VictorJuiz/thesis huggingface dataset:
On the JLO Character and Loop Quantum Gravity

In type II noncommutative geometry, the geometry on a C∗-algebra A is given by an unbounded Breuer–Fredholm module (ρ,N,D) over A. Here ρ:A→N is a ∗-homomorphism from A to the semi-finite von Neumann algebra N⊂B(H), and D is an unbounded Breuer–Fredholm operator affiliated with N that satisfies certain axioms. Each Breuer–Fredholm module assigns an index to a given element in the K-theory of A. The Breuer–Fredholm index provides a real-valued pairing between the K-homology and the K-theory of A. When N=B(H), a construction of Jaffe-Lesniewski-Osterwalder associates to the module (ρ,N,D) a cocycle in the entire cyclic cohomology group of A for D is theta-summable. The JLO character and the K-theory character intertwine the K-theoretical pairing with the pairing of entire cyclic theory. If (ρ,N,F) is a finitely summable bounded Breuer–Fredholm module, Benameur-Fack defined a cocycle generalizing the Connes's cocycle for bounded Fredholm modules. On the other hand, given a finitely-summable unbounded Breuer–Fredholm module, there is a canonically associated bounded Breuer–Fredholm module. The first main result of this thesis extends the JLO theory to Breuer–Fredholm modules (possibly N does not equal B(H)) in the graded case, and proves that the JLO cocycle and Connes cocycle define the same class in the entire cyclic cohomology of A. This extends a result of Connes-Moscovici for Fredholm modules. An example of an unbounded Breuer–Fredholm module is given by the noncommutative space of G-connections due to Aastrup-Grimstrup-Nest. In their original work, the authors limit their construction to the case that the group G=U(1) or G=SU(2). Another main result of the thesis extends AGN’s construction to any connected compact Lie group G; and generalizes by considering connections defined on sequences of graphs, using limits of spectral triples. Our construction makes it possible to equip the module (ρ,N,D) with a Z_2-grading. The last part of this thesis studies the JLO character of the Breuer–Fredholm module of AGN. The definition of this Breuer–Fredholm module depends on a divergent sequence. A concrete condition on possible perturbations of the sequence ensuring that the resulting JLO class remains invariant is established. The condition implies a certain functoriality of AGN’s construction.

Keywords: noncommutative geometry
quantum gravity
mathematical physics
Advisor: Eckhard, Meinrenken
The Neurophysiological Correlates of Children's and Adults' Judgments of Moral and Social Conventional Violations

Adults and young children have been found to distinguish between moral and social conventional acts, which are considered to entail distinct domains of reasoning (e.g., Turiel 1983). Recently, research has begun to examine the neural basis of moral judgments (e.g., Greene et al., 2001), but these studies did not examine the development of neurocognitive processing of judgments in these two domains. The present study focused on detection of cognitive conflict as a neurocognitive process that distinguished judgments of moral and conventional violations. The N2 component of the ERP was examined in order to determine whether the two types of violation are associated with different neurophysiological correlates and whether they change with development. In a series of five experiments, reaction times and ERPs were recorded from 12- to 14-year-old children and undergraduates who read scenarios that had one of three possible endings: (1) moral violations, (2) conventional violations, (3) no violation (neutral acts). Participants judged whether the act was acceptable or unacceptable when a rule was assumed or removed. Results indicate that reaction times were faster for moral than conventional violations when a rule was assumed for both undergraduates and children, as well as when a rule was removed for children but not for undergraduates. ERP data indicated that adults’, but not children’s, N2 amplitudes were larger (i.e., more negative) for conventional than iii moral violations when a rule was assumed. Furthermore, source analysis indicated generators for the N2 in dorsomedial and ventromedial prefrontal cortices. The results suggest that judgments of conventional violations involve increased conflict detection as compared to moral violations, and these two domains are processed differently across development. The findings were explained by the idea that judgments of conventional violations are more explicitly dependant on rules, whereas judgments of moral violations are based more directly on the intrinsic negative consequences of the act.

