VictorJuiz/thesis huggingface dataset:
An Archaeobotanical Contribution to Foodways, Wood Collecting Strategies, and Niche Construction at the Late and Terminal Archaic Site of Côte Rouge in Southern Québec

This thesis illustrates the varied contributions of archaeobotany to our understanding of precontact groups in southern Québec, using the site of Côte Rouge (CeEt-481 and CeEt-211) as a case study. This location has been known to First Nations since at least the Late Paleoindian period (11 200-9500 cal. BP), and gained popularity during the Laurentian/Late Archaic (6800-4500 cal. BP) and post-Laurentian/Terminal Archaic (4500 to 3200 cal. BP) to become a significant place that was still sporadically visited during the Woodland period (3200 cal. BP-contact). Euro-Canadian settlement added to the palimpsest of the archaeological deposits characterized by a thin soil with active bioturbation. Different strategies, including the systematic collection of large samples, the inclusion of control samples, and abundant radiocarbon dates, led to the isolation of contaminated areas and to the detection of waste disposal patterns. Because hunter-gatherers tend to abandon their hearths frequently and favor mobility over trash relocation, the analysis focused on the hearths and their close periphery. The cooking techniques recognized include pit roasting, hot rock boiling and direct cooking on rock griddles. The wood charcoal assemblages did not reveal a correlation between the types of hearths and the wood taxa found in them, suggesting wood collection practices followed the principle of least effort. The size of the hearths decreased through time, which may be a linked to a change in the social context of meal consumption or an increase of plants in the diet. Charred seeds and fruits are documented only for the Terminal Archaic, in the samples dated from 3800 to 3300 BP (4200 and 3500 cal. BP). More frequent visits to Côte Rouge may have enhanced gap phase succession and favored the establishment and maintenance of nuts, fleshy fruits, and berries, an ecological inheritance that subsequent groups benefited from. The low densities of charred nuts and the absence of processing or storage features suggest they were not amassed to be stored at the site. Acorns have not been attested in the form of charred nutshells or starch granules on pebble tools. Finally, the potential for a local pollen analysis was judged poor but the observation of a selection of stone tools under high magnification revealed the presence of a few starch grains and brown and red residues thought to be resin and/or birch bark pitch.

Keywords: Archaeobotany
Archaic
Cooking techniques
Hunter-gatherers
Niche construction
Northeastern America
Advisor: Crawford, Gary W.
Maintenance Modeling and Optimization for Multi-unit Systems

Unplanned downtimes caused by system failures incur high costs for many complex systems such as wind turbines, aircrafts, and advanced medical equipment. It is crucial to prevent failures for such systems by applying maintenance policies. Maintenance models can be classified as corrective or preventive maintenance (PM). PM is performed to prevent severe deterioration or failure of the system. The most advanced PM program is known as condition-based maintenance (CBM) which is a maintenance approach that takes into account collected information concerning the working condition of a system to determine the optimal maintenance actions. Studies in the area of CBM have focused mainly on single unit systems, however in reality most of the systems consist of more than one unit. Maintenance models for single unit systems cannot be applied to multi-unit systems when there is a dependency between units. This research presents a new framework for maintenance modeling of multi-unit systems. We proposed CBM policies for multi-unit systems taking into account external demand and production rates which depend on the state of a unit. Units of the system are subject to gradual deterioration and deterioration process of each unit is a three-state continuous time homogeneous Markov chain with two working states and a failure state. We have applied semi-Markov decision process (SMDP) framework to formulate the maintenance decision problem and to determine the optimal control parameters. Two computational approaches were proposed to find the optimal policy by applying 1) the first step of policy iteration algorithm, and 2) the first and second steps of policy iteration algorithm. We showed that a lower average cost rate can be obtained by applying the second approach. We also derived an analytical formula for the average cost considering a corrective maintenance policy for multi-unit systems applying Markov renewal processes. We also developed a powerful model for joint CBM and just-in-time spare parts provisioning policies for a multi-unit production system. SMDP framework is applied to formulate the maintenance problem to determine the optimal control parameters.

