VictorJuiz/thesis huggingface dataset:
Quantum Cryptography in Rreal-life Applications: Assumptions and Security
Keywords: quantum information
quantum optics
quantum cryptography
communication security

Quantum cryptography, or quantum key distribution (QKD), provides a means of unconditionally secure communication. The security is in principle based on the fundamental laws of physics. Security proofs show that if quantum cryptography is appropriately implemented, even the most powerful eavesdropper cannot decrypt the message from a cipher. The implementations of quantum crypto-systems in real life may not fully comply with the assumptions made in the security proofs. Such discrepancy between the experiment and the theory can be fatal to the security of a QKD system. In this thesis we address a number of these discrepancies. A perfect single-photon source is often assumed in many security proofs. However, a weak coherent source is widely used in a real-life QKD implementation. Decoy state protocols have been proposed as a novel approach to dramatically improve the performance of a weak coherent source based QKD implementation without jeopardizing its security. Here, we present the first experimental demonstrations of decoy state protocols. Our experimental scheme was later adopted by most decoy state QKD implementations. In the security proof of decoy state protocols as well as many other QKD protocols, it is widely assumed that a sender generates a phase-randomized coherent state. This assumption has been enforced in few implementations. We close this gap in two steps: First, we implement and verify the phase randomization experimentally; second, we prove the security of a QKD implementation without the coherent state assumption. In many security proofs of QKD, it is assumed that all the detectors on the receiver's side have identical detection efficiencies. We show experimentally that this assumption may be violated in a commercial QKD implementation due to an eavesdropper's malicious manipulation. Moreover, we show that the eavesdropper can learn part of the final key shared by the legitimate users as a consequence of this violation of the assumptions.
Experimental Investigation of the Dynamics and Structure of Lean-premixed Turbulent Combustion
Keywords: premixed turbulent combustion
flame surface density
flame curvature
flame front thickness
G-equation
turbulent burning velocity

Turbulent premixed propane/air and methane/air flames were studied using planar Rayleigh scattering and particle image velocimetry on a stabilized Bunsen type burner. The fuel-air equivalence ratio was varied from Φ=0.7 to 1.0 for propane flames, and from Φ=0.6 to 1.0 for methane flames. The non-dimensional turbulence intensity, u'/SL (ratio of fluctuation velocity to laminar burning velocity), covered the range from 3 to 24, equivalent to conditions of corrugated flamelets and thin reaction zones regimes. Temperature gradients decreased with the increasing u'/SL and levelled off beyond u'/SL > 10 for both propane and methane flames. Flame front thickness increased slightly as u'/SL increased for both mixtures, although the thickness increase was more noticeable for propane flames, which meant the thermal flame front structure was being thickened. A zone of higher temperature was observed on the average temperature profile in the preheat zone of the flame front as well as some instantaneous temperature profiles at the highest u'/SL. Curvature probability density functions were similar to the Gaussian distribution at all u'/SL for both mixtures and for all the flame sections. The mean curvature values decreased as a function of u'/SL and approached zero. Flame front thickness was smaller when evaluated at flame front locations with zero curvature than that with curvature. Temperature gradients and FSD were larger when the flame curvature was zero. The combined thickness and FSD data suggest that the curvature effect is more dominant than that of the stretch by turbulent eddies during flame propagation. Integrated flame surface density for both propane and methane flames exhibited no dependance on u'/SL regardless of the FSD method used for evaluation. This observation implies that flame surface area may not be the dominant factor in increasing the turbulent burning velocity and the flamelet assumption may not be valid under the conditions studied. Dκ term, the product of diffusivity evaluated at conditions studied and the flame front curvature, was a magnitude smaller than or the same magnitude as the laminar burning velocity.
Life History, Maternal Quality and the Dynamics of Harvested Fish Stocks
Keywords: walleye
Sander vitreus
maternal influences
maternal effects
recruitment
density-dependence
temperature
growing degree day
age
lifespan
maturity
sustainable
cod
Gadus morhua
egg
Ricker
reproductive rate
demographics
stock-recruitment
fecundity
mortality
growth
life history

