VictorJuiz/thesis huggingface dataset:
Slavery, conversion, and religious geography in Portuguese India in the sixteenth and seventeenth centuries [electronic resource]
Keywords: History.

Slaves toiled in Portuguese India in the sixteenth and seventeenth centuries, originating from a variety of places, including East Africa, East Asia, Southeast Asia, and different parts of India. Yet, the legal status they occupied, the types of tasks they completed, and their ethnic origins were not the only ways in which they were identified. In the early modern Portuguese world, their religious affiliation formed a key component of identity. Through the establishment of the Goan Inquisition, detailed information about slaves' religious choices, words, and actions entered the written historical record. This dissertation examines the complex world of slavery in sixteenth and seventeenth- century Portuguese India. It utilizes detailed Goan and Lisbon Inquisition cases of slaves and slaveholders, contextualizing the cases with 2254 Goan Inquisition case summaries. This dissertation explores the flights of slaves and freed slaves in the context of overlapping political and religious spatial boundaries, investigating the political implications of slaves' conversions to Islam. Most slaves prosecuted by the Goan Inquisition were converts to Islam from Catholicism, which I argue is significant given that in this era Muslims were considered both religious and political enemies. Drawing from the Lisbon Tribunal cases of New Christians residing in Goa, this dissertation also examines the nature of master-slave relations, during an era in which inquisitors intervened in the master-slave hierarchy.
Social networks [electronic resource] : the making of female migrant sex workers in post-socialist China
Keywords: Anthropology.

While estimates vary dramatically, roughly 6 to 10 million women are working in the sex trade (Fu and Choy 2010). This dissertation examines the role of social networks in making and remaking female sex worker communities (xiaojie) as the sex trade, involving migration, has become an increasingly common means of livelihood in post-socialist China. Drawing on theories of social relations as well as studies of gendered migration in anthropology and relevant fields, I specifically explore the complex social mechanisms through which migrant sex workers make and remake their lives with attention to their daily interactions, multiple discourses, and negotiated practices. This study draws on fieldwork I conducted for twenty-six months between 2006 and 2009, primarily in a red-light neighborhood in Haikou, the capital city of the southernmost province of Hainan. As I became a part of the mobile women's networks, my research naturally extended beyond the geographic boundaries of the neighborhood into multiple sites, from urban red-light neighborhoods to suburban brothels, from observations of sex workers' business activities to public health interventions, from discussions with their neighbors to holidays with their families. It is a unique and important characteristic of my study that I interacted not only with sex workers, but also with various social actors embedded in their networks (i.e., family members, urban neighbors, boyfriends, colleagues, madams, and clients). This is a research method that allows for a fuller understanding of the inter-relationships and mutual perceptions among sex workers and those around them. The central argument of my dissertation develops out of this fieldwork. Much to my surprise, I discovered that, rather than being socially isolated, the sex workers have strong social connections, and their social networks mold this community and, by extension, restructure its cultural ideologies and social structures. I learned that, the women shape, and are shaped by, their social networks and that these networks are interwoven with gender and class to form their values, aspirations, and practices, and, by extension, their suffering (e.g., STIs), subjectivity, and lived experiences. Interestingly, the social networks make it possible for migrant women in the sex trade to cross what otherwise might appear to us to be fixed social boundaries (e.g. boundaries between "prostitute" and "general public," and between relations of commodified intimacy and genuine emotional connection). While these women have strong agency, realize upper social mobility, and change social association (guanxi) patterns, they concurrently suffer emotionally and physically, and social networks play a critical role in the process as 21st China goes through dramatic transformations.
Society theater [electronic resource] : a laboratory for esthetic and social change (1715-1815)
Keywords: French and Italian.

