VictorJuiz/thesis huggingface dataset:
Improving the Design Analysis of Prognosis Studies in Rare Diseases
Keywords: Childhood-onset lupus
Longitudinal Analytic Methods
Longitudinal design
Prognosis
Rare diseases

Prognosis studies examine outcomes and identify factors associated with or predictive of observed outcomes. In rare diseases, prognosis studies play an especially important role in informing patients and guiding treatment. Yet the current prognosis literature is plagued by design issues limiting clarity of information. Objectives: This thesis aims to improve on the design and analysis of prognosis studies in rare diseases. The objectives are: 1) to evaluate the quality of current Systemic Lupus Erythematosus (SLE) prognosis literature and identify areas of deficits; 2) to apply the longitudinal study design to a childhood-onset SLE (cSLE) cohort to study longitudinal evolution of organ damage and disease activity; and 3) to explore the application of modern longitudinal analytic methods in analyzing an observational cohort. Methods: A systematic review of the literature was performed. A cSLE cohort was studied longitudinally. Longitudinal modelling of an irregular-visit-schedule observational cohort was performed using marginal and random effect models, along with Bayesian latent class growth mixture modelling. Results: I have identified study design elements at high risk of bias within the SLE literature. Using the longitudinal design, I demonstrated that cSLE patients accrued damage throughout their disease courses and determined prognostic factors with clear temporal predictive relationships with damage evolution. I applied latent class technique to group patientsâ disease activity trajectories into more homogeneous classes and identified early factors that predicted patterns of disease activity evolution. Conclusions: I have demonstrated that the design and analysis of prognosis studies can be improved in rare diseases. I identified areas of deficits in prognosis study design. I have successfully applied the longitudinal study design and modern longitudinal analytic techniques to provide more precise prognostication in cSLE. Given this body of work, we now have the tools to design robust prognosis studies to achieve maximal gain in clarity of information.
The Structure of Diagonally Constructed ASH Algebras
Keywords: Operator Algebras

We introduce a class of recursive subhomogeneous algebras which are constructed using a type of diagonal map similar to those previously defined for homogeneous algebras. We call these diagonal subhomogeneous (DSH) algebras. Using homomorphisms that also exhibit a kind of diagonal structure, we study certain limits of DSH algebras. Our first result is that a simple limit of DSH algebras with diagonal maps has stable rank one. As an application we show that whenever X is a compact Hausdorff space and σ is a minimal homeomorphism thereof, the crossed product algebra C*(Z, X,σ) has stable rank one. We also define mean dimension in the context of these limits. Our second result is that mean dimension zero implies Z-stability for simple separable limits of DSH algebras with diagonal maps. We also show that the tensor product of any two simple separable limit algebras of this kind is Z-stable.
Response of periodic systems to electromagnetic fields: multipole expansion, microscopic charge-current density, polarization and magnetization
Keywords: metamaterials
multipole expansion
optical properties of materials
periodic systems
polarization and magnetization

Polarization and magnetization fields are central concepts in the theory of light-matter interaction, because they describe the distribution of charges and currents induced in the material medium due to an application of electromagnetic fields. Here I develop strategies to treat polarization and magnetization fields in periodic structures and I analyze the radiation spectrum emitted by them. The methods are based on the multipole expansion of charge-current distributions and on its extensions to account for the motion of charges between lattice sites. In the first part of this thesis I treat the optical response of 2d nanoparticle arrays, with the focus on collective effects that arise due to higher order multipolar response. First, I evaluate the interaction constants that describe the collective radiative interactions between nanoparticles in magneto-electric quadrupolar arrays, in an approach that gives the radiative damping in an exact analytic form. Then I find the radiation spectrum from an array of gold spheres with large electric quadrupolar response. The spectrum is dominated by surface-lattice resonances (SLRs) which are of a mixed multipolar character, with significant contributions from multipoles that would be negligible if the sphere was isolated. I link the SLRs to an excitation of the normal modes of the array, and propose a simplified model of the normal mode dispersion relations to explain the SLR properties. In the second part of this thesis I develop strategies to describe charges and currents and polarization and magnetization fields in regular solids. The formalism is based on gauge-invariant dynamical equations of electron Green functions. I derive and categorize the descriptions of dynamics introduced via Peierls transformation of the Green function. Then I apply the formalism to treat the linear response of an insulator to electromagnetic fields. I find the microscopic charge and current densitites in a form such that their expansion around lattice sites follows in a natural way. Restricting myself to static and uniform fields I introduce microscopic polarization and magnetization fields, and derive all the response coefficients within one formalism that makes no reference to energy or thermodynamic potentials.
Economics of Parking: Short, Medium, and Long-Term Planning
Keywords: Autonomous vehicles
Enforcement
Parking
Transportation

