VictorJuiz/thesis huggingface dataset:
Novel Photonic Crystal Architectures for Optoelectronics

The discovery of photonic crystals made over two decades ago sparked great excitement in the scientific community as this breakthrough brought with it the promise of novel and highly advanced photonic devices for a broad range of new technologies. Surprisingly, for a myriad of reasons, a few of which will be discussed in this thesis, little headway has been made in the development of commercial devices based on photonic crystals. Indeed, a disproportionate amount of research has been devoted to more fundamental studies and thus confined to the academic arena. In this thesis, we demonstrate the fabrication of novel bottom-up or combined bottom-up and top-down photonic crystals and demonstrate their integration into viable optoelectronic technologies. In particular, we highlight the fabrication of colloidal one-dimensional and three-dimensional photonic crystals with color reflectivity that is electrically tunable throughout the entire visible spectrum. In our methodology, a requisite material for the preparation of an electrically tunable one-dimensional photonic crystal, was a porous one-dimensional photonic crystal fabricated entirely from nanoparticles. We thus fabricated and highlight here the preparation of one-dimensional photonic crystals from various combinations of SiO2, TiO2, SnO2, and Sb:SnO2 (ATO) nanoparticles. We also demonstrate that these nanoparticle one-dimensional photonic crystals are also capable of serving as the resonator structure in organic dye and polymer based distributed feedback lasers. Finally, we also describe the fabrication of the first example of electrically conductive one-dimensional photonic crystals for optical wavelengths based entirely on conducting and optically transparent metal oxides. Owing to the conductivity and optical transparency of such materials, they are particularly well suited for serving simultaneously as the anode and mirror of a Light Emitting Diode microcavity for enhanced color purity.

Advisor: Ozin, Geoffrey Alan
Manners, Ian
3D Magnetic Resonance Image-based Cardiac Computer Models of Cardic Electrophysiology

There is a clear need for improved methods (e.g. computer modelling, imaging) to characterize the substrate of abnormal rhythms like ventricular tachycardia (VT) developed by patients who have suffered a heart attack. Progress leading to improved disease management and treatment planning (based on predictive models) as well as outcomes assessment will have immediate impact on the quality of life in this large patient population. Prior to integration into clinical applications, the predictive models have to be properly validated using experimental techniques selected to reflect the electrophysiological phenomena at spatio-temporal scales similar to those considered in simulations. This thesis advanced us toward this goal by addressing the challenge of building more accurate models of electrophysiology for individual hearts. A novel construction of a realistic 3D cardiac model from Magnetic Resonance Images (MRI), with a long-term aim to predict propagation of the electrical impulse in normal and pathologic large hearts (translatable to human hearts), and associated inducibility of VT is described. To parameterize the model, an original evaluation method of electrophysiological (EP) characteristics of the heart tissue was used. The method combined state-of-the-art experimental physiology tools like optical fluorescence imaging using voltage-sensitive dyes and a CARTO electro-anatomical system, with a cardiac computer model generated from high resolution MR scans of explanted normal and pathologic porcine hearts. Several input model parameters (e.g., conductivity, anisotropy, restitution) were successfully adjusted using the ex-vivo measurements of action potential to yield close correspondence between model output and experiments. Moreover, a simple, fast, and macroscopic mathematical model was used with computation times less than 1h, attractive for clinical EP applications.

Keywords: cardiac modelling MRI
Advisor: Wright, Graham
The Evolutionary Ecology of Sexual Conflict and Condition-dependence in an Insect Mating System

Sexual conflict and condition-dependent trait expression have emerged as major themes in sexual selection. There is now considerable evidence suggesting that both conflict and condition-dependence can drive the evolution and expression of sexual traits; still, important questions remain concerning the extent to which conflict shapes sexual traits and the role of condition in mediating conflict. Here, I address these two themes in studies of a ladybird mating system. One set of studies investigates the function and economics of potentially antagonistic traits – nuptial gifts and female mating resistance – while another examines condition-dependence in mating resistance and male ejaculate composition. Nuptial gifts are often considered beneficial to females, but recent thinking suggests they may also allow males to manipulate females, raising the possibility of conflict. I demonstrate that male ladybirds benefit from nuptial feeding by their mates through reduced re-mating frequency. Benefits to female reproduction and lifespan, however, are weak or non-existent. These results show that although males gain from transferring gifts that influence female behaviour, females experience neither harm nor benefit. I next tested the hypothesis that nuptial feeding is maintained – despite an absence of benefits – because female foraging is generally elevated after mating. However, although females indeed display strongly increased foraging after mating, this response did not increase nuptial feeding. Recent studies suggest that individual condition may affect the economics of mating and extent of conflict. Female ladybirds vigorously resist mating, and I show that (1) resistance is condition-dependent, with low-condition females displaying more resistance, and (2) resistance functions to minimize superfluous matings (sexual conflict), rather than to select among males (indirectly benefiting females). Resistance generates selection favouring large males; thus, this work demonstrates that ecological circumstances, through influencing condition, affect the strength of sexual selection. Finally, male condition may influence investment in ejaculate components, but condition-dependence in ejaculate composition is currently poorly understood. I show that, in agreement with theory, males in poor condition transfer smaller ejaculates that nonetheless contain more sperm, but less seminal fluid. Taken together, this work highlights both the value of economic studies in evaluating sexual conflict, and the significance of condition-dependence for sexual selection.

