VictorJuiz/thesis huggingface dataset:
The Genetic Basis of Fecundity Variation in Caenorhabditis briggsae

Identifying the genetic basis for phenotypic variation is a central question in evolutionary biology and can be studied in detail using model organisms. Fecundity variation in different isolates of C. briggsae has been observed previously, but the genetic causes of this variation are unclear. Crosses between C. briggsae advanced-intercross recombinant inbred lines (AI-RILs) and parental strains yield near isogenic line (NIL) strains, which I created to provide a powerful genetic resource to fine-map the basis for fecundity and other trait differences. Phenotypic analysis of the NILs shows the complexities of possible epistatic interactions on phenotypic expression. These NIL strains contribute a valuable genetic resource toward the long-term goal of identifying the genes responsible for differences in fecundity in this species. The elucidation of the basis for this trait variation will also contribute further into the mechanisms for how genotype and phenotype and environment all interact.

Keywords: quantitative genetics
fecundity
Caenorhabditis briggsae
Advisor: Cutter, Asher
Functional Plasmonic Mesh Architectures

The aim of this thesis is to establish a platform for implementing nanoscale plasmonic slot waveguide (PSW) devices that can interface with dielectric technology for hybrid silicon-plasmonic interconnect applications. For waveguide excitation, an orthogonal junction coupler that operates based on momentum matching is analyzed and then experimentally demonstrated to have coupling efficiency of 50 +/- 2 % between 450 nm wide silicon waveguide and 50 nm wide PSW across a 200 nm bandwidth. Next, for designing scalable optical components with multiple-input multiple-output capability and high fabrication tolerance, two dimensional PSW mesh structure that utilizes simultaneous power distribution and interference within a network of intersecting PSW junctions is introduced. Finally, a closed-form model for PSW mesh structures is derived by incorporating the characteristic impedance model into the scattering matrix formalism. The model can handle arbitrary combination of junctions and has less than 5 % discrepancy when compared to Finite-Difference Time-Domain results.

Keywords: Plasmonic Slot Waveguides
Advisor: Helmy, Amr S.
A Call For Autonomy And Compassion

The current blanket prohibition of assisted death in Canada continues to be the subject of much debate. This thesis examines the shortcomings and strengths of the Belgium Law on Euthanasia of 2002 and discusses whether similar legislation could be implemented in Canada. More particularly, the thesis looks at the spirit and intent of the law, the conditions under which assisted death is permitted, and the control mechanism present in the Belgian law. The analysis of Belgium’s ten years of experience with assisted death allows us to argue that the risks inherent in assisted death regime can be controlled in a system where an exception is made for competent people in a situation of unbearable suffering. Important safeguards to prevent abuse and protect people from vulnerable groups are identified in the Belgian statute. This thesis recommends in its conclusion to regulate assisted death as an expression of compassion for suffering patients, in line with Canada’s longstanding commitment to respect for patient autonomy.

Keywords: Euthanasia
Assisted suicide
Assisted death
Belgium Law
Compassion
Patient Autonomy
Advisor: Lemmens, Trudo
Six4/5 Family Transcription Factor UNC-39 Controls the Development of RID Neuron in Caenorhabditis elegans

Members of the Six4/5 family of homeobox transcription factors have been implicated in multiple human disorders, including type I mytonic dystrophy, branchio-oto-renal syndrome, and holoprosencephaly, suggesting a role for these factors in the nervous system development. Using a forward genetics approach, we identified unc-39, a C. elegans homologue of the human SIX5 gene, as a novel regulator of the development of a specific neuron, called RID. Our data support the role of unc-39 early in C. elegans development and suggest a possibility of complete absence of RID neuron in unc-39 mutants. unc-39 mutant has a similar locomotion phenotype to the RID-ablated animals, which provides further support to the hypothesis that the absence of RID contributes to the locomotion phenotype observed in the mutant. We show that unc-39 functions at multiple points in the lineage that gives rise to the RID neuron, and that its function is context-dependent.

