VictorJuiz/thesis huggingface dataset:
Contributions of Epstein-Barr Nuclear Antigen 1 (EBNA1) and the Family of Repeats (FR) Region to oriP-mediated Replication and Segregation Functions in Nasopharyngeal Carcinoma
Keywords: Epstein-Barr
virus
EBNA1
oriP
nasopharyngeal carcinoma

The Epstein-Barr virus (EBV) EBNA1 protein mediates the replication and mitotic segregation of the EBV genomes via interactions with the viral oriP sequences. C666-1 is the only known nasopharyngeal carcinoma (NPC) cell line that stably maintains EBV in culture and I investigated whether this is due to differences in oriP-mediated functions in replication and segregation. I found that both C666-1 and EBV-negative NPC cell lines can replicate and maintain oriP plasmids for extended periods but that high EBNA1 levels interfered with plasmid segregation. The segregation element within oriP was recently shown to contain 29 repeated sequences instead of the 20 repeats in initial oriP isolates. I compared the functions of oriP with 20 or 29 repeats and found that the higher number of repeats decreased plasmid replication but increased plasmid maintenance, consistent with a segregation effect. Finally, I identified a potential role for promyelocytic leukemia nuclear bodies in oriP plasmid replication.
Latch-based Performance Optimization for FPGAs
Keywords: time borrowing
FPGA
CAD
latches
clock skew
retiming
optimization

We explore using pulsed latches for timing optimization -- a first in the academic FPGA community. Pulsed latches are transparent latches driven by a clock with a non-standard (i.e. not 50%) duty cycle. As latches are already present on commercial FPGAs, their use for timing optimization can avoid the power or area drawbacks associated with other techniques such as clock skew and retiming. We propose algorithms that automatically replace certain flip-flops with latches for performance gains. Under conservative short path or minimum delay assumptions, our latch-based optimization, operating on already routed designs, provides all the benefit of clock skew in most cases and increases performance by 9%, on average, essentially for "free". We show that short paths greatly hinder the ability of using pulsed latches, and further improvements in performance are possible by increasing the delay of certain short paths.
Economic Impacts of Forest Stewardship Council Certification on International Trade of Forest Products
Keywords: Forest certification
international trade

The objective of this study is to investigate the economic impacts of Forest Stewardship Council (FSC) certification on global trade of forest products. Global Forest Products Model (GFPM) is used to predict export, import and net trade quantity of several forest products from year 2006 to 2056. The simulation findings suggest that: (1) Under the assumption that FSC certification plays negative effects on forest stock, Europe reduced sawnwood export; while Ireland became the net importer of sawnwood and wood pulp for next fifty years. (2) Under the assumption that FSC certification has no effects on forest stock, North America, Europe and Asia became the three major sawnwood importers; Europe and North America dominated sawnwood export; Africa significantly expanded its market share of sawnwood export from 1.3% in 2006 to 8.8% in 2056. Africa and Asia became the two largest importers of fuelwood. (3) Under the assumption that FSC certification plays positive effects on forest stock, Europe increased its export of sawnwood; Ireland became the net exporter of sawnwood and wood pulp since 2026. However, FSC certification has no impact on the trend of forestry stocks and products in Canada.
Impact of Current Waveforms on Battery Behaviour
Keywords: battery
electrical engineering
electrochemical
model

With increasing emphasis on renewable energy sources and efficient energy use, energy storage devices, and in particular electrochemical storage devices, are becoming more prevalent. In order to interface batteries to systems, converters are used to maintain the desired voltage, current or power. In this thesis, we explore the response of the battery to commonly seen current waveforms to understand the impact of the converter on the battery. An electrochemical model of the electrode-electrolyte is studied to first understand its operating principles and then to pinpoint the causes of the observed battery response. A circuit was built to test the response of the battery to current waveforms. Experiments consisting of constant current, triangular and sinusoidal currents of varying frequency and ripple currents, and pulsed currents were conducted. Using electrochemical principles, an explanation of the results is presented along with the impact of the experimental results on converter design specifications.
Factors Affecting the Resistivity of Recovery Boiler Precipitator Ash
Keywords: Electrostatic Precipitator
Resistivity
Recovery Boiler
Kraft Pulping Process
Precipitator Dust

