VictorJuiz/thesis huggingface dataset:
Parallel Anisotropic Block-based Adaptive Mesh Refinement Algorithm For Three-dimensional Flows

A three-dimensional, parallel, anisotropic, block-based, adaptive mesh refinement (AMR) algorithm is proposed and described for the solution of fluid flows on body-fitted, multi-block, hexahedral meshes. Refinement and de-refinement in any grid block computational direction, or combination of directions, allows the mesh to rapidly adapt to anisotropic flow features such as shocks, boundary layers, or flame fronts, common to complex flow physics. Anisotropic refinements and an efficient and highly scalable parallel implementation lead to a potential for significant reduction in computational cost as compared to a more typical isotropic approach. Unstructured root-block topology allows for greater flexibility in the treatment of complex geometries. The AMR algorithm is coupled with an upwind finite-volume scheme for the solution of the Euler equations governing inviscid, compressible, gaseous flow. Steady-state and time varying, three-dimensional, flow problems are investigated for various geometries, including the cubed-sphere mesh.

Keywords: AMR
adaptive mesh refinement
finite volume
anisotropic
block based
unsteady
parallel
binary tree
body fitted
multi block
3D
three dimensional
CFD
computational fluid dynamics
Euler equations
Advisor: Groth, Clinton P. T.
Generation of Anti-CD133 Human Synthetic Antibodies as Tools for Exploring CD133 Function

Two synthetic human antibody fragments against the human pentaspan membrane protein CD133 were isolated using a novel selection method involving direct selections on cells coupled with Illumina deep sequencing. The antibody fragments were isolated through a PCR-based recovery strategy developed in the lab and subsequently converted to full length IgGs. Termed RW01 and RW03, the antibodies bind separate epitopes on CD133 and are able to detect the protein using various molecular techniques. Finally, experiments have shown that RW01 and RW03 treatment affect the stability of CD133 on live cells. Additional experiments are required to reveal the specific epitope recognized by each antibody, which organelles they are targeted to when internalized and whether they have an effect on cellular differentiation or cellular viability. In addition to the therapeutic potential of these antibodies, they will have many applications towards expanding our knowledge concerning the CD133 protein and its role in cancer.

Advisor: Moffat, Jason
Sidhu, Sachdev
A Functional, Immunological, and Physiological Comparison of Cold-water Immersion for Recovery from High-intensity Intermittent Exercise

Cold-water immersion (CWI) is a common recovery modality used to facilitate restoration of pre-exercise muscle force generation and soreness following high-intensity exercise. Although it is commonly used by athletes and commonly studied in sport science, evidence is equivocal regarding its efficacy. We compared 4 CWI protocols (10 or 30 minutes at 10 or 20°C) of different durations and temperatures with passive rest for their effects on drop jump and squat jump height, inflammation (IL-6, IL-10, IL-8, MPO, IL-1β, TNFα, IFNγ, GM-CSF, IL-2), and ratings of soreness/impairment following high-intensity intermittent sprint-exercise. CWI for 10 minutes at 10°C promoted restoration of force generation, while CWI for 30 minutes at 10°C was associated with lower ratings of soreness/impairment, but higher plasma IL-8 and MPO at 2 hours post-exercise. Overall, minor functional benefits of CWI for 10 minutes at 10°C were observed, while longer duration CWI protocols may increase post-exercise inflammation.

Keywords: Recovery
Exercise-induced inflammation
Skeletal Muscle
Exercise
Advisor: Wells, Gregory D.
Framework for the Integration of a Parameterized Logit Captivity Model for Morning Commuting in the Greater Toronto and Hamilton Area with an Agent Based Dynamic Traffic Micro Simulation

This thesis proposes a framework that combines a mode choice model with a large scaled agent-based multimodal traffic microsimulation. Both components are discussed with respect to their development as separate entities. The mode choice model uses a formulation that explicitly considers latent modal captivity despite using conventional travel survey data. An existing multimodal microsimulation traffic assignment model used in the study area is enhanced and partially calibrated for use with the MATSIM traffic assignment tool. Both of the components are then tested independently in terms of statistical and behavioral validity and a conceptual procedure to test the implications of the mode choice model on mode switching behaviour within the traffic assignment model is presented. Other applications of both the travel assignment model and mode choice model are discussed. In order for the framework to become operational, further development with respect to the traffic assignment model is required.

