VictorJuiz/thesis huggingface dataset:
Application of Compressive Sensing and Belief Propagation for Channel Occupancy Detection in Cognitive Radio Networks

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.

Keywords: spectrum sensing
compressive sensing
belief propagation
sparsity level detection
Advisor: Valaee, Shahrokh
Design and Development of a Novel Device for Tissue Viscoelasticity Measurement

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.

Keywords: Vibration
Viscoelastic
Advisor: Zu, Jean W.
Spray Drying Based Technologies for the Double Fortification of Salt with Iron and Iodine

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.

Keywords: Spray Drying
Encapsulation
Iron
Iodine
Food Fortification
Advisor: Diosady, Levente L.
Cheng, Yu-Ling
Anti-plasmodium Activity of Small Imidazolium-and Triazolium-based Compounds

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.

Keywords: Plasmodium falciparum
Imidazolium salts
Triazolium salts
Malaria
antimalarial drugs
invasion
Advisor: Crandall, Ian E.
Acceleration of Coevolution Detection for Predicting Protein Interactions

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.

Keywords: bioinformatics
algorithms
computer hardware
Advisor: Rose, Jonathan S.
Burst-train Generation for Femtosecond Laser Filamentation-driven Micromachining

Bursts of femtosecond laser pulses with a repetition rate of 38.5MHz were created by integrating a purpose-built burst resonator system with a Ti: Sapphire laser system. The timing control system in this work provided flexibility for generation of any desirable pulse train profile in the burst envelope. These laser pulses further have been used for high aspect ratio hole drilling inside glass materials. High repetition rate of the pulses produces heat accumulation effects during the laser machining interaction which provided the possibility of deeper etching, increased the aspect ratio, and mitigated cracks and damages effects of single pulses. During the process, time-resolved nanosecond scale side-view images have been recorded with a time-gated intensified-CCD camera enabling the observation of transient effects during the laser machining process. These side-view images further have been used to assess the physics of burst interaction and illustrate benefits and disadvantages of high repetition rate laser pulses.

Advisor: Herman, Peter R.
Development of Simulator Training to Reduce Head Motion Artifact in fMRI

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.

Keywords: fMRI
motion
simulator
artifact
Advisor: Graham, Simon James
Modulation of Aryl Hydrocarbon Receptor-dependent Transcription by Halogenated Compounds and Pharmaceuticals

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.

Keywords: Aryl Hydrocarbon Receptor
Coactivators
Dioxin
Omeprazole
Furans
Advisor: Matthews, Jason
The Role of 3-deoxy-D-arabino-heptulosonate 7-phosphate Synthase 1 in Arabidopsis thaliana Metabolism

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.

Keywords: Arabidopsis
DAHP synthase
Advisor: Christendat, Dinesh
The Navigation of Non–English Speaking Elderly Hispanic Immigrants through the Service System

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.

Keywords: non-English Speaking
older Hispanic adults
Advisor: McDonald, Lynn
Orthologous Gene Identification in 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.

Keywords: Orthologs
Comparative Genomics
Expressologs
Neutral Evolution
Expression Profile
Plant Species
Advisor: Provart, Nicholas
Shear Behaviour of Deep Reinforced Concrete Members Subjected to Uniform Load

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.

Keywords: Reinforced concrete
Shear
Uniform load
Shear behaviour
Clamping
Strut and tie
Sectional shear
Concrete
Deep beams
Continuous beams
Pre-cracking
Crack orientations
Advisor: Collins, Michael P.
Bentz, Evan
Design and Characterization of a Multi-modality Phantom for Contrast Enhanced Ultrasound and Magnetic Resonance Imaging

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.

Keywords: Imaging
Contrast Agents
Advisor: Chopra, Rajiv
Mechanisms of Vts1-Mediated Repression in S. cerevisiae

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.

Keywords: Vts1
post-transcriptional regulation
Advisor: Smibert, Craig
Endothelial Cells Guided by Immobilized Gradients of Vascular Endothelial Growth Factor on Porous Collagen Scaffolds

A key challenge in tissue engineering is overcoming cell death in the scaffold interior due to the limited diffusion of oxygen and nutrients therein. We hypothesized here that immobilizing a gradient of vascular endothelial growth factor (VEGF-165) would guide endothelial cells into the interior of the scaffold thereby enhancing angiogenesis. The protein was immobilized onto a collagen scaffold through carbodiimide chemistry by one of the three methods experimented: placing 5 µl of the solution at the center of the scaffold to create a ~2 ng/ml/mm gradient in a radial direction. D4T endothelial cells were observed to be guided by this VEGF-165 gradient deep into the center of the scaffold compared to both uniformly immobilized VEGF-165 and VEGF-free controls. We concluded that the VEGF-165 gradient scaffolds promoted the migration, and not proliferation, of cells deep into the scaffold. These gradient scaffolds provide the foundation for future in vivo tissue engineering studies.

