VictorJuiz/thesis huggingface dataset:
The effects of neuroinflammation on the subventricular zone neurogenic compartment following Theiler's Murine Encephalomyelitis virus infection and its regulation by Galectin-3
Keywords: Galectin-3
Theiler's
neuroinflammation
multiple sclerosis

The subventricular zone (SVZ) is an adult neurogenic niche that contains multipotent stem/progenitor cells that may be a viable target for remyelination in Multiple Sclerosis. In response to demyelination, SVZ progenitors are recruited into myelin lesions. Currently, the effect of inflammation on the endogenous brain stem cell compartment remains poorly characterised. Theiler's murine encephalomyelitis virus (TMEV) induces a demyelinating disease in susceptible SJL/J mice, due to persistence of the virus, which models the chronic progressive form of multiple sclerosis. In contrast, virus is rapidly cleared in TMEV resistant C57BL/6 mice. This viral clearance is critically dependent on infiltration of CD4+ and CD8+ T cells during the first 3-14 days after infection, through the blood vessels and meninges. This project aimed to characterise the impact of TMEV induced inflammation on SVZ homeostasis.
In both strains of mice the most pronounced and consistent inflammation in the CNS was observed in periventricular regions and in particular, the SVZ, which showed targeted infection by the TMEV virus. However, the time course and kinetics for infiltration at 3,7 and 14 days post infection have very different profiles between resistant C57BL/6 and susceptible SJL mice. Using RT-PCR arrays and ELISA I have shown that these differences in T cell infiltration to the SVZ may be due to much higher chemokine and cytokine expression levels in B6 mice. TMEV infection decreases SVZ cell proliferation and results in a loss of neuroblast numbers.
Galectin-3 (Gal-3) is a β-galactoside binding protein that is constitutively expressed specifically in the SVZ. Following TMEV infection Gal-3 levels are significantly upregulated in the SVZ, with higher expression in B6 mice compared to SJL mice. Primary SVZ astrocytes secrete extracellular Galectin-3 at much higher levels than cortical astrocytes. Galectin-3 is a pro-inflammatory mediator which upon secretion is able to activate immune and inflammatory signaling events and amplify pro-inflammatory cytokine production. Both SJL and B6 Gal-3-/- KO mice have decreased expression of CCL2, CCL5 CXCL10 and CCL8 chemokines in the SVZ after TMEV infection. Deletion of Gal-3 prevents the loss of SVZ proliferation and in B6 mice decreases hematopoietic cell infiltration and enhances ectopic neuroblast emigration. These data implicate Galectin- 3 as a novel regulator of the SVZ inflammatory response and may provide a new target for regulating T cell CNS immigration in autoimmune disease.
Play, risk and children's sociality in urban Vancouver
Keywords: friendship
risk
games
childhood
toys
play

This thesis demonstrates how children challenge the boundaries adults place on them, out of concern for their safety, through child-specific cultural practises. The thesis argues that these boundaries emerge from contemporary changes in the perception of risk to children and have driven the systematic limitation of spaces that children are allowed to experience on their own. Based on data collected among elementary school-age children during twelve months of fieldwork (2008-2009), across multiple sites in the city of Vancouver, Canada, I argue that children creatively adapt to spatial and social limits imposed on them through play, consumption and exchange. Moreover, the research demonstrates that through gathering social knowledge and experimenting with self-presentation and systems of social order, children create a sophisticated peer culture. This incorporates social differentiations and hierarchies that differ from those of adult society however, are interdependent with it. My work thus challenges the position of children as objects and ‘anecdotes’ in anthropology: considered ‘works in progress’ and lacking full status as persons in society. Rather, I argue that they should be treated as competent social actors in their own right with their own social meanings and cultural practises.
Neuroanatomical screening and analysis of transgenic and ENU induced mutagenised mice
Keywords: gene mapping
KO
CNS development
neuroanatomy
Intellectual disability
brain development
ENU
mental retardation

I have sought to discover genetic causes of neuroanatomical defects by conducting N-ethyl-N-nitrosourea mutagenesis and transgenic knock out screens in mice. The rationale behind this is that mutations causal to structural defects will be informative about developmental neurobiology and the biological basis of behaviour. Direct screening for behavioural abnormalities in mice has historically been arduous and yielded few findings due to small effect sizes and limited statistical power. My approach sought to bypass these problems by screening for highly penetrant morphological phenotypes. This thesis details my screens and the histological, genetic and behavioural characterisation of lines of interest. These include models of hydrocephalous, pyramidal cell layer ectopia, abnormal neurogenesis, corpus callosum agenesis, hippocampal enlargement, elevated cell death and hypomyelination.
Whilst N-ethyl-N-nitrosourea mutagenesis screening has been conducted since the twilight of the 20th century, systematic transgenic knock out screening is currently in its infancy. By discovering gene-phenotype associations through both approaches, I have been able to compare the relative yields, strengths and weaknesses of the two screening methods. Additionally, I have discussed the significant of the gene-phenotype associations produced from both screens.
Selection along the HIV-1 genome through the CTL mediated immune response
Keywords: MHC
phylodynamics
HIV
HLA
HIV-1
escape
selection
CTL

