VictorJuiz/thesis huggingface dataset:
!-Logic

Equational reasoning with string diagrams provides an intuitive method for proving equations between morphisms in various forms of monoidal category. !-Graphs were introduced with the intention of reasoning with infinite families of string diagrams by allowing repetition of sub-diagrams. However, their combinatoric nature only allows commutative nodes. The aim of this thesis is to extend the !-graph formalism to remove the restriction of commutativity and replace the notion of equational reasoning with a natural deduction system based on first order logic.
The first major contribution is the syntactic !-tensor formalism, which enriches Penrose’s abstract tensor notation to allow repeated structure via !-boxes. This will allow us to work with many noncommutative theories such as bialgebras, Frobenius algebras, and Hopf algebras, which have applications in quantum information theory.
A more subtle consequence of switching to !-tensors is the ability to definitionally extend a theory. We will demonstrate how noncommutativity allows us to define nodes which encapsulate entire diagrams, without inherently assuming the diagram is commutative. This is particularly useful for recursively defining arbitrary arity nodes from fixed arity nodes. For example, we can construct a !-tensor node representing the family of left associated trees of multiplications in a monoid.
The ability to recursively define nodes goes hand in hand with proof by induction. This leads to the second major contribution of this thesis, which is !-Logic (!L). We extend previous attempts at equational reasoning to a fully fledged natural deduction system based on positive intuitionistic first order logic, with conjunction, implication, and universal quantification over !-boxes. The key component of !L is the principle of !-box induction. We demonstrate its application by proving how we can transition from fixed to arbitrary arity theories for monoids, antihomomorphisms, bialgebras, and various forms of Frobenius algebras. We also define a semantics for !L, which we use to prove its soundness.
Finally, we reintroduce commutativity as an optional property of a morphism, along with another property called symmetry, which describes morphisms which are not affected by cyclic permutations of their edges. Implementing these notions in the !-tensor language allows us to more easily describe theories involving symmetric or commutative morphisms, which we then demonstrate for recursively defined Frobenius algebra nodes.

Advisor: Coecke, B
Kissinger, A
Combining single-molecule fluorescence and single-channel recording in droplet interface bilayers

Single-channel recordings (SCR) and single-molecule Fluorescence (SMF) are invaluable tools for studying membrane proteins. Combining these two techniques would allow for structural dynamics to be correlated with function at the single-molecule level. However, the different requirements of SCR and SMF measurements present a long-standing challenge. Droplet interface bilayers (DIBs) are a model membrane system in which parallelisation of such measurements is possible using optical single-channel recording to resolve the conductance of multiple proteins simultaneously. In this project, two approaches were evaluated for obtaining simultaneous measurements in DIBs: the first sought to report on structural changes associated with a gating bacterial mechanosensitive channel, MscS; the second sought to resolve kinetics of the spontaneous β-barrel folding mechanism. For both approaches, functional, labelled protiens were produced and characterised using ensemble measurements to confirm that the state-transition of interest was accompanied by a change in fluorescent signal. Characterisation of MscS in DIBs revealed that control of lateral tension (a requirement to stimulate mechanosensitive channel gating) posed a major experimental challenge, rendering further pursuit of this candidate impossible. However in the case of β-barrel folding, the single-molecule fluorescence alone revealed a rare but fast transition from a membrane-associated unfolded to a folded state. While further work is needed to fully exploit simultaneous measurements, significant progress towards this goal is presented in this work, in particular the development of reagents, experimental procedures and analytical tools.