Keywords: Condition-based maintenance
Markov renewal theory
Multi-unit system
Policy iteration algorithm
Semi-Markov decision process
Advisor: Makis, Viliam
Living Reliquaries: Monasticism and the Cult of the Saints in the Age of Louis the Pious

At the genesis of this dissertation is the observation that numerous Carolingian monasteries of the ninth century were more than just enclaves for a spiritual elite following the Rule of St. Benedict but also functioned as popular religious shrines. These communities almost invariably identified with a patron saint particular to their institutions, whose bodily remains they protected and memorialized, and whose cults they actively promoted. This contrasts sharply with the early Merovingian period when monasteries and the shrines of the saints were mostly separate endeavors. My study aims to understand how and why this development came about, and what, if anything, the cult of the saints and their relics had to do with the monastic life and its ideals. It also serves to complicate the prevailing view that Carolingian monasteries were essentially “Benedictine” and functioned foremost as “powerhouses of prayer” for the aristocratic society that supported them. A preliminary chapter provides historical context and introduces key themes by analyzing Queen Balthild’s decision, ca. 650, to organize the premier saints’ shrines of the Frankish realm as monasteries. The remaining chapters are then devoted to detailed case studies of the monastery-shrines of Saint-Wandrille, Saint-Denis, and Saint Gall, and are based on close readings of hagiographical works composed during the early decades of the ninth century in the midst of major institutional transformations. While scholars have previously focused on the adoption of the Rule of St. Benedict by these communities in the context of an imperially sponsored monastic reform, the changes are shown here to have been much more comprehensive, entailing large-scale building projects, artistic enhancements, liturgical renewal, and the production of new hagiographic literature. The larger aim, it is argued, was to create integrated complexes of sacred space, more worthy of the relics housed within, as the basis for Christian communities that comprised more than just their monks. The reformed monasteries themselves are represented, in effect, as living reliquaries, whose sacred duty was to protect, honor, and mediate the power of the relics entrusted to their care.

Keywords: Carolingians
Cult of the saints
Merovingians
Monasticism
Rule of St. Benedict
Sacred Space
Advisor: Cochelin, Isabelle
Diem, Albrecht
Recruitment and Mechanism of the Bacterial Type IV Pilus Motors

The type IVa pilus system can be used for adhesion, natural competence, phage adsorption, folded-protein secretion, surface sensing, and surface associated motility. Likewise, it is a major virulence factor in many bacterial pathogens. This system extends and retracts a thin and long protein fibre from the bacterial inner membrane. PilB and PilT are the cytoplasmic ATPases that power pilus extension and retraction, respectively. PilC is an inner membrane protein that bridges the cytoplasmic ATPases to the pilus. PilM is a cytoplasmic protein that is predicted to recruit PilB or PilT, and also binds to the cytoplasmic N-terminal residues of PilN, another inner membrane protein. Herein crystal structures of PilM alone and bound to the N-terminal residues of PilN demonstrate that PilN-binding causes structural changes in PilM. PilM bound to PilB and PilT, and evidence was provided that PilN-binding to PilM inversely modulates these interactions. This is consistent with a model in which PilM recruits PilB or PilT to decide whether the pilus system extends or retracts. The crystal structures of the core ATPase domains of PilB bound to ADP and a non-hydrolyzable ATP analogue were determined. Analysis of the differences between structures permitted the deduction of the catalytic mechanism and domain movements of PilB, which with PilC would support the assembly of a right-handed helical pilus. Extrapolating this analysis to a previously published structure of PilT suggests a mechanism for how PilT would enable right-handed pilus disassembly. However, the available crystal structures of PilT, as well as new structures determined herein, are heterogeneous and not obviously consistent with the structure used for this analysis. CryoEM analysis revealed PilT, but not PilB, has preferences for conformation that are obscured by crystal lattice formation. The physiologic importance of these conformations was validated, allowing for the proposal of the most comprehensive model of PilT function to date.