In France, the 18th century was a time of great enthusiasm for the theater. Princes, aristocrats and bourgeois could not slake their passion by attending the official theaters and they staged plays in their private residences to recreate the dramatic experience. People became amateur actors with unprecedented fervor and participated in a new form of sociability known as "society or private theater." Although long dismissed by critics as minor and unimportant, society theater had a lasting impact on the development and evolution of French theater during the 18th century. In addition, because society plays were closer to contemporary life than official dramatic works, they reveal that this practice introduced, tested, and disseminated new social ideas among the participants. Using the metaphor of the laboratory, this study advances a reevaluation of society theater as medium of esthetic and social change. The first chapter traces the history of the practice from its inception to the end of the Napoleonic Empire. Esthetic innovations and main characteristics of the genre are then analyzed before presenting an account of the reception and treatment of society theater in the 18th-century official and unofficial press. The unique social functions of this practice are then revealed through discussion of laughter. An illustration of the way society theater introduced, tested, and disseminated new ideas is presented through examination of the treatment of love in society plays. Finally, the subversive side of the practice is underlined using a couple of representative case studies. Works by Charles Collé, Carmontelle, Marivaux, and Beaumarchais are analyzed.
Soft X-ray spectroscopy and X-ray scattering of ice and water in aqueous solutions [electronic resource]
Keywords: Chemistry.

Water has many anomalous thermodynamic and physical properties as a result of the intermolecular hydrogen-bonding (H-bonding). In this dissertation, several synchrotron x-ray techniques were used to investigate the structure of ice and liquid water, both neat, pure water, and in aqueous solutions. First, the effect of protons and hydroxide ions was explored using x-ray Raman Scattering (XRS) and small angle x-ray scattering (SAXS). Both excess protons and hydroxide ions induce strong H-bonds in water molecules in their vicinity. However, proton appears to have only a local effect while hydroxide induces more density fluctuations on the long length scale. Then the effect of ionic charge was explored using SAXS. It was observed that multivalent cations such as magnesium and aluminum ions form "quasi-lattice" in the solution due to the repulsive interactions between the hydrated cations. Higher-charged molecular anions such as sulfate and phosphate do not have such a pronounced effect due to the fundamental difference in cation and anion hydration mechanisms in water. Following the study of molecular anions, the perchlorate anion, a most structure-breaking anion, was studied in more depth using x-ray absorption spectroscopy (XAS) and SAXS. It was observed that perchlorate not only breaks H-bonds in water, but also interacts with water in the hydration shells of multivalent cations such that the "quasi-lattice" structure is significantly disrupted. Finally, temperature-dependent XAS of supercooled water was studied and the absorption cross section was compared with ice data to further understand the interpretation of XAS in this dissertation.
A solid-state doping technology for carbon nanotubes [electronic resource]
Keywords: Electrical Engineering.

Single wall carbon nanotubes (SWCNTs) have great potential of becoming the channel material for future high-speed transistor technology. Despite tremendous progress in the recent years, certain challenges still remain to be addressed to realize a scaled CNT based transistor technology. In this thesis I address three fundamental challenges that are essential to realizing a SWCNT-based transistor technology. One of the fundamental issues in carbon nanotube transistor technology originates from material synthesis which provides us a mixture of metallic and semiconducting CNTs. To use the semiconducting CNT as the transistor channel material, we developed a solution-based carbon nanotube sorting process where semiconducting CNTs can be sorted from metallic CNTs to a > 99% of purity. The main application of CNTs following this sorting process is for thin film transistors (TFTs) that can be utilized on flexible transparent substrates. In order to achieve carbon nanotube field effect transistors (CNTFETs) with excellent gate control, it is essential to understand the interactions between CNTs and gate insulation materials - ALD high-k dielectrics. In the second section I will investigate the effects of atomic layer deposited (ALD) high-k dielectrics (Al2O3 & HfO2) on SWCNTs. We study the ALD nucleation and growth on SWCNTs and we confirm our findings and gain insightful information using Raman Spectroscopy. In the third part of the thesis I present a novel, VLSI-compatible solid-state doping technique to fabricate n-type carbon nanotube transistors using low work-function metal oxides as gate dielectrics. Using this technique we demonstrate wafer-scale, aligned CNT transistors with yttrium oxide (Y2Ox) gate dielectrics that exhibit excellent n-type behavior. We confirm this mechanism by carrying out a variety of characterization techniques and provide a general guideline for CNT doping that could also be applicable for MoS2 and graphene. This thesis paves the way to exploiting a wide range of materials for an effective n-type carbon nanotube transistor for a complementary (p- and n-type) transistor technology.
Solution-processing of organic semiconductors for field-effect transistors [electronic resource]
Keywords: Materials Science and Engineering.