Keywords: C. elegans
neuronal development
RID
Six4/5
Six5
unc-39
genetics
cell fate
transcription factor
homeobox
homeodomain
Advisor: Zhen, Mei
Development and Validation of a Novel Quantitative Assay for Cell surface Expression of GPCRs using a Receptor β-lactamase fusion Protein and the Colourometric Substrate Nitrocefin

Trafficking of GPCRs is a dynamic process that is tightly regulated and sometimes defective in human diseases. Therefore it is important to develop new methods to allow simple and quantitative measurement of surface expression of membrane proteins. Here we describe the development and validation of a new assay for quantification of cell surface expression of GPCRs using β-lactamase as a reporter. For this assay we N-terminally fused β-lactamase (βlac) to the β2-adrenergic receptor (β2AR) and GABA b R1 (GBR1). The results obtained by the βlac assay are quantitatively and qualitatively similar to well established ELISA when measuring agonist induced internalization of β2AR. We also show that measurement of GBR1 surface expression with GBR2 co-expression is quantitatively identical between the βlac and ELISA. In conclusion, our results show that our newly developed βlac assay is quantitatively similar while being less expensive, more robust and higher throughput compared to an ELISA.

Keywords: GPCR
Assay
β-lactamase
Nitrocefin
Surface Expression
ELISA
Internalization
Pharmacological Chaperone
Molecular Chaperone
Advisor: Salahpour, Ali
Somatostatin Receptor Type 2 Antagonism Improves Glucagon Counter-regulation in Biobreeding Diabetes-prone Rats

Impaired counterregulation during hypoglycemia in type 1 diabetes (T1D) is partly due to inadequate pancreatic islet alpha-cell glucagon secretion. We hypothesized that hypoglycemia can be prevented in autoimmune T1D by selective somatostatin receptor type 2 (SSTR2) antagonism of alpha cells to relieve SSTR2 inhibition, thereby increasing glucagon secretion. Diabetic biobreeding diabetes prone (BBDP) rats (D) vs non-diabetic BBDP (N) rats, underwent infusion of vehicle or SSTR2 antagonist (SSTR2a) during insulin-induced hypoglycaemia. D rats, treated with SSTR2a, needed little or no glucose to maintain hypoglycemia. To monitor real-time glucagon secretory response directly, we developed the technique of thin slices of the pancreas from D and N rats as well as normal human pancreas, subjected to perifusion with vehicle vs SSTR2a. SSTR2a treatment enhanced glucagon secretion in N and D rats and human pancreas. We conclude that SSTR2 antagonism can enhance hypoglycemia-stimulated glucagon release sufficient to achieve normoglycemic control.

Keywords: Type1 diabetes
Somatostatin receptor type 2 anatgonist
Glucagon
counterregulation
Advisor: Gaisano, Herbert Young
Vranic, Mladen
Functional Electrical Stimulation as a Neuroprosthesis for Sitting Balance: Measuring Respiratory Function and Seated Postural Control in Able-bodied Individuals and Individuals with Spinal Cord Injury

The level and completeness of spinal cord injury (SCI) above the first lumbar vertebra determine the degree of multi-system impairments including altered respiratory function and decreased capacity to maintain upright posture and seated postural stability in humans. Both systems were studied in able-bodied (AB) subjects and individuals with tetraplegia to explore the potential of functional electrical stimulation (FES) as a neuroprosthesis for seated postural control without compromising respiratory function. Data for AB participants (n=10) indicated higher tidal volumes, greater trunk extensor muscle activity, and different values of seated postural stability in upright sitting compared to slouch sitting. In three case studies of individuals with tetraplegia, surface FES was applied to trunk muscles. Changes in tidal volume, respiratory rate, and seated postural stability were case specific. These studies inform the development of a strategy for non-invasive FES as a neuroprosthesis for sitting balance while preserving respiratory function in individuals with SCI.

Keywords: neuroprosthesis
functional electrical stimulation
postural control
respiratory function
spinal cord injury
seated postural stability
Advisor: Verrier, Molly
Popovic, Milos R.
Stoichiometric Hydrogenated Amorphous Silicon Carbide Thin Film Synthesis Using DC-saddle Plasma Enhanced Chemical Vapour Deposition

Abstract Silicon carbide is a versatile material amenable to variety of applications from electrical insulation to surface passivation, diffusion-barrier in optoelectronic and high-frequency devices. This research presents a fundamental study of a-SiC:H films with variable stoichiometries deposited using novel technique, DC saddle-field plasma-enhanced chemical-vapour deposition, a departure from conventional RF PECVD commonly used in industry. DCSF PECVD is an alternative technique for low temperature large area deposition. Stoichiometric a-SiC:H obtained by fine-tuning precursor gas mixture. Annealing up to 800oC showed no significant change in elemental composition; particularly indicating thermal stability at stoichiometry. Ellipsometry showed wide range of optical gaps whose maximum surpasses values reported in literature. Refractive index measured and change in values studied as function of increasing carbon content in the films. Also attainment of very smooth surface morphology for stoichiometric a-SiC:H films reported. Surface roughness of 1 nm rms demonstrated for films grown at temperature as low as 225oC.

