VictorJuiz/thesis huggingface dataset:
Virtually inconceivable: Ontological insecurities and the rise of geopolitics and sovereignty in EU cybersecurity policy

The policy domain of cybersecurity has become inundated with geopolitical concepts and sovereignty appeals over the last decade, arousing the interest of scholars and policymakers alike regarding how such a notable shift has implicated the behaviour of actors in cyberspace. Scholarship conventionally expects state actors with cyberwarfare and intelligence capabilities to voice geopolitical reasoning and sovereigntist claims, overlooking the presence of such discourse within the European Union’s (EU) cyber policies. Yet, the EU’s agenda of ‘technological sovereignty’ and its invocation of geopolitical metaphors have become increasingly prevalent in its cybersecurity policy, whereupon ‘European sovereignty’ has emerged as a priority—defying expectations based upon the EU’s traditional eschewal of geopolitics, and scholarly assumptions about its capabilities as a cyber actor. Thus, to explore this development, I ask how, and why, such geopolitical and sovereigntist language has emerged in EU cybersecurity policy, and the implications of such language upon the EU’s self-conception as a cyber actor. Adhering to an interpretive- qualitative methodology, I develop a chronology of EU cybersecurity policy development from 2009-2020 and conduct discourse analyses of documents and elite interviews. My dissertation undertakes a sustained focus upon the ontological dimension to cyber policymaking, particularly ontological insecurity—an approach not yet leveraged in this empirical context. Through the lens ontological insecurity, I argue that the emergence of geopolitical and sovereigntist language in EU cybersecurity policy is a consequence of how EU cybersecurity policy has centred upon the management of particular ontological insecurities in cyberspace, for which policymakers have leveraged discursive strategies oriented around the delegitimization, and later legitimization, of geopolitics. Sovereignty, in turn, emerged as a response to insecurities elicited by the EU’s decision to ‘speak in geopolitical terms’, and has become prevalent as a means of differentiating the EU from geopolitical actors in cyberspace. Overall, my dissertation illustrates how insecurities about the EU’s past, cyberspace as an environment, and relations with cyber actors have shaped the dominant ideas and policy responses over the course of 2009-2020, enabling the emergence of sovereigntist and geopolitical language in this contemporary stage of the EU’s development. Significantly, it unmasks a key tension underlying EU cybersecurity policy: while the EU has increasingly articulated traditional, state-centric assumptions about geopolitics in cyberspace; simultaneously, EU policymakers have sought to represent the EU as transcendent of this dynamic for which the vocabulary of ‘European sovereignty’ has been leveraged to differentiate the EU from geopolitical actors in cyberspace.

Keywords: European Union
delegitimization
sovereignty
cyberspace
ontological security
cybersecurity
geopolitics
Advisor: Johnson, R
Vulnerable bodies: the poetics of protection in the Old English Metrical Charms

This thesis offers the first complete metrical and stylistic analysis of the twelve Old English metrical charms. The verse found in these texts is rife with apparent irregularities, and scholars have historically labeled them poor verse, or have neglected discussions of style in favour of anthropological and source studies. Those who have addressed the poetics of the charms have largely dismissed them as meaningless features meant only to hypnotise the listener. Yet this thesis argues the metrical charms are not arbitrary sound, but narrative verse, containing powerful imagery that invokes themes appearing elsewhere in the Old English literary corpus. They also feature significant rhetorical and ornamental features lauded as aesthetic achievements in other Old English verse.
Drawing on past scholarship on Old English style and merging close reading with rigorous metrical analysis, this thesis argues that the unusual metrical and stylistic features of the charms are not defects but a function of their genre, the substance of a meaningfully different Old English poetic style. This study explores the ways in which the charms’ stylistic ornamentation, imagery, and word choice highlight their central ideologies and anxieties, and the ways in which supposed metrical ‘irregularities’ in fact serve aesthetic purposes and accommodate prescribed magical formulae. It invites us to reconsider the criteria by which we judge Old English verse, and to challenge dichotomies of ‘correct’ and ‘incorrect’ metre, rigorous ‘classical’ verse and ‘decayed’ late verse.
Stylometric analysis and close reading offer literary insight into the charms as well, and this thesis explores the ways in which the charms safeguard human individuals and communities against invasive agents. I argue that the charms equate disease, physical and spiritual dangers, and even falling victim to theft, with submission, defeat, or loss of control in intimate conflict with the Other. These texts seek to reinstate boundaries that have been violated — civilization and wilderness, inside and outside — by maintaining or restoring human bodies and spaces as inviolate wholes.

