VictorJuiz/thesis huggingface dataset:
The pathless sky: violence and culture in First World War air services

The First World War has almost always been the impetus behind new developments in critical studies of violence, in fields as diverse as psychology, strategic studies, and cultural history. Western Front infantry soldiers remain central to cross-disciplinary interpretations of combatant experience, identity, and community. This thesis reframes these fundamental relationships between war violence and community by considering an under-explored First World War battlefield: the air. It explores French, British, and American fighter pilots as a transnational combat culture emerging in dialogue with a distinctive, new type of warfare.
Though still largely relegated to popular history and one-dimensional stereotypes, First World War flyers vividly expose the wartime processes of navigating ‘unprecedented’ violence. Air services began the war affiliated with older military services and without a clear picture of what an aerial conflict entailed. As such, pilots themselves were disproportionately important to shaping the practices, rules, language, and uses of military aviation. The thesis follows fighter pilots through the process of learning to fly into informally organised combat, establishing their under-explored reliance on peacetime transnational aviation networks and elite flying ‘aces’ to share information and create communal practices. Pilots who flew in the three-dimensional battle space above the Western Front relied upon complex embodied relationships with their rapidly militarising aircraft to survive, a process that directly informed the ways in which they did, suffered, and survived aerial violence. The thesis explores the impact of these shared experiences, demonstrating First World War aerial violence’s profound disruption of military and class hierarchies and its post-war commodification as a cultural tool.
Allied aviators’ transnational combat culture was shaped by what this thesis terms ‘violent flight’, or the embodied experience of flying in a dangerous combat zone. As pilots considered this to be work, the thesis establishes a materially informed, geographically specific interpretation of pilots as gendered labourers to elucidate the development of their wartime communities into a unified combat culture. This deliberately transnational, multi-disciplinary approach urges new, post-centenary conversations about the place of violence in First World War historiography and establishes a specific, complex symbiosis between violence and war cultures.

Keywords: aviation
violence studies
history of war
Royal Air Force
Service Aéronautique
First World War
British military
air forces
French military
fighter pilots
World War I
aviation history
American military
military psychology
aerial combat
war violence
military history
military culture
transnational history
cultural history of war
history of medicine
combat culture
Royal Flying Corps
US Army Air Service
Advisor: Gregory, A
Gildea, R
Graphical ekphrasis in contemporary music

This thesis is, primarily, a treatise supporting a new approach to ekphrastic frameworks within contemporary music. Deriving from the Greek for ‘description’ [ἔκφρασις], ekphrasis traditionally relates to descriptions of art works as literary devices, with Keats’ Ode on a Grecian Urn (1819) being a well-known example. Through a re-evaluation and extension of Siglind Bruhn’s seminal work on ekphrasis within a musical context, I suggest that the construction of compositional grammars deriving from distinctly visual stimuli allows for a deeply embedded poetic and formal connection between the two media, which I deem a 'graphical ekphrasis'. To demonstrate this concept, three case studies are used which exhibit a variety of compositional methods and graphical sources. The first two studies adopt a largely work-centric focus, taking score analysis as the key interrogative method, supported by composer testimony or writings. The final case study explores the place of graphical ekphrasis in my own music, highlighting the potential of the rhetorical model and compositional method. Finally, an argument is proposed for the ways in which this concept may be developed, focusing on the construction of a composite framework for ‘transmedial’ aesthetics which can cut across both historical periodisation and disciplinary boundaries.

Keywords: ekphrasis
composition
transmediality
contemporary music
Advisor: Saxton, R
Cross, J
Probing iron-sulfur clusters redox states by incorporating an unnatural amino acid

