VictorJuiz/thesis huggingface dataset:
Engineering Boronsubphthalocyanine for Organic Electronic Applications

Boronsubphthalocyanines (BsubPcs) are a class of organic semiconducting materials which are relatively underdeveloped in their synthetic methods and organic semiconducting applications. A comprehensive investigation of these materials is explored in a rigorous and strategic manner progressing through each stage of the materials development cycle: materials selection from computational screening, organic/organometallic synthesis of target materials using known methods or by the development of new synthetic methods, physical and chemical analysis of new materials, and device implementation in organic light emitting diodes and organic photovoltaic cells. The result is the formation of new compositions of BsubPc specifically engineered for application as organic semiconductors in devices. Specifically, phenoxy-boronsubphthalocyanine derivatives are investigated starting with a computational study of their molecular orbitals – a property that dictates their function (donor or acceptor behaviour) in organic electronic devices. The nature of the axial phenoxylate is found to vary the energy level of the frontier molecular orbitals minimally, by up to ~0.4 eV while the nature of the BsubPc periphery can shift the energy levels of the frontier molecular orbitals by >1 eV. The differential sensitivity of the axial phenoxylate and the BsubPc periphery becomes a key design element allowing controlled adjustments of the frontier molecular orbitals by peripheral modification and isolating the design physical chemical properties essential to device fabrication to the axial phenoxylate. Subsequently, an investigation into the solubility and sublimability of these materials is performed, which leads to their investigation in OLED and OPV devices. The success from the phenoxy-BsubPcs study has led to the exploration of new chemistry to expand the available axial nucleophiles beyond phenoxylates. Previously unattainable sulphur and nitrogen nucleophiles are synthesised using two methods (1) the condensation of Cl-BsubPc with phthalimides and (2) the activation of Cl-BsubPc using aluminum chloride to access thiols and anilines. The phthalimido-BsubPcs synthesized from this method are incorporated in OLEDs.

Keywords: Organic Electronics
Subphthalocyanine
Photovoltaics
Light Emitting Diodes
Advisor: Bender, Timothy
Kleinian Reparation: A Psychoanalytic Exploration of Residential School Apology in Canada

The work of mid-twentieth century psychoanalyst Melanie Klein stresses the importance of the phantasy world and its role within the human psyche. For Klein innate human destructive phantasies coexist with feelings of love, guilt, and reparation. Love and hate exist in tension with one another and one must cope with balancing these feelings. I will use the psychoanalytic concept of reparation as understood by Klein to explore the performance of apology and reparation. Reparation, for Klein, refers to the psychological need to make things good, that is to say, to mend and repair relationships with others. Using this concept this work will examine the United Church of Canada's 1986 and 1998 apologies to First Nations peoples for its involvement in the residential school system, as well as the Canadian government's “Statement of Reconciliation” and 2008 apology for residential schools. This work asks the question: are these apologies effective in their attempts to make amends for past injustices or are they examples of what Klein calls “manic reparation”, which works to conceal, hide, or preserve phantasies of aggression? Klein's theories will provide a new and evaluative theoretical lens to discuss apology. The academic study of apology currently seeks to find “categorical elements”, which are then used to decide if the apology is a “success.” But this approach is missing the important component of the implied reparative concept within an apology. An apology is not only a written text but also an act that can work to conceal or reveal the perpetrators’ view of their transgressions. Exploring the manifest and latent content of apologies will provide a richer insight into the apology process.

Keywords: Religion
United Church of Canada
History
Psychoanalysis
Canadian Government
Melanie Klein
Apology
Residential Schools
Advisor: Hewitt, Marsha
Modeling Evolution

Evolution by natural selection began as a biological concept, but since Darwin it has been recognized to have broader application than biology. Applying evolutionary ideas beyond biology requires that the principles of evolution by natural selection be abstracted and generalized from the biological case. The received view of evolution by natural selection in biology is itself seriously flawed, which understandably renders the project of abstracting it and applying it elsewhere challenging. This thesis develops a generalized account of models of evolution by natural selection which is used to resolve various outstanding issues in the philosophy of biology. This also clarifies the methods and prospects of applying evolution by natural selection to non-biological domains. It does so by analyzing models of evolution both within biology and outside it, relying in particular on the contrast provided by models of firm competition in evolutionary economics. This analysis highlights those aspects of the classical view which must be abandoned or revised, and leads to the development of a neo-dynamical model of evolution, which is developed, explained, defended, and applied to problems in evolutionary biology and multi-level selection theory.