Keywords: history of medicine
Old English
metre
gender
metrical charms
style
poetics
Advisor: Leneghan, F
O'Donoghue, H
Investigating the roles of CDA and DCTD in cancer nucleotide metabolism

Nucleotides play essential roles in cellular function, including as components of the nucleic acids DNA and RNA. Cancer cells have elevated proliferation and DNA replication, necessitating a reliable supply of nucleotides from the nucleotide de novo synthesis and salvage pathways. These have consequently been exploited as targets for nucleotide analogue chemotherapy. Resistance to chemotherapy can arise from enzymes in the synthesis and salvage pathway, including upregulation of the pyrimidine salvage enzyme cytidine deaminase (CDA). CDA functionally overlaps with the salvage enzyme deoxycytidylate deaminase (DCTD), and it is uncertain whether either enzyme is the principal deaminase and whether they deaminate cytidine nucleotides derived from nucleotide synthesis, in crosstalk between the synthesis and salvage pathways. I investigated these queries by setting up and optimising targeted HPLC-MS/MS systems for nucleic acid composition and nucleotide pool analysis, using them to measure isotopically labelled nucleotide precursor incorporation into cell lines and observe effects of CDA and DCTD siRNA knockdown (KD). The nucleoside analysis platform I developed is capable of sensitive analysis of nearly 20 nucleosides, whereas the free nucleotide analysis platform has analyte sensitivity comparable to or lower than those reported in literature and can detect most nucleotide phosphates without sample purification steps. The KD and pulse-chase experiment provided evidence that CDA and DCTD are mutually redundant in deaminated 2’-deoxycytidine nucleotides and validates previous reports that DCTD has low activity against cytidine monophosphate. Additionally, there was no impact of CDA and DCTD KD on L-glutamine labelling of cytidine nucleotides, suggesting that de novo synthesis-derived cytidine nucleotides are not dephosphorylated and deaminated in significant amounts. It was also observed that nucleotide phosphate interconversion occurs at much shorter timeframes than one hour.
Taken together, the studies in this thesis, using targeted and sensitive MS analytical methods, support the theory of redundancy of the CDA and DCTD, with implications for their roles in resistance to cancer chemotherapy as well as in other disease states.

Keywords: nucleotide
cancer
metabolism
Advisor: Kriaucionis, S
Kessler, B
Goding, CR
Computational analysis of host/pathogen coevolution

In this thesis, I present my research on host/pathogen coevolution in several different systems and on different time scales. The thesis comprises multiple parts and shows how advances in computational methods can be applied to a broad range of questions, from basic research to issues of immediate clinical relevance.
Chapter 1 examines this host pathogen coevolution in a nonhuman system, looking at giant viruses, satellite viruses, related transposable elements found in eukaryotes and giant viruses, and individual 'jumping' homing endonuclease genes (HEGs) found in all three. Unfortunately, due to enormous amounts of time over which some of the elements involved have diverged, it is difficult to draw reliable conclusions here. However, the novel identification of HEGs in satellite and giant viruses shows a likely solution to the question of the mechanism for the horizontal gene transfer of HEGs between dissimilar phyla.
Chapter 2 focuses on the coevolution of humans with pathogens. This can be seen in the influence of archaic hominid immune genes on the modern immune system, and what appears to be the introgression of archaic hominids' granular adaptation to local pathogens when modern humans expanded out of Africa. The fact that these archaic HLAs have retained this regional granular adaptation for tens of thousands of years suggests some sort of survival advantage. While previous work has shown that there is different selective pressures acting on different class I HLAs, this chapter shows that this relationship is retained when looking exclusively at archaic derived HLAs. Selective pressures acting on HLA-A but not HLA-B have not previously been described, and Chapter 2 identifies the suppression of endogenous retroviruses as possibly being one such selective pressure.
Chapter 3 examines the granular adaptation of HIV-1M to humans in Sub-Saharan Africa by looking at correlations between human genetic diversity and HIV diversity. Unfortunately, widespread genotyping of HIV patients in Sub-Saharan Africa is not available, but linguistic diversity has previously been specifically shown to correlate with human genetic diversity in Sub-Saharan Africa, providing a useful proxy with which to make comparisons. My results show that linguistic diversity, and by extension human genetic diversity, does indeed correlate with both HIV subtype and amino acid sequence diversity in the region. This runs contrary to the dominant paradigm that HIV subtypes are artefacts of founder effects and may explain some of the difficulties in creating an HIV vaccine despite over 30 years of research on the subject.