Solution-processability is a key advantage of organic semiconductors, enabling us to easily deposit these materials at low-cost. Among organic semiconductors, small molecule semiconductors are typically highly crystalline and thus exhibit high carrier mobilities; however, small molecules are generally difficult to deposit into uniform films by solution-processing. In this thesis, we focus on developing solution-processing methods for semiconducting small molecules and understanding the mechanism behind film formation / charge transport in these systems for applications in organic field-effect transistors (OFETs). First, a modified capillary force lithography (MCFL) technique is introduced for fabricating highly textured micro-patterns of a crystalline semiconducting small molecule, C8-BTBT. As this technique is based on soft lithography, various geometries can be patterned onto substrates of interest and the size of the patterns is also easily controlled. Detailed characterizations reveal that the walls of the PDMS stamp used for patterning play an important role in controlling nucleation and growth of C8-BTBT crystals. Fabricated micro-line patterns for high-performance active layers in OFETs are shown to exhibit field-effect mobilities as high as 2.6 cm2/Vs. Secondly, blending semiconducting small molecules with polymer binders is investigated for simultaneously utilizing the exceptional electronic property of small molecules and the good film-forming property of polymers. Our results reveal that residual solvent in blend films following spin-coating plays a critical role in inducing vertical phase separation. In addition, we deduce specific characteristics of polymer binder that are required to generate vertical phase separation and show how annealing temperature affects the type of crystalline phase of rubrene formed in blend films. Lastly, solvent effects are also investigated on the properties of rubrene small molecule blended with a polymer binder. The properties of blend films are analyzed in terms of morphology, crystallinity, and charge transport with various characterization techniques. From our results, we found that there exists a strong correlation between the properties of blend films and solvent characteristics such as solubility, boiling temperature, and surface tension.
Some problems in multiplicative number theory [electronic resource]
Keywords: Mathematics.

Let q be a power of a prime p. In the first part of this thesis, we establish the upper bound of the least prime primitive root mod q by p^3.1. We say a polynomial in F_q [T] is m-smooth if all of its irreducible factors are of degree less than or equal to m. Let N(n, m) be the number of solutions to the polynomial equation X+Y=2Z where all variables are m-smooth polynomials of degree n. In the second part of this thesis, we establish a lower bound on N(n, m) when (8+d) log_q n < = m < = n^1/2 for small d, and prove the analog of the xyz conjecture of Lagarias and Soundararajan in the polynomial rings over finite fields.
Space, mind, and discursive knowledge [electronic resource]
Keywords: Philosophy.

Two major philosophical debates are explored - one concerning the reality of space, and one concerning the physicality of qualia. What binds these explorations together is a set of observations Kant made concerning incongruent counterparts. Chapter 1 presents a novel reformulation of Kant's attempt to refute the relational theory of space using these observations. I argue that standard relationist replies fail to engage his 'handless body' thought-experiment, by treating the body as enantiomorphic rather than homomorphic. I then present novel relational replies to Kant's argument as properly understood. In Chapter 2 presents a novel refutation of Frank Jackson's Knowledge Argument (KA). I consider the advances made by John Perry and Torin Alter in identifying the 'discursive learnability' assumption central to KA. I show that this 'discursive learnability' criterion for physical facts must be rejected because straightforwardly physical facts about 'parity-violating' phenomena are not discursively learnable, and I substantiate this claim using Kant's observations about incongruent counterparts. Chapter 3 presents a critique of some popular strategies for rejecting KA, including those of David Lewis, Brian Loar, and Daniel Stoljar. I also propose a distinction between two ways that words fail to communicate concepts and knowledge, and suggest that this clarifies the debate concerning KA.
Spectroscopic and computational studies of mononuclear nonheme iron enzymes [electronic resource] : insights into the priming of oxygen-activating Fe(II) enzymes and the mechanism of nitrile hydratase
Keywords: Chemistry.