Worldwide surveys have shown that cruising for parking substantially increases the travel time of individuals and leads to higher traffic congestion as well. Motivated by the need to mitigate adverse effects of parking, this thesis investigates the impact of emerging short, medium, and long-term parking policies. Hourly parking pricing is a short-term policy whereby vehicles pay based on their dwell time. We show that hourly parking pricing can actually increase congestion if imposed imprudently, but if devised optimally, it can lead to better traffic management. Parking enforcement is a medium-term policy comprised of a citation fine and a level-of- enforcement (e.g., number of inspection cameras in streets). We quantify the effect of enforcement policies and we investigate the impact of enforcement technology (i.e., on-foot inspection or camera-based inspection) on illegal parking behaviour. For long-term planning, we model the impact of autonomous vehicles (AV) on parking. With the anticipated growth in AVs, passengers no longer need to park near their final destination. Instead, passengers are dropped off by AVs at their final destination and the AVs travel to the nearest and most affordable available parking lot. We investigate the parking patterns of AVs and show that they substantially decrease parking search time.
Yours, Mine Ours: What Ancient Egyptian Possessives Can Tell Us About Language Change and Stable Variation
Keywords: Ancient Egyptian
Egyptology
historical linguistics
language variation and change
morphology
sociolinguistics

Natural language variation can be thought of as two or more variants competing for use (Kroch 2001,1989). Under this model, two outcomes are possible: language change or specialization. Specialization can be then broken down into specialization for different functions, and partial specialization – stable variation (Wallenberg 2013; Fruehwald and Wallenberg 2013). In this historical sociolinguistic investigation, I analyze differences between stable variation and language change in Ancient Egyptian. Observing two Egyptian possessive variables – clitic possession and nominal possession – I compare factors affecting variant choice in each, using a dataset with a total of 4,656 possessive tokens and 495 demonstrative tokens. I use a theoretical syntactic account to make testable predictions about language change and to inform my choice of continuous factor, which provides the mechanism for stable variation (Wallenberg 2013; Fruehwald and Wallenberg 2013) – in this case, phrase complexity. Using distributional results, logistic regression, and logistic curves, I find that clitic possession is an instance of language change. I then combine results for demonstrative tokens with a theoretical syntactic account to explain the emergence of the innovative variant in clitic possession, and use logistic regression and conditional inferences trees to illustrate the spread of this variant across Egypt over time. I also find that possessum and text type have an effect on clitic possessive variation, supporting Egyptology-based predictions of stigmatization of the innovative variant, but providing evidence against Egyptological claims of an alienability split for this variable. Phrase complexity has an effect on clitic possession as well, perhaps the reason for the slowness of this particular language change. Conversely, I find that nominal possession is an instance of stable variation. Possessum and possessor interact in their effect on nominal possessive variation, an effect which provides an understanding of the social meaning attached to the nominal possessive variants: one for high-status nouns, one for other types of nouns. Effects of text type and location are also present in nominal possession, but minimal. Phrase complexity is a significant factor as well, constraining variation along a continuum and supporting the claim that a continuous factor is the reason for stable variation.
Effects of Model Salivary Esterases and MMP Inhibition on the Restoration's Marginal Integrity and Potential Degradative Contribution of Cariogenic Bacteria
Keywords: biodegradation
esterase
gene response
resin composite
secondary caries
Streptococcus mutans

Enzyme-catalyzed degradation of the restoration-tooth interface compromises interfacial integrity, thereby contributing to secondary caries, which is a major cause of resin-based restoration failure. It is hypothesized that in addition to salivary esterases, the cariogenic bacterium Streptococcus mutans has specific esterases that degrade the resin-dentin interface, releasing biodegradation by- products (BBPs) such as bis-hydroxy-propoxy-phenyl-propane (BisHPPP). In turn, BisHPPP affects S. mutans by stimulating the expression of esterases. Another hypothesis is that the biostability of the resin-dentin interface is affected by simulated salivary esterases, dentinal matrix metalloproteinase (MMP) inhibition, and restorative materials. To test the first hypothesis, putative esterase genes in S. mutans UA159 were identified, purified, and characterized. SMU_118c was identified as the dominant esterase in S. mutans UA159 and showed a similar hydrolytic activity profile to salivary esterases. BisHPPP upregulated expression of the SMU_118c gene and related protein in a concentration-dependent manner. This positive feedback process could accelerate the degradation of the restoration-tooth interface and lead to premature restoration failure. To test the second hypothesis, an in vitro model was established to evaluate the effects of salivary esterases, MMP inhibition and restorative materials on interfacial integrity. It was confirmed that interfacial integrity was compromised with time and was further deteriorated by simulated salivary esterases, as indicated by the greater depth of bacterial ingress and more bacterial biomass of biofilm along the interface. However, this process could be modulated by using different restorative materials and MMPs inhibition.This project elucidated the mechanistic interaction between oral bacteria and restorative materials and established a new, in vitro, and physiologically relevant model to assess the effect of material chemistry, properties, and application modes on bacterial penetration and biofilm formation. These findings offer the oral health community practical ways to reduce secondary caries by altering material composition and restorative procedures.
Home Caregiver Safety when Assisting with Bathing and Toileting
Keywords: aging in place
assistive devices
ergonomics
home care provider

