VictorJuiz/thesis huggingface dataset:
Quantifying plasma membrane protein reduction during immune activation using mass spectrometry

The communication of immune cells through cell surface receptors is crucial for maintaining immune homeostasis, coordinating the immune response and pathogen clearance. The interaction of cell surface receptors with their cognate ligands is dependent on a key-lock principle and therefore only allows binding of partners in their correct conformational state. Reductive cleavage of labile disulfide bonds is a post-translational modification, capable of controlling protein function by mediating a conformational change. Activation of the immune system leads to the secretion of thiol isomerases that catalyse labile disulfide bond reduction and thereby are able to modulate protein function. A bioinformatics study and a mass spectrometry based screen have shown that many different plasma membrane proteins potentially contain labile disulfide bonds. To identify proteins with biologically relevant labile disulfide bonds it is necessary to quantify the reduction occurring as it is expected that only proteins that are reduced to a substantial amount affect cellular function.
In this study, a mass spectrometry based method to screen for proteins with labile disulfide bonds and quantify their reduction in primary cells was developed. It was then applied to study the plasma membrane redox proteome during immune activation and identified several proteins, mainly activating (CD132, gp130) and adhesion (integrins, ICAM1 and CD44) molecules, that are reduced to a major degree during immune activation. Furthermore, functional studies on the shared cytokine receptor gp130 showed that thioredoxin reduction inhibits IL-6 signalling.
These observations in conjunction with the literature suggest that labile disulfide bond reduction during immune activation is a mechanism to prevent over-activation of the immune system and excessive accumulation of leukocytes in sites of inflammation. Presenting a method to identify altered redox control of proteins in diseases such as autoimmunity provides the basis for the rational design of novel redox drugs.

Advisor: Barclay, A
Metcalfe, C
Prophetic rhetoric in the early Stuart period

This is a study of the political prophecy in England in a period delimited by the accession of King James I (1603) and the end of the Interregnum (1660). It combines the analysis of hitherto obscure manuscript texts with that of printed works to provide a nuanced account of the uses and reception of prophecies in this period.
Chapter One (which focuses on the first decade of James’s reign) and Chapter Two (which covers the period 1613-19) approach the analysis of dramatic treatments of political prophecy through the study of prophecy both as a rhetorical buttress to the Jacobean state and as a protest genre. Attentive to the elite bias of the legal documents wherein allegedly oppositionist uses of prophecy are recorded, these chapters heed the counsel of historians who have found literary scholars insufficiently suspicious of the rhetoric of these materials. A focus on dramatic texts, neglected by the historians, reveals that Jacobean playgoers were encouraged to regard both official prophetic rhetoric and official rhetoric about prophecy with scepticism.
Chapter Three considers how native and continental prophetic traditions were expanded and repurposed in England around the beginning of the Thirty Years’ War, when belief in the purportedly inspired status of prophecies was rare but recognition of their utility as a vehicle for political discussion was nonetheless widespread.
Chapter Four explores the adaptation and tendentious exposition of medieval, sixteenth-century, and Jacobean manuscript prophecies in printed propaganda for both the royalist and parliamentarian causes in the mid-seventeenth century.
This study of literary and archival sources finds that previous scholarship has overestimated the extent of popular faith in the authenticity of allegedly ancient and inspired prophecies in the early Stuart period. The longevity of purported prophecies, it concludes, was ensured through the recognition, appreciation, and exploitation of their rhetorical affordances.

Keywords: prophecy in literature
politics and literature
James I, King of England, 1566-1625
Charles I, King of England, 1600-1649
Lilly, William, 1602-1681
Shakespeare, William, 1564-1616
prophecy
Advisor: Kean, M
A study of superplasticity in Ti-6Al-4V: characterisation, modelling and applications

Superplasticity is vital in many industries - medical, defense, aerospace, transport and sports amongst others -- for the fabrication of metallic components of complex geometry. The inherent peculiarity of the effect has kept theorists fascinated for many years. But significant controversy exists concerning the exact deformation mechanisms which are operative. In particular, precise details of the accommodation mechanics - whether those are diffusion, dislocation-accommodated, a combination of both or some sort of cooperative grain boundary sliding - are still matter of debate. In this thesis, superplasticity is first experimentally studied under constant strain-rate tensile conditions; this has allowed the regime of superplasticity to be pinpointed and it forms the basis of the computational material model. In addition, a method for the rapid quantification of superplastic properties using sub-scale specimens is presented: the approach is validated and then applied to a series of different titanium alloys. Results allowed to assess critically the main factors influencing superplasticity in titanium alloys. For the elucidation of the accommodation mechanisms accompanying grain boundary sliding during superplasticity, surface observations are carried out. For this, an in-situ scanning electron microscope testing module is employed. Different regimes of the phenomenon in the Ti-6Al-4V alloy are targeted: results provided important details of the mechanics at the grain level. For design purposes, this understanding is translated into validated material laws which are accurate and which capture the relevant phenomena. Microstructurally explicit material laws are proposed based upon the micromechanical modes of deformation which are shown to be operating with aim of incorporating those into the finite element analysis of superplastic forming. In the final part of the thesis, modelling is used to simulate an industrially-relevant manufacturing process which exploits superplasticity: the construction of hollow wide-chord fan blades which are of significant importance for the aerospace sector. The modelling is used to highlight the importance of microstructurally-based models and their influence on processing optimisation.

