VictorJuiz/thesis huggingface dataset:
The Caribbean Cold War: between exile and revolution, 1945-1960

In the late 1940s, the governments of Cuba, Venezuela, Guatemala or Costa Rica saw themselves as engaged in a regional conflict between democracy and dictatorship. These countries were led by political parties born from anti-dictatorial struggles, opposing military dictatorships through exiled activism, armed struggle, and diplomacy. While they aspired to democratise their countries, and legislated to that effect, they identified a group of dictatorships as their enemy: in the Dominican Republic, Nicaragua, and Honduras. Between 1945 and 1960, two regional blocs emerged and traded blows: governments plotted coups in neighbouring countries, armed proxy armies of exiles, and denounced their rivals at international gatherings.
In this thesis I seek to explore this conflict. My argument is that it can be understood as a ‘Caribbean Cold War’: an ideological rivalry between two transnational blocs, which fought indirectly via proxies. At the centre of this conflict was the question of democracy: how should it be defined and implemented? While the self-proclaimed democratic bloc saw their rivals as military autocrats, the latter engaged in their own language and definitions of democracy. At stake was the meaning of the concept itself in the region, and its future.
Viewing this conflict as a regional cold war changes the way we understand the broader, global Cold War between the United States and the Soviet Union. It highlights the need to acknowledge the existence of alternative ideological cleavages at the regional level, where some governments contested the supremacy of the socialist-capitalist binary with an alternative axis that better reflected their grievances. This thesis thus uncovers a Caribbean position on the global Cold War which defied, and did not align neatly, with the superpowers of the time.
To examine this conflict, this thesis is divided into six chapters. The first chapter analyses the creation of the anti-dictatorial political parties through the 1920s and 1930s, and their rise to power in the mid-1940s. The second chapter explores the emergence of the regional conflict in the late 1940s, and how democratic governments coordinated their actions internationally. The third chapter focuses on Cuba, analysing the insurrection against Fulgencio Batista (1952-1958) as a flashpoint in this regional conflict with far-reaching consequences. Chapter four explores how military leaders in authoritarian regimes justified their rule and proposed their own understanding of democracy. The fifth chapter contextualises this regional conflict within attitudes by the superpowers of the Cold War towards democracy in Latin America. Finally, the sixth chapter examines how the Cuban Revolution of 1959 divided the unity of the anti-dictatorial bloc by introducing a new understanding of democracy, which in turn unravelled the ideological axis which had underpinned conflict in the region.

Keywords: democracy
exile
Latin America
Caribbean
revolution
Cold War
Advisor: Posada-Carbo, E
All things hydrogen: hydrogen imaging in atom probe tomography and its application to tungsten

This thesis investigates the fundamental behaviour of contaminant hydrogen in Atom Probe Tomography (APT), develops an APT imaging method for sample hydrogen, applies it to deuterium implanted tungsten, and describes a large-scale APT data analysis and its application to hydrogen.
Rate cycling experiments are introduced, where the evaporation rate or frequency is repeatedly changed during experiments. Contaminant hydrogen is, other than sample hydrogen, rate dependent, therefore this allows estimating the true amount of sample hydrogen. By undertaking APT experiments below the evaporation threshold, it could then be investigated how the electric field influences the contaminant signal on tungsten. Beyond a critical field strength, the contaminants are found to evaporate with a detectable energy deficit. This allows differentiation between contaminant and sample hydrogen, which evaporates without any energy deficit, enabling development of a method for direct hydrogen imaging using pulsed laser APT.
The technique is applied to image deuterium in self-ion irradiated, deuterium implanted tungsten. The deuterium is retained with a characteristic depth distribution, which is imaged by APT with high spatial resolution. The highest deuterium concentrations are found in a layer directly under the material surface (up to 20 nm deep), corresponding to the depth reached by the deuterium during implantation, and in a deeper layer (ca 120 to 170 nm below) due to radiation damage. The scatter of measured concentrations across samples is large, and potentially requires further study.
Finally, a large-scale data analysis, covering 848 archival datasets from the Oxford APT group is presented. It is shown that many APT spectra can be regarded as a point cloud, in which a similarity metric based on the city block distance is well suited to search spectra by similarity. The point cloud contains clusters, mostly due to chemical composition of the underlying APT specimens. The dependence of contaminant hydrogen behaviour on material, voltage and electric field strength is studied.