Keywords: Evolution
Philosophy of Science
Advisor: Walsh, Denis
Development and Application of a Novel Method to Detect Mammalian Protein-protein Interactions

Understanding normal and cancer cell biology requires the development and application of systems biology approaches capable of probing the functional human proteome, and the protein-protein interactions (PPIs) within it. Such technologies will facilitate our understanding of how molecular events drive phenotypic outcomes, and how these processes are perturbed in disease conditions. In this thesis, I first describe the development of a mammalian, Gateway compatible, lentivirus-based protein-fragment complementation assay (magical-PCA), for the in vivo high-throughput identification of PPIs in mammalian cells. This technology provides a vast improvement over current PCA methodologies by allowing for pooled, proteome-scale mapping of PPIs in any mammalian cell line of interest, using any bait protein of interest. A proof-of-concept pooled genome-scale screen using the magical-PCA approach was performed using the human mitochondrial protein TOMM22 as a bait, providing evidence that this technology is amenable to proteome-wide screens. Moreover, the TOMM22 screens offered novel insight into links between TOMM22 and proteins involved in mitochondrial organization, apoptosis, and cell cycle dynamics. Second, I performed a pooled genome-scale magical-PCA screen with the oncoprotein BMI1, a component of the E3 ubiquitin ligase complex involved in histone H2A mono-ubiquitination and gene silencing, to identify novel BMI1 protein interactors. Consequently, I have uncovered a novel physical and functional association between BMI1 and components of the mammalian splicing machinery. I further discovered that BMI1 knockdown influenced the alternative splicing of a number of cellular pre-mRNAs in colon cancer cell lines, suggesting that the association between BMI1 and cellular splicing factors impinges on pre-mRNA processing. Importantly, BMI1 expression was shown to influence the alternative splicing of the SS18 oncoprotein towards an exon 8-excluded isoform, which was shown in this study to promote cell proliferation when assessed in an anchorage-independent growth assay. Together, these studies highlight the development of a new methodology for the detection and proteome-scale screening of mammalian PPIs. A proof-of-concept screen with human TOMM22 highlighted the utility of the approach, as I was able to detect both strong and weak or transient PPIs. Application of my screening methodology to BMI1 provided crucial insight into the function of this oncoprotein, and BMI1-driven tumorigenesis.

Keywords: Protein-protein interactions
Cancer
Alternative splicing
Advisor: Moffat, Jason
Expanding the Capabilities of Constraint-based Metabolic Models for Biotechnology Purposes

Over the past decade, the constraint-based approach to metabolic modeling has become an important tool for understanding and controlling biology. Unfortunately, the application of this novel approach to systems biology in biotechnology has been limited by three significant technical issues: existing metabolic modeling methods cannot completely model the overflow metabolism, cannot model the metabolism of microbial communities, and cannot design strains optimized for productivity and titer. Three computational methods – the Flux Balance Analysis with Membrane Economics (FBAME) method, the Dynamic Multi-species Metabolic Modeling (DyMMM) framework, and the Dynamic Strain Scanning Optimization (DySScO) strategy – have been developed to resolve these issues respectively. First, the FBAME method, which adopts the membrane occupancy limitation hypothesis, was used to explain and predict the phenomenon of overflow metabolism, an important metabolic phenomenon in industrial fermentation, in Escherichia coli. Then, the DyMMM framework was used to investigate the community metabolism during uranium bioremediation, and demonstrated that the simultaneous addition of acetate and Fe(III) may be a theoretically viable uranium bioremediation strategy. Lastly, the DySScO strategy, which combines the DyMMM framework with existing strain design algorithms, was used to design commodity-chemical producing E. coli optimized for a balanced product yield, titer, and volumetric productivity. These novel computational methods allow for broader applications of constraint-based metabolic models in biotechnology settings.

Keywords: metabolism
modeling
optimization
Advisor: Mahadevan, Radhakrishnan
The Evolution of the Hellenistic Polis: Case Studies in Politics and Political Culture

The following dissertation sets out to explore the evolution of a handful of civic institutions in the Hellenistic era. The first chapter focuses on the institution of the ephebeia and citizen-training. It centres on three documents: the gymnasiarchic law of Beroea (I. Beroeae 1 [ca. 167 BCE]), the oath of the agelaoi of Dreros (I. Cret. 1.9.1 [ca. 200 BCE]) and the honorary decree for Menas of Sestos. It argues first that citizen training programs of the Hellenistic period had higher rates of participation than the Athenian evidence seems to suggest, and second that three virtues of gymnastic training, euexia, eutaxia and philoponia, were also political and social virtues. The second chapter focuses on Zosimos of Priene (I. Priene 113 [ca. 100 BCE]) and the connection between his two most important reforms: instituting a system of duplicate record-keeping and funding rhetorical training for ephebes. It argues that the speeches of envoys and ambassadors (presbeutic rhetoric) constituted the dominant mode of Hellenistic rhetoric; within that genre, arguments based on history and on official records were considered the most effective. The third chapter focuses on Fabius' letter to Dyme (Syll.3 684 [144 BCE]). It argues that the destruction of Dyme's public archives was not part of a 'socialist' revolution, but rather was a means of rejecting changes to the citizen body forced on the city by Rome. The final chapter turns to the island of Kos. It explores Diokles' decree (IG XII.4.1 75 [ca. 200 BCE]) as an example of how the balance between self-interest and communal interests were negotiated.