Advisor: Reed, R
Complicating articulation in narrative film: tracing the relationship between inarticulate form and character

This thesis explores the relationship between film form and character expression, both of which are seen as articulated structures, that is utterances in which separable parts operate cooperatively to create meaning. The specific films examined present characters who struggle to express themselves. These inexpressive characters are combined in each case with a disrupted form which displays its own many-jointed structure. The thesis argues that the dynamic relationship between inarticulacies of character, narrative, and form generates an indeterminate dialectic. The unresolved relationship between parts and whole (reminiscent of a complex mosaic structure) complicates the process of reading for univocal meaning. The operation of this dual inarticulacy is discussed in Chapter One. Each subsequent chapter is devoted to a single film and a particular example of formal disjuncture: contrapuntal narrative levels, clashing styles, discontinuous editing, bricolage, the dislocation of genre signifiers from conventional meanings, and intermedia. The films discussed at length in connection with these theories are: 'Journal d'un curé de campagne' (1951); 'Germania anno zero' (1948); 'Belle de Jour' (1967); 'Distant Voices, Still Lives' (1988) and 'The Long Day Closes' (1992); 'Meek's Cutoff' (2010); 'The Pillow Book' (1996).

Keywords: Genre
Discontinuity
Post-structuralism
Surrealism
Intermedia
Indeterminacy
Neo-realism
Advisor: Klevan, A
Ambitwistor strings: worldsheet approaches to perturbative quantum field theories

Tree-level scattering amplitudes in massless theories not only exhibit a simplicity entirely unexpected from Feynman diagrams, but also an underlying structure remarkably reminiscent of worldsheet theory correlators, yet essentially algebraic. These features can be explained by ambitwistor strings - two-dimensional chiral conformal field theories in an auxiliary target space, the complexified phase space of null geodesics, known as ambitwistor space. The aim of this thesis is to explore the ambitwistor string approach to understand these structures in amplitudes, and thereby provide a new angle on quantum field theories.
In the first part of this thesis, the wide-ranging impact of ambitwistor strings on the study of tree-level amplitudes is highlighted in three developments: an extension of ambitwistor string worldsheet models to an extensive family of massless theories, emphasising the universality of ambitwistor strings for massless theories; a beautiful proof of the duality between asymptotic symmetries and the low energy behaviour of a theory, relying on the contact geometry of the ambitwistor target space; and finally a twistorial representation of ambitwistor strings in four dimensions, leading to remarkably simple formulae for scattering amplitudes in Yang-Mills and gravity with any degree of supersymmetry.
The second part of this thesis focusses on proving a conjectured ambitwistor string formula for loop amplitudes, and extending the formalism to more general theories. Remarkably, residue theorems reduce the computationally challenging ambitwistor higher-genus expressions to simple formulae on nodal Riemann spheres. This idea is developed into a widely applicable framework for loop integrands, that is shown to be applicable to both supersymmetric and non-supersymmetric theories. In the case of supergravity, this provides strong evidence for the validity of the ambitwistor string at loop level, and explicit proofs are given for non-supersymmetric theories. Notably, this leads to a proposal for an all-loop integrand for gravity and Yang-Mills.

