VictorJuiz/thesis huggingface dataset:
Information Transmission using the Nonlinear Fourier Transform
Keywords: Communication theory
Information theory
Optical fiber communication
Nonlinear dispersive waves
Stochastic partial differential equations
Orthogonal frequency-division multiplexing (OFDM)
Nonlinear Fourier transform
Integrable systems
Channel capacity
Solitons
Nonlinear Schrodinger equation
Interference channel
Fiber-optic

The central objective of this thesis is to suggest and develop one simple, unified method for communication over optical fiber networks, valid for all values of dispersion and nonlinearity parameters, and for a single-user channel or a multiple-user network. The method is based on the nonlinear Fourier transform (NFT), a powerful tool in soliton theory and exactly solvable models for solving integrable partial differential equations governing wave propagation in certain nonlinear media. The NFT decorrelates signal degrees of freedom in such models, in much the same way that the Fourier transform does for linear systems. In this thesis, this observation is exploited for data transmission over integrable channels such as optical fibers, where pulse propagation is governed by the nonlinear Schr\"odinger (NLS) equation. In this transmission scheme, which can be viewed as a nonlinear analogue of orthogonal frequency-division multiplexing commonly used in linear channels, information is encoded in the nonlinear spectrum of the signal. Just as the (ordinary) Fourier transform converts a linear convolutional channel into a number of parallel scalar channels, the nonlinear Fourier transform converts a nonlinear dispersive channel described by a \emph{Lax convolution} into a number of parallel scalar channels. Since, in the spectral coordinates the NLS equation is multiplicative, users of a network can operate in independent nonlinear frequency bands with no deterministic inter-channel interference. Unlike most other fiber-optic transmission schemes, this technique deals with both dispersion and nonlinearity directly and unconditionally without the need for dispersion or nonlinearity compensation methods. This thesis lays the foundations of such a nonlinear frequency-division multiplexing system.
The Role of Tort Liability in Improving Governmental Accountabilty in the Health Sector
Keywords: governmental liability
health policy
tort law
accountability
negligence
health system organization

Over the past decade, concerns with the accessibility and quality of health services have led several individuals to bring tort claims against provincial governments. Unlike other types of health sector legal claims, which have been the subject of much commentary, this thesis provides the first treatment of the tort cases against governmental defendants. To date, Canadian courts have not been receptive to these claims, striking nearly all of them on pre-trial motions, on the basis that government defendants did not owe the plaintiffs a duty of care. In order to situate the health sector tort claims within the judiciary’s broader approach to governmental liability, I compiled a dataset of all tort cases against Canadian governmental defendants from the past decade. My dataset indicates that judges have dismissed more health sector tort claims than those arising from nearly all other sectors of government activity, even accounting for other explanatory variables. I also develop a framework to categorize the judicial approaches to the test for establishing a duty of care. Canadian judges now generally conduct a comprehensive analysis of the closeness and directness of the parties’ relationship and the policy implications of tort liability in determining whether a defendant owes a plaintiff a duty of care. However, judges adjudicating health sector claims fail to appreciate the government’s modern role in the health sector and are almost singularly concerned with the policy implications of their decisions. I conclude with two policy recommendations. First, I argue that judges should more frequently permit these claims to proceed beyond the pre-trial dismissal stage to a full trial, in order to evaluate the policy concerns both for and against governmental liability with the benefit of a full evidentiary record. Second, I argue that judges should more frequently permit health sector tort claims to proceed beyond the duty of care stage of the negligence analysis to an assessment of whether the government met the standard of care. While this approach would allow judges to scrutinize the reasonableness of the government’s decisions, improving transparency and potentially motivating an improved decision-making process, it would not necessarily lead to widespread liability.
Resource Allocation in Autonomous Cellular Networks
Keywords: Resource allocation
Cellular network
Self-configuration