Iron-sulfur clusters (FeS) are crucial redox cofactors in nature. They are involved in complex enzyme catalysis, acting as electron-relays. Techniques focusing on studying the electron loading on FeS-cluster relays during enzyme catalysis are rather scarce. Here, a novel approach is described to probe the redox state of FeS clusters by infrared (IR) spectroscopy, exploiting the versatility of this technique across a range of sample conditions and during turnover.
In this work, an unnatural amino acid p-cyano-L-phenylalanine (pCNF) was incorporated into the model protein spinach ferredoxin, which contains a [2Fe-2S] cluster. It is shown that pCNF can be used as infrared probe to prove the redox states of the [2Fe-2S] cluster. The integrity and correct functioning of the [2Fe-2S] cluster upon pCNF incorporation was confirmed by UV-Vis spectroscopy and electrochemistry. A small but reproducible shift in the streching frequency of the CN group of pCNF upon chemical or electrochemical reduction of the protein was observed by IR spectroscopy. Furthermore, detailed crystallographic characterisation was performed to compare the structures of the oxidised and reduced pCNF-containing ferredoxin, suggesting that the IR shift does not arise from a structural change but rather from the reduction of the [2Fe-2S] cluster.
Then this method was applied to more complex metalloenzymes containing FeS clusters. Experiments were then conducted on E. coli [NiFe] hydrogenase I to test whether an overexpression system could be suitable for extending the pCNF incorporation to Hyd-1. Although the overexpressed protein was found to behave normally comparing to the chromasomally encoded enzyme, it was decided not to continue with this enzyme due to difficulties in crystallising the overexpressed protein, unusual IR active site spectra features and limitation in yield.
Instead, the method was applied to [FeFe] hydrogenases from the sulfate reducing bacterium Desulfovibrio desulfuricans (DdHydAB), to investigate how the FeS clusters interact with the diiron prosthetic group to allow efficient catalysis. pCNF was incorporated successfully close to the proximal cluster in DdHydAB. From the preliminary IR results, there is a detectable difference in the band position of the cyano group in the F27CNF variant between the oxidised and reduced states on both apo- (lacking the binuclear site) and holo- (containing the full active site H-cluster) enzymes.
Overall, the research work in this thesis demonstrated a novel approach that applying an unnatural amino acid pCNF to metalloenzymes which contain FeS clusters to study the redox state of the FeS cluster by IR spectroscopy.

Advisor: Vincent, K
Electrochemistry of hydrazine

The electrochemical oxidation of hydrazine is of widespread importance particularly in the area of fuel cells and also provides the basis for chemical sensors for this toxic chemical. In this thesis, electrochemical methods including cyclic voltammetry, chronoamperometry and nano-impacts are employed to develop a comprehensive understanding of the reaction mechanistically and kinetically.
Chapter 1 introduces the basic principles of electrochemistry and electrochemical techniques while the generic chemicals, reagents and instrumentation used in this thesis are summarised in Chapter 2.
Chapter 3 reports the electrochemical characterisation of Palladium nanoparticles decorated graphene oxides nanoplatelets (Pd/GO) via nano-impacts in terms of the hydrogen evolution (HER) and oxidation reactions (HOR). The key conclusion is that only the zone of the individual platelets physically close to the electrode surface is effectively catalytic, and this insight provides the basis of the study of the Pd/GO catalytic ability towards hydrazine oxidation in Chapter 6.
The investigation into hydrazine oxidation starts in Chapter 4 where the focus is placed on the interpretation of the mechanism and kinetics of hydrazine oxidation at generic carbon surfaces, necessarily prior to any catalysis study. It was found that the Marcus-Hush theory is more appropriate for describing the voltammetry of hydrazine oxidation in comparison with the well-recognized Butler-Volmer theory.
In Chapter 5, the mechanism of hydrazine oxidation is probed further at carbon surfaces meanwhile with focus on the variation of the pH and buffer capacity of the electrolytes. It is revealed that the oxidation reaction is self-inhibited as the protons released from the oxidation easily combines with the electro-active N2H4 molecules (local to the working electrode surface) to form inactive N2H5+.
Chapter 6 targets the catalysis of the above-mentioned Pd/GO nanoplatelets towards hydrazine oxidation via studies using both macroelectrodes modified by drop-casting and by single entity electrochemistry using nano-impacts, demonstrating that the first electron transfer of the four electron, four proton oxidation of hydrazine is rate-determining and involves no proton loss in the initial step. The electro-catalysis towards hydrazine oxidation is then extended to bulk Palladium (Chapter 7) and Palladium nanoparticles (Chapter 8). Chapter 7 evidences the existence of a long-lived radical di-cation N2H5•2+ on the voltammetric timescale. Finally in Chapter 8, the markedly reduced over-potential for the oxidation at the surface of Palladium nanoparticles is identified quantitatively to arise from partly the increased surface area of the interface and partly an increased catalytic ability of the nanoparticles relative to the bulk Palladium.

