VictorJuiz/thesis huggingface dataset:
Trapping and Removal of Bubbles in a Microfluidic Format

Unwanted gas bubbles are a challenge for microfluidic-based systems, as adherence to channel networks can disrupt fluid delivery. This is especially true for devices with biological applications, as the presence of a single bubble creates thin fluid films with extremely high shear stresses, which can damage biological samples. Current strategies to remove bubbles require complicated fabrication or off-chip components. This thesis describes an on-chip microfluidic strategy utilizing permeation for in-plane trapping and removal of occasional gas bubbles. The trap was demonstrated with nitrogen bubbles, which were consistently removed at a rate of 0.14 µL/min for a single trap, and shown to have long-term operation capability by removing approximately 4,000 bubbles during one day without failure. The trap was integrated with a microfluidic system for the study of small blood vessels. Experiments were complemented with analytical and numerical models to characterize the bubble removal process.

Keywords: microfluidic
bubble trap
bubbles
trap
Advisor: Guenther, Axel
Surface Plasmon Polariton Based Polarization Modulators Using Metal-polymer Waveguides

A tunable polarization modulator based on the periodic metal strips embedded in a polymer waveguide is presented. The periodic metallic structure is analyzed by Finite Element simulation (COMSOL). The calculation results show that the giant birefringence is formed by the selective cut-off of TE polarization over TM polarization, which makes it possible to design an efficient polarization modulator with a short conversion length. The metallic strips are made by using four-layer lift-off fabrication technology. The transmission and group indices of TE and TM modes are measured. However, it is observed that TE and TM modes cut off at same time, which does not agree with our predictions. The reason for failure is that the change in refractive indices is different from what we expected, which makes the device perform in opposite way. Finally, further suggestions are provided to modify the design so that the device can achieve its expected function.

Keywords: polarization modulator
surface plasmon polariton
Advisor: Poon, Joyce
Miniaturized Electrochemical Immunosensors for the Detection of Growth Hormone

The first part of this research involves the development of a gold-nanoparticle based sandwich type immunosensor to identify trace amounts of human chorionic gonadotropin hormone based on the direct electrochemical detection of Au nanoparticles. The second part of this research is to design a biosensor that can be easily handled, has higher specificity, sensitivity, low-cost, and rapid response and has a better detection of growth hormone (GH). Current bioanalytical techniques have reported the difficulty to detect GH doping. This research aims to address the issue of measuring GH in small volumes, which has been challenging the limits of analytical detection systems. The electrochemical measurements utilize the redox activity of ferro/ferricyanide in cyclic voltammetry and impedance spectroscopy. The detection limit 10 pg/mL was observed for GH in 20 μL sample volume, which indicated that this versatile platform can be easily adapted for decentralized electrochemical immunosensing of clinically important proteins.

Keywords: Immunosensor
Growth hormone
Advisor: Kerman, Kagan
Stress-constrained Structural Topology Optimization with Design-dependent Loads

Topology optimization is commonly used to distribute a given amount of material to obtain the stiffest structure, with predefined fixed loads. The present work investigates the result of applying stress constraints to topology optimization, for problems with design-depending loading, such as self-weight and pressure. In order to apply pressure loading, a material boundary identification scheme is proposed, iteratively connecting points of equal density. In previous research, design-dependent loading problems have been limited to compliance minimization. The present study employs a more practical approach by minimizing mass subject to failure constraints, and uses a stress relaxation technique to avoid stress constraint singularities. The results show that these design dependent loading problems may converge to a local minimum when stress constraints are enforced. Comparisons between compliance minimization solutions and stress-constrained solutions are also given. The resulting topologies of these two solutions are usually vastly different, demonstrating the need for stress-constrained topology optimization.

Keywords: topology optimization
design dependent loads
pressure loads
self-weight
stress constraints
block aggregated constraints
Advisor: Martins, Joaquim R. R. A.
The Thermal Grill Illusion of Pain: Effects of Altering Placements of Warm and Cool Grill Elements

The simultaneous application of interlaced innocuous warm and cool stimuli can elicit sensations of burning heat (the Thermal Grill Illusion, TGI). The TGI is thought to reflect changes in the central interactions between somatosensory sub-modalities (i.e. cold-inhibition of pain). Previous studies used multiple alternating warm and cool bars to elicit a TGI. The primary objective of this study was to evaluate the effects of altering the placements of warm and cool grill elements on the intensities of perceived pain and unpleasantness in 26 male subjects. Arranging the thermal grill elements in a warm flanking cool (WCW) pattern evoked significantly higher intensities of pain and unpleasantness than a cool flanking warm (CWC) pattern and a uniform warm stimulus. Conversely, CWC did not elicit significantly different intensities of perceived pain and unpleasantness than a uniform cool stimulus. This finding may reflect differences in the level of activation of central neurons.

