VictorJuiz/thesis huggingface dataset:
Path/Action Planning for a Mobile Robot

This thesis consists of two parts united by the theme of path/action planning for a mobile robot. Part I presents the Second Opinion Planner (SOP), and Part II presents a new paradigm for navigating, growing, and planning on a Network of Reusable Paths (NRP). Path/action planning is common to both parts in that the planning algorithm must choose the terrain assessment or localization technique at the path-planning stage. Terrain-assessment algorithms follow the trend of low-fidelity at low-cost and high-fidelity at high-cost. Using a high-fidelity method on all the raw terrain data can drastically increase a robot's total path cost (cost of driving, planning, and doing the terrain assessment). SOP is a path-planning algorithm that uses a hierarchy of terrain-assessment methods, from low-fidelity to high-fidelity, and seeks to limit high-cost assessment to areas where it is beneficial. The decision to assess some terrain with a higher-fidelity method is made considering potential path benefits and the cost of assessment. SOP provides a means to triage large amounts of terrain data. The system is demonstrated on simulated problems and in real terrain from an experimental field test carried out on Devon Island, Canada. The SOP plans are quite close to the minimum possible cost. Growing a NRP is an approach to navigation that allows a mobile robot to autonomously explore unmapped, GPS-denied environments. This new paradigm results in closer goal acquisition and a more robust approach to exploration with a mobile robot, when compared to a classic approach to guidance, navigation, and control. A NRP is a simple Simultaneous Localization And Mapping system that can be shown to be a physical embodiment of a Rapidly-exploring Random Tree planner. Simulation results are presented, as well as the results from two different robotic test systems that were tested in planetary analogue environments. NRP offers benefits to planetary exploration by allowing a rover to be used for the parallel scientific investigations. This increases the number of sites that can be investigated in a short time, as compared to a serial approach to exploration. Two mock missions were carried out at planetary analogue sites.

Keywords: mobile robot
autonomy
field robotics
path planning
Advisor: Barfoot, Timothy D.
Prophetic Scribalism: A Semantic, Textual and Hypertextual Study of the Serek Texts

This thesis challenges the position that the serek texts are primarily prescriptive and legal, as they have been customarily defined. It argues that the term serek should be reconceptualized according to descriptive analysis, with the purpose of creating what C. Newsom terms a ‘Gestalt structure.’ In order to achieve this, four serek texts (M, S, Sa, and D) will be analyzed at three literary levels—semantic, textual and hypertextual—explaining how the elements at these levels interact as cohesive wholes, thus serving to create a more complete picture of this group of texts as a literary unity. Thus, while the separate, constituent semantic, textual and hypertextual parts must be analysed as separate elements, the fundamental questions posed regarding these elements will be different in a Gestalt paradigm as compared to a traditional, definitional analysis. Going from the micro to the macro, the first chapter will look at the serek texts through the ‘microscope’ of close philological analysis, examining how the term serek functions atomistically within the Dead Sea Scrolls. Building upon these results, the second chapter will more broadly analyse the structure, themes and narrative apparent in the serek texts, thus creating a fuller understanding of how the serek texts relate to one another and respond to circumstances in community life. Finally, the last chapter seeks yet more broadly to understand the serek texts in the wider literary milieu of the Second Temple Period. Here, a scribal technique present in the serek texts will be compared to a similar technique used in the Book of Isaiah—arguably the most important prophetic work for the Qumran sectarians.

