VictorJuiz/thesis huggingface dataset:
Chromatin Reassembly following a DNA Double-Strand Break Repair: The Ctf18-complex and Ctf4 work in concert with H3K56 Acetylation
Keywords: yeast
genetic interaction
DNA repair
acetylation
cohesion
histone

The budding yeast, Saccharomyces cerevisiae, serves as an excellent model for identifying fundamental mechanisms of DNA repair. A Local Coherence Detection (LCD) algorithm that uses biclustering to assign genes to multiple functional sub-groups was applied on the chromosome E-MAP containing genetic interactions among genes involved in nuclear processes. Using this method, we found that Asf1 and Rtt109, genes that are together required for histone H3K56 acetylation, cluster together with Ctf4, Ctf18, Ctf8 and Dcc1, genes important for efficient sister chromatid cohesion. It is known that H3K56 acetylation is required for post-repair chromatin reassembly at sites of DNA double-strand breaks (DSBs). The cohesion genes were previously implicated in the repair of some DNA DSBs, but the nature of their involvement has not been reported. The experimental data in my thesis work suggest that Ctf4, Ctf8, Ctf18 and Dcc1 function in the post-repair chromatin reassembly pathway.
Measurement of T1 in the Vessel Wall Using MRI
Keywords: Magnetic Resonance Imaging
Atherosclerosis
T1
MRI
Vessel Wall
Imaging

This thesis presents a high-resolution volumetric technique to measure the longitudinal relaxation time T1 in the vessel wall using MRI. The method of Variable Flip Angles (VFA) was applied using a new strategy for flip angle selection that allows measurement of T1 with high accuracy (< 10% mean error) and precision (T1-to-noise ratio > 10) over the wide range of anticipated values (300-3000ms) in the vessel wall. This strategy was validated in simulation, phantom and volunteer spinal cord experiments. Initial validation of vessel wall T1 measurements was performed in ex-vivo thoracic aorta samples from cholesterol-fed rabbits. For in-vivo vessel wall T1 mapping, the technique was augmented with spatial saturation bands for flow suppression and applied to the carotid arteries of three volunteers. Preliminary results from volunteers suggest that this approach may be useful in characterizing T1 changes associated with high-risk atherosclerotic disease.
Disruption of the Toll-like Receptor 4 Signaling Pathway by Salmonella Effector SigD
Keywords: Salmonella
SigD

The enteropathogenic bacteria Salmonella are the main cause of food borne gastroenteritis worldwide. The activation of Toll-like receptor 4 (TLR4) by LPS triggers an immune response to counter infection. Signaling by TLR4 requires the adaptor proteins, TIRAP and TRAM. Recruitment and activation of these molecules is dependent on the membrane lipid, PIP2. The Salmonella effector, SigD, is a 4-phosphatase that depletes PIP2 from the host plasma membrane during invasion. Thus, we investigated if SigD could lead to the interruption of the TLR4 pathway. We observed that SigD expression caused the disappearance of TIRAP from the Salmonella containing vacuoles (SCVs) in HeLa cells. Furthermore, we demonstrated that SigD attenuates NF-κB activation, implicating SigD in the disruption of the MyD88 dependent pathway. In addition, the observed inhibition of PKCε phosphorylation suggests SigD may also block the other branch of the TLR4 signaling cascade, the MyD88 independent pathway.
Generating Reliable and Predictable Lower-Limb Torque Vectors using Functional Electrical Stimulation
Keywords: Functional Electrical Stimulation
Standing Balance

Recovery of the ability to maintain balance during standing is one of the primary and essential goals of rehabilitation programs for individuals with Spinal Cord Injury (SCI). Regaining functionality during standing by means of a neuroprosthesis would decrease secondary complications and increase independence, and would consequently improve the quality of life of these individuals. However, the development of a standing neuro- prosthesis requires techniques to generate reliable and predictable torque vectors in the lower limbs. We proposed and tested a method based on surface Functional Electrical Stimulation (FES) and the idea that three independent muscles can form a basis that would span the joint torque vector space. We tested the proposed stimulation technique on the quadriceps muscles that produce knee extension. The results of this study suggest that the quadriceps muscle basis vectors are insufficient to cover the knee joint vector space.
Rights Without Remedies: The Court Party Theory and the Demise of the Court Challenges Program
Keywords: Court Challenges Program
access to justice
Charter of Rights and Freedoms
equality rights
Court Party Theory
litigation
intervener
intervenor
interest groups
judicial activism
judicial review
legal aid
section 15
s. 15
Rainer Knopff
Ian Brodie
F. L. Morton
CCP
human rights
statistics
study
quantitative

