VictorJuiz/thesis huggingface dataset:
A Defence of Separatism

Philosophers commonly distinguish between an experience’s intentional content—what the experience represents—and its phenomenal character—what the experience is like for the subject. Separatism—the view that the intentional content and phenomenal character of an experience are independent of one another in the sense that neither determines the other—was once widely held. In recent years, however, separatism has become increasingly marginalized; at present, most philosophers who work on the issue agree that there must be some kind of necessary connection between an experience’s intentional content and phenomenal character. In contrast with the current consensus, I believe that a particular form of separatism remains the most plausible view of the relationship between an experience’s intentional content and phenomenal character. Accordingly, in this thesis I explain and defend a view that I call “moderate separatism.” The view is “moderate” in that the separatist claim is restricted to a particular class of phenomenal properties: I do not maintain that all the phenomenal properties instantiated by an experience are independent of that experience’s intentional content but only that this is true of the sensory qualities instantiated by that experience. I argue for moderate separatism by appealing to examples of ordinary experiences where sensory qualities and intentional content come apart. First I argue that an experience’s intentional content does not determine the sensory qualities it instantiates by appealing to cases where two experiences share the same intentional content but instantiate different sensory qualities. Then I argue that the sensory qualities instantiated by an experience do not determine its intentional content by appealing to cases where two experiences that instantiate the same sensory qualities differ with regard to intentional content. I consider a number of alternatives to my account of the intentional content and phenomenal character of the experiences at issue and argue that none is plausible. If so, it follows that the intentional content and sensory qualities instantiated by an experience are independent of one another.

Keywords: intentionality
phenomenal consciousness
perception
representationalism
phenomenal intentionality
separatism
Advisor: Seager, William
Violent Conflict and Social Capital in Ethnically-polarized Developing Countries

This dissertation explores the problem of violent ethnic conflict in ethnically polarized developing countries using the concept of social capital. Ethnically polarized developing countries typically have high levels of intra-ethnic social capital (social capital existing within groups) but low levels of inter-ethnic social capital (social capital existing between groups). Violent conflict can be averted by cultivating higher levels of inter-ethnic social capital. High levels of inter-ethnic social capital create incentives for elites to adopt moderate strategies. A civic compact emerges when the general population internalizes the norms of inter-ethnic social capital (the rule of law; the right to participation; and the right to continued physical and cultural existence). The civic compact is associated with a general expectation that elites will not pursue extra-institutional strategies such as violence to advance their interests. Peace processes that originate in “hurting stalemates” afford fragile opportunities to begin to cultivate inter-ethnic social capital. At such moments, elite incentive structures align in such a way as to overcome barriers to reform associated with path dependence. The cultivation of inter-ethnic social capital is initiated by integrating the norms of inter-ethnic social capital into the structure of the peace process, although eventually state institutions (which must incorporate these norms into their design) will also re-enforce these norms. Elites begin to internalize the norms of inter-ethnic social capital by repeatedly engaging with each other during the peace process in a manner that actualizes these norms into their experiences. I explore how the norms of inter-ethnic social capital can be integrated meaningfully into the peace process so that elites begin to absorb these norms and so that the institutions that emerge from the process are perceived to be legitimate. Inter-ethnic social capital is developed among the masses primarily through the interactions that the masses have with state institutions. The peace process must focus on rehabilitating the relationship between the masses and the state. This dissertation assesses how this relationship may be rehabilitated and how the norms of inter-ethnic social capital can be integrated into the process of rehabilitating this relationship so that the masses can begin to internalize these norms.