Electrostatic precipitators (ESPs) are commonly used to control particulate emissions from recovery boilers in the kraft pulping process. The electrical resistivity of entrained particulates is known to affect the performance of ESPs. There are many factors which influence resistivity of particulate matter, such as field strength, time of exposure, particle size, particle composition, temperature, and flue gas composition. The objective of this study was to identify the ideal operating conditions and dust particle characteristics which lead to an optimum dust resistivity and maximized ESP efficiency. The effect of these factors was examined through a variety of experimental and analytical techniques on kraft recovery boiler ash samples and synthetically prepared samples. It was concluded that particle composition, gas composition, and ambient temperature had the most pronounced effects, while the other factors, such as field strength and exposure time, had a smaller impact on particle resistivity.
The Effect of a Low Glycemic Index Diet on Glucose Challenge Test Results in Women at risk for Gestational Diabetes Mellitus
Keywords: carbohydrates
pregnancy
glycemic index
glucose challenge test

Gestational Diabetes Mellitus develops in 3.7-18% of Canadian women, and can cause serious maternal-fetal complications. Low-GI foods have been shown to increase β-cell function in subjects with impaired glucose tolerance. Theoretically, this effect should improve glucose tolerance and reduce the risk of gestational hyperglycemia. Thus, we aimed to explore the effects of a low-GI diet on glucose challenge test (GCT) results in women at risk for GDM. Women were randomized to receive education during pregnancy focused on incorporation of low- or medium- to high-GI foods. Key foods were provided to assist compliance. Information was obtained from medical records and questionnaires. Ninety-four (94) women completed the study. After adjustment for confounding variables, there was no significant difference in GCT values between intervention groups. Results suggest that low-GI foods do not affect blood glucose control during pregnancy.
A Transformerless High Step-up DC-DC Converter For DC Interconnects
Keywords: Energy Systems
High Voltage DC
DC Interconnect
High Step-Up
DC-DC Converter
Distributed Energy Resources

The proliferation of distributed energy resources (DER)s has prompted interest in the expansion of DC power systems. The technological limitations that hinder the expansion of DC power systems are the absence of DC circuit breakers and high step-up/high step-down DC converters for interconnecting DC systems. This thesis presents a transformerless high step-up DC-DC converter intended for use as an interconnect between DC systems. The converter is required to operate at medium to high voltage (>1kV) and provide high voltage gain (>5). This work details the steady state operation and dynamic model of the proposed converter. The component ratings are identified and converter design limitations are investigated. A 100V:1kV/4kW prototype is produced to verify the analytic steady state model and measure efficiency. An experimental efficiency of 90% was achieved at a step-up ratio of 1:10, however efficiency at low power is limited due to the need to circulate power.
Precast Segmental Double-T Girder Systems for Multi-span Highway Overpass Bridges
Keywords: bridge
concrete
post-tension
double-T
external unbonded tendons
fibre-reinforced
precast
segmental

An alternative structural system for short span bridges is presented: a precast segmental double-T with external, unbonded post-tensioning tendons. Single-span designs from 20 to 45 m long show that the system can be implemented over a wide range of spans and that the system’s sensitivity to post-tensioning losses reported in previous literature can be reduced by aligning the prestressing force more concentrically. Designs for multi-span bridges using this system are presented using simply supported spans connected by thin flexible linking slabs made of ultra high-performance fibre-reinforced concrete and using sections made fully continuous over intermediate supports. A simplified method of geometry control is presented to facilitate the proper alignment of precast segments without the use of match casting. The precast segmental double-T bridge is compared to sixteen existing slab on girder bridges and found to be a competitive alternative in terms of material use, cost, construction schedule, and aesthetic merit.
Life Cycle Modelling of Multi-product Lignocellulosic Ethanol Systems
Keywords: Lignocellulosic Ethanol
Biofuels
Life Cycle Analysis
Environment