Keywords: Stoichiometric, Hydrogenated, Amorphous, Silicon Carbide, DC-Saddle
Advisor: Kherani, Nazir P.
Sex and Strain Differences in Acute Hepatotoxic and Inflammatory Responses to Liver Procarcinogens in the Developing Mouse

We previously observed that postnatal exposure of mice to the procarcinogen 4-aminobiphenyl (ABP) produced liver tumors only in wild-type males, while arylamine N-acetyltransferase deficient males and females of either strain were protected. Others have also observed a sex difference in liver tumors in mice using the procarcinogen diethylnitrosamine (DEN). Reasons for these sex and strain differences are unclear, but differences in acute hepatotoxicity and inflammation may be involved. In this thesis we found that neither ABP nor DEN produced overt hepatotoxicity in postnatally exposed mice, and only DEN caused an increase in levels of the pro-inflammatory cytokine interleukin-6 but was not sex-dependent. The lack of sex difference suggests that sex hormone modulation of inflammation following sexual maturation might favour growth of initiated cells in males. However, the lack of detectable inflammation following ABP exposure may be due to localized responses, or that inflammation may be a DEN-specific effect.

Keywords: 4-aminobiphenyl
Aromatic amines
Diethylnitrosamine
Carcinogenesis
Hepatocellular carcinoma
Hepatotoxicity
Inflammation
Advisor: Grant, Denis M.
Oxidative Stress and Global DNA Methylation in Patients with Bipolar Disorder and an Excellent Response to Lithium

Correlation between 8-hydroxy-2-deoxyguanosine (8-OHdG) and/or redox imbalance and 5-methylcytosine (5mc) levels was studied in patients with bipolar disorder (BD) and an excellent response to lithium treatment, their affected and unaffected relatives (AR and UR, respectively) and controls. We demonstrated that global methylation was decreased in BD subjects and their relatives compared to controls and remained so after lithium treatment in BD subjects, while UR and AR were no longer different than controls. 8-OHdG levels and Complex I activity did not differ between groups before and after lithium treatment. Finally, glutathione peroxidase activity was higher in relatives of patients before and after lithium treatment and negatively correlated with 5mc levels. The methylation pattern in BD subjects may be specific for BD and that lithium may be involved in regulating global methylation. This study supports the antioxidant properties of lithium through regulation of glutathione system.

Keywords: Bipolar Disorder
Oxidative Stress
DNA Methylation
Lithium
Advisor: Young, L. Trevor
The Effects of Substrate Oxidation on Post-exercise Food Intake in Pre-pubertal, Normal-weight Boys and Men

The relationship between substrate oxidation (RER) and food intake (FI) is undefined. This study examined the effects of RER modified by a glucose pre-load (GL), exercise (EX) and GL with EX on, FI and energy balance (NEB) in normal-weight boys (9-12 y) and men (20-30 y). Subjects (15 boys, 15 men) were randomized with treatments of either water or GL followed by either EX or rest. Measures included RER, energy expenditure (EE)(kcal/kg), subjective appetite, FI(kcal/kg) measured at a pizza lunch and NEB (kcal/kg). FI(kcal/kg) was reduced by GL(p < 0.0001), and further decreased with GL ingested prior to EX(p = 0.0254). RER was increased with GL(p < 0.0001) and EX(p = 0.0043), and was higher in men compared to boys (p = 0.007). There was no association between RER and FI(kcal/kg). In conclusion, there was no relationship between RER and FI, suggesting that FI is not affected by substrate oxidation.

