VictorJuiz/thesis huggingface dataset:
Endothelial Cells Guided by Immobilized Gradients of Vascular Endothelial Growth Factor on Porous Collagen Scaffolds
Keywords: gradient
VEGF
Tissue Engineering
collagen
immobilization

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.
Testing the Cruciferin Deficient Mutant, ssp-1, of Arabidopsis thaliana, as a Vehicle for Overexpression of Foreign Proteins
Keywords: seed storage protein mutant 1
Arabidopsis thaliana
12S cruciferins deficiency
‘empty container’ hypothesis

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.
Rac2 is Required for Formation of Extracellular Traps in Neutrophils
Keywords: neutrophils
neutrophil extracellular traps
Rac
NETs

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.
Evaluation of UWB Beamformers in a Wireless Channel and Potential Microwave Implementations
Keywords: beamformer
UWB

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.
Network Clustering in Vehicular Communication Networks
Keywords: clustering algorithm
network

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.
Fabrication and Characterization of Nano-FET Biosensors for Studying Osteocyte Mechanotransduction
Keywords: NanoFET
nanowire
biosensor
osteocyte
mechanotransduction
nanomanipulation
MEMS
NEMS
bone
bone remodelling

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.
Application of Gaussian Moment Closure Methods to Three-Dimensional Micro-Scale Flows
Keywords: CFD
Micro-scale

A parallel, block-based, three-dimensional, hexahedral finite-volume scheme with adaptive mesh refinement has been developed for the solution of the 10-moment Gaussian closure for the modelling of fully three-dimensional micro-scale, non-equilibrium flows. The Gaussian closure has been shown to be a more effective tool for modelling rarefied flows lying within the transition regime than the Navier-Stokes equations, which encounter mathematical difficulties approaching free-molecular flows, and is computationally less expensive than particle-based methods for flows approaching the continuum limit. The hyperbolic nature of the moment equations is computationally attractive and the generalized transport equations can be solved in an accurate and efficient manner using Godunov-type finite-volume schemes as considered here. Details are given of the Gaussian closure, along with extensions for diatomic gases and slip-flow boundaries. Numerical results for several canonical flows demonstrate the potential of these moment closures and the parallel solution scheme for accurately predicting fully three-dimensional non-equilibrium flow behaviour.
The Effects of Helium on Deuterium Retention in Tungsten Under Simultaneous Irradiation
Keywords: Fusion
Tungsten
Deuterium
Helium
Plasma Surface Interactions
Simultaneous irradiation

The trapping behavior of deuterium and helium in polycrystalline tungsten (PCW) under D+-only, He+-only, sequential and simultaneous irradiation was studied as a function of incident ion fluences and irradiation temperature. Deuterium implanted at 300 and 500 K gets trapped at surface adsorption sites, vacancy-related traps, or extended defects. No deuterium was trapped for 700 K implantations. Results were affected by tungsten-carbide impurities in PCW specimens. It is suggested that He trapping occurs via the formation of He clusters, at impurity sites, or as part of He-vacancy complexes. For sequential implantations, D and He were found to de-trap each other, with He impeding the trapping of D when implanted first at 300 K. Under simultaneous irradiation a decrease in D inventories was observed for all cases, and a re-distribution of He to higher energy traps (associated with He-vacancy complex formation) was observed for higher fluences and temperatures.
Effect of Selective/Non-selective COX Inhibition on Rosuvastatin-Mediated Protection from Ischemia-reperfusion Induced Endothelial Dysfunction in the Human Forearm Vasculature
Keywords: statin
ischemia reperfusion injury
preconditioning
cox

