiratory nerves which is the neural correlate of breathing). A reduction in artificial cerebral spinal fluid (aCSF) pH increased fictive breathing frequency (fR) and total fictive ventilation (TFV). Cold temperature reduced and hot temperature increased fR and TFV under control conditions. CH attenuated fictive breathing independently of temperature. Additional experiments in which the aCSF temperature was varied indicate that the effects of temperature acclimation result from neural plastic changes within respiratory control centres in the brain.

Keywords: Control of Breathing
Temperature
Hypoxia
Amphibian
in vitro brainstem-spinal cord
Advisor: Reid, Stephen G.
Metabolic Modeling of Spatial Heterogeneity of Biofilms in Microbial Fuel Cells

Microbial fuel cells (MFCs) are alternative energy resources that generate electricity from organic matter, where microorganisms such as the Geobacter species oxidize organic waste and transfer electrons to an electrode. Mathematical models are used to study biofilm processes, in hopes of developing MFCs into commercial applications. Existing biofilm models are based on Nernst-Monod type expressions, and are restricted to studying extracellular electrochemical/microbiological components, separated from the metabolic behavior of microorganisms. In this thesis, a model was developed combining extracellular biofilm conditions, with the intracellular metabolic fluxes of microorganisms under spatial heterogeneities (electron donor/acceptor levels) across the biofilm. This model predicts biofilm processes under varying extracellular conditions (presence/absence of NH4+, shear stress in continuous mode MFCs), and intracellular conditions (ATP maintenance fluxes); and also provides a preliminary evaluation of the pH changes across the biofilm. A sensitivity analysis based on the cell density and the biofilm conductivity was also conducted.

Keywords: Microbial fuel cells
Metabolic Modeling
Advisor: Mahadevan, Radhakrishnan