With a fixed number of terminals and a fixed system spectrum, it can be shown that increasing the number of BSs in a cellular network results in a better network performance. However, a regular organized deployment of a cellular network with small cells is both prohibitively expensive and complicated. A possible solution is to allow the network to grow in an organic fashion. This calls for self-configurable approaches for resource allocation which not only improve the performance but also decrease the network planning as well as maintenance costs. Over the past few years, a particular type of small BSs known as femto-BSs has attracted tremendous attention from the industry and academia alike. Femto BSs operate on the licensed spectrum allocated to the cellular network. They are small, inexpensive and transmit at low power levels. Although the deployment of these small BSs result in significant improvements in the indoor coverage for both voice and data services, they only satisfy the immediate needs of the present cellular networks — namely the improvement of the indoor coverage. They do not provide a fundamental solution for a scalable architecture which can organically grow and adapt to the short and long term changes in the network. In this thesis, we propose a practical unified framework for the system design and resource allocation of cellular networks with various types of base stations (with different power budgets) deployed in an irregular fashion. We refer to these networks as autonomous cellular networks. To this end, we first introduce an adaptive localized approach to resource allocation in traditional cellular networks. We show that localized resource assignment at the cost of partial loss of orthogonality at the cell edges can provide significant gains in the network performance. In the second part of the thesis, we propose an adaptive self-configurable resource allocation framework for cellular networks. A network clustering technique is proposed which enables coordinated resource allocation in a network with irregular deployment of BSs. The performance of the proposed framework is evaluated with the regular as well as the irregular deployment of BSs.
Paired Associative Plasticity in Human Motor Cortex
Keywords: Neuroplasticity
Associative plasticity
Transcranial Magnetic Stimulation

This thesis consists of four chapters. In this thesis we explored associative plasticity of human motor cortex with the use of noninvasive transcranial magnetic stimulation (TMS). Paired Associative Stimulation (PAS) has grown in popularity because of its potential clinical applications. We used TMS techniques in combination with electromyographic (EMG) measurements to study cortical excitability and kinematic features of arm movement. This work has focused in a cohesive approach to answer certain fundamental questions about a) the rules of cortical plasticity and mechanism of PAS, b) the interaction between the state of neuronal excitability at the targeted cortical network and the effects of PAS, and c) translation of these effects into obvious measurable kinematic changes starting from network level changes and ending up with the behavioral modulation of arm movement. First we explored the role of GABAergic intracortical networks and intracortical facilitation on modulation of cortical excitability by showing for the first time that PAS can be conditioned by these inhibitory and facilitatory intracortical networks. Next, using standard indirect approaches utilizing peripheral EMG measures, we showed a graded excitability response for the PAS technique and showed that interactions of PAS with motor learning depends on the degree as well as the state of cortical excitability. Rules governing the interactions of brain stimulation techniques and motor learning are important because brain stimulation techniques can be used to modify, improve or disrupt motor adaptation and skill learning with great potential for clinical applications such as facilitation of recovery after stroke. TMS provide us with a unique opportunity to study the rules of plasticity at a systems level, which is a combination of synaptic and nonsynaptic (metaplastic) changes. These changes can occur either in the direction to limit the physiological range of neuronal functioning (homeostatic) or against the direction established state of neurons.
Search for Neutral Minimally Supersymmetric Standard Model Higgs Decaying to Two Hadronic Taus with the ATLAS Detector in pp collisions at 7 TeV Center of Mass Energy
Keywords: MSSM Higgs
hadronic tau

This thesis presents the first search for a neutral Minimal Supersymmetric Standard Model Higgs boson decaying to a pair of hadronic taus in proton-proton collisions with a center-of-mass energy of √s = 7 TeV. Results are presented for an integrated lumi- nosity of 1.056 fb−1 using data from the ATLAS detector at the Large Hadron Collider. After signal selection, 245 events are observed. The number of events is consistent the background estimate of 256 ± 26. An exclusion limit for the Higgs boson production is derived as a function of (cross-section)×(branching ratio). This limit is presented as a function of two parameters: mA and tanβ in the mmax scenario. A point in the (mA, h tanβ) phase space is excluded if the signal hypothesis is rejected at the 95% confidence level.
Conservation Genetics of Freshwater Turtles
Keywords: microsatellite
spatial genetics
Emys blandingii
Chelydra serpentina
Clemmys guttata
Apalone spinifera

Turtles have long life spans, overlapping generations and promiscuous mating systems. Thus, they are an ideal system with which to investigate the application of conservation genetics methods and assumptions to long-lived organisms. Turtles are also one of the most threatened groups of vertebrates and conservation genetics studies are essential to effective recovery of turtle species. This thesis has two main objectives: 1) to evaluate some common population genetics assumptions with respect to turtles and other long-lived organisms, and 2) to collect important information on the population genetics of threatened turtles in Ontario, which can be used to inform species recovery. In Chapters Two and Three, I describe the development of novel microsatellite markers for the snapping turtle and spiny softshell. In Chapter Four I demonstrate significant genetic structure in populations of the endangered spotted turtle in Ontario, and find that “bottleneck tests” may fail to detect recent population declines in small turtle populations. I also show that spotted turtles do not show the typical correlation between population size and genetic diversity. In Chapter Five I use microsatellite markers developed in Chapter Two and document population structure in the widespread snapping turtle for the first time. I compare these results with results from Chapter Four to test the traditionally accepted hypothesis that genetic diversity is reduced in small, isolated populations compared to large, connected populations. As in Chapter Four, my results suggest that the usual patterns of genetic structure and loss of diversity may not apply to turtles. In Chapter Six I conduct a conservation genetics study of the endangered Blanding’s turtle. Finally, in Chapter Seven I combine results from spotted, snapping and Blanding’s turtles to test whether vagility predicts population structure, genetic diversity and significant barriers to gene flow in three species sampled across a single landscape. Analyses reveal minimal congruence in barriers to gene flow and the three species show unexpected and contrasting patterns of diversity across the landscape. Discordant patterns among species highlight areas for further research and shed light on possible cryptic behaviour, and I discuss potential further directions for research in the Summary.
Observational Studies of Interacting Galaxies and the Development of the Wide Integral Field Infrared Spectrograph
Keywords: Galaxy Evolution
Optical Design