Keywords: hydrazine oxidation
catalysis
electrochemistry
Palladium
Advisor: Compton, R
A model-based approach to address the commercialisation challenges of autologous cell therapies

Whilst many cell therapy products have been approved over the last 20 years, very few have achieved commercial success. With the increasing number of clinical trials and approved autologous cell therapy products, and high-value investment activities in the sector, making informed decisions for the commercialisation of these therapies is more and more critical.
This thesis makes an original contribution to knowledge by systematically breaking down the commercialisation challenges of autologous cell therapies into operational, tactical, and strategic level problems and employ a model-based approach in (1) modelling and assessing the needle-to-needle supply chain of autologous cell therapies, (2) capacity planning, and (3) further understanding the uncertainties in the commercialisation of autologous cell therapies.
Three models were designed and implemented to address this multi-level problem. Firstly, a discrete event simulation is used to identify the patient-to-patient supply chain bottlenecks to inform decisions to improve efficiency. Secondly, a mixed-integer linear programming problem was formulated to simultaneously optimise capacity planning and product portfolio selection. Finally, a risk-adjusted net present value valuation model, supported by an adaptive neuro-fuzzy inference system, was proposed to aggregate the learnings from past commercialised products and the operational and tactical models to aid investment and global entry decisions for the commercialisation of autologous cell therapies.
The developed supply chain and capacity planning models were used to simulate hypothetical United Kingdom case studies based on data collected from industry. The final valuation model was applied to a global case study to evaluate project valuation under uncertainties. The results of the modelling studies were found to be consistent with realworld observations and the models obtained can be useful for the cell therapy industry to make better decisions in commercialising life-saving therapies.

Advisor: Yang, A
Cui, Z
Meinert, E
Demoicratic authority: nature and ground of the EU’s right to rule

This thesis examines the nature and ground of the EU’s legitimate authority. It provides an original account of the preferred moral standard to evaluate such authority and studies its effects on the practical reasoning of those subject to the EU’s authority. The overarching objective of the thesis is to overcome court-centred discussions about conflicting claims to ultimate authority and Kompetenz-Kompetenz, and to initiate a debate on the more substantial and prior question of the moral grounds of the EU’s authority. The thesis draws on the rich literature concerning the political authority of states and the emerging discussions on international authority. It shows that searching for the moral ground of the EU’s authority can provide a fresh perspective on important legitimacy challenges in the EU, especially in relation to the authority of the Member States. This is not only theoretically important in that it highlights a previously neglected perspective on the EU’s authority claim. Beyond that, a whole range of factors illustrate the practical relevance of this investigation: growing nationalism in the Member States, ever more opposition from national constitutional courts, and ultimately Brexit highlight the fact that the authority of the EU is under strain. The three parts of the thesis reflect the three main steps of the argument. Part I makes the case that the concept of political authority (both the study of the nature and of the legitimacy of authority) is applicable to political communities and organisations beyond the state. Part II focuses on the nature, scope and addressees of the EU’s authority claim. It uses the notions of institutions and membership to understand the EU’s authority claim and to relate it to national and international authority claims. The main goal is to gain analytical clarity about what kind of authority the EU claims that is in need of legitimation. Part III engages with the appropriate moral standard to ground and evaluate the EU’s authority. It looks at both the EU institutions’ vision as well as at various implicit and explicit academic models used to evaluate the legitimate authority of EU law. In the final two chapters, the thesis proposes an original account of demoicratic authority, which takes the EU’s constitutional peoples as principal sources of the EU’s authority and is based on the value of the EU’s institutional set-up to allow the peoples to exercise joint self-determination beyond the state and thereby secure their autonomy as constitutional collectives.

Keywords: Political Obligation
Legitimacy
Demoicracy
Authority
Authority Claims
EU
Advisor: Eleftheriadis, P
Insights into viral RNA synthesis by the influenza A virus and SARS-CoV-2 RNA polymerases

Influenza A virus and SARS-CoV-2 are RNA viruses which cause severe respiratory disease and death in humans. Both encode RNA-dependent RNA polymerases (RdRps), which are responsible for synthesising viral RNA as part of a larger complex of viral proteins; for influenza A virus this complex is called a ribonucleoprotein (RNP), and for SARS-CoV-2 the replication- transcription complex (RTC). In this work I elucidate mechanisms used by influenza A virus and SARS-CoV-2 to synthesise viral RNA.
I first present evidence that the influenza A virus RdRp maintains the structural integrity of RNPs during transcription by binding to the 3′ end of viral genomic RNA. I then go on to demonstrate that in order to initiate viral RNA synthesis, the influenza A virus RdRp requires trans-activation through dimerization. Furthermore, I show that the influenza A virus RdRp co-opts the host protein ANP32A to help it form a second structurally-distinct dimer, which has the role of encapsidating nascent viral RNA into progeny RNPs. Collectively, these findings allow me to present a more detailed molecular model for how influenza viral RNA is synthesised and assembled into new RNPs.
One role of the influenza A virus RNP is to hide highly immunogenic viral RNA from cellular innate immune receptors such as RIG-I. The SARS-CoV-2 RTC instead synthesises 7- methylguanosine (m7G)-capped viral RNA which does not activate RIG-I. In this work I also show that one of the domains in the SARS-CoV-2 RdRp is a guanylyltransferase enzyme, which resolves a missing link in the mechanism of coronavirus m7G cap synthesis. Together, these studies improve understanding of the diverse mechanisms used by RNA viruses to synthesise viral RNA, and identify multiple functionally important sites on the influenza A virus and SARS- CoV-2 RdRps which could be exploited for future antiviral strategies.

