VictorJuiz/thesis huggingface dataset:
Characterizing effects of prebiotics and human milk oligosaccharides on the intestinal epithelial barrier

Prebiotics are non-digestible compounds that enhance the growth of certain microbes within the gut microbiota and confer benefits on the host, but whether they can also elicit direct immune-regulatory effects is unknown. This thesis addresses this gap through three specific aims: (1) to characterize the effects of prebiotics on the intestinal epithelial barrier, (2) to delineate the underlying signaling mechanisms underlying barrier- and immune-regulation, and (3) to evaluate the effects of human milk oligosaccharides using relevant models of human disease. In the first part of this thesis, two prebiotics, inulin and short-chain fructooligosaccharides (scFOS), were tested in an in vitro bacterial challenge system with enterohemorrhagic Escherichia coli serotype O157:H7. Inulin and scFOS increased the resistance of Caco-2Bbe1 monolayers, reduced permeability and increased the expression of select tight junction proteins. These changes were associated with the activation of protein kinase C isoform Î´ - a host kinase enzyme that controls multiple cell functions. The second part of this thesis expands on PKCÎ´ signaling and characterizes the global signaling of inulin and scFOS using Caco-2Bbe1 cells. This was performed using a kinome peptide array to profile kinase phosphorylation levels, which revealed several immune pathways and functional networks that were regulated by prebiotics. These findings were then validated in vivo using a neonatal endotoxemia model, which showed that prebiotics dampened intestinal inflammation without altering the composition of gut microbiota. In the third part of this thesis, I demonstrate a unique mechanism whereby HMOs promote barrier function by inducing the production of mucus. This finding was confirmed using a neonatal mouse model of necrotizing enterocolitis (NEC), where HMOs prevented the development of NEC by enhancing intestinal goblet cell production. Taken together, these data demonstrate that prebiotics are not biologically inert. In fact, prebiotics directly trigger host cell signaling to alter epithelial barrier integrity and gut inflammation â indicating previously unrecognized mechanisms of prebiotics and HMOs.

Keywords: Fructans
Human milk oligosaccharides
Kinome
Necrotizing enterocolitis
Prebiotics
Advisor: Sherman, Philip M.
Biogenic-Anthropogenic Interactions in Secondary Organic Aerosol Formation and Health Effects of Atmospheric Organic Aerosol

Secondary organic aerosol (SOA) formed from oxidation of volatile organic compounds (VOCs), comprises a major fraction of atmospheric submicron particulate matter, which is crucial for global climate change and human health. While biogenic VOCs are naturally emitted and cannot be directly controlled, field measurements and satellite observations have shown that biogenic SOA (BSOA) formation correlates well with anthropogenic pollutants and may be anthropogenically controlled. In this work, the formation of the “anthropogenically controllable BSOA” was examined. BSOA from α-pinene ozonolysis was investigated in the presence of laboratory-generated or ambient organic aerosol such as Toronto ambient particles. It is shown that SOA was not equally miscible with all organic species. Aerosol mixing thermodynamics in the atmosphere is composition dependent. Based on laboratory observations, an empirical framework using bulk elemental ratios was developed to predict atmospheric organic miscibility and SOA yield enhancements. Besides organic aerosol, interactions between BSOA formation and SO2 was also examined. Synergistic effects were observed between BSOA formation and SO2 oxidation through Criegee and peroxide chemistry under atmospherically relevant RH conditions. In addition to the physicochemical properties of SOA, health impacts of SOA were examined. An atmospheric simulation reactor (ASR) was developed to investigate the health effects of air pollutants by permitting controlled chronic in vivo exposure of mice to combine particulate and gaseous pollutants at ‘real-life’ concentrations. Results show that daily exposure to SOA from naphthalene photooxidation led to increased airway hyperresponsiveness (AHR) to methacholine in a dose-dependent manner. Multi-pollutant exposures with ozone and/or NO2 in conjunction with a sub-toxic concentration of SOA resulted in additive effects on AHR to methacholine. Inflammatory cell recruitment to the airways was not observed in any of the exposure conditions, indicating the increased AHR was not associated with airway inflammation and may occur through other mechanisms.

