VictorJuiz/thesis huggingface dataset:
Neutrophil Responses to Borrelia burgdorferi Infection are Aberrant in a Murine Model of Obesity Independent Diabetes

The incidence of both Lyme disease and diabetes is rising in many countries. Metabolic, cardiovascular and/or immune dysregulation associated with diabetes could alter host susceptibility to infection or inflammatory outcomes of infection by the Lyme disease pathogen,

Keywords: Borrelia burgdorferi
Diabetes
Lyme disease
Neutrophil
Advisor: Glogauer, Michael
Active Control of Separation on a Low Reynolds Number Airfoil Using Synthetic Jet Actuation

Wind tunnel experiments were used to study the effect of excitation amplitude and frequency on flow separation using synthetic jet actuation. A synthetic jet actuator was located near the leading edge of a NACA0025 airfoil at a chord-based Reynolds number of 100,000 and angle-of-attack of 10 degrees. Under these flow conditions, the boundary layer separated from the suction surface and failed to reattach. Low-frequency excitation was used to target flow instabilities, while high-frequency excitation was performed at time scales an order of magnitude smaller. Low-frequency excitation at the separated shear layer frequency was found to be the most effective technique for flow reattachment and drag reduction. The results suggested that flow reattachment depended on exceeding a threshold momentum coefficient that varied with excitation frequency. Furthermore, a local minimum in drag independent of excitation frequency was achieved when the momentum coefficient corresponded to an average jet velocity that matched the freestream velocity.

Keywords: Boundary layer
Flow control
Fluid mechanics
Synthetic jet
Advisor: Lavoie, Philippe
Maintenance Models for A Two-unit Series System

We consider two maintenance models for a two-unit series system with economic dependence, composed of one deteriorating expensive unit and one cheaper unit with low replacement cost. In the first model, we apply the opportunistic age-based preventive replacement policy with two different age thresholds for the expensive unit, in order to save the system set-up cost. In the second model, we use condition based maintenance (CBM) with multivariate Bayesian control chart to calculate the posterior probability of the expensive unit in its warning state. Also, the OM control limit is introduced to provide opportunities for its full inspection when the cheaper unit fails during sampling intervals. In both two models, the semi-Markov decision process (SMDP) algorithms are developed to find two optimal control limits and minimum average costs in a long-run horizon.

Keywords: Bayesian control chart
CBM
two-unit series system
Advisor: Makis, Viliam
Self-similar Based Time Series Analysis and Prediction

Fractals have been observed in many natural phenomena, and self-similarity is the most important statistical property of fractals. In the literature, the concepts of self-similarity and long-range-dependence (LRD), the increment process of a self-similar signal when the Hurst parameter is between 0.5 and 1, are often confused. On the other hand, the forecasting of many real-life signals exhibiting these properties is useful yet remains challenging. The objective of this thesis is to provide the readers with a clear and detailed explanation of the relevant concepts, and then to compare forecasting models (including FARIMA, HAR-RV, wavelet-based and average-VAR) for self-similar and LRD signals via real-life data (arterial blood pressure signals and volatility indexes). Numerical studies show that the four models perform similarly, while the FARIMA model is not recommended due to its time-consuming computation; and the performance of detecting large decrease is more accurate than that of detecting large increase.

Keywords: Fractals
Hurst parameter
LRD
Prediction
Self-similar
Advisor: Lee, Chi-Guhn
Abundances of Cavity-nesting Birds and their Dead Wood Resources in Closed-canopy Managed and Unmanaged Mixedwood Forests of Boreal Northeastern Ontario

In eastern boreal forests harvesting has displaced forest fires as the dominant disturbance, changing the natural age mosaic and reducing old-growth forest and standing dead wood supplies. Herein, eleven cavity nesting bird species and their habitats are compared among three stand histories (mid-rotation and mature regenerated stands (31-40 and 47-64 years post-harvest, respectively) and uncut forest (80+ years old)) surveyed in boreal mixedwood sites in northeastern Ontario. Yellow-bellied sapsucker, northern flicker and red-breasted nuthatch abundances were greater in uncut sites. While large live tree density and basal area increased with time since disturbance, a U-shaped pattern in large dead stem density was observed with old-cut sites having low supplies. Resource use based on breeding and feeding evidence was examined relative to availability and large dead trembling aspen was found to be important. Results indicate a diminished ability of post-harvest stands to supply similar habitat attributes to those of uncut forest.