The author argues that the Court Challenges Program’s 2006 cancellation was based on claims that judicial review is undemocratic, including those made by three academics, Rainer Knopff, F.L. Morton and Ian Brodie; the Court Party Theorists (the “CPT”). Through a study of Charter equality cases, this paper examines the CPT’s arguments regarding judicial activism, interest groups and interveners and finds they are largely unsupported by statistical evidence. Further, the debate about judicial review and democracy obscures judicial review’s important auditing function over the legislature’s constitutional adherence. This audit depends on individuals’ capacity to pursue Charter litigation, an ability compromised by the access to justice crisis. The author examines this crisis and the efforts to fill the funding gap left by the CCP’s cancellation and concludes that a publicly-funded program like the CCP is best-placed to ensure that the Charter remains a relevant tool for enforcing fundamental human rights in Canada.
Intrinsic Properties of Rhodamine B and Fluorescein Gas-phase Ions Studied using Laser-Induced Fluorescence and Photodissociation in a Quadrupole Ion Trap Mass Spectrometer
Keywords: Analytical
Chemistry
Mass Spectrometry
Laser-induced fluorescence
Photodissociation

Studying the intrinsic properties of molecules in the gas-phase is advantageous, since it reduces the complexity present in solution that arises from interactions between the molecule of interest and other species present in the local environment, including those with the solvent itself. In this report, the photophysical properties of gaseous cationic rhodamine B (RBH+) were determined and photodissociation reaction kinetics and power dependence of three prototropic forms of fluorescein; the cation ([F + H]+), monoanion ([F - H]-), and dianion ([F – 2H]-2), each of which possesses their own distinct spectral properties, were measured. The analyte ions of interest were formed via electrospray ionization, mass-selected and stored in a quadrupole ion trap mass spectrometer which has been customized to enable gas-phase spectroscopic studies. Knowledge of the intrinsic photophysical properties of such chromophores in the gas-phase will enable a better understanding of how the local environment of the molecule alters its properties.
Robustness Analysis of Simultaneous Stabilization and its Applications in Flight Control
Keywords: Aerospace Engineering
Flight Control
Simultaneous Stabilization
Control Robustness
Aircraft Stability and Control

Simultaneous stabilization is an important problem in the design of robust controllers. It is the problem of designing a single feedback controller which will simultaneously stabilize every member of a finite collection of liner time-invariant systems. This provides simplicity and reliability which is desirable in aerospace applications. It can be used as a back-up control system in sophisticated airplanes, or an inexpensive primary one for small aircraft. In this work the robustness of the simultaneous stabilization problem, known as the Robust Simultaneous Stabilization (RSS) problem, is addressed. First, an optimization methodology for finding a solution to the Simultaneous Stabilization (SS) problem is proposed. Next, in order to provide simultaneous stability while maximizing the stability robustness bounds, a multiple-robustness optimization design methodology for the RSS problem is presented. The two proposed design methodologies are then compared in terms of robustness of the designed controller.
Application of Compressive Sensing and Belief Propagation for Channel Occupancy Detection in Cognitive Radio Networks
Keywords: spectrum sensing
compressive sensing
belief propagation
sparsity level detection