Life cycle assessment is an important tool to evaluate the impact of 2nd generation lignocellulosic ethanol, and its potential greenhouse gas (GHG) emissions benefits relative to gasoline. The choice of feedstock, process technology, and co-products may affect GHG emissions and energy metrics. Co-products may improve both the financial and environmental performance of the biorefinery. 26 well-to-wheel models of future lignocellulose-to-ethanol pathways were constructed, considering corn stover, switchgrass, and poplar feedstocks, three pre-treatment technologies, four co-product options, and the use of ethanol in a light-duty vehicle. Model results showed that all pathways with lignin pellet co-production had significantly lower net GHG emissions relative to gasoline and corresponding pathways producing only electricity. Pathways co-producing xylitol had at least 66% greater GHG emission reductions relative to pathways co-producing only lignin pellets. All feedstock/pretreatment/co-product combinations led to GHG reductions of at least 60%, meeting the threshold stipulated under the Energy Independence and Security Act.
The Effect of Muscle Mass during Priming Exercise on Pulmonary Oxygen Uptake and Cardiac Output Kinetics
Keywords: Cardiac Output
Pulmonary Oxygen Uptake
Priming Exercise
Kinetics

The effective of additional muscle mass in a priming exercise on cardiac output (Q) and pulmonary oxygen uptake (VO2) kinetics (mean response time, s) were determined in cyclists. Outcomes were measured over four trials, each consisting of a 6-minute legs alone (UAL) or arms and legs (ULO) warm-up, 3 minute passive recovery, then 6 minutes leg cycling (PAL, PLO; respectively). Q was significantly higher preceding exercise onset with PAL compared to PLO or ULO (0.72 ± 0.13 vs. 0.58 ± 0.09, 0.43 ± 0.09 L∙min-1; respectively, P < 0.05). Q kinetics did not differ between unprimed (ULO: 38.9 ± 8.6) and primed exercise regardless of muscle mass (PLO: 38.6 ± 11.0; PAL: 40.7 ± 11.3). VO2 kinetics were faster (P < 0.05) with PAL (36.9 ± 6.0) compared to ULO (58.7 ± 10.5). Muscle mass employed during priming exercise had only slight effect on subsequent VO2 and Q responses.
Regulation of the Timing of Puberty: Exploration of the Role of Epigenetics
Keywords: puberty
epigenetics
DNA methylation
histone acetylation
C57BL/6 female mice
histone deacetylase inhibitor
methyl-donor
microarray
growth
Hoxa11
variation in complex traits
epigenome wide association study
L-methioine
suberoylanilide hydroxamic acid

Pubertal timing displays wide, normally distributed variation in a healthy population of sexually maturing adolescents. However, like many complex traits, factors contributing to the variation are not well understood. Epigenetic regulation may contribute to some of the population variation. The role that epigenetics, specifically DNA methylation and histone acetylation, may play in regulating pubertal timing was investigated in C57BL/6 female mice: investigating whether population variation in pubertal timing among inbred mice could be explained by environmental factors; whether perturbing the epigenome using a histone deacetylase inhibitor or methyl-donor would alter pubertal timing; and examining genome-wide methylation patterns in hypothalami of early versus late maturing mice. Results demonstrate that measurable micro-environmental factors have only negligible effects on pubertal timing; pubertal timing was significantly altered by administration of epigenetic modifying agents; differences in methylation patterns are subtle. This initial evidence supports the involvement of epigenetic mechanisms in regulating pubertal timing.
Application of Vertical-cavity Surface-emitting Lasers for Simultaneous Laser Speckle Contrast and Intrinsic Optical Signal Imaging: Toward Chronic Portable Cortical Hemodynamic Imaging
Keywords: biophotonics
hemodynamics
imaging
speckle
optics
ischemia
vcsel
coherence