Statins can act as preconditioning agents against ischemia reperfusion (IR)-injury through a mechanism involving cyclooxygenase (COX)-2 and the upregulation of prostaglandin synthesis. The following study investigated the effect of selective and non-selective COX inhibition on rosuvastatin-mediated protection against IR-induced endothelial dysfunction in the human forearm vasculature. Healthy volunteers were randomized to drugs with different COX-inhibiting properties: 81mg aspirin (OD), 325mg aspirin (OD), 400mg ibuprofen (QID), 200mg celecoxib (BID) or placebo. A single dose of 40mg rosuvastatin was also administered 24-hours prior to IR. Endothelial function before and after IR was assessed by measuring flow-mediated dilation of the radial artery. Our results show that 81mg and 325mg aspirin (more COX-1 selective), 400mg ibuprofen (similar selectivity for COX-1/2) and 200mg celecoxib (COX-2 selective) all effectively abolished statin-mediated protection against IR-induced endothelial dysfunction in the forearm (2-way ANOVA, p<0.05). These findings indicate that even partial COX-2 inhibition is sufficient to attenuate statin-induced preconditioning.
Acoustic Streaming Pump for Microfluidic Applications
Keywords: Microfluidics
MEMS
Ultrasound
Piezoelectric

A prototype acoustic streaming pump for microfluidic applications was developed. A novel integration scheme was devised based on the acoustic reflector concept. Numerical simulations were conducted to predict the flow patterns around the transducer. Ultrasound transducers using P(VDF-TrFE) as the piezoelectric element were fabricated using lithography-based microfabrication technology. Silicon channels were fabricated using anisotropic etching. A heat-press bonding technique was adopted to bond the transducers with the silicon chips using CYTOP fluoropolymer as the adhesive. The piezoelectric transducers were characterized to have a resonance frequency of 82 MHz. Micro-PIV experiments were performed in the near and far-fields of the ultrasonic transducer/pump. The near field experiments showed complex flow patterns that could enhance mixing. Estimates of the pumping pressure were obtained using transient flow velocities in the far-field. Conservative estimates indicate the total back pressure the micropump can pump against is 39 Pa. Future research directions were suggested.
Quantifying the Influence of Crown Size on Mechanical Wood Properties in White Spruce (Picea Glauca)
Keywords: Wood Quality
Crown Size
White Spruce
Forestry

Conceptual models of wood formation suggest that trees with large crowns produce low quality wood, but few studies have explicitly examined the relationship between crown size and wood quality. In this study, I examine how crown size influences the strength and stiffness of wood, as measured by Modulus of Elasticity (MOE) and Modulus of Rupture (MOR), using 42- and 72-old year plantation white spruce (Picea glauca) from Ontario, Canada. Mechanical properties were determined from 10x10x140 mm mini-clear samples (n=657), selected from a radial gradient at three heights within the stems. Non-linear mixed-effects models showed that strength and stiffness significantly decreased with crown size, and that MOE and MOR were best predicted by cambial age and crown ratio. The results suggest that the models could be used in conjunction with remotely sensed data to identify high quality timber prior to harvest.
Patterns of Post-zygotic Isolation among Genetically Diverse Strains of Caenorhabditis briggsae and Caenorhabditis sp. 9
Keywords: evolution
speciation
Caenorhabditis
Haldane's rule
Darwin's corollary to Haldane's rule
DMI
intraspecific variation
Caenorhabditis briggsae
Caenorhabditis sp. 9

The study of speciation is key to understanding the origins of biodiversity. Model organisms, with a host of genetic and molecular tools, are crucial to dissecting the genetics of speciation. Crosses between the recently-discovered Caenorhabditis sp. 9 and the well-known C. briggsae produce fertile F1 hybrid females, opening the door to genetic studies of speciation for the first time within the genus. I crossed eight different isogenic strains of C. briggsae reciprocally with six inbred lines of C. sp. 9 to investigate: Haldane’s rule, systematic asymmetries in hybrid viability, and whether genetic variation for hybrid viability segregates within each species. Results of these crosses confirm Haldane’s rule and demonstrate strong asymmetric parent-of-origin effects. Furthermore, I observed genotype-dependent differences in the number of F1 hybrid progeny. This provides evidence for genetic variation for hybrid viability within both species, allowing insights into the genetic forces driving the evolution of incompatibility loci.
ASPIRE: Adaptive Service Provider Infrastructure for VANETs
Keywords: VANET
Clustering
Network Architecture
NEMO
Criticality
vehicular network
Mobile Network
network mobility
Service Provider
vehicle communication