Keywords: cavity nesters
forestry management
habitat suitability
mixedwood boreal forest
standing dead trees
woodpeckers
Advisor: Malcolm, R Jay
Phosphorylation of Neuralized at Serine 94 and 96 is Required for Notch Signaling during Drosophila Development

The Notch (N) signaling pathway defines one of the most fundamental signaling pathways that govern metazoan development. Neuralized (Neur) and Mindbomb (Mib), E3 ubiquitin ligases, are essential activators of the N pathway. They are responsible for ubiquitinating and mediating the endocytosis of N ligands, Delta (Dl) and Serrate (Ser). Whereas the functions of Neur are well characterized, how Neur itself is regulated is less well understood. I have identified several phosphorylated residues in Neur including residues S94 and S96. I have determined that phosphorylation of these residues is required for Neur function in embryonic neurogenesis and shown that overexpression of phosphorylation defective mutants leads to defects in sensory organ development in

Keywords: Delta endocytosis
Drosophila
lateral inhibition
Neuralized
Phosphorylation
third instar larvae
Advisor: Boulianne, L. Dr. Gabrielle
Dexmedetomidine as an Oral Premedication to Facilitate Mask Induction for General Anesthesia for Pediatric Dentistry

Dexmedetomidine is a relatively new alpha-2 agonist sedative agent that has many beneficial properties of a premedication. In this randomized clinical trial, oral dexmedetomidine was compared to oral midazolam for its efficacy in gaining cooperation for mask acceptance for induction of general anesthesia. Study subjects consisted of 28 children aged between 3-8 years and ASA I-II status who demonstrated poor cooperation at a prior dental appointment that were randomized to receive either dexmedetomidine 6 micrograms/kg or midazolam 0.7mg/kg 15 minutes prior to induction of anesthesia. The midazolam group had a significantly greater level of sedation but there was no significant difference in cooperation behavior during induction. No differences were found in time to discharge and there were no cases of hypotension and bradycardia requiring treatment. Under the context used in this study, oral dexmedetomidine can be a viable alternative oral premedication to midazolam prior to induction of GA.

Keywords: anesthesia
children
Dexmedetomidine
premedication
Advisor: Haas, A. Daniel
Design of a Comprehensive Evidence-based Laparoscopy Curriculum for Gynecology Residents

Simulation has become the cornerstone of teaching surgical procedures in all surgical subspecialties. Limited operating room resources and patient safety drive this trend. Gynecology lacks any standardized curriculum for teaching residents about surgical procedures, specifically laparoscopy. The purpose of this study was to design a comprehensive laparoscopic surgery curriculum for gynecology residents.The initial step of the study determined that there was a desire to implement a standardized laparoscopy-training program in obstetrics and gynecology residency programs. Residency Program Directors were surveyed as to their current methods of laparoscopy education as well as their interest in a standardized curriculum. The second step of the study used a Delphi technique to determine the elements that should be included in the standardized curriculum. Expert gynecologic laparoscopists performed the identified virtual reality tasks in order to set proficiency benchmarks in the final part of the study.

Keywords: Gynecology
Laparoscopy
Resident Education
Simulation
Surgical Curriculum
Advisor: Grantcharov, P Teodor
Joint Optimization of Manufacturing Quantities and Maintenance for a Deteriorating Production System

The aim of this thesis is to jointly optimize manufacturing quantities and maintenance policies for deteriorating production systems under the age-based and the condition-based maintenance. In the age-based maintenance model, the time to component failure, the preventive maintenance time and the corrective maintenance time are all assumed to be random variables. Lost sales due to repair delay are permitted and shortage costs are also considered. Preventive maintenance is performed after M production runs to restore the production facility to the 'good as new' condition. Corrective maintenance is performed upon failure. In the condition-based maintenance model, deterioration of the production facility is caused by ageing and environmental factors. The proportional hazards model is employed to evaluate the production facility's hazard rate and the condition-based control limit policy is used to minimize the average cost and guarantee the system's reliability. The deterioration is modeled as a semi-Markov decision process.

