VictorJuiz/thesis huggingface dataset:
Physical Models of Shear Zones: on the Relationship between Material Properties and Shear Zone Geometry

I present physical shear-box experiments investigating the relationship between geometrical properties of shear zones and mechanical properties of deformed rocks. Experimental methodology is also examined critically and new materials for analogue modelling of shear localization are presented. First, I tested experimentally whether meaningful rheological information can be deduced from finite geometrical shear zone data. The results predict characteristic geometrical responses for certain end-member materials. However, it will be difficult to constrain such responses in the field. In the second part physical controls on deformation in the shear box are analysed for Newtonian and power-law fluids and an elastoviscoplastic strain-softening material. Since models always represent simplifications of the natural problem, it is essential to understand fully the physics of a given simulation. I show that displacement boundary conditions, model geometry, and rheology control shear zone geometry. Practical applications of the shear box for modelling natural shear localization and limitations of isothermal physical models with displacement boundary conditions in general are discussed. In the third part, new data on the rheology of highly-filled silicone polymers are introduced. Since dynamic similarity must be satisfied in analogue models to permit scaled, quantitative simulations of deformation processes, the choice of suitable rock analogues is critical for physical experiments. In particular, we address the problem of designing power-law fluids to model rocks deforming by dislocation creep. We found that highly-filled polymers have complex rheologies. Hence, such materials must be used with care in analogue modelling and only for certain experimental stress-strain rate conditions. Finally, I investigated whether fault network geometry and topography of brittle strike-slip faults are influenced by the degree of compaction of the host rock. Analogue shear experiments with loose and dense sand imply that the degree of sediment compaction may be a governing factor in the evolution of fault network structure and topography along strike-slip faults in sedimentary basins. Therefore, models of strike-slip faults should consider potential volume changes of deformed rocks.

Keywords: shear zones
physical modelling
strain localization
rheology
Advisor: Cruden, Alexander R.
Strategic Forest Management Planning Under Uncertainty Due to Fire

Forest managers throughout Canada must contend with natural disturbance processes that vary over both time and space when developing and implementing forest management plans designed to provide a range of economic, ecological, and social values. In this thesis, I develop a stochastic simulation model with an embedded linear programming (LP) model and use it to evaluate strategies for reducing uncertainty due to forest fires. My results showed that frequent re-planning was sufficient to reduce variability in harvest volume when the burn fraction was low, however, as the burn fraction increased above 0.45%, the best strategy to reduce variability in harvest volume was to account for fire explicitly in the planning process using Model III. A risk analysis tool was also developed to demonstrate a method for managers to improve decision making under uncertainty. The impact of fire on mature and old forest areas was examined and showed that LP forest management planning models reduce the areas of mature and old forest to the minimum required area and fire further reduces the seral area. As the burn fraction increased, the likelihood of the mature and old forest areas satisfying the minimum area requirements decreased. However, if the seral area constraint was strengthened (i.e., the right hand side of the constraint was increased) the likelihood improved. When the planning model was modified to maximize mature and old forest areas, the two fixed harvest volumes (i.e., 2.0 and 8.0 M. m3/decade) had much different impacts on the areas of mature and old forest when the burn fraction was greater than 0.45%. Bootstrapped burn fraction confidence intervals were used to examine the impact of uncertain burn fraction estimates when using Model III to develop harvest schedules. I found that harvest volume bounds were large when the burn fraction was ≥0.45%. I also examined how the uncertainty in natural burn fraction (i.e., estimates of pre-fire suppression average annual area burned) estimates being used for ecosystem management can impact old forest area requirements and the resulting timber supply.