Keywords: Transportation
Travel Behaviour
Microsimulation
Transit
Advisor: Habib, Khandker
Filling the Gap:How Should ESA vs. SOCAN Interact with the New Making Available Right

The main issue that this thesis deals with is the interaction between the Supreme Court of Canada’s recent decision in ESA vs. SOCAN and the new making available right introduced in Canada’s Copyright Modernization Act. The thesis analyzes the approach of the Supreme Court of Canada in ESA vs. SOCAN and examines the legislative history of the making available right on both global and domestic levels. A conclusion drawn by this thesis is that, the scope of the communication right in Canada’s Copyright Act should be expanded after the introduction of the making available right in order to cover a variety of digital transmissions including downloading, P2P file sharing and other interactive transmissions.

Keywords: copyright
the making available right
Advisor: Drassinower, Abraham
A 1.25GS/s 8-bit Time-interleaved C-2C SAR ADC for Wireline Receiver Applications

Many wireline communication systems are moving toward a digital based architecture for the receiver that requires a front-end high-speed ADC. This thesis proposes a two-level time-interleaving topology for realizing such an ADC, comprising front-end time-interleaved sub-rate track-and-holds each followed by a sub-ADC which is further time-interleaved to a slower clock frequency. The design, implementation and measurement of the 1.25GS/s sub-ADC fabricated in 65nm CMOS technology is presented. The SAR architecture is chosen for its low power and digital friendly nature along with an unconventional C-2C capacitive DAC implementation for higher bandwidth. The time-interleaved C-2C SAR ADC runs with a 1.0V supply, and it has a full input range of 1.0V\subscript{pp} differential, while consuming 34mW. The SNDR is 39.4dB at low frequency and the FOM is 360fJ/conv-step and 428fJ/conv-step at low and Nyquist input frequencies respectively. The SNDR is 34dB at 4GHz input frequency, which is more than 6 times the Nyquist frequency.

Advisor: Carusone, Anthony Chan
Sex Differences in the Connectivity of the Subgenual Anterior Cingulate Cortex: Implications for Pain Habituation

Women exhibit greater habituation to painful stimuli than men. The neural mechanism underlying this sex difference is unknown. However, pain habituation has been associated with pain-evoked activity of the subgenual anterior cingulate cortex (sgACC), implicating a connection between the sgACC and the descending pain antinociceptive system. Therefore, the thesis hypothesis was that women have stronger connectivity than men between the sgACC and the descending antinociceptive system. Healthy subjects provided informed consent. 3T MRI images included anatomical diffusion-weighted imaging for structural connectivity analyses (SC) with probabilistic tractography and resting-state functional images for functional connectivity (FC) analyses. Women had stronger sgACC FC with nodes of the descending pain modulation system (raphe, PAG) and the medial thalamus. In contrast, men had stronger sgACC FC with nodes of the salience/attention network (anterior insula, TPJ) and stronger sgACC SC with the hypothalamus. These findings implicate a mechanism for pain habituation and its associated sex differences.

Keywords: Functional magnetic resonance imaging
Diffusion tensor imaging
Sex differences
Pain
Habituation
Subgenual anterior cingulate cortex
Neuroscience
Functional connectivity
Structural connectivity
Neuroimaging
Clinical
Programming
Descending pain modulation
Advisor: Davis, Karen
Association of Five-factor Model Personality Traits with Prefrontal Cortical Activation during Motor Inhibitory Control

The ability to control one’s behaviour is a fundamental cognitive function subserved by the prefrontal cortex (PFC). Whereas the neural basis of inhibitory control is reasonably well-established, the possible influence of individual differences in personality on cortical activity associated with this ability remains largely unexplored. The present study obtained self-report ratings of Five-Factor Model personality traits from 42 healthy adults while hemodynamic oxygenation in the PFC was recorded during a Go/No-Go task. Results indicated that Neuroticism, Agreeableness and Openness to Experience were associated with attenuated activity in the lateral PFC, a region critical for emotion regulation and behavioural control, whereas Extraversion and Conscientiousness were associated with greater activation in these regions. Activity within the medial PFC, an area linked to task engagement and self-monitoring, shared a positive association with Agreeableness. These findings provide important insights into how neural systems supporting inhibitory control may be affected by individual differences in personality.

