VictorJuiz/thesis huggingface dataset:
On Improving Spectrum Utilization through Cooperative Diversity and Dynamic Spectrum Trading
Keywords: cooperative diversity
dynamic spectrum trading
secondary spectrum
cognitive radio networks
network coding

The prime wireless spectrum is inherently a critical yet scarce resource. As the demand of wireless bandwidth grows exponentially, it becomes a crucial issue to improve the spectrum utilization for the development and deployment of any new wireless technologies. In this thesis, we seek to address this problem through cooperative diversity and dynamic spectrum trading, in the context of the envisioned primary-secondary dynamic spectrum sharing paradigm. For an OFDMA-based cellular primary network which owns an exclusive right to access a certain spectrum band, we propose XOR-assisted cooperative diversity to improve the spectral efficiency of the allocated band, as well as an optimization framework to address the resource allocation problem. For the secondary network that utilizes cognitive radios to opportunistically exploit the spectrum white spaces, we establish a spectrum secondary market, design the market institution based on double auctions, and solve the decision making problem using reinforcement learning, to improve spectrum utilization via trading among secondary users.
Delivery of Helper-dependent Adenoviral Vectors to the Subretinal Space of Mice
Keywords: eye gene therapy
viral vectors
helper dependent adenovirus
subretinal injections
retina
photoreceptors

The helper-dependent adenoviral (HD-Ad) vector is the latest generation of Ad vectors. It ameliorates the vector-associated immunogenic problems with increased capacity for carrying DNA because all viral coding genes are removed. I hypothesize that HD-Ad vectors can be effective vehicles for retinal gene delivery. The objectives of this study are to determine if HD-Ad vectors can deliver reporter genes, GFP or lacZ, driven by a CMV or a MOPS promoter, into specific retinal layers. Subretinal injections were performed and eyes removed at time points from 1 week to 3 months, processed for fluorescent microscopy, X-gal staining, and H&E staining. Transgene expression was detected for at least 3 months. A dose dependent relationship was revealed between the level of transgene expression and viral vector dose. Distinctively, the MOPS promoter drove photoreceptor cell specific expression. Notably, no sign of inflammation or tissue toxicity was detected, demonstrating the benefits of the HD-Ad vector.
A Real-time Mediated Reality Platform for Outdoor Navigation on Mobile Devices and Wearable Computers
Keywords: Mediated Reality
Wearable Computing

Wearable computing systems have been researched and developed for several decades. With the advent of the head-mounted display, augmented and mediated reality systems became an important example of wearable computing. However, due to certain factors such as computational constraints, cost, obtrusiveness, practicality, and social acceptance, mediated reality systems have been leveraged in only very specific application domains and have yet to see mainstream adoption. This dissertation describes the research and development of a real-time mediated reality platform developed for modern mobile devices to provide a more reasonable transition in overcoming the mainstream adoption barrier of mediated reality systems. In particular, an outdoor navigational application that provides contextually-relevant information about a user’s surroundings is developed using the platform as a proof-of-concept for evaluation. In addition, the server infrastructure required to support the application is discussed, as well as the evaluation of a hybrid orientation tracking approach using sensors and computer vision.
W-Band Passive and Active Circuits in 65-nm Bulk CMOS for Passive Imaging Applications
Keywords: mm-wave
CMOS
passive imaging
LNA
switches
noise figure
peak detector

The design and implementation of mm-wave switches, variable attenuators, and a passive imaging system in 65-nm CMOS are presented. The design and analysis of shunt switches is presented with a demonstration circuit showing record performance for a single-pole single-throw switch with 1.6dB loss and 30dB isolation at 94GHz. Single-pole double-throw (SPDT) switches are shown, with 4dB insertion loss in the W-band (75-110GHz), and the only reported SPDT switch operating in the D-band (110-170GHz). A novel technique for implementing digitally controlled variable attenuation is presented, resulting in variable attenuation between 4 and 30dB in the W-band. Finally, a W-band radiometer is described integrating a record-high gain CMOS LNA, SPDT switch, and peak detector. This is the highest-frequency imaging system in CMOS with this level of integration, offering a responsivity over 90kV/W, and a noise-equivalent power less than 0.2pW/√Hz.
Charaterization of Beta-cell Specific Knockout of UCP2
Keywords: diabetes
UCP2

