VictorJuiz/thesis huggingface dataset:
Type III Secreted Effectors as Molecular Probes of Eukaryotic Systems

Successful bacterial pathogens manipulate crucial intracellular host processes as a virulence strategy. One particular potent mechanism utilized by bacterial phytopathogens is to inject virulence factors (effectors) directly into the host cell. While many effectors have been identified and shown to suppress plant immune responses, very few have well-characterized enzymatic activities or host targets. To overcome the challenges of functional analysis of effectors, I designed two heterologous screens to characterize effector proteins of the bacterial phytopathogen Pseudomonas syringae. Specifically, my objective was to identify those P. syringae effectors that target evolutionarily conserved host proteins or processes and to subsequently elucidate the molecular mechanisms of these effectors. The first heterologous screen that I performed was to utilize tandem-affinity-purification (TAP)-tagged effectors in human cells to identify potential interacting host proteins. The second heterologous screen iii utilized a high-throughput genomics approach in yeast, known as the pathogenic genetic array (PGA), to characterize P. syringae effectors. Using the first heterologous approach, I have identified HopZ1a as the first bacterial phytopathogen effector that binds tubulin. I have shown that HopZ1a is an acetyltransferase activated by the eukaryotic co-factor, phytic acid. In vitro, activated HopZ1a acetylates itself and tubulin. In Arabidopsis thaliana, activated HopZ1a causes microtubule destruction, disrupts the secretory pathway and suppresses cell wall-mediated defense. The acetyltransferase activity of HopZ1a is dependent on the conserved catalytic cysteine residue (C216) and a conserved lysine residue (K289). Using the second heterologous screen in yeast, I have shown that HopZ1a may target the mitogen-activated protein kinase (MAPK) signaling cascades. Together, my work has identified novel eukaryotic targets and elucidated the virulence functions of HopZ1a.

Keywords: host-pathogen interaction
type III effectors
Advisor: Guttman, David S.
Desveaux, Darrell
Plato on Pleasure, Intelligence and the Human Good: An Interpretation of the Philebus

The Philebus is devoted to the question what constitutes the good for a human being. Although Socrates initially favors a life of pure intelligence against the hedonist’s life of pure pleasure, he quickly concedes that some pleasures actually enhance the life of intelligence. In order to determine which pleasures deserve a place in the best life, Socrates undertakes a lengthy investigation into the nature of pleasure. Commentators have long been frustrated in their attempt to uncover a single, unified account that explains in a plausible way the extraordinary variety of pleasures analyzed in the dialogue. I argue that this search for a generic account of pleasure is misguided, because one of the main purposes of Socrates’ division of pleasure is to expose its essentially heterogeneous nature. Pleasures can be bodily or psychic, pure or mixed with pain, truth apt or not, healthy or diseased, and inherently measured or unmeasured, and there are no essential properties which all of these diverse phenomena share. The inclusion of some pleasures in the final ranking of the goods at the end of the Philebus represents a dramatic shift in Plato’s attitude towards certain pleasures, and so it is not surprising that many scholars misinterpret the force of this conclusion. Even in the Republic where the pleasures of reason are favorably compared to the pleasures of spirit and appetite, intellectual pleasures are judged to be more pleasant and real than other pleasures, but they are nowhere judged to be better or praised as genuine goods. In the Philebus, not only are some pleasures unambiguously ranked among the highest goods, but Socrates gives no indication that these pleasures are good only in some qualified or extrinsic way. Instead, certain pleasures make their own positive contribution to the goodness of the best human life, making the mixed life more valuable and choiceworthy than the unmixed life of intelligence.

