VictorJuiz/thesis huggingface dataset:
Exploring the causes and consequences of phenological change in a wild bird population

Changes in climate shape biological populations. They can alter spatial distributions, the timing of life history events, and even the species themselves. We are now experiencing a period of rapid directional climate change, alongside seasonal fluctuations. This thesis investigates temporal changes in life history events, phenology, as a climate response. I explore the causes and population level consequences of change in breeding phenology of two wild bird populations from Wytham Woods, UK.
I test how great tits (Parus major) and blue tits (Cyanistes caeruleus) achieve temporal synchrony between the peak demands of their breeding and the peak abundance of their prey species (winter moth caterpillars - Operophtera brumata) in an inter-annually variable environment. I demonstrate great tit (Parus major) incubation behaviour fine-tunes the timing of hatching in response to ambient temperatures right up until hatching (Chapter two). Temperatures within the nest box, however, appear to play little role in the breeding phenology of blue tits (Cyanistes caeruleus) (Chapter two). I discuss the merits and limitations of statistical approaches for cue identification (Chapter six), finding the method and time period of data used both affect the cue identified and predictive accuracy.
The second part of this thesis explores the influence of a directionally changing environment on great tit phenology. I use an integral projection model (IPM) to predict population dynamics over the 21st century, showing that if the cues used by both interacting species change sufficiently closely, temporal synchrony can be maintained through both phenotypic plasticity and micro-evolution (Chapter 5). However, if the cues diverge mismatch will arise (Chapter 5) causing population declines when certain thresholds are passed (Chapter 4).
This work contributes to understanding how phenological synchrony is achieved, how it might change in the future, and its population impacts. In Wytham Woods it appears that great tits have a great deal of flexibility in multiple components of their breeding cycle, allowing them to retain synchrony with their caterpillar prey in a fluctuating environment. These birds are relatively resilient to negative phenological impacts from climate change. Only if the cues used by the predator and prey completely diverge do we predict consistent declines in population size during this century.

Keywords: Great tit
Population dynamics
Climate change
Phenology
Advisor: Coulson, T
Sheldon, B
Cole, E
Salience, authority, and resources: explaining victims' compensation in postwar Bosnia and Herzegovina

The aim of this thesis is to probe subnational varieties in compensation enacted for war victims in post-war Bosnia and Herzegovina. The current literature in transitional justice posits that mainly the nature of previous conflicts, democratic and economic development, international normative pressures, and the regional clustering of justice explain why only some post-war countries award material assistance to victims (Olsen et al. 2010; Kim 2012; Risse and Sikkink 2013; Powers and Proctor 2015). While these explanations provide critical insights into the processes behind compensation adoption across states, they do not explain why only some victim categories within a state secure compensation. Drawing on a large database of qualitative data ranging from interviews to newspaper articles collected during fieldwork in Bosnia, this thesis explores compensation for military and civilian war victims, victims of torture and sexual violence, and families of missing people. By zooming in on these victim categories in the Bosnian context, this thesis advances a new understanding of compensation for victims as an outcome of complex political, external, and economic influences exerted on the main domestic policymakers. This thesis uses a new analytical framework about the inter-category varieties in compensation that draws upon arguments about bounded agency of war victims who are constrained by the parameters of post-war political structures that to a large degree shape their strategies. I show that the different compensation outcomes can primarily be explained by the varying effectiveness of victims in convincing domestic political authorities that compensation is in their political interest by using framing and advocacy strategies at the domestic and international level. While such strategies are limited by the political and socioeconomic characteristics of the state, victim categories that are able to strategically frame their demands and access resources to mobilize are more likely to secure compensation adoption. Therefore, this thesis introduces three tools that victims can leverage – international salience, moral authority, and mobilization resources – that are shaped by both structural conditions and the victims’ agency.

Keywords: Sarajevo
Transitional justice
Srebrenica
Veterans
War
Bosnia and Herzegovina
Victims
Prijedor
Advisor: Power, T
Organizational modes of non-state armed groups

