VictorJuiz/thesis huggingface dataset:
A 'Mitey' Influence? Life History, Impacts and Distribution of a Gall-inducing Arthropod in a Temperate Forest Canopy
Keywords: ecology

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.
Biomedical and Psychosocial Factors Associated with Pain and Disability after Peripheral Nerve Injury
Keywords: peripheral nerve
injury
outcome
disability
upper extremity

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.
Genomic Characterization of Medulloblastoma
Keywords: Medulloblastoma
Genomics
Cancer
Bioinformatics

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.
Kernel-based Copula Processes
Keywords: copula
time-series analysis

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.
Extracellular Fluid Systems in the Brain and the Pathogenesis of Hydrocephalus
Keywords: lymphatic CSF absorption
beta 1 integrins

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.
Configuration Optimization of Underground Cables inside a Large Magnetic Steel Casing for Best Ampacity
Keywords: Cables
eddy current
hysteresis
underground
optimization
losses
power
pipe

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.
Indigeneity, Warfare & Representation: The Zapatista Case (1994-2003)
Keywords: Indigeneity
Warfare
Zapatistas
EZLN
Chiapas
Indigenous

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.
A Defence of Separatism
Keywords: intentionality
phenomenal consciousness
perception
representationalism
phenomenal intentionality
separatism

Philosophers commonly distinguish between an experience’s intentional content—what the experience represents—and its phenomenal character—what the experience is like for the subject. Separatism—the view that the intentional content and phenomenal character of an experience are independent of one another in the sense that neither determines the other—was once widely held. In recent years, however, separatism has become increasingly marginalized; at present, most philosophers who work on the issue agree that there must be some kind of necessary connection between an experience’s intentional content and phenomenal character. In contrast with the current consensus, I believe that a particular form of separatism remains the most plausible view of the relationship between an experience’s intentional content and phenomenal character. Accordingly, in this thesis I explain and defend a view that I call “moderate separatism.” The view is “moderate” in that the separatist claim is restricted to a particular class of phenomenal properties: I do not maintain that all the phenomenal properties instantiated by an experience are independent of that experience’s intentional content but only that this is true of the sensory qualities instantiated by that experience. I argue for moderate separatism by appealing to examples of ordinary experiences where sensory qualities and intentional content come apart. First I argue that an experience’s intentional content does not determine the sensory qualities it instantiates by appealing to cases where two experiences share the same intentional content but instantiate different sensory qualities. Then I argue that the sensory qualities instantiated by an experience do not determine its intentional content by appealing to cases where two experiences that instantiate the same sensory qualities differ with regard to intentional content. I consider a number of alternatives to my account of the intentional content and phenomenal character of the experiences at issue and argue that none is plausible. If so, it follows that the intentional content and sensory qualities instantiated by an experience are independent of one another.
Violent Conflict and Social Capital in Ethnically-polarized Developing Countries
Keywords: social capital
ethnic conflict
development
law
peace process

This dissertation explores the problem of violent ethnic conflict in ethnically polarized developing countries using the concept of social capital. Ethnically polarized developing countries typically have high levels of intra-ethnic social capital (social capital existing within groups) but low levels of inter-ethnic social capital (social capital existing between groups). Violent conflict can be averted by cultivating higher levels of inter-ethnic social capital. High levels of inter-ethnic social capital create incentives for elites to adopt moderate strategies. A civic compact emerges when the general population internalizes the norms of inter-ethnic social capital (the rule of law; the right to participation; and the right to continued physical and cultural existence). The civic compact is associated with a general expectation that elites will not pursue extra-institutional strategies such as violence to advance their interests. Peace processes that originate in “hurting stalemates” afford fragile opportunities to begin to cultivate inter-ethnic social capital. At such moments, elite incentive structures align in such a way as to overcome barriers to reform associated with path dependence. The cultivation of inter-ethnic social capital is initiated by integrating the norms of inter-ethnic social capital into the structure of the peace process, although eventually state institutions (which must incorporate these norms into their design) will also re-enforce these norms. Elites begin to internalize the norms of inter-ethnic social capital by repeatedly engaging with each other during the peace process in a manner that actualizes these norms into their experiences. I explore how the norms of inter-ethnic social capital can be integrated meaningfully into the peace process so that elites begin to absorb these norms and so that the institutions that emerge from the process are perceived to be legitimate. Inter-ethnic social capital is developed among the masses primarily through the interactions that the masses have with state institutions. The peace process must focus on rehabilitating the relationship between the masses and the state. This dissertation assesses how this relationship may be rehabilitated and how the norms of inter-ethnic social capital can be integrated into the process of rehabilitating this relationship so that the masses can begin to internalize these norms.
Extragalactic Stellar Populations in the Near and Mid-infrared: 1-30 Micron Emission from Evolved Populations, Young and Dusty Star Forming Regions and the Earliest Stellar Populations
Keywords: Extragalactic astrophysics
Stellar populations
Near and mid-infrared

The near- through mid-infrared offers a unique and, as this thesis aims to show, essential view of extragalactic stellar populations both nearby, at intermediate redshifts and at very high redshift. In chapter 2, I demonstrate that rest-frame near-IR photometry obtained by the Spitzer Space Telescope provides more robust stellar mass estimates for a spectroscopic sample of ~100 galaxies in the redshift desert (0.5<z<2), and is crucial for modeling galaxies with young star-forming populations. From this analysis, a surprising result emerges in the data. Although the rest-frame light short of 2 micron improves stellar mass estimates, the models and observations disagree beyond 2 micron and emission from non-stellar sources becomes significant. At wavelengths from 1-30 micron, stellar and non-stellar emission contribute equally to a galaxy's global spectral energy distribution. This is unlike visible wavelengths where stellar emission dominates or the far-IR where dust emission provides the bulk of a galaxy's luminosity. Using the sample of high-z galaxies, in chapter 3, I quantify the statistical significance of the excess emission at 2-5 micron and find the emission to correlate with the OII luminosity, suggesting a link between the excess emission and star formation. The origin of the excess emission is not clear, although I explore a number of non-stellar candidates in this chapter. Nearby resolved observations provide a clearer picture of the excess by spatially resolving 68 nearby galaxies. By analyzing the pixel-by-pixel near-IR colours within each galaxy at ~1-5 micron, increasingly red near-IR colors are mapped to spatial regions in chapter 4. For regions with red NIR colors and high star formation rates, I find the broad near- through mid-IR spectrum is constant, varying only in amplitude as a function of the intensity of star formation, suggesting the infrared emission of a young, dusty stellar populations can be added to stellar population synthesis models as an additional component tied to the star formation rate. In closing the thesis, the focus is moved to the detection of stellar populations in the earliest star-forming galaxies. By z>6, all visible wavelength emission is redshifted into near-IR wavelengths. In chapter 5, I show how a tunable near-IR filter I have helped develop holds promise for finding bright Lyman alpha emitting galaxies at redshifts of 8<z<11.