Keywords: Aerosol Miscibility
Biogenic-anthropogenic Interaction
Health Effects
Secondary Organic Aerosol
Sulfur Dioxide
Advisor: Chan, Arthur W. H.
Reducing the computational cost of UV reactor performance calculations

The performance of a UV reactor can be described using the concept of UV dose, which is the product of the residence time of a microbe or particle and the intensity, or fluence rate, of UV light hitting that particle in a reactor. The process to model the reactor performance of a UV reactor, hereby known as the reactor performance process (RPP), consists of three separate models: 1) the computational fluid dynamics (CFD) model: the UV fluid flow field modeling, typically performed using commercial software; 2) the fluence rate model: the physics of the intensity of the UV irradiation; and 3) the reactor performance model: RED, for example, an organism-specific metric for delivered UV dose. The combination of these three models to numerically estimate the UV reactor performance has never been subjected to scrutiny for relevancy, efficiency, nor computational expense. The aim of this thesis was to examine and reduce the computational cost of the RPP and as a result of this work, in certain scenarios, the cost of calculating the reactor performance of a UV reactor was reduced from over 300 billion steps to less than 12,000. This was accomplished by optimizing each of the models of the RPP: by focusing on four key factors in CFD modeling (initial condition, mesh size, time step, and particle tracking), the computational cost of that step was reduced by five times; by systematizing fluence rate model implementation, the computational cost of that step was reduced by at least nine times; by using mixing as a proxy for reactor performance in certain lamp orientations, the computational cost was reduced by over 99%. Further scenarios need to be examined where mixing can be used as a proxy for reactor performance; this optimization offered the best reduction in computational cost. This optimization would reduce the overall computational cost of the RPP for more general UV reactors but also provide a different perspective from which to examine the performance of UV reactors.

Keywords: mixedness
Shannon entropy
UV disinfection
wastewater disinfection
Advisor: Lawryshyn, Yuri
The Association of Health Literacy and Self-Efficacy to Cancer Chemotherapy Self-Management Behaviours and Health Service Utilization

Abstract Background Increasing demands on Canadaâ s healthcare system require patients to take on more active roles in their health [1]. Effective self-management has been linked to improved health outcomes; and there is evidence that effective behaviours are linked to health literacy, however, this link has had minimal testing in the cancer context [2, 3]. Firmly establishing this link is important because those aged 65 years and older comprise the majority of the users of the cancer care system, and these individuals are most at risk for inadequate health literacy [4]. As such, the cancer care system may require increased self-management by patients least able to do so and, in doing so, fail to provide adequate care and incur substantial cost [5-7]. Objectives To examine the association between health literacy and cancer chemotherapy self-management behaviours (CSMB) and health service utilization (HSU) and test the hypothesized relationship between self-efficacy and these outcomes. Design Cross-sectional survey. Methods Participants completed a questionnaire package with socio-demographic information and validated measures of health literacy, cancer coping self-efficacy, symptom severity, symptom interference, CSMB score, and HSU. Multivariate modeling using hierarchical linear regression was used to examine the association of health literacy to CSMB health services utilization. Results Education and language spoken at home explained a significant amount of variance (22.5%) in health literacy score. Health literacy was not significantly associated with any of the dependent variables in multivariate analysis. The analyses conducted to explore the association of self-efficacy to CSMB score and HSU showed that self-efficacy contributed to explaining variation in CSMB score but did not contribute significantly to explaining HSU. Conclusion This study provides new knowledge that advances understanding of the association of health literacy and self-efficacy on CSMBs and HSU in the context of cancer care.

Keywords: Cancer
Health Literacy
Neoplasm
Self-Efficacy
Self-Management
Advisor: Howell, Doris M
The Aesthetics of Redemption in fin de siècle Literature and the Arts

This dissertation explores a cluster of texts in fin de siècle aestheticism from a Nietzschean perspective, questioning whether their claims about art and life are, at bottom, world-affirming or world-denying. I argue that the aesthetic worldviews of Friedrich Nietzsche, Walter Pater and Oscar Wilde manifest a struggle against Christian (especially Protestant) values, a struggle that, however, periodically and sometimes fatally capitulates to the otherworldliness it seeks to overcome. Chapter 1 delineates the theoretical framework for my investigation. Drawing on the work of Nietzsche and Max Weber, I begin by examining the diverse strains of otherworldliness, some more implicit than others, that run through the aesthetic theories of Arthur Schopenhauer, Richard Wagner, Joris-Karl Huysmans, and Charles Baudelaire. In Chapter 2, I consider the evolution of Nietzsche’s own aesthetic philosophy from his youthful embrace of the Wagnerian Gesamtkunstwerk to his mature view that the Dionysian artist exemplifies the individual who has vanquished all decadent urges to be redeemed from worldly suffering, and is thus able to affirm life through his work. Chapter 3 demonstrates how Pater’s contemplative aestheticism, which originally sets out to counteract the antipathy to the ‘here and now’ associated with ascetic Protestantism, ends up reproducing the hierarchy between the temporal world and a more desirable ‘otherworld.’ In the fourth and final chapter, I suggest that Wilde overcomes the otherworldliness of Paterian aestheticism but only by advancing a secularized version of aesthetic incarnation. This dissertation argues that aestheticism is neither an inevitable offshoot of secularization nor a particular phase of Christian theology, but rather a struggle to work through the complex moral and philosophical dilemmas that arise from the rigorous commitment to valuing life on its own terms.