Keywords: Personality
Inhibitory Control
Prefrontal Cortex
fNIRS
Five-Factor Model
Advisor: Ruocco, Anthony Charles
The Neural Correlates of Working Memory in Children and Adolescents with ASD and the Effects of Cognitive Load

Research on the neural bases of cognitive deficits in autism spectrum disorder (ASD) has shown that working memory (WM) difficulties are associated with abnormalities in the prefrontal cortex. However, few studies have examined the impact of cognitive load on WM and its neural underpinnings in children and adolescents. We used fMRI and an n-back task with four levels of difficulty to compare the cortical activation patterns associated with WM in children with and without ASD across cognitive load. Findings revealed impaired modulated activity as a function of cognitive load in prefrontal and parietal cortices in children with ASD relative to typical controls. Results suggest that children with ASD rely mainly on posterior brain regions associated with lower-level visual processing, whereas controls showed activity in frontal lobes related to the classic WM network. Findings will help guide future longitudinal work by localizing areas of vulnerability to developmental disturbances.

Keywords: working memory
autism spectrum disorder
cognitive load
fMRI
Advisor: Taylor, Margot
The Characterization of a Novel Cell Migration Gene with a Maternal-effect and Temperature Sensitivity in Caenorhabditis elegans

The nematode Caenorhabditis elegans is a unique resource for the study of axon guidance and cell migration. Genetic data collected from C. elegans research is integral to advancing our knowledge of genetic pathways that control axon and cell guidance, such as the UNC-6/netrin pathway, within a developing organism. In this thesis, I describe the characterization of ev821, an allele isolated from a screen for novel guidance mechanisms or components of the UNC-6 pathway. Furthermore, I show that ev821 is a maternal-effect and temperature-sensitive mutation with defects in phase 2 of distal tip cell migration in the C. elegans hermaphrodite, as well as ray-1 displacement and a blister phenotype in the C. elegans male. My research on ev821 could broaden our understanding of the mechanisms driving UNC-6 guidance, and has the potential to identify unknown factors that act within or in parallel to the UNC-6 signaling pathway.

Keywords: Caenorhabditis
elegans
Migration
Maternal
Temperature
Distal
Advisor: Culotti, Joseph
Visualizing Protein Interactions at Supported Bilayer Surfaces

Understanding the mechanisms by which proteins act on membrane surfaces is fundamental if we are to exploit their capabilities or halt the progression of the diseases they are associated with. Arguably, the best way to study these interactions is by using techniques that can obtain molecular-scale information, in real time and under physiologically relevant conditions. Studying supported lipid bilayer systems with high spatial resolution tools, such as atomic force microscopy (AFM), and high temporal resolution techniques, such as polarized total internal reflection fluorescence microscopy (pTIRFM), allows us to meet these requirements [1]. The goal of this project is to use methods that are currently available and further their applications and capabilities to provide insight into the mechanisms by which amyloidogenic and antimicrobial peptides act on membranes.

Keywords: atomic force microscopy
polarized total internal reflection fluorescence
antimicrobial
amyloid
bilayer
order parameter
Advisor: Yip, Christopher M.
Social Anxiety Disorder: Behavioural Characteristics Associated with the Cortisol Stress Response

The present study evaluated the cortisol stress response and its relationship to several behavioural measures in SAD participants. It is hypothesized that SAD participants will show an exaggerated cortisol response to the Trier Social Stress Test (TSST) and differing positive and negative affects compared to controls, as well as correlations between the two measures. SAD (n=12) and controls (n=12) underwent the TSST. Serial plasma cortisol samples were taken and self-report measures were completed. The plasma cortisol levels were numerically higher in SAD at all time points compared to controls but the difference was not statistically significant. Cortisol response correlated inversely with childhood emotional abuse (p=0.01) and directly with positive affect (p=0.02) in SAD participants. Furthermore, SAD participants reported greater negative affect (prior to and after TSST) and more frequent emotional abuse than controls. SAD is associated with changes in HPA axis activity and affective states that differ from controls.