Keywords: ion channel
droplet interface bilayer
fluorescence spectroscopy
single-molecule
Advisor: Wallace, M
Imaging nociceptive brain activity in the newborn infant

In this thesis electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) are used to investigate the temporal and spatial patterns of noxious-evoked brain activity in newborn infants. EEG was used to investigate responses to graded intensities of experimental noxious stimulation, and evoked brain activity was compared with behavioural and spinal cord activity constituting common surrogate measures of pain in infants. Nociceptive-specific brain activity was elicited in response to all forces of experimental noxious stimulation (applied forces: 32 - 128 mN). In addition, the magnitude of the noxious-evoked response was positively correlated with the magnitude of reflex leg withdrawal, and this relationship was observed in the absence of changes in facial expression.
As fMRI had not previously been used to investigate nociceptive processing in infants at 3 Tesla, initial experiments were conducted to optimise the acquisition parameters. The results from optimisation showed that an echo time of approximately 50 ms should be used in future fMRI studies in infants. Experiments conducted alongside this optimisation used fMRI to investigate the cortical and subcortical structures activated by experimental noxious stimulation (applied forces: 32 - 128 mN) in newborn infants (0 - 11 days old). This was compared with noxious-evoked brain activity in adults (applied forces: 32 - 512 mN). Experimental noxious stimulation evoked a widespread pattern of brain activity in newborn infants that overlapped with the network of brain regions activated by nociceptive processing in adults.

Keywords: Pain
Neonates
Infants
EEG
fMRI
Brain imaging
Advisor: Slater, R
Clare, S
Symmetries in physics, metaphysics, and logic

This thesis examines the idea that when a physical theory contains symmetries, the theory should be interpreted in such a way that symmetry-related models represent the same physical state of affairs. It argues that we can best do so by drawing on analogies to ideas in philosophy of logic and language: specifically, by thinking of symmetries as a means of translating a theory into itself. It consists of six chapters, together with an introduction and conclusion.
In Chapter 1, I set up the main ideas needed to more precisely frame the question at hand: namely, the notions of symmetry, interpretation, and possibility. I make some remarks about how I take these to be connected.
In Chapter 2, I argue that isomorphic models should be interpreted as equivalent. After giving some motivations for doing so, I consider the main obstruction: how to provide an account of de re modality. I review how counterpart theory may be used to overcome this obstruction, and clarify how counterpart theory relates to other positions in the debate over modality de re.
In Chapter 3, I show that the metaphysical debate over quidditism can be made precise by drawing on notions of translation from model theory, and argue in favour of an anti-quidditist attitude towards interpreting theories. I then consider the special case of translating a theory into itself: how such a theory should be interpreted, and what reformulations of the theory such an interpretation suggests.
In Chapter 4, I turn my attention to physics. I define the notion of an internal symmetry for a theory, and argue that they may be regarded as translations from a theory into itself (in the sense of Chapter 3); and, hence, that symmetry-related models should be interpreted as equivalent. Drawing on the analogy further, I look at how the theory may be reformulated to take this interpretation into account.
In Chapter 5, I look at external symmetries. I argue, drawing on ideas from Chapters 2 and 3, that models related by external symmetries should also be interpreted as equivalent. I discuss how implementing this interpretational lesson bears on finding the spacetime structure appropriate to a theory.
In Chapter 6, I consider a specific external symmetry: the accelerative symmetry of Newtonian gravitation. I show that one can reformulate the theory to take this into account, setting gravitation on a spacetime structure that has absolute rotation but no absolute acceleration.

Keywords: Symmetries
Equivalence
Translation
Advisor: Wallace, D
Pooley, O
Graphs of algebraic objects