To what extent can two 'Modes' be found amongst non-state armed groups (NSAGs)? The Modes theory hypotheses that NSAGs are organized into two distinct Modes, either the 'Imagistic' or the 'Doctrinal' Mode, with each Mode characterised by a particular organisational structure and type of resource extraction. Previous preliminary research on this had three limitations: 1) it used a sample of only five groups; 2) "Galton's problem", i.e. non-independence of groups was not taken into account, and 3) the theory of resource extraction was underdeveloped. The present research overcomes each of these limitations.
First, can the patterns found in the 5-group case study be replicated with a larger sample? A dataset with 50 NSAGs was constructed, with variables that were derived from the theory and resembling those used for the 5-group case study. Analysis results showed that a few 'Doctrinal' variables were significantly correlated and 'Doctrinal' rituals had a frequency distribution as predicted. Yet, most correlations between all Modes variables were not significant, and analyses did not convincingly show that there were two distinct Modes.
Second, to what extent does "Galton's problem" (autocorrelation) play a role amongst NSAGs regarding their Modes properties? Data on relations between armed groups and their geographical locations were added to the sample. Using Moran's I, it appeared that two to four Modes properties were significantly autocorrelated. With geographical region as covariate, analyses were redone. Results remained basically the same as without regional covariate.
Third, what is the relationship between Modes and the type of Resource extraction? Resource types were operationalized and Resource type data were added to the sample of NSAGs. A theory on Risk, and a ROI (Return on Investment) and Risk index were developed. Regressions showed no change in ROI or Risk over time. Low ROI did not typically predict Doctrinal-related Modes properties, and high-ROI did not typically predict Imagistic-related Modes properties. The significance of relations between Modes properties and Resource types strongly depended on whether the analysis was a correlation or a regression. Overall, only a few relationships were significant and no consistent pattern emerged.
Limitations of the present research, and suggestions for further research are discussed, as well as an overall assessment of the Modes theory.

Keywords: group property
Modes theory
cultural evolution
Galton's problem
resource extraction
armed group
ritual
Advisor: Whitehouse, H
Atkinson, Q
Distributive interaction of algebraic effects

While monadic effects are widespread in modern functional programming, the idea of formulating computational effects as algebraic theories seems a less familiar one to programmers. One appealing feature of such algebraic effects is the clear decoupling between specification and implementation (or in more model-theoretic terms, syntax versus semantics). With monads, this distinction is arguably less clear.

But perhaps the most compelling reason for considering algebraic effects is the relative ease by which such effects can be combined. This point is clearly of much relevance to the semantics of programming languages since in much of modern software development, one often deals with multiple interacting effects. As a simple example, we may want a program that not only keeps track of some state across the computation (e.g. a parser consuming a string of text), but also account for the possibility of failure.

But it is well known that there is more than one way to combine these state and exception effects, each corresponding to a different composition. Neither can be considered canonical, since both have their use cases. It turns out that under the lens of algebraic effects, both interactions can be understood in terms of straightforward amalgamations of the respective equational laws. Both of these constructions arise naturally from the categorical structure of Lawvere theories, a more abstract formulation of equational theories as categories.

In this dissertation we seek to further the understanding of combining effects, especially from this more algebraic perspective. Of particular interest is a distributive tensor construction on Lawvere theories that does not seem to be very widely known. The distributive tensor plays a leading role in many examples of computational interest, and two such applications will be considered in some depth.

Firstly, from the observation that various combinatorial search strategies are characterised by two equivalent formulations as bunch monadic types and as more structured theories of monoids, we give a number of correspondence results. Furthermore, it is also shown that the list monad transformer is exactly a distributive tensor from the theory of monoids.

The second application considers in some detail a derivation of the geometrically convex monad, that is the combination of probabilistic and nondeterministic choice effects, called combined choice. As it is no easy task to capture the equational properties between probabilistic and nondeterministic choice, a technique is explored for reasoning about such equations visually by taking a geometric interpretation of the free models of combined choice, as convex polygons on a plane.

Advisor: Gibbons, J
Abou-Saleh, F
Improving geospatial models of risk for vector-borne, zoonotic diseases

Public health surveillance data are often incomplete, particularly where resources are lacking, but geospatial models can help to fill the gaps by providing estimates where data are sparse. By combining information on locations where diseases have been recorded with geographic data on environmental and socioeconomic covariates known to affect disease transmission using machine-learning models (such as boosted regression trees), niche modelling can generate fine-resolution, evidence-based risk maps for a variety of diseases of public health importance.
This thesis investigates the geographical distribution of two vector-borne, zoonotic diseases of public health importance: Plasmodium knowlesi malaria and yellow fever (YF). A number of new methodological approaches to niche modelling are developed for: mapping diseases whose distributions are impacted by multiple host and vector species, ameliorating spatial bias in disease reporting rates, and accounting for human vaccination coverage.
Chapter 2 investigates spatial variation in risk of human P. knowlesi infection across Southeast Asia. The infection risk model for P. knowlesi malaria is based on improvements to a standard niche modelling approach, and incorporates a novel joint distribution model to leverage data from a number of host species.
Chapter 3 estimates YF vaccination coverage through time across all age cohorts in every district/municipality of countries at risk of YF, globally. These estimates are used to estimate the additional vaccination coverage needed to prevent further YF outbreaks, and they provide information needed to account for population immunity when estimating YF infection risk.
Chapter 4 describes the development of a novel Poisson point process niche model, which is then used to predict YF infection risk in humans and demonstrates how vaccination coverage can be efficiently accounted for in disease niche models.
The disease risk maps of P. knowlesi malaria and YF produced through this thesis will act as resources to improve the targeting, implementation and evaluation of disease prevention, surveillance and control strategies. Methods developed to account for vaccination coverage, reporting rate biases, and complex transmission systems will be applicable to risk mapping for a range of vector-borne, zoonotic diseases of public health importance.