Keywords: Aestheticism
Friedrich Nietzsche
Oscar Wilde
Religion of Art
Secularization
Walter Pater
Advisor: Comay, Rebecca
Identification and in vivo Characterization of a Potential TAAR1 Antagonist

TAAR1 is a G-protein coupled receptor expressed in monoaminergic regions in the brain and represents a potential novel therapeutic target for the treatment of neurological disorders. While success has been made with discovering novel selective agonists for TAAR1, only one TAAR1 antagonist has been described thus far. We used an in silico screen on a TAAR1 homology model and identified several novel agonists and potential antagonists for TAAR1. One of the identified antagonists (compound 22) was predicted to have favourable physicochemical properties that should allow it to cross the blood brain barrier. In vivo studies were therefore carried out and showed that compound 22 potentiates amphetamine- and cocaine-mediated locomotor activity, consistent with behaviours observed in Taar1-KO animals. In order to assess whether the effects of compound 22 are mediated through antagonism of TAAR1, experiments were carried out on Taar1-KO mice. Our results show that compound is also able to enhance amphetamine- and cocaine-mediated locomotor activity in Taar1-KO mice, suggesting that the in vivo effects of compound 22 are not mediated by TAAR1. In collaboration with Psychoactive Drug Screening Program at UNC-Chapel Hill, we attempted to determine the target for compound 22. PDSP results suggested several potential targets for compound 22. These include, the dopamine, norepinephrine and serotonin transporters; as well as sigma 1 and 2 receptors. Furthermore, the dopamine D2 receptor was also an initial hit in a functional assay performed by PDSP. Our follow-up studies using heterologous cell systems showed that neither DAT nor dopamine D2 dopamine receptors are targets of compound 22. Therefore, the biological target of compound 22 mediating its psychoactive effects remain unknown.

Keywords: Amphetamine
Cocaine
Homology Model
Locomotion
TAAR1
Trace Amines
Advisor: Salahpour, Ali
Culture, Identity and Attitudes of Adult Immigrant Learners of German in the Context of the German Integration Course

Inspired by pioneering studies in the field of adult immigrants and second language acquisition, my dissertation research seeks to bridge the classroom as an inside space and the outside as lived social reality and to draw conclusions on how the interplay of these experiences affects and is affected by aspects of culture, attitudes and identity formation. Set in the specific context of the German Integration Course, this qualitative study is based on a series of guided conversations with and the written accounts of five adult immigrants enrolled in the Integration Course in Frankfurt, Germany in 2012. I am predominantly interested in socio-psychological factors affecting the learning process, including learnersâ perspectives on learning a second language in a compulsory setting in Germany, and the influence as well as the dependence of such perspectives on their identities and as result on their learning behavior. In my work, I donâ t draw a straight line between attitudes and language achievements. Much like water refracts light and produces images, I assert that our attitudes form interpretive stances through which we explain and make sense of our experiences. This process, in turn, affects our identity work and consequently our learning behaviour in and outside the classroom. As of today, research on the linguistic development in adult immigrant learners enrolled in the German Integrationskurs and the sociocultural factors that shape it is scarce. Consequently, the present study will contribute to the small but constantly growing body of research trying to shed light on the Integration courseâ s potential and capacity to meet its own goals. My work also has the intention to contribute to modern SLA pedagogy by shedding more light on the process-oriented, socio-psychological realm of language acquisition in migration contexts.

Keywords: adult education
Integrationskurs
second language acquisition
Advisor: Hager, Michael
Topological Phases in Perovskite Iridates with Strong Spin-Orbit Coupling

The study of topological phases of matter has attracted much attention recently, providing a promising route to understanding the classification of various phases in condensed matter physics. The Iridates, which are Iridium-based compounds, have already shown rich physical phenomena and can be a perfect platform to reveal topological phases in materials with strong spin-orbit coupling. This thesis focuses on possible exotic topological phases that stem from the interplay between strong spin-orbit coupling and non-trivial band structure in three-dimensional perovskite Iridates and other layered Iridate materials. Firstly, motivated from previous band structure results of SrIrO 3, we predict that three-dimensional perovskite Iridates can realize a new class of metals dubbed “topological crystalline metals” with surface states protected by lattice symmetry and a pair of topological invariants. We show that these novel metallic phases can give rise to various non-trivial topological phases when different symmetries are broken, including a Weyl and nodal-line semimetal. Secondly, we provide a generic condition to identify a novel three-dimensional topological semi-metallic phase in materials with strong spin-orbit coupling. Such a semi-metallic phase is featured by bulk gapless four-fold degenerate nodal-line excitations. By using perovskite Iridates SrIrO3 as an example, we give an explicit mathematical proof on the validity of this condition as well as verify the existence of such bulk nodal-line band degeneracy in the tight-binding model. Thirdly, we propose that a topological insulator can exist in a two-dimensional single layer Iridium oxide superlattice under certain lattice distortions; a tight-binding model is constructed using the basis of an effective J eff=1/2 pseudo-spins. A topological magnetic insulator with quantum anomalous Hall effect is found in the bilayer superlattice when a magnetic order or magnetic field is present in the system. Lastly, a pair of helical Majorana fermions emerges at the interface of a two-dimensional Weyl semimetal and a d-wave superconductor. We focused on the most promising and feasible realization: Iridium oxide layer without inversion symmetry, which is classified as Weyl semimetal, in proximity to d-wave high temperature Cuprates. In conclusion, we provide some future directions related to the topological phases in Iridates.