Keywords: Thermal Grill Illusion
Psychophysics
Pain
Thermoreception
Advisor: Dostrovsky, Jonathan O.
Hunter, Judith
In Vitro Examination of Secondary Caries Using Infrared Photothermal Radiometry and Modulated Luminescence

Dental secondary caries is the carious lesion developed around existing restoration margins. Many new technologies have been developed for caries detection purposes, but their performance is unsatisfactory for the specific purpose of secondary caries diagnosis. Therefore, the development of a novel technology to detect secondary caries has been highly necessary. The objective of this research was to investigate the ability of photothermal radiometry and modulated luminescence to detect secondary caries: wall lesions and outer lesions. Changes in experimental PTR-LUM signals due to sequential demineralization on vertical walls of sectioned tooth samples were investigated. Another study was conducted to investigate how two different types of secondary caries, wall lesions and outer lesions, affect the PTR-LUM signals. The studies demonstrated that PTR-LUM is sensitive to progressive demineralization and remineralization on vertical walls of sectioned tooth samples, as well as to the presence of wall lesions and outer lesions developed around composite restorations.

Keywords: Photothermal Radiometry and Luminescence
Secondary Caries
Advisor: Mandelis, Andreas
The Effects of Green Tea on Salivary Production and Viscosity, and on Quality of Life in Patients with Sjögren’s Syndrome: A Pilot Study

Several beneficial effects of green tea polyphenols (GTPs) have been shown in both in vitro and animal studies. This pilot study tested their effects on relief of dry mouth and quality of life (QoL) in Sjögren’s syndrome (SS) patients. After one month of green tea consumption in 18 SS patients, and three months in 7 patients, there was an improvement in the patients’ oral health and QoL. In addition there was an increase in the unstimulated salivary flow rate and a decrease in the viscosity of stimulated saliva, although not statistically significant. Furthermore, 83% of the patients reported that they would continue to drink green tea. Although the mechanism of action of the GTPs is unknown in this patient population, we have shown that regular green tea consumption by SS patients is a simple yet effective and enjoyable means of dry mouth relief.

Keywords: Sjögren’s syndrome
Green tea
Advisor: Laing, Leslie P.
Investigation of the Oncogenic Role of Sox2 in the Pathogenesis of Lung Squamous Cell Carcinoma using Normal Human Lung Basal Progenitors

Sox2 is the most frequently amplified oncogene in lung squamous cell carcinoma (SCC). Lung SCC arises in the proximal to central airways and is thought to originate from the p63-positive basal progenitor cells. Since Sox2 amplification occurs early in SCC pathogenesis, we investigated the oncogenic role of Sox2 using normal primary human lung basal progenitor cells. Although Sox2 is highly expressed in normal basal progenitors in a quiescent tracheal epithelium in vivo, we found that Sox2 expression decreases substantially during in vitro proliferation. When Sox2 expression is elevated in the proliferating basal cells in vitro to a level clinically observed in lung SCCs, Sox2 causes hyperplasia and promotes both squamous and Mucin16-positive glandular lineages at the expense of ciliated cell differentiation. Furthermore, our data suggest that the squamous and glandular-differentiating activity of Sox2 is differentially modulated by Receptor tyrosine kinase (RTK) and/or PI3-kinase signaling to promote squamous metaplasia of basal progenitor cells during SCC development.