Home care workers who assist with personal care have much higher rates of musculoskeletal disorders (MSDs) of the back and shoulder than the general working population. This thesis identifies and describes activities that are likely to contribute substantially to the development of MSDs, then identifies and evaluates ways to reduce risk. Physically demanding activities and aspects of the home care context that contribute to MSD risk are identified through a literature review and through focus groups with home care providers, leading to a focus on toileting and bathing. An observational study was used to analyze providers’ postures and related lower back loads while assisting with these activities in a simulated home care scenario. During toileting, exposures to MSD risk factors were highest when managing clothing, providing posterior perineal care and during transfers. One third of providers’ exposure to severely flexed trunk postures, which are powerful predictors of lower back MSD risk, could be eliminated if bidet seats were used for perineal cleaning. During bathing, the highest exposures to MSD risk factors were observed during transfers and while providing lower limb care. Four tools to reduce exposures were evaluated in a follow-up study. Shoulder muscle activity and exposure to non-neutral postures were reduced when using a short-handled leg-lifter to transfer the legs, while sitting to lift the legs improved back postures but increased demands on the shoulders. A sliding, rotating bench reduced back muscle activity despite an increased use of awkward postures. All participants judged the leg-lifter and sliding, rotating bench to be feasible and desirable for use in the community. The identified tools reduce providers’ exposure to MSD risk factors when assisting with two of the most demanding homecare activities. There is a need to improve access to assistive devices to ensure providers’ occupational safety while preserving their ability to provide client care.
Habits of Peace: The Foundations of Long-Term Regional Cooperation in Southeast Asia and South America
Keywords: Constructivism
Diplomacy
Habit
Practice Theory
South America
Southeast Asia

The regions of Southeast Asia and South America are often cited as puzzling cases of long peace among nation-states. Absent hard power balancing behaviours, liberal democratic development, and economic interdependence, both present unlikely cases for prolonged periods of time absent large scale inter-state violence. This research begins with an inquiry into the foundations the long peace of each region: practices of conflict management. More narrowly, this project asks: How can we understand cooperation and community building alongside persistent militarized violence? Upon what foundations have these largely illiberal states been able to build relative but lasting peace despite pervasive territorial disputes? In answering these questions, this research argues that distinct and diplomatic habits shape the management of peace and conflict in each region. The underlying argument of this work is that the habitual and dispositional qualities of regional diplomatic practice inform the long peace of these regions and regional relations more generally. In each region, distinctive and discrete qualities of regional relations shape crisis response, but also shape how crises, themselves, are understood by regional diplomatic officials. These â habits of peaceâ make possible long-term regional cooperation and relative peace alongside persistent intra-regional violence. After articulating the conflictual nature of peace in each regional case, I suggest that existing understandings of regional long-peace overlook the practical and tactical foundations upon which interstate cooperation rest. I offer a theoretical framework and particular set of methods attentive to the habitual and dispositional qualities of inter-state relations. In the subsequent empirical cases I demonstrate the existence and effect of a particular regional habitual disposition in each region, with a particular focus on episodes of regional crisis including the 2011 Preah Vihear border dispute in Southeast Asia and the 1995 Cenepa conflict between Peru and Ecuador.
Children's and adolescents' judgments about social responsibility: Moral identity and the public good
Keywords: Identity development
Moral development
Moral reasoning
Political Psychology
Political socialization

The current research sought to assess children's (10-11 years), adolescents' (13-14 years), and adult's (Psy100 students) perceptions regarding the importance and obligation to engage in various civic activities. Drawing from previous research on the topic of civic obligation, participants were presented with five different types of civic acts (voting, volunteering, charity work, clubs sports, and petitions/protests) and were asked to assess the extent to which these acts were important, obligatory, and legally mandatory. Of interest was also participants' justifications for their responses, which were coded according to moral reasoning, personal choice, or practical factors which mitigated responses. Finally, measures of moral identity were administered to explore the extent to which individual differences in the personal importance of moral qualities influenced responses. Results suggested that younger participants rated charitable endeavors as more obligatory and legally mandatory than did the young adults. Conversely, the young adults tended to prioritize voting more highly relative to the younger participants. Supplementing these findings were the justification analyses, which suggested that younger participants used more moral reasoning in their responses to questions about charitable organizations compared to the young adults. Results also suggested that moral identity was related to the quantitative evaluations of the different civic activities. Moral identity was also positively associated with the use of moral reasoning within morally salient activities across all situations. Regression models indicated that this link between moral identity and moral cognition persisted when age effects were controlled.
Investigating the Metal-like Optical Behavior of Boron Nitride
Keywords: boron nitride
graphene
Phonon polariton
SNOM
surface waves