Knowledge of offspring production (recruitment) is fundamental to understanding and forecasting the dynamics of a population. In this thesis, I focus on two demographic characteristics of fish stocks that are important to recruitment: population density and age structure. First, populations produce more recruits at low density, but quantifying this response has proven difficult. Using data from hundreds of populations of walleye (Sander vitreus), an economically important freshwater fish, I demonstrate that the growing-degree-day metric (a temperature index) is better than age at explaining variation in density-dependent growth and maturity both within and among populations. I then incorporate multi-lake measures of density-dependent life history change into a temperature-based biphasic model of growth and reproduction to predict sustainable rates of mortality for walleye throughout most of their range. Second, the age (or size) structure of a population may also affect recruitment because of positive effects of maternal age on offspring production and survival; however, evidence for these ‘maternal influences’ on recruitment is limited. Using both an analytical model and a meta-analysis of stock-recruitment data from 25 species of exploited marine fish, I show that (i) maximum reproductive rate increased with the mean age of adults in a population, and (ii) the importance of age structure increased with a species’ longevity. I then demonstrate a similar effect of maternal influences on reproductive rate in a detailed study of Lake Erie walleye. By highlighting the importance of fisheries-induced demographic change to recruitment, this thesis provides insight into past and present failures. However, it also demonstrates clearly the benefits of proactive management strategies that (i) identify and respect the limits of exploitation, (ii) protect from exploitation reproductively valuable individuals—principles that apply generally to any freshwater, marine, or terrestrial species that is of recreational, commercial, or conservation value.
Modelling Effects of Partial Harvesting on Wildlife Species and their Habitat
Keywords: Forest management
Wildlife

In Canada’s eastern boreal forest region, partial-harvest silviculture has garnered increasing support for maintaining wildlife species and habitat structure associated with late-successional forests. If late-successional species can find suitable habitat in managed stands that retain a certain number, type, and pattern of live trees, then partial harvesting might represent a viable tool for maintaining species associated with old and complex forests. I used several indirect forms of inference to evaluate whether late-successional vertebrate species can be maintained within partially harvested stands in the eastern boreal forest. A meta-analysis of studies across North America showed that no bird species decreased in abundance by half where light harvesting retained at least 70% of live trees. However, adverse effects occurred at lower levels of retention, with some bird species unlikely to use harvested stands with less than 50% retention until appropriate habitat structure returned. A spatially explicit stand dynamics model showed that while partial harvesting can promote development of understory saplings, downed wood, and heterogeneity, it can also induce long-term decreases in the abundances of large trees and snags. Consequently, species dependent on the latter, such as brown creepers (Certhia americana) and northern flying squirrels (Glaucomys sabrinus), were projected to be more susceptible to partial harvesting than those associated with other types of structure. At a more detailed scale, a neighbourhood model developed from live-trapping data revealed that southern red-backed voles (Myodes gapperi) exhibited local associations with several late-successional features within boreal mixedwood stands. Their associations with some features depended on stand-level habitat conditions, which suggested that vole habitat in managed stands could be improved by retaining live trees and downed wood. A spatially explicit model of optimal home range establishment that incorporated these relationships fit vole abundance data marginally better than an aspatial habitat model. When the home range model was applied to simulated partially harvested stands, it predicted that spatial heterogeneity could have a positive effect on vole abundance, but only at harvest intensities of 70-90% with suppressed shrub cover. With careful attention to issues such as these, partial-harvest silviculture could be useful in maintaining vertebrate biodiversity within eastern boreal forests.
Birth Outcomes of Immigrants to Urban Ontario. A Population-based Study
Keywords: epidemiology
immigrants
Ontario
perinatal

