VictorJuiz/thesis huggingface dataset:
Biotic filters in fungal endophyte community assembly

My work focuses on the community ecology of symbioses, specifically of fungal endophytes and their hosts. This thesis describes how plant defense compounds and a seed endophyte influence community structure of maize fungal endophytes. Maize produces benzoxazinoids (BXs), compounds toxic to microbes and insects. I assessed the influence of three factors on endophyte communities: host BX production, host neighbor identity and presence of a BX-detoxifying endophyte, Fusarium verticillioides (FV). To determine the influence of BXs on communities, two BX-producing (BX+) and one BX-nonproducing (BX–) genotype were planted in Ridgetown and Harrow, Ontario (triculture). Fungi were isolated and tested for tolerance to 2-benzoxazolinone (BOA), a toxic BX byproduct. Species and functional diversity (community distribution of BOA tolerance levels) was calculated. In seedling roots and mature leaves, the community proportion with low BOA tolerance was greater in BX– than BX+ plants. Fusarium abundance was up to 35 times higher in mature leaves of BX+ than BX– plants. Next, to assess the effect of host neighbor identity on communities, BX– monocultures were planted, and communities from BX– plants in monoculture and triculture compared. Monoculture root communities had higher species diversity than those in triculture. In vitro experiments were conducted to evaluate the influence of BOA on endophyte species interactions. FV facilitated species with lower BOA tolerance in the presence of BOA. Finally, fields were planted with a BX+ and BX– genotype in Ontario, Canada and Georgia, USA. Seed was inoculated with FV (FV+) or sterilized (FV–). FV abundance was highest in BX+FV+ plants, and Fusarium abundance was greater in BX+ than BX– plants in mature leaves. In Georgia, BX+FV+ communities in below ground tissue had lower abundance of BOA sensitive species than BX+FV–. Overall, results suggest that BXs are a habitat filter that increased colonization by horizontally transmitted and seed-born Fusarium species. This invokes the hypothesis that selective breeding for enhanced BX concentrations increased abundance of Fusarium species in maize. The in vitro study indicated that FV could facilitate other species. In contrast, field results suggest that FV interacts competitively with community members, a trait enhanced in the presence of BXs.

Keywords: fungal endophytes
Fusarium
Advisor: Kohn, Linda M.
Methodological Examination of Screening Prenatal Exposure to Alcohol and Illicit Substances

Fetal alcohol spectrum disorder (FASD) is the leading non-genetic cause of brain damage. In an effort to reduce alcohol-exposed pregnancies, steps are needed to identify at risk women as early as possible so that appropriate intervention can occur. The objective of this dissertation was to examine screening methods validated in identifying pregnant women at risk for consuming alcohol and illicit drugs during pregnancy. A systematic review identified three main approaches including maternal self-report, use of standardized questionnaires and detection via biological markers. Since most screening tools were developed in alcoholic women, it was important to examine performance in problem drinkers. Alcohol screening tools (ASQ), currently the best method of predicting prenatal problem drinking, were not effective in a cohort representative of problem drinkers. ASQ performance improved minimally, using higher thresholds, but not enough to be used alone. Provider’s knowledge of complexities inherent in women under their care is an important component in screening. As illicit drug use is an important predictor of problem drinking, identifying maternal risk factors associated with substance use was necessary. Increased rates of STD’s, untreated psychiatric disorders, binge drinking and heavy smoking were all identified as predictors of prenatal methamphetamine (MA) use. These factors, combined with high rates of unplanned pregnancies have serious adverse implications for the fetus. The most widely used method to screen for illicit substance use is based on a practice-based approach that relies heavily on maternal self-report. Most providers do not ask about alcohol and substance use in the absence of a high index of suspicion due to the assumption that patient will deny use. But evidence suggests that maternal account can be accurate in a supportive environment. The last study examines the agreement between self-reported data, in comparison to illicit drug use based on positive hair test results. A reasonable agreement between the two approaches of identification demonstrates that maternal self-report can be reliable in women who are motivated enough to seek prenatal care. No single approach is sufficient to effectively identify at risk women. However, combining two or more methods will improve screening and help reduce the number of alcohol-exposed pregnancies.