The whole body UCP2 knockout (UCP2−/−) have enhanced insulin secretion and higher ATP content. However, these changes could be due to indirect effects of extra-pancreatic deletion and therefore, generating beta-cell specific knockout mice (UCP2BKO) is essential. A 90% knockdown of UCP2 protein was observed in beta-cells of UCP2BKO mice. No significant differences were observed in body weight accumulation, fasting blood glucose, plasma insulin or glucagon. UCP2BKO had impaired oral glucose tolerance with no differences in insulin secretion or sensitivity. Enhanced ROS accumulation was observed in the beta-cells of UCP2BKO and upregulation of antioxidant enzyme genes. Morphometric analysis showed an increased glucagon positive area in the pancreata of UCP2BKO mice. Results obtained from UCP2BKO were contrary to the phenotype observed in UCP2−/− mice. Overall, the characterization of UCP2BKO demonstrates that UCP2 in the beta-cell is involved in modulating ROS production.
A Novel Biosensing Interface Preparation Method for ElectroMagnetic Piezoelectric Acoustic Sensor
Keywords: biosensor
self-assembling monolayer
EMPAS
thiolsulfonate

Preliminary work towards the development of novel biosensing interfaces for EMPAS (ElectroMagnetic Piezoelectric Acoustic Sensor) is presented in this manuscript. This method involves the use of unprecedented thiosulfonate-based linkers to construct robust and durable SAMs (Self-Assembling Monolayer) onto piezoelectric quartz crystals, which can chemoselectively immobilize thiol-containing biomolecules under aqueous conditions in a single, straightforward, reliable and coupling-free manner. Initial efforts are devoted to the construction of SAMs and the subsequent immobilization of thiol-containing biomolecules, and then characterization by CAMs (Contact Angle Measurement) and ARXPS (Angle-Resolved X-ray Photoelectron Spectroscopy). This method is then implemented into the construction of biosensing interfaces dedicated to the detection of avidin. With the incorporation of OEG (Oligo(Ethylene Glycol)) backbone and diluent in the method, 14-fold difference in signal response of EMPAS was observed between biotinylated and unfunctionalized SAMs.
Roko: Balancing Performance and Usability in Coarse-grain Parallelization
Keywords: Programming Model
Parallelization
Synchronization
Concurrency Control
Multi-core Systems
FPGA Applications

We present Roko, a system that allows parallelization of sequential C codes with a modest user intervention. The user exposes parallelism at the function level by annotating the code with pragmas. Roko defines only two pragmas: the parallel pragma is used to denote function calls that will be executed asynchronously, and the exposed pragma is used to describe data usage of the marked function calls. Architecturally, Roko consists of three components: a compiler that analyzes pragmas, a software environment that spreads the execution over multiple processors, and a hardware support that implements a novel synchronization scheme, versioning. We have designed, implemented and evaluated an FPGA-based prototype of Roko. Our experimental evaluation shows: (i) that few simple pragmas are all that is needed to expose parallelism in benchmark applications and (ii) that Roko can deliver good performance in terms of application speedup.
Characterization of the Role of CXCL10 and CXCR3 in Breast Cancer
Keywords: Breast Cancer
Lymphocytic Infiltration
Chemokine
Basal
CXCL10
CXCR3

Lymphocytic infiltration is a feature of basal breast cancer tumors. CXCL10 is a chemokine that was found expressed higher in basal tumor RNA compared to estrogen receptor positive tumor RNA. Both CXCL10 and its receptor CXCR3 were expressed in familial breast cancer tissues, a proportion of which have a basal phenotype. CXCL10 expression was associated with lymphocytic infiltration, and with CXCR3 expression. CXCL10 ligand and receptor were overexpressed individually or together in the human MCF7 cell line. Recombinant human CXCL10 was found to dose dependently decrease cell proliferation. CXCR3 and CXCL10-CXCR3 expressing cells had the potential for increased migration independent of CXCL10 concentration. Co-expression of both genes increased proMMP-2 levels, and conditioned media from one of these clones chemoattracted more of the CXCR3 clones, CXCL10-CXCR3 clones, and CD4+ T-lymphocytes. CXCL10 neutralization suggested that CXCL10 could play a role in this chemoattraction, though it is likely not the only factor involved.
Optimization of Purification Conditions for the Pseudomonas syringae HopZ1a Type III Secreted Effector Protein for Structural and Functional Studies
Keywords: Molecular biology
microbiology