Keywords: PilB
PilM
PilN
PilT
pilus
T4P
Advisor: Howell, P. Lynne
"For the Honour and Good of the Republic": Institutional Enclosure in Spanish Colonial Manila, 1590-1790

In this study, I examine the place of institutional enclosures, including religious houses, colegios (schools, orphanages, and female reform houses), and hospitals, in Spain’s colonial project in Manila from the end of the sixteenth to the end of the eighteenth century. The immediate goals of these institutions, predominantly founded within the walled city of Intramuros, varied: they sought to regulate monastic life, educate the city’s orphaned and non-orphaned children, reform ‘scandalous’ women, and both physically and spiritually heal the city’s ill. However, the overarching objective of these institutions was to contribute to the creation and maintenance of an idyllic republic in what was represented as a remote but significant colony in the Pacific. This long-term approach to Manila’s institutions reveals how ideas about social propriety, reform, and urban order were not only a result of the ‘enlightened’ Bourbons across the Spanish colonies. Such expressions of colonial paternalism can be seen from the earliest foundations of Manila’s institutions at the end of the sixteenth century, and evolved and endured over the seventeenth and eighteenth centuries. Manila’s institutional enclosures were perceived to benefit the republic because they had implications for the world beyond their walls; the supervised communities within the walls were to provide models of behaviour and morality for unenclosed city dwellers to emulate. Each institution offered a protected environment in which caste categories and gendered models could be constructed and regulated. Institutional administrators and inhabitants were involved in the process of delineating a caste system which would contribute to the creation of a racialized hierarchy in Manila. Administrations also emphasized models of femininity and masculinity that conformed to a monastic model of gender because the idyllic female and male religious represented a controlled, moral population. Despite the goal of establishing an orderly republic, the personal desires and ambitions of enclosed individuals could, and did, take priority over institutional rules, potentially causing scandal. Across this study, we see that institutional enclosure was not only a colonial projection and strategy, but was also an individual, lived experience for a range of women, men, and youths.

Keywords: Colonial Latin America
Early Modern Spanish World
Gender History
Religious History
Advisor: Mills, Kenneth
Poésie et idéologie libertine dans l’œuvre de Charles de Sigogne (1560 – 1611)

Charles-Timoléon de Beauxoncles, mieux connu sous son nom de plume, Charles de Sigogne, compte parmi les nombreux auteurs restés longtemps dans l’oubli et auxquels la recherche dix-septièmiste a récemment redonné la place qu’ils méritaient. Notre étude s’inscrit dans ce même mouvement de réhabilitation en s’intéressant à Sigogne. Ce poète, associé aux recueils collectifs satiriques, marque la première décennie du XVIIe siècle en faisant la transition avec le siècle précédent. Bien que jouissant d’une popularité certaine, son succès littéraire est paradoxal puisqu’il n’a jamais publié d’œuvre en son nom. La poétique de Sigogne repose sur une langue ordurière, une énonciation proche de l’invective ainsi que sur la description de realia et de corps répugnants dans leurs représentations hyperboliques. Son outrance verbale répond à un antipétrarquisme virulent et se fonde sur le renversement systématique des valeurs qui annonce l’esthétique burlesque. Cette étude, qui cherche d’abord à mieux faire connaître la production de ce poète méconnu, s’articule autour des notions d’œuvre et d’auteur, et analyse les ressorts de son écriture satirique en s’appuyant notamment sur le concept polysémique du libertinage. Afin de comprendre l’altérité et la singularité de la satire de Sigogne, nous nous interrogeons sur les usages et les réappropriations du genre en faisant l’analyse des éléments parodiques propres à sa poésie. L’analyse des recueils collectifs, en se fondant sur l’étude de la réception et de la production de l’écriture sigognienne, nous permet de comprendre et de déterminer la place prédominante qu’y occupe Sigogne. L’étude de son style et de son utilisation constante de métaphores relatives au bas corporel et aux isotopies de la nature, permet de montrer comment sa poétique s’inscrit dans une véritable esthétique de dégoût. Finalement, il s’agit de comprendre comment Sigogne mobilise la performativité de la parole en offrant une place de choix à l’invective, l’insulte et l’énonciation ordurière et en refusant toute forme d’argumentation.