We demonstrated simultaneous intrinsic optical signal imaging (IOSI) and laser speckle contrast imaging (LSCI) using coherence modulation of vertical-cavity surface-emitting laser (VCSEL) diodes. The unique properties of VCSELs were exploited to deliver rapidly switched coherent and non-coherent illumination suitable for high resolution LSCI and IOSI, respectively. Utilizing three near-infrared VCSELs we were able to map changes in cortical blood oxygenation and flow during ischemia. Additionally, the subtle reflectance changes associated with cortical spreading depression were imaged using non-coherent VCSEL illumination. We are currently using two-photon laser-scanning microscopy to quantify the accuracy of LSCI and IOSI implementations. The small size and efficiency of VCSELs and modern photo diodes, makes the development of implantable dual-mode imaging devices feasible. Devices capable of chronic imaging of cortical hemodynamics could significantly enhance the range of studies available to neuroscientists and significantly aid clinicians postoperatively. The research presented in this thesis significantly furthers this objective.
Homo and Hetero-assembly of Inorganic Nanoparticles
Keywords: nanoparticles
quantum dots
gold nanorods
zeta potential

This thesis describes the synthesis and assembly of metal and semiconductor nanoparticles (NPs). The two research topics include i) hetero-assembly of metal and semiconductor NPs, ii) effect of ionic strength on homo-assembly of gold nanorods (GNRs). First, we present hetero-assembly of GNRs and semiconductor quantum dots (QDs) in a chain using biotin-streptavidin interaction. We synthesized alloyed CdTeSe QDs and modified them with mercaptoundecanoic acid to render them water-soluble and to attach streptavidin. We synthesized GNRs by a seed-mediated method and selectively modified the ends with biotin. Hetero-assembly of QDs and GNRs depended on the size, ligands, and ratio of QDs and GNRs. Second, we controlled the rate of homo-assembly of GNRs by varying the ionic strength of the DMF/water solution. The solubility of polystyrene on the ends of GNRs depended on the ionic strength of the solution, which correlated with the rate of assembly of GNRs into chains.
Characterization of the Reflection and Dispersion Properties of 'Mushroom'-related Structures and their Applications to Antennas
Keywords: Electromagnetic Bandgap Structure
surface-wave band gap
mushroom structure
High Impedance Surface

The conventional mushroom-like Sievenpiper structure is re-visited in this thesis and a relationship is established between the dispersion and reflection phase characteristics of the structure. It is shown that the reflection phase frequency at which the structure behaves as a Perfect Magnetic Conductor (PMC) can be predicted for varying angles of incidence from the modal distribution in the dispersion diagrams and corresponds to the supported leaky modes within the light cone. A methodology to independently tune the location of the PMC frequency point with respect to the surface wave band-gap location is then presented. The influence of having said PMC frequency point located inside or outside the surface wave band-gap on a dipole radiation pattern is then studied numerically. It is demonstrated that the antenna exhibits a higher gain when the PMC frequency and band-gap coincide versus when they are separated. Two design cases are then presented for when the aforementioned properties coincide and are separated and a gain improvement of 1.2 dB is measured for the former case.
Search for DNA Methylation Biomarkers in the Circulating DNA of Prostate and Colorectal Cancer
Keywords: cancer
biomarkers
epigenetics
circulating DNA
early diagnosis
DNA methylation

Early diagnosis represents an effective way to improve patient prognosis in cancer. New opportunities for cancer diagnosis and screening may arise from identification of cancer-specific epigenetic alterations in the cell-free circulating DNA (cirDNA). This study investigated biomarkers at the level of DNA methylation in the plasma cirDNA of individuals affected with prostate cancer or colorectal cancer. A methylation-sensitive restriction enzyme-based method was used to enrich methylated DNA fractions, which were interrogated on CpG island and human genome tiling microarrays. A number of genes and non-coding loci exhibited differential methylation between prostate cancer patients and controls. The candidate loci identified from these microarray experiments underwent verification by bisulfite modification coupled with pyrosequencing. Our results suggest that microarray-based studies of DNA methylation in the cirDNA can be a promising avenue for the identification of epigenetic biomarkers in cancer.
An in silico Characterization of Microbial Electrosynthesis for Metabolic Engineering of Biochemicals
Keywords: in silico
bioelectrosynthesis
metabolic engineering
flux balance analysis
microbial electrosynthesis
SPEEQ