Keywords: Forest Management
Linear Programming
Risk
Uncertainty
Simulation
Re-planning
Burn Fraction
Fire
Advisor: Martell, David Lee
A Thick Multilayer Thermal Barrier Coating: Design, Deposition, and Internal Stresses

Yttria Partially Stabilized Zirconia (Y-PSZ) plasma-sprayed coatings are widely used in turbine engines as thermal barrier coatings. However, in diesel engines Y-PSZ TBCs have not met with wide success. To reach the desirable temperature of 850-900˚C in the combustion chamber from the current temperature of 400-600˚C, a coating with a thickness of approximately 1mm is required. This introduces different considerations than in the case of turbine blade coatings, which are on the order of 100µm thick. Of the many factors affecting the durability and failure mechanism of TBCs, in service and residual stresses play an especially important role as the thickness of the coating increases. For decreasing the residual stress in the system, a multi-layer coating is helpful. The design of a multilayer coating employing relatively low cost materials with complementary thermal properties is described. Numerical models were used to describe the residual stress after deposition and under operating conditions for a multilayer coating that exhibited the desired temperature gradient. Results showed that the multilayer coating had a lower maximum stress under service conditions than a conventional Y-PSZ coating. Model validation with experiments showed a good match between the two.

Keywords: Plasma sprayed coatings
ceramics
oxide
thermal barrier coating
residual stress
mullite
spinel
forsterite
Advisor: Coyle, Thomas W.
Regulation of mRNA Decay in S. cerevisiae by the Sequence-specific RNA-binding Protein Vts1

Vts1 is a member of the Smaug protein family, a group of sequence-specific RNA-binding proteins that regulate mRNA translation and degradation by binding to consensus stem-loop structures in target mRNAs. Using RNA reporters that recapitulate Vts1-mediated decay in vivo as well as endogenous mRNA transcripts, I show that Vts1 regulates the degradation of target mRNAs in Saccharomyces cerevisiae. In Chapter Two, I focus on the mechanism of Vts1-mediated mRNA decay. I demonstrate that Vts1 initiates mRNA degradation through deadenylation mediated by the Ccr4-Pop2-Not deadenylase complex. I also show that Vts1 interacts with the Ccr4-Pop2-Not deadenylase complex suggesting that Vts1 recruits the deadenylase machinery to target mRNAs, resulting in transcript decay. Following poly(A) tail removal, Vts1 target transcripts are decapped and subsequently degraded by the 5’-to-3’ exonuclease Xrn1. Taken together these data suggest a mechanism of mRNA degradation that involves recruitment of the Ccr4-Pop2-Not deadenylase to target mRNAs. Previous work in Drosophila melanogaster demonstrated that Smg interacts with the Ccr4-Pop2-Not complex to regulate mRNA stability, suggesting Smaug family members employ a conserved mechanism of mRNA decay. In Drosophila, Smg also regulates mRNA translation through a separate mechanism involving the eIF4E-binding protein Cup. In Chapter Three, I identify the eIF4E-associated protein Eap1 as a component of Vts1-mediated mRNA decay in yeast. Interestingly Cup and Eap1 share no significant homology outside of the seven amino acid eIF4E-binding motif. In eap1 cells mRNAs accumulate as deadenylated capped species, suggesting that Eap1 stimulates mRNA decapping. I demonstrate that the Eap1 eIF4E-binding motif is required for efficient degradation of Vts1 target mRNAs and that this motif enables Eap1 to mediate an interaction between Vts1 and eIF4E. Together these data suggest Vts1 influences multiple steps in the mRNA decay pathway through interactions with the Ccr4-Pop2-Not deadenylase and the decapping activator Eap1.