Keywords: History
Epigraphy
Hellenistic
City-State
Polis
Classics
Greek History
Ancient History
Sestos
Kos
Dyme
Priene
Advisor: Rubincam, Catherine
Lytle, Ephraim
Microfluidic Studies of Biological and Chemical Processes

This thesis describes the development of microfluidic (MF) platforms for the study of biological and chemical processes. In particular the thesis is divided into two distinct parts: (i) development of a MF methodology to generate tunable cell-laden microenvironments for detailed studies of cell behavior, and (ii) the design and fabrication of MF reactors for studies of chemical reactions. First, this thesis presented the generation of biopolymer microenvironments for cell studies. In the first project we demonstrated a high-throughput MF system for generating cell-laden agarose microgels with a controllable ratio of two different types of cells. The MF co-encapsulation system was shown to be a robust method for identifying autocrine and/or paracrine dependence of specific cell subpopulations. In the second project we studied the effect of the mechanical properties on the behavior of acute myeloid leukemia (AML2) cancer cells. Cell-laden macroscopic agarose gels were prepared at varying agarose concentrations. A modest range of the elastic modulus of the agarose gels were achieved, ranging from 0.62 kPa to 20.21 kPa at room temperature. We observed a pronounced decrease in cell proliferation in stiffer gels when compared to the gels with lower elastic moduli. The second part of the thesis focuses on the development of MF platforms for studying chemical reactions. In the third project presented in this thesis, we exploited the temperature dependent solubility of CO2 in order to: (i) study the temperature mediated CO2 transfer between the gas and the various liquid phases on short time scales, and (ii) to generate bubbles with a dense layer of colloid particles (armoured bubbles). The fourth project involved the fabrication of a multi-modal MF device with integrated analytical probes. The MF device comprised a pH, temperature, and ATR-FTIR probes for in-situ analysis of chemical reactions in real-time. Furthermore, the MF reactor featured a temperature controlled feedback system capable of maintaining on-chip temperatures at flow rates up to 50 mL/hr.

Keywords: Microfluidic
Cell Encapsulation
Multi-modal Analysis
Microenvironments
Biopolymers
High-throughput
Advisor: Kumacheva, Eugenia
Dynamic Structures of Protein Interaction Networks Predict Complex Phenotypes of Biological Systems

This work focuses on the use of network graph theory in biological networks. I explore how network graph theory informs our understanding of biological networks such as protein interaction networks. I show that the human protein interaction network forms dynamic, modular structures that organize cell signaling pathways into higher order units. The misregulation of the dynamic, modular structure of the protein interaction network in breast cancer tumours is associated with outcome of the disease, suggesting that the altered structure of the protein interaction network is directly related to the phenotype of the tumour. I also demonstrate that the human protein interaction network is fractal in nature and thus forms self-similar structures within the network. The fractal skeletons of the protein interaction network contain critical information and therefore can be used alone in determining the phenotype of breast cancer tumours by examing the disruption of dynamic network structures. The self-similar fractal backbones deconvolve the protein interaction network into layers of independent function, resulting in improved description of breast cancer outcome using the dynamic network modularity algorithm. Finally, I discuss how the discoveries and technologies described within can be improved and how these discoveries can lead to a network based modality of medicine.

Keywords: network biology
cancer
systems biology
Advisor: Wrana, Jeffrey
Supply Chain Design - Competitive and Financial Perspectives

In this thesis we study problems in the context of inventory control and facility location. In chapter 2 we study the competition among risk averse newsvendors. We showed that the well-known result for the single-product monopoly firm, which states higher risk aversion causes the firm to reduce its order quantity, cease to hold under the competition. We concluded that the higher risk aversion does not necessarily cause both firms to reduce their order quantity. We showed that the impact of risk aversion on equilibrium quantities is a trade-off between two effects: (a) Own risk aversion increment which causes that the firm reduces its order quantity and (b) Effect of spillover demand from competitor which causes that the firm increases its order quantity. We also show which firm raises its order quantity as both firms become more risk averse depending on their attributes: profitability ratio (overstocking to understocking ratio), initial risk aversion level and demand characteristic (distribution and substitution). In Chapter 3, we study how the operational decisions of a firm's manager depend on her own incentives, the capital structure, and financial decisions in the context of the newsvendor framework. We showed that in contrast to common practices, tying the manager's compensation to stock price (equity value) may not be optimal for shareholders. We propose to tie the managers' compensation to the firm value or include a debt-like instrument in the compensation package to mitigate the risk taking behaviour of the managers. We also show how the board of directors can modify the compensation structure based on the state of the economy and publicly available information about company's demand. In Chapter 4, we study the effect of risk attitude of decision makers on well-known location problems with uncertain demand. In addition to providing mathematical formulations for those problems, we also discussed how we can solve these problems using linearization techniques. We also shed some light on the importance of considering the volatility and correlation structure. Furthermore, we apply a Bayesian updating method, a useful tool for updating the probability distribution to incorporate the consultants' view about uncertain factors in location problems.