Advisor: Moyes, C
Golding, N
Hay, S
Lagrangian perspectives on ocean ventilation

Within the global climate system, the ocean operates as a vast store of important components such as heat and carbon dioxide that it exchanges with the atmosphere on timescales from days to millennia. Its facility to do so is in large part due to the process of ocean ventilation by which water is moved from the surface mixed layer, where it is in contact with the atmosphere, and transported through the subsurface. An understanding of ocean ventilation, therefore, is crucial in establishing the magnitudes and timescales of ocean-atmosphere exchange.
In this thesis, a predominantly Lagrangian approach is adopted, evaluating trajectories in an eddy-permitting numerical ocean circulation model to explore different aspects of the ventilation process. Following critical assessment of the fidelity of the trajectory analysis, a dynamical systems approach is applied to assess the role of ocean turbulence in the transport of ventilated water in the subsurface, with application to the subtropical gyre of the North Atlantic. The pathways of ventilation, represented by Lagrangian maps, are found to be highly chaotic and characterised by a non-dimensional filamentation number that compares the ventilation and filamentation timescales of the flow. Subsequently, the mechanisms and variability of ventilation of dense water masses in the high-latitude North Atlantic are considered, a crucial component in present-day oceanic uptake of heat and carbon dioxide. A Lagrangian approach allows us to link surface processes to their subsurface signature, and reveals that variations in annual re-entrainment establish substantial inter-annual variability in the water that enters the deep ocean. Furthermore, the results reveal that mechanisms of ventilation in the numerical simulation differ substantially from observations, with possible implications for the fidelity of future climate projections. Finally, the translation into the ocean interior of a biologically and chemically active tracer, such as carbon dioxide, is considered, and how this is dependent on the interaction between ventilation, circulation and biogeochemical processes. From observations in the Weddell Gyre, it is shown that biological export and the horizontal circulation are critical in sustaining regional uptake of carbon dioxide from the atmosphere.
Broadly, these various results serve to emphasise the complexity of the ventilation process and its associated role in the oceanic storage of climate-relevant components, from the chaotic nature of pathways, short timescales of variability, its difficulty of representation in numerical models, and its interaction with the biogeochemical system.

Advisor: Johnson, H
Marshall, D
Correlation of optical anisotropy with structural changes in Ge2Sb2Te5

Ge2Sb2Te5 (GST) is an established phase-change material that undergoes fast reversible transitions between amorphous and crystalline states with a high electro-optical contrast, enabling applications in non-volatile optical and electronic memories and optically-switchable structured metamaterials. This work demonstrates that optical anisotropy can be induced and recorded in pure and doped GST thin films using circularly polarised light (CPL), opening up the possibility of controlled induction of anisotropic phase transition in these and related materials for optoelectronic and photonic applications. While the amorphous-to-crystalline phase transition in GST has generally been understood to proceed via a thermal mechanism, significant optical anisotropy (measured by circular dichroism (CD) spectroscopy in this work) strongly suggests that there is an electronic athermal component of the phase change induced by the handedness of circularly polarised nanosecond laser pulses and implies the existence of chiral structures or motifs. Optically active and inactive regions in the films have also been studied using X-ray and electron diffraction and spectroscopic techniques in order to obtain a structural picture that can be correlated to the optical changes observed and the findings offer surprising evidence of the nature of the phase transition. Regions exhibiting higher CD signal intensities were found to be mostly amorphous with elemental phase separation observed within modified surface features. Several mechanisms are proposed for the observed phenomena, including the retention of chiral crystalline fragments in laser- irradiated and melt-quenched amorphous regions, which could explain the results of CD spectroscopy. This may be extended to other material systems and harnessed in potential metamaterials, plasmonics, photonics or chiroptical applications.