Keywords: Plato
Philebus
Timaeus
pleasure
intelligence
knowledge
the human good
the good life
moral psychology
cognition
perception
sensation
intentionality
consciousness
aisthēsis
phronēsis
nous
hēdonē
health
disease
animals
gods
soul
body
desire
expectation
memory
recollection
false pleasure
pain
Advisor: Barney, Rachel
An Integrated Two-stage Innovation Planning Model with Market Segmented Learning and Network Dynamics

Innovation diffusion models have been studied extensively to forecast and explain the adoption process for new products or services. These models are often formulated using one of two approaches: The first, and most common is a macro-level approach that aggregates much of the market behaviour. An advantage of this method is that forecasts and other analyses may be performed with the necessity of estimating few parameters. The second is a micro-level approach that aims to utilize microeconomic information pertaining to the potential market and the innovation. The advantage of this methodology is that analyses allow for a direct understanding of how potential customers view the innovation. Nevertheless, when individuals are making adoption decisions, the reality of the situation is that the process consists of at least two stages: First, a potential adopter must become aware of the innovation; and second the aware individual must decide to adopt. Researchers, have studied multi-stage diffusion processes in the past, however a majority of these works employ a macro-level approach to model market flows. As a result, a direct understanding of how individuals value the innovation is lacking, making it impossible to utilize this information to model realistic word-of-mouth behaviour and other network dynamics. Thus, we propose a two-stage integrated model that utilizes the benefits of both the macro- and micro-level approaches. In the first stage, potential customers become aware of the innovation, which requires no decision making by the individual. As a result, we employ a macro-level diffusion process to describe the first stage. However, in the second stage potential customers decide whether to adopt the innovation or not, and we utilize a micro-level methodology to model this. We further extend the application to include forward looking behaviour, heterogeneous adopters and segmented Bayesian learning, and utilize the adopter's satisfaction levels to describe biasing and word-of-mouth behaviour. We apply the proposed model to Canadian colour-TV data, and cross-validation results suggest that the new model has excellent predictive capabilities. We also apply the two-stage model to early U.S. hybrid-electric vehicle data and results provide insightful managerial observations.

Keywords: Product Planning
Diffusion
Discrete Choice
Bayesian Learning
Advisor: Lee, Chi-Guhn
The Influence of Synthesis Temperature on the Crystallographic and Luminescent Properties of NaYF4-based Upconverters and their Application to Amorphous Silicon Photovoltaics

There are several factors which conspire to limit the efficiency of solar cells. One of these is the fact that a solar cell is unable to absorb photons of energy less than the band gap of the semiconductor from which it is made; in the case of some high-band gap materials such as amorphous silicon – the model system used in this study – this can mean that as much as 50% of the solar spectrum is unusable. Upconversion phosphors – materials which can, by way of two or more successive photon absorptions, convert low energy (typically near infrared) light into high energy (typically visible) light – offer a potential solution to this problem as they can be used to convert light, which would otherwise be useless to the cell, into light which can be used for power generation. In this thesis we work towards the application of NaYF4-based upconverters to enhanced efficiency amorphous silicon (a-Si) photovoltaic power generation. We begin by synthesizing these upconverters at a range of temperatures and studying the crystallographic and spectroscopic properties of the resulting materials, elucidating heretofore undocumented trends in their luminescence and crystallography, including the effect of synthesis temperature on upconversion intensity, crystallite size, and lattice parameter. We also investigate the emission quantum yield of these materials, beginning with an in depth discussion and investigation of two methods for recording absolute quantum yields. We demonstrate that the quantum yields of the materials may vary by a factor of over 100, depending on the synthesis conditions. After we have fully characterized these properties we turn our attention to the application of these materials to amorphous silicon solar cells, for which we provide a proof of concept by demonstrating the effect of upconversion luminescence on the photoconductance of an a-Si film. We conclude by developing a roadmap for future improvements in the field.

Keywords: Upconversion
Photovoltaics
Solar
Rare Earth
Advisor: Kherani, Nazir P.
Ozin, Geoffrey Alan
Perovic, Doug
Investigating the Factors that Govern the Induction of an In vivo Cytotoxic T-lymphocyte Response against a Tissue-borne Antigen