Keywords: homing endonuclease gene
Denisovans
HIV
HLA
virophage
polinton
linguistics
Neanderthals
phylogenetics
Advisor: Iversen, A
Thomas, A
Safe and certified reinforcement learning with logical constraints

Reinforcement Learning (RL) is a widely employed machine learning architecture that has been applied to a variety of decision-making problems, from resource management to robot locomotion, from recommendation systems to systems biology, and from traffic control to superhuman performance in video games. However, RL has experienced limited success beyond rigidly controlled or constrained applications, and successful employment of RL in safety-critical scenarios is yet to be achieved. A principal reason for this limitation is the lack of a systematic formal approach to specify requirements as tasks (or learning constraints), and to provide guarantees with respect to these requirements and constraints, during and after learning. This work addresses these issues by proposing a general method that leverages the success of RL in learning high-performance controllers, while developing the required assumptions and theories for the satisfaction of formal requirements and guiding the learning process within safe configurations. Given the expressive power of Linear Temporal Logic (LTL) in formulating control specifications, we propose the first model-free RL scheme to synthesise policies for unknown black-box Markov Decision Processes (MDPs), where the reward function is formally shaped by an LTL specification. We convert the given property into a Limit Deterministic Buchi Automaton (LDBA), namely a finite-state machine expressing the property. Further, by exploiting the structure of the LDBA, we shape a synchronous reward function on-the-fly, and we discuss the assumptions under which RL is guaranteed to synthesise control policies whose traces satisfy the LTL specification with maximum probability possible. This probability (certificate) can also be calculated in parallel with policy learning when the state space of the MDP is finite: as such, the RL algorithm produces a policy that is certified with respect to the property. We also show that our method produces "best available" control policies when the logical property cannot be satisfied. The performance of the proposed method is evaluated via a set of numerical examples and benchmarks, where we observe an improvement of one order of magnitude in the number of iterations required for the policy synthesis, compared to existing approaches whenever available.

Keywords: formal methods
Markov decision processes
reinforcement learning
policy synthesis
temporal logics
Advisor: Abate, A
Kroening, D
Immunological responses to retinal gene therapy

Dose-dependent inflammatory responses in adeno-associated virus (AAV)–mediated retinal gene therapy trials have restricted the use of high vector doses and impeded the ability to enhance therapeutic efficacy. Characterising the nature of this response, and devising methods to overcome it, are thus becoming increasingly important in the clinical application of gene therapies. In the experiments herein, I investigated the composition, timing, and magnitude of the cellular immune response to retinal gene therapy in mice using quantitative flow cytometric analysis. I observed a significant increase in retinal leukocytes from 14 days after subretinal injection of an AAV8 vector expressing green fluorescent protein (GFP). These consisted of a constant population of resident microglia and infiltrating peripheral leukocytes including macrophages, natural killer cells, CD4 and CD8 T cells, and natural killer T cells. An identical vector at an equivalent dose encoding a human therapeutic transgene elicited a diminished response compared to paired injections with a GFP vector. However, the proportions of the leukocyte populations remained similar, suggesting a common mechanism of immunity. In addition to the induction of a cell-mediated immune response, innate detection of AAV vectors may directly restrict transgene expression. Preliminary evidence suggested in vitro AAV transduction may be limited by the anti-viral nucleic acid sensors Toll-like receptor 9 and cyclic GMP AMP synthase, suggesting possible detection of transgenic AAV genomes. I also showed that the immunomodulatory drug hydroxychloroquine can significantly enhance AAV transduction in vitro, ex vivo, and in vivo, with indirect indication of the partial antagonism of TLR9. The lack of structural change in the retina following subretinal hydroxychloroquine delivery indicates that it could be a safe adjunct for improving retinal gene therapy efficacy.

Keywords: immunity
adeno-associated virus
AAV
hydroxychloroquine
inflammation
retinal gene therapy
Advisor: Xue, K
Maclaren, R
A problem of industries and regions: unemployment and structural change in Britain during the interwar years and 1980s

The most serious employment crises in twentieth-century Britain occurred during the interwar years and the early 1980s, when, in both cases, the unemployment rate climbed to over 10% in aggregate and remained high for many years. Both downturns also coincided with periods of structural change in the economy: in the interwar years, export-oriented heavy industries lost out to expanding light manufacturing industries, and, during the early 1980s, the decline of manufacturing accelerated as the economy pivoted toward service industries and finance. A large literature on these recessions has dealt with aggregate demand fluctuations and supply factors, but this mainly macroeconomic focus has limited our understanding of the impacts of structural change. This thesis investigates the interaction of structural change and the business cycle in both the crises using newly-digitized industry microdata and econometric methods. How did structural change affect these employment downturns, and what were the consequences for workers and the labor market? I find that in both periods, secular structural change contributed significantly to, and was amplified by, the cyclical downturn. This interaction caused the im- pact of the interwar and early 1980s recessions to vary across industries, regions, gender, and demographic groups, with some workers experiencing persistent disadvantage.
Chapter I reviews how structural and cyclical unemployment were understood by economists in a pre-Keynesian setting. Chapter II analyzes interwar unemployment with novel data, finding that structurally-disadvantaged industries had higher unemployment and that the labor market was more flexible for some workers than others. On the early 1980s, Chapter III argues that structural change caused a jobless recovery from the 1980-1981 recession. Finally, Chapter IV uses individual-level data to demonstrate that this recession disproportionately affected workers from particular industries, regions, and demographic groups.