Keywords: anitpétrarquisme
Charles
libertine
poésie
satire
Sigogne
Advisor: Holtz, Grégoire
Gentrification and Displacement in U.S. Shrinking Cities: The Role of Planning Policy and Housing Subsidies in Detroit

As shrinking cities implement regeneration initiatives to recover from years of decline, planners have been struggling with how to promote equitable development. A weak housing market with high vacancy rates does not necessarily mean increased housing affordability, especially for low-income residents. To the contrary, it can mean a precarious housing situation given the decreasing supply of decent housing that is affordable to low-income households. Revitalization efforts to improve the housing stock can create even more housing precarity, as these efforts typically attract wealthier in-movers and result in increased competition for a scarce supply of decent housing. This research shows how the conceptual boundaries between regeneration and gentrification have blurred in Detroit, as there is evidence of direct and indirect displacement. Through a critical examination of the social and housing impacts of regeneration initiatives in the greater downtown, a distinct picture of gentrification emerges and illustrates how the process occurs in a resurgent declining city. This research employs a mixed-methods approach to explore the impacts of gentrification on the housing affordability landscape in Detroit. I do this by examining the housing impacts of revitalization initiatives from three different perspectives. First, I examine how the affordable housing opportunities of low-income households in the greater downtown have been affected by recent intense reinvestment. Second, I explore displacement effects by using evictions data as a proxy for direct displacement and by conducting in-depth qualitative interviews to explore tenant experiences with indirect displacement in a rapidly gentrifying downtown. Third, I interrogate the role that place-based subsidies and planning policies have played in helping to facilitate gentrification.

Keywords: Displacement
Gentrification
Housing
Resurgent Declining Cities
Revitalization
Shrinking Cities
Advisor: Hackworth, Jason
Evaluation of the Greenhouse Gas Emissions of Oil Sands Upgrading Technologies Using a Novel Life Cycle-based Model

As the production of oil sands bitumen and associated final products (e.g., transportation fuels) continues to grow, so do the environmental impacts associated with the life cycle of fuel production and use. This has motivated research on developing novel analytical methods that model these impacts on a life cycle basis. Upgrading generated 23% of the greenhouse gas (GHG) emissions from oil sands operations or 2% of Canada’s GHG emissions in 2016. Upgrading is a stage in the production of oil sands-derived transportation fuels that transforms bitumen into higher value products, most of them refinery feedstocks. A novel life cycle-based model, the Oil Sands Technologies for Upgrading Model (OSTUM), that assesses the direct and indirect energy use and GHG intensities of current and emerging upgrading technologies, was developed and implemented using publicly available data. OSTUM is applied to commercial upgrading technologies operating in Canada in 2018: delayed coking based- (DC), hydroconversion based- (HC), and combined hydroconversion and fluid coking based upgrading (HC/FC). Two emerging partial upgrading technologies are also modeled: the HI-Q® Process and EST technology. These latter applications demonstrate OSTUM’s flexibility to produce adequate assessments as the oil sands industry evolves. DC’s baseline intensity is 8.5 grams of carbon dioxide equivalent per megajoule of synthetic crude oil (g CO2e/MJ SCO) and range is 6.3–11.2 g CO2e/MJ SCO. HC’s baseline intensity is 10.8 g CO2e/MJ SCO (range: 8.6-14.3 g CO2e/MJ SCO) and HC/FC’s is 12.2 g CO2e/MJ SCO (range: 9.7-14.8 g CO2e/MJ SCO). The baseline, low and high scenario GHG intensities for HI-Q® are 3.7, 2.3 and 6.4 g CO2e/MJ of partially upgraded bitumen (PUB), respectively, and 8.3, 6.6 and 12.3 g CO2e/MJ PUB for EST. Contributions include 1) the development of a framework to systematically assess/compare the GHG intensities of upgrading technologies using consistent boundaries, assumptions, sources, and methodologies; 2) comprehensive and transparent results obtained with a well-documented model; 3) improved characterization of emission sources/drivers of variability; 4) improved estimation of hydrogen consumption; and 5) estimation of GHG intensities of upgrading co-products of different qualities. OSTUM can provide insight and assist stakeholders in regulating and mitigating upgrading GHG emissions.