Keywords: mRNA decay
Advisor: Smibert, Craig
Teaching the Creed and Articles of Faith in England: Lateran IV to Ignorantia sacerdotum

This study examines how English laypeople and clergy of lower ranks were taught the basic principles of Christian doctrine as articulated in the Apostles’ Creed and Articles of Faith. Chapter one addresses the theological and historical background. Over the course of the twelfth century, school-based theologians came to place an increasing emphasis on faith as a cognitive state while at the same time moral theologians sought to make sure that all Christians had a basic participation in the life of the Church. These trends led to an effort by the Church as an institution to make sure that all Christians had at least a basic understanding of the Christian religion. Chapter two examines how the episcopate carried out a drive to ensure this basic level of understanding through the venues of councils, synods, and deanery and archdeaconry meetings. In all three of these venues, the requirements of making sure the laity know the Creed and Articles of Faith were passed on to parochial clergy, and through these clergy to the laity. Chapter three concerns one particular aspect of presenting the basics of doctrine to the laity, viz., preaching. An examination of a sample of three works of religious instruction for clergy and three sets of model sermons shows how parochial clergy, Franciscans, and Dominicans preached the basics of Christian doctrine. The distribution of the manuscripts of these works shows a broad distribution among parochial clergy, Augustinian canons, and Franciscan and Dominican friars. Such a broad distribution suggests that the Augustinian canons may have been carrying out a good deal of pastoral care and catechetical instruction and that the ready access of preaching aids to clergy indicates that those with responsibility of preaching Christian doctrine to laypeople would have had resources available to do so. Chapter four concerns vernacular literature as a means of religious instruction. Most thirteenth-century literature of religious instruction was in Anglo-Norman, a language spoken and read by aristocrats, clergy, and the upwardly mobile. Three Anglo-Norman works, the Château d’amour by Robert Grosseteste, the Mirour de Seinte Eglyse by Edmund of Abingdon, and the Manuel des pechez by William of Waddington all contain the foundational Christian doctrines contained in the Articles of Faith. The manuscript distribution of all three show that they were owned by both clergy and laity, indicating that they served as teaching aids for clergy, and also that they served to provide laypeople who could afford copies of them with unmediated religious instruction. The broad conclusion of this thesis is that the available evidence shows that the basic principles of Christian doctrine were available both to the lower clergy who would preach and teach the Creed and Articles of Faith and also to the laity who would receive this preaching and instruction.

Keywords: Medieval Church
Religious Education
Medieval Preaching
Medieval Catechesis
Anlgo-Norman
Religious Literature
Advisor: Goering, Joseph
Maintaining Habitat Connectivity for Conservation

Conserving biodiversity in human-dominated landscapes requires protecting networks of ecological reserves and managing the intervening matrix to maintain the potential for species to move among them. This dissertation provides original insights towards (1) identifying areas for protection in reserves that are critical to maintain biodiversity and (2) assessing the potential for species' movements among habitat patches in a reserve network. I develop and test methods that will facilitate conservation planning to promote viable, resilient populations through time. The first part of this dissertation tests and develops reserve selection strategies that protect either a single focal species in a dynamic landscape or multiple interacting species in a static landscape. Using a simulation model of boreal forest dynamics, I test the effectiveness of static and dynamic reserves to maintain spatial habitat requirements of a focal species, American Marten (Martes americana). Dynamic reserves improved upon static reserves but re-locating reserves was constrained by fragmentation of the matrix. Management of the spatial and temporal distribution of land-uses in the matrix will therefore be essential to retain options for re-locating reserves in the future. Additionally, to include essential consumer-resource interactions into reserve selection, a new algorithm is presented for American marten and its two primary prey species. The inclusion of their interaction had the benefit t of producing spatially aggregated reserves based on functional species requirements. The second part of this dissertation evaluates and synthesizes the network-theoretic approach to quantify connectivity among habitat patches or reserves embedded within spatially heterogeneous landscapes. I conduct a sensitivity analysis of network-theoretic connectivity analyses that derive least-cost movement behavior from the underlying cost surface which describes the relative ecological costs of dispersing through different landcover types. Landscape structure is shown to aff ect how sensitive least-cost graph connectivity assessments are to the quality (relative cost values) of landcover types. I develop a conceptual framework to classify network connectivity statistics based on the component of habitat connectivity that they quantify and the level within the network to which they can be applied. Together, the combination of reserve design and network connectivity analyses provide complementary insights to inform spatial planning decisions for conservation.