Keywords: social capital
ethnic conflict
development
law
peace process
Advisor: Trebilcock, Michael
Extragalactic Stellar Populations in the Near and Mid-infrared: 1-30 Micron Emission from Evolved Populations, Young and Dusty Star Forming Regions and the Earliest Stellar Populations

The near- through mid-infrared offers a unique and, as this thesis aims to show, essential view of extragalactic stellar populations both nearby, at intermediate redshifts and at very high redshift. In chapter 2, I demonstrate that rest-frame near-IR photometry obtained by the Spitzer Space Telescope provides more robust stellar mass estimates for a spectroscopic sample of ~100 galaxies in the redshift desert (0.5<z<2), and is crucial for modeling galaxies with young star-forming populations. From this analysis, a surprising result emerges in the data. Although the rest-frame light short of 2 micron improves stellar mass estimates, the models and observations disagree beyond 2 micron and emission from non-stellar sources becomes significant. At wavelengths from 1-30 micron, stellar and non-stellar emission contribute equally to a galaxy's global spectral energy distribution. This is unlike visible wavelengths where stellar emission dominates or the far-IR where dust emission provides the bulk of a galaxy's luminosity. Using the sample of high-z galaxies, in chapter 3, I quantify the statistical significance of the excess emission at 2-5 micron and find the emission to correlate with the OII luminosity, suggesting a link between the excess emission and star formation. The origin of the excess emission is not clear, although I explore a number of non-stellar candidates in this chapter. Nearby resolved observations provide a clearer picture of the excess by spatially resolving 68 nearby galaxies. By analyzing the pixel-by-pixel near-IR colours within each galaxy at ~1-5 micron, increasingly red near-IR colors are mapped to spatial regions in chapter 4. For regions with red NIR colors and high star formation rates, I find the broad near- through mid-IR spectrum is constant, varying only in amplitude as a function of the intensity of star formation, suggesting the infrared emission of a young, dusty stellar populations can be added to stellar population synthesis models as an additional component tied to the star formation rate. In closing the thesis, the focus is moved to the detection of stellar populations in the earliest star-forming galaxies. By z>6, all visible wavelength emission is redshifted into near-IR wavelengths. In chapter 5, I show how a tunable near-IR filter I have helped develop holds promise for finding bright Lyman alpha emitting galaxies at redshifts of 8<z<11.

Keywords: Extragalactic astrophysics
Stellar populations
Near and mid-infrared
Advisor: Abraham, Roberto
A Novel Access Technology Based on Infrared Thermography for People with Severe Motor Impairments

Many individuals with severe motor impairments are cognitively capable, but because of their physical impairments, unable to express their intention through conventional means of communication. Access technologies are devices that attempt to translate the intention of these individuals into functional activity by harnessing their residual physical or physiological abilities. The primary objective of this thesis was to design and develop a novel non-invasive and non-contact access technology based on infrared thermal imaging. This access technology translates the local temperature change associated with voluntary mouth opening to activation of a binary switch such as a mouse click or key press. To this end, an algorithm based on motion and temperature analyses, and morphological and anthropometric filters was designed to detect mouth opening activity in thermal video in real-time. The secondary objective of this thesis was to introduce a mutual information measure for objective assessment of binary switch users’ performance. A model was suggested, in which combination of cognitive and physical abilities of the human user of a binary access switch constitute a communication channel. The proposed mutual information measure estimates the rate of information transmission in the ‘human communication channel’ during stimulus response tasks. Using this measure, in a study with ten able-bodied participants, the infrared thermal switch was validated against a conventional chin switch. Impairments in body functions and structures that may contraindicate the use of the infrared thermal switch were explored in a study with seven clients, with severe disabilities. Potential hard and soft technological solutions to mitigate the effect of these impairments on infrared thermal switch use were recommended. Finally the infrared thermal switch was tailored to meet the needs of a young man with severe spastic quadriplegic cerebral palsy, who had no other means of physical access.

Keywords: rehabilitation engineering
assistive technology
infrared thermography
image processing
infrared thermal imaging
access technology
human-computer interaction
mutual information
communication channel
contextual factors
severe motor impairments
people with disability
client-centred design
international classification of functioning disability and health (ICF)
video processing
access switch
access pathway
paediatric
non-invasive
non-contact
biomedical engineering
algorithm
Advisor: Chau, Tom
Venetsanopoulos, Anastasios N.
"Unchaste" Goddesses, Turbulent Waters: Postcolonial Constructions of the Divine Feminine in South Asian Fiction

