VictorJuiz/thesis huggingface dataset:
Cell fate mechanisms in colorectal cancer
Keywords: mathematical biology
intestine
colorectal cancer
Notch
cancer modelling
computational biology
gut
Wnt

Colorectal cancer (CRC) arises in part from the dysregulation of cellular proliferation, associated with the canonical Wnt pathway, and differentiation, effected by the Notch signalling network. In this thesis, we develop a mathematical model of ordinary differential equations (ODEs) for the coupled interaction of the Notch and Wnt pathways in cells of the human intestinal epithelium. Our central aim is to understand the role of such crosstalk in the genesis and treatment of CRC.
An embedding of this model in cells of a simulated colonic tissue enables computational exploration of the cell fate response to spatially inhomogeneous growth cues in the healthy intestinal epithelium. We also examine an alternative, rule-based model from the literature, which employs a simple binary approach to pathway activity, in which the Notch and Wnt pathways are constitutively on or off. Comparison of the two models demonstrates the substantial advantages of the equation-based paradigm, through its delivery of stable and robust cell fate patterning, and its versatility for exploring the multiscale consequences of a variety of subcellular phenomena.
Extension of the ODE-based model to include mutant cells facilitates the study of Notch-mediated therapeutic approaches to CRC. We find a marked synergy between the application of γ-secretase inhibitors and Hath1 stabilisers in the treatment of early-stage intestinal polyps. This combined treatment is an efficient means of inducing mitotic arrest in the cell population of the intestinal epithelium through enforced conversion to a secretory phenotype and is highlighted as a viable route for further theoretical, experimental and clinical study.
An LFG approach to Old English constituent order
Keywords: Old English
constituent order
lexical-functional grammar
syntax
word order

Old English (OE) differs from Present Day English (PDE) in many ways although the most noticeable is perhaps consituent order. Many generative analyses from van Kemenade (1987) to Pintzuk (1999) have sought to explain Old English word order, but no purely transformational account has successfully explained the data. In this thesis, I show how the multi-projection architecture of Lexical-Functional Grammar (LFG) can explain the data in a way unavailable to transformational accounts. While the thesis treats several different areas of grammar, there are consistent themes that emerge throughout. I will first survey the basic data that an analysis of Old English should seek to explain. This will be the focus of of Chapter 1. From there, I will consider previous analyses of OE including head-first accounts, head-final accounts, the competing grammars account, and Clark’s 2004 OT-LFG analysis in Chapter 3. Chapter 4 will introduce the basics of LFG with specific reference to Old English. The main body of the paper will focus on elements of my own lexical-functional analysis of Old English, which has been developed and tested using XLE (Crouch et al., 1998). Through the interplay of the f-structure and c-structure, LFG improves our understanding of OE syntax. Chapter 5 builds upon Clark (2004) by proposing a novel hierarchical verb cluster. Chapter 6 offers a discourse-based account of OE constituent order within the LFG framework. And Chapter 7 points the way towards an improved formal analysis of word order freezing in LFG. My conclusion offers final thoughts and directions for future research.
Although this project grew out of a desire to analyze Old English systematically and without stipulation, it has largely become an effort to develop and analyze the relationships between the multiple projections available in LFG, specifically the effects of these relationships on the constituent structure. Besides just offering a fascinating laboratory for testing the bonds that hold together various parts of syntactic structure, Old English is an important language to study for its diachronic implications. If we can develop a coherent picture of Old English syntax and understand how and why consitutents get ordered in OE in the way that they do, we are a step closer to understanding how and why the language has changed in the way that it has. For example, it is not insignificant that the verb cluster I propose in Chapter 5 is rare in Middle English and vanishingly rare by Shakespeare’s time. In the space available in this thesis, I will be unable to delve too deeply into these diachronic considerations. But I believe that much of what is presented here is essential to that project and can point to exciting new directions in diachronic syntax and ultimately contribute to a clearer picture of language change. And language change is a powerful window into the way that language works as a whole.
Compound shock waves and creep behaviour in sediment beds
Keywords: clay
consolidation