Advisor: Makis, Viliam
The Kalamazoo River Spill: Pipelines, Politics, and Economies of Knowledge

In July 2010, an oil pipeline ruptured in southwest Michigan, spilling approximately one million gallons of diluted bitumen (dilbit) from the Alberta tar sands into the Kalamazoo River. As the first major pipeline release of dilbit, the story of the Kalamazoo River spill is often cited in growing debates about dilbit pipeline projects in North America. This thesis provides an ethnographic account of the aftermath of the spill. Drawing on research conducted in Michigan in 2013, I examine how knowledge claims about the spill have been produced and mobilized in Michigan, focusing in particular on impacted residents' responses to the disaster. Informed by my involvement with environmental justice groups in Toronto, the thesis also explores how the story of the spill has been brought to bear on debates about a proposed pipeline project in Eastern Canada. Together, the chapters engage themes of risk, uncertainty, comparison, and knowledge production in environmental politics.

Advisor: Gilbert, Emily
Photoactive Lipid-gold Nanoconstructs for Molecular Imaging and Photo-therapy

The ubiquitous presence of porphyrins in nature is a testament to their versatility and utility. This thesis examines the utility of novel synthetic porphyrin derivatives, metallo-pyrolipid, as surface-enhanced Raman scattering (SERS) contrast agents for molecular imaging and monitoring of photodynamic therapy (PDT). Chapter 2 illustrates the refinement and optimization of manganese-pyrolipid gold nanoparticles for optical imaging of endothelial growth factor receptor overexpression in early stage lung cancer. In chapter 3, the use of palladium-pyrolipid gold nanoparticles as a new platform for SERS reporting photosensitizers is presented, allowing for real-time PDT and molecular imaging. These nanoparticles are demonstrated to be promising as photobleaching-dependent SERS reporting agents for PDT dosimetry. It is my hope that the studies presented in this thesis will set the stage for the development of simple and multifunctional SERS agents for medical imaging and therapeutic-use relevant to current unmet needs in medicine.

Keywords: Dosimetry
Molecular Imaging
Nanoparticle
PDT
Porphyrin
SERS
Advisor: Zheng, Gang
Improving the Mechanical Performance of Wood Fiber Reinforced Bio-based Polyurethane Foam

Because of the environmental impact of fossil fuel consumption, soybean-based polyurethane (PU) foam has been developed as an alternative to be used as the core in structural insulated panels (SIPs). Wood fibers can be added to enhance the resistance of foam against bending and buckling in compression. The goal of this work is to study the effect of three modifications: fiber surface treatment, catalyst choice, and mixing method on the compression performance of wood fiber-reinforced PU foam. Foams were made with a free-rising process. The compression performance of the foams was measured and the foams were characterized using Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), and X-ray computed tomography (CT). The foam reinforced with alkali-treated fibers had improved compression performance. The foams made with various catalysts shared similar performance. The foam made using a mechanical stirrer contained well-dispersed fibers but the reinforcing capability of the fibers was reduced.

Keywords: Compression behaviors
Foam density
Non-destructive test
Polymer-matrix composites
Polyurethane foams
Sandwich Panel
Advisor: Kortschot, T Mark
Particle Size Influences Fibronectin Internalization and Degradation by Fibroblasts

Particle size is a crucial factor that influences the fate and biological impact of particles and their surface proteins upon internalization. Here, using fibronectin-coated polystyrene nanoparticles and microparticles we examined the effect of particle size on degradation of fibronectin. Microparticle uptake depended primarily on integrins and actin filaments, while nanoparticle uptake relied mainly on lipid rafts and specifically on clathrin-mediated endocytosis. Further, biotinylated fibronectin when coated on microparticles underwent more intracellular processing than fibronectin coated on to nanoparticles. Thus, particle size affects actin and clathrin-dependent internalization, which in turn regulates intracellular fibronectin degradation.

Keywords: actin
clathrin
flow cytometry
receptor mediated endocytosis
toxicity
Advisor: McCulloch, A Christopher
Influence of Material and Technique on Occlusal Chipping of All-ceramic Molar Crowns

Objective: To evaluate the effect of material and fabrication technique on chipping behavior of all-ceramic molar crowns. Materials methods: A molar tooth with crown preparation was used to make fifty identical replicas from epoxy resin (n=10). Porcelain-fused-to-metal crowns (PFM) constituted the control group. There were four experimental groups: monolithic CAD/CAM lithium disilicate glass-ceramic crowns (LDG); Zirconia core 0.5 mm thick veneered with feldspathic porcelain added by hand-layering (ZVL), by heat-pressing (ZVP) and CAD/CAM milled lithium disilicate glass-ceramic veneer (CAD-on). All crowns were subjected to compressive cyclic loading at mesio-buccal cusp at 30° angle in universal testing machine. Results: All LDG and CAD-on crowns survived fatigue test; while all specimens of PFM, ZVP and ZVL groups failed at different stages of the 500,000 cycles fatigue test (P

Keywords: All-Ceramic
Chipping
Crowns
Fracture
Advisor: El-Mowafy, Omar
Expression Analysis of CTHRC1 in the Murine Embryo during Mid-facial Development

Collagen Triple Helix Repeat Containing 1 (CTHRC1) has been shown to regulate collagen expression, cell migration and interact with the Wnt/planar cell polarity pathway. Objective: Determine CTHRC1 expression in the midface of mouse embryos during craniofacial development. Methods: qPCR and immunohistochemistry were used to determine the expression of Cthrc1 at embryonic (E) days of development E8.5-E13.5. Results: CTHRC1 expression was in the notochord and neural tube at E8.5, mesenchyme of the midface at E9.5-E10.5 and areas of cartilage formation at E11.5-E13.5. Conclusions: The expression of CTHRC1 in the developing craniofacial region suggests a role of CTHRC1 in migration of cranial neural crest cells and in chondrocyte proliferation and differentiation. We speculate the functions of CTHRC1 during craniofacial development are via its interactions with the Wnt/PCP pathway, shown previously to play a significant role during craniofacial development. Support: Donald G. Woodside Fund and NSERC.

Keywords: craniofacial development
Cthrc1
Midface
Murine embryo
Advisor: Gong, Siew-Ging
Articulatory Compensation in Amyotrophic Lateral Sclerosis: Tongue and Jaw in Speech

This study investigated range, maximum speed, and duration of tongue and jaw movements in Amyotrophic Lateral Sclerosis (ALS; n=26) and healthy controls (n=16). The study objectives were to examine tongue and jaw movements and their interactions at varying stages of bulbar impairment. The patient group was classified based on the severity of bulbar impairment, via the measure of speaking rate. Kinematic measures were obtained from a sentence produced at individual's comfortable speaking rate and loudness. With ALS, the jaw movements decreased in maximum speed at a later stage of disease compared to the tongue. A positive correlation between range of tongue and jaw movements was observed at an early stage of disease. This correlation was lost at a later stage. Changes in jaw movements may be a compensatory response to tongue impairment. The findings of this study contribute to the understanding of disease progression and speech preservation in ALS.

Keywords: Amyotrophic Lateral Sclerosis
Bulbar ALS
Jaw
Speech Kinematics
Tongue
Advisor: Yunusova, Yana
The Role of Ovarian and Fetal Factors in Fetoplacental Microvascular Growth and Placental Development in Late Gestation in Mice

In late gestation, the rate of fetal growth increases significantly which must be matched by proper nutrient delivery. Although there is little change in placental weight at this stage, there is a large increase in fetoplacental capillaries resulting in an increased surface area for maternal-fetal exchange. The objective of this thesis was to determine the role of maternal ovarian or fetal signals in mediating fetoplacental angiogenesis. Changes in fetoplacental vascularity were assessed upon the removal of one or both ovaries in late gestation, or upon removal of fetal factors by inducing fetal cardiac arrest. Results suggest that ovarian and fetal factors promote fetoplacental microvascular growth while diminishing non-blood space components in the exchange region of the placenta in late gestation. Further studies are required to elucidate the specific factors involved, which is imperative for understanding why and how blunted fetoplacental capillarization occurs in pregnancy complications such as intrauterine growth restriction.

Keywords: Estradiol
Fetectomy
Fetoplacental capillaries
Late gestation
Ovariectomy
Placenta
Advisor: Adamson, Lee
BarTLB: Barren Page Resistant TLB for Managed Runtime Environments

This thesis observes that many translation look-aside bu_er (TLB) misses in managed runtime language workloads originate from barren pages. That is, pages that contain mostly dead objects sprinkled with only a few live objects. The main contribution of this work is that it characterizes the barren page phenomenon. This work also proposes (1) a low-cost barren page identi_cation technique, and (2) two simple, low-cost techniques for improving TLB performance: (a) The Barren Page First (BPF) replacement policy extends an existing TLB replacement policy to prefer barren pages on evictions. (b) Selective In-Cache Translation Caching (SICTC) avoids installing barren pages in the TLB by augmenting one way of a virtually-indexed, physically-tagged L1 data cache with virtual tags. Experiments _nd that for those Dacapo and SPECJBB2005 workloads thatexhibit barren pages BPF and SICTC improve performance by 4% and 9.2% on average.

Keywords: manage runtime environment
TLB
virtual memory
Advisor: Moshovos, Andreas
Dynamic Regulation of CD8+ T cell Signalling by the Adaptor Protein 3BP2

AbstractDynamic Regulation of CD8+ T Cells by the Adaptor Protein 3BP2Korris Lee © 2014 MSc Department of Immunology, University of TorontoCD8+ T cells fill an important niche under the aegis of the adaptive immune system by killing transformed and/or infected host cells. Their activity is initialized by T cell receptor (TCR) signalling, which consists of a complex network of signalling molecules that can be modulated by adaptor proteins. 3BP2 is an adaptor protein expressed in hematopoietic cells, including T cells. These data establish that 3BP2 in T cells is inducible in a time-dependent manner upon TCR stimulation, and that it interacts with important early signalling molecules (Lck, ZAP-70, Vav-1, SLP-76) and increases the phosphorylation of others (Src/Lck, ZAP-70, PLC-γ, NFAT, Erk). Lastly, 3BP2 affects T cell functions: adhesion, proliferation, cytokine production and signalling, and lastly cytotoxicity potential. Future work would address 3BP2 and CD4+ T cells, the biological implications of cherubic 3BP2, and the effect of 3BP2 in vivo.

Advisor: Rottapel, Robert
Evaluation of a 4-Phase Bioimplant as a Delivery Vehicle for rhBMP-2

Current recombinant BMP-2 (BMP) bioimplants use an acellular collagen sponge (ACS) as a carrier. However these bioimplants produce a large initial burst of BMP which is linked to ectopic bone formation, inflammation and cancer.The objective of this thesis was to evaluate a novel 4-phase scaffold (4PS) as a BMP carrier. BMP release kinetics in vitro and bone formation in vivo were evaluated for various 4PS bioimplant designs.BMP placement at different sites within the 4PS bioimplant modified the release profile, with some bioimplants showing a reduced initial burst and total cumulative release compared to ACS. In vivo the 4PS bioimplants produced bone ossicles of the same total volume, but significantly greater bone content than ACS. This study demonstrates that certain 4PS bioimplants produced a reduced burst release and formed denser bone ossicles than ACS, suggesting that these bioimplants may be safer and more effective than ACS bioimplants.

Keywords: 4-Phase Carrier
BMP-2
BMP delivery
Advisor: Peel, A Sean
A Study of Scheduling a Neuro-imaging Application on a Heterogeneous CPU-GPU Cluster

The ever increasing complexity of scientific applications has led to utilization of new HPC paradigms such as Graphical Processing Units (GPUs). However, modifying applications to run on GPU is challenging. Furthermore, the speedup achieved by using GPUs has added a huge heterogeneity to HPC clusters. In this dissertation, we enabled NPAIRS, a neuro-imaging application, to run on GPUs with slight modifications to its original code. This important feature enables current users of NPAIRS, i.e. bio-medical scientists, to utilize GPUs without applying fundamental changes to their application. Our experiments show a 7-fold speedup for NPAIRS. Then, we investigated several scheduling algorithms for a heterogeneous CPU-GPU cluster. We show that scheduling can highly improve makespan of a CPU-GPU cluster.Finally, we propose a dynamic scheduling that estimations task execution times on various resource types. Our scheduling scheme obtains performance samples on-the-fly and distributes the tasks based on the historical execution data.

Keywords: GPU
Heterogeneous clusters
NPAIRS
Scheduling
Advisor: Amza, Cristiana