This dissertation explores the presence of the divine feminine in Indic river myths of the Ganga, the Narmada, and the Meenachil as represented in the three novels: Amitav Ghosh’s The Hungry Tide, Gita Mehta’s A River Sutra, and Arundhati Roy’s The God of Small Things. It challenges masculinist nationalistic narratives, and identifies itself as a feminist revisionist work by strategically combining Indian debates on religious interpretations with Western phenomenological and psychoanalytical perspectives to open up productive lines of critical enquiry. I argue that the three postcolonial novelists under survey resurrect the power of the feminine by relocating this power in its manifestation as the turbulent and indomitable force of three river goddesses. In their myths of origin, the goddesses are “unchaste,” uncontainable, and ambiguous. Yet, Mahatma Gandhi and the Indian patriarchy manipulated and coerced women for their political purposes. They denied female agency in order to promote a brand of nationalism bordering on religious zeal and subjugation through imposed paradigms of chastity. The patriarchy conflated the imaginary chastity of the mother goddess in her multiple manifestations--including but not limited to the River Ganga--with the exalted position forced upon the young Indian widow. Popular art of the colonial period in India dismantled the irrepressible sexual ambiguity of the divine feminine for the Indian population, and reinvented her as a chaste, mother figure (Bharat Mata, or Mother India), desexualized her, and held her up as an iconic, pervasive figurehead of the Motherland. Ironically though, the makeover of the uncontrollable, “chaotic” feminine into this shackled entity during and after the Indian freedom struggle is just the kind of ambiguity that appears in discourses of nation building. By reaffirming the archaic myths of the feminine, Ghosh, Mehta, and Roy dislodge the colonial project and the patriarchal Indian independence movement that sought to “chastise” the divine feminine. I suggest that in these three novels pre-colonial images of the river goddesses--presented in all their ambiguous, multiple, and fluid dimensions--are a challenge to the Indian nationalist project that represents the goddesses one dimensionally as an iconic figure, unifying the geo-body of India and symbolically projecting her as the pure, homogenous Bharat Mata.

Keywords: Postcolonial, Gender Studies, Modern South Asia, Feminism, Resistance, Hegemony, Goddesses, Water, Rivers, Patriarchy, English Literature, World Literature, Nationalism
Advisor: Kanaganayakam, Chelva
Genome Graphs

Whole-genome shotgun sequencing is an experimental technique used for obtaining information about a genome’s sequence, whereby it is broken up into many short (possibly overlapping) segments whose sequence is then determined. A long-standing use of sequencing is in genome assembly – the problem of determining the sequence of an unknown genome, which plays a central role for the sequencing of novel species. However, even within the same species, the genomes of two individuals differ, and though these variations are relatively small, they account for the observed variation in phenotypes. A large portion of these are copy number variants (CNVs), or genomic segments which appear a different number of times in different individuals. The unifying theme of this thesis is the use of genome graphs for both CNV detection and genome assembly problems. Genome graphs, which have already been successfully used for alignment and assembly, capture the structure of a genome even when its sequence is not fully known, as with the case of sequencing data. In this thesis, we extend their uses in several ways, culminating in a method for CNV detection that is based on a novel genome graph model. First, we demonstrate how the double-stranded nature of DNA can be efficiently incorporated into genome graphs by using the technique of bidirected network flow. Furthermore, we show how genome graphs can be efficiently used for finding solutions that maximize the likelihood of the data, as opposed to the usual maximum parsimony approach. Finally, we show how genome graphs can be useful for CNV detection through a novel construction called the donor graph. These extensions are combined into a method for detecting CNVs, which we use on a Yoruban human individual, showing a high degree of accuracy and improvement over previous methods.