User desire for ubiquitous applications on-board a vehicle motivates the necessity for Network Mobility (NEMO) solutions for Vehicular Ad-Hoc Networks (VANETs). Due to the dynamic topology of VANETs, this approach incurs excessive infrastructure cost to maintain stable connectivity and support these applications. Our solution to this problem is focused on a novel NEMO-based Network Architecture where vehicles are the main network infrastructure. Within this Architecture, we present a Network Criticality-based clustering algorithm, which adapts to mobility changes to form stable self-organizing clusters of vehicles and dynamically builds on vehicle clusters to form more stable Mobile Networks. Simulation results show that the proposed method provides more stable clusters, lower handoffs and better connectivity compared to popular density-based vehicle clustering methods. In addition, they confirm the validity of the proposed Network Architecture. The proposed method is also robust to channel error and exhibits better performance when the heterogeneity of vehicles is exploited.
The Fanconi Anaemia Protein FANCJ is Involved in the Alternative Lengthening of Telomeres (ALT) Mechanism in Human Cells
Keywords: Fanconi anaemia
Telomeres
Cancer
FANCJ

Approximately 15% of human cancers utilize a recombination-based mechanism termed Alternative Lengthening of Telomeres (ALT) to maintain the lengths of their telomeres. The Fanconi anaemia protein FANCJ localizes to telomeric foci in human ALT cells, but not in telomerase-positive or primary cells. Telomere-associated FANCJ frequently localizes with FANCD2 and BRCA1, and primarily localizes to ALT-associated PML nuclear bodies. Depletion of FANCJ in human ALT cells causes the loss of BRCA1 at telomeric foci and a decrease in telomeric repeat DNA content primarily as a result of the loss of the brightest telomeric repeat DNA foci. In contrast, depletion of the FANCD2 results in increased telomeric repeat DNA synthesis and this is suppressed upon the codepletion of FANCJ. Together, data from this study suggest that FANCJ is required for telomeric repeat DNA synthesis in human ALT cells, which may or may not be dependent on BRCA1, and FANCD2 restrains this synthesis.
Development and Characterization of a Controlled Expression System for Osteogenic Genes
Keywords: BMP-2
Controlled Expression
pRTS-1
Transfection

Current treatment methods for non-union bone defects present problems. The objective of this study was to genetically engineer primary and immortalized cell types to express osteogenic molecules BMP2, RUNX2, OSX, or VEGF in a doxycycline dose-dependent manner for tissue regeneration. Coding cDNA sequences for all four factors were sub-cloned into the pRTS-1 expression plasmid and transfected into HUCPVCs, RBMCs, ROS cells. Electroporation was the most effective method of transfection for all cells but stably transfected cells could only be established for RBMCs and ROS cells. Cells achieved maximum expression within 72hours of induction and returned to basal levels after 18 days. Enhanced osteogenic bioactivity was only observed upon activation of BMP-2. The tight regulation of the pRTS-1 system allowed for a controlled gene expression. Future transplantation experiments using these engineered RBMC and ROS cells in vivo will evaluate the usefulness of the dox-inducible gene expression system in bone defects.
An Analysis and Recommendations for Improvements to the Oakville Trafalgar Memorial Hospital Emergency Department
Keywords: health care
management

In an attempt to improve patient care and compensate for growing demands, new tools and strategies are under constant review and development for improvements and analyses. Advances in technology, analyses of the use of public funding, acquiring additional capital, and adapting practical tools and resources from other industries are commonly considered to improve the situation. This work provides a series of recommendations and analyses of solutions for emergency healthcare developed with Oakville Trafalgar Memorial Hospital (OTMH) in mind that can be scaled and adapted for all hospitals and emergency departments. Solutions applied were analyzed for their effect on patient care and health care providers. Recommendations for future improvements and work have been made and numerous concepts were drawn from previous studies and applications in other industries, and adapted for OTMH. It is concluded that the solutions had a positive effect on both the staff experience as well as patient throughput.
Controlling Iron Defeciency Anemia and Preventing Calcium Deficiency in Bangladesh Children: A Novel Approach Using a Multi-micronutrient Powder (MNP) Formulation
Keywords: Iron Deficiency Anemia
Calcium Deficiency
Nutrient-Nutrient Interaction
Micronutrient Powder