A rack on [𝑛] can be thought of as a set of permutations (𝑓𝑥)𝑥 ∈ [𝑛] such that 𝑓(𝑥)𝑓y = 𝑓y-1𝑓x𝑓y for all 𝑥 and y; additionally, a rack such that (𝑥)𝑓𝑥 = 𝑥 for all 𝑥 is a quandle, and a quandle such that 𝑓x2 = ɩ for all 𝑥 is a kei. These objects can be represented by loopless, edge-coloured directed multigraphs on [𝑛]; we put an edge of colour y between 𝑥 and z if and only if (𝑥)𝑓y = z. This thesis studies racks and kei via these graphical representations.
In 2013, Blackburn showed that for any ε &GT; 0 and 𝑛 sufficiently large, the number of isomorphism classes of kei on [𝑛] is at least 2(1/4 - ε)𝑛2, while the number of isomorphism classes of racks on [𝑛] is at most 2(c+ε)𝑛2 for a constant c. The main result of this thesis is that the lower bound is asymptotically correct; for any ε &GT; 0 the number of isomorphism classes of racks on [𝑛] is at most 2(1/4 + ε)𝑛2, for 𝑛 sufficiently large. We also show that in almost all of these racks almost all components of the corresponding graph have size 2. Additionally, we show several more detailed results regarding kei, including a full classification of all kei in which each component has size equal to an odd prime.
This thesis also contains several partial results on another topic. The commuting graph of a finite group is defined to be the graph on the non-trivial cosets of G/Z(G) where x̄ȳ is an edge if and only if 𝑥 and y commute. In 2012, Hegarty and Zhelezov proposed a family of random groups and published some results on the corresponding family of random graphs; this thesis contains some generalisations and extensions of these results.

Keywords: Enumeration
Racks
Commuting Graph
Advisor: Riordan, O
The development of a biosensor for the detection of pathogenic bacteria in water

Pathogenic bacteria are causative agents of epidemics and deaths worldwide; water is a vector for the transport of bacteria and their consequent consumption by humans. The accepted "gold standard" for assessing bacterial concentrations in water is by traditional plate counts. However, this globally accepted technique takes longer than 24 hours. An alternative method to rapidly detect and to continuously assess bacterial concentration is required. A biosensor that provides near real-time information on the bacterial loading of a waterbody is proposed. This thesis describes the development of a microfluidic-magnetophoretic device to detect bacteria in water.
Escherichia coli is a well-reported bacterium found in the intestinal tract of mammals. Particular strains of E. coli are pathogenic to humans. E. coli is used as an "indicator" for water contamination and was chosen as the target for the biosensor. Magnetic particles (MPs) were functionalised with an anti-E. coli antibody. The functionalised MPs were used to capture E. coli from drinking water by forming MP-bacterial complexes.
A microfluidic device was designed, incorporating magnetophoresis, to separate and concentrate MPs suspended within a sample. A separation efficiency of approximately 80% of the MPs from a sample flow was achieved. Using a magnetic gradient and video tracking of the MPs, the magnetic-drift velocities of unbound and bound MP-bacterial complexes was determined. It was found that viable and non-viable MP-bacterial complexes had different magnetically-induced drift velocities. A single viable E. coli bound to an MP travelled at 0.49 times the velocity of an unbound MP, and a single non-viable E. coli travelled at 0.75 that of an unbound MP. As such, this novel magnetophoretic separation technique can be used to determine the viability of bacteria. The developed biosensor provides the ability to concentrate, separate and enumerate viable E. coli from drinking water, with the potential for automation and sampling from continuous flow.

Advisor: Thompson, I
Sheard, S
The role of aspirations and identities in decisions to invest in children’s schooling

I demonstrate that household investments in children's education in Ethiopia are affected by parents' self-beliefs (such as their locus of control), parents' aspirations for children's educational attainment, children's conceptions of their roles and identities in the household and at school, and children’s own preferences, all concepts not widely studied in development economics.
Two empirical chapters report on a field experiment in which randomly selected adults watched documentaries about role models who were poor but succeeded in agriculture or small business. Six months later, parents' self-beliefs and aspirations for children's education were higher in the treatment than in the placebo and control groups. Enrolment of children in school, spending on education, saving and use of credit also increased.
A third empirical chapter draws on longitudinal qualitative research to argue that children's preferences for their time allocation between work and school are strongly influenced by the desire to comply with valued identities as students and as independent earners and contributors to the household.
The fourth chapter suggests that understanding children's preferences might improve predictions about their reaction to education policies. The literature predicts an increase in time in school will not improve test scores: children will reduce effort because they desire a limited amount of learning. I find a reform to lengthen the Ethiopian primary school day improves test scores. Although this could occur through many mechanisms, one possibility is that children do not prefer to limit their desired amount of learning. This suggests that better evidence on children's preferences might improve prediction of the effects of policies to alter school inputs.
The conclusion reflects on whether the empirical relevance of concepts of self-beliefs, aspirations and identities implies that assumptions in standard models of decision-making in economics about the characteristics of beliefs and preferences ought to be rejected. I argue that these ideas can be captured by existing economic concepts of beliefs and preferences and by standard assumptions about these concepts. I suggest that, contrary to recent accounts building on human capital theory, self-beliefs should be viewed as beliefs, not non-cognitive skills. I consider aspirations as a type of preference, shaped by both objective constraints and self-beliefs. I consider identity as a preference for complying with a social role, but highlight that such preferences are often altruistic, rather than self-interested. In conclusion, I argue that economics should draw further on other social sciences, including psychology, to develop substantive theories of the formation and characteristics of beliefs and preferences. Doing so will suggest when it is appropriate to apply standard models and how their assumptions can be modified if their predictions do not hold.

Keywords: primary education
instructional time
identity
aspirations
Ethiopia
Advisor: Dercon, S
Camfield, L
Awkwardness in Marcel Proust's 'A la recherche du temps perdu'

This thesis examines awkwardness between characters in Marcel Proust's A la recherche du temps perdu. It offers the first full-length study of awkwardness in literary fiction, and provides a new prism through which to analyse many major characters in Proust's novel, and, crucially, their interactions. While the word "awkwardness" poses translation challenges, the thesis identifies a rich lexicon of French terms used by Proust to denote various aspects of the phenomenon: through close analysis of passages containing these terms, a coherent vision of awkwardness and its importance in the novel emerges. Awkwardness occurs in very different types of relationship – family, social, friendship and love – because, Proust stresses, human interaction is rarely easy. This latter point is not a new argument, but by focusing directly on the feelings of awkwardness which arise, original insights can be made about the specific challenges of communication, cohesion and desire in the Recherche. The thesis explores the degrees of togetherness and separation Proust depicts, and compares well-known scenes and neglected moments to their mutual illumination. We find that awkwardness is essential to the novel’s depiction of society in a state of rapid flux – the consequence of accelerated social change is escalated awkwardness – and that uncomfortable encounters with other people develop the protagonist’s relation with his own mind.

Keywords: Awkwardness
Advisor: Yee, J
'Free Schools': the role of Conservative and Liberal political thought in shaping the policy

'The landscape of schooling in England has been transformed over the last five years' (House of Commons Education Committee, 2015:3). More than half of secondary schools in England have become academies, independent of local authorities and funded directly by central government. The programme was begun by New Labour in 2002, and by the time they left office at the 2010 General Election 203 academies had been established. The policy was considerably extended between 2010-2015 by the Conservative and Liberal Democrat coalition, and 'Free Schools' were introduced by Education Secretary Michael Gove: that is, schools 'set up in response to what local people say they want and need in order to improve education for children in their community' (DfE, 2013/2015). By the time of the 2015 general election, there were 4,674 newly-sponsored or converter academies and 252 'Free Schools', representing 64% of secondary school students (47% of all state school students), and 51% of secondary schools (32% of all state schools). This research argues the hypothesis that there is a high degree of philosophical continuity on this policy across the main political parties in England. It also analyses the extent to which the policy-makers invoke historical expressions of conservatism and/or liberalism in their articulation of that convergence. Drawing on past associations with politicians, the principal expositors and key architects of the 'Free Schools' policy were interviewed, and these transcripts have given insight into how the themes of policy are conceptualised and understood. The data suggests that there are convergent philosophical views across the main political parties, and agreement on the course of history of the policy. There are, however, ethical concerns about the pace of reform, the primacy of the 'market', and the extent to which democratic public goods are consistent with schools that are 'free'.

Advisor: Gearon, L
McLean, I
Sammons, P
Neuropsychiatry and the management of aerial warfare: the Royal Air Force neuropsychiatric division in the Second World War

This work is a critical assessment of the role of neuropsychiatry in the management of aerial warfare. Focussing almost exclusively on the Second World War (1939-45), the thesis demonstrates how the Royal Air Force (RAF) mobilised specialist medical knowledge to improve wastage and combat efficiency in flying personnel. Neurological and psychiatric expertise was enlisted to improve service performance and reduce the burden of neuropsychiatric disorders. To meet these key objectives, the RAF neuropsychiatric division undertook important administrative and therapeutic duties in the areas of personnel selection, service discipline, neuropsychiatric research, and the treatment of mental disorders. The work therefore assesses how the division responded to these challenges and contributed to the management of aerial warfare.
The thesis assesses the factors that shaped the practice of neuropsychiatry in the service. Historically, the training and personal interests of specialists and the context of therapeutic practice guided the development of mental health specialties. To gain a fuller appreciation of the administrative and therapeutic duties of the division, this work explores the medical, social, military, and professional factors that shaped neuropsychiatric thought and practice. Secondly, the work engages with the 'human element' of aerial combat. The physical and mental health of aircrew was fundamental to the conduct of the air war and underpinned the administrative decisions of the air force. It was the primary objective of the neuropsychiatric division to preserve and develop these vital human resources. Neuropsychiatric disorders represented a challenge to efficiency, for they could affect the performance and motivation of a flyer. The thesis will examine how the neuropsychiatric division attempted to sustain aircrew by preventing and treating the disorders that compromised their efficiency.

Advisor: Harrison, M
Resistance mechanisms to mTOR inhibition in renal cancer

Introduction: Advanced clear cell renal cell cancer (CCRCC) is incurable, but molecularly targeted treatments have improved the prognosis. One such molecular target is the mammalian target of rapamycin (mTOR) and two rapalogues (everolimus and temsirolimus) have been licensed for the treatment of advanced CCRCC, but resistance to treatment is a significant problem. Novel mTOR kinase inhibitors show more complete blockade of mTOR downstream targets, and greater in vitro anti proliferative activity, although resistance remains a problem.
Hypotheses: 1) CCRCC cell lines, resistant to mTOR kinase inhibition could be generated in vitro through continuous culture in drug, and 2) mediators of resistance could be identified through screening cells at the mRNA and protein/phosphoprotein level, or by examining the signalling in resistant cells to identify the re-activation of key mTOR targets.
Methods: Resistant cells were created by continuous culture in the PI3K-mTOR kinase inhibitor BEZ235. Resistance was assessed by CellTiter-Glo viability assays and clonogenic assays. mRNA microarray and antibody arrays were conducted. Intra-cellular signalling was assessed by western blotting. The functional relevance of identified markers of resistance were assessed with small molecule inhibitors and siRNA protein depletion.
Results: BEZ235 resistant cells were created and had a 14 fold higher growth inhibitory 50 (GI50) concentration compared to sensitive cells (99 nM vs. 7 nM). Array screening of the cells identified markers, but not mediators of resistance (MET, Abl, MEK/ERK and the Notch pathway).
In BEZ235 resistant cells, the downstream mTOR target 4E-BP1 was rephosphorylated, despite evidence of on-going blockade of another mTOR target, S6. Recovery of 4E-BP1 phosphorylation was associated with increased protein expression of the mTOR binding partner RAPTOR, and could be reduced by depletion of RAPTOR, or by the addition of rapamycin. Both of these interventions partially reversed BEZ235 resistance.
Conclusions: RAPTOR protein up-regulation, represents a novel mechanism of resistance to mTOR kinase inhibition and can be partially overcome by rapamycin. The combination of BEZ235 and rapamycin warrants further investigation to evaluate its potential to overcome resistance to mTOR kinase inhibition in RCC.

Advisor: Macaulay, V