HopZ1a is a type III secreted effector (TTSE) protein from Pseudomonas syringae. The goal of this study was to obtain a 3D crystal structure of HopZ1a to provide insight into its biochemical function. The first objective was to obtain HopZ1a protein that was sufficiently abundant and pure for crystallographic studies. Purification conditions were optimized and multiple constructs of HopZ1a were generated using secondary structure prediction programs as well as structural characteristics inherent to TTSEs. Truncations of HopZ1a from the N- and C-terminus led to a soluble, proteolytically resistant construct, HopZ1a66-261. This protein formed granular precipitates in crystallography screens. These conditions will provide the basis for refinement screens aimed at optimizing the HopZ1a crystallization conditions. Overall, the soluble constructs described in this study will provide invaluable tools for future in vitro functional and structural studies of this important family of type III secreted effector proteins.
Cough Detection and Forecasting for Radiation Treatment of Lung Cancer
Keywords: cough detection
arma forecasting
respiratory gating
breathing measurement
gaussian mixture model
4DCT

In radiation therapy, a treatment plan is designed to make the delivery of radiation to a target more accurate, effective, and less damaging to surrounding healthy tissues. In lung sites, the tumor is affected by the patient’s respiratory motion. Despite tumor motion, current practice still uses a static delivery plan. Unexpected changes due to coughs and sneezes are not taken into account and as a result, the tumor is not treated accurately and healthy tissues are damaged. In this thesis we detail a framework of using an accelerometer device to detect and forecast coughs. The accelerometer measurements are modeled as a ARMA process to make forecasts. We draw from studies in cough physiology and use amplitudes and durations of the forecasted breathing cycles as features to estimate parameters of Gaussian Mixture Models for cough and normal breathing classes. The system was tested on 10 volunteers, where each data set consisted of one 3-5 minute accelerometer measurements to train the system, and two 1-3 minute accelerometer measurements for testing.
Sex Differences in Sensorimotor Mu Rhythms During Selective Attentional Processing
Keywords: sex differences
attention
somatosensory processing
mu rhythms

Magnetoencephalography was used to investigate the effect of directed attention on changes in sensorimotor mu (8-12Hz) response (mu reactivity) to non-painful electrical stimulation of the median nerve in healthy adults. Results indicated attention-related sex differences in mu reactivity, with females showing i) prolonged mu suppression when attending to somatosensory stimuli indicating active processing of the sensory stimuli; ii) task-dependent attentional modulation of the mu response, which was absent in males, and iii) a trend for greater neuronal excitability of the primary somatosensory region suggesting greater physiological responsiveness to stimulation overall. Sex-related differences in attentional modulation of sensorimotor rhythms suggest that females and males use different top-down control strategies when processing somatosensory information. These sex differences in attention may underlie well-documented sex-related biases in pain processing wherein females typically report greater sensitivity to experimental and clinical pain.
Quantifying the Spatial Relationship between Landcover Hheterogeneity and Species' Distributions
Keywords: boundary analysis
species range
birds
spatial heterogeneity
conservation
Ontario

Although considerable research has been invested in disentangling the factors limiting species’ ranges at local and continental spatial scales, less attention has been granted to the relationship between species’ spatial distributions and landscape attributes at intermediate spatial scales. This research investigates the spatial relationship between avian species’ distributions (Ontario Breeding Bird Atlas [2001-2005] data) and landcover heterogeneity (Ontario Land Cover [1991-1998] data) in terms of their respective boundary locations (i.e., high rates of change in landcover composition and avian species turnover) in a vulnerable transitional zone in southern Ontario. Significant spatial overlap was found between landcover and avian boundaries. Given that land management decisions are most often made at the regional or landscape scales, this positive spatial relationship has important implications for conservation efforts. Future research should focus on assessing the spatial relationship between landcover heterogeneity and avian species’ distributions for different functional and taxonomic groups.
Automated Microfluidic Sample Preparation for Laser Scanning Cytometry
Keywords: microfluidics
laser scanning cytometry
automated