Advisor: Kee, Hae-Young
X-ray Investigations of Liquid Water Transport in Polymer Electrolyte Membrane Fuel Cell Gas Diffusion Layers

Understanding the liquid water transport behaviour in a polymer electrolyte membrane (PEM) fuel cell is key to achieving high performance. The gas diffusion layer (GDL) provides transport pathways for electrons, reactant gases, and product water. However, when liquid water accumulates within the pores of the GDL, the effective porosity of the material is decreased, resulting in a reduced effective diffusivity of reactant gases. This can lead to reactant starvation at the catalyst during high current density operation, causing significant efficiency losses. The aim of this thesis is to investigate the impact of the GDL microstructural properties on water transport in an operating fuel cell. Synchrotron X-ray radiography was used as a probing tool for identifying the water distribution in the GDL in situ. The role of the microporous layer (MPL) on liquid water management was identified through investigating in-plane water distribution in the GDL. Nanopores of the MPL reduced the amount and the size of water clusters in the GDL. Next, the influence of MPL thickness on the water accumulation in the GDL was investigated. The application of a thick MPL on the carbon fibre substrate resulted in less water content at the MPL-substrate interface than that in the GDL with a thin MPL. The effect of substrate thickness was also studied in terms of the fuel cell performance and liquid water distribution. The fuel cell incorporating a thin substrate exhibited superior electrochemical performance; however, unusual material movements were observed in the synchrotron images. It was concluded that the thin substrate was not able to provide necessary mechanical support to prevent material movements (e.g. membrane swell). Lastly, performance benefit of an MPL based on multiwall carbon nanotubes (MWCNTs) was studied. The MWCNTs additive to the MPL resulted in a high-porosity GDL compared to the conventional MPL. The high porosity region was prone to liquid water accumulation, but it also facilitated improved oxygen transport. The main findings of this thesis provide insights to fuel cell manufactures for design next generation GDLs.

Keywords: Computed tomography
Gas diffusion layer
Liquid water transport
Polymer electrolyte membrane fuel cell
Porous medium
Synchrotron imaging
Advisor: Bazylak, Aimy
Performance Analysis and Optimization of Virtualized Cloud-RAN Systems

Cloud radio access networks (C-RAN) are a promising solution against the ossification of wireless systems. C-RANs provide a platform for rapid innovation and deployment of new wireless technologies. However, they also present a set of challenges un-encountered in traditional systems. The goal of this thesis is to identify, study and provide solutions for those challenges. The challenges studied in this thesis fall into two broad categories; the first set of challenges is about multiplexing several network slices on the same physical infrastructure. The second set of challenges stems from the cloud computing concept itself and how it affects the wireless systems architecture. For the first part, we start at the PHY-layer, and focus on the question of how multiple network slices can be accommodated on the same infrastructure. We conduct a performance analysis of the alternative multiplexing and scheduling schemes that can be used for slicing and interference coordination. Next, we show how we can integrate the effects of statistical multiplexing into PHY-layer performance indicators, and provide an algorithm for admission control combined with resource slicing using both FDMA and SDMA. For the cloud computing challenges, we start by looking at how the cloud computing model combined with the demands of wireless networks raise the need for efficient distributed scheduling schemes. We provide a completely distributed solution that achieves up to 92% efficiency and discuss the effects of the nature of the scheduler on the performance. One of the main goals of C-RAN is providing more energy-efficient systems through dynamic resource scaling. We investigate this problem from both the radio access part as well as the cloud computing part. For the radio access, we propose an optimization and control framework for the activation, association and clustering of remote radio heads (RRH). The problem is solved using the successive geometric programming approach for signomial optimization. For the cloud computing part, we propose a predictive control framework for anomaly-aware scaling of computing resources. Our proposed scheme is based on the Gaussian process model and provides 95% prediction accuracy and 90% anomaly detection accuracy.

Advisor: Leon-Garcia, Alberto