During human immunodeficiency virus 1 (HIV-1) infection, the viral population is in constant battle with the host immune system. The cytotoxic T-lymphocyte (CTL) response, a branch of the adaptive immune response, is implicated in viral control and can drive viral evolution in the infected host population. Endogenous viral peptides, or ‘epitopes’, are presented to CTLs by human leukocyte antigen (HLA) class I molecules on the surface of infected cells where they may be identified as non-self. Mutations in or proximal to a viral epitope can result in ‘escape’ from CTLs targeting that epitope. The repertoire of epitopes which may be presented is dependent upon host class I HLA types. As such, reversion may occur after transmission due to changes in viral fitness and selection in the context of a new HLA background. Thus, parameters describing the dynamics of CTL escape and reversion are key to understanding how CTL responses within individuals relate to HIV-1 sequence evolution in the infected host population. Escape and reversion can be studied directly using biological assays and longitudinal viral sequence data, or indirectly by considering viral sequences across multiple hosts. Indirect approaches include tree based methods which detect associations between host HLA and viral sequence but do not estimate rates of escape and reversion, and ordinary differential equation (ODE) models which estimate these rates but do not consider the dependency structure inherent in viral sequence data. We introduce two models which estimate escape and reversion rates whilst accounting for the shared ancestry of viral sequence data. For our first model, we lay out an integrated Bayesian approach which combines genealogical inference and an existing epidemiological model to inform escape and reversion rate estimates. Using this model, we find evidence for correlation between escape rate estimates across widely separated geographical regions. We also observe a non-linear negative correlation between in vitro replicative capacity and escape rate. Both findings suggest that epistasis does not play a strong role in the escape process.
Although our first model worked well, it had some key limitations which we address in our second method. Notably, by making a series of approximations, we are able account for recombination and analyse very large datasets which would be computationally infeasible under the first model. We verify our second approach through extensive simulations, and use the method to estimate both drug and HLA associated selection along portions of the HIV-1 genome. We test the results of the model using existing knowledge, and determine a collection of putative selected sites which warrant further investigation. Finally, we find evidence to support the notion that the CTL response played a role in HIV-1 subtype diversification.
Contextuality and noncommutative geometry in quantum mechanics
Keywords: functional analysis
contextuality
quantum mechanics
quantum physics
k-theory
noncommutative geometry
operator algebras

It is argued that the geometric dual of a noncommutative operator algebra represents a notion of quantum state space which differs from existing notions by representing observables as maps from states to outcomes rather than from states to distributions on outcomes. A program of solving for an explicitly geometric manifestation of quantum state space by adapting the spectral presheaf, a construction meant to analyze contextuality in quantum mechanics, to derive simple reconstructions of noncommutative topological tools from their topological prototypes is presented.
We associate to each unital C&ast;-algebra A a geometric object--a diagram of topological spaces representing quotient spaces of the noncommutative space underlying A—meant to serve the role of a generalized Gel'fand spectrum. After showing that any functor F from compact Hausdorff spaces to a suitable target category C can be applied directly to these geometric objects to automatically yield an extension F∼ which acts on all unital C&ast;-algebras, we compare a novel formulation of the operator K0 functor to the extension K∼ of the topological K-functor. We then conjecture that the extension of the functor assigning a topological space its topological lattice assigns a unital C&ast;-algebra the topological lattice of its primary ideal spectrum and prove the von Neumann algebraic analogue of this conjecture.
Conceptual Art: What is it?
Keywords: Conceptual Art
philosophy
aesthetics