Keywords: Social Anxiety
Stress
Cortisol
Advisor: Ravindran, Arun
Effects of Acute Aerobic Exercise on the Pharmacokinetics of the Anti-anxiety/Anti-depressant Drug Sertraline

This study examined the effects of 30 minutes of cycle exercise at 65% V̇O2max on the pharmacokinetics of the S.S.R.I. sertraline. Blood samples were taken over 48 hours from 14 healthy males (23.9±2.5 years, 80.3±12.6 kilograms) following oral ingestion of a single 100 mg dose of sertraline. Participants completed two sertraline trials separated by at least two weeks; one trial while resting and the other trial with exercise as described above. With exercise, the absorption rate constant and volume of sertraline in the central compartment decreased, while the elimination half-life increased. Maximum concentration, time of maximum concentration, and area under the curve were unchanged. Fitness level had little impact on the concentration of sertraline, as compartmental modeling was unchanged when relative V̇O2max was added as a covariate. However, controlling for participant body weight improved the model estimate. These results indicate that acute aerobic exercise has the potential to change the concentration of sertraline in vivo.

Keywords: Exercise
Sertraline
Physical activity
Pharmacokinetics
Anxiety
Depression
Mental health
Medication
Exercise pharmacology
Advisor: Jacobs, Ira
The Requirement for Oxygen in the Maturation and Secretion of Soluble urokinase Plasminogen Activator Receptor (uPAR)

TTumor hypoxia (poor oxygenation) adversely affects patient prognosis by promoting therapeutic resistance and an aggressive tumor phenotype. We aimed to understand how urokinase plasminogen activator receptor (uPAR), a cysteine-rich protein implicated in the malignant phenotype and poor patient prognosis, matures in hypoxia. We hypothesized that secretion of uPAR during hypoxia is conferred by a superior ability to form disulfide bonds without oxygen. A model and assay was established to monitor the oxygen-dependency of suPAR (a soluble secreted isoform of uPAR) folding and secretion. We found that suPAR maturation involves disulfide formation and N-linked glycosylation in normoxia. In anoxia, suPAR disulfide formation was impaired, but suPAR was nevertheless secreted. We propose that suPAR has low dependency on disulfide formation for efficient secretion in comparison to other disulfide-containing proteins. Mechanisms supporting protein expression during hypoxia may potentially be targeted to mitigate the adverse effects of tumor hypoxia and ultimately improve cancer therapy.

Keywords: Biochemistry
Oncology
Advisor: Koritzinsky, Marianne
Germany's Embrace of a Rescue Culture - A Comparison Between the Approaches Taken in Germany, Canada and the United States

An increasing number of restructuring proceedings in both the United States and Canada end in the liquidation of the debtor company. This might prejudice the rescue culture approach which is deeply rooted in both countries bankruptcy laws. At the very least, it is the expression of different economic circumstances and of a different creditors&rsquo; structure which has excited for a little over a decade. This thesis gives an overview of the different approaches available in Germany, Canada and the United States to rescue a debtor and explains what exactly is meant by a rescue culture policy. Furthermore, it examines the extent to which each legislator has embraced the rescue culture approach. Finally, it looks at the reasons and consequences of the above mentioned current North-American trend and examines the extent to which these developments may influence the outcome of restructuring proceedings in Germany.

Keywords: bankruptcy
insolvency
rescue culture
Germany
restructuring
chapter 11
CCAA
BIA
United States
Canada
insolvency plan proceedings
Advisor: Duggan, Anthony
Carbon and Nutrient Dynamics of Downed Woody Debris in a Northern Hardwood Forest

Downed woody debris (DWD) is a carbon-rich form of forest litter and plays a unique role in carbon and nutrient cycling. I present a novel modeling approach describing DWD decomposition and nutrient storage in a managed northern hardwood forest. The predicted half-life of DWD carbon was 7 years, less than previously observed in similar northern hardwood forests. A stage-based nutrient model indicated that harvest slash DWD was a net nitrogen and phosphorus sink for eight years following harvest and accumulated calcium during decay. Field observations of respiration and leaching supported model results with a respired C half-life of 8 years, while leached carbon export constituted 1.37% of the respired flux. DWD leachate carbon and nitrogen concentrations were 11× and 2× greater than from litter, respectively, and DWD leachate contributed disproportionately to soil C stocks. This work represents an expedient means of forecasting DWD abundance and partitioning carbon flux from DWD.