Keywords: Newsvendor
Game Theory
Location Problem
Risk Preference
Capital Structure
Executive Incentives
Advisor: Berman, Oded
Psalms Unbound: Ancient Concepts of Textual Tradition in 11QPsalms-a and Related Texts

This dissertation investigates ways in which early Jewish communities conceptualized the production and collection of writing. Through a study of 11QPsalms-a, the Qumran Psalms Scroll, it shows how modern book culture (shaped by the canon, codex, print, authorial copyright, and scholarly editing) has distorted our understanding of ancient texts and fostered anachronistic questions about their creation and reception. Taking seriously what early Jewish texts have to say about their own writtenness and building upon earlier scholarship on scriptural multiformity, the dissertation also uses theoretical insights from the field of Book History to study the identity, assembly, and literary context of the Psalms Scroll as an example of the ancient textual imagination. Physical and discursive evidence suggest that no concept of a “Book of Psalms” existed as a coherent entity in the ancient Jewish imagination, but that psalms collections were conceptualized and created in looser, unbounded ways. New metaphors made possible by electronic text, which likewise cannot be constrained into the categories of print book culture, can encourage new ways of imagining ancient concepts of fluid textuality as well. After a study of the status and compilation of the Psalms Scroll (Ch. 1-2), the dissertation engages the question of Davidic authorship (Ch. 3). David was not imagined as the author of a particular psalms collection, but as the inaugurator of a variety of liturgical traditions. The identity between an individual figure and a specific text should be unbound in favour of a looser relationship, allowing for the continuing growth of traditions inspired by the figure. Chapters 4 and 5 present a reading of the Psalms Scroll and Davidic lore alongside two other traditions: Ben Sira and angelic ascent literature. Both possess literary links with the Psalms Scroll, but also shed light on the ways in which ancient communities imagined writing and understood their own relationship to their texts. Thus, reading across canonical and generic boundaries embeds psalms traditions in a richer context of reception and provides a fuller picture of the ancient textual imagination. The conclusion makes a comparative gesture toward the Nachleben of psalms collecting in Syriac Christianity.

Keywords: Dead Sea Scrolls
Psalms
Book History
Early Judaism
Advisor: Najman, Hindy
Welfare Reforms in Post-Soviet States: A Comparison of Social Benefits Reform in Russia and Kazakhstan

Concerned with the question of why governments display varying degrees of success in implementing social reforms, (judged by their ability to arrive at coherent policy outcomes), my dissertation aims to identify the most important factors responsible for the stagnation of social benefits reform in Russia, as opposed to its successful implementation in Kazakhstan. Given their comparable Soviet political and economic characteristics in the immediate aftermath of Communism’s disintegration, why did the implementation of social benefits reform succeed in Kazakhstan, but largely fail in Russia? I argue that although several political and institutional factors did, to a certain degree, influence the course of social benefits reform in these two countries, their success or failure was ultimately determined by the capacity of key state actors to frame the problem and form an effective policy coalition that could further the reform agenda despite various political and institutional obstacles and socioeconomic challenges. In the case of Kazakhstan, the successful implementation of the social benefits reform was a result of a bold and skilful endeavour by Kazakhstani authorities, who used the existing conditions to justify the reform initiative and achieve the reform’s original objectives. By contrast, in Russia, the failure to effectively restructure the old Soviet social benefits system was rooted largely in the political instability of the Yeltsin era, and a lack of commitment to the reforms on the part of key political actors. And when the reform was finally launched, its ill-considered policies and the government’s failure to form the broad coalition and effectively frame the problem led to public protests and subsequent reform stagnation. Based on in-depth fieldwork conducted in Russia and Kazakhstan in 2006 and 2008, my study enriches the literature on the transformation of post-communist welfare regimes, and contributes important insights to the central question in the literature on public policy, that is, when, why and how policies change. It also enhances our understanding of political and public policy processes in transitional and competitive authoritarian contexts.

Keywords: welfare reform
Russia
policy implementation
Kazakhstan
Advisor: Solomon, Peter