Keywords: sexual conflict
condition dependence
Advisor: Rowe, Locke
A 'Mitey' Influence? Life History, Impacts and Distribution of a Gall-inducing Arthropod in a Temperate Forest Canopy

Mature forest canopies worldwide sustain an enormous diversity of arthropods, many of which are specialist natural enemies. However, with the exception of species that exhibit massive outbreaks, host-specific canopy arthropods are thought to have relatively little influence on tree health and overall forest productivity. My thesis examines the role of one such arthropod in a temperate forest stand in central Ontario. The maple spindle gall mite Vasates aceriscrumena (Riley) (Acari: Eriophyoidae) is a host-specific canopy parasite that induces galls on leaves of sugar maple Acer saccharum Marsh. I examine three diverse topics related to this host-parasite system: 1) the seasonal phenology of this mite in mature sugar maple canopies, 2) the impacts of galling on host physiology and growth and 3) the distribution of this mite across host ontogeny and within the broader context of the local forest community. With respect to phenology, I document a previously unobserved interaction between the gall-inducer and a gall-invading mite (ubiquitous in the canopy but new to science) and consequences of this on the bionomics of galling mite populations. This work is also the first to examine differential physiological responses to galling across two distinct stages in the ontogeny of the host. Infected leaves in mature trees show drastic reductions in gas-exchange processes (photosynthesis, stomatal conductance and water use efficiency) while infected sapling leaves show no such detectible responses. Further, I find a significant negative correlation between radial increment growth in mature trees and levels of mite galling, as well as significantly increased galling frequency in mature trees compared with understory saplings. Finally, I explore the relationship between galling abundance and abiotic and biotic variables within a large mapped forest plot and show that gall densities are most strongly correlated with local species diversity and less so with host densities. Overall, my research provides a new perspective on the influence of host-specific, dispersal-limited canopy arthropods as major drivers of ‘age-dependent’ reductions in physiological performance and growth of older trees and as natural enemies that are strongly associated with local forest community distribution patterns.

Keywords: ecology
Advisor: Thomas, Sean C.
Smith, Sandy
Biomedical and Psychosocial Factors Associated with Pain and Disability after Peripheral Nerve Injury

The main objective of my dissertation was to evaluate the biomedical and psychosocial factors associated with pain and disability in patients following traumatic upper extremity nerve injuries. This was approached by conducting 3 studies. The first study surveyed peripheral nerve surgeons regarding the assessment of pain in patients with nerve injury. The results showed that only 52% of surgeons always evaluate pain in patients referred for motor/sensory dysfunction. Pain assessment frequently includes verbal response and assessment of psychosocial factors is infrequent. The second study was a retrospective review to assess disability, as measured by the Disabilities of the Arm, Shoulder and Hand (DASH), in patients with chronic nerve injury. Results showed substantial disability (mean DASH 52 + 22) and a significantly lower health status (p < 0.001) compared with well-established norms. In the regression model, the factors associated with the DASH (R2 = 44.5%) were pain, older age and nerve injured. The third study was a cross-sectional evaluation of the biomedical and psychosocial factors associated with pain and disability after upper extremity nerve injury in 158 patients. DASH scores were significantly higher in patients with workers’ compensation or litigation (p = 0.03), brachial plexus injuries (p < 0.001) and unemployed patients (p < 0.001). In the multivariable regression analysis, the final model explained 52.7% of the variance with these predictors; pain intensity (Beta = .230, p = 0.006), nerve injured (Beta = -.220, p = 0.000), time since injury (Beta = -.198, p = 0.002), pain catastrophizing (Beta = .192, p = 0.025), age (Beta = .187, p = 0.002), work status (Beta = .179, p = 0.008), cold sensitivity (Beta = .171, p = 0.015), depression score (Beta = .133, p = 0.066), workers’ compensation/litigation (Beta = .116, p = 0.049) and gender (Beta = -.104, p = 0.09). Future investigation regarding treatments of the factors that are associated with disability and chronic pain will assist to improve health related quality of life in patients with traumatic nerve injury.