Keywords: lung squamous cell carcinoma
Sox2
basal cells
lung progenitor
Advisor: Moghal, Nadeem
Quantifying the Fuel Load, Fuel Structure and Fire Behaviour of Forested Bogs and Blowdown

A study was undertaken to characterize two dynamic fuel types not included in the Canadian Forest Fire Behaviour Prediction System: forested bogs and blowdown. Fuel load and structure were measured at ten forested bog sites in central Alberta along a 108 year post-fire chronosequence. Canopy bulk density increased following a sigmoidal curve between 0.00 and 0.54 kg•m-3. Crown fire potential was modeled using a general crown fire behaviour model and found to follow a similar sigmoidal pattern increasing with time-since-fire. Blowdown fuel loads were measured at six sites in northwestern Ontario and ranged from 13.4 to 18.9 kg•m-2. Elevated fine blowdown fuels were found to have faster reaction times and dry more rapidly than predicted by the Fine Fuel Moisture Code. Detailed observations were also made of fire behaviour in blowdown fuels

Keywords: Wildfire
Fuel Type
Fire Behaviour
Blowdown
Forested Bog
Advisor: Martell, David Lee
Wotton, Brian Michael
Elucidating the Role of TDP-43 in the Pathogenesis of Amyotrophic Lateral Sclerosis

Amyotrophic Lateral Sclerosis (ALS) is a devastating neurodegenerative disease with no cure. TAR-DNA binding protein 43 (TDP-43) is the major component of the cytoplasmic inclusions characteristic of ALS. Transgenic Drosophila lines expressing wild-type, mutant and splice variants of human TDP-43 were generated. I find that ubiquitous expression of all TDP-43 transgenes, except for TDP-43∆C-term, is sufficient to cause lethality. I also show that eye-specific expression of a TDP-43∆N-term splice variant, which localizes diffusely to the cytosol, results in increased cell toxicity suggesting an association between cytosolic localization and toxicity. Consistent with this model, I find that the TDP-43∆N-term splice variant is capable of recruiting full length TDP-43 into the cytoplasm, and I suggest this may represent an initiating event in TDP-43-linked ALS. Altogether, my results seem to indicate that exclusion of TDP-43 from the nucleus rather than its presence in aggregates is linked to increased cytotoxicity and lethality in ALS.

Keywords: ALS
Drosophila
TDP-43
Neurodegeneration
Advisor: Boulianne, Gabrielle
Correlates of Condom Use among Single, Sexually Active Ontario Adults: Data from the 1996/97 Ontario Health Survey

OBJECTIVE: To examine the past-year prevalence and frequency of condom use and to identify correlates of condom use among young, unattached heterosexual Ontarians. METHODS: Descriptive statistics and multiple logistic regression were used to analyze the 1996/97 Ontario Health Survey (OHS), a cross-sectional, random digit-dialling (RDD) survey of 36,892 Ontario residents of households with a telephone line. RESULTS: Between 1996 and 1997, 61.3% (95% CI=58.5%-64.1%) of the study sample (aged 15-44, n=1,949) reported consistent (always) condom use and 11.8% (95% CI=10.2%-13.5%) reported never using condoms. Significant correlates included, for both sexes, health planning region, age, ethnic origin, and type of smoker; for females only, socio-economic status, age at first sexual intercourse, and past-month oral contraceptive use ; and for males only, number of past-year sexual partners, HIV testing history, and past-year frequency of religious attendance. CONCLUSIONS: Findings constitute a cross-sectional component for examining the long-term trend of condom use in Ontario.

Keywords: condom use
correlates
Advisor: Calzavara, Liviana
Studies in Palladium Catalyzed Carbohalogenation Chemistry

Since recognizing the significance of reversible oxidative addition of palladium into aryl halides in the synthesis of 2-bromo-indoles, the Lautens group has focused on unusual carbon-halogen reductive eliminations. These efforts led to the discovery of the novel palladium-catalyzed inter- and intramolecular carbohalogenation reaction – the formal addition of an sp2 carbon–iodide bond across an alkene. One current research direction is utilizing a range of aryl halides and pseudohalides as starting materials for carbohalogenation chemistry. This thesis describes complementary research, focusing on the expansion of functional group scope. Carbohalogenation has been developed to synthesize novel products including heteroaromatic compounds and 7-membered rings. Polyunsaturated aryl iodide substrates were investigated with the goal of performing domino carbohalogenation. Ultimately, the successful halogen exchange process was combined with domino carbohalogenation in an efficient halogen-exchange domino reaction. Additionally, preliminary studies on enantioselective carbohalogenation, and functionalization of the neopentyl iodide products are also discussed.

