VictorJuiz/thesis huggingface dataset:
Ocean heat uptake: drivers, variability and impacts

Attributions of causes in the fully coupled atmosphere-ocean system are difficult due to a wide range of interactions in the climate system. One way to address this is to break down the fully coupled closed system into two open systems. Such studies often depend on the specification of sea surface temperature to link ocean and atmosphere. Instead, in this thesis we focus on understanding the impacts of perturbations to surface heat fluxes as this gives a better handle on imposing changing processes and improves the realism of air-sea interactions.
We identify (Chapter 2) the local and non-local response of ocean heat content to idealised surface heat flux perturbation patterns, demonstrating the importance of circulation change in communicating the non-local response. The global heat content response pattern is shown to be a linear combination of the responses to flux perturbations in individual ocean basins, primarily the North Atlantic and the Southern Ocean.
We further investigate (Chapter 3) processes and forcings that regulate the ocean heat content change in the South Pacific Gyre, finding an important cooling contribution from a weakening of the ocean circulation as a response to high-latitude Southern Ocean heat flux forcing. This mechanism is not robust in CMIP5 but is identified in the MPI-GE fully-coupled large ensemble.
In order to investigate the impact of changing ocean circulation on atmospheric extreme events, we introduce, develop and validate (Chapter 4) the novel HadSM4 slab ocean-atmosphere model configuration. Using large ensembles of HadSM4, we quantify the impact of the ocean heat convergence anomaly that occurred in the North Atlantic in the 2013-14 winter season. Our results indicate that the 2013-14 anomaly induced a warming of around 1 K in the North Atlantic, 0.5 K in Western Europe, and an increase in winter precipitation that up to halves the return times of extremely wet winters over parts of Europe.
To isolate the impact of air-sea feedbacks on mean state, variability and extreme events, sea surface temperature realisations from this slab ensemble are used to force an atmosphere-only sister ensemble (Chapter 5). Disabling the feedback of heat fluxes onto SST strongly increases the ensemble spread of seasonal mean air-sea heat flux components, as the first-order impact of coupling is a negative feedback. Regionally important changes in extreme events indicate the importance of representing atmosphere-ocean coupling for studies exploring the impact of external forcing on weather extremes.
This work improves our understanding on how ocean and atmosphere force each other’s dynamics and variability through surface energy exchange, by the way of the centennial impact of atmospheric forcing on ocean dynamics, the seasonal impact of ocean forcing on atmospheric dynamics, and the atmospheric impact of mixed-layer coupling.

Keywords: slab ocean
ocean heat uptake
large ensemble modelling
ocean dynamics
climate dynamics
Mixed-layer feedbacks
air-sea interactions
climate modelling
extreme value analysis
Advisor: Allen, M
Zanna, L
Free groups and Stallings' folding

In the present work we investigate various aspects of free groups and their automorphisms, utilizing Stallings' folding techniques introduced in 1983. These techniques have provided new insights into several classical results and have been widely applied over the years to study various properties of free groups and to generalize results to wider families of groups.
We apply folding techniques to uncover a fine property of the classical Whitehead's algorithm for recognizing primitive elements and free factors in a free group. This property is then used to the study of the complex of free factors, a crucial object on which Out(F_n) acts. We also make use of these techniques to investigate echelon subgroups of F_n, a particular type of subgroup which is relevant to the study of fixed-point subgroups of automorphisms of F_n.
Next we turn our attention to the problem of studying equations in a free group. Given two free groups H≤F and an element g ∈ F, we study the ideal of the equations w(x) in H* ⟨x⟩ with g as a solution. In particular, we focus on the relationship between equations and their degree, providing an algorithm that determines the minimum integer d that appears as the degree of an equation in a given ideal. More generally, we study the subset of the equation in a given ideal of a fixed degree d. This is done using two different techniques, one based on Stallings' folding operations and the other using context-free languages.