Keywords: Dead Sea Scrolls
Serek Texts
Isaiah
Second Temple Judaism
Prophecy
Legal Texts
War Scroll
Community Rule
Damascus Document
Allusion
Advisor: Metso, Sarianna
Physical and Functional Characterization of the SUMO System and SUMO Chains in S. cerevisiae

The ubiquitin-like proteins (Ubls) are small polypeptides that function as post-translational modifiers. Like ubiquitin, most Ubls are covalently attached to a lysine residue on target proteins. The small ubiquitin-related modifiers (SUMO) play important roles in a number of critical biological processes, such as proliferation and regulation of the cell cycle, yet their specific cellular functions have remained poorly understood. Like ubiquitin, SUMO proteins can also form oligomeric “chains”, but the functions of these structures were even less well understood. To this end, I created the first spectral library for the identification of Ub/Ubl proteins and Ub/Ubl chain linkages in mass spectrometry experiments. This tool has dramatically improved our ability to use MS to analyze the contents of biological samples for Ub and Ubls, and to identify specific types of Ub and Ubl chains in model organisms. I also used MS to conduct the first comprehensive SUMO system protein-protein interactome in any organism. In total, 452 high confidence protein-protein interactions were detected for S. cerevisiae SUMO system proteins, encompassing a total of 321 interacting partners. Yeast SUMO system components were found to interact with proteins involved in a number of different biological processes, and my mapping effort increased the number of known SUMO system interacting partners >50-fold. This study revealed that a number of transcriptional co-repressors and chromatin remodelling proteins interact physically with specific SUMO system components, with a clear division of labour between SUMO system enzymes. Finally, I conducted the first global analysis of SUMO chain function, using a combination of genetic, high-content microscopy, and high-density transcriptomics screens. Consistent with my interactomics work, this study demonstrated that inhibition of SUMO chain synthesis leads to severe chromatin condensation defects, which in-turn leads to chromosome missegregation, unscheduled transcription of stress-and nutrient-regulated genes, and aberrant intragenic transcription. Together, my work thus revealed a major role for the SUMO system in the maintenance of higher order chromatin structure and transcriptional repression.

Keywords: yeast
SUMO
Proteomics
AP-MS
Advisor: Raught, Brian
Settling for Less out of Fear of Being Single

The present research explores a novel construct of fear of being single, without a romantic partner. This research demonstrates that those who fear being single may lower their relationship standards without realizing it, even accounting for constructs typically examined in relationship research such as anxious attachment and neuroticism. Study 1 explored the content of people’s thoughts about being single. Studies 2A and 2B involved the development and validation of the Fear of Being Single scale. Study 2C provided preliminary support for the hypothesis that fear of being single predicts settling for less in ongoing relationships, showing that fear of being single predicted greater dependence on unsatisfying relationships. Studies 3A and 3B explored the predictive ability of fear of being single for self-reported dating standards. Across both samples, fear of being single was unrelated to self-reported standards for a mate, with the exception of consistently higher standards for parenting. However, Studies 4 and 5 explored romantic interest in targets that were manipulated to vary in responsiveness (both Studies 4 and 5) and physical attractiveness (Study 5 only). These studies found that fear of being single consistently predicted higher levels of romantic interest in less responsive and less attractive dating targets. Taken together, the present research suggests that fear of being single is a meaningful predictor of settling for less in relationships.

Keywords: Social Psychology
Romantic Relationships
Advisor: MacDonald, Geoff
The Effectiveness of an Alternative Alcohol Taxation Method in a Middle-income County: A Case Study of Thailand