Keywords: Moral development
Social conventions
Neuroscience
ERP
N2
Advisor: Helwig, Charles C.
Zelazo, Philip D.
Exploring Many-body Physics with Ultracold Atoms

The emergence of many-body physical phenomena from the quantum mechanical properties of atoms can be studied using ultracold alkali gases. The ability to manipulate both Bose-Einstein condensates (BECs) and degenerate Fermi gases (DFGs) with designer potential energy landscapes, variable interaction strengths and out-of-equilibrium initial conditions provides the opportunity to investigate collective behaviour under diverse conditions. With an appropriately chosen wavelength, optical standing waves provide a lattice potential for one target species while ignoring another spectator species. A “tune-in” scheme provides an especially strong potential for the target and works best for Li-Na, Li-K, and K-Na mixtures, while a “tune-out” scheme zeros the potential for the spectator, and is pre- ferred for Li-Cs, K-Rb, Rb-Cs, K-Cs, and 39K-40K mixtures. Species-selective lattices provide unique environments for studying many-body behaviour by allowing for a phonon-like background, providing for effective mass tuning, and presenting opportunities for increasing the phase-space density of one species. Ferromagnetism is manifest in a two-component DFG when the energetically preferred many-body configuration segregates components. Within the local density approximation (LDA), the characteristic energies and the three-body loss rate of the system all give an observable signature of the crossover to this ferromagnetic state in a trapped DFG when interactions are increased beyond kF a(0) = 1.84. Numerical simulations of an extension to the LDA that account for magnetization gradients show that a hedgehog spin texture emerges as the lowest energy configuration in the ferromagnetic regime. Explorations of strong interactions in 40K constitute the first steps towards the realization of ferromagnetism in a trapped 40K gas. The many-body dynamics of a 87Rb BEC in a double well potential are driven by spatial phase gradients and depend on the character of the junction. The amplitude and frequency characteristics of the transport across a tunable barrier show a crossover between two paradigms of superfluidity: Josephson plasma oscillations emerge for high barriers, where transport is via tunnelling, while hydrodynamic behaviour dominates for lower barriers. The phase dependence of the many-body dynamics is also evident in the observation of macroscopic quantum self trapping. Gross-Pitaevskii calculations facilitate the interpretation of system dynamics, but do not describe the observed damping.

Keywords: ultracold atoms
many-body physics
Bose-Einstein condensate
quantum degeneracy
ferromagnetism
Josephson effects
Advisor: Thywissen, Joseph H.
The Need for a Physical Education: Examining Physical Activity During The Transition to University

While physical activity (PA) declines across the lifespan, this does not occur linearly. Declines are most pronounced during the transition into early adulthood. This dissertation consisted of three studies examining PA decline during the transition into early adulthood: (1) to understand patterns of PA and other health behaviours of Canadians; (2) to understand reasons for PA declines during entry into university; and (3) to examine the feasibility and effects of a website-delivered PA intervention. Study 1 utilized multilevel modeling to identify patterns of PA, binge drinking and smoking among a nationally-representative cohort of adolescents (N = 640). Results found PA decline evident among all young adults transitioning into early adulthood regardless of educational trajectory – declines being most pronounced among college/university males – highlighting the saliency of PA decline, as other health behaviours stabilized or declined during early adulthood. Given justification for intervening with the university population, study 2 explored students’ perceptions of PA, and their preferences towards a PA intervention. Eight focus groups were conducted with first-year university students (N = 45). Results found students being concerned with PA decline, and were receptive to an Internet-based intervention. However, such concerns are inflected with ambivalence, potentially posing a challenge for interventionists. Findings from studies 1 and 2 informed the development of a website-delivered PA intervention – ‘Active Transition’. Pre-testing was conducted with first-year students (N = 15) and PA experts (N = 7), which found the website and its content being acceptable and usable. Results of the efficacy trial (N = 65) found Active Transition to successfully attenuate declines in PA cognitions, and to some extent, PA behaviours. This confirms the Internet being a useful tool for delivering PA interventions in this population. However, given modest compliance in terms of usage, future work is required to evaluate the addition of more current/popular strategies for engaging students. Overall, this dissertation has provided justification for why it is critical that research continues work with this population, and has provided the foundations in helping with the long-term vision of implementing a population-level initiative to help students attenuate the significant declines in their PA behaviours.

Keywords: Physical Activity
Transition
Advisor: Faulkner, Guy
Prediction of Protein-protein Interactions and Essential Genes through Data Integration

