VictorJuiz/thesis huggingface dataset:
Neuroanatomical screening and analysis of transgenic and ENU induced mutagenised mice

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.

Keywords: gene mapping
KO
CNS development
neuroanatomy
Intellectual disability
brain development
ENU
mental retardation
Advisor: Flint, J
Selection along the HIV-1 genome through the CTL mediated immune response

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.

Keywords: MHC
phylodynamics
HIV
HLA
HIV-1
escape
selection
CTL
Advisor: McVean, G
McLean, A
Electron spin echo envelope modulation spectroscopy of radical pairs in photosynthetic bacteria

Electron spin echo envelope modulation (ESEEM) spectroscopy is widely used to study the radical pairs created during the primary steps of photosynthesis. In this thesis the analysis of ESEEM spectra is improved, and some new applications and variations of this experiment suggested.
Experimental spectra from species such as P+Q-A, the secondary radical pair formed in the reaction centre of the bacterium Rhodobacter sphaeroides, give information about the exchange and dipolar couplings between the radicals. The model used to analyse the data affects the results; this thesis suggests two improvements. First, the effect of anisotropic hyperfine couplings in the radicals is considered by the addition of a single spin-1/2 nucleus to the model. This approach suggests that previous models neglecting the effect of nuclei may have been slightly in error. Secondly, several model fittings are performed in the time domain. This approach avoids the Fourier transformation to the frequency domain so that experimental dead-time does not corrupt the data. An excellent fit to experimental data is found with a model containing one spin-1/2 nucleus on each radical. The hyperfine coupling parameters resulting from the fit are consistent with independent experimental results.
Use is made of the method of Cramér-Rao lower bounds to assess the precision to which experimental parameters are determined from a time domain curve fitting. It is shown that the lower bounds may also be used to determine the optimum sampling strategy for the experiment.
An example is given of the novel use of ESEEM to determine the distance between the radicals in the strongly coupled, uncorrelated radical pair Q-AQ-B ESEEM has not yet been used for this purpose, and the simulated spectra produced here indicate that the experiment could be used to evaluate the dipolar coupling and hence the inter-radical distance.
This thesis considers the possibility of performing ESEEM at higher frequencies than are usually considered. Calculations show that the increased resolution of the g-tensors allow an experiment performed at the W-band frequency of 95 GHz to make a correlation between the relative orientations of the radicals and the dipolar axis, information which has previously been unavailable from a single experiment.
Thomas Traherne's view of language in Restoration England

The aim of this thesis is to demonstrate that the seventeenth-century religious writer Thomas Traherne an individual who is almost never included in philological enquiries was aware of linguistic issues and added his own unique view to the debatesoftheage. Theprojectisdividedintofourmainchapters. ChapterI, "Traherne's Word Definitions," analyzes Traherne's word definitions and places him withinthecontextofphilosophicallanguagemovements. Ifocusuponhisunpublished CommentariesofHeaven,alargeencyclopediawhichpurportstoopen"TheMysteries ofFelicitie"anddefine"AllThings"asobjectsofhappiness. Despitetheidentification of this manuscript in 1982, much of Traherne scholarship ignores its existence. Chapter n, "Language and the Fall," investigates Traherne's view of prelapsarian speech. It discusses notions of Adam's language, the dumbness of infants, the Tower of Babel, and the way in which these are all sites of linguistic "falls." Chapter in, "Silence in Traherne's Writings," looks at the role of silence in religious practice, politics,andself-identity. AttimesTrahernecelebratessilenceasaspecialincubatory condition which nurtures the individual and blocks out the nefarious forces of language. Atothertimeshedescribesitasdormantandsterile. Thechapteroffersan explanationastowhyhefluctuatesbetweentheseextremes. ChapterIV,"Traherne and the Seventeenth-Century Debate Over Metaphor," analyzes the conformist and nonconformist debate over metaphor which was indicative of deep theological and political controversies of the time. My Epilogue offers a discussion of Traherne's manuscriptTheCeremonialLaw,aworkrecentlydiscoveredin1996. InmythesisI define Traherne's theological and linguistic views, while at the same time I call attention to the manuscripts Commentaries ofHeaven and The Ceremonial Law, and their crucial position in the Traherne canon.
Contextuality and noncommutative geometry in quantum mechanics

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.

Keywords: functional analysis
contextuality
quantum mechanics
quantum physics
k-theory
noncommutative geometry
operator algebras
Advisor: Abramsky, S
Coecke, B
Conceptual Art: What is it?

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.

Keywords: Conceptual Art
philosophy
aesthetics
Advisor: Stock, K
A Functional and Monadic Proof Assistant for Streams

Streams, which are infinite sequences of elements, are defined by a coinductive datatype and operations on streams are corecursive pro­grams. Equations that define streams, under light restrictions, have a unique solution. This project presents the discussion and imple­mentation of a proof assistant that supports this proof method. The tool is implemented in the purely functional language Haskell and makes extensive use of monads. The emphasis of the project is pla­ced on simplicity, clarity and terseness.
Distributed representations for compositional semantics

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.

Keywords: deep learning
compositional semantics
natural language processing
Advisor: Pulman, S
Blunsom, P
From Romans to Goths and Franks:  ethnic identities in sixth- and seventh-century Spain and Gaul

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.

Keywords: Identity
Medieval History
Ethnicity
Advisor: Wickham, C
Ward-Perkins, B
Black candidates facing white electorates

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.

Keywords: Deracialisation
racial campaign strategies
black electoral politics
Advisor: King, D
The artistic relationship between John Ruskin and Dante Gabriel Rossetti

This is the first single study of the relationship between John Ruskin and Dante Gabriel Rossetti, and the first to claim a similarity between their Aesthetic ideas. The assumption that Rossetti merely tolerated Ruskin for the sake of his patronage has discouraged the search for any significant intellectual exchange. No previous explanation has been sought for Ruskin's insistence, despite even Rossetti's opposition, that Rossetti was the intellectual leader of the Pre-Raphaelite Movement. This analysis reveals that Ruskin favoured Rossetti's art for qualities which he is not usually held to have admired in Pre-Raphaelitism, and which he began to emphasise soon after meeting Rossetti.
Although Rossetti's reputed indifference to Ruskin is partly the result of the one-sided impression afforded by the imbalance of the extant correspondence it is also because all previous accounts of the relationship have been selective and have therefore perpetrated a superficial impression of conflict. A comprehensive and detailed examination of the correspondence has revealed that the particular disagreements were made possible by a fundamental sympathy. The relationship which emerged seems to have been, contrary to prevailing opinion, initiated by common aims, sustained by mutual professional respect, and dissolved by developing ideological differences.
Having established the possibility of mutual influence between Ruskin and Rossetti, the thesis analyses the common theory of creativity underlying the work produced during their ten-year friendship. There follows a discussion of two aspects of Rossetti f s creative practice towards which Ruskin showed unequalled sensitivity, presumably as a result of his own artistic preoccupations: the Symbolic or Grotesque power, and the reliance upon Memory. Ruskin's collection of Rossettis;- is discussed, and an explanation offered for the apparent discrepancy between his public and private opinions of Rossetti's work. Finally it is claimed that Rossetti's affinity with Ruskin modifies his links with Aestheticism. This study hopes not only to justify the analysis of the Aesthetic ideas common to Ruskin and Rossetti, but also to consider its implications for both Pre-Raphaelitism and Aestheticism.

Advisor: Richards, B
ASKNet: automatically creating semantic knowledge networks from natural language text 

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.

Keywords: ASKNet
large scale knowledge acquisition
semantic network
Advisor: Clark, S