This research is a theoretical, experimental and numerical study of the one-dimensional deformation of suspensions. The study is focussed on the transition between sedimentation and consolidation, and creep during soil consolidation. In the literature, sedimentation, traditional large strain consolidation and creep are explored independently. The theory of sedimentation has been derived in parallel with the mathematical description of shock waves. The large strain consolidation theory of Gibson et al. (1981) has been adopted, and attention is given to the material properties of compressibility and permeability. Traditionally creep has been studied on thin samples, and a review is given to identify parallels with creep behaviour of the thick samples studied here. The experimental work was carried out in the laboratory using settling column tests. During the sedimentation stage, when the soil particles are fluid supported, shock waves were monitored and tracked by means of an X-ray absorption technique to allow for the calculation of experimental flux functions. Settling column experiments on different natural soils have been performed to study the consolidation behaviour by means of the measurement of pore water pressure and X-ray density measurements. An in-depth study of the development of effective stress has been performed to quantify the creep behaviour of the soils studied in a strain rate surface. The sedimentation equation is classified as a hyperbolic partial differential equation. In this kind of equation, discontinuities can propagate, and standard solution methods, eg finite differences, fail to give adequate results. For this reason codes have been developed using the finite volume method (FVM) to solve the sedimentation equation numerically. A standard numerical code has been developed for the solution of the large strain consolidation equation, while for the unified sedimentation-consolidation model the finite volume method (FVM) has been used. The shock waves monitored in the experiments are successfully predicted by the sedimentation model using experimentally derived flux functions. This study made it possible to formulate a physically and mathematically correct definition of the transition from sedimentation to consolidation. The strengths and weaknesses of the traditional large strain consolidation model have been identified by means of an international Class A prediction seminar. A new unified sedimentation-consolidation model is proposed using a flux function, a permeability relationship and a strain rate surface as material functions. Successful predictions of experiments have been performed, showing the transition from sedimentation to consolidation and the inclusion of creep.
Silver nanowire transparent conductors for quantum dot photovoltaics
Keywords: quantum dot
photovoltaics
nanowire

This thesis studies the application of silver nanowire transparent conductors in PbS quantum dot photovoltaics.
Silver nanowires were synthesized using a colloidal method and characterized using scanning electron microscopy. Nanowires were deposited on glass substrates by a stamp transfer process to generate a low density continuous network of conductive nanowires. This resulted in a highly conductive and transparent film appropriate for optoelectronic applications. Nanowire synthesis, deposition, and processing were optimised to produce transparent conductors suitable for thin film photovoltaics.
These nanowire films were used to fabricate lead sulphide (PbS) colloidal quantum dot solar cells. In this structure, p-type PbS quantum dots form a junction with a n-type ZnO nanoparticle layer. A variety of fabrication and processing treatments were developed in order to reduce short-circuiting of devices and to enhance cell performance. Moderate nanowire density, improved ZnO adherence, slight device aging, and increased PbS film thickness proved to result in the highest quality devices. The champion device developed in this thesis achieved a power conversion efficiency of 2.2%.
The signature of a rough path: uniqueness
Keywords: signature
rough paths
G-Brownian
Jordan curves
nonlinear heat flow

The main contribution of the present thesis is in two aspects.
The first one, which is the heart of the thesis, is to explore the fundamental relation between rough paths and their signatures. Our main goal is to give a geometric characterization of the kernel of the signature map in different situations. In Chapter Two, we start by establishing a general fact that a continuous Jordan curve on a Riemannian manifold can be arbitrarily well approximated by piecewise minimizing geodesic interpolations which are again Jordan. This result enables us to prove a generalized version of Green’s theorem for planar Jordan curves with finite p-variation 1 ≤ p < 2, and to prove that two such Jordan curves have the same signature if and only if they are equal up to reparametrization. In Chapter Three, we investigate the problem for general weakly geometric rough paths. In particular, we show that a weakly geometric rough path has trivial signature if and only if it is tree-like in the sense we will define later on. In Chapter Four, we study the problem in the probabilistic setting. In particular, we show that for a class of stochastic processes, with probability one the sample paths are determined by their signatures up to reparametrization. A fundamental example is Gaussian processes including fractional Brownian motion with Hurst parameter H > 1/4, the Ornstein-Uhlenbeck process and the Brownian bridge.
The second one is an application of rough path theory to the study of nonlinear diffusions on manifolds under the framework of nonlinear expectations. In Chapter Five, we begin by studying the geometric rough path nature of G-Brownian motion. This enables us to introduce rough differential equations driven by G-Brownian motion from a pathwise point of view. Next we establish the fundamental relation between rough (pathwise theory) and stochastic (L2-theory) differential equations driven by G-Brownian motion. This is a crucial point of understanding nonlinear diffusions and their generating heat flows on manifolds from an intrinsic point of view. Finally, from the pathwise point of view we construct G-Brownian motion on a compact Riemannian manifold and establish its generating heat flow for a class of G-functions under orthogonal invariance. As an independent interest, we also develop the Euler-Maruyama scheme for stochastic differential equations driven by G-Brownian motion.
The ethics of Otium: pastoral, privacy and the passions 1559-1647.
Keywords: Pastoral
Comus
Milton
Montemayor
Melancholy
Gomberville
Suffocation of the Mother
Otium
Sidney