Keywords: reserve selection
network theory
Advisor: Fortin, Marie-Josee
The Integration of Pitch and Time in Music Perception

Nine experiments were conducted to explore pitch-time integration in music. In Experiments 1-6, listeners heard a musical context followed by probe events that varied in pitch class and temporal position. When evaluating the goodness-of-fit of the probe (Experiment 1), listeners’ ratings showed more influence of pitch class than of temporal position. The tonal and metric hierarchies contributed additively to ratings. Listeners again rated goodness-of-fit in Experiment 2, but with instructions to ignore pitch. Temporal position dominated ratings, but an effect of pitch consistent with the tonal hierarchy remained. Again, these two factors contributed additively. A speeded classification task in Experiments 3 and 4 revealed asymmetric interference. When making a temporal judgment (Experiment 3), listeners exhibited a response bias consistent with the tonal hierarchy, but the metric hierarchy did not affect their pitch judgments (Experiment 4). Experiments 5 and 6 ruled out alternative explanations based on the presence of pitch classes and temporal positions in the context, unequal numbers of pitch classes and temporal positions in the probe events, and differential difficulty of pitch versus temporal classification. Experiments 7-9 examined the factors that modulate the effect of temporal variation on pitch judgments. In Experiment 7, a standard tone was followed by a tonal context and then a comparison tone. Participants judged whether the comparison tone was in the key of the context or whether it was higher or lower than the standard tone. For both tasks, the comparison tone occurred early, on time, or late with respect to temporal expectancies established by the context. Temporal variation did not affect accuracy in either task. Experiment 8 used the pitch height comparison task, and had either a tonal or an atonal context. Temporal variation affected accuracy only for atonal contexts. Experiment 9 replicated these results and controlled for potential confounds. The findings imply that the tonal contexts found in typical Western music bias attention toward pitch, increasing the salience of this dimension at the expense of time. Pitch salience likely arises from long-term exposure to the statistical properties of Western music and is not linked to the relative discriminability of pitch and time.

Keywords: Music
Dimensional interactions
Pitch
Time
Advisor: Schmuckler, Mark
Molecular and Cellular Function of the Listeria Monocytogenes Virulence Factor InlC

Several pathogenic bacteria, including Listeria monocytogenes, use an F-actin-dependent motility process to spread between mammalian cells. Actin ‘comet tails’ propel Lm through the cytoplasm, resulting in bacteria-containing membrane protrusions that are internalized by neighboring cells. The mechanism by which L. monocytogenes overcomes cortical membrane tension to generate protrusions is unknown. In this work, I identify bacterial and host proteins that directly regulate the formation of protrusions. First, I show that efficient cell-cell spread in polarized epithelial cells requires the secreted Lm virulence protein, InlC. I next identify the mammalian adaptor protein Tuba as a ligand of InlC. InlC binds to a C-terminal SH3 domain in Tuba, which normally engages the human actin regulatory protein N-WASP. InlC promotes protrusion formation by inhibiting Tuba and N-WASP function, most likely by impairing binding of N-WASP to the Tuba SH3 domain. Tuba and N-WASP are known to control the structure of apical junctions in epithelial cells [1]. I demonstrate that, by inhibiting Tuba and N-WASP, InlC transforms taut apical cell-cell junctions into structures with a “slack” morphology. Experiments with Myosin II inhibitors indicate that InlC-mediated perturbation of cell junctions accounts for the role of this bacterial protein in protrusion formation. Collectively, my results suggest that InlC enhances bacterial dissemination by relieving cortical tension in apical junctions, thereby enhancing the ability of motile bacteria to deform the plasma membrane into protrusions to allow their spread into neighbouring cells.