A critical concern in metabolic engineering is the need to balance the demand and supply of redox intermediates. Bioelectrochemical techniques offer a promising method to alleviate redox imbalances during the synthesis of biochemicals. Broadly, these techniques reduce intracellular NAD+ to NADH and therefore manipulate the cell’s redox balance. The cellular response to such redox changes and the additional reducing can be harnessed to produce desired metabolites. In the context of microbial fermentation, these bioelectrochemical techniques can improve product yields and/or productivity. We have developed a method to characterize the role of bioelectrosynthesis in chemical production using the genome-scale metabolic model of E. coli. The results elucidate the role of bioelectrosynthesis and its impact on biomass growth, cellular ATP yields and biochemical production. The results also suggest that strain design strategies can change for fermentation processes that employ microbial electrosynthesis and suggest that dynamic operating strategies lead to maximizing productivity.
Identifying Mechanisms Used by Adherent-invasive Escherichia coli Associated with Crohn Disease to Evade the Immune System
Keywords: Crohn Disease (CD)
Adherent-Invasive Escherichia coli (AIEC)
Interferon gamma (IFNγ)
Signal transducer and activator of transcription 1 (STAT1)

Background: Adherent-invasive Escherichia coli (AIEC) is a pathogen isolated from the ileum of patients with CD. IFNγ is a key mediator of immunity, which regulates inflammatory responses to microbial infections. Previously, we showed enterohemorrhagic E. coli prevents STAT1 activation. Aims: To determine; 1) whether activation of STAT1 by IFNγ was prevented following AIEC infection, and 2) define the mechanisms used. Methods: Human epithelial cells were infected with AIEC strains or other pathogenic and commensal E. coli strains. Following infection, cells were stimulated with IFNγ. Activation of STAT1, was monitored by immunoblotting. Results: AIEC strains prevented STAT1 phosphorylation in response to IFNγ. Effect required live bacteria with active protein synthesis. A bacterial product was responsible for blocking STAT1 signalling and interfered with downstream signalling cascades. Conclusion: Suppression of epithelial cell STAT1 signal transduction by AIEC strains represents a novel mechanism by which the pathogen evades host immune responses to the infection.
Differential Roles of Tryptophan Residues in the Functional Expression of Human Anion Exchanger 1
Keywords: Anion exchanger 1
Membrane protein
Tryptophan
Protein expression
Protein function
Trafficking
Cell surface expression
N-glycosylation

Anion exchanger 1 (AE1) is a 95 kDa glycoprotein that facilitates Cl-/HCO3- exchange across the erythrocyte plasma membrane. Seven conserved tryptophan (Trp) residues are in the AE1 membrane domain; at the membrane interface (Trp648, Trp662, and Trp723), in transmembrane segment (TM) 4 (Trp492 and Trp496), and in hydrophilic loops (Trp831, and Trp848). All 7 Trp residues were individually mutated into alanine (Ala) and phenylalanine (Phe) and transiently expressed in human embryonic kidney (HEK)-293 cells. The 7 Trp residues could be grouped into three classes according to the impact of the mutations on the functional expression of AE1: class 1, normal expression, class 2, expression decreased, and class 3, expression decreased by Ala substitution. These results indicate that Trp residues play differential roles in AE1 expression depending on their location in the protein and suggest that Trp mutants with a low expression are misfolded and retained in the ER.
The Effects of Immigrant Status and Ethnicity on the Propensity and Intensity of Informal Care Received in Canada
Keywords: Informal Care
Immigrant Status

The literature on the effects of race and ethnicity on informal caregiving is sparse and incomplete. Furthermore, most caregiving studies do not control for immigrant status. In the few studies that have analyzed the impact of ethnicity on informal care, ethnicity was categorized as African American, Hispanic, or non-Hispanic White. In Canada, the relationship between informal care and immigrant status and ethnicity needs to be better understood as the country has a growing population of immigrants and individuals who will require informal care in the future. This thesis aims to understand how immigrant status and ethnicity affects the propensity and intensity of care received by using probit and ordinary least squares models. Throughout the thesis, immigrant status was measured as binary variable (0/1) and as year of immigration and region of origin.