Keywords: SARS
influenza
virus
coronavirus
polymerase
RNA
Advisor: Fodor, E
Optimising network modelling methods for fMRI

The activity of functional brain networks is responsible for the emergence of time-varying cognition and behaviour. Accordingly, functional connectivity (FC) in fMRI has been shown to be predictive of behavioural traits and psychiatric and neurological conditions.
Many studies estimate FC by calculating the average correlation across an entire fMRI scanning session data (static FC). A major goal of such neuroimaging studies is to develop predictive models to analyze the relationship between whole-brain FC patterns and behavioural traits. However, there is no single widely accepted standard pipeline for analyzing static FC. We proposed six steps for designing FC-based predictive models. This standardized framework for estimating static FC should accelerate both congruence and scientific progress within the neuroscientific community.
However, there is also increasing interest in studying the time-varying nature of FC in fMRI (time-varying FC). Typically, methods that measure time-varying FC have several limitations that bias the estimation of time-varying FC, to appear more stable over time than it actually is. We designed a new method, MAGE, that offers a potential explanation and a solution for the homogeneity of time-varying FC seen in existing approaches. This new framework for estimating time-varying FC showed that FC is not static over time and fluctuates on a sub-minute time-scale during resting-state fMRI.
This work also investigates the clinical applications of both static and time-varying FC. We found that MAGE estimated time-varying FC can provide a more precise understanding of how brain networks are related to cognitive abilities, both in health and disease. Lastly, we demonstrated thatMAGE can reliably capture the time-varying changes in FC across a range of behavioral and cognitive tasks, overcoming the limitations of most popular existing methods.

Keywords: deep learning
fMRI
time-varying functional connectivity
machine learning
functional connectivity
Advisor: Smith, S
Woolrich, M
Fine root dynamics and morphological traits in tropical forest ecosystems

A major challenge in tropical belowground carbon allocation ecology is to understand how fine root dynamics and traits change across different ecosystems and environmental gradients. This study examines the spatial variation of fine root carbon stock, productivity, fractional carbon allocation of total productivity to the fine roots, and residence time across pantropical forest types. At a regional scale, this thesis investigates the vertical distribution and seasonal variation of fine root carbon stock, productivity, mortality, and residence time in lowland Amazon rainforests and Andean montane forests. In addition, this thesis examines how fine root morphological traits are related to soil properties and climatic variables from lowland to montane forests.
My first study was the largest fine root carbon stock and dynamics study across tropical forests in South America, Africa, and Southeast Asia. The analysis was carried out separately in lowland and montane forests to understand the spatial variation and the effect of soil properties and climate variables. Root dynamics were better predicted by soil properties, such as soil sand content, soil pH, and soil phosphorus content than by climatic variables, and a different set of predictors were identified for lowland and montane forests. Lower values of mean annual productivity of fine roots were observed in upper montane forests and Southeast Asian lowland forests.
My second study examined the vertical and seasonal variation in fine root dynamics in the Amazon-Andes region. The vertical distribution of fine root carbon stock and productivity in the soil profile showed proportionally more stock and productivity in the surface soil in montane forests, particularly in lower montane forests, than in lowland forests, which was related to the thickness of the organic layer. Root mortality increased in the dry season in both lowland and montane forests.
I concluded my thesis by analyzing fine root morphological traits and the root-environment relationships. These features were strongly related to soil properties and some root dynamics traits. Root tissue density emerged as the principal trait in determining the variation in root morphological traits and the rate of root foraging for resources.
This is one of the first pan-tropical studies to explore fine root dynamics along environmental gradients in neotropical and paleotropical regions. I worked with the Global Ecosystems Monitoring network teams across old-growth tropical forests ecosystems. Ultimately, my thesis provides a common analytical framework for estimating below-ground dynamics in different environmental gradients across the tropics, and the results may be used for improving global vegetation models.

Keywords: Fine roots
allocation
productivity
residence time
fine root morphological traits
biomass
Advisor: Malhi, Y
Riutta, T
Girardin, C