Wide-band spectrum sensing is an approach for finding spectrum holes within a wideband signal with less complexity/delay than the conventional approaches. In this thesis, we propose four different algorithms for detecting the holes in a wide-band spectrum and finding the sparsity level of compressive signals. The first algorithm estimates the spectrum in an efficient manner and uses this estimation to find the holes. The second algorithm detects the spectrum holes by reconstructing channel energies instead of reconstructing the spectrum itself. In this method, the signal is fed into a number of filters. The energies of the filter outputs are used as the compressed measurement to reconstruct the signal energy. The third algorithm employs two information theoretic algorithms to find the sparsity level of a compressive signal and the last algorithm employs belief propagation for detecting the sparsity level.
Design and Development of a Novel Device for Tissue Viscoelasticity Measurement
Keywords: Vibration
Viscoelastic

This thesis presents a novel device for measuring the viscoelastic properties of biological tissue. The ability to measure the mechanical properties of tissue is of special interest for many medical applications; ranging from disease diagnostics to surgical operations and simulations. In practice, physicians use a technique called palpation to detect the presence of viscoelastic property changes which are associated with the healthiness of tissue. Palpation relies exclusively on the expertise and experience of the physician and is only effective if the difference in tissue stiffness is profound. Current technologies for the measurement of tissue healthiness, including ultrasound, have been shown to be incapable of detecting isoechoic lesions even though they were significantly stiffer than surrounding tissue. The new device presents a reliable, accurate and quantitative method for determining the mechanical properties of soft tissue. Consequently, the healthiness of the tissue or the presence of lesions can be found.
Spray Drying Based Technologies for the Double Fortification of Salt with Iron and Iodine
Keywords: Spray Drying
Encapsulation
Iron
Iodine
Food Fortification

The fortification of salt with iron may reduce the prevalence of iron deficiency globally, but fortification is complicated by iron-iodiate interactions. To minimize this interaction, a spray dry microencapsulation system was developed. This study evaluated the creation and use of this system, and produced engineered iron premixes for integration into coarse iodized salt. Bioavailable ferrous fumarate powders were encapsulated to produce small particles (<20μm). Feed systems containing both suspended and dissolved ferrous fumarate were compared to find optimal conditions. The premixes were blended into iodized salt at 1000ppmiron and stored at 40C, ~60%RH. The salt was sampled periodically for 6 months to evaluate iodine stability. All encapsulated samples showed increased stability. The capsules ability to adhere to the salt as well as its colour and apparent bioavailability were evaluated. The evaluated samples indicate that stable double-fortified salt based on inexpensive, coarse, unrefined salt may be obtained economically by this approach.
Anti-plasmodium Activity of Small Imidazolium-and Triazolium-based Compounds
Keywords: Plasmodium falciparum
Imidazolium salts
Triazolium salts
Malaria
antimalarial drugs
invasion

In response to growing levels of resistance to currently used antimalarials, there is an urgent need to develop drugs that exhibit novel mechanisms to kill Plasmodium parasites. The objective of this study was to examine the antiparasitic activity of newly synthesized compounds based on imidazolium and triazolium rings. According to our structure/activity relationship studies the key components appear to be their positively charged rings and hydrophobic side groups, and bivalent compounds, which incorporate two positively charged rings, show even greater potency than monovalent compounds. Depending on the concentration used, our compounds appear to primarily inhibit intracellular parasite development or invasion into red blood cells. Selected compounds have been tested in vivo using a P. berghei ANKA murine model. Together, our findings demonstrate that small imidazolium- and triazolium-based compounds display both in vitro and in vivo activity through a novel mechanism of action that may involve inhibition of erythrocyte invasion.
Acceleration of Coevolution Detection for Predicting Protein Interactions
Keywords: bioinformatics
algorithms
computer hardware

Protein function is the ultimate expression of the genetic code of every organism, and determining which proteins interact helps reveal their functions. MatrixMatchMaker (MMM) is a computational method of predicting protein-protein interactions that works by detecting co-evolution between pairs of proteins. Although MMM has several advanced features compared to other co-evolution-based methods, these come at the cost of high computation, and so the goal of this research is to improve the performance of MMM. First we redefine the computational problem posed by the method, and then develop a new algorithm to solve it, achieving a total speedup of 570x over the existing MMM algorithm for a biologically meaningful data set. We also develop hardware which has not yet succeeded in further improving the performance of MMM, but could serve as a platform that could lead to further gains.
Development of Simulator Training to Reduce Head Motion Artifact in fMRI
Keywords: fMRI
motion
simulator
artifact