Keywords: downed woody debris
modeling
carbon
wood decay
wood respiration
dissolved organic carbon
leaching
nitrogen
hardwood
forestry
Advisor: Caspersen, John
The Relationship between Very Long Chain Plasma Ceramides and Anxiety in Coronary Artery Disease

Anxiety is a highly prevalent comorbidity in coronary artery disease (CAD) and confers increased risk of subsequent cardiac events and mortality. However, biological mechanisms of this relationship are not well understood. Ceramides are sphingolipids involved in inflammatory signaling and cell viability in the periphery and nervous system, and are implicated in pathophysiological mechanisms associated with anxiety. This study aimed to investigate relationships between plasma ceramide concentrations and anxiety symptomology as assessed by the Spielberger State-Trait Anxiety Inventory trait subscale (STAI-T) in CAD patients with linear regressions. High performance liquid chromatography coupled electrospray ionization tandem mass spectrometry was used to assay sphingolipid species. Plasma C22:0 ceramide (β=-0.232, p=0.018) concentrations and 8 other species of sphingolipids (SM18:0, SM20:1, C18:0, C20:0, C18:1, DHC22:0, LacC22:0, LacC24:1) were negatively correlated with STAI-T score when controlling for gender, BMI, and CES-D. Findings suggest specific sphingolipids to be potential markers for anxiety severity in CAD.

Keywords: anxiety
coronary artery disease
ceramide
biological markers
mood
inflammation
sphingolipid
Advisor: Lanctôt, Krista
Cholecystokinin in the C57BL/6J Mouse: Effects on Acoustic Startle Response and Anatomical Distribution in the Amygdala

Cholecystokinin (CCK) causes panic attacks in humans and increases fear-associated behaviours in rodents by way of CCK-B receptors. The aim of this thesis was to investigate the CCK system behaviourally and anatomically in C57BL6/J mice and to assess the suitability of CCK-IRES-Cre mouse lines for amygdala manipulation. The behavioural results failed to support the startle-activating effect of CCK-4 or the startle-inhibiting effects of CCK-B receptor antagonists, in spite of evidence showing CCK-4 induced activation of c-Fos in the central amygdala. The anatomical results show that CCK-8 expression in the basolateral amygdala (BLA) is comparable to the CCK mRNA expression pattern. These results suggest that viral manipulations in the CCK-IRES-Cre line will induce changes in endogenous CCK systems in the mouse amygdala.

Keywords: cholecystokinin
startle
amygdala
mouse
Advisor: Yeomans, John S.
The Impact of Pregnancy on Breast Cancer Survival in Women who Carry a BRCA1 or BRCA2 Mutation

Background: Young BRCA mutation carries with a history of breast cancer often inquire about the impact of pregnancy upon their risks of cancer recurrence and survival. Methods: We identified 128 BRCA carriers who were diagnosed with breast cancer while pregnant or who became pregnant after breast cancer diagnosis. Women were matched to 269 controls. Women were followed from the date of breast cancer diagnosis until the date of death. The Kaplan-Meier method and a left-truncated Cox proportional hazard model were used to estimate 15-year survival rates. Results: The adjusted hazard ratio associated with 15-year survival for women diagnosed with breast cancer who were or became pregnant after breast cancer diagnosis, compared to women who did not become pregnant was 0.76 (95% CI 0.31 to 1.91 p = 0.56). Conclusion: Pregnancy concurrent with or after a diagnosis of breast cancer does not appear to adversely affect survival among BRCA1/2 mutation carriers.

Keywords: Epidemiology
Survival
Oncology
Pregnancy
Advisor: Narod, Steven
Matrix Metalloproteinase-7 Degradation of Fetuin Blocks Fetuin-mediated Inhibition of Mineralization

Mechanisms underlying the association between atherosclerosis and periodontitis are not defined. Matrix metalloproteinases (MMPs) are increased in untreated periodontitis. Fetuin, a serum protein, inhibits vascular mineralization in humans. I hypothesized that MMP-7 affects fetuin function. In vitro mineralization was conducted based on methods developed by Hunter and colleagues. Mineralization was quantified using absorbance measurements (at 540 nm) of alizarin red bound to nascent crystals. Mineralization assays included intact MMP-3 and MMP-7-treated human and bovine fetuin (0-2 &mu;M).The inhibition of mineralization mediated by fetuin (2 &mu;M) was maximal at 3.5-4 hours. Transmission electron microscopy and electron diffraction analysis of crystals formed revealed the presence of hydroxyapatite. SDS-PAGE demonstrated that MMP-7 is more effective in digesting fetuin than MMP-3. The inhibitory effect of fetuin on mineralization was more reduced by MMP-7 digestion compared to MMP-3. Fetuin inhibits mineralization in vitro and this effect is reduced by MMP-7 degradation.

Keywords: fetuin
periodontitis
Advisor: McCulloch, Christopher