VictorJuiz/thesis huggingface dataset:
A cryogenic trap for microwave-driven quantum logic using 43Ca+ ions

The encoding and manipulation of information using the quantum states of trapped ions currently represents one of the most promising routes towards the realisation of a universal quantum computer. Although quantum gates in this system were originally driven by lasers, an alternative approach that uses the magnetic field gradients generated by current-carrying structures integrated directly into the trap has gained traction in recent years. This laser-free approach offers a few advantages, but the implementation of fast two-qubit gates with fidelities below the threshold required for quantum error correction remains challenging. In this thesis I describe progress in an ion trap system aimed at improving the fidelity and speed of two-qubit gates driven by magnetic field gradients oscillating near the transition frequency of the qubit. Work is based on a hyperfine qubit in 43Ca+ that has not been used for quantum logic before. We operate at a static magnetic field of 28.8 mT, at which point the qubit frequency of approximately 3.1 GHz becomes to first order insensitive to field fluctuations, enabling an internal coherence time that is orders of magnitude larger than the duration of quantum gates. The strong magnetic field results in a complex energy level structure, with adjacent states in the ground level being split by several multiples of the linewidths of the cooling lasers. Nevertheless, we demonstrate cooling to a temperature of 0.5mK for a single ion, close to the Doppler limit, by exploiting dark resonances that form between fine-structure levels. Furthermore, we implement resolved-sideband cooling using two laser beams driving a Raman transition, achieving an average occupation number ¯n = 0.08 for the two-ion motional mode of interest. Experiments are carried out in a surface trap that is suitable for operation at room and cryogenic temperatures. It features a U-shaped microwave electrode, which produces a microwave magnetic field such that the field component coupling the qubit states exhibits a strong gradient, but significantly reduced amplitude around the trap centre. I discuss measurements of parameters that will impact twoqubit gate fidelity, such as heating rates, drifts in motional frequencies, ac Zeeman shifts and the spatial dependence of the microwave magnetic field. Furthermore, we demonstrate spin-motion entanglement for a single ion using the Mølmer-Sørensen scheme and present the results of initial attempts at a twoqubit gate, for which we measure a fidelity of 0.77(2). I also provide a brief analysis of dominant sources of error that will have to be addressed in future experiments.

Keywords: surface trap
trapped ions
calcium 43
microwave gates
laser cooling
two-qubit gates
laser-free gates
Advisor: Steane, A
Essays in finance

This thesis presents three empirical analyses that contribute to our understanding of how financial securities and intermediaries facilitate the allocation of resources between firms, consumers, and the government. Each paper investigates a distinct asset class and aspect of the resource allocation problem. The first paper explores the role of information in financial markets and the wisdom of crowds. The analysis uses a recently developed statistical technique to infer overlap in information sets of security analysts and develops a profitable trading strategy using analyst stock ratings. This finding highlights the prevalence of information diversity. The second paper focuses on government debt managers in national treasuries and finds that they actively choose the maturity structure of government bonds to minimize the expected costs of debt service while responding to demographic factors so as to enable risk-sharing across generations. The third paper leverages the new phenomenon of equity crowdfunding campaigns to disentangle entrepreneurial choices from investor preferences, differentiating the fundraising strategies that entrepreneurs pursue based on their experience and gender, and the funding outcomes they achieve. Taken together, these three studies contribute to our understanding of how intermediaries and securities allocate resources in various financial settings.

Keywords: financial markets
equity crowdfunding
maturity structure
gender
government debt management
information
wisdom of crowds
fundraising strategy
Breaking boundaries: a study of socio-cultural identities in archaic and classical western Sicily

This thesis investigates the burial practices of western Sicilian settlements during the late Archaic and Classical periods, incorporating comparative epigraphic evidence. Specifically, it explores the processes of creation and assertion of socio-cultural identities among migrant and indigenous communities, rather than focusing solely on their pre-defined outcomes. The prioritisation of ethnicity in the definition of collective identities in this region and period continues to influence the ways the agents and dynamics of contact are conceptualised. Such ‘ethnic labelling’ is not only unwarranted in view of the available evidence, but also obfuscates our understanding of other types of identities and historical processes. To challenge these existing frameworks and heuristic models, this thesis analyses the burial evidence from Palermo, Monte Castellazzo di Poggioreale, Monte d'Oro di Montelepre, Himera and Solunto, and draws on comparative epigraphic evidence from the curse tablets and Meilichios horoi of Selinunte, and the tophet of Mozia. By examining the markers and features used by western Sicilian communities to assert and negotiate their social identities, this thesis reveals the complex ways in which social hierarchies, economic drivers, historical circumstances and regional intervisibility shaped funerary and epigraphic practices. This thesis argues that patterns (and discontinuities) in these practices were not imposed by pre-defined ethnic rationales, but were rather selected by local communities in response to their unique context of social mobility, polity interaction and regional connectivity.

Keywords: ancient Mediterranean
death and burial
ancient Sicily
identity
epigraphy
Advisor: Prag, J
Crawley Quinn, J
Conflict and society in the Anglo-Saxon landscape

This thesis is about the communication of collective identity in the landscape of Anglo-Saxon England. The goal of this research is to examine the way landscape was perceived in historical writing, and how landscape shaped the strategies by which political authority and collective identity was transmitted. Thus, this thesis is concerned with the relationship between practice and perception. From a historiographical perspective, this work will bring together three aspects of research that are sometimes not in simultaneous dialogue, namely: landscape, identity, and political history, providing an opportunity to synthesise major historiographical work, and demonstrate the interconnectedness of topics often dealt with in isolation. The central contention of this work is that the landscape was not ‘passive’ or mute; it was ideologically charged and fiercely contested. Not only did this guide political and social strategies, but it also underpinned historical writing, and the landscape itself could be used for rhetorical effect. The first major argument of this thesis is that Anglo-Saxon collective identity was layered and flexible, and it cannot be entirely determined or discussed in ethnic terms. As such, techniques that communicated collective identity needed to be robust enough to incorporate complex layers of Anglo-Saxon self-perception. It will be argued that ‘conflict’, as a broad process and set of interactions which were interpreted and communicated in historical writing, was an important way to locate collective identity in a landscape context. The places where battles took place and were memorialised, where assemblies publicly asserted the status of the military elite, and where acts of reconciliation took place were perceived as being significant and were incorporated into wider landscapes. Thus, the perception of the landscape, and the layers of meaning that it evoked in Anglo-Saxon society could subvert the traditional dichotomy of ‘core-and-periphery’ by emphasising the ideological significance of landscapes that might traditionally be understood as ‘peripheral’, such as forests, moors, or fens.

Keywords: Anglo-Saxon
kingship
community
England
identity
warfare
landscape