Laser scanning cytometry (LSC) is a slide-based method that is used clinically for Quantitative Imaging Cytometry (QIC). A “Clatch” slide, named after the inventor, which is used in conjunction with the LSC for immunophenotyping patient cell samples, has several drawbacks. The slide requires time consuming and laborious pipette steps, making the slide prone to handling errors. The Clatch slide also uses a significant amount of cell sample, limiting the number of analyses for fine needle aspirate (FNA) samples. This thesis details an automated microfluidic system, composed of an embedded circuit, a plastic and polymer microfluidic device, and an aluminum frame, which can perform the same immunophenotyping procedures. This new system reduces the labor from 36 pipette steps to 8, it reduces the amount of cell sample from 180 μL to 56 μL, and it shortens the entire procedure from 75 minutes to 42 minutes.
An Investigation of the Exocyst Complex and its role in Compatible Pollen-pistil Interactions in Arabidopsis
Keywords: Exocyst Complex
Arabidopsis
Molecular signaling
Plant Reproduction
Pollen-Pistil Interactions
Compatibility
Self-Incompatibility
Exo70A1
Vesicle Trafficking
Docking Complexes
Brassica
Stigma
Papillae Cells

Compatible interactions between male gametophytes (pollen) and the female reproductive organ (pistil) are essential for fertilization in flowering plants. Recognition at a molecular level allows “compatible” pollen grains to adhere/germinate on the stigma while pollen grains from unrelated plant species are largely ignored. The exocyst is a large eight subunit complex that is primarily involved in polarized secretion or regulated exocytosis in eukaryotic cells where it functions to tether vesicles to the plasma membrane. Recent research has implicated one of the Exo70 family members, Exo70A1, in compatible pollen-pistil interactions in Arabidopsis and Brassica. The loss of Exo70A1 in Arabidopsis Col-0 stigmas leads to the rejection of compatible pollen producing a “female sterile” phenotype. Through my research I have demonstrated that, driven by a stigma-specific promoter, an RFP:Exo70A1 fusion protein rescues this defect in exo70A1-1 mutant and Exo70A1 is found to be localized to the plasma membrane at flower opening.
Effects of Rosiglitazone on Nitrolgycerin-induced Endothelial Dysfunction
Keywords: rosiglitazone
endothelial dysfunction

Sustained nitroglycerin (GTN) therapy impairs endothelial function in healthy volunteers and patients with cardiovascular disease, caused by an increase in vascular oxidative stress. This study aims to estimate the effect of rosiglitazone on vascular endothelial function in healthy volunteers continuously dosed to transdermal GTN (0.6mg/hr) for 7 days. To assess endothelial function, forearm blood flow was measured by venous occlusion strain-gauge plethysmography in response to intra-brachial infusions of acetylcholine. GTN-treated subjects experienced significant attenuation of endothelium-dependent responses to acetylcholine (p<0.05; compared to placebo), but was reversed with vitamin C (p=ns; compared to placebo). Endothelium-dependent responses to acetylcholine were blunted in groups randomized to rosiglitazone alone (p<0.05; compared to placebo) and rosiglitazone + GTN (p<0.05 compared to placebo). Interestingly, this effect was not modified by vitamin C. In conclusion, rosiglitazone impairs endothelial function and concurrent therapy with rosiglitazone does not attenuate the adverse effects of transdermal GTN on the vasculature.
Ultrastructural and Histochemical Characterization of the Zebra Mussel Adhesive Apparatus
Keywords: Zebra Mussel
Dreissena polymorpha
byssus
ultrastructure
bioadhesive
adhesive
3,4-dihydroxyphenylalanine
DOPA
TEM
transmission electron microscopy
bio-adhesive
catechol oxidase
immunogold labeling
histochemistry
histochemical methods
adhesive plaque
cryoultramicrotomy
TEM biological sample preparation

Since their accidental introduction into the Great Lakes in mid- to late-1980s, the freshwater zebra mussels, Dreissena polymorpha, have colonized most lakes and waterways across eastern North America. Their rapid spread is partly attributed to their ability to tenaciously attach to hard substrates via an adhesive apparatus called the byssus, resulting in serious environmental and economic impacts. A detailed ultrastructural study of the bysuss revealed a 10 nm adhesive layer at the attachment interface. Distributions of the main adhesive amino acid, 3,4-dihydroxyphenylalanine (DOPA), and its oxidizing (cross-linking) enzyme, catechol oxidase, were determined histochemically. It was found that, upon aging, DOPA levels remained high in the portion of the byssus closest to the interface, consistent with an adhesive role. In contrast, reduced levels of DOPA corresponded well with high levels of catechol oxidase in the load-bearing component of the byssus, presumably forming cross-links and increasing the cohesive strength.
Development of an Enzyme Immunoassay and Cellular Function Assays to Probe the Function of Teneurin C-terminal Associated Peptide (TCAP)
Keywords: ELISA
reporter
TCAP
teneurin
cFos
solubility
solution
immunoassay
peptide
signal transduction
neuron
promoter element