Keywords: peripheral nerve
injury
outcome
disability
upper extremity
Advisor: Katz, Joel
Genomic Characterization of Medulloblastoma

Medulloblastoma is the most common malignant pediatric brain tumour. Although survival rates have improved in recent years, long-term survivors exhibit a significantly diminished quality of life complicated by neurological, endocrine, intellectual, and social sequelae as a result of conventional therapies. In order to improve the current outlook for patients with medulloblastoma, rational, targeted therapies that are more efficient and less toxic are required. Despite insight gained from the study of hereditary tumour syndromes and candidate gene approaches, the molecular basis of medulloblastoma remains poorly defined, with more than half of all cases remaining unaccounted for at the genetic level. The intent of my PhD research program was to use high-resolution genomics in an attempt to gain an improved understanding of the medulloblastoma genome and potentially uncover novel genes and pathways driving its pathogenesis. By applying a combination of single nucleotide polymorphism (SNP) arrays, exon arrays, and microRNA arrays to a large cohort of primary medulloblastoma samples, we have identified novel oncogenes and tumour suppressors, implicated deregulation of the histone code as an important event in the pathogenesis of medulloblastoma, and refined the definition of medulloblastoma subgroups. This thesis demonstrates the extent of heterogeneity that exists in the medulloblastoma genome, showing that relatively few genomic aberrations are common when studying medulloblastoma as a single disease. In spite of this heterogeneity, we have identified novel candidate genes and processes that may serve as potential targets for future therapies. Importantly, we have established an improved method of classifying medulloblastomas into distinct molecular variants, showing that certain genomic changes are enriched and occasionally restricted to a specific subgroup. Finally, in addition to genomic differences, we have confirmed that medulloblastoma subgroups differ in their demographics and clinical behavior, and propose that medulloblastoma subgroup affiliation should become an integral component of patient stratification in the future.

Keywords: Medulloblastoma
Genomics
Cancer
Bioinformatics
Advisor: Taylor, Michael
Rutka, James T.
Kernel-based Copula Processes

The field of time-series analysis has made important contributions to a wide spectrum of applications such as tide-level studies in hydrology, natural resource prospecting in geo-statistics, speech recognition, weather forecasting, financial trading, and economic forecasts and analysis. Nevertheless, the analysis of the non-Gaussian and non-stationary features of time-series remains challenging for the current state-of-art models. This thesis proposes an innovative framework that leverages the theory of copula, combined with a probabilistic framework from the machine learning community, to produce a versatile tool for multiple time-series analysis. I coined this new model Kernel-based Copula Processes (KCPs). Under the new proposed framework, various idiosyncracies can be modeled compactly via a kernel function for each individual time-series, and long-range dependency can be captured by a copula function. The copula function separates the marginal behavior and serial dependency structures, thus allowing them to be modeled separately and with much greater flexibility. Moreover, the codependent structure of a large number of time-series with potentially vastly different characteristics can be captured in a compact and elegant fashion through the notion of a binding copula. This feature allows a highly heterogeneous model to be built, breaking free from the homogeneous limitation of most conventional models. The KCPs have demonstrated superior predictive power when used to forecast a multitude of data sets from meteorological and financial areas. Finally, the versatility of the KCP model is exemplified when it was successfully applied to non-trivial classification problems unaltered.

Keywords: copula
time-series analysis
Advisor: Jaimungal, Sebastian
Extracellular Fluid Systems in the Brain and the Pathogenesis of Hydrocephalus