Functional MRI (fMRI) is a primary tool in the study of brain function. The primary cause of data corruption in fMRI is head motion while scanning. This problem is compounded by the fact that subjects are asked to perform behavioural tasks, which can promote head motion. Random and/or large head motions are often not handled well in post-processing correction algorithms. This thesis investigates the use of an alternate method: an MRI simulator to help reduce head motion in subjects through training. A simulator environment was developed where subjects could be trained to reduce their head motion through closed loop visual feedback. The effect of simulator training was investigated in young, old and stroke subjects. Performance of subjects with respect to head motion was investigated prior, during and after feedback training, including subsequent fMRI scans. This research helps improve fMRI image quality by reducing head motion prior to scanning.
Modulation of Aryl Hydrocarbon Receptor-dependent Transcription by Halogenated Compounds and Pharmaceuticals
Keywords: Aryl Hydrocarbon Receptor
Coactivators
Dioxin
Omeprazole
Furans

The aryl hydrocarbon receptor (AHR) mediates the toxic effects of halogenated aromatic hydrocarbons (HAHs), including 2,3,7,8-tetrachlorodibenzo-p-dioxin, 2,3,4,7,8-pentachlorodibenzofuran and 2,3,7,8-tetrachlorodibenzofuran. Y322 is believed to play a role in binding-independent activation of AHR by atypical inducers, such as omeprazole. I examined AHR-mediated regulation of and coactivator recruitment to CYP1A1, CYP1B1, HES1 and TiPARP in T-47D and HuH7 cells. All compounds induced expression of each gene in both cell lines, with some temporal differences between the HAHs and omeprazole. Chromatin immunoprecipitation assays demonstrated activator-, cell line- and gene-selectivity in AHR coactivator recruitment. Omeprazole induced AHR degradation which was prevented by MG-132 pre-treatment. Y322 was found to be important for maximal AHR activation by 2,3,7,8-TCDD and 2,3,4,7,8-PeCDF, but required for 2,3,7,8-TCDF and Omp in an AHR-deficient MCF-7 cells. My findings provide further evidence for cell-, gene- and ligand-dependent differences in AHR-mediated gene expression and coactivator recruitment, and a role for Y322 in AHR activation.
The Role of 3-deoxy-D-arabino-heptulosonate 7-phosphate Synthase 1 in Arabidopsis thaliana Metabolism
Keywords: Arabidopsis
DAHP synthase

The enzyme 3-deoxy-D-arabino-heptulusonate 7-phosphate synthase (DHS) catalyzes the first step of the shikimate pathway. In bacteria, the regulation of the pathway is mediated by allosteric inhibition of DHS by the aromatic amino acids tyrosine, phenylalanine and tryptophan. The regulation of the pathway in plants remains elusive but the aromatic amino acids are involved as suggested by the hypersensitivity of dhs1 knockout mutant to tyrosine. In this study the effects of the dhs1 mutation on endogenous levels of aromatic amino acids and of downstream metabolites are explored. HPLC analysis is used to measure levels of tyrosine and phenylalanine and 5-methyltryptophan sensitivity is used to probe levels of tryptophan. Additionally, the auxin content of whole seedlings was quantified by LC/MS and its local levels at the root apex are visualized with the DR5::GUS reporter system.
The Navigation of Non–English Speaking Elderly Hispanic Immigrants through the Service System
Keywords: non-English Speaking
older Hispanic adults

This qualitative study examined three areas of social service provision through the experiences of non-English speaking older Hispanic immigrants. These three areas included availability and accessibility of services and culturally competent practices of service providers. The qualitative approach of phenomenology was used to interview ten participants in order to explore their experiences with service provision. An analysis of the interviews pointed to the following themes: (a) experiences with services were deeply connected to issues of immigration and adaptation; (b) language barriers were especially difficult to overcome in services; (c) the role of families as primary supports needed to be reconsidered in order to offer better quality of services; and (d) culturally competent practices needed to be reinforced at the organizational level of workers, agencies and government in order to become more effective. From these themes, recommendations and implications for social work and services for non-English speaking elderly Hispanics are detailed.
Orthologous Gene Identification in Plant Species
Keywords: Orthologs
Comparative Genomics
Expressologs
Neutral Evolution
Expression Profile
Plant Species