Iron deficiency anemia (IDA) and calcium deficiency affect millions of children globally. Sprinkles is a multi-micronutrient powder (MNP) that has successfully treated anemic infants and can be modified to include additional micronutrients. The efficacy for treating IDA and preventing calcium deficiency requires evaluation due to potential nutrient interactions. We assessed the efficacy of Sprinkles MNP including iron with and without calcium on hemoglobin (Hb) response in 100 anemic rural Bangladeshi infants for 2 months. Sprinkles MNP with and without calcium resulted in a significantly higher Hb concentrations in both groups (P<0.0001 and P<0.0001). However, infants who received Sprinkles MNP without calcium had a significantly higher change in Hb concentration (P=0.024) and rate of recovery from anemia (P=0.008). No differences in socio-demographic or dietary characteristics were documented between groups. Although both groups had an improvement in Hb status, the antagonistic interaction between iron and calcium requires further study.
Role of TAp73 in the Transformation of Mouse Ovarian Surface Epithelium
Keywords: p73
OSE
ovarian cancer

Tumour suppressor 73 (Trp73) gene shares structural and functional homology with p53. Trp73 encodes multiple isoforms with opposing effects. The TAp73 isoform is a transcription factor and is classified as a tumour suppressor where as the DNp73 isoform is a putative oncogene. Imbalance of the two opposing isoforms has been reported in human malignancies including ovarian cancer. TAp73 deficiency results in a dramatic increase in the DNp73 isoform, mimicking the altered isoform balance observed in human ovarian cancer. The effects of TAp73 deficiency in mouse OSE cells were assessed. TAp73 deficiency is not sufficient to induce ovarian cancer in mice. However, TAp73 deficiency compromises cellular proliferation in OSE cell lines. Furthermore, expression of p73 isoforms and epithelial markers is altered in TAp73 deficient cell line. Further studies are needed to determine if TAp73 deficiency in conjunction with other molecular alterations can mediate transformation of OSE cells leading to ovarian cancer.
Structural Studies of the Inhibitory Role of Tctex-1 for the Microtubule-associated RhoGEF Lfc
Keywords: biochemistry
structural biology
molecular biology
nuclear magnetic resonance
protein-protein interaction
small GTPases
guanine nucleotide exchange factors
dynein motor complex

Lfc is a guanine nucleotide exchange factor (GEF) for RhoA and is negatively regulated by its association with the microtubule array. Tctex-1, a light chain subunit of the dynein motor complex, was identified as an Lfc-interacting protein in a yeast two-hybrid screen. In mouse embryonic fibroblast (MEF) cells, over-expression of Tctex-1 represses Lfc-induced actin stress fiber and focal adhesion complex formation. Here, we present biochemical evidence obtained from a real-time, nuclear magnetic resonance (NMR)-based assay indicating that the microtubule exerts its inhibitory effect on Lfc through a mechanism that is dependent on the presence of Tctex-1. We also present NMR structure data showing that Lfc and the dynein intermediate chain (DIC) bind to different surfaces of Tctex-1. The biochemical and structural data together support a model in which Lfc is recruited to the microtubules through the dynein cargo adaptor function of Tctex-1, resulting in inhibition of Lfc function.
Engineering the (S)-3-O-Geranylgeranylglyceryl Phosphate Synthase (GGGPS) Monomer from its Dimer
Keywords: Protein Engineering
TIM Barrel evolution
Archaea
GGGPS
Archaeal Membrane Lipid Synthesis

(S)-3-O-Geranylgeranylglyceryl Phosphate Synthase (GGGPS) is a TIM (βα)8 barrel protein found in Archaea and the enzyme catalyzing the first step in the biosynthesis of archaeal membrane lipids. The TIM (βα)8 barrel protein fold is thought to have evolved by duplication and fusion of (βα)4 half barrels. We propose that the GGGPS has also evolved from (βα)4 half barrels. One way to test this hypothesis is to generate putative half-barrels experimentally. GGGPS from Archaeaglobus fulgidus, is a dimer of (βα)8 barrels. Thus, before constructing half barrels, a stable monomer is needed to be engineered. Introducing three substitutions into the dimer interface formed the GGGPS monomer. AUC showed ~50 % of the protein is in the monomeric state. CD experiments confirmed that the engineered protein was properly folded but had decreased thermal stability. In an enzymatic assay, the monomeric GGGPS protein proved as active as the WT protein on a subunit basis.