In addition to their activity against intracellular pathogens, it is now clear that CD8+ T-lymphocytes also mediate anti-tissue responses. In order to manipulate these responses in the setting of tumor immunity or autoimmunity, it is necessary that we understand the parameters that promote CD8+ activation. In the first section of this thesis, a transgenic mouse model was used to explore the effectiveness of peptide/adjuvant-based and dendritic cell (DC)-based vaccination techniques at eliciting CD8-mediated anti-pancreatic responses. It was found that, while peptide vaccines were unable to stimulate autoimmunity, the transfer of DCs promoted autoimmune diabetes in a manner that was dependent upon the toll-like receptor (TLR)-based maturation of the DCs. Furthermore, the diabetes induction was dependent upon the engagement of the immunodominant CD8+ population and a second T-cell specificity, indicating that polyclonal responses may be required for effective tissue destruction. In the second section of this thesis, I explored the requirements for CD28-signaling during the activation of naïve self-reactive CD8+ T-cells. The transfer of mature DCs was insufficient to promote diabetes in CD28-deficient animals, whereas infection with lymphocytic choriomeningitis virus could induce diabetes in the same animals. Anti-tissue responses were further explored in tumor-bearing mice following DC transfer and demonstrated that a critical determinant of the induction of anti-tissue immunity in the absence of CD28-derived costimulatory signals, was the persistence of antigen presentation. In the final section of this thesis, I explored the role of nuclear factor kappa B 1 (NF-κB1) in DC maturation using the DC transfer model described above. Surprisingly, NF-κB1-deficient DCs were capable of inducing diabetes without the need for external stimulation. Furthermore, the absence of NF-κB1 in unstimulated DCs was associated with dysregulated production of tumor necrosis factor alpha (TNF-α), and this cytokine was required for the proper upregulation of the cytotoxic effector molecule granzyme B in CD8+ T-cells that infiltrated the pancreatic islets. This work therefore presents a novel model of autoimmune tissue destruction, in which defined genes and pathways that contribute to DC-T-cell interactions can be explored in an in vivo non-TCR transgenic setting.

Keywords: dendritic cells
T-lymphocytes
Advisor: Pamela, Ohashi
Estimating Urban Scale Semi-volatile Organic Compound Emissions and Fate Using a Coupled Multimedia and Atmospheric Transport Model

Cities are sources of persistent organic pollutants (POPs), such as polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs), to surrounding regions and beyond. A spatially resolved, (5×5 km2), dynamic contaminant fate model named Spatially Oriented or SO-MUM was developed by coupling the fugacity based Multimedia Urban Model (MUM) (Diamond et al., 2001; Diamond et al., 2010c) and the Boundary Layer Forecast Model and Air Pollution Prediction System (BLFMAPS) which was developed at Environment Canada (Daggupaty et al., 2006). MUM was updated to contain a revised surface film sub-model which takes into account the dynamic nature of surface films. SO-MUM was illustrated by application to the City of Toronto, Canada. Spatially resolved air emissions of Σ88PCB were estimated to be ~230 (40-480) kg y-1, 280 (50-580) g y-1 km-2, and 90 (16-190) mg y-1 capita-1 and Σ26PBDE were estimated to be 28 (6-63) kg y-1, 34 (7-77) g y-1 km-2 and 11 (2-25) mg y-1 capita-1. These emissions were back-calculated from measured air concentrations and spatial chemical mass inventories yielding emission rates per mass inventory of 0.4 (0.05-1.6) and 0.1 (0.01-0.7) g kg-1inventory y-1, for Σ88PCBs and Σ26PBDEs, respectively. Approximately 30% and 16% of PCB and PBDE emissions emanate from the city’s downtown. Air advection accounted for ~95% (PCB) and ~70% (PBDE) of total air emission losses with the remaining balance depositing to the city. The metric “Urban Travel Distance” or UTD was introduced for quantifying the extent of an urban plume resulting from spatially heterogeneous emissions. For PCBs and PBDEs the UTDs were ~25 and ~30 km. The updated surface film sub-model indicated that films “bounce” higher vapor pressure semi-volatile organic compounds (SVOCs) back into the air but they act as a transient sink from air for lower vapor pressure SVOCs, thereby facilitating transport to surface waters. Model calculations suggest that if the PCB inventory is reduced, volatilization from near-shore Lake Ontario will become a net source of PCBs to air, but that neither near-shore Lake Ontario nor soil would become a significant volatilization PBDE source to air.