Keywords: screening
alcohol
pregnancy
illicit substances
Advisor: Koren, Gideon
Chemical Kinetic Modeling of Biofuel Combustion

Bioalcohols, such as bioethanol and biobutanol, are suitable replacements for gasoline, while biodiesel can replace petroleum diesel. Improving biofuel engine performance requires understanding its fundamental combustion properties and the pathways of combustion. This study's contribution is experimentally validated chemical kinetic combustion mechanisms for biobutanol and biodiesel. Fundamental combustion data and chemical kinetic mechanisms are presented and discussed to improve our understanding of biofuel combustion. The net environmental impact of biobutanol (i.e., n-butanol) has not been studied extensively, so this study first assesses the sustainability of n-butanol derived from corn. The results indicate that technical advances in fuel production are required before commercializing biobutanol. The primary contribution of this research is new experimental data and a novel chemical kinetic mechanism for n-butanol combustion. The results indicate that under the given experimental conditions, n-butanol is consumed primarily via abstraction of hydrogen atoms to produce fuel radical molecules, which subsequently decompose to smaller hydrocarbon and oxygenated species. The hydroxyl moiety in n-butanol results in the direct production of the oxygenated species such as butanal, acetaldehyde, and formaldehyde. The formation of these compounds sequesters carbon from forming soot precursors, but they may introduce other adverse environmental and health effects. Biodiesel is a mixture of long chain fatty acid methyl esters derived from fats and oils. This research study presents high quality experimental data for one large fatty acid methyl ester, methyl decanoate, and models its combustion using an improved skeletal mechanism. The results indicate that methyl decanoate is consumed via abstraction of hydrogen atoms to produce fuel radicals, which ultimately lead to the production of alkenes. The ester moiety in methyl decanoate leads to the formation of low molecular weight oxygenated compounds such as carbon monoxide, formaldehyde, and ketene, thereby reducing the production of soot precursors. The study concludes that the oxygenated molecules in biofuels follow similar combustion pathways to the hydrocarbons in petroleum fuels. The oxygenated moiety's ability to sequester carbon from forming soot precursors is highlighted. However, the direct formation of oxygenated hydrocarbons warrants further investigation into the environmental and health impacts of practical biofuel combustion systems.

Keywords: biofuel
combustion modeling
Advisor: Thomson, Murray J.
Liquefaction of Early Age Cemented Paste Backfill

Modern mines require systems that quickly deliver backfill to support the rock mass surrounding underground openings. Cemented Paste Backfill (CPB) is one such backfilling method, but concerns have been raised about CPB’s liquefaction susceptibility especially when the material has just been placed, and if it is exposed to earthquakes or large mining induced seismic events. Conventional geotechnical earthquake engineering for surface structures is now relatively advanced and well accepted, and so the objective of this thesis is to consider how that framework might be extended to assess the liquefaction potential of CPB. Seismic records were analyzed for earthquakes and for large mining induced events. Important seismological trends were consistent for rockbursts and earthquakes when the signals were recorded at distances as proximate as one kilometre, suggesting that the conventional earthquake engineering approach might plausibly be adapted for such design situations. For production blasts and for more proximate locations to rockbursts, much higher frequencies dominate and therefore new design methods may be required. Monotonic triaxial tests conducted on normally consolidated uncemented mine tailings demonstrated that the material is initially contractive up to a phase transition point, beyond which dilation occurs. Most importantly the material never exhibits unstable strain softening behaviour in compression, and only temporary or limited liquefaction in extension. The addition of 3% binder results in initial sample void ratios that are even higher than their uncemented counterparts, and yet the material friction is slightly enhanced when tested at 4 hours cure. These results suggest that the flow liquefaction phenomenon commonly associate with undrained loose sand fills will not occur with paste backfill. Cyclic triaxial test results analyzed in terms of number of cycles to failure for a given cyclic stress ratio exhibited a trend consistent with previous tests on similar materials. However, the addition of 3% binder and testing at 4 hours cure resulted in an order of magnitude larger number of cycles to failure – a surprising and dramatic increase, suggesting good resistance of the material to cyclic mobility. Future research is recommended to build on these results and develop more robust methods for liquefaction assessment of CPB.

Keywords: Monotonic and Cyclic Liquefaction
cemented paste backfill
Mining-induced seismicity
Silt-sized tailings
Advisor: Grabinsky, Murray
Functional Partitioning of the Human Lumbar Multifidus: An Analysis of Muscle Architecture, Nerve and Fiber Type Distribution using a Novel 3D in Situ Approach