The total number of births among immigrants is on the rise and currently exceeds one fifth of live births within industrialized countries. The relation between adverse birth outcomes and migration remains unclear. The objectives of this thesis are to undertake a literature review to clarify the relation between migration and adverse birth outcomes, and to examine the interplay between duration of residence, maternal country of origin, and the residential environment using data on immigrants to Ontario Census Metropolitan Areas. The findings indicate that: a) Analyzing disparities in birth outcomes by migrant status with migrants defined as a single category is not informative. Rather, ethnicity and country of origin are important predictors of birth outcomes among immigrants. b) Duration of residence is linearly associated with low infant birth weight and preterm birth, mainly driven by decreases in gestational age with prolonged stay in Canada. c) The detrimental effects of long duration of residence on preterm birth are modestly attenuated, but not prevented, among immigrants living in urban neighbourhoods characterized by low material deprivation. d) Neighbourhood material deprivation has little, if any, influence on birth outcomes of recent immigrants, and only becomes influential after 15 years of stay in Canada. Maternal world region of origin constitutes a stronger predictor of adverse birth outcomes among recent immigrants. These findings stress the importance of the maternal country of birth and duration of residence as key predictors of immigrants’ health. They also support further research aimed at clarifying the nature of the association between time spent in Canada after migration and decreases in gestational age at delivery, and the identification of immigrant groups at high risk of adverse birth outcomes, based on these two key predictors.
Mapping Specificity Profiles and Protein Interaction Networks for Peptide Recognition Modules
Keywords: Phage display
Protein domain
Protein interaction network
PDZ domain
SH3 domain
endocytosis

Protein-protein interactions are of vital importance to the cell as they mediate the assembly of protein complexes that carry out diverse biological functions. Many proteins involved in cellular signaling are built by the combinatorial use of peptide recognition modules (PRMs), which are small protein domains that bind to their cognate ligands by recognizing short linear peptide motifs. Thousands of PRMs are found in nature, requiring improved methods to better elucidate their molecular determinants of binding and to allow accurate mapping of their interaction networks. In this thesis, I describe the development and application of phage-displayed peptide libraries to map the binding specificities of two common PRMs. First, I generated specificity profiles for 82 C. elegans and human PDZ domains that could be organized into a specificity map. The map revealed that PDZ domains have far greater substrate sequence specificity than previously believed, providing significant insights into the relationships between PDZ structure and specificity, and allowing specificity prediction for uncharacterized domains. My results were used to predict both endogenous and pathogenic PDZ interactions. This analysis revealed that viruses have evolved ligands that specifically mimic PDZ domains to subvert host cell immunity. Second, I analyzed the binding specificity for the SH3 domain family in S. cerevisae. I found that, like PDZ domains, SH3 domains have binding specificities that are more detailed than the conventional classification system. The phage-derived specificity profiles were combined with data from oriented peptide and yeast two-hybrid screening to generate a highly accurate SH3 domain interaction network. Given the prominent role of SH3 domains in endocytosis, the SH3 domain interaction data was used to predict the dynamic localization of several uncharacterized endocytosis proteins, which was subsequently confirmed by cell-based assays. The application of the techniques described here to other PRM families will significantly improve protein interaction maps for signaling pathways, which will illuminate our understanding of the cell circuitry, allow the use of PRMs as general affinity reagent and detection tools, and guide the development of small molecule inhibitors that mimic their peptide ligands for therapeutic intervention.
The Role of Ceramide in Oxidant-mediated Priming of Macrophages for LPS Signaling
Keywords: oxidative stress
macrophage
ceramide