Keywords: Food Intake Regulation
Metabolic Flexibility
Substrate Oxidation
Fat Oxidation
Carbohydrate Oxidation
Energy Balance
Energy Intake
Advisor: Anderson, G. Harvey
Thomas, Scott
An Ultra-wideband Spatial Filter for Time-of-arrival Localization in Tunnels

An ultra-wideband (UWB) spatial filter is proposed to mitigate multipath effects in a one-way, one-dimensional time-of-arrival (TOA) localization system for use inside a tunnel. The spatial filter is a weighted array of judiciously placed antennas and it exploits the fact that electromagnetic waves propagate as modes in a tunnel by selectively extracting these mode(s). The design of several spatial filters is presented alongside vigorous analyses to characterize the localization performance afforded by them in a noisy environment. The filters are evaluated using data from an analytical equation waveguide model, a ray tracer model and measurements. These spatial filters deliver accurate localization estimates across distance and well-designed filters can operate at higher SNRs and further distances than single sensors. Insights into successful spatial filter design are provided and this spatial filtering technique has created a new branch of multipath-aware localization systems.

Keywords: Ultra-wideband
Localization
Time-of-arrival
Tunnel
Advisor: Hum, Sean Victor
The Production of Protein Isolates from the Aqueous Extraction of De-hulled Yellow Mustard Flour and Determination of their Functional Properties

Two types of protein isolates were prepared from de-hulled yellow mustard flour by aqueous extraction, membrane processing and acid precipitation of proteins at the isoelectric point (IEP 5.5). Their electrophoretic, main functional properties and protein composition were determined. The precipitated and acid soluble protein isolates had 83.0 and 96.0% protein content on a moisture and oil free basis, respectively. The acid soluble protein isolate had comparable functional properties to those of commercially available soybean and other protein isolates. The precipitated protein isolate exhibited less desirable functionality than the soluble isolate, due to its high lipid content (~25%); however, it was still comparable to soybean isolates. Storage temperature had limited effect on lipid oxidation, and hence the stability of the precipitated protein isolate at 25-45ºC. Taste and texture of wieners and bologna prepared with 1-2% of this isolate as binder were comparable to those prepared with soy protein isolates.

Keywords: Yellow mustard
Aqueous extraction
Functional properties
Membrane processing
Advisor: Diosady, Levente L.
Properties and Performance of Photocatalytic Concrete

This research program is focused on the photocatalytic cement with emphasis on evaluating impacts on concrete’s physical, transport and durability properties. The scope of this project is to examine three key aspects of photocatalytic concrete including: a critical review of currently reported applications; an examination of air pollution concentrations in Ontario to assess the potential effectiveness of photocatalytic concrete, with respect to NOx; and an experimental study to characterize the material properties. Research findings revealed comparability between photocatalytic concrete and conventional concrete in mechanical and fluid transport properties. Although photocatalytic concrete resisted rapid freeze and thaw damage very well, in terms of de-icer salt scaling performance, only formed surface performed well and highly variable results for photocatalytic and GU concrete was observed for the finished surface.

Keywords: Photocatalytic
Concrete
Advisor: Panesar, Daman
Hooton, Robert Douglas
MIMO Performance of Low Mutual Performance of Low Mutual Coupling Antennas in Indoor and Hallway Environments

In this thesis, the 2×2 MIMO performance of several low mutual coupling antennas has been investigated in indoor and hallway scenarios. Three compact antennas intended for mobile applications with low mutual coupling between the input ports are presented in this thesis. To gauge the performances of the three designed antennas, two reference antennas are also used. Channel capacity measurements were conducted in Bahen Center Antenna Lab room 8175 and the Bahen Center 8th floor hallway by using the five antennas as receivers. The antenna spatial location, orientation, line-of-sight and non-line-of-sight situation and richness of multipath effect were considered in the measurements. By averaging the results, it is found that in an indoor environment, low mutual coupling antennas can outperform the reference high mutual coupling antennas especially in higher SNR scenarios. In the hallway environment, low mutual coupling antennas always outperform the reference high mutual coupling antennas due to pattern diversity.