Muscle architecture, innervation pattern and fiber type distribution of lumbar multifidus (LMT) throughout its volume was quantified. Musculotendinous (n=10) and neural components (n=3) were dissected and digitized from thirteen embalmed cadaveric specimens. The data were imported into Autodesk® Maya® 2008 to generate 3D neuromuscular models of each specimen. Architectural parameters (fiber bundle length, FBL; fiber bundle angle, FBA; tendon length) were quantified from the models using customized software. The medial branch of the posterior rami (L1-L5) was traced through LMT to determine its distribution. Using immunohistochemistry, Type I/II muscle fibers were identified in 29 muscle biopsies from one fresh frozen specimen. The total area and number of each cell type was calculated using Visiopharm® (image analysis software). Architectural and fiber type data were analyzed using ANOVA with Tukey’s post-hoc test (p ≤ 0.05). From L1-L4, LMT had three architecturally distinct regions: superficial, intermediate and deep. At L5, intermediate LMT was absent. Mean FBL decreased significantly from superficial (5.8 ± 1.6cm) to deep regions (2.9 ± 1.1cm) as did volume (superficial, 5.6 ± 2.3ml; deep, 0.7 ± 0.3ml). In contrast, mean FBA increased from superficial to deep. The medial branch of the posterior ramus (L1-L5) supplied the five bands of LMT. Each medial branch in turn divided to supply the deep, intermediate and superficial regions separately. The area occupied by Type I fibers was significantly less (p< 0.01) in the deep (56%) compared with the superficial regions (75%). Based on architecture and morphology, superficial LMT with the longest FBL and relatively small FBA is well designed for torque production and controlling the lumbar lordosis. Intermediate LMT with significantly longer FBL compared with the deep region and with its caudal to cranial line of action may help to control intersegmental stability. Furthermore, the absence of intermediate LMT at L5 and may contribute to the higher incidence of instability observed at the lumbosacral junction. Deep LMT with its short FBL, large FBA and proximity to the axis of spinal rotation may function to provide proprioceptive input to the CNS rather than a primary stabilizer of the lumbar spine.

Keywords: lumbar multifidus
muscle architecture
3D modeling
fiber type distribution
innervation
morphology
Advisor: Agur, Anne M. R.
Buoyant Plumes with Inertial and Chemical Reaction-driven Forcing

Plumes are formed when a continuous buoyant forcing is supplied at a localized source. Buoyancy can be created by either a heat flux, a compositional difference between the fluid coming from the source and its surroundings, or a combination of both. In this thesis, two types of laminar plumes with different forcing mechanisms were investigated: forced plumes and autocatalytic plumes. The forced plumes were compositionally buoyant and were injected with inertial forcing into a fluid filled tank. The autocatalytic plumes were produced without mechanical forcing by buoyancy that was entirely the consequence of a nonlinear chemical reaction -- the iodate-arsenous acid (IAA) reaction. This reaction propagates as a reacting front and produces buoyancy by its exothermicity, and by the compositional difference between the reactant and product. Both the forced and autocatalytic plumes were examined in starting and steady states. The starting, or transient, state of the plume occurs when it initially rises through a fluid and develops a plume head on top of a trailing conduit. The steady state emerges after the plume head has risen to the top of a fluid filled tank leaving only a persistent conduit. Plume behaviour was studied through experimentation, simulation, and by using simple theoretical analysis. We performed the first ever study of plumes as they crossed over the transition between buoyancy-driven to momentum-driven flow. Regardless of the driving mechanism, forced plumes were found to exhibit a single power law relationship that explains their ascent velocity. However, the morphology of the plume heads was found to depend on the dominating driving mechanism. Confined heads were produced by buoyancy-driven plumes, and dispersed heads by momentum-driven plumes. Autocatalytic plumes were found to have rich dynamics that are a consequence of the interplay between fluid flow and chemical reaction. These plumes produced accelerating heads that detached from the conduit, forming free vortex rings. A second-generation head would then develop at the point of detachment. The detachment process for plumes was sensitively dependent on small fluctuations in their initial formation. In some cases, head detachment could occur multiple times for a single experimental run, thereby producing several generations of autocatalytic vortex rings. Head detachment was reproduced and studied using autocatalytic plume simulations. Autocatalytic flame balls, a phenomenon closely related to autocatalytic plumes, were also simulated. Flame balls were found to have three dynamical regimes. Below a critical radius, the smallest flame balls experienced front death. Above this radius, they formed elongating, reacting tails. The largest flame balls formed filamentary tails unable to sustain a reaction.

Keywords: Fluid Dynamics
Chemo-hydrodynamics
Buoyancy-driven flow
Plumes
Advisor: Morris, Stephen W.
William of Ockham's Early Theory of Property Rights: Sources, Texts, and Contexts

This dissertation examines William of Ockham's theory of property rights in the Opus nonaginta dierum (1332) in the context of the other major Michaelist texts of the period. A corollary of the project is to examine to what extent Ockham, a theologian with no formal training in law, was able to exploit the resources of Roman and canon law to justify his theory of property rights. The first chapter outlines general methodological concerns. The second chapter describes John XXII's theory of property rights as it can be found in his major bulls of the 1320s. The subsequent chapters adopt a thematic approach. Chapters three through five analyse in turn the concepts of ius, dominium, and usus, which are hierarchically related concepts in the Michaelist texts. Chapter three examines ius in traditional legal discourse in order to provide a framework for understanding how the Michaelists employed the term; both the issue of positive and natural rights and the interaction of divine, natural, and positive law are examined. Chapter four examines dominium, here primarily understood as proprietary lordship, as it is justified in divine, natural, and positive law; the Franciscan position on the origin of private property also becomes clear. The fifth chapter deals with the Franciscan argument that usus must be understood not only in a legal sense. Franciscan use, they argue, is a rightless and legally indefensible sort of use because it lacks a connection to ius. The sixth chapter explores how the Michaelists explained that one may justly use something that is consumed through use without ever holding property rights over it, while the seventh explores the Franciscan theory of corporate rights in the face of Innocent IV's and John XXII's arguments about the supposedly fictive personality of corporations. A concluding chapter and three appendices round out the dissertation. The first appendix illustrates how Michael of Cesena adapted Bonaventure's theory of a 'fourfold community of temporal things'. The second compares the structural interrelationship of the Michaelist texts. The final appendix tabulates Ockham's use of canon and Roman law with respect to the writings of the pope and the other Michaelists.