Background: While specific taxation has been found to be effective in reducing alcohol consumption and its related harms in High-Income Countries, it theoretically encourages drinking initiation in Low- and Middle-Income Countries (LMIC) with a high prevalence of lifetime abstainers. This dissertation aims to systematically review the existing evidence of the effects of taxation in LMIC on alcohol consumption, alcohol-related harms, and the rate of drinker initiation, and to examine how changes in Thailand’s Two Chosen One (2C1) taxation rates affect alcohol consumption, related harms and drinking initiation. Method: (1) A systematic review and meta-analysis that examines the effects of taxation policy on alcohol consumption, alcohol-related harms and the rate of drinker initiation in LMIC. (2) A quasi-experimental study using interrupted time-series analysis that examines the effects of alcohol taxation increases in Thailand on alcohol consumption and traffic fatalities. (3) An analysis of four consecutive national surveys on alcohol consumption behaviours to examine the effect of alcohol tax increases on drinking initiation prevalence in Thailand. Result: There were only 10 published studies that quantitatively examined the effect of alcohol taxation policy on consumption in LMIC. In LMIC the price elasticity of demand was -0.64 for all alcohol consumption, -0.50 for beer consumption, and -0.79 for consumption of other alcohol. No studies were found that examined the effects of taxation policy on alcohol-related harms and drinking initiation in LMIC. Thailand’s alcohol taxation increase in 2009 was associated with a reduction in alcohol consumption (tax elasticity of -1.95) and in traffic fatalities (tax elasticity of -1.90). Increased taxation prevented drinking initiation among young people 15 – 24 years of age during 2001-2011 in Thailand (tax elasticity of -0.40). Conclusion: Increases in taxation under the 2C1 taxation method were associated with decreases in alcohol consumption, alcohol-related harms and drinking initiation.

Keywords: alcohol
taxation
consumption
harm
drinking initiation
middle-income country
Thailand
policy
Advisor: Rehm, Jürgen
A Generic Simulation-based Perioperative Decision Support Tool for Tactical Decision

In Canada and around the world, there has been an increased focus on the efficiency, cost and access to health care services. One area of particular focus is surgical procedures, often with government funding and policies focused on reducing wait times through pay for performance and volume target initiatives. In Ontario, an expert panel was assembled to evaluate the current state of surgical processes and provide recommendations to improve access, efficiency and quality. This thesis addresses the panel's recommendation for a simulation-based decision tool to help hospitals inform decisions that can lead to improved access and efficiency. A generalised, simulation based perioperative decision tool is presented that can be used to test a variety of tactical decisions. The generic model has been applied to six hospitals of varying sizes, ranging from large academic centres to small rural community hospitals. The model remains in use at some of the hospitals to regularly inform decisions. The model is also being applied to additional hospital sites. During application of the generic model, challenges in design decisions and validation were encountered. As a result, a series of principles are proposed to guide future generic modelling design and achieving user acceptance. These principles add to the generic simulation modelling and healthcare modelling research fields by laying some groundwork for a formalised approach to designing effective generic simulation models and achieving confidence in results. Finally, the research demonstrates two uses of the generic model: as decision tool and as a demonstrative tool. As a decision tool the model is used to compare numerous potential tactical decision options under consideration. As a demonstrative tool, the model is used to quantify the effect of poor practices on hospital performance. The design of the generic model only considers efficient processes and best practices. When model results are compared to historical performance, decision makers are able to quantify the effect of existing poor practices on their performance and decision making. The tool enables users to base their tactical level decisions on the assumption that good practices and procedures are followed.

Keywords: simulation
healthcare
surgery
perioperative
generic modelling
decision support
Advisor: Carter, Michael W.
Performance Excellence: Toward a Model of Factors Sustaining Professional Voice Performance in Opera

While considerable research has explored the skills elite professionals use to sustain performance excellence in a multitude of disciplines, much less research has focused on professional musicians. Multi-faceted skills are needed to maintain performance excellence. This research investigates the deliberate skills and processes professional opera singers employ to preserve elite performance. Data drawn from individual semi-structured interviews with ten professional opera singers, with a minimum career length of ten to twenty years, were analyzed within the methodology of grounded theory. Results revealed a strong role for creation of a music "road-map" in the context of deliberate preparedness in both physical and mental skills, which contributed to high levels of learning self-efficacy. High-level skills cultivated in the preparation phase were applied directly within the context of live performance, facilitated "flow" experiences, involved energy exchanges with other performers and audiences, and resulted in higher levels of performing self-efficacy.