Keywords: Circular dichroism spectroscopy
Reduced density function (RDF) analysis
Phase change material
Chalcogenide
Athermal amorphous-to-crystalline phase transition
Optically-induced chirality
Advisor: Kirkland, A
Borisenko, K
Raising European citizens? European narratives, European schools and students' identification with Europe

Fostering identification with Europe among citizens could legitimise European integration. Whether such an identity exists, however, remains an on-going debate among scholars. This research returns to the foundations of how a European identity is constructed, transmitted and transformed. It explores narratives of European identity in a carefully chosen context – European Schools for children of EU officials – where identification with Europe should mirror official EU visions. A qualitative content analysis explores narrations of 101 students collected during interviews and focus groups across three schools, and analyses documents and interviews with EU officials, school directors and teachers. This analysis reveals a descriptive puzzle: official EU and European School propositions of (multi-) national narratives differ markedly from teachers' and students' conceptions of cosmopolitan and transnational identities. The EU constructs an out-group of its own nationalist past and non-EU citizens. On the other hand, students construct an explicitly European in-group, but differentiate themselves from more national and less mobile lifestyles. This disparity, in turn, reveals a causal puzzle about how differences in narratives emerge. I use process tracing to elucidate the relationship between European schooling and students' identification with Europe. The results show a distorted transmission where broader EU goals are elaborated and transformed by teachers and further fuelled by interactions amongst students with similarly mobile and multilingual backgrounds. I develop a dual mechanism to understand how the varieties of identification with Europe develop: the concept of "doing Europe" explains how students nourish a transnational social network; "telling Europe", on the other hand, considers students' exposure to European symbols and stories in school and both national and anti-nationalist narratives provided by teachers and peers. Together, this leads to a transformed but ultimately European in-group understanding. Overall, this project underlines the complexity of identity construction, given that top-down transmission gets altered even in this favourable case. Specifically, it informs future research on European identity by detailing peculiar narratives and offering a causal approach to how these narratives emerge.

Keywords: education
Europe
process tracing
citizenship
European identity
nationalism
identity
teachers
European Union
schools
narratives
Advisor: Fisher, S
Impact of tidal turbine support structures on realizable turbine farm power

This thesis discusses the importance of tidal turbine support structures through analytical and computational modelling. A head-driven analytical channel model was first developed to determine the sensitivity of the flow to the presence and type of support structures. It showed that there was a significant potential reduction in farm power output even when only considering approximate force coefficients for rotor and support structure. To confirm these findings, computational simulations were performed on a full-scale turbine to obtain more accurate force coefficients considering full rotor-support structure interactions.
The flow interaction effects between the rotor and its support structure were studied using Computational Fluid Dynamics (CFD) for different support structure shapes for a range of tidal velocities including the power-capping zone. The integrated rotor force coefficients were higher in the presence of the cylindrical support structure than the elliptical support due to the higher opposing thrust from the cylinder in the channel redirecting the flow and increasing the flow velocity over the top half of the rotor. The presence of rotor caused a drop in the stream-wise forces on the support structure. The amplitude of the stream-wise sectional forces along the support structure height was lower in the case of an elliptical than a circular cylinder due to more streamlined shape of the ellipse.
At device scale, the computational model was used to study the turbine performance in the power-capping zone by pitching the blades to feather. The influence of pitch-to- feather power-capping strategy was examined by studying the forces and angle of attack on the turbine blades, and the wake at three different blade pitch angles. Increasing blade pitch angle resulted in a significant drop in the average load on the blade. Also since the tidal channel flow has a shear in its velocity profile, the influence of shear on turbine performance was studied by comparing it to the same turbine in a uniform flow.
The analytical channel flow model was used to investigate the characteristics of tidal stream energy extraction for large tidal farms deployed in tidal channels with specific focus on the limitations to realizable farm power due to turbine support structure drag and constraints on volume flow rate reduction. The force coefficients dataset from computational modelling was used to obtain a better estimate of the farm power output. Support structures were seen to contribute significantly to the overall resistive force in the channel and thus reduce the overall flow rates in the channel, leading to losses in realizable power. Over a wide range of channel characteristics, realistic levels of support structure drag lead to up to a 10% reduction in realizable power, and an associated reduction in the number of turbines that can be economically installed.

Keywords: CFD
tidal
Advisor: Willden, R
Galois actions on non-abelian finite groups and applications

In this thesis, we consider the Galois actions on some finite characteristic quotients of the geometric fundamental groups of once-punctured elliptic curves. In particular, those of which can be naturally regarded as non-abelian lifts of usual mod &ell; Galois representations attached to elliptic curves. We also find its applications to some questions in the realm of Diophantine geometry.

Advisor: Kim, M