Keywords: William of Ockham
John XXII
Bonagratia of Bergamo
Michael of Cesena
Francis of Marchia
Franciscan poverty
property rights
corporation theory
Advisor: King, Peter
Diapirism on Venus and the Early Earth and The thermal effect of fluid flows in AECL's Tunnel Sealing Experiment

Flow instabilities occur at all scales in planetary systems. In this thesis we examine three cases of such instabilities, on three very different length scales. In the first part, we test the idea that Archean granite-greenstone belts (GGBs) form by crustal diapirism, or Rayleigh-Taylor instabilities. GGBs are characterized by large granitic domes (50-100 km in diameter) embedded in narrow keel-shaped greenstones. They are ubiquitous in Archean (> 2.5 Ga) terrains, but rare thereafter. We performed finite element calculations for a visco-elastic, temperature-dependent, non-Newtonian crust under conditions appropriate for the Archean, which show that dense low-viscosity volcanics overlying a felsic basement will overturn diapirically in as little as 10 Ma, displacing as much as 60 % of the volcanics to the lower crust. This surprisingly fast overturn rate suggests that diapiric overturn dominated crustal tectonics in the hot conditions of the Early Earth, becoming less important as the Earth cooled. Moreover, the deposition of large volumes of wet basaltic volcanics to the lower crust may provide the source for the formation of the distinctly Archean granitic rocks which dominate Earth's oldest continents. The second part examines the origin of Venusian coronae, circular volcanic features unique to Venus. Coronae are thought to result from small instabilities (diapirs) from the core-mantle boundary, which are typical of stagnant-lid convection. However, most young coronae are located in a region surrounded by long-lived hotspots, typical of a more active style of mantle convection. Using analogue experiments in corn syrup heated from below, we show that the co-existence of diapirs and long-lived mantle plumes are a direct consequence of the catastrophic overturn of the cold Venusian lithosphere thought to have occurred ~ 700 Ma ago. In the last part we analyze the thermal effect of fluid flow through a full-scale experiment testing clay and concrete tunnel seals in a Deep Geological Repository for nuclear was finite element software, we were able to show that the formation of fissures in the heated chamber between the two seals effectively limited heat flow, and could explain the discrepancy between the predicted and measured temperatures.

Keywords: Archean crustal diapirism
geophysical fluids
nuclear waste disposal
Archean geodynamics
Venusian mantle convection
Advisor: Bailey, Richard
Open Networking in Central America: The Case of the Mesoamerican People's Forum

This dissertation considers the case of the Mesoamerican People’s Forum (MPF), a Central American ‘cousin’ of the World Social Forum, and manifestation of the Global Justice Movement. It argues that the MPF cannot be adequately understood as a transnational social movement or as an ‘open space.’ Rather, it is best understood as a political playing field on which the leaders of locally rooted social movements contested the future of the Central American left within an uncertain and changing political context. Based on extensive ethnographic field work and grounded analysis, it argues that well-placed actors within forum spaces can best be thought of as ‘mediators’ between state and society. The emergence of de facto federated governance structures in Central America, plus weak democratic institutions, have placed new pressures on mediators. Leaders within the Central American left find that they need to build up and/or maintain power bases to shield their positions within an uncertain political environment. They mobilize people to participate in transnational forum spaces because of the legitimating benefits, but shape networked flows within these spaces to limit the potential for networking to erode established positions. Thus I conclude that openness is neither the condition nor the objective of social forums, but rather a pawn strategically deployed or retracted in the course of networked interactions. The work advances thinking about the nature of collective political subjectivity in an era of transformationalist globalization. It also argues in favor of critical realist perspectives on collectivization in a post-development, globalizing world. Specifically, scholars can best advance an ‘epistemology of the south’ by promoting and protecting cognitive justice, which in turn can be achieved through the use of realist approaches that serve to uncover the practices of power at work within networked spaces.

Keywords: Global Justice Movement
Mesoamerican People's Forum
Central America
Globalization
Open Space
Collective Political Subjectivity
Advisor: Deibert, Ronald J.