Keywords: catalysis
palladium
domino chemistry
carbohalogenation
Advisor: Lautens, Mark
Dynamic Analysis of Whiplash

This study is concerned with whiplash injuries resulting from the sudden acceleration and deceleration of the head relative to the torso in vehicle collisions. Whiplash is the most common automobile injury, yet it is poorly understood. The objective of this thesis is to develop a representative rigid linkage lumped parameter model using Lagrangian mechanics to capture the relative motion of the head and cervical spine. Joint locations corresponding to the intervertebral centers of rotation are used to simulate the normal spinal movements and an inverse analysis is applied to determine the viscoelastic parameters for the spine, based on cadaver test results. The model is further validated using ANSYS dynamic finite element analysis and experimentally validated using a newly designed and fully instrumented whiplash test fixture. Our findings reveal the effectiveness of the simplified model which can be easily scaled to accommodate differences in collision severity, posture, gender, and occupant size.

Keywords: whiplash
dynamic
lumped-parameter
rigid linkage
inverse analysis
multi-body
analytical
numerical
experimental
Advisor: Meguid, Shaker A.
Factors Governing Sorption of Dissolved Organic Matter and Pharmaceuticals in Soil

Pharmaceuticals, personal care products and dissolved organic matter (OM) are introduced to soil via irrigation with reclaimed wastewater. This thesis examines the basic factors that influence sorption of these components in soil. Sorption of dissolved OM samples of varying composition to clay surfaces was examined. Results indicate that preferential sorption is dependent on clay type but not necessarily OM composition. Analysis of soils revealed aliphatic components, carbohydrates and amino acids are prevalent at the soil-water interface whereas aromatics are inaccessible at the soil-water interface. No clear relationship between sorption affinity of 17β-estradiol, sulfamethoxazole, carbamazepine and phenanthrene and soil OM aromaticity or aliphaticity was observed. A negative relationship between sorption and O-alkyl content may be due to these components blocking contaminant access to high affinity sorption sites. Therefore, application of reclaimed wastewater to soils with O-alkyl-rich OM may result in higher mobility of contaminants.

Keywords: sorption
organic matter
pharmaceuticals
soil
nuclear magnetic resonance spectroscopy
Advisor: Simpson, Myrna J.
The Directive on Alternative Investment Fund Managers: Comparative Analysis of Certain Aspects of the Regulatory Regimes of Europe, Canada and the United States of America

The Alternative Investment Fund Managers Directive ("AIFMD"), adopted by the European Union on 11 November 2010, has introduced a harmonized set of rules for alternative investment funds (“AIFs”) in Europe. This thesis discusses potential financial risks for the AIFs industry arising from the European regulatory reform, which started before the current financial crisis, and compares relevant European, Canadian and US rules governing AIFs. This comparative analysis is based on four main criteria: i) registration and authorization requirements, ii) general financial transparency requirements, iii) capital requirements, and iv) remuneration restrictions. The analysis of AIFs regulatory reform in Europe leads to three main conclusions. First, the AIFMD requirements are much stricter than analogue regimes in Canada and the United States. Second, as a consequence of this regulation, European AIFs may be in disadvantage. Third, the complexity of the present European institutional framework is not able to fully implement the European regulatory reform.

Keywords: Financial Regulation
Alternative Investment Fund Managers
Advisor: Iacobucci, Edward
Control of Dopant Type and Density in Colloidal Quantum Dot Films

Colloidal quantum dots (CQDs) are an inexpensive and solution processable photovoltaic(PV) material reaching modest efficiencies of 6%. However, doping quantum dots still remains a challenge. This thesis explores the level of doping in lead sulfide (PbS)CQDs by surface ligands and bulk doping within the quantum dot lattice using metals. In light of the knowledge that oxygen creates traps on the surface of PbS CQDs, we have turned to the use of oxygen-free fabrication. We find that under a nitrogen environment, PbS CQD films are n-type and tunable in doping by use of halide ions. We show for the first time control over the doping density of n-type CQD films over a wide range. We also show the ability to fabricate p-type PbS films with high doping density that are compatible with n-type films. This compatibility enabled us to make the world’s first CQD homojunction PV device.