This thesis studies the literary genre of pastoral between 1559 and 1647. The first of these dates is that of a work that changed the course of early modern pastoral, Montemayor’s Diana; and the second marks the English translation of Gomberville’s Polexandre, a pastoral romance which exemplifies the shifts in cultural values that re-shaped Montemayor’s model over the century that followed its publication.
My study focusses on the significance for this genre of the ethical quality known to classical moral philosophy as otium, and translated in early modern English by words such as peace, leisure, retirement, ease and idleness. Otium has strong historical associations with the tradition of Virgilian pastoral. Its significance in early modern pastorals, however, has been largely overlooked, despite the fact that early modern interest in otium had been revitalised by the rediscovery of some of its most important classical discussions. This renewed interest in otium, I argue, was essential to the development of early modern pastoral.
My argument challenges both old and new critical perspectives on pastoral, and engages with key issues in early modern culture which literary scholars have neglected. Older studies understood pastoral otium simply as idyllic retreat; newer ones accept this view, but argue against its privileged and quietist political implications, preferring to concentrate on the tradition of interpreting pastoral as political allegory. Otium’s principal connotations, however, were neither quiet nor idyllic. Though its restorative qualities were sometimes cautiously acknowledged, otium’s potential to corrupt was ever-present, and affected a range of areas including privacy, politics, moral psychology and medicine. When people wanted to imaginatively explore those effects, I argue, pastoral was the genre to which they were most likely to turn. Listening to what pastorals say about otium can play an important role in reconstructing this crucial and misunderstood aspect of early modern culture.
Re-conditioning England: George Orwell and the social problem novel
Keywords: Englishness
England
George Orwell

"What can the England of 1940 have in common with the England of 1840? But then, what have you in common with the child of five whose photograph your mother keeps on the mantelpiece? Nothing, except that you happen to be the same person".
This comes from George Orwell's wartime pamphlet The Lion and the Unicorn in which, according to Tosco Fyvel, he sought "to identify himself with England in its finest hour". Orwell offered a more prosaic justification – "I don't share the average English intellectual's hatred of his own country" – in one of his regular "London Letters" to the American Partisan Review and from these three sources a complex constellation of questions emerges. The issue at stake is Orwell's relationship with his country and it involves ideas of identity, history, ownership, love, hatred, community and, crucially, his position as spokesperson. Drawing and expanding upon work on Orwell and Englishness, focusing on Orwell's often overlooked originality as a novelist and challenging Raymond Williams' influential account in Orwell and Culture and Society, "Re-Conditioning England" seeks to negotiate a path through this complex of questions. This path, as the title and opening quotation imply, is guided by the past and by Orwell's engagement with the mid-nineteenth century mode of social realism. It is informed by Williams' conception of the novel as a "knowable community" and Benedict Anderson's of the nation as an "imagined community". A chronological and contextual study, the thesis pays attention, throughout, to both when and where Orwell wrote. It places his work within contemporary debates over the status of Charles Dickens, poetry, language and the nation to the end of arguing: in his engagement with contemporary social-problems, Orwell first consciously updates and then self-consciously critiques the nineteenth-century genre of condition-of-England writing.
Miscarriages of justice: a definition
Keywords: wrongful convictions
criminal justice
evidence
miscarriages of justice
appeals