Keywords: gradient
VEGF
Tissue Engineering
collagen
immobilization
Advisor: Radisic, Milica
Shoichet, Molly
Testing the Cruciferin Deficient Mutant, ssp-1, of Arabidopsis thaliana, as a Vehicle for Overexpression of Foreign Proteins

ssp-1 is a seed storage protein mutant which is deficient in one of the major seed storage proteins in Arabidopsis thaliana, the 12S cruciferins. To determine if this mutant can drive a higher level expression of a transgene than that found in wild type, the mutant was transformed with the phytohemagglutinin (PHA) gene and single copy PHA homozygotes were identified. These PHA transformants were crossed to wild type so that each PHA gene would be in the same copy number and chromosomal context in a wild type background. Immunoblotting was employed to compare the PHA levels of the single copy transformants in both genetic backgrounds. PHA levels ranged from 4.52% to 7.7% of the total protein in transformants. Two of the transformants showed 30.33% and 44.18% more PHA than that of their backcross. Therefore, a mutant such as ssp-1 may provide a means for overexpression of foreign proteins.

Keywords: seed storage protein mutant 1
Arabidopsis thaliana
12S cruciferins deficiency
‘empty container’ hypothesis
Advisor: Riggs, C. Daniel
Rac2 is Required for Formation of Extracellular Traps in Neutrophils

Recently, it was found that pathogens are trapped and killed by neutrophil extracellular traps (NETs). The role of Rac small GTPases is explored in the formation of NET using neutrophils lacking Rac1, Rac2 or both isoforms. NET formation was observed in both wild-type and Rac1-null neutrophils. In contrast, NET formation was markedly impaired in cells lacking either Rac2 or both Rac2 and Rac1. The defect in NET formation in Rac2-null cells was rescued in the presence of exogenous reactive oxygen species sources, suggesting that Rac2-mediated ROS generation is required. In addition, the role of nitric oxide in NET formation is assessed. Blocking NO production with the nitric oxide synthase inhibitor L-NAME significantly reduced NET formation. Moreover, Rac2-null cells produced significantly less NO than Rac1-null cells or their wild type counterparts. Our data suggest that Rac2 is essential for NET formation via pathways involving both ROS and NO.

Keywords: neutrophils
neutrophil extracellular traps
Rac
NETs
Advisor: Glogauer, Michael
Evaluation of UWB Beamformers in a Wireless Channel and Potential Microwave Implementations

Ultra-wideband (UWB) wireless communication is a topic of intense research. It has the potential for superior performance over comparable narrowband wireless systems. UWB wireless systems transmit pulses that have energy concentrated mainly from 3.1 GHz to 10.6 GHz. These pulses are transmitted at very low energy levels so as not to interfere with many existing wireless systems that operate in the same band. UWB communication systems can benefit significantly from beamforming networks where the received signal strength depends on angle of arrival. This thesis focuses on the characterization of a digital beamformer in a real wireless channel. The beamformer is evaluated using various methods to judge its performance impact on a real UWB communication system. An analog UWB beamformer in hardware is derived by taking advantage of a simple microwave circuit realization. The analog UWB beamformer is studied and its feasibility is evaluated.

Keywords: beamformer
UWB
Advisor: Hum, Sean Victor
Network Clustering in Vehicular Communication Networks

This thesis proposes a clustering algorithm for vehicular communication networks. A novel clustering metric and an improved clustering framework are introduced. The novel clustering metric, network criticality, is a global metric on undirected graphs which quantifies the robustness of the graph against changes in environmental parameters, and point-to-point network criticality is also defined to measure the resistance between different points of a graph. We localize the notion of network criticality for a node of a vehicular network which can potentially be promoted as the cluster header. We use the localized notion of node criticality in conjunction with a universal link metric, Link Expiration Time (LET), to derive a clustering algorithm for the vehicular network. We employ a distributed multi-hop clustering algorithm based on the notion of network criticality. Simulation results show that the proposed clustering algorithm forms a more robust cluster structure.

Keywords: clustering algorithm
network
Advisor: Leon-Garcia, Alberto
Fabrication and Characterization of Nano-FET Biosensors for Studying Osteocyte Mechanotransduction

Nano-FET biosensors are an emerging nanoelectronic technology capable of real-time and label-free quantification of soluble biological molecules. This technology promises to enable novel in vitro experimental approaches for investigating complex biological systems. In this study, we first explored osteocyte mechanosensitivity under different mechanical stimuli and found that osteocytes are exquisitely sensitive to different oscillatory fluid flow conditions. We therefore aimed to characterize protein-mediated intercellular communication between mechanically-stimulated osteocytes and other bone cell populations in vitro to elucidate the underlying mechanisms of load-induced bone remodeling. To this end, we devised a novel nano-manipulation based fabrication method for manufacturing nano-FET biosensors with precisely controlled device parameters, and further investigated the effect of these parameters on sensor performance.

Keywords: NanoFET
nanowire
biosensor
osteocyte
mechanotransduction
nanomanipulation
MEMS
NEMS
bone
bone remodelling
Advisor: Sun, Yu
You, Lidan