Keywords: Listeria monocytogenes
InlC
Tuba
cell-cell spread
Advisor: Gray-Owen, Scott
Study of the Physiological and Molecular Mechanisms Underlying Peptide-induced Cell Death and Biofilm Formation in Streptococcus mutans

Biofilms are complex and highly adapted communities of microorganisms found attached to surfaces. Among the best characterized infectious multi-cellular biofilms is the oral community known as dental plaque. Streptococcus mutans resides in the oral biofilm, and is one of the main causative agents of dental caries. Streptococci are known to monitor their population density using a peptide pheromone (CSP)/two component signalling system (ComDE) in a process classically known as quorum sensing (QS). Previous work in S. mutans has implicated the QS system in genetic competence, the stress response, bacteriocin production and biofilm formation. Our objective in this work was to thoroughly characterize the transcriptional and phenotypic response to CSP in S. mutans, and determine its role in biofilm formation. We have shown that the CSP pheromone is more than simply a QS signal, and is also an inducible ‘alarmone’ capable of communicating stress in the population. We have demonstrated that elevated concentrations of CSP such as those that occur during stress trigger autolysis in a fraction of the population. Importantly, we have shown that autolysis in S. mutans occurs via a novel mechanism of action: intracellular accumulation of a self-acting bacteriocin. We have also identified and characterized the autolysis immunity protein, which is differentially regulated from the bacteriocin to allow survival at low cell density. A second regulatory system was shown to govern expression of autolysis immunity in the absence of CSP signaling, and also contribute to the oxidative stress response in the biofilm. Finally, we present evidence that autolysis is involved in the release of DNA in the biofilm, which contributes to the architecture of the extracellular matrix and may provide a mechanism for the dissemination of fitness-enhancing genes under stress. Together, our data provides a mechanistic link between phenotypes previously ascribed to the CSP pheromone in S. mutans.

Keywords: biofilm
competence
Streptococcus
quorum sensing
Advisor: Cvitkovitch, Dennis
Lévesque, Céline
The Contribution of Physical, Mental and Social Dimensions of Health to Predicting Self-rated Health Over the Course of Recovery Following Total Joint Replacement Surgery

Background: Self-rated health (SRH) is among the most frequently assessed health perceptions in epidemiological research. While the predominant focus has been the predictive relevance of SRH, there is increasing interest in understanding the nature of SRH. Recently a conceptual interpretation of SRH was proposed. Purpose: To assess the tenability of the recently proposed distinctions of self-rated health, as a spontaneous assessment of overall health, or as an enduring self-concept, or both, and to determine the significance of mental well-being, physical and social health for SRH. Methods: A cohort of individuals undergoing total joint replacement (TJR) for hip or knee osteoarthritis (OA) was followed over 6 months of recovery. Participants (n=449) completed (pre-surgery, 3 and 6 months post-surgery) measures associated with physical health: pain, physical function, sports/recreation, fatigue; mental well-being: anxiety, depression; and social health: social participation, passive/active recreation, community access. Using structural equation modeling, confirmatory factor analyses (CFA) investigated 3 latent health variables, and the responsiveness of SRH to current and changing health status, as well as its predictive significance for future health status was investigated. Results: CFA analyses confirmed relationships between observed health measures and hypothesized latent health dimensions. SRH was responsive to current and changing mental well-being. The effects of physical and social health were mediated through mental well-being. SRH was a strong predictor of future SRH and future health status. Conclusion: SRH displayed features of both an enduring self-concept and spontaneous assessment of health status; evidence is provided that both operate simultaneously. While aspects of physical health have always been perceived as the major determinants of SRH, these findings indicate that mental and social health explain much of the relationship between physical health and SRH. These results are particularly unexpected since this is a sample of individuals undergoing TJR surgery, for which pain and restricted physical function are primary indicators. Since SRH is a significant predictor of health status, TJR outcomes, health care utilization and mortality, this study suggests that health research and care, treatment and management modalities should consider a broad range of health dimensions, not only physical aspects of health, and SRH.

Keywords: Self-Rated Health
Physical Health
Mental Well-Being
Social Health
Advisor: Badley, Elizabeth Mary