Keywords: Performance excellence
Opera
Deliberate practice
Self-efficacy
Advisor: Bartel, Lee
Understanding Private Law's Remedies

The fundamental question of private law’s remedies is how do subsequent remedial actions rationally address prior failures. This question can be approached either intrinsically or extrinsically. While the former justifies and explains the remedial action from within the original plaintiff-defendant relationship, the latter welcomes external principles and goals. The arguments of this thesis fit within an intrinsic approach to private law’s remedies. To this end, several arguments are levied against the extrinsic perspective, and, in particular, its confidence in the separation of rights and remedies. For positive inspiration, it looks to two leading intrinsic theoretical accounts—those of Ernest Weinrib and John Gardner, respectively—with an eye to revealing what, if any, meaningful differences there are between the two. Using the language and logic of practical reasons and reasoning, this dissertation suggests that remedies can be understood in one of two ways. First, the remedy is just the same as the original reason. If I fail to pay my debt on the date it is due, my subsequent remedial action in paying it later is carried out because of the original reason, namely, that I owe a debt to someone. Second, the remedy is a reflection of certain second-order reasons that are part of the original (operative) reason. These are reasons not to act for certain other reasons that counsel against the performance of the first-order reason to do the obligatory action. These reasons stick around and tell you to do something; that doing nothing is not optional. If I break your toe, I can no longer satisfy the original reason not to break your toe; however, I can and must do something to address my initial failure. The content of this reparative action is constrained by the original reason not to break your toe. While its first-order strength is no longer available—one can no longer act for the reason it recommends—it can nonetheless provide guidance with respect to what the next-best thing might be.

Keywords: "private law"
remedies
Advisor: Weinrib, Ernest
The Evolutionary and Ecological Consequences of Partner Variation in the Mutualism between Legumes and Symbiotic Nitrogen Fixing Bacteria

A fundamental goal in ecology and evolutionary biology has been to understand how microevolutionary forces affect the origin and maintenance of mutualisms over ecological and evolutionary time scales. Mutualistic partners vary in the reciprocal benefits they provide, yet the role of partner variation on microevolutionary forces that impact the maintenance of mutualisms is unclear. Using the mutualism between legumes and nitrogen fixing symbionts, my dissertation investigated the ecological and evolutionary consequences of variation in partner quality. In the first experiment, I demonstrate how insect herbivory can change the costs and benefits of associating with exploiters, and that some degree of exploitation from non-beneficial rhizobia can reduce insect herbivory, thus removing the fitness advantage of associating purely with beneficial rhizobia. In the second study, I examine how rhizobia genotype modifies competition between hosts grown in kin and non-kin groups. I show that lower fitness in plant kin groups can simply be a by-product of genetic variance in plant size and non-linear relationships between plant size and fitness. I further show that the symbiotic community can change difference in fitness between kin and non-kin groups independent of these by-product effects. In my last chapter, I provide the first empirical evidence that an important mechanism for mutualism stability-- the ability for hosts to preferentially associate with beneficial rhizobia-- is genetically variable and can evolve in response to exploitation. I also show that host preference for beneficial rhizobia can be maintained in legume populations, even in the absence of exploitation. My dissertation provides insight into the potential evolutionary dynamics of stabilizing mechanisms by suggesting that the agents of selection that affect the level of host exploitation can come from biotic factors other than the exploiters themselves. My dissertation has also shown that inclusion of other ecological interactions, such as herbivory, can provide valuable perspective on fitness effects of symbionts on their hosts, and can even change our fundamental assumptions about the effects of exploitation on host fitness, which has formed the backbone of mutualism theory.