The currently known network of human protein-protein interactions (PPIs) is providing new insights into diseases and helping to identify potential therapies. However, according to several estimates, the known interaction network may represent only 10% of the entire interactome - indicating that more comprehensive knowledge of the interactome could have a major impact on understanding and treating diseases. The primary aim of this thesis was to develop computational methods to provide increased coverage of the interactome. A secondary aim was to gain a better understanding of the link between networks and phenotype, by analyzing essential mouse genes. Two algorithms were developed to predict PPIs and provide increased coverage of the interactome: FpClass and mixed co-expression. FpClass differs from previous PPI prediction methods in two key ways: it integrates both positive and negative evidence for protein interactions, and it identifies synergies between predictive features. Through these approaches FpClass provides interaction networks with significantly improved reliability and interactome coverage. Compared to previous predicted human PPI networks, FpClass provides a network with over 10 times more interactions, about 2 times more proteins and a lower false discovery rate. This network includes 595 disease related proteins from OMIM and Cancer Gene Census which have no previously known interactions. The second method, mixed co-expression, aims to predict transient PPIs, which have proven difficult to detect by computational and experimental methods. Mixed co-expression makes predictions using gene co-expression and performs significantly better (p < 0.05) than the previous method for predicting PPIs from co-expression. It is especially effective for identifying interactions of transferases and signal transduction proteins. For the second aim of the thesis, we investigated the relationship between gene essentiality and diverse gene/protein features based on gene expression, PPI and gene co-expression networks, gene/protein sequence, Gene Ontology, and orthology. We identified non-redundant features closely associated with essentiality, including centrality in PPI and gene co-expression networks. We found that no single predictive feature was effective for all essential genes; most features, including centrality, were less effective for genes associated with postnatal lethality and infertility. These results suggest that understanding phenotype will require integrating measures of network topology with information about the biology of the network’s nodes and edges.

Keywords: protein-protein interactions
data mining
Advisor: Jurisica, Igor
Investigating the Safety and Therapeutic Potential of Vitamin D3 with Calcium Supplementation in Patients with Multiple Sclerosis

Low vitamin D status has been consistently associated with an increased risk of multiple sclerosis (MS). Further, preclinical and in vitro data demonstrate immune regulatory properties of 1,25-dihydroxyvitamin D that may be beneficial for patients with MS. To date evidence of beneficial in vivo immunomodulation by supplementation with vitamin D3 in humans is lacking. In a one-year, open-label, phase I/II dose-escalation study of vitamin D3 (average ~14,000 IU/d over one year) with calcium (1,200mg/d) in patients with MS, we compared the effects of treatment on safety outcomes, clinical outcomes and selected biomarkers of immune system activity, relative to matched MS patients [age, sex, disease duration, disease modifying therapy, and expanded disability status scale (EDSS)] randomized to receive no supplementation. Mean serum 25(OH)D concentrations were 78.1±27.0 nmol/L at baseline and at one-year were 82.7±34.8 and 179.1±76.1 nmol/L in control and treated groups, respectively. Serum and urinary calcium and all other safety outcomes were unchanged throughout the trial. Compared to controls, treated patients tended to have fewer relapses (McNemar, p=0.09) and a greater proportion had a stable or improved EDSS at study end (p=0.018). We observed significantly reduced lymphocyte proliferative responses to antigenic challenge in the treatment group at one year, compared to baseline and control group responses. High serum 25(OH)D concentrations were not associated with short-term adverse effects in patients with MS, but with evidence of clinical improvement and beneficial immunomodulation.

Keywords: Vitamin D
multiple sclerosis
Advisor: Vieth, Reinhold
Intentional traumatic brain injury in Ontario, Canada

Violence and traumatic brain injury (TBI) are two major public health concerns. This thesis is comprised of three different research topics; the epidemiology of intentional TBI in Ontario, discharge against medical advice (DAMA) as an undesirable outcome of acute stage, and functional changes after receiving rehabilitation care. To study these areas, three different datasets from the Canadian Institute for Health Information (CIHI) were used. The first epidemiological study on intentional TBI identified 1,409 (8.0%) intentional TBIs and 16,211 (92.0%) unintentional TBIs. Of the intentional TBIs, 389 (27.6%) were self-inflicted TBI (Si-TBI) and 1,020 (72.4%) were other-inflicted TBI (Oi-TBI). The most common causes of Si-TBI were “jumping from high places” and “firearms”. Major causes of Oi-TBI were ‘fight and brawl” and “struck by objects”. Si-TBI was associated with younger age, female gender, and having a history of alcohol/drug abuse. Oi-TBI was also associated with younger age and having an alcohol/drug abuse history and also with male gender. The second study on discharge against medical advice found that 446 (2.84%) TBI patients left hospitals without medical advice. DAMA was significantly associated with intentional injuries in those with self-inflicted TBI and other-inflicted TBI. DAMA was also associated with younger age and a history of alcohol/drug abuse. Using univariate analyses, the third study found that people with intentional TBI had significantly lower FIM gains in the motor area and significantly lower relative function gains (as measured by Montebello Rehabilitation Factor Score) in the cognitive area. Multivariate analyses of the same data showed that intentional TBI was also associated with lower cognitive relative gains, while controlling for age, gender, alcohol/abuse history, and other demographic and clinical variables. Persons with intentional TBI were found to be less likely to be discharged home, controlling for other relevant confounders. In conclusion, a person who has been injured due to assault or suicidal attempt may need more individualized care as they may be at greater risk for adverse rehabilitation outcomes. These findings regarding people with intentional TBI provide a basis for enhancing efforts on prevention of violence-related TBI and DAMA, and also for improving rehabilitation programs and discharge plans for this vulnerable population.