Keywords: Ambitwistor Strings
Quantum Field Theory
Advisor: Mason, L
Unravelling haematopoietic stem cell dysfunction in isolated Del(5q) myelodysplastic syndromes

Myelodysplastic syndromes (MDS) represent a heterogeneous group of haematological malignancies. A subgroup of MDS patients are characterized by heterozygous deletion of the long arm of chromosome 5, Del(5q), as the only karyotypic abnormality. The commonly deleted region (CDR) on chromosome 5 contains approximately forty-two genes and haploinsufficiency of one or more of these genes is thought to be the basis for Del(5q) MDS pathogenesis.
The 5q deletion originates in the Hematopoietic Stem Cell (HSC) compartment and Del(5q) HSCs have a clonal advantage, outcompeting healthy HSCs in the bone marrow of patients. Although they have a competitive advantage in situ, Del(5q) HSCs perform poorly in functional stem cell assays in vitro and in vivo.
A mouse model of Del(5q) MDS, the Cd74-Nid67 model, carries a heterozygous deletion of eight genes located within the CDR. Cd74-Nid67 haploinsufficiency causes macrocytic anaemia and bone marrow dysplasia in mice. However, the impact of Cd74-Nid67 haploinsufficiency on HSC function has not previously been investigated.
The results presented, herein, demonstrate that haploinsufficiency of Cd74-Nid67 has a significant impact on HSC self-renewal and repopulation potential. Furthermore, two genes within this region, Rps14 and Rbm22, are identified as likely candidates responsible for Cd74-Nid67 HSC dysfunction. Finally, we demonstrate that Cd74-Nid67 HSC dysfunction is driven by a P53-dependent mechanism.
This study provides important insights into the mechanistic basis for disease development and propagation, which may facilitate the development of improved therapeutic avenues for Del(5q) MDS patients.

Advisor: Jacobsen, S
Applications of the virtual fields method to the mechanical behaviour of rubbers under dynamic loading

Experimental techniques for measuring the mechanical response of rubbers under dynamic loading are developed utilising the virtual fields method (VFM), to inversely identify constitutive behaviour from experimental observations. Rubbers and other ‘soft’ materials are difficult to characterize using traditional dynamic techniques such as the split Hopkinson bar: the low sound speed makes it difficult to achieve static equilibrium and the small supported forces give low signal-to-noise ratios in the experimental data. In this research, the dynamic VFM with the aid of high-speed imaging is applied to dynamic tensile experiments to resolve these difficulties. The VFM is a mathematical technique that makes use of the principle of virtual work. Manipulation of this equation enables us to remove the need for traditional force measurement, instead exploiting acceleration full-field data as a virtual load cell. Thus, the aforementioned difficulties are no longer of concern: the technique requires that the specimen is not in static equilibrium and that inertial forces are significant compared to material forces. Two dynamic tests and dynamic VFMs are developed and applied to tensile drop-weight and gas-gun driven experiments. The first uses small amplitude dynamic deformation superposed on static pre-stretching. Dynamic identifications at a number of pre-strains are collated to identify the complete nonlinear behaviour. The second utilizes a large strain amplitude of dynamic loading: one experiment characterizes the full response. Further applications of the dynamic VFM are explored in order to improve the first method and to extend the identification capability, and experiments performed at non-ambient temperatures allow a preliminary exploration of time-temperature superposition.

Advisor: Siviour, C
The mid Upper Palaeolithic of European Russia: chronology, culture history and context: a study of five Gravettian backed lithic assemblages

This thesis examines the Mid Upper Palaeolithic (MUP) of Russia (ca. 30,000–20,000 14C BP). During this time, as in the rest of Europe, the principal archaeological industry is known as the Gravettian. However, in Russia two other industries, the Streletskayan and the Gorodtsovian, are also known from the beginning of the MUP. Historically, there have been significant problems integrating the Russian MUP record with that from the rest of Europe.
The research described in this thesis concentrates on backed lithic assemblages (including Gravette points, microgravettes, other backed points and backed bladelets) from five Russian Gravettian sites: Kostenki 8 Layer 2, Kostenki 4, Kostenki 9, Khotylevo 2 and Kostenki 21 Layer 3. These are studied from an explicitly Western European theoretical perspective, using standard techno-typological methods to construct typological groupings and describe the variation between and within sites. Alongside this, new radiocarbon dates from several sites Kostenki 8 Layer 2, Kostenki 4 and Borshchevo 5) were obtained. These radiocarbon dates are critically analysed alongside published dates and unpublished dates made available to this research.
The results of the research constitute a new culture history for the Russian MUP. Each stage of the MUP is dated and described, and the uncertainties in our knowledge outlined. One new lithic index fossil is defined and two others are re-assessed. The Russian record is compared with the contemporary archaeological record elsewhere in Europe, in order to describe large-scale synchronic variation and changes through time in the homogeneity and regionalisation of material culture. The relationship between these dynamics and climate change are discussed.