Introduction: Civilian trauma remains a significant health care problem in North American society. Hemorrhagic shock and resuscitation (S/R) have been shown to prime the immune system for an exaggerated response to subsequent otherwise innocuous inflammatory stimuli such as lipopolysaccharide (LPS), resulting in multiple organ failure or death. Using a rodent model of lung injury, we previously demonstrated that antecedent S/R leads to augmented LPS-induced lung injury by way of heightened NF-κB nuclear translocation, resulting in increased elaboration of pro-inflammatory cytokines in alveolar macrophages. Further studies revealed that oxidative stress generated during S/R is responsible for this priming phenomenon. Our group recently identified two significant alterations to LPS signaling under oxidative stress conditions in macrophages: 1) the rapid recruitment of the LPS receptor Toll-like receptor 4 (TLR4) to membrane lipid rafts, and 2) the reprogramming of LPS signaling to a Src-dependent pathway involving phosphatidylinositol 3-kinase (PI3K). Major Objective and Hypothesis: The objective of this thesis is to elucidate the molecular mechanisms underlying the augmented cellular responsiveness observed in macrophages following oxidative stress. The central hypothesis is that oxidative stress regulates LPS signaling by altering the activation and assembly of TLR4 receptor signaling components through generation of the lipid ceramide. Summary of Findings: In the first paper, we demonstrate that the antioxidant stilbazulenyl nitrone (STAZN), a novel second-generation azulenyl nitrone, is protective in a rodent two-hit model of lung injury involving hemorrhagic S/R and subsequent intra-tracheal LPS injection. Resultant oxidative stress and lung injury in vivo were significantly reduced by STAZN following S/R and LPS. In the second paper, we explore the mechanism underlying oxidant-induced surface up-regulation of TLR4 in macrophages. Using immunofluorescence microscopy and flow cytometry techniques, hydrogen peroxide in vitro and hemorrhagic S/R in vivo are shown to induce TLR4 translocation in macrophages in a ceramide and Src-dependent manner, and the enzyme acid sphingomyelinase (ASM) is shown to mediate ceramide generation. In the third paper, the role of ceramide in oxidant-induced macrophage priming for LPS signaling is investigated. Ceramide generation via ASM is shown to have a prominent upstream role in oxidant activation of the PI3K/Akt pathway via Src kinases in macrophages. Furthermore, oxidative stress is shown to reprogram LPS signaling to a ceramide dependent pathway. Conclusion: Together, these findings highlight the role of oxidative stress in mediating augmented cellular responsiveness following S/R, and describe the role of ceramide as a central upstream mediator of oxidant priming in macrophages. The hierarchy of signaling molecules and interactions described herein represent novel targets for modulating oxidative stress in the treatment of critical illness and organ injury.
Option Pricing using Fourier Space Time-stepping Framework
Keywords: option pricing
Fourier Space Time-stepping
partial integro-differential equation
fast Fourier transform

This thesis develops a generic framework based on the Fourier transform for pricing and hedging of various options in equity, commodity, currency, and insurance markets. The pricing problem can be reduced to solving a partial integro-differential equation (PIDE). The Fourier Space Time-stepping (FST) framework developed in this thesis circumvents the problems associated with the existing finite difference methods by utilizing the Fourier transform to solve the PIDE. The FST framework-based methods are generic, highly efficient and rapidly convergent. The Fourier transform can be applied to the pricing PIDE to obtain a linear system of ordinary differential equations that can be solved explicitly. Solving the PIDE in Fourier space allows for the integral term to be handled efficiently and avoids the asymmetrical treatment of diffusion and integral terms, common in the finite difference schemes found in the literature. For path-independent options, prices can be obtained for a range of stock prices in one iteration of the algorithm. For exotic, path-dependent options, a time-stepping methodology is developed to handle barriers, free boundaries, and exercise policies. The thesis includes applications of the FST framework-based methods to a wide range of option pricing problems. Pricing of single- and multi-asset, European and path-dependent options under independent-increment exponential Levy stock price models, common in equity and insurance markets, can be done efficiently via the cornerstone FST method. Mean-reverting Levy spot price models, common in commodity markets, are handled by introducing a frequency transformation, which can be readily computed via scaling of the option value function. Generating stochastic volatility, to match the long-term equity options market data, and stochastic skew, observed in currency markets, is addressed by introducing a non-stationary extension of multi-dimensional Levy processes using regime-switching. Finally, codependent jumps in multi-asset models are introduced through copulas. The FST methods are computationally efficient, running in O(MN^d log_2 N) time with M time steps and N space points in each dimension on a d-dimensional grid. The methods achieve second-order convergence in space; for American options, a penalty method is used to attain second-order convergence in time. Furthermore, graphics processing units are utilized to further reduce the computational time of FST methods.
Crosstalk between Insulin and Wnt Signaling Pathways
Keywords: colorectal cancer
Type 2 Diabetes
beta-catenin
insulin