In order to identify expressologs (orthologs exhibiting the highest expression profile ranking) among a variety of plant species, bioinformatic methods were used in order to first identify sequence orthologs and subsequently to rank these orthologs based on expression profile similarity. Analyses conducted on these data suggested that expressologs exhibited greater functional equivalency. A comparison of drought response in A. thaliana and Populus showed that expressologs exhibited a higher correlation when computed using stress data as opposed to developmental data. This suggested that the use of condition-specific data sets is more appropriate when examining specific conditions. Analysis was conducted in order to investigate the hypothesis that neutral evolution was a predominant factor in gene expression divergence. Some evidence was found for selection acting on expression pattern maintenance. Further analysis will be required in order to confirm the type of selection acting to maintain expression patterns across species.
Shear Behaviour of Deep Reinforced Concrete Members Subjected to Uniform Load
Keywords: Reinforced concrete
Shear
Uniform load
Shear behaviour
Clamping
Strut and tie
Sectional shear
Concrete
Deep beams
Continuous beams
Pre-cracking
Crack orientations

Experiments were conducted to investigate the shear behaviour of large deep beams subjected to uniform load. Six tests were performed on specimens with identical cross sections and reinforcing, but under different loading configurations. Variables included: span, degree of cracking prior to loading, proximity to a disturbed region near a reaction, and type of flexural stress on the loaded face. The findings indicate a specific set of variables resulting in unconservative predictions made using a strut-and-tie model for simply-supported beams subjected to uniform load, confirming and validating recent results by other researchers. A fanning strut model is proposed and is shown to provide more conservative results. The emerging trend of high capacity in continuous uniformly-loaded specimens is supported by the experimental results, as is the high capacity of specimens uniformly-loaded on their flexural tension face. Further, the high strength of specimens with suboptimal crack orientations supports recent experimental work.
Design and Characterization of a Multi-modality Phantom for Contrast Enhanced Ultrasound and Magnetic Resonance Imaging
Keywords: Imaging
Contrast Agents

Multi-modality imaging is a possible solution for overcoming individual modality limitations. With the use of modality specific contrast agents, contrast-enhanced multi-modality imaging may provide a more comprehensive evaluation of tumour characteristics. This may be possible by combining ultrasound and magnetic resonance imaging, whose contrast agents behave differently within the microvasculature. A novel, microvascular, and leaky phantom is presented that permits ultrasound contrast agents to remain entirely within the mimicking vascular compartment while the magnetic resonance contrast agents may freely diffuse between the mimicking vasculature and tissue compartments. The results show that the phantom is a useful tool for investigating the combination of contrast-enhanced ultrasound and magnetic resonance imaging. This work motivates further combined contrast-enhanced imaging studies, with future work to incorporate additional modalities.
Mechanisms of Vts1-Mediated Repression in S. cerevisiae
Keywords: Vts1
post-transcriptional regulation

Vts1p is the Saccharomyces cerevisiae member of the Smaug family of post-transcriptional regulators, which is a group of sequence-specific RNA-binding proteins that regulate target mRNA expression. Vts1p is known to mediate deadenylation-dependent degradation of target transcripts through the recruitment of the Ccr4p/Pop2p/Not deadenylase complex. By conducting a functional analysis of Vts1p deletion mutants, I demonstrate that two regions within Vts1p are independently capable of downregulating the expression of an mRNA reporter. I provide both genetic and biochemical evidence that suggests residues 170-523 regulate reporter expression at the level of mRNA stability and function through a mechanism that requires the Ccr4p/Pop2p/Not deadenylase, whereas residues 1-237 repress reporter expression at the level of translation and function through a novel mechanism. In addition, I map a direct interaction between the eIF4E-binding protein, Eap1p, and the Vts1p SAM domain, which suggests a model in which residues 170-523 recruit Eap1p to mediate efficient target transcript degradation.