Keywords: Antenna
MIMO
channel capacity
mutual coupling
Advisor: Eleftheriades, George V.
Electrochemical Based Detection of Influenza

Influenza is the infectious agent of the seasonal flu. Flu symptoms from influenza infection are similar to the symptoms caused by bacterial upper respiratory tract infections. This similarity causes the inappropriate diagnosis and prescription of antibiotics, leading to drug resistant bacterial strains. Moreover, the limitations of the current viral detection methods prevent the clinical diagnosis of influenza. The objective of this project is to design a rapid and sensitive influenza diagnostic method based on the highly sensitive Nanostructured microelectrode biosensing assay. The diagnostic method was designed by selecting probe sequences, controlling the quality of the probes and the sensing chips, and optimizing the deposition conditions. This diagnostic method was shown to be capable of differentiating influenza sequences from non-complementary sequences, detecting influenza sequences in the form of ~1000-nucleotide RNA molecules, sensing the target influenza RNA within a complex mixture of cell lysates, and achieving a clinically relevant detection limit.

Keywords: Nanostructured Micro Electrode
Influenza
Advisor: Kelley, Shana O.
Possible Modifications to the Accelerated Mortar Bar Test (ASTM C1260)

The Accelerated Mortar Bar test (AMBT) is rapid, reproducible, and perhaps the most widely used technique for examining the potential alkali-silica reactivity of aggregates. Unfortunately, this test is often unreliable as it may identify non-reactive aggregate as reactive and vice versa. With the aim of improving the accuracy of AMBT, two modifications to the current procedure were evaluated: 1) the maturity of mortar bars prior to alkali hydroxide exposure and 2) reduction of the storage temperature. The original and modified versions were performed on six aggregates with alkali-silica reactive (ASR) components, and their expansions and ASR classifications were compared. Results show that increasing the maturity had no significant impact on expansions. However, modifying the storage temperature to 60˚C and extending the period of testing to 28 days can be very effective in terms of more reliably identifying the existing falsely identified aggregates.

Keywords: Alkali-Silica Reaction
Accelerated Mortar Bar Test
ASTM C 1260
CSA A23.2-25A
Advisor: Hooton, Robert Douglas
The Effect of Bisphosphonate Therapy on Neutrophil Function: A Potential Biomarker Preliminary Findings

Bisphosphonate-related osteonecrosis of the jaws (BRONJ) occurs subsequent to intravenous and oral bisphosphonate exposure in a small subset of patients. Evidence of concurrent bacterial colonization at sites of bone necrosis, previous reports of neutrophil-related complications in some patients taking bisphosphonates along with perturbed neutrophil function in bisphosphonate-treated mice suggests an innate immune role in the development of bisphosphonate-related osteonecrosis of the jaws. This study investigates neutrophil function in BRONJ patients to determine if neutrophil functional defects may serve as a potential biomarker for BRONJ susceptibility. Patients with BRONJ and patients beginning intravenous pamidronate were studied. Eighteen patients with BRONJ and five patients beginning pamidronate therapy provided oral and blood neutrophil samples. Neutrophils from the population of patients with bisphosphonate-related osteonecrosis of the jaws and from those post-pamidronate treatment showed lower reactive-oxygen species production. These data suggest that a compromise in neutrophil function may be a potential biomarker for BRONJ susceptibility.

Keywords: Bisphosphonate
Neutrophils
Osteonecrosis
Biomarker
Advisor: Glogauer, Michael
Clokie, Cameron
MR Diffusion Measurements of Apoptotic Changes in Tumour Cells

Monitoring treatment efficacy is a large area of cancer research as it can increase the effectiveness of therapy regimens. Diffusion weighted Magnetic Resonance imaging (DWI), allows assessment of tissue microstructure without exogenous contrast agents. In this thesis, two different DWI techniques were used to acquire data from acute myeloid leukemia cells undergoing apoptosis, and data was fitted to an analytical model of re- stricted diffusion. Results indicated a decrease in average restriction size from 6.4 to 2.7μm, and an increase in the restricted diffusion coefficient from 0.17 to 0.82μm^2/ms in untreated versus treated cells. The free diffusion coefficient was constant indicating changes in restrictions, rather than any intrinsic changes in the intra-cellular or extra- cellular fluid. This combination of techniques has the potential for use in preclinical and clinical settings as it demonstrates that apoptotic changes may be measured consistently.

Keywords: imaging
magnetic resonance imaging
cancer
diffusion
apoptosis
medical physics
acute myeloid leukemia
cisplatin
Advisor: Stanisz, Greg