Mononuclear nonheme iron enzymes (NH Fe enzymes) catalyze a variety of biological reactions. A large group of NH Fe enzymes use a ferrous active site to activate dioxygen towards reaction with substrate, and require an additional cofactor as a source of electrons necessary for catalysis. The main part of this thesis involves the application of a circular dichroism (CD), magnetic circular dichroism (MCD) and variable temperature, variable-field MCD (VTVH MCD) spectroscopic methodology to a series of alpha-ketoglurate-dependent (alpha-KG-dependent) enzymes for the purpose of understanding how this enzyme family and the NH Ferrous enzymes in general induce the dissociation the generation of a 5C site for dioxgyen reactivity, as well as how dioxygen binding is oriented for proper catalysis. In addition to catalyzing oxidation of organic substrates, NH Fe enzymes are also involved in the catalytic hydrolysis and hydration of substrates. A prominent example of this is nitrile hydratases (NHases), unusual low-spin (LS) Ferric or Cobaltic enzymes that catalyze the conversion of nitriles to amides in soil bacteria. Another part of this thesis involves the spectroscopic characterization of a ferric NHase for the determination of its active site geometric and electronic structure, which are used to calibrate a computational model which is extended to explore the NHase catalytic mechanism.
Statistical analyses on high-thoughput sequencing of B cell and T cell receptors [electronic resource]
Keywords: Biomedical Informatics.

The immune system is typically described as having two major branches: the adaptive branch, and the innate branch. In the adaptive immune system, T cells and B cells learn to discern foreign pathogens from self. B cell repertoires mediate the host's ability to mount appropriately pathogen-specific humoral responses against immunological challenges. VDJ somatic recombination of the immunoglobulin chains, affinity maturation, and B cell clonal selection all contribute to the generation of a healthy B cell repertoire. Despite starting from only a limited number of genomic segments, these processes lead to diverse and optimized repertoires of clones, where each clone has its own distinct binding specificity for foreign antigens. High depth sequencing data on the repertoire of B cell receptors has enabled us to examine the diverse receptors in great detail. My thesis will showcase three aspects of the B cell repertoire in terms of how they relate to ageing and/or pathology: clonal convergence, clonal expansion, and phylogenetic hypermutation. In a separate but related work, we apply a novel combination of sequencing method and statistical techniques to examine T cell receptors. We raised the lower bounds on T cell receptor repertoires beta chain richness in healthy humans, and examined how T cell receptor diversity relates to age.
Statistical Analysis of the Epistasis Between ApoE and its Genetic Neighbors on Hippocampal Atrophy
Keywords:  Department of Biology
Biology
Alzheimer's disease
ApoE
GWAS
Thesis