Keywords: bioinforamatics
Advisor: Brudno, Michael
Borodin, Allan
Ex vivo Binding of the Agonist PET Radiotracer [11C]-(+)-PHNO to Dopamine D2/D3 Receptors in Rat Brain: Lack of Correspondence to the D2 Recepor Two-affinity-state Model

The dopamine D2 receptor exists in vitro in two states of agonist affinity: a high-affinity state mediating dopamine’s physiological effects, and a physiologically-inert low-affinity state. Our primary goal was to determine the in vivo relevance of this two-affinity-state model for the agonist PET radiotracer [11C]-(+)-PHNO, developed for measurement of the D2 high-affinity state. Our second goal was to characterize the regional D2 versus D3 pharmacology of [3H]-(+)-PHNO binding and assess its utility for measuring drug occupancy at both receptor subtypes. Using ex vivo dual-radiotracer experiments in conscious rats, we showed that, contrary to the two-affinity-state model, the binding of [11C]-(+)-PHNO and the antagonist [3H]-raclopride were indistinguishably inhibited by D2 partial agonist (aripiprazole), indirect agonist (amphetamine) and full agonist ((-)-NPA) pretreatment. Furthermore, ex vivo [11C]-(+)-PHNO binding was unaffected by treatments that increase in vitro high-affinity state density (chronic amphetamine, ethanol-withdrawal), whereas unilateral 6-OHDA lesion, which increases total D2 receptor expression, similarly increased the ex vivo binding of [11C]-(+)-PHNO and [3H]-raclopride. These results do not support the in vivo validity of the two-affinity-state model, suggesting instead a single receptor state for [11C]-(+)-PHNO and [3H]-raclopride in conscious rat. Importantly, we also demonstrated that the increased amphetamine-sensitivity of the agonist radiotracers [11C]-(+)-PHNO and [11C]-(-)-NPA, commonly seen in isoflurane-anaesthetized animals and cited as evidence for the two-affinity-state model, is due to the confounding effects of anaesthesia. Using in vitro and ex vivo autoradiography in rat and the D3 receptor-selective drug SB277011, we found that [3H]-(+)-PHNO binding in striatum and cerebellum lobes 9 and 10 was due exclusively to D2 and D3 receptor binding, respectively, but in other extra-striatal regions to a mix of the two receptor subtypes. Surprisingly, the D3 contribution to [3H]-(+)-PHNO binding was greater ex vivo than in vitro. Also surprising, several antipsychotic drugs, at doses producing 80% D2 occupancy, produced insignificant (olanzapine, risperidone, haloperidol) or small (clozapine, ~35%) D3 occupancy, despite similarly occupying both receptor subtypes in vitro. These data reveal a significant discrepancy between in vitro and ex vivo measures of dopamine receptor binding and suggest that the D3 occupancy is not necessary for the therapeutic effect of antispychotic drugs.

Keywords: positron emission tomography
dopamine D2 receptor
dopamine D3 receptor
agonist D2/D3 radiotracer
antagonist D2/D3 radiotracer
rat
antipsychotic drugs
autoradiography
ex vivo
Advisor: Wilson, Alan A.
Development of a High Resolution Microvascular Imaging Toolkit for Optical Coherence Tomography

This thesis presents the development of new optical coherence tomography imaging systems and techniques to improve in vivo 3D microvascular imaging. Specifically these systems and techniques were proposed to address three main problems with 3D Doppler optical coherence tomography imaging: (a) Motion artefacts, (b) angle dependence of the signal, and (c) relatively high minimum detectable velocity of conventional color Doppler algorithms (~500 μm/s). In order to overcome these limitations a multi-pronged strategy was employed: (1) Construction of a retrospectively gated OCT system for the mitigation of periodic motion artefacts. Proof of principle in vivo B-mode imaging of Xenopus Laevis (embryo of African clawed frog) cardiovascular function up to 1000 frames per second (fps) from data acquired at 12 fps. Additionally, 4D imaging of the Xenopus Laevis heart at 45 volumes per second was demonstrated. (2) Construction of a Fourier domain mode locked laser for high speed swept source optical coherence tomography imaging. This laser was capable of reaching sweep rates of 67 kHz and was optimized to function in the SNR limited phase noise regimes upto approximately 55 dB structural SNR. (3) Development of a novel speckle variance image processing algorithm for velocity and angle independent 3D microvascular imaging. The velocity and angle independence of the technique was validated through phantom studies. iii In vivo demonstration of the speckle variance algorithm was performed by imaging the capillary network in the dorsal skin-fold window chamber model, with the results being validated using fluorescence confocal microscopy. In the final part of this thesis, these newly developed technologies were applied to the assessment of anti-vascular and anti-angiogenic therapies in preclinical models, specifically, photodynamic therapy and targeted degradation of HIF-α.