Keywords: GHG emissions
Life cycle assessment
Modeling
Oil sands upgrading technologies
Advisor: MacLean, Heather L
Unraveling an Evolutionary Enigma: Investigation of Population Dynamics, Species Diversification, Phylogeny, and Biogeography of the Common Mastiff Bats (Molossus)

Understanding the spatial distribution of genetic diversity for a particular group is critical to understanding patterns of biodiversity and biogeography and informing conservation and management decisions, especially when studying cryptic species. Bats are one of the few native groups of mammals present in both the Antilles and the mainland Neotropics. However, not much is known about how geographic and oceanic barriers affect gene flow and the patterns of diversity in this group and the capacity of different species to disperse among islands. In addition, mechanisms underlying the evolution of species-specific echolocation signals and its correlation with morphology are not well understood. I address these evolutionary questions using the mastiff bats (Molossus) as a study group. The genus Molossus is widely distributed in the Neotropics, occupying both sides of prominent geographic and oceanic barriers. I used the genotype by sequencing (GBS) approach to test the utility of next generation sequencing to understand phylogenetic relationships, population structure, biogeography, and evolution of characters among genetically conserved groups. I clarified the taxonomy of Molossus and elevate the number of species in the genus from 11 to 14, revealing three complexes of cryptic species. I also showed that phylogeographic patterns vary according to habitats preferences, to levels of population isolation, and to historical fluctuations in climate. Biogeographic analyses suggest that the ancestor of Molossus had its origin in South America and that most of the speciation in the genus occurred relatively recently, within a short period of time, consistent with a hypothesis of diversification in Pleistocene refugia. I did not find much support for mainland geographic barriers acting to disrupt gene flow, but oceanic straights seem to genetically isolate some species. Previously a taxonomic black-box, the evolution of Molossus has been painted with an alchemist’s admixture of stasis, convergence, genetic divergence, and conservatism to render the seemingly mundane house-bat a fascinating model in which to explore evolutionary patterns in a broadly distributed Neotropical group comprising both relatively ancient and recently derived lineages.

Keywords: Bats
Biogeography
Evolution
Morphology
Phylogeny
Population Genetics
Advisor: Engstrom, Mark
Investigation of the Immunogenicity and Specificity of the Transferrin Binding Proteins from Bovine Pathogenic Bacteria

Through trying to survive and proliferate within their hosts, pathogens have developed creative mechanisms of acquiring iron. A nutrient required for survival by most organisms, iron is both highly sought and jealously guarded. Hosts sequester iron using iron-binding proteins. These iron sinks keep the extracellular concentration of free iron at a level that does not support microbial proliferation. Transferrin is a bilobal iron carrying protein found in the blood and cerebrospinal fluid, and on mucosal surfaces. It is targeted by a number of microbial transferrin binding proteins and siderophores. This thesis focuses on one of the best-studied bacterial transferrin receptors, which consists of the transporter TbpA and its associated surface lipoprotein TbpB. TbpA and TbpB have been studied for years as potential vaccine antigens. Recently, mutants of TbpB that do not bind transferrin have been shown to provide improved protection against infection compared to wild-type TbpB. In this thesis, I develop a method for rapidly screening TbpB mutants, measure loss of affinity for multiple mutations, and investigate the effectiveness of a mutant in generating transferrin blocking antibodies. Furthermore, I investigate multiple methods of measuring binding specificity in Tbp-transferrin interactions in order to lay the groundwork for identifying functionally important residues in Tbps, and for designing improved animal models of infection.

Keywords: bacterial membrane proteins
host-pathogen interactions
nutritional immunity
protein-protein interactions
Advisor: Moraes, Trevor F