Advisor: Haley, D
Bagot, P
Moody, M
The role of biodiversity in Southeast Asian tropical forest restoration

Tropical forests in Sabah, Malaysian Borneo, are threatened by land use change and continued overexploitation. Active restoration of dipterocarp-dominated forests is used to increase the restoration value of these landscapes, and knowledge of the ecological mechanisms that promote tropical forest functioning is critical to realising this goal..
In this thesis, I use a long-term, field-scale experiment to investigate the effectiveness of active restoration techniques in a once-logged lowland dipterocarp forest. I show that enrichment planting of dipterocarp seedlings increases satellite-derived metrics of aboveground biomass, canopy cover, and leaf area index. I then show a clear relationship between ecosystem functioning and the biodiversity of enrichment planted seedlings. This relationship is likely driven by species-specific niche differences which generate stronger complementary effects through a more functionally diverse seedling cohort and is unlikely to be generated via stochastic processes as hypothesised under neutral theory. .
At the local scale, I demonstrate that the survival of enrichment planted seedlings in a selectively logged forest may benefit from increasing densities of the surrounding tree matrix as a result of potential positive density-dependence. I also add to the evidence base that light is a primary driver of growth and survival within selectively logged dipterocarp forests. More data concerning the seedling environment, including microclimate variation, will help to provide a more comprehensive assessment of logged forest dynamics..
Finally, I show that survival and growth of enrichment planted seedlings are similar for most investigated species across an old-growth and secondary forest, demonstrating the capacity for old-growth forests to provide restoration target information from which to compare active restoration success. I also identify a growth-survival trade-off in both primary and secondary forests and demonstrate that my studied selectively logged dipterocarp forest is in an early successional stage and has not experienced a collapse in seedling growth and recruitment. However, I call for more work to understand the variables underlying species-specific responses to habitat perturbation..
This thesis helps to inform future restoration design, implementation, and monitoring across Sabah. To maximise the benefits of forest restoration to climate security, economic growth, and social wellbeing, a data-driven approach to forest restoration projects that utilises current ecological theory will become increasingly important.

Keywords: enrichment planting
dipterocarpaceae
remote sensing
Malaysia
Sabah
restoration
Advisor: Hector, A
Fernandez-Miranda Cagigal, E
Learning cell representations in temporal and 3D contexts

Cell morphology and its changes under different circumstances is one of the primary ways by which we can understand biology. Computational tools for characterization and analysis, therefore, play a critical role in advancing studies involving cell morphology.
In this thesis, I explored the use of representation learning and self-supervised methods to analyze nuclear texture in fluorescence imaging across different contexts and scales. To analyze the cell cycle using 2D temporal imaging data, as well as DNA damage in 3D imaging data, I employed a simple model based on the VAE-GAN architecture. Through the VAE-GAN model, I constructed manifolds in which the latent representations of the data can be grouped and clustered based on textural similarities without the need for exhaustive training annotations. I used these representations, as well as manually engineered features, to perform various analyses both at the single cell and tissue levels.
The application on the cell cycle data revealed that common tasks such as cell cycle staging and cell cycle time estimation can be done even with minimal fluorescence information and user annotation. On the other hand, the texture classes derived to characterize DNA damage in 3D histology images unveiled differences between control and treated tissue regions. Lastly, by aggregating cell-level information to characterize local cell neighborhoods, interactions between DNA-damaged cells and immune cells can be quantified and some tissue microstructures can be identified.
The results presented in this thesis demonstrated the utility of the representations learned through my approach in supporting biological inquiries involving temporal and 3D spatial data. The quantitative measurements computed using the presented methods have the potential to aid not only similar experiments on the cell cycle and DNA damage but also in exploratory studies in 3D histology.

Keywords: representation learning
histology
machine learning
cell cycle
Advisor: Rittscher, J
Waithe, D
Multidimensional mass photometry

Mass Photometry (MP), an emergent technology based on interferometric scattering principles, has revolutionised the field of biophysics by enabling label-free, solution-phase mass measurements at the single-molecule level. Traditionally, MP analysis and experiments focus on discrete events, characterising distributions of measurements from single molecules interacting with a glass surface. Our research challenges this convention, demonstrating that these events are not isolated but interconnected, encoding deeper insights of the underlying particle.
In this context, we introduce Tandem-MP, a novel approach that assigns binding and unbinding events to individual particles, thereby facilitating the measurement of dissociation at the single-molecule level. This method reveals intricate patterns that illuminate the structural organisation of protein complexes in unprecedented detail.
Recognising that conventional analysis methods utilise only a small fraction of the information encoded within the data, we developed an innovative particle-centric analysis pipeline. This framework automatically tailors the analysis to each molecule, enabling continuous tracking of both mass and position of particles without the need for experimental adjustments. This approach not only addresses the limitations inherent in standard MP methodologies, but also unveils a wealth of quantitative, orthogonal information.
To exemplify the utility of our approach, we investigated two distinct systems: citrate synthase and adeno-associated viruses. For citrate synthase, our method uncovered complex dissociation pathways at the level of individual molecules. In the study of adeno-associated viruses, we identified unique signatures of their surface interactions, a means to directly report capsid stability, and a way to differentiate between equal-mass serotypes.
This research demonstrates the true capabilities of MP by providing a proof-of-concept framework that leverages and exploits single-molecule measurement, paving the way for new discoveries in molecular biophysics.