Keywords: Optical Coherence Tomography
Microvascular Imaging
Advisor: Vitkin, Alex
Literary Developments of the Table of Nations and the Tower of Babel in Anglo-Saxon England

This dissertation examines the various ways Anglo-Saxon authors interpreted and adapted Genesis 10–11: the Table of Nations and the Tower of Babel narrative. Although Genesis 10–11 offered Christians of Late Antiquity and the Middle Ages a scripturally authorized understanding of the origins of ethnic and linguistic diversity of the world, its nature as an ancient Jewish text that deals with matters more suitable to its original audience than to its late antique and medieval readers allowed these later readers to transform the meaning of the text in order to give it a significance more fitting to their own times. In the first section of my dissertation, I treat the topos of the number 72, which becomes prominent when authors of Late Antiquity and the Middle Ages read it into the Table of Nations as the number of descendants of Noah’s three sons. My first chapter deals with the initial development of this topos in Christian and Jewish writings of Late Antiquity; my second chapter with the topos in the Latin writings of early Anglo-Saxons, from the biblical commentaries from the School of Canterbury to Alcuin; and my third chapter with the topos in the writings of later Anglo-Saxons, from King Alfred to the Old English texts of the eleventh century. In the second section of my dissertation, I treat the interpretations of the Tower of Babel as they form and are informed in Late Antiquity and Anglo-Saxon England. As in the first section, three chapters are presented: the first on the initial developments in Late Antiquity; the second on the continual development into the Latin authors of early Anglo-Saxon England; and the third on the mainly Old English authors of the later Anglo-Saxon period.

Keywords: Table of Nations
Babel
Old English
Aldhelm
Aldhelm
Bede
Aelfric
King Alfred
seventy-two
ethnicity
Genesis
Biblical interpretation
Advisor: Orchard, Andy
Towards a Mechanistic Understanding of the Molecular Chaperone Hsp104

The AAA+ chaperone Hsp104 mediates the reactivation of aggregated proteins in Saccharomyces cerevisiae and is crucial for cell survival after exposure to stress. Protein disaggregation depends on cooperation between Hsp104 and a cognate Hsp70 chaperone system. Hsp104 forms a hexameric ring with a narrow axial channel penetrating the centre of the complex. In Chapter 2, I show that conserved loops in each AAA+ module that line this channel are required for disaggregation and that the position of these loops is likely determined by the nucleotide bound state of Hsp104. This evidence supports a common protein remodeling mechanism among Hsp100 members in which proteins are unfolded and threaded along the axial channel. In Chapter 3, I use a peptide-based substrate mimetic to reveal other novel features of Hsp104’s disaggregation mechanism. An Hsp104-binding peptide selected from solid phase arrays recapitulated several properties of an authentic Hsp104 substrate. Inactivation of the pore loops in either AAA+ module prevented stable peptide or protein binding. However, when the loop in the first AAA+ was inactivated, stimulation of ATPase turnover in the second AAA+ module of this mutant was abolished. Drawing on these data, I propose a detailed mechanistic model of protein unfolding by Hsp104 in which an initial unstable interaction involving the loop in the first AAA+ module simultaneously promotes penetration of the substrate into the second axial channel binding site and activates ATP turnover in the second AAA+ module. In Chapter 4, I explore the recognition elements within a model Hsp104-binding peptide that are required for rapid binding to Hsp104. Removal of bulky hydrophobic residues and lysines abrogated the ability of this peptide to function as a peptide-based substrate mimetic for Hsp104. Furthermore, rapid binding of a model unfolded protein to Hsp104 required an intact N-terminal domain and ATP binding at the first AAA+ module. Taken together, I have defined numerous structural features within Hsp104 and its model substrates that are crucial for substrate binding and processing by Hsp104. This work provides a theoretical framework that will encourage research in other protein remodeling AAA+ ATPases.

Keywords: molecular chaperone
thermotolerance
Hsp104
yeast
disaggregation
protein folding
Advisor: Glover, John R.