Keywords: persistent organic pollutants
environmental fate modeling
fugacity
urban pollution
Advisor: Diamond, Miriam L.
Towards A Poetics of Marvellous Spaces in Old and Middle English Narratives

From the eighth to the fourteenth century, places of wonder and dread appear in a wide variety of genres in Old and Middle English: epics, lays, romances, saints’ lives, travel narratives, marvel collections, visions of the afterlife. These places appear in narratives of the other world, a term which in Old and Middle English texts refers to the Christian afterlife: Hell, Purgatory, even Paradise can be fraught with wonder, danger, and the possibility of harm. But in addition to the other world, there are places that are not theologically separate from the human world, but that are nevertheless both marvellous and horrifying: the monster-mere in Beowulf, the Faerie kingdom of Sir Orfeo, the demon-ridden Vale Perilous in Mandeville’s Travels, or the fearful landscape of the Green Chapel in Sir Gawain and the Green Knight. Fraught with horror or the possibility of harm, these places are profoundly different from the presented or implied home world of the text. My dissertation investigates how Old and Middle English narratives create places of wonder and dread; how they situate these places metaphysically between the world of living mortals and the world of the afterlife; how they furnish these places with dangerous topography and monstrous inhabitants, as well as with motifs, with tropes, and with thematic concerns that signal their marvellous and fearful nature. I argue that the heart of this poetics of marvellous spaces is displacement. Their wonder and dread comes from boundaries that these places blur and cross, from the resistance of these places to being known or mapped, and from the deliberate distancing between these places and the home of their texts. This overarching concern with displacement encourages the migration of iconographic motifs, tropes, and themes across genre boundaries and theological categories.

Keywords: marvellous
wonder
medieval
landscape
geography
Faerie
Hell
Purgatory
Paradise
monsters
Beowulf
Sir Orfeo
Sir Gawain and the Green Knight
Mandeville
poetics
oral tradition
traditional referentiality
displacement
Advisor: Orchard, Andy
The Culmination of Tradition-based Tafsīr: The Qurʼān Exegesis al-Durr al-manthūr of al-Suyūṭī (d. 911/1505)

This is a study of Jalāl al-Dīn al-Suyūṭī’s al-Durr al-manthūr fi-l-tafsīr bi-l-ma’thur (The scattered pearls of tradition-based exegesis), hereinafter al-Durr. In the present study, the distinctiveness of al-Durr becomes evident in comparison with the tafsīrs of al-Ṭabarī (d. 310/923) and Ibn Kathīr (d. 774/1373). Al-Suyūṭī surpassed these exegetes by relying entirely on ḥadīth (tradition). Al-Suyūṭī rarely offers a comment of his own. Thus, in terms of its formal features, al-Durr is the culmination of tradition-based exegesis (tafsīr bi-l-ma’thūr). This study also shows that al-Suyūṭī intended in al-Durr to subtly challenge the tradition-based hermeneutics of Ibn Taymīyah (d. 728/1328). According to Ibn Taymīyah, the true, unified, interpretation of the Qurʼān must be sought in the Qurʼān itself, in the traditions of Muḥammad, and in the exegeses of the earliest Muslims. Moreover, Ibn Taymīyah strongly denounced opinion-based exegesis (tafsīr bi-l-ra’y). By means of the traditions in al-Durr, al-Suyūṭī supports several of his views in contradistinction to those of Ibn Taymīyah. Al-Suyūṭī’s traditions support the following views. First, opinion-based exegesis is a valid supplement to tradition-based exegesis. Second, the early Muslim community was not quite unified. Third, the earliest Qur’ānic exegetes did not offer a unified exegesis of the Qur’ān. Fourth, Qur’ānic exegesis is necessarily polyvalent since Muslims accept a number of readings of the Qur’ān, and variant readings give rise to various interpretations. Al-Suyūṭī collected his traditions from a wide variety of sources some of which are now lost. Two major exegetes, al-Shawkānī (d. 1250/1834) and al-Ālūsī (d. 1270/1854), copied some of these traditions from al-Durr into their Qur’ān commentaries. In this way, al-Suyūṭī has succeeded in shedding new light on rare, neglected, and previously scattered traditions.