Interacting galaxies are thought to be the essential building blocks of elliptical galaxies under the hierarchical galaxy formation scenario. The goal of my dissertation is to broaden our understanding of galaxy merger evolution through both observational studies and instrument developments. Observationally, I approach the goal photometrically and spectroscopically. The photometric studies better constrain the number density evolution of wet and dry mergers through five CFHTLS broad band photometry up to z~1. Meanwhile, by comparing the merger and elliptical galaxy mass density function, I discovered that the most massive mergers are not all formed via merging processes, unless the merging timescale is much longer than the expected value. Spectroscopically, the kinematic properties of close pair galaxies were studied to understand how star formation were quenched at z~0.5. I discovered that the number of red-red pairs are rare, which does not support the gravitational quenching mechanism suggested by the hot halo model. In instrumentation, one efficient way to study galaxy mergers is to use the integral field spectroscopic technique, capitalizing its intrinsic capability of obtaining 2-D spectra effectively. However, the currently available integral field spectrographs are inadequate to provide the required combination of integral field size and spectral resolution for merger studies. I, therefore, have developed two optical designs of a wide integral field infrared spectrograph (WIFIS), which I call WIFIS1 and WIFIS2, to satisfy the requirements of merger studies. Both the designs provide an integral field of 12" x 5" on 10-m telescopes (or equivalently 52" x 20" on 2.3-m telescopes). WIFIS1 delivers spectral resolving powers of 5,500 covering each of JHK bands in a single exposure; WIFIS2 does a lower power of 3,000 focusing on a shorter wavebands of zJ and H bands. All the WIFIS2 optical components have either been or being fabricated, and some of the components have been characterized in the laboratory, including its integral field unit, gratings, and mirrors. The expected completion of WIFIS based on WIFIS2 is 2013 summer, which will be followed by WIFIS1-based spectrograph in a few years.
Evaluating the Interaction of HIV and the Immune System in Mucosal Tissues
Keywords: HIV
Mucosa

90% of Human Immunodeficiency Virus (HIV) infections are acquired across the genital or gastrointestinal mucosa, and infection leads to profound depletion of CD4+ lymphocytes. Antiretroviral therapy can restore blood CD4+ T cells. However, immune dysfunction and defects in mucosal antimicrobial defence persist. Some CD4+ T-subsets, particularly antimicrobial Th17 cells, show enhanced susceptibility to HIV infection and are also preferentially depleted in the course of HIV infection; the latter may allow microbial translocation into the bloodstream. Genital infections have been shown to have direct mucosal immune effects and to increase susceptibility to HIV; however, the effect of systemic infections, such as Malaria (which is holo-endemic in some HIV prevalent regions) is unknown. Understanding the relationship between HIV, highly susceptible immune cells, immune activation and malaria infection on mucosal tissues has been the main focus of my thesis. In HIV-infected individuals, I explored whether HIV antiretroviral therapy restores gut Th17 populations and improves gut antimicrobial defences. Therapy restored gut Th17 populations in some, but not all individuals, but antimicrobial defence remained impaired. I then piloted a novel mucosal-optimized PCR assay to measure cervical immune gene responses, as standard mucosal assays are inadequate. I succeeded in measuring mitogen-induced, but not HIV-specific, cervical immune responses in HIV-infected individuals. Next, using this PCR platform I examined mitogen-induced cervical immune responses in individuals demonstrating reduced susceptibility to HIV, and found that they had reduced production of both Th17-associated and pro-inflammatory cytokines from cervical cells. Finally, in a murine model I found that malaria caused genital and gastrointestinal mucosal immune activation, and increased both the expression of mucosal HIV susceptibility immune markers, and mucosal T cell immune activation. In summary, insufficient gastrointestinal Th17 cells restoration does not underlie persistent mucosal immune activation and microbial translocation in HIV-infected people on therapy. A reduced frequency of highly susceptible Th17 cells in the cervix of HIV-exposed but uninfected individuals was identified as a correlate of reduced HIV susceptibility. Malaria, a common systemic infection in HIV-endemic countries, may enhance susceptibility to HIV through increasing putative immune markers of HIV susceptibility and immune activation in potential mucosal sites of HIV exposure.
The Role of Intercellular Contacts in EpithelialL-mesenchymal/-myofibroblast Transition
Keywords: cell contacts
myofibroblast
myogenic program
EMT