Keywords: single particle
Mass photometry
Advisor: Benesch, J
Corporate criminal liability under European Union law

This thesis advances a solution to corporate crime in the European Union (EU). It is specially designed to fit in the current framework of EU criminal law, and to be accepted by the Member States, which have sometimes appeared reluctant towards new developments in this field of law.
Following an assessment of various national and international doctrines of corporate criminal responsibility, and a critical analysis of the current situation of corporate liability in EU criminal law, the thesis proposes a general framework for specific corporate offences to be adopted at EU level. However, the main objective here is not to advance a defined, specific corporate offence to be enacted by EU law – a quite unrealistic goal – but rather to develop the common elements and concepts to be used every time a specific corporate offence is intended to be introduced in different fields of criminal law, at EU level.
This common conceptual framework for specific corporate offences contains the general features of such offences. The actus reus is a failure to prevent subordinate individuals from committing an offence. With regard to the mens rea, the model is one of strict liability, supplemented by a due diligence defence.
This model is very flexible and can accommodate even stigmatic offences. It respects due process requirements and the principles of criminal law but, at the same time, it is an efficient instrument in the fight against corporate crime, focusing not only on deterrence and retribution, but also on compliance and prevention.
Therefore, this solution pursues, as an ultimate goal, one of the objectives of the EU, namely the promotion of social justice and protection through the rule of law. However, the model also has an intermediate objective: to be an efficient tool for the EU in its efforts to address corporate crime.

Keywords: strict liability
rule of law
corporate omission
corporate  law
EU criminal law
specific corporate offence
due diligence defence
corporate mens rea
corporate criminal liability
criminal law
Advisor: Williams, R
Analytical approaches to the modelling of multi-row turbine arrays


The increasing recognition of wind turbines as an effective source of renewable power generation that can deliver a net zero carbon future, has led to the construction of larger turbine arrays. Predicting the performance of large turbine arrays requires consideration of many physical factors, such as array geometry, turbine operation, inflow conditions and turbulent wake mixing. Due to the large parameter space that an array may be optimised over, low-order models with low computational cost are often employed. This thesis is concerned with the extension of one of those low-order models; the hybrid inviscid-viscous model of multi-row turbine arrays.
The first extension presented is to the inviscid portion of the model by generalising the linear momentum actuator disk theory, such that the system with non-uniform inflow may be analytically solved utilising a single cubic equation. The impact of shear on a single turbine is then explored, followed by an analysis of a multi-row turbine, which indicates possible performance gains due to varying turbine resistance at each row.
The second extension is in the construction of a novel wake mixing model based on the momentum deficit and self-similarity of Reynolds stresses. This self-similar mixing model is then compared with the results of a "uniform" mixing model. It is shown that the predictions made by each model are similar when the mixing rate parameterised in the uniform model is accurate for a given turbine resistance and array configuration.
The final extension presented in the thesis concerns itself with “anisotropic blockage”, in which a turbine is not equidistant from all nearby boundaries or lines of symmetry with other turbines. A range of Reynolds-averaged Navier-Stokes (RANS) simulations are conducted, followed by a new theoretical method of estimating the turbine efficiency based on scale-separation arguments. This method is benchmarked against an existing "isotropic blockage" model and is found to agree better with the RANS simulations.

Keywords: wind energy
tidal energy
Advisor: Nishino, T
Plantiness: Re-evaluating plant human relationships across temporal landscapes in Britain

‘Plantiness’ explores the notion that plants are lively, active beings with the ability to shape and change us as we have also done to them. This theory of reciprocity considers plant intelligence and plant materiality, while incorporating ideas of making-in-growing, aesthetics, labour, and edibility. This provides a framework for approaching plant-human relationships in a way that is accessible to those outside of plant studies/sciences. With the help of a range of disciplines — including plant biology, ethnobotany, critical plant studies, and archaeobotany — plantiness can expand the vegetal world and encourage us to consider the ‘planty’ perspective within archaeology.
In order to explore such planty perspectives, archaeological work is set within the highly dynamic landscapes of the Fens of eastern England. Moving chronologically and temporally, sites including Etton, Haddenham, Barleycroft/Over, and Holme I/II, will be discussed, providing unique examples of the reciprocal relationships that are negotiated between humans and plants. Further sites from within the Flag Fen Basin, including Flag Fen, Bradley Fen, and Must Farm demonstrate different studies of how we can understand plant-human relationships within geographically linked places. The plants discussed within these case studies are both trees and cereals, two significantly different types of plants within the plant kingdom, but the two most likely to be preserved by charring (carbonisation) in archaeological contexts. These trees and cereals negotiated relationships with humans in unique ways, which can be explored via a number of different theoretical approaches. Engaging with plantiness provides insight into human inter-relationships of the past, considering notions of what it means to be human while also adding to larger ideas of human becoming.