Keywords: Qurʼān
Tafsīr
al-Durr al-manthūr
al-Suyūṭī
Exegesis
ḥadīth
al-Ṭabarī
Ibn Kathīr
al-Shawkānī
al-Ālūsī
Ibn Taymīyah
Ibn Taymiya
Muslim Tradition
Quran Commentary
Advisor: Saleh, Walid
Developing Self-regulated Learning Skills To Overcome Lexical Problems in Writing: Case Studies of Korean ESL Learners

The study examined how 5 adult Korean learners of English developed self-regulated learning (SRL) skills to overcome lexical problems in their English writing. Empirical studies have consistently shown that many of the greatest problems for ESL learners in writing are lexical in nature. The goal of the present study was to help participants to address these problems, first through tutored assistance and then more independently by controlling their uses of strategies through planning, monitoring, and evaluation processes. The study involved two phases: Phase 1 was exploratory in nature, in which I attempted to identify typical lexical problems Korean learners of English encounter in writing. Phase 2 included an intervention in the form of one-on-one tutoring that followed the cyclic model of SRL proposed by Zimmerman, Bonner, and Kovach (1996). I worked with 5 participants through the SRL cycle individually as they wrote and revised 3 argumentative essays. The intervention lasted for 9 weeks, focusing on developing the participants’ SRL skills in writing through the use of various strategies that were devised in Phase 1 and refined throughout Phase 2. I analyzed the participants’ difficulties and uses of strategies, self-ratings on their essays, and several measures of essay quality to examine changes in their SRL skills, self-efficacy, and writing skills. The participants initially encountered various types of difficulties in their English writing and primarily relied on self-employed strategies to cope with their difficulties. Over the course of the intervention, the participants’ attention to their difficulties and uses of various linguistic resources became progressively more focused and specific. Initially, the participants largely depended on their L1 to write their L2 essays, being chiefly occupied with the grammatical encoding of their communicative intentions. Subsequently, the participants displayed unique patterns in developing their SRL skills, which exerted positive influences on building their self-efficacy beliefs as writers and on improving the quality of their essays. Based on these findings, I emphasize the growing need for L2 writing teachers to incorporate language-focused, vocabulary-centered, and corpora-based instruction into their teaching practices. In turn, students require individual support and untimed writing tasks to develop SRL skills in writing.

Keywords: second language writing
self-regulated learning
lexical knowledge
Advisor: Cumming, Alister
The Relationships Among Emotional Intelligence, Gender, Coping Strategies, and Well-being inthe Management of Stress in Close Interpersonal Relationships and the Workplace

People with high levels of emotional intelligence (EI) seem to possess emotional skills that allow them to cope effectively with the challenges they face and promote well-being. Considering the role of EI in coping research may yield significant benefits for individuals because EI has consistently been linked with positive outcome measures, including life and work satisfaction, interpersonal functioning, healthy relationships, job performance, psychological well-being, physical health, and psychophysiological measures of adaptive coping (Martins, Ramalho, & Morin, 2010). Although the theoretical significance of EI to coping has been recognized (e.g., Bar-On & Parker, 2000; Snyder, 1999), relatively few studies explore the relationships among these constructs. The current research explores and compares how emotional intelligence (EI) facilitates adaptive coping across both interpersonal and occupational contexts – two central areas of our lives. It provides evidence in support of an extended adaptational model contextualizing EI within the transactional model of stress and coping (Lazarus & Folkman, 1984). In general, results from an online survey (N = 300) showed that most participants (approximately 66%) did not cope adaptively with stress. Results are consistent with a model which suggests that EI and the coping strategies people use when dealing with interpersonal and occupational stressors have significant effects on psychological well-being. The findings linked EI with adaptive coping behaviour, exposing both similarities and differences in the types of coping strategies people implement across interpersonal and occupational contexts, as well as their relationships to well-being. In addition, the results demonstrated that certain coping strategies (i.e., social support, venting/self-blame, and alcohol/drug use) partially mediated the relationship between emotion skills and well-being in these two contexts. Finally, gender differences in both EI and coping strategies emerged, with the differences being mostly attributed to the socialization of gender role (i.e., the degree of agentic and communal traits) rather than sex (i.e., being male or female). Moderation models suggested that gender did not interact with EI to influence coping strategy choice (i.e., social support, venting/self-blame, alcohol/drug use) or well-being. These results are discussed in terms of their implications for the therapeutic context, organizational policy, theoretical considerations, as well as future research directions.

Keywords: Emotional Intelligence
Coping
Gender
Stress
Interpersonal
Occupational
Well-Being
Advisor: Watson, Jeanne