Keywords: quantum dots
photovoltaics
doping
transistors
homojunction
Advisor: Sargent, Edward H.
Proteolytic Processing of Nlrp1b in the FIIND Domain is Required for Inflammasome Activity

Nlrp1b is a NOD-like receptor of the innate immune system that upon sensing of anthrax lethal toxin oliogmerizes and forms a protein scaffold that binds to and activates pro-caspase-1; this complex is called an inflammasome. Nlrp1b is highly polymorphic and different alleles display an all or none ability to sense lethal toxin. Here I show that Nlrp1b is cleaved in the FIIND domain, and that the cleaved fragments remain associated even after activation by lethal toxin. The inflammasome activity of an inactive allele was restored by three mutations, one of which also restored cleavage. A heterologous cleavage site was inserted into an uncleaved mutant of Nlrp1b; induced proteolysis of the cleavage site rescued inflammasome activity. An uncleaved mutant of Nlrp1b showed no deficiency in FIIND self-association, but did have reduced recruitment of pro-caspase-1. These data provide evidence that cleavage of Nlrp1b is required for proper recruitment and activation of caspase-1.

Keywords: Microbiology
Immunology
Nlrp1b
Nalp1b
Inflammasome
Anthrax
Lethal toxin
pyroptosis
caspase-1
NLR
Nlrp1
IL-1
NOD
CARD8
Cleaved
Cleavage
Proteolysis
Innate immune
Pattern recognition receptor
Inflammation
FIIND
CARD
Advisor: Mogridge, Jeremy
Understanding the Role of Ribosomal Proteins and Aberrant FLVCR1 Splicing in Diamond Blackfan Anemia

Diamond Blackfan Anemia is a rare congenital disease that is primarily characterized by reduced erythroid progenitors. DBA pathogenesis has been associated with genes encoding ribosomal proteins (RPs) which are important in translation. However, this fails to explain why erythropoiesis is specifically disrupted. Our lab previously found that aberrant splicing of the human transcript encoding heme exporter, FLVCR1, is involved in DBA pathogenesis; and that RPS19 implicated in 25% of DBA patients, regulates FLVCR1 transcript splicing. This thesis investigated the role of another DBA associated gene encoding RPS17, in the regulation of FLVCR1 splicing and disrupted erythropoiesis in DBA. My findings further support the role of FLVCR1 aberrant splicing in DBA and provide evidence suggesting that RPS17 may not be a candidate DBA gene. Furthermore, my study implicates a potential role for RPS19 transcript levels in defective erythroid differentiation observed in DBA.

Keywords: Diamond blackfan anemia
Ribosomal proteins
Advisor: Tailor, Chetankumar
Combining Decomposition and Hybrid Algorithms for the Satellite Range Scheduling Problems

Multiple-resource satellite scheduling problem (MuRRSP) is a complex and difficult scheduling problem, which schedules a large number of task requests onto ground-station antennas in order to communicate with the satellites. We first examined several exact algorithms that were previously implemented in the machine scheduling field. They are column generation and logic-based Benders decomposition. A new hybrid approach that combines both column generation and logic-based Benders decomposition is proposed. The hybrid performed well when there is a large number of machines. Next, we presented a connection between the parallel machine scheduling problem and MuRRSP in order to solve MuRRSP with exact algorithms. Furthermore, we proposed a strengthened cut in the sub-problem of the logic-based Benders decomposition. The resulting algorithm proved to be very effective. Barbulescu’s benchmark problems were solved and proved optimal with an average run-time less than one-hour. To the best of our knowledge, previous efforts to solve MuRRSP were all heuristic based and no optimal schedules existed.

Keywords: Satellite Scheduling
Hybrid Algorithm
Logic-Based Benders Decomposition
Advisor: Beck, J. Christopher
Effect of NAFLD on Regulation of Hepatic Transporters and Metaboic Enzymes Using a High Fat/ High Cholesterol Dietary Model in Rats

Non-alcoholic fatty liver disease is affecting an increasing population worldwide. NAFLD is closely associated with obesity and diabetes. Research has shown that the expression of some important hepatic transporters and enzymes are altered under inflammatory conditions. We examined the effect of NAFLD on the gene expression of several hepatic transporters and enzymes, as well as the impact of exercise in attenuating the effect of NAFLD. We have demonstrated that the mRNA expression of several hepatic transporters and enzymes, as well as FXR were significantly downregulated in liver of rats treated with a HFHCD. We concluded that HFHCD-induced hepatic steatosis, together with the reduced expression of FXR, contributed to the downregulation of expression of hepatic transporters and enzymes. The mRNA expression of TNF-α and IL-1β were unaffected. Interestingly, exercise was found to improve the expression levels of some transporters and enzymes.

Keywords: Non-alcoholic fatty liver disease
Transporters
Advisor: Piquette-Miller, Micheline