Recent advances in scanning near-field optical microscopy (SNOM) have led to rapid growth of the field of phonon polaritonics. Due to strong vibrational resonances, which are responsible for negative permittivity in the mid-infrared (mid-IR) region, hexagonal boron nitride (hBN) is of high interest in the field. Here, we investigate the metal-like optical properties of hBN governed by phonons. We demonstrate one of the first experimental observations of surface phonon polaritons (SPhPs) in boron nitride nanotubes (BNNTs), which exhibits a very high effective index (neff ~70), yet a long propagation length. We show that the apparent periodicity can be controlled by varying the nanotube size and the supporting substrate. We also observed IR polaritonic interaction between graphene plasmons and surface phonon polaritons of BNNT, which are capable of coherently exchanging their energies at the nanoscale. 2D hBN films were also studied, and we report a metal-free method of launching phonon polaritons by making use of the intrinsic property of the material itself. To support these studies, we also developed and implemented an opto-mechanic stabilization mechanism for the SNOM and showed improved phase stability. Our reported modification of the SNOM setup to work with 2 IR continuous wave (CW) lasers opens further doors for studying inter-mode energy transductions by performing IR pump-probe CW spectroscopy.
Circuits, Architectures, and CAD for Low-Power FPGAs
Keywords: CAD
Circuit design
FPGA
Interconnect
Low Power
Reconfigurable Computing

Field Programmable Gate Arrays (FPGAs) are becoming an ever more prominent platform for the implementation of digital systems. In contrast to traditional processors that map computations onto a series of predefined instructions, an FPGA maps a computation onto a custom tailored digital circuit, thus yielding performance benefits. FPGAs can also provide cost and time-to-market benefits compared to Application Specific Integrated Circuits (ASICs). However, these advantages do not come for free as FPGAs typically have higher power consumption than the aforementioned platforms. FPGA power consumption is specifically of great concern presently given the growing demand for compute power in power constrained environments such as in mobile devices and data centres. To that end, in this thesis we explore circuit and architectural techniques to reduce power dissipated in FPGAs, and present the necessary CAD tools to implement our proposed power optimization schemes. First, we present a technique to reduce the dynamic power dissipation that arises because of glitches. For this technique we designed a programmable glitch filter which we propose to augment a conventional FPGA; the proposed circuit can be configured to eliminate glitches for a range of different pulse-widths. Our second power reduction technique is motivated by observing that there exists an abundance of unused routing conductors in FPGAs. We show that by tri-stating these unused routing conductors we can reduce the effective wire capacitance seen by adjacent conductors, thereby reducing dynamic power. Moreover, we show how tri-stated wires also results in reduced routing leakage. The third power reduction technique also seeks to leverage unused routing conductors; in this case we employ the unused routing conductors as charge reservoirs to enable a charge recycling technique to reduce dynamic power. Finally, this thesis presents a technique to aggressively reduce leakage power dissipated in the routing network of an FPGA by tri-stating both used and unused routing buffers; the used routing buffers in this case are temporarily activated when they are needed â i.e. when they are in the process of transmitting data. Ensuring that all circuits are effectively shut-off at all other times allows us to reduce leakage power.
Confirmation bias in visual attention
Keywords: Attention
Cognition
Confirmation bias
Decision making
Vision

This dissertation evaluates the proposal that visual attention is biased towards stimuli that could potentially verify a perceptual hypothesis, compared to stimuli that might falsify it. To do so, I use a visual search task with two, mutually exclusive, coloured targets (e.g., a red p or a blue p). Before each set of searches, one target colour is designated positive, or confirmatory, information and one is designated negative information by requiring affirmative responses or negative responses to one of the two targets (e.g., press Z if the p is red, press M if it is not). The first set of experiments, reported in Chapter 2, showed that confirmatory search patterns were observed for both novel and practiced hypotheses, were observed despite instructions to the contrary, and were mitigated by a search colour-preview. Chapter 3 measured the ocular correlates of the search bias, showing that more fixations indeed go towards confirmatory stimuli, but showed that when stimulus inspections took longer, search became les confirmatory and more efficient. Finally, Chapter 4 demonstrated that confirmatory search did not occur when hypotheses referred to visually heterogeneous stimuli and also did not occur when hypotheses included a negation, suggesting that a visual matching bias underlies confirmatory search. Confirmation bias thus appears to be a side-effect of goal-directed cognition in general, and the present results are discussed in relation to theories likening reasoning to foraging and information search.