Late-onset Alzheimer’s disease (AD), in comparison to familial AD, accounts for 95% of all AD cases. Previous genomic association studies have shown the e4 allele of the apolipoprotein E gene (ApoE4) to significantly increase the risk of late-onset AD. Using single nucleotide polymorphism (SNP) and structural magnetic resonance imaging (MRI) data of 1018 subjects from the Alzheimer’s Disease Neuroimaging Initiative, this study investigated how SNPs in 50 genes functionally related to, or co-expressed with ApoE modulate the risk associated with ApoE4 and whether any genetic variant within these 50 genes shows sex-specific interaction. Three linear models were constructed to separately quantify the effect of 1) SNP only 2) SNP-by-ApoE4 interaction 3) SNP-by-Sex interaction on hippocampal gray matter density extracted from structural MRIs. After filtering for SNPs with a minor allele frequency over 0.05, a total of 7760 SNPs were tested. No SNP remained significant after adjusting for multiple comparisons (adjusted p-value threshold = 5.04 x 10-5). A SNP in the aminolevulinate dehydratase gene, rs818691, came close to the threshold in the SNP-by-Sex model with a p-value of 5.26 x 10-5. Our results suggest that no common polymorphisms in genes known to be functionally related to, or co-expressed with ApoE, contributes significantly to hippocampal atrophy and that ApoE modulates risk of AD through pathways that have yet to be clarified.
Statistical methods on graphs [electronic resource]
Keywords: Statistics.

In relational data the most basic statistical questions focus on modeling the structure of the network and on making inferences about the nodes. These questions are addressed separately with a simple but novel model for each. On the side of graph structure, a class of "monotone random graphs" are examined where n vertices are totally ordered such that independent edge probabilities satisfy the partial ordering p_{i, j} ≤ p_{k, l} for i ≤ k and j ≤ l. The MLE of the graph's edge parameters can be solved by isotonic regression (equivalent to projection onto a convex cone), and this MLE is a consistent estimator. On the nodal inference side, the focus is specifically on multi-relational networks. This approach constructs a design matrix by multiplying a vector of nodal features with each adjacency matrix in which the nodes are embedded. After constructing this design matrix through nodal diffusion, standard statistical learning techniques can be applied to the design matrix.
Stochastic effects in the grammar [electronic resource] : toward a usage-based model of copula contraction
Keywords: Linguistics.

The aim of this analysis of conversational English corpus data is to unearth living effects of phonological, syntactic, and frequency information in an area of the grammar prone to variation: copula contraction. "Living" effects arise during active language processing and may be contrasted with the products of diachronic coalescence of sev- eral forms into fused units. Researchers have found that English auxiliary contraction (have > 've, has > 's, be > 'm/'re/'s, will/shall > 'll ) is subject to phonological, processing, and grammatical constraints. These constraints are most evident in the study of the copula, as "to be" contracts with a wider range of hosts than other auxiliaries, or preceding words, i.e., with pronominal and lexical noun phrase hosts. The analysis reveals three novel e ndings about copula contraction. First, copula con- traction is sensitive to both the collocational frequency of the copula and its host and the following word, even when lexical noun phrase hosts (as opposed to pronominal hosts) are considered in light of known grammatical constraints. The more frequent the host or the following word, the more likely the copula is to contract. The results also suggest that the role of preceding phonology in predicting contraction may be more sensitive to voicing than the vowel/consonant distinction that has generally been observed. Persistence is also shown to play a role in predicting contraction . Finally, the results suggest that copula reduction and contraction are sensitive to many of the same factors and argue that this is evidence of the same constraints creating allomorphic variation at the morphological level.
String theory, geometry and (mock) modular forms [electronic resource]
Keywords: Physics.

Monstrous moonshine (Conway and Norton, c. 1980) is a relation between the "monster", the largest of the sporadic finite simple groups, and the j-function, the unique holomorphic weight zero modular function under SL(2, Z) with a simple pole at the infinite cusp. Recently, string theory has been the impetus for the discovery of a host of similar such relations, connecting many smaller finite groups to mock modular forms, the recalcitrant cousins of the j-function. Here I discuss some of these mysterious new connections, and progress we have made in understanding them by studying string theory on K3 manifolds. This thesis is based on the papers [157], [153], and [127] written with Miranda Cheng, Xi Dong, John Duncan, Shamit Kachru, Natalie Paquette, and Timm Wrase. It should not be cited without also referencing those papers.