Keywords: traumatic brain injury
intentional injury
Advisor: Colantonio, Angela
The Effect of Nonconscious Goals on Conscious Goal-based Preferences

This dissertation examines whether a nonconscious goal can change preferences between binary options, one favoring a conscious goal (e.g., undiluted but non-healthy iced tea) and the other a nonconscious goal (e.g., diluted but healthy iced tea). Across four laboratory experiments, we demonstrate that when participants are only given a conscious goal (e.g., to choose the tastier drink), the majority of them seek the alternative that is more instrumental to this goal. However, when a nonconscious goal is also primed (e.g., to be healthy), their preferences can shift to the alternative that is perceived to be instrumental to this goal but is inferior from the conscious goal standpoint. We propose a two-stage model to explain these findings. In the first stage, when a nonconscious goal is primed, individuals attend to goal-relevant cues (e.g., health-signaling label) and automatically form a positive evaluation toward the option that facilitates the nonconscious goal relative to the option that does not satisfy the goal. In the second stage, the positive automatic evaluation is then used to distort perceptions of the option’s conscious goal instrumentality such that the option is perceived as having a more favorable taste compared to when the goal is not primed. While the positive automatic evaluation influences the option’s taste, it does not affect the evaluation of the option’s other attributes (e.g., scent, color). By manipulating the timing of nonconscious goal activation and by adopting an evaluative conditioning task, we find support for our conceptual model while ruling out alternative explanations and identifying a boundary condition of task difficulty. The findings of the experiments contribute to the literature on nonconscious goals 1) by showing that these goals can play a central role in decision making when choice options pit them against conscious goals, and 2) by identifying a mechanism (i.e., attribute distortion) that can resolve goal competition in choice.

Keywords: nonconscious goals
preference
multifinality
taste
Advisor: Mitchell, Andrew
Characterization and Modeling of the Remodeling Process that Occurs in Modular Tissue Engineered Constructs Assembled Within Microfluidic Perfusion Chambers

Using a modular approach, a vascularized tissue construct is created by embedding functional cells within submillimeter-sized collagen cylinders (modules) while the outside surfaces are seeded with endothelial cells (EC). The void spaces created by randomly packing modules into a container form EC-lined perfusion channels. Upon implantation, the tissues are remodeled by and integrated into the host and experience, to some degree, immune and inflammatory responses. This work utilized microfluidic techniques to study and model the tissue remodeling in vitro in the absence of the host response. When the construct’s tortuous perfusion channels were reproduced in poly(dimethylsiloxane) microfluidic devices and lined with EC, perfusion at higher flow rates reduced EC activation and maintained the desired quiescent EC phenotype. When applying these results to collagen constructs, higher flow rates were not achievable due to the weak mechanical properties of collagen. To increase the collagen’s mechanical strength, a semi-synthetic collagen/poloxamine-methacrylate hydrogel was examined but due to its heterogeneous surface composition, there was inadequate EC attachment and the material was deemed unsuitable for this application. Proceeding with lower flow rates, tissues assembled within microfluidic perfusion chambers from EC-seeded collagen modules showed that over the course of 24 hours, perfusion did not significantly increase activation but instead increased KLF2 expression, a transcription factor involved in the establishment of EC quiescence, and disrupted VE-cadherin bonds between adjacent EC. However, after 1 week of perfusion, the majority of EC were lost. To ameliorate this loss, mesenchymal stromal cells (MSC) were embedded within the modules in order to take advantage of their anti-apoptotic and immunomodulation effects. The MSC temporarily mitigated the loss of the EC but did not prevent it. They did, however, take on a phenotype similar to smooth muscle cells and migrated towards the EC. Perhaps this indicates that the combination of EC, MSC and perfusion drives the creation and assembly of pseudo vessels. Together, the microfluidic techniques used in this study to assemble and perfuse modular tissues revealed new insights into the remodeling process and exposed critical issues surrounding the adaptation of the EC to the combination of perfusion, remodeling and changing flow fields.

Keywords: tissue engineering
microfluidics
perfusion
endothelial cells
mesenchymal stromal cells
activation
differentiation
remodeling
model
collagen
poloxamine
activation
shear stress
disturbed flow
vascular
modular
Advisor: Sefton, Michael