Keywords: evolutionary ecology
mutualisms
legume
Rhizobia
nitrogen-fixation
microbial symbiont
exploiter
cheater
herbivory
competition
selection
context-dependency
Advisor: Stinchcombe, John
B Cell Development: The Impact of the Environment

B lymphocytes develop from pluripotent stem cells, and differentiate to plasma cells (PCs) in reaction to signals from the supportive microenvironment. Different sets of signals, which are derived from multiple sources such as soluble cytokines and cell-cell contacts, are required at different stages of development. For instance, murine B cell progenitors require the action of interleukin-7 (IL-7) in the early phase of their development in the bone marrow (BM). The necessity for IL-7 decreases as the cell matures, and this event is correlated with the appearance of CD22. The first two chapters of this thesis focus on the early stages of B cell development that take place in the BM. In chapter 1, I examine the IL-7 response and, although I do not show a specific role for CD22 in the loss of sensitivity to IL-7, my data suggest that cis interactions involving sialic acids might modulate the IL-7 response. This section is followed by the analysis of the effect of IL-21 on B cell progenitors in the BM. IL-21 is known to regulate the terminal stages of B cell differentiation. In collaboration with Dr. Danijela Konforte, I present evidence that B cell progenitors in the BM also express a functional IL-21 receptor and that stimulation of this receptor with IL-21 accelerates the maturation pace of B cells. I further demonstrate that proB cells stimulated with IL-21 and anti-CD40 can differentiate into immunoglobulin (Ig)-secreting cells, and discuss the possibility that IL-21 plays a role during inflammation for the development of B cell progenitors in peripheral lymphatic organs. Finally, in the last chapter, in collaboration with the laboratory of Dr. Gommerman, I investigate how the microenvironment can shape the development of B cells. It has been demonstrated by my collaborators that IgA+ PCs present in the gut produce iNOS and display traits commonly associated to the myeloid lineage, and in this chapter, I describe a co-culture system with BM and gut stroma to study the conditions that sustain the generation of IgA+iNOS+ cells. In particular, I show that the presence of microbial products is one of the key factors required for their development.

Keywords: B cell development
Advisor: Paige, Christopher J.
The Time-course of Lexical Influences on Fixation Durations during Reading: Evidence from Distributional Analyses

Competing models of eye movement control during reading disagree over the extent to which eye movements reflect ongoing linguistic and lexical processing, as opposed to visual/oculomotor factors (for reviews, see Rayner, 1998, 2009a). To address this controversy, participants’ eye movements were monitored in four experiments that manipulated a wide range of lexical variables. Specifically, Experiment 1 manipulated contextual predictability by presenting target words (e.g., teeth) in a high-predictability prior context (e.g. “The dentist told me to brush my teeth to prevent cavities.”) versus a low-predictability prior context (e.g., “I'm planning to take better care of my teeth to prevent cavities.”), Experiment 2 manipulated lexical ambiguity by presenting biased homographs (e.g., bank, crown, dough) in a subordinate-instantiating versus a dominant-instantiating prior context, and Experiments 3A and 3B manipulated word frequency by contrasting high frequency target words (e.g., table) and low frequency target words (e.g., banjo). In all four experiments, I used distributional analyses to examine the time-course of lexical influences on fixation times. Ex-Gaussian fitting (Staub, White, Drieghe, Hollway, & Rayner, 2010) revealed that all three lexical variables (i.e., predictability, lexical ambiguity, word frequency) were fast-acting enough to shift the entire distribution of fixation times, and a survival analysis technique (Reingold, Reichle, Glaholt, & Sheridan, 2012) revealed rapid lexical effects that emerged as early as 112 ms from the start of the fixation. Building on these findings, Experiments 3A and 3B provided evidence that lexical processing is delayed in an unsegmented text condition that contained numbers instead of spaces (e.g., “John4decided8to5sell9the7table2in3the9garage6sale”), relative to a normal text condition (e.g., “John decided to sell the table in the garage sale”). These findings have implications for ongoing theoretical debates concerning eye movement control, lexical ambiguity resolution, and the role of interword spaces during reading. In particular, the present findings provide strong support for models of eye movement control that assume that lexical influences can have a rapid influence on the majority of fixation durations, and are inconsistent with models that assume that fixation times are primarily determined by visual/oculomotor constraints.

Keywords: reading
eye movements
distributional analysis
lexical processing
Advisor: Reingold, Eyal M.