Type II diabetes and hyperinsulinemia are associated with increased risks of developing colorectal cancer (CRC). Detailed mechanisms underlying this correlation, however, are yet to be explored. The present study demonstrates that insulin increases the expression of proto-oncogenes c-Myc and cyclin D1 via both translational and transcriptional mechanisms. We show here that insulin stimulates c-Myc gene translation via an Akt/PKB-dependent mechanism involving the mTOR signaling pathway. More importantly, we show for the first time that transcriptional stimulation of c-Myc and cyclin D1 expression by insulin involves a novel Akt/PKB-independent signal crosstalk between insulin and canonical Wnt signaling pathways. We then identified p21-activated protein kianse 1 (PAK-1) as a novel mediator for insulin and Wnt/beta-catenin (b-cat) molecular crosstalk, involving MEK/ERK signaling. Furthermore, we found that insulin treatment leads to increased b-cat phosphorylation at Ser675, and this is associated with increased b-cat nuclear content and increased b-cat interaction with Tcf/Lef-binding elements (TBEs) of the human c-Myc gene promoter. Lastly, we demonstrated that insulin signaling directly alters the expression levels of components of the Wnt signaling pathway, including fizzled homology 4 (Fdz-4) and TCF7L2 (=TCF-4). This study not only demonstrated the existence of signaling crosstalk between insulin and canonical Wnt signaling pathways at multiple levels, it reveals molecular mechanisms for observed correlation between CRC and hyperinsulinemia. The growing evidence implicating PAK-1 in various human tumorigenesis has emerged PAK-1 as a potential therapeutic target. Our discovery of PAK-1 functioning as a novel central mediator for insulin and Wnt signaling crosstalk in intestinal cells suggests that PAK-1 may potentially be a good target candidate for treating patients with CRC, especially those who have Type II diabetes or experience hyperinsulinemia.
The Tie2 RTK: Regulation and Downstream Signaling
Keywords: Tie2
signal transduction

Tie2 is a receptor tyrosine kinase (RTK) involved in numerous aspects of both normal and pathological angiogenesis. Proper functioning of this receptor is essential for normal development of the vasculature in the embryo as well as vessel maintenance and at sites of active angiogenesis in the adult. A growing list of pathological states has been attributed to a disruption of the angiogenic ‘balance’ including psoriasis, arthritis, atherosclerosis and diabetic retinopathy. Elucidating the molecular mechanisms behind this important biological process will provide insight into the various molecules involved as well as provide potential targets for novel angiogenic therapies. In an attempt to better understand the signaling pathways downstream of the Tie2 receptor we have studied tyrosine residues on the receptor believed to play an important role in Tie2 function. Of these, we have identified Y1111 as a negative regulatory site on Tie2. Mutation of this site affects receptor phosphorylation and kinase activity. Furthermore, protease digestion studies indicate that mutation of Y1111 may alter receptor conformation and potentially relieve negative inhibition imparted by the C-tail of Tie2. As well, we examined potential Tie2 downstream binding partners, specifically the novel Grb7 family of proteins. This work describes for the first time tyrosine phosphorylation of Grb14, an adaptor molecule previously shown to bind Tie2 in vitro. Moreover, our data suggests a role for this adaptor in Tie2 signal transduction involving two tyrosine residues in the receptor C-terminal tail; Y1100 and Y1106. These studies provide important insight into both signal transduction downstream of Tie2 as well as help us understand some of the molecular mechanisms behind the intrinsic ability of this RTK to regulate its own activity.