Epithelial mesenchymal/-myofibroblast transition (EMT/EMyT) has emerged as one of the central mechanisms in wound healing and tissue fibrosis. The main feature of EMyT is the activation of a myogenic program, leading to the induction of the α-smooth-muscle actin (SMA) gene in the transitioning epithelium. Recent research suggests that intercellular contacts are not merely passive targets, but are active contributors to EMT/EMyT. Indeed, our group showed previously that contact uncoupling or injury is necessary for TGFβ to induce EMyT (two-hit paradigm). Further, our previous work also revealed that Smad3, the main TGFβ-regulated transcription factor, binds to the Myocardin Related Transcription Factor (MRTF), the prime driver of SMA promoter, and inhibits MRTF’s transcriptional activity. During EMyT, Smad3 eventually degrades, which liberates the MRTF-driven myogenic program. However the mechanisms whereby cell contacts regulate the fate of Smad3 and MRTF during EMyT are poorly understood. Accordingly, the central aim of my studies was to explore the role of intercellular contacts, in particular that of Adherens Junction (AJs) in the induction of the myogenic reprogramming of the injured epithelium. This thesis describes two novel molecular mechanisms through which AJs impact EMyT. In the first part, we show β-catenin, an AJs component and transcriptional co-activator counteracts the inhibitory action of Smad3 on MRTF. Moreover we reveal that β-catenin is necessary to maintain MRTF stability via protecting MRTF from proteasomal degradation. Thus, β-catenin is an indispensable permissive factor for SMA expression. In the second part, we demonstrate that contact injury and TGFβ suppress the expression of the phosphatase PTEN. EMyT-related reduction or absence of PTEN potentiates Smad3 degradation. EMyT is associated with enhanced phosphorylation of the T179 residue in Smad3 linker region, and this event is necessary for Smad3 degradation. PTEN silencing increases the stimulatory effect of contact uncoupling and TGFβ on SMA promoter activity and SMA protein expression. Thus, the integrity of intercellular contacts regulates the level of PTEN, which in turn controls Smad3 stability through impacting on T179 phosphorylation. This new knowledge holds promises for targeted therapies and more effective prevention of the currently incurable fibroproliferative and fibrocontractile diseases.
Freight Market Interactions Simulation (FREMIS): An Agent-based Modelling Framework
Keywords: Freight Modelling
Agent-Based Modelling

Freight transport is the output of an economic market, which converts commodity flows into vehicle flows. Interactions in this market influence vehicle flows and since freight market characteristics (product differentiation and economies of scale/scope) violate perfect competition conditions, the output of this market cannot be predicted directly, unless these interactions are represented in the forecasting models. Traditional freight modelling frameworks do not consider these interactions and consequently they may provide inaccurate freight flow forecasts. In this dissertation, a freight modelling framework is proposed using simulation of freight agent interactions in the economic market to forecast freight flows. The framework is named FREMIS (FREight Market Interactions Simulation). The FREMIS framework consists of two demand models to represent shipper decisions (bundling of shipments and carrier selection) in the market and functions based on profit maximizing behaviour to simulate carrier proposals for contracts. Besides that, learning models are proposed to simulate agent learning processes based on their interactions. The framework was developed aiming to create a realistic representation of freight markets using feasible data collection methods. To illustrate the feasibility of the data collection, a customized web survey was implemented with shippers and carriers in a freight market. Two probabilistic models were developed using the data. The first model, a shipment bundling model was proposed combining a probabilistic model and a vehicle routing algorithm. The results of the probabilistic model are presented in this dissertation, where the locations of shipments (origin and destination) influence the probability of bundling them. Second, three carrier selection models were developed aiming to analyse the nonresponse bias and non-attendance problem in the survey. All of these models assumed heteroskedasticity (different scale or variance) in shipper behaviour. In all models, the hypothesis of agents’ heteroskedasticity cannot be rejected. Besides that, nonresponse bias and non-attendance problem were identified in the survey. In conclusion, the models obtained from the survey were consistent with their behavioural assumptions and therefore they can be adopted during FREMIS implementation.