Keywords: more-than-human
plants
archaeobotany
theory
prehistory
Advisor: Gosden, C
Structural studies of prokaryotic surface layer proteins

Many prokaryotic organisms are encapsulated by a flexible two-dimensional proteinaceous surface layer (S-layer) consisting of repeating units of surface layer proteins (SLPs). SLPs are often the highest copy-number macromolecules in these cells, playing key roles in essential cellular functions including cell-shape maintenance, protection against predators and interaction with the environment. Using recently developed electron cryomicroscopy (cryo-EM) and electron cryotomography (cryo-ET) techniques, I have determined the structures of several S-layers across domains of life, from archaeal and bacterial model organisms and investigated their molecular function.
In the Gram-negative bacteria model organism Caulobacter crescentus, the S-layer is anchored to the cell envelope via lipopolysaccharide (LPS). Using cellular cryo-ET coupled with subtomogram averaging (STA) I resolved a 3.5 Å resolution in-situ structure of the complete S-layer, showing how the native S-layer is anchored at the tip of the lipopolysaccharide.
Combining structural studies with deep-homology bioinformatics (in collaboration) for Haloferax volcanii archaeal and Deinococcus radiodurans bacterial SLPs, I showed that immunoglobulin containing S-layers are widespread in prokaryotes. Additionally, I structurally characterised an abundant outer membrane β-barrel protein from D. radiodurans, elucidating its multidomain architecture and how it tethers the outer membrane to the underlying peptidoglycan layer and thereby shapes and maintains the cell envelope.
Finally, I elucidated the in-situ structure of the S-layer of the ammonia-oxidising archaeon Nitrosopumilus maritimus. Using whole cell isothermal titration calorimetry and molecular dynamics simulations (in collaboration), I showed that this S-layer is required for ammonium enrichment from a dilute marine environment, facilitating the conversion of ammonium oxidation to nitrite.
Taken together, these findings revealed common principles of S-layer arrangement and assembly, advancing our understanding of this important and widespread cellular organelle.

Keywords: S-layer
cryo-ET
cryo-EM
Caulobacter crescentus
Deinococcus radiodurans
subtomogram averaging
Nitrosopumilus maritimus
Haloferax volcanii
prokaryotic cell surfaces
Advisor: Bharat, T
Sattentau, Q
A longitudinal study of child mental health in the UK: the role of income and other risk factors

Background
Previous evidence suggests child mental health is associated with family income, with poorer mental health amongst those in less affluent families. This DPhil research investigates the relationship between family income and child mental health from early childhood to adolescence, potential variation with age, and the factors that may explain the relationship.
Methods
Three complementary analytical approaches were employed to analyse data for a consistent cohort of children when they were aged 3, 5, 7, 11, 14 and 17 years, using data from the UK Millennium Cohort Study. Cross-sectional analyses were used to examine the association between family income and child mental health while exploring the role of child, family, and peer-related factors in elucidating the association. Panel data analyses were used to investigate the variation of the longitudinal association over time. Finally, the concentration index approach, coupled with its decomposition method, was used to quantify the degree of income inequalities in child mental health and analyse underlying factors contributing to the inequalities.
Results
Higher family income was associated with fewer child mental health problems; the magnitude of this gradient varied with age, being larger in adolescence than in childhood. The strength of the association was reduced after adjustment for factors reflecting Parental Stress and Investment theories, with the larger attenuation driven by Parental Stress factors. Accounting for peer-related factors during adolescence did not markedly attenuate the association further. The presence of income-related inequalities in child mental health was observed in childhood and adolescence, affirming the reported link between income and child mental health. Maternal depression and parent-child relationship emerged as the key contributors to inequalities across all ages.
Conclusions
The income gradient and income inequalities in child mental health observed in this research, along with the factors that underpin the relationship, suggest that income-support interventions may be a way to reduce child mental health problems, while also benefiting the wider family. Adolescence emerges as an important stage for implementing income interventions, offering a greater potential for reducing child mental health problems compared to other periods.

Keywords: health inequality
child mental health
income gradient
Advisor: Violato, M
Carson, C