Keywords: Gravettian
Kostenki-Borshchevo region
Russia
radiocarbon dating
Kostenki
chronology
Upper Palaeolithic
lithic technology
Mid Upper Palaeolithic
backed lithics
Advisor: Barton, N
Higham, T
The people’s princess:  Grayson Perry and English cultural identity

This thesis will consider the art and persona of Grayson Perry in relation to ideas of national identity. In particular, it will argue that Perry has been occupied with ideas of class and national identity throughout his career, but that these underlying concerns have often been subsumed, or obfuscated, by the foregrounding of other more obvious aspects of his work, such as his transvestism. At the centre of this thesis is the argument that Perry’s vision of England, and the purportedly ambivalent way in which he presents it, functions as a way of negotiating – and repatriating – English national identity at a time of crisis. I want to further argue, however, that this has been complicated by Perry’s self-positioning, and I propose that he has cultivated an air of subversion and transgression that has tempered the more affirmative aspects of his work. This half-subversive, half-affirmative stance allows him and his work to resonate with both those critical of the usual institutions of contemporary art – including many sections of the public and certain newspapers, tabloid and broadsheet alike – as well as the institutions themselves. This stance has implications not only for Perry’s engagement with contemporary art but for his considerations of national identity as well, enabling an enquiry into, and ultimately a restitution of, ‘Englishness’ (and, to a lesser extent, ‘Britishness’), by framing it within a rhetoric of ambivalence and diminishment rather than overt nationalism, the latter of which would have more problematic associations. Similarly, I want to suggest that it is this stance and its mediatory properties, coupled with his earlier self-positioning and his subtle but consistent foregrounding of domestic and demotic issues of national identity throughout his career, that has made Perry such a popular candidate to take on the task of reinvigorating this identity now.

Keywords: Englishness
Young British Artists
cross-dressing
cultural identity
contemporary art
Grayson Perry
Tracey Emin
transvestism
Britishness
YBAs
national identity
history of art
Apophasis, contemplation, and the kenotic moment in Anglo-Saxon literature

This thesis reveals the considerable influence of contemplation (sometimes referred to as mysticism) on Anglo-Saxon literature, manifested through the arrangement of narratives according to the theological concepts of apophasis and kenosis. This is demonstrated through a lengthy contextual discussion of the place of contemplation in Anglo-Saxon spirituality, and close analysis of four poems and a prose text.
Although English mysticism is commonly thought to start in the High Middle Ages, this thesis will suggest that this terminus post quem should instead be resituated to the Anglo-Saxon period. The first chapter seeks to reveal the centrality of contemplation to Anglo-Saxon spirituality through analysing a range of diverse material, to evidence the monastic reader borne from this culture capable of reading and composing the texts that make up the rest of the thesis in the manner suggested.
The thesis places chronologically diverse Anglo-Saxon texts in a contemplative context, with close reference to theology, phenomenology, and narrative structure, to suggest that our interpretation of them should be revised to apprehend the contemplative scheme that they advocate: to cleanse the reader of sin through inspiring penitence and kenosis (humility and emptying of one’s will) and direct the mind intellectually beyond the words, images and knowledge of the terrestrial sphere (apophasis), so as to prepare them for the potential coming of God’s grace in the form of a vision. This reading is supported by the close taxonomical resemblance of each text’s narrative structure. The thesis thus suggests that contemplation was central to Anglo-Saxon spirituality, producing an elite contemplative audience for whom certain texts were designed as preparative apparatus.

Keywords: apophasis
Anglo-Saxon literature
kenosis
mysticism
Advisor: Gillespie, V
Orchard, A
Big effects of a little sector: the structural effects of venture capital on the macroeconomy

We explore certain structural elements of venture capital investment, focusing on the role of venture capital as an asset class dedicated to technology investment. The structural role of technology as contributing to the total factor productivity is captured through the use of endogenous growth mechanisms as found in Romer (1990) and Rivera-Batiz and Romer (1991). In the first chapter, we explain certain elements of the two recessions in the first decade of the 21st century by combining these endogenous growth mechanisms with a financial accelerator in the market for production capital to capture the financial elements associated with decreased leverage after a financial crisis. In the second chapter, we assess the impact of policies in the late 1970s which largely created venture capital by encouraging technology investment to occur through debt contracts rather than equity contracts. We explain a set of stylized facts by contrasting a debt mechanism and an equity mechanism for an asset that derives its value from returns to technology goods in a stochastic endogenous growth model. Our final chapter deals with the disposition of venture capitalists towards Knightian uncertainty. We show that an uncertainty-loving behavior of venture capitalists leads to a Pareto improvement in the economy. However, the magnitude of the effect of changes in disposition towards uncertainty is small, implying that bubbles in the venture capital market caused by this type of uncertainty-loving behavior should not be a great concern for investors and policy makers.

Advisor: Ellison, M