Conceptual Art (henceforth CA) has the peculiar status of being at once a neglected topic in philosophical aesthetics, and one on which a degree of philosophical weight disproportionate to the attention it has received is placed. On the one hand it is frequently mentioned by philosophers as a problematic case, one that general theories of art have difficulty dealing with, but on the other, there is a notable lack of philosophical research taking CA as its focus. It is largely taken as a given that CA is radically different from other art in various ways and thus poses problems for some of the general statements about art that philosophers tend to make. But it is striking that these claims are not, for the most part, grounded in a thorough investigation into the nature of CA. The purpose of my research is to conduct such an investigation; to address the question of what CA is, and what makes it different from other art, in order to come to a clearer view of what particular philosophical issues or difficulties CA raises for the philosophy of art. In existing literature on CA, it is standard to take CA’s distinctiveness to have something to do with the importance of ‘ideas’. I investigate what could be meant here by ‘idea’, and identify two broad schools of thought as to what form this emphasis on ideas in CA takes: Priority Accounts, which claim that in CA ideas are the most important aspect of the work and Constitution Accounts, which claim that works of CA are ideas. I identify serious problems for Constitution Accounts, in general, and for some kinds of Priority Account. I then put forward a new kind of Priority account which I think overcomes the problems faced by its rivals.
Distributed representations for compositional semantics
Keywords: deep learning
compositional semantics
natural language processing

The mathematical representation of semantics is a key issue for Natural Language Processing (NLP). A lot of research has been devoted to finding ways of representing the semantics of individual words in vector spaces. Distributional approaches—meaning distributed representations that exploit co-occurrence statistics of large corpora—have proved popular and successful across a number of tasks. However, natural language usually comes in structures beyond the word level, with meaning arising not only from the individual words but also the structure they are contained in at the phrasal or sentential level. Modelling the compositional process by which the meaning of an utterance arises from the meaning of its parts is an equally fundamental task of NLP.
This dissertation explores methods for learning distributed semantic representations and models for composing these into representations for larger linguistic units. Our underlying hypothesis is that neural models are a suitable vehicle for learning semantically rich representations and that such representations in turn are suitable vehicles for solving important tasks in natural language processing. The contribution of this thesis is a thorough evaluation of our hypothesis, as part of which we introduce several new approaches to representation learning and compositional semantics, as well as multiple state-of-the-art models which apply distributed semantic representations to various tasks in NLP.
Part I focuses on distributed representations and their application. In particular, in Chapter 3 we explore the semantic usefulness of distributed representations by evaluating their use in the task of semantic frame identification.
Part II describes the transition from semantic representations for words to compositional semantics. Chapter 4 covers the relevant literature in this field. Following this, Chapter 5 investigates the role of syntax in semantic composition. For this, we discuss a series of neural network-based models and learning mechanisms, and demonstrate how syntactic information can be incorporated into semantic composition. This study allows us to establish the effectiveness of syntactic information as a guiding parameter for semantic composition, and answer questions about the link between syntax and semantics. Following these discoveries regarding the role of syntax, Chapter 6 investigates whether it is possible to further reduce the impact of monolingual surface forms and syntax when attempting to capture semantics. Asking how machines can best approximate human signals of semantics, we propose multilingual information as one method for grounding semantics, and develop an extension to the distributional hypothesis for multilingual representations.
Finally, Part III summarizes our findings and discusses future work.
From Romans to Goths and Franks:  ethnic identities in sixth- and seventh-century Spain and Gaul
Keywords: Identity
Medieval History
Ethnicity

Within a few centuries after the collapse of the Roman Empire in the West, the descendants of Romans who had envisioned the world in terms of moral, civilized Romans and the savage barbarian ‘other’ had come to identify with those very barbarians. This thesis explores this shift from ‘Roman’ to ‘Gothic’ and ‘Frankish’ identities in sixth- and seventh-century Spain and Gaul through an examination of the ways ethnonyms were used in contemporary sources. Within the first section on Visigothic Spain, chapter one discusses the ‘Romans’ of the East—that is, the Byzantines—as portrayed by Isidore of Seville and John of Biclar. Chapter two covers ‘Romans’ of the West—the Hispano-Romans—who appear in John of Biclar’s Chronicle, a hagiographical Life, and civil and canon law. Chapter three discusses the use of ‘Goth’ as an ethnic descriptor, a religious identifier, and a political term. Chapter four begins the Gaul section with an examination of Gregory of Tours’ writings, showing that he wrote with a Roman mindset. Chapter five illustrates that Gregory’s contemporary, Venantius Fortunatus, selected ethnic labels like ‘Roman’ and ‘barbarian’ in his poems as rhetorical tools to allude and flatter. Chapter six shows how Fredegar, in the seventh century, employed ‘Frank’ as a political term more than his predecessors had, suggesting a change in mindset. Chapter seven confirms this change in hagiographical texts across the two centuries. Chapter eight examines the contemporary expectation that separate law codes should be written for each ethnic group and concludes that, while this encouraged ethnic diversity, it did not prevent individuals from identifying with the Franks politically. By distinguishing among different modes of identification these ethnonyms represented, we see that changes in political language facilitated changes in more traditionally ethnic language, and the shift from ‘Roman’ to other ethnic identities.
Black candidates facing white electorates
Keywords: Deracialisation
racial campaign strategies
black electoral politics