To date, debate and discussion about ‘miscarriages of justice’ has occurred without any firm understanding of what the term does, or should, signify. This thesis argues that in light of the significant conceptual distinctions which must be drawn between the numerous flaws and injustices which can arise at each stage of the criminal justice system, the best approach is to aim for a principled and consistent functional definition. The definition offered here is functional in that it provides a means by which attempts to identify and remedy miscarriages of justice can be analysed.
Key to the proposed definition is the act of convicting an individual of a criminal offence. This act is central to the criminal process, and therefore central to any meaningful account of miscarriage of justice. Furthermore, it is an act which is conceptually distinct from any other activity in the criminal justice system, and one which is of such significance that its improper imposition is of such concern that it warrants consideration in isolation.
In a criminal justice system which is premised on the fair and equal treatment of its citizens as moral actors, there are three distinct circumstances in which a conviction cannot stand. The first two concern themselves with situations where an individual is either innocent, or has been put at unfair jeopardy of conviction in circumstances where they may not be guilty. That is: when the individual is factually innocent of the crime of which they have been convicted or when there has been a material breach of a due process protection provided by positive law. The final situation where a conviction ought not to be upheld is not one in which the innocence of an individual is in doubt, but rather where the integrity of the criminal justice system as a whole is impugned.
Other definitions are both possible and plausible, as the distinctions drawn in order to arrive at this point are contestable. However, taken together, these three categories provide a consistent and principled account of the matters which an entity charged with reviewing criminal convictions ought to concern themselves with, and therefore a tool for analysing their success or failure.
Starving for their art: hunger, modernism and aesthetics in Samuel Beckett, Paul Auster and J. M. Coetzee
Keywords: Knut Hamsun
modernism
hunger in literature
Paul Auster
Franz Kafka
aesthetics
J. M. Coetzee
Samuel Beckett

As literary modernism was emerging in the late nineteenth and early twentieth centuries, a number of its most important figures and precursors began to talk about their own writing as a kind of starvation. My doctoral thesis considers the reasons for and development of this previously little-explored trope, arguing that hunger becomes a focal point for modernism’s complex relationship to aesthetic autonomy. I identify a specific tradition of writers, beginning in the nineteenth century with proto-modernists such as Melville and Rimbaud, flourishing in the pivotal figures of Knut Hamsun, Franz Kafka and Samuel Beckett, and expiring with modernist-influenced contemporary writers such as Paul Auster and J. M. Coetzee. Although these writers are avid readers and devoted disciples of one another, mine is the first study to read them alongside one another as a coherent literary tradition. Reading them in this way, I am able to trace the development of the ‘art of hunger’ as a locus for a crisis in aesthetic autonomy that spans the twentieth century.
I develop this line of argument in two phases. In the first, I trace the emergence of an art of hunger out of modernist engagements with philosophical aesthetics and its notions of aesthetic autonomy. Readings of the “art of hunger” in Herman Melville, Arthur Rimbaud, Knut Hamsun, Franz Kafka and Samuel Beckett’s post-war work reveal that starvation carries autonomy to an extreme and hyper-literal endpoint, revealing both its desirability as an aesthetic ideal and the impossibility of art’s complete autonomy from the body, the market or the social dimensions of language.
In the second phase, I consider how this trope has animated later twentieth-century engagements with modernism. For authors writing in the aftermath of modernism, hunger provides a way of considering new complications to aesthetic autonomy in the light of both their debt to modernism and their specific historical circumstances. In this light, I consider three different extensions of the modernist art of hunger: its absorption into high formalism in Beckett’s late prose; its collapse in the face of an emerging concern with the social in Paul Auster; and its transformation into an ethical aesthetics of food taboos, restriction and asceticism in J. M. Coetzee.
Stochastic population oscillators in  ecology and neuroscience
Keywords: stochastic processes
mathematical neuroscience
mathematical ecology
dynamical systems

In this thesis we discuss the synchronization of stochastic population oscillators in ecology and neuroscience. Traditionally, the synchronization of oscillators has been studied in deterministic systems with various modes of synchrony induced by coupling between the oscillators. However, recent developments have shown that an ensemble of uncoupled oscillators can be synchronized by a common noise source alone.
By considering the eﬀects of noise-induced synchronization on biological oscillators, we are able to explain various biological phenomena in ecological and neurobiological contexts - most importantly, the long-observed Moran eﬀect. Our formulation of the systems as limit cycle oscillators arising from populations of individuals, each with a random element to its behaviour, also allows us to examine the interaction between an external noise source and this intrinsic stochasticity. This provides possible explanations as to why in ecological systems large-amplitude cycles may not be observed in the wild. In neural population oscillators, we were able to observe not just synchronization, but also clustering in some pa- rameter regimes.
Finally, we are also able to extend our methods to include coupling in our models. In particular, we examine the competing eﬀects of dispersal and extrinsic noise on the synchronization of a pair of Rosenzweig-Macarthur predator-prey systems.
We discover that common environmental noise will ultimately synchronize the oscillators, but that the approach to synchrony depends on whether or not dispersal in the absence of noise supports any stable asynchronous states. We also show how the combination of correlated (shared) and uncorrelated (unshared) noise with dispersal can lead to a multistable steady-state probability density. Similar analysis on a coupled system of neural oscillators would be an interesting project for future work, which, among other future directions of research, is discussed in the concluding section of this thesis.