Keywords: structural change
interwar
1980s
unemployment
Advisor: Offer, A
O'Rourke, K
On the adversarial robustness of Gaussian processes

We study the robustness of Bayesian inference with Gaussian processes (GP) under adversarial attack settings. We begin by noticing how the distinction between model prediction and decision in Bayesian settings naturally leads us to give two different notions of adversarial robustness. The former, probabilistic adversarial robustness, is concerned with the behaviour of the posterior distribution, formally characterising its worst-case attack uncertainty. On the other hand, adversarial robustness is concerned with local stability of the model decision, and is strictly correlated with bounds on the predictive posterior distribution of the model.
In the first part of this thesis we show how, by relying on the Borell-TIS inequality, the computation of probabilistic adversarial robustness can be translated to the solution of a set of optimisation problems defined over the GP posterior mean, variance and specific derived quantities. In order to solve these, we develop a general framework for the lower- and upper-bounding of GP posterior parameters, which relies on interval bound propagation techniques, the computation of linear and lower upper bounding functions and the solution of linear and convex-quadratic programming problems. Employing the central limit theorem for stochastic processes, we then demonstrate how the derived bounds can also be used for the adversarial analysis of infinitely-wide deep BNN architectures.
In the second part of this thesis, we show how a suitably defined discretisation of the GP latent space can be used to convert the computation of adversarial robustness to the solution of a finite number of optimisation problem over a set of uni-dimensional Gaussian integral functions. We proceed by extending and adapting the GP optimisation framework developed in the context of probabilistic robustness to the formal solution of these integrals. We rely on the theory of branch-and-bound optimisation algorithms to formally prove that our method is guaranteed to terminate in finitely-many steps to an ϵ
-exact solution of the problem, for any ϵ>0
selected a-priori. Furthermore, the method developed is anytime, in that it can be stopped at any point during its computation and still provide formal lower and upper bounds that can be used to certify the GP adversarial robustness. By carefully designing suitable prior functions, we then show how GPs provide us with competitive and state-of-the-art models for their application in affective computing. We finally rely on three datasets for affect recognition from physiological signals as a real-world testbed to analyse the scalability and the practical feasibility of the methods we have developed for the verification and interpretation of GP models, which we argue are crucial for the development of machine learning systems that have to interact with humans in clinical situations.

Advisor: Kwiatkowska, M
Stronger than they seem: 'parchment barriers' and the state of judicial independence in Hungary and Poland

Judicial independence has been a particularly salient issue in the context of the rule of law in democracies and hybrid regimes in recent years. Actions to encroach on this independence are taken very seriously, evidenced by the Article 7 procedures against Hungary and Poland. A political consensus seems to exist that certain legal changes to their constitutional courts should be condemned as threats to judicial independence. In empirical works on the subject, however, a very different consensus exists, finding no strong relationship between ‘parchment barriers’, or de jure independence, and de-facto judicial independence. The gap between the political and scholarly consensuses is an important one, because resolving it should dictate policy responses to the very real problem of captured courts. This begs an interesting question– how have legal changes to the regulation and makeup of judiciaries affected actual judicial outcomes? This paper first inspects and reconsiders the key characteristics of de jure judicial independence, showcasing the need for more conceptual clarity between the relevant legal or constitutional provisions and the actual changes to the structures which judges, governments, and citizens operate within. It then analyzes constitutional court behavior in two country cases: Hungary and Poland. A two-part analysis is performed for each country case. First, the effects of all legal changes which occurred on overall court outcomes are estimated. Second, the specific mechanism of how changes to the judicial appointment process can influence individual judge behavior is investigated. The results of these analyses provide tentative evidence that the legal changes to the constitutional courts of both countries are related to a decrease in the likelihood of a case being decided against the preferences of the ruling government. In both cases, this appears to be at least partly driven by the behavior of judges appointed through more politicized appointment processes, which rule in favor of the government more often. Ultimately, the paper provides support for the notion that formal rules can and do affect behavior. It also highlights the inherent relationship between calls to increase the democratic representation and legitimacy within minority institutions, and the greater possibilities of their majoritarian capture.

Keywords: Democratic Backsliding
Poland
Hungary
Central Europe
Judicial independence
Judicial Politics
CEE
Constitutional politics
Advisor: Zubek, R