The teneurin C-terminal associated peptides (TCAP) are a family of four predicted peptides that are expressed in all metazoans where the teneurins have been studied to date. Of the four peptides, TCAP-1 has been studied most extensively. In vitro, TCAP-1 increases neuronal proliferation and neurite outgrowth. In vivo, the peptide reduces CRF-induced behavioural responses in rats. Despite the large body of evidence indicating a strong biological role for TCAP-1, little is known about the chemistry and solubility of the peptide, or the signaling pathway(s) mediating these effects. The aim of this research was to appropriately solubilize the peptide and to develop detection assays for its study in greater detail. I have now established an appropriate formulation of TCAP-1 and developed an immunoassay to assess its concentrations in tissues and in circulation. Also, by examining a number of transcriptional response elements, I have found two assays for probing the signal transduction mechanisms of this peptide.
Transparent Conductive Oxides for Organic Photovoltaics
Keywords: organic electronics
transparent conductors

Organic solar cells and organic light emitting diodes are on the forefront of emerging technologies aimed at harnessing light in ways never thought possible. Largear installations of OLED solid state lighting (SSL), as well as organic photovoltaics(OPVs), will become possible as the efficiencies of these devices continue to rise. All organic solar cells and OLEDs require the use of transparent conductive electrodes.Indium oxide (ITO) is currently the transparent conductor of choice for these applications, due to its unique combination of transparency, high conductivity, durability,and favourable surface properties. Indium, however, is a rare and expensive metal; proposed large-area installations of OPV cells and OLEDs will add further strain to global indium supply. Transparent conductive materials that are abundant, inexpensive, and which enable efficient and robust organic devices must therefore be developed. In the present work, suitable ITO anode replacement materials are demonstrated for OLEDS, small-molecule, polymer, and PbS colloidal quantum dot photovoltaics.
Optical and Structural Characterization of Amorphous Carbon Films
Keywords: amorphous carbon
optical

A fundamental study of the correlations between ion energy, substrate temperature, and plasma density with hydrogen content, percent sp2 bonding, optical gap, and refractive index of hydrogenated amorphous carbon (a-C) films is presented. A strong dependency between the ion energy used during deposition and the film’s microstructure is shown. Moreover, it is revealed that the optical properties of the a-C films are controlled by the concentration and size of sp2 clusters in the film. Through N2 mixing in the source gas, room-temperature nitrogen doped polymeric-like a-C films were demonstrated for the first time. X-ray Photoelectron Spectroscopy revealed an increase in the Fermi level of these films with increased nitrogen content. A proof-of-concept a-C based transparent heat mirror (THM) was demonstrated. It was shown that a-C acts as an oxygen-free protective barrier and anti-reflective coating for Ag films in the THM, increasing the transmission in the visible region by 10-20%.
The Role of Rac1 and Rac2 in Determining Bone Quality in Aged and Osteoporotic Female Mouse Models
Keywords: Rac GTPases
bone remodeling
osteoclastogenesis
bone quality

The osteoclasts, the bone cells responsible for bone degradation, have a crucial role in the age-related bone loss and post-menopause osteoporosis. Rac1 and Rac2, members of the Rho-family of small GTPases, are known for having a key role in osteoclast formation and activity, which could be translated to bone quality. In this study, we characterize the roles of Rac1 and Rac2 on bone quality using an aged and osteoporotic mouse model. Bones from wild type, Rac1KO and Rac2KO mice were harvested for mechanical tests, bone densitometry, micro-computed tomography and histomorphometric analyses to evaluate bone mineralization and architecture. We observed that the deletion of Rac1 or Rac2 in pre-osteoclasts minimized bone loss in both age-related and post-menopause osteoporosis. These results highlight the importance of the two small GTPases in bone remodeling and identify Rac1 and Rac2 as potential targets for the development of new therapies for the treatment of osteoporosis.