Fundamental questions related to the locations of Cerebrospinal Spinal Fluid (CSF) absorption deficit and causes of the pressure gradients that expand the ventricles with hydrocephalus remain largely unanswered. Work in the Johnston lab over a 15 year period has demonstrated that CSF moves through the cribriform plate foramina in association with the olfactory nerves and is absorbed by a network of lymphatic vessels located within the olfactory turbinates. A kaolin-based rat model of communicating hydrocephalus was developed as a collaborative effort with Drs. McAllister, Wagshul and Li. After developing a method to quantify lymphatic CSF uptake in rats, we examined and observed that the movement of a radioactive tracer into the nasal turbinates was significantly reduced in the kaolin-injected animals compared to saline injected controls. However, it was possible that while lymphatic CSF uptake was compromised, other CSF absorption pathways may have compensated. To answer this, we measured the CSF outflow resistance (Rout) and observed it to be significantly greater in the kaolin group compared with animals receiving saline and there was a significant positive correlation between CSF Rout and ventricular volume. Nonetheless, it is not clear how impaired CSF clearance could lead to a dilation of the ventricles since the ventricular and subarachnoid compartments are in communication with one another and pressure would likely increase equally in both. At this point, we came across a theoretical paper that postulated that a drop in periventricular interstitial fluid pressure might provide an intraparenchymal pressure gradient favouring ventricular expansion. In addition, studies in non-CNS tissues indicated that a disruption of beta-1 (β1) integrin-matrix interactions could lower tissue pressure. Based on these suppositions and data, we examined if these concepts had relevance to the brain. For this, we measured pressure in the brain and observed a decline in periventricular pressures to values significantly below those monitored in the ventricular system following the injection of the anti integrin antibodies. Many of the animals developed hydrocephalus over 2 weeks post antibody injection. These data provide a novel mechanism for the generation of intraparenchymal pressure gradients that is likely contributing to ventricular expansion.

Keywords: lymphatic CSF absorption
beta 1 integrins
Advisor: Johnston, Miles
Configuration Optimization of Underground Cables inside a Large Magnetic Steel Casing for Best Ampacity

This thesis presents a method for optimizing cable configuration inside a large magnetic cylindrical steel casing, from the total ampacity point of view. The method is comprised of two main parts, namely: 1) analytically calculating the electromagnetic losses in the steel casing and sheathed cables, for an arbitrary cables configuration, and 2) implementing an algorithm for determining the optimal cables configuration to obtain the best total ampacity. The first part involves approximating the eddy current and hysteresis losses in the casing and cables. The calculation is based on the theory of images, which this thesis expands to apply to casings having both high magnetic permeability and high electric conductivity at the same time. The method of images, in combination with approximating the cable conductors and sheaths as multiple physical filaments, is used to compute the final current distributions in the cables and pipe and thus the associated losses. The accuracy of this computation is assessed against numerical solutions obtained using the Maxwell finite element program by Ansoft. Next, the optimal cable configuration is determined by applying a proposed two-level optimization algorithm. At the outer level, a combinatorial optimization based on a genetic algorithm explores the different possible configurations. The performance of every configuration is evaluated according to its total ampacity, which is calculated using a convex optimization algorithm. The convex optimization algorithm, which forms the inner level of the overall optimization procedure, is based on the barrier method. This proposed optimization procedure is tested for a duct bank installation containing twelve cables and fifteen ducts, comprising two circuits and two cables per phase, and compared with a brute force method of considering all possible configurations. The optimization process is also applied to an installation consisting of a single circuit inside a large magnetic steel casing.

Keywords: Cables
eddy current
hysteresis
underground
optimization
losses
power
pipe
Advisor: Anders, George
Iravani, Mohammad Reza
Indigeneity, Warfare & Representation: The Zapatista Case (1994-2003)

This thesis deals with issues of indigeneity, warfare and representation as they relate to the Zapatista struggle in Chiapas, Mexico between the years of 1994-2003 –a period widely known as a period of low intensity warfare. During this period, militants of the Zapatista National Liberation Army (EZLN) engaged fiercely in the creation and defence of de facto “indigenous” municipalities and territories, posing a direct challenge to the legitimacy of the Mexican “state” and its faculty to govern. The environment of war, accompanied by a prevalent Indianist discourse, highly structured the ways in which Zapatista lives came to be represented by activist and academic writings alike. Generic images of Zapatista militants came to dominate the literature. Within this context, my thesis argues for the importance of moving away from images of Zapatistas as public figures and investigating, instead, everyday Zapatista lives. I argue that a refocus on specific-situated-local-everyday politics necessarily entails engaging with “internal” conflict, division, hierarchies, and power differentials. Framed by an ethnographic approach, the analysis presented here is based on 17 months of fieldwork. My discussion on indigenous autonomy and self-determination, therefore, goes well beyond claims to indigenous rights and engages, instead, historical as well as on-the-ground expressions of what self-determination looked like on an everyday basis. My discussion on warfare, moves beyond condemnations of militarization in the area and pays attention to some of the ways in which warfare worked to structure peoples’ lives and daily perceptions as well as outsiders’ understanding of the conflict. While generally my analysis is confined by the particularities of time and space, a generous examination of an ample literature gives it theoretical depth and political relevance beyond the Zapatista case.

Keywords: Indigeneity
Warfare
Zapatistas
EZLN
Chiapas
Indigenous
Advisor: Napolitano, Valentina