It has long been assumed that when African American candidates compete in majority-white election environments, they adopt a 'deracilaised' campaign model that discards their racial identity in order to win white support. This paper finds that the ‘deracialised’ campaign model is conceptually limited and not substantiated empirically. The thesis proposes three alternative models of racial appeal, which acknowledge the ability of black candidates to preserve black racial identity while appealing to whites for support. These models are applied in case studies of several significant senatorial campaigns (Brooke 1966, Gantt 1990, Braun 1992, Steele 2006, Ford 2006), which have been sourced using newspaper articles, television and radio advertisements, printed campaign literature, internal campaign documents, opinion polls, demographic data, and fifty interviews with candidates and campaign staff.
ASKNet: automatically creating semantic knowledge networks from natural language text 
Keywords: ASKNet
large scale knowledge acquisition
semantic network

This thesis details the creation of ASKNet (Automated Semantic Knowledge Network), a system for creating large scale semantic networks from natural language texts. Using ASKNet as an example, we will show that by using existing natural language processing (NLP) tools, combined with a novel use of spreading activation theory, it is possible to efficiently create high quality semantic networks on a scale never before achievable.
The ASKNet system takes naturally occurring English text (e.g., newspaper articles), and processes them using existing NLP tools. It then uses the output of those tools to create semantic network fragments representing the meaning of each sentence in the text. Those fragments are then combined by a spreading activation based algorithm that attempts to decide which portions of the networks refer to the same real-world entity. This allows ASKNet to combine the small fragments together into a single cohesive resource, which has more expressive power than the sum of its parts.
Systems aiming to build semantic resources have typically either overlooked information integration completely, or else dismissed it as being AI-complete, and thus unachievable. In this thesis we will show that information integration is both an integral component of any semantic resource, and achievable through a combination of NLP technologies and novel applications of spreading activation theory. While extraction and integration of all knowledge within a text may be AI-complete, we will show that by processing large quantities of text efficiently, we can compensate for minor processing errors and missed relations with volume and creation speed. If relations are too difficult to extract, or we are unsure which nodes should integrate at any given stage, we can simply leave them to be picked up later when we have more information or come across a document which explains the concept more clearly.
ASKNet is primarily designed as a proof of concept system. However, this thesis will show that it is capable of creating semantic networks larger than any existing similar resource in a matter of days, and furthermore that the networks it creates of are sufficient quality to be used for real world tasks. We will demonstrate that ASKNet can be used to judge semantic relatedness of words, achieving results comparable to the best state-of-the-art systems.
Extrusion processing of chocolate crumb paste
Keywords: Shear Wave Rheometry
Pastes
Thermogravimetric Analysis
Cone Penetrometry
Food Engineering
Twin Screw Extrusion
Multiphoton Microscopy
Mixing Analysis
Foods

This project considers the co-rotating twin screw extrusion of a confectionery paste comprising powdered proteins, sugars, water and fats. As is the case with many food industry products, this process has been developed experimentally with little quantitative understanding of how variations in processing conditions influence the formation of the extrudate. A variety of techniques have therefore been developed to characterise and quantify the dispersive mixing, distributive mixing and rheological flow properties of this complex, multiphase, viscoelastic, unstable material. These techniques have then been utilised in a pilot plant extruder study of the mechanics of mixing and paste formation during extrusion, considering the influence of both processing conditions and screw profile. The internal evolution of paste microstructure has been successfully tracked along the length of screw profile using dead-stop extractions of the screws.
A rigorous off-line assessment of shear yield strength behaviour using cone penetrometry has shown the use of conventional off-line rheometers to be unviable due to rapid post extrusion hardening. This highlighted the need for an in-line rheological measurement technique for continuous extrusion analysis where the extruded material is severely time dependent and not extractable. In pursuit of this, a novel arrangement of bender elements is proposed and trialled, to rapidly characterise material parameters of viscoelastic pastes. A second technique looking to extend the application of shear wave interface reflection to multiphase pastes is also trialled.
A novel analysis of thermogravimetric data (TGA) has generated a viable index of distributive mixing, suitable for use on complex multi-component materials where thermal decomposition temperatures of the components are not well defined. Quantitative image analysis of pastes using scanning electron microscopy (SEM), optical microscopy protein staining and a novel application of multiphoton microscopy (MPM) have been used to visualise paste microstructure and quantify dispersive mixing.
From the pilot plant extruder study, the application of these techniques was successful in mapping the evolution of paste mixing and the resulting microstructure, as well as identifying key differences between pastes mixed by twin screw extrusion and batch mixing.