Keywords: free non-abelian groups
free factors
equations over groups
Whitehead's algorithm
Advisor: Bridson, M
A study of foam targets for direct-drive inertial confinement fusion

Recent experiments using DT-wetted-foam layers in inertial confinement fusion capsules have demonstrated that the convergence of the implosion can be controlled through varying the initial capsule temperature. These experiments also demonstrated low amounts of hydrodynamic instability growth at low convergence ratio. In this thesis, simulations and an experiment relevant to these capsules are presented.
Simulation campaigns are discussed which explore the fusion performance that could be achieved in experiments using wetted-foam capsules, in a newly identified regime (based around limits to convergence ratio and other implosion parameters) where instability growth is expected to be minimal. Performance is explored first for third-harmonic of Nd:glass laser drivers, and then for higher frequency ArF drivers and a novel ‘two-colour’ laser scheme. Further simulations are then performed which explore how such capsules could be heated using electron beams, and the impact this has on fusion performance is discussed. ‘Hydrodynamic-equivalent’ capsules are also presented, which are surrogate targets where the DT-wetted-foam layer is replaced instead with an equivalent density layer of dry foam. Such capsules have comparable hydrodynamic performance, and could facilitate room temperature experiments to validate the low instability regime.
The equation of state of these foams is not well characterised. An experiment is therefore also presented which measured principal Hugoniot data of TMPTA foam at 260 mg cm−3, equivalent to the foam layer in the hydrodynamic-equivalent capsules. VISAR was used to measure shock transit times through an α-quartz reference layer and a TMPTA foam layer in a multi-layer target and impedance matching performed to enable calculation of the foam shock state, while the foam shock temperature was estimated using streaked optical pyrometry. The results demonstrate that for the pressure range probed in the experiment the TMPTA foam was well described by existing QEOS and SESAME models, suggesting that this foam can be well approximated as a low density homogenous plastic.

Advisor: Norreys, P
Revival to revolution: medieval narratives in Irish republicanism

Medieval narratives that had been celebrated in the Gaelic Revival (c.1880-1916) became a tool of republican self-fashioning in the revolutionary era (c.1912-23). As revolutionary nationalism developed into a movement distinct from Revivalism, it acquired its own flavour of engagement with medieval history and literature. This project argues for the continued cultural relevance of medieval narratives throughout the revolutionary period. Employing a hybrid methodology and incorporating a wide range of source material, this study adds nuance to our understanding of the transition from Revival to Revolution. The project demonstrates that medieval narratives not only remained a part of revolutionary culture after the Rising, but were selected, reimagined and deployed in ways specific to this context.
This project brings together the fields of medieval Irish literature, nineteenth and early twentieth century translations and twentieth century Irish history. Ultimately, it is a historiographical project, but an interdisciplinary one. The project interrogates how literature and mythology circulated in the national imaginarium and shaped identity. The research framework suits the multifaceted nature of the subject.
As Joep Leerssen wrote in Remembrance and Imagination, ‘tradition’ is not ‘a discreet heirloom’ but ‘a vast and chaotic curiosity shop.’ Fin de siècle revolutionaries in Ireland inherited a wealth of narratives that took multiple forms in the middle ages and were then passed through centuries of time and translations. Entering twentieth century culture, the tales were mediated not only through translation but through their modern audiences’ values. New translations, retellings, and derivative works of art–and the context of each reader’s own particular Weltanschauung–all create new frameworks for using old narratives in the service of identity.
Following the Revival, the medieval cultural inheritance continued to solidify identity and advance the political case for independence. Medieval narratives allowed people to understand, define and legitimise the present in terms of the past.

Keywords: Irish
Irish republicanism
Irish mythology
Irish Revolution
Gaelic revival
Irish Civil War
Ireland
Irish War of Independence
Easter Rising
medieval Irish literature
Irish volunteers
Advisor: Williams, M
McBride, I
Mendicant ecclesiology and the apostolic life in the thought of the Oxford Masters, c.1250-1325

This thesis examines the texts and contexts in which three mendicants at the University of Oxford discussed certain ecclesiological themes in the late thirteenth and early fourteenth centuries. Although the secular-mendicant disputes at the University of Paris certainly provided a major impetus for the articulation of ideas about both the vita apostolica, as well as the structure of the contemporary Church and its orders, modern scholars have tended to impose certain artificial limitations upon their investigation into the effect of the mendicant orders’ emergence upon the development of ecclesiological thought. Firstly, they have generally limited their examination to the Parisian schools, which bore witness to the fiercest episodes of antifraternal polemic; secondly, they have tended to downplay the role that burgeoning intrafraternal tensions played in the way that ecclesiological concepts continued to be explored and refined. By examining the works of three mendicant theologians associated with the University of Oxford – the Franciscans, Thomas of York and William de la Mare, and the Dominican, Nicholas Trevet – this thesis traces the articulation of mendicant ‘aspects ecclésiologiques’ beyond the antifraternal debates at Paris. In doing so, it begins to illuminate the vitality and originality of much of the ecclesiological thought produced by mendicant theologians during this period.

Keywords: University of Oxford
religious orders
friars
apostolic life
Dominican order
Franciscan order
medieval universities
ecclesiology
Mendicant orders
Advisor: Kempshall, M
Behavioural drivers of fertility in red junglefowl Gallus gallus and commercial chicken flocks

The fowl, Gallus gallus, has been used to study sexual behaviour and sexual selection for many years: its combination of reproductive biology that is fairly typical of birds and a polygynandrous mating system makes it an ideal model species for studying the effects of pre- and post- copulatory competition and of conflict between the sexes. There is a large body of research spanning many decades on these processes in domestic chickens and their wild ancestor, the red junglefowl. As well as being an ideal model system, the sexual behaviour and fertility of this species is of great significance to the poultry industry, where the reproductive efficiency of broiler breeders (birds whose commercial purpose is to produce hatching eggs) is a key concern. However, the behaviour of broiler breeders in a commercial setting, and how their behaviour links to fertility, is little understood.
Females of this species are subject to intense sexual harassment, and some behavioural strategies exhibited by females in response to sexual harassment have been described. However, we lack a detailed and systematic understanding of the suite of female responses to sexual harassment, despite these having the potential to significantly affect reproductive success for males and females.
In this thesis, I build on existing knowledge of sexual behaviour and its influence on fertility, with a focus on female responses to sexual coercion and on commercially relevant insights in broiler breeders. I use a mix of approaches, from a theoretical model, to an experiment on a captive population of junglefowl, to translational research in broiler breeders. The findings of this thesis add new detail to our understanding of female resistance against sexual coercion, both in this species and in general, and inform suggestions for husbandry optimisations that could be trialled in broiler breeders.

Keywords: sexual selection
broiler breeders
sperm competition
Gallus gallus
red junglefowl
chickens
broilers
poultry farming
polyandry
Coolidge effect
Advisor: Pizzari, T
Bath, E
McDonald, G
War and Peace: analysis of the Egyptian presence in the Levant during the 18th dynasty

This thesis investigates the establishment of the Egyptian “Empire” in the Levant at the beginning of the Late Bronze Age, and aims at reconstructing the reasons that brought Thutmose III and its successors to conquer and control the region. This reconstruction is based upon an analysis of their military actions, namely their campaigns and the development of a network of installations able to logistically support the army in enemy territory. Given the scattered nature of the sources, written and archaeological evidence are used in concert, and the subject at hand is seen through the new and different perspectives of modern military theory. In this way, there emerges a picture of a complex and calculated Egyptian effort, aimed at developing and controlling a buffer state in the region. In particular, it is argued that the Egyptian efforts appear to have been specifically designed to respond to the socio-political characteristics of each area they entered, and to the mutation of the objectives through time. Such an adaptability has been hitherto unrecognized, and opens new avenues in the study of the Levant under the Egyptian occupation.

Keywords: military theory
18th dynasty
Levant
grand strategy
Advisor: Mynářová , J
Dahl, J
Micro-patterns of violence: disaggregating Provisional Irish Republican Army activity, 1969-1979

This thesis examines the first ten years of the campaign of political violence that was waged by the Provisional Irish Republican Army (PIRA) during the Northern Ireland Troubles (c.1969–1998). The primary aim is to understand how and why the PIRA chose to apply violence, and the consequences of these decisions. What is significant about this thesis, is the volume and range of PIRA violence that has been disaggregated and assessed – fatal and non-fatal acts of violence; targeted assassinations that were planned and executed as intended; operations that were stillborn, off-target, or thwarted by the security forces; attacks that maimed or killed unintended targets; and acts that were never intended to and did not cause physical harm to others. The work uncovers a richer account of the relationship between PIRA agency, chance, and the character and consequences of PIRA violence than has hitherto been possible.
The research has involved a detailed investigation of the PIRA’s activity to establish how, when where and why the violence took different forms. The PIRA’s operations have been examined in minute detail to identify and evaluate the significance of various characteristics that are apparent in each stage of the process: its design, execution, outcome, and reception. This has involved first, identifying why the PIRA selected certain targets and tactics, and the extent to which they perpetrated violence with accuracy and discrimination in each scenario. Second, the different outcomes that are produced – directly or indirectly – as a result of PIRA violence (including the material damage, deaths and injuries caused) and the relationship between these outcomes and the actions taken by the perpetrator(s), have been explored. Finally, the thesis considers how and why the armed struggle was perceived in disparate ways by others.

Keywords: violence studies
Northern Ireland Troubles
Provisional Irish Republican Army
Advisor: Mulholland, M
McBride, I
Axonal membrane trafficking regulation and its failure in cargo delivery

Regulation of axonal trafficking of membrane-bound compartments is important for delivery of various neuronal cargoes towards the distal synapses and for quality control of damaged cellular components/toxic proteins. The contribution of Rab GTPase pathways in neurodegenerative pathologies and the regulatory mechanism to replenish various Rab proteins in the axonal periphery remain unclear. In the Encalada lab, we modeled familial prion disease axonopathies in primary murine hippocampal neurons, to determine (1) the biogenesis pathway that forms neurotoxic mutant prion protein (PrPmut) aggregates and (2) the consequences of PrPmut aggregate formation on cytoskeletal-organelle interactions within swollen axons that PrPmut aggregates reside. Firstly, I, and the research team, identified that the small GTPase ARL8 recruits kinesin-1 and HOPS for axonal transport and fusion, respectively, that generates neurotoxic PrPmut aggregates in non-degradative endolysosomes, called ‘endoggresomes.’ This axonal rapid endosomal sorting and transport-dependent aggregation (ARESTA) mechanism forms endoggresomes rapidly, and as a result impair calcium dynamics and neuronal viability. Inhibition of ARESTA reduces axonal endoggresome densities and rescues neuronal dysfunction, providing an anti-aggregation target to ameliorate prionopathies. Secondly, axonal micro-domain analysis of live organelle dynamics within endoggresome sites showed deficits to the MT-based active transport system, that result in enhanced mitochondrial-Rab7 endosomal contacts that induce mitochondrial fission via Rab7 activity and render retained mitochondria dysfunctional. In the Davis lab, I studied post-transcriptional fate of rab GTPase mRNA towards their axonal localization and function at the Drosophila larval neuromuscular junction (NMJ) pre-synapse. I found that a conserved RNA-binding protein Imp and kinesin-1 are required for rab11 mRNA delivery to axon termini and are required for synaptic plasticity and unimpaired locomotory behavior. Furthermore, I detected transcripts of multiple important rab GTPases for endosome recycling at the axonal and glial periphery at the NMJ, uncovering an unorthodox regulatory mechanism of axonal membrane trafficking.

Keywords: Rab GTPase
neurodegeneration
axonal transport
synaptic plasticity
mitochondria
PrP
neuromuscular junction
membrane trafficking
mRNA
drosophila
microtubule
Studies of beam instabilities and associated beam-loss on a high-intensity proton synchroton

High-intensity hadron accelerators provide beams for many different applications around the world: from high energy particle physics to drivers of spallation neutron sources such as ISIS. These facilities face a common, significant challenge: the control and mitigation of beam-loss, often defining the limit to the beam intensity achievable.
Beam-loss may be driven by many different processes including transitions between accelerators, RF capture and non-linearities in the accelerator’s magnetic lattice. Collective effects, such as space charge and beam instabilities, may also be a major source of beam-loss, particularly in accelerators pushing for higher intensities. The interaction of space charge with beam instabilities is a key topic of current research and development.
The head-tail instability drives beam-loss on a number of high intensity hadron accelerators around the world. Measurements of the instability are shown from the ISIS Neutron and Muon Source at the Rutherford Appleton Laboratory in the UK. These are shown in normal, Rapid Cycling Synchrotron, operation as well as in a new operating mode: bunched beams stored at injection energy. The new mode is utilised to explore the instability on ISIS systematically, with a simplified experimental setup for comparison with established theory, as a function of the vertical betatron tune and the vertical beam size.
Particle-in-cell tracking simulations of ISIS in the new operating mode are performed, varying the associated beam and accelerator parameters, and the results compared to observed instability characteristics. Further simulations include a self-consistent model of the beam’s transverse space charge field, allowing analyses of its effect on the instability characteristics.
Experimental and simulation results are compared with predictions derived from a well established theory of head-tail dynamics which does not include the effects of space charge. Recent theories including these effects are summarised and the results discussed in the light of those theories.
Key agreements and discrepancies between experiment, simulation and theory are presented together with directions for future research. Finally, the impact of this research on the operation of current and future high intensity hadron accelerators is discussed with particular focus on current ISIS operations.

Keywords: beam
ISIS
space charge
instability
proton
beam-loss
head-tail
RAL
accelerator
Advisor: Warsop, C
Foster, B
Towards a new theory of reparative justice under authoritarian states



Injustices are ubiquitous throughout countries governed by authoritarian states, given their fundamentally anti-plural and anti-liberal nature, and unchecked executive powers. Such injustices, ranging from the murder and suppression of dissidents, targeted ostracisation of citizens, the exploitation of resources and land confiscation, to the perpetration of deeply unjust social hierarchies, often leave substantial devastation in their wake. The task of repairing such injustices is likely to impose substantial costs on populations under such states. On what grounds, and by what parameters should such responsibilities of reparative justice be assigned to individual citizens - especially if culpable state actors do not take up such responsibilities?
Existing accounts for reparative justice and citizens’ responsibilities for state injustices tend to suffer from a number of issues when applied to authoritarian contexts. First, some are exclusively centered around liberal democratic contexts. Second, most fail to fine-grain and conceptualise comprehensively the limits to agency of individual citizens. Third, even accounts that purportedly advance non-blame-centric conceptions of moral responsibility, strain to articulate why citizens residing under highly coercive and radically uncertain circumstances ought to be held responsible.
Drawing upon robust empirics on authoritarian regimes, this thesis advances the view that authorisers of states in relation to state-perpetrated injustices are responsible for repairing injustices, on grounds that they have either subjectively avowed voluntary uptake of responsibilities qua authorisers of their state, or objectively authorised their state via being capable of influencing or benefiting from state policies and their outcomes.
Reparative justice calls for compensation, opposition, apology and commemoration for injustices, as well as fundamental reforms to faulty institutions. As compared with other surveyed accounts anchored in concepts of moral liability and blameworthiness, collective responsibility, complicity, structural injustice, and intentional citizenship, this account is demonstrably more descriptively accurate, explanatorily precise, and compatible with our broader normative commitments.

Keywords: responsibilities
authority
citizenship
injustices
authoritarianism