VictorJuiz/thesis huggingface dataset:
Using Phase-Change Droplets for Indicator Dilution Measurements of Hepatic Perfusion Index

There is a need to determine the extent to which areas within the liver are supplied by blood from the hepatic compared relative to blood from the portal vein, as this may provide a method to earlier detect tumours. Measuring this ratio in practice, however, has proven to be difficult. This thesis presents a method to separate the phases of liver enhancement using contrast enhanced ultrasound by vaporizing phase-change nanodroplets to locally create microbubbles. Droplets vaporized during the arterial phase produce contrast enhancement from the hepatic artery only. A following vaporization at a later point in time will produce bubbles in both the hepatic artery and the portal vein. By subtraction, the enhancement pattern resulting from the hepatic portal vein may be determined. The relative flow rate may then be calculated using indicator dilution methods. This method is validated by in vitro experiments.

Keywords: Contrast Enhanced
Droplets
Hepatic Metastases
Hepatic Perfusion
Microbubbles
Ultrasound
Advisor: Burns, Peter N
Adsorption of Organic Pollutants from Oil Sands Process-affected Water Using NaOH-activated Delayed Coke

Adopting the strategy of treating waste with waste, NaOH-activated delayed coke (ADC) was explored as an adsorbent for removing total dissolved organics (TOC) from oil sands process-affected water (OSPW). NaOH activation enlarged specific surface area and improved adsorption capacity of ADC for methylene blue (MB) by nearly 1000 times, from 0.24 mg/g to 228 mg/g. The affinity of TOC towards carbon is weaker than that of MB. The highest TOC adsorption capacity is 44 mg/g, recorded with ADC at pH 4 and 16 ℃. The equilibrium adsorption isotherms of both TOC and MB follow the Freundlich model. Although both are likely physisorption, TOC displays some behavior of cooperative adsorption that could result in multilayer adsorption at high TOC concentrations. Kinetic data of ADC for MB and TOC fit the pseudo-2nd-order model with high R2. The intraparticle diffusion was found to be the rate-limiting step in both MB and TOC adsorption with ADC.

Keywords: acid-extractable organics
activated carbon
delayed coke
naphthenic acids
oil sands process-affected water
petroleum coke
Advisor: Jia, Charles Q
Staying in Time: Does the Temporal Proximity of Related Events Drive Memory Integration?

Flexible behaviour relies on our capacity to effectively use information gathered over the aggregate of our experiences. This requires memory to go beyond the act of simply recalling individual events; instead, it must be sensitive to relationships connecting our experiences. Prominent theories argue that this is possible through the formation of interconnected memory structures in the brain, whereby related experiences become integrated into overlapping neural populations. However, the conditions required for such integration are still not well understood. Emerging evidence suggests that the temporal proximity of two related events may influence how their content is integrated into memory. I first develop a training procedure for creating robust memories over short and long delay periods, and between distinct environments. Next, I evaluate participants’ tendency to integrate memory learned across related experiences separated by short and long delay periods. Together, these lay the foundation for investigating integration time windows in humans.

Keywords: Cognition
Hippocampus
Learning
Memory
Psychology
Spatial
Advisor: Duncan, Katherine
The Influence of Fluorinated Divinyl Urethane Monomers and Fluorinated Fillers on Resin Composite Physical Properties and Chemical Biostability

Background: Salivary enzymes contribute to loss of resin composite material integrity and release of degradation products, suggesting that improving composite physical and chemical stability is required. Objectives: To study fluorine/urethane incorporation into resin composites and assess their influence on enzyme-mediated ester hydrolysis and mechanical strength. Methods: Fluorinated monomers and silanated barium borosilicate fillers were prepared and characterized by 1H-NMR [monomers] and thermogravimetric analysis (TGA)/X-ray photoelectron spectroscopy (XPS) [fillers], respectively. Composite formulations were assessed for mechanical strength, hydrophobicity, and biodegradation resistance using simulated human salivary esterase incubation conditions and ultra-high-performance liquid chromatography. Results: Eight different fluoro-monomers were assessed after incorporation into resin formulations at 35-55wt%. The best performing monomer was used alongside a fluoro/methacrylate silane and showed comparable mechanical/hydrophobicity properties but lower biostability relative to the control. Increasing the fluoro-contribution showed an optimum between reduced physical properties and improved biostability. Conclusions: Novel monomers should seek to remove/replace all vulnerable ester-containing monomers.

Keywords: biodegradation
composites
dental materials
dimethacrylates
fluorinated monomers
plasticization
Advisor: Santerre, J Paul
Finer, Yoav
Current Ultrasound Technology for Guiding Intraoral Inferior Alveolar Nerve Blockade: A Feasibility Study

In this multi-phase, randomized split-mouth study, a total of 80 volunteers received two different inferior alveolar (IAN) blocks: one side using a traditional landmarking technique and the other side an ultrasound (US)-guided technique. We also studied different US-guided approaches when the original approach was found to be unsuccessful. We used a visual analogue scale to evaluate pain caused by the US probe and by the different injection techniques. An electrical pulp test device was used to evaluate onset and success of the two techniques. In-plane US-guided nerve blockade was not technically feasible given the required position of the US transducer needed to appropriately visualize the IAN. US-guided with out-of-plane technique does not improve IAN block success rate. There was more pain associated with free-hand out-of-plane US-guided approach compared to a landmarked technique. There were no adverse events noted with any of the techniques or approaches.

Keywords: inferior alveolar nerve blockade
local anaesthesia
sonography
ultrasound
Advisor: Lam, David K
Investigating the Impact of Long-Known Music Exposure on Brain Activity in Cognitively Impaired Older Adults

There is interest in developing preventative measures to mediate the manifestation AD in persons at risk for the disease. This study utilized a structured music-listening intervention to long-known, autobiographically salient music in older adults with cognitive impairment, where participants listened to long-known music for at least one hour per day for three weeks. A network involving frontal and limbic areas, as well areas involved in autobiographical memory, was preferentially activated during long-known music compared to recently-heard music. Post-intervention, our investigation revealed decreases in brain activity during music listening and statistically significant improvement in memory scores. These results are interpreted as improved neural efficiency associated with the implemented intervention. As a secondary analysis, it was revealed that non-musicians saw greater effect of intervention than musicians. These results provide preliminary evidence that long-known music listening intervention can induce brain plasticity to facilitate cognitive reserve to reduce risk of developing AD.

Keywords: Alzheimer's disease
Brain Plasticity
Intervention
Mild Cognitive Impairment
Music
Music Based Intervention
Advisor: Fischer, Corinne E
Memory and Network Interface Virtualization for Multi-Tenant Reconfigurable Compute Devices

Field Programmable Gate Arrays (FPGAs) have increasingly been deployed in datacenters. These devices have proven effective at performing certain compute tasks better (faster, lower latency, higher throughput, and/or more efficiently) than traditional compute devices. In this work, we explore the application of the virtualization concept to multi-tenant FPGAs, with a specific focus on enabling multiple applications to securely share an FPGA and preventing snooping and/or errant behaviour. Conceptually, the traditional shell concept in FPGA design is extended to the hard shell and soft shell components. The hard shell focuses on the logical isolation of hardware applications on the same FPGA. For memory and networking interfaces on the FPGA, this work introduces hardware components aimed at enabling this isolation. In particular, the design of a new component that is termed the Network Management Unit (NMU) is presented in detail. The NMU enables the isolation of network traffic.

Keywords: Cloud
FPGA
Memory
Networking
Reconfigurable
Virtualization
Advisor: Chow, Paul
Sex differences in neutrophil extracellular trap formation

Immune responses vary between men and women. The female sex is considered protective in combatting acute infections, but disadvantageous in chronic inflammatory diseases. As neutrophils play a central role in innate immunity, they may mediate the sexual dimorphism in immune responses. Neutrophils can combat invading microbes by forming neutrophil extracellular traps (NETs). We hypothesize that females release higher amounts of NETs, leading to more robust acute immune responses. To test our hypothesis, neutrophils isolated from healthy human males and females were induced to form NETs in response to various pharmacological and biological stimuli. Total DNA content was higher in neutrophils from females compared to males. Female neutrophils released decreased levels of DNA in response to the calcium ionophore A23187. PMA, LPS, ionomycin and bacteria stimulation did not result in significant sex differences. Correlating the serum levels of the sex hormones testosterone, estradiol and progesterone to NETosis levels in the above conditions revealed a negative correlation between testosterone and A23187-mediated DNA release. No correlation was detected in relation to endogenous estradiol and progesterone levels, but a combination effect has not been fully explored. Exogenous estradiol or progesterone treatment at physiological concentrations did not influence DNA release. Given the results thus far, a sex difference in NETosis was detected with A23187 treatment but not from biological stimuli in the context of healthy neutrophils.

Keywords: Infection
Inflammation
Neutrophil
Neutrophil extracellular trap
Sex
Sex hormone
Advisor: Palaniyar, Nades
Sweezey, Neil B
Plasma Membrane Recruitment Patterns of Glucose Transporters (GLUT) 1, 2, 3, and 5 in Response to Feeding in the Ruby-throated Hummingbird, Archilochus colubris.

Hummingbirds, among the smallest vertebrate endotherms, have high resting and active metabolic rates and subsist almost exclusively on nectar sugar; they face extreme challenges to energy homeostasis and blood sugar regulation. Transmembrane sugar transport, and thus some control over energy flux, is mediated by facilitative glucose transporters, GLUTs. I determined relative protein abundance and subcellular localization via Western Blot for several GLUTs in flight muscle and liver from fed or fasted ruby-throated hummingbird (Archilochus colubris). I observed GLUT5 protein in flight muscle PM, consistent with its hypothesized uniquely high flux of fructose. GLUT1 protein was absent in hepatocytes, contradicting previously observations of transcript. Finally, glucose-specific GLUT1 abundance was increased in flight muscle PM of fed birds, while liver PM was increased in GLUT3 and glucose/fructose-transporting GLUT2. This suggests muscle glucose uptake capacity is dynamically regulated in response to feeding, while both glucose- and fructose-uptake capacity respond in the liver.

Keywords: Feeding
Glucose transporters (GLUTs)
Hummingbird
Liver
Muscle
Sugar
Advisor: Welch, Jr., Kenneth C.
Reid, Stephen G.
Rational Design and Synthesis of sub-15 nm Upconverting Nanoparticles for Improved LRET Efficiency

Herein, sub-15 nm β-NaGdF4:Yb@NaYF4:Yb,Tm@NaYF4 upconverting nanoparticles (UCNPs) were synthesized to improve efficiency in luminescence resonance energy transfer (LRET) with fluorescein in solution. Analysis of luminescence intensity and lifetime associated with blue emission channel of as-synthesized UCNPs reveal superior protection against solvent-related quenching as compared to conventional homogeneous core-shell UCNP constructs of similar size, composition, and shell thickness. The NaGdF4-NaYF4 core-shell design offered vibrational and spatial separation of sensitizer from solvent environment. Additionally, activators confined to a thin NaYF4 shell close to particle surface decrease the distance between energy donating centers and accepting fluorophore bound to particle surface. Consequently, core-shell-shell UCNP constructs demonstrate a two-fold improvement in sensitivity to fluorescein as compared to homogeneous core-shell constructs. The relatively high LRET efficiency (62±2%) presented in this work has yet to be reported in literature at particle sizes of

Keywords: bioassay
core-shell
lifetime
LRET
nanomaterials
Upconverting nanoparticles
Advisor: Krull, Ulrich J
Prosser, Scott R
Upconversion nanoparticles coated with Alendronate and PEG-conjugated Alendronate

Upconverting nanoparticles (UCNPs) have gained traction as diagnostic and imaging probes for biological applications due to their many unique optical properties. This thesis describes the exploration of alendronate and polyethylene glycol (PEG) surface chemistries to impart NaYF4:Yb3+ /Er3+@NaYF4 core shell UCNPs with the colloidal and optical stability required for biological applications upon transference into aqueous environments. Prior to evaluating colloidal and optical stability, NMR studies to confirm binding and surface coverage studies of alendronate and alendronate PEG 5kDa were conducted yielding ligand densities of 2.56 +/- 0.16 nm-2 and 0.085 +/- 0.02 nm-2 , respectively. Alendronate PEG 5kDa coated UCNPs demonstrated enhanced colloidal stability in comparison to alendronate coated UCNPs in 1X PBS buffer. Both alendronate and alendronate PEG coating led to a significant decrease in optical intensity of the main green emission peak at 537 nm by 84% and 93%, respectively.

Keywords: Alendronate
Colloidal Stability
Optical Stability
Polyethylene Glycol
Surface Density
Upconvering Nanoparticles
Advisor: Krull, Ulrich J
Prosser, Scott R
The Robust Canadian Traveler Problem and Its Application to Robot Routing

The stochastic Canadian Traveler Problem (CTP), which finds application in robot route selection under uncertainty, aims to find the traversal policy with the minimum expected cost. This thesis extends the stochastic CTP to what we call the Robust Canadian Traveler Problem (RCTP), in which the variability of the policy cost is also considered. An optimal algorithm and an approximate algorithm are then proposed to compute the policy that has a good balance of both mean and variation of the traversal cost. The benefit of the proposed framework versus traditional approaches is shown by doing simulations in randomly generated worlds as well as on a map of 5 km of paths built from robot field trials. Specifically, the RCTP framework is able to search for policy alternatives with significant lower worst-case cost and less computational time compared against the optimal CTP policy, but with little sacrifice on the expected cost.

Keywords: Canadian Traveler Problem
Path Planning
Planning Under Uncertainty
Advisor: Barfoot, Timothy D.
Examining Representations of Relevant and Irrelevant Items in Visual Working Memory: An Analysis of Age-related Memory Differences

The inhibitory deficit hypothesis suggests that older adults fail to suppress irrelevant information, resulting in impaired memory for task-relevant items and increased priming of distractors (Hasher et al., 1988). In contrast, younger adults seem to filter out extraneous information and ultimately remember target items better. We set out to explore these differences by investigating how relevant and irrelevant items are represented in the brain. Using a classifier trained on four image categories, we found that while younger adults were unaffected by the representational similarity of simultaneously presented categories, older adults actually performed better when category similarity was higher. This contradicted our hypothesis that greater representational similarity would result in increased interference between studied stimuli, adding strain to already weak inhibitory mechanisms and further impairing memory for targets in older adults. These surprising results may lead to fruitful new avenues of research and opportunities to build on existing theoretical frameworks.

Keywords: Inhibitory Deficits
Memory
Neural Representations
Advisor: Buchsbaum, Bradley
Real-Time Data Acquisition System for Monitoring Focused Ultrasound Blood-Brain Barrier Opening

Sunnybrook Hospital’s Focused Ultrasound Lab has designed a new 256 element hemisphere dome for the purpose of blood brain barrier (BBB) disruption. This dome requires a receiver system that can digitize reflected ultrasonic pulses in order to determine the safety of the treatment and modify transmission settings in a closed feedback manner. Current commercial receiver systems do not address this problem in a cost effective manner. In order to address this issue a 32 channel, with the capability to expand to 256 channels, data acquisition system was designed to capture subharmonic reflections from ultrasonic pulses generated during blood brain barrier opening therapy. All channels of this device were characterized and a single channel was used to determine if inertial cavitation could be detected. The results indicate that the device is capable of detecting this and can be incorporated into a blood brain barrier disruption machine for monitoring purposes.

Keywords: Blood Brain Barrier
Data Acquisition System
Focused Ultrasound
FPGA
PCB
Ultrasound
Advisor: Hynynen, Kullervo
A Field Study of Exterior Airtightness Testing in Five Multi-Unit Residential Buildings

The airtightness of a multi-unit residential building (MURB) enclosure is an important factor when considering energy consumption. There is limited data available on the airtightness of MURBs. The complexity of the MURB geometry complicate standard testing procedures; this is especially true when measuring the isolated exterior enclosure airtightness where the adjacent zones must be taken into consideration. This thesis explored three alternative suite-based methods from the literature used to measure the isolated exterior pressure boundary leakage. A field study took place in five MURBs where the goal was to compare the results from these methods to pressure neutralization test results. Of the three testing methods, the testing method that used adjacent pressure differentials in its calculation was the most similar. Ideally, these results and lessons learned will aid future researchers in developing airtightness testing methods and standards for conducting efficient and accurate tests.

Keywords: Air Leakage
Airtightness
Blower Door
Exterior Airtightness
Multi-Unit Residential Buildings
MURB
Advisor: Touchie, Marianne
Separate mesolimbic dopaminergic pathways mediate the opposing motivational effects of acute caffeine

Caffeine is the most commonly consumed psychoactive drug in the world, yet little is known about the neural substrates that underlie its rewarding and aversive properties. Using male Wistar rats in a place conditioning procedure, we showed that systemic caffeine at a low intraperitoneal dose of 2 mg/kg (or 100μM injected directly into the rostral, but not caudal, ventral tegmental area) induced reward. By contrast, high doses of systemic caffeine (10 and 30 mg/kg) produced aversions that were not recapitulated by a caffeine analog restricted to the periphery. We demonstrated that pharmacological blockade of dopamine receptors using α-flupenthixol injected into the nucleus accumbens shell, but not core, blocked caffeine reward. Conversely, α-flupenthixol injected into the nucleus accumbens core, but not shell, blocked caffeine aversions. Thus, our findings reveal two dopamine-dependent and functionally dissociable mechanisms for processing caffeine motivation that are segregated between nucleus accumbens subregions.

Keywords: caffeine
core
dopamine
nucleus accumbens
shell
ventral tegmental area
Advisor: van der Kooy, Derek
Impact Studies of Containment Ring during Blade Shed in Turbofan Engines

The catastrophic failure of fan blades in turbofan engines, referred to as fan blade-out (FBO), can cause severe damage to aircraft and result in fatal incidents. Recent accidents indicate that the protective containment structures (rings) used to limit the consequences of such failures may be inadequate. Accordingly, this study involves the design and analysis of a novel containment ring using dynamic nonlinear finite element (FE) simulations of ballistic impacts and FBO events, and the development of a novel instrumented test rig to calibrate the finite element simulations and study blade-out in turbofan engines. The predictions of the finite element method reveal that Kevlar is suitable for use in containment structures and that the optimal multilayered target has an exposed aluminum foam surface with a Kevlar fabric backing. This is confirmed in the containment of blade-out with a single trailing blade and fully bladed fan disk.

Keywords: Aircraft
Blade-Out
FBO
Turbofan
Advisor: Meguid, Shaker A
Late Cenozoic reconstructions of precipitation isotopes and climate in continental Alaska and Yukon

This thesis presents late Cenozoic reconstructions of hydrogen isotope ratios in mean annual precipitation (dDMAP) from fossil plant waxes (n-C28 alkanoic acids) and hydrated volcanic glass shards in tephra that are archived in sediments in south-east Alaska and central Yukon. The leaf wax dDMAP estimates, spanning 6.2 to 2.8 Ma, are negative compared to modern which is unexpected for a warmer-than-modern climate as indicated by other proxies. Tephra-dDMAP estimates spanning 6.7 to 0.025 Ma are consistent with North Pacific sea surface temperatures, documenting low dDMAP values during the latest Miocene, peak values during high pCO2 warm intervals (~5 and 3 Ma), and transition to the lowest values on record in the Late Pleistocene. The difference in trends between the two dDMAP reconstructions most likely owes to an inappropriate net-fractionation assumption associated with the leaf wax proxy which remains one of the largest uncertainties in fossil leaf wax derived paleoclimate reconstructions.

Keywords: Climate
Hydrogen isotope
Leaf wax
Pliocene
Subarctic
Tephra
Advisor: Porter, Trevor J
GABA: a Potential Agent of Beta-Cell Proliferation

Studies have shown that GABA can increase the β-cell mass and improve glucose tolerance in normal and STZ treated mouse models. Herein we explored the applicability of GABA to a pre-diabetes setting. We showed that 10 weeks of GABA administration via drinking water ad libitum to normal CD1 mice stimulated almost a 2-fold increase in β-cell mass. Inhibition of the GABAA receptor abolished ex-vivo GABA-induced increase in Ki-67+ staining in β-cells. Additionally, the OCR and MMP were unchanged with GABA treatment suggestive of no effect of GABA on cellular metabolism which is linked to the GABA shunt. Lastly, the HFD-induced pre-diabetic CD1 mice treated with GABA prior to and after pre-diabetes onset did not show an enhancement in the β-cell mass, glucose tolerance or insulin sensitivity. Thus, GABA may increase β-cell mass in normoglycemic CD1 mice, potentially through the GABAA receptor, but it does not reverse or prevent pre-diabetes.

Keywords: Beta-cell mass
Cell proliferation
GABA
Glucose tolerance
Metabolism
Pre-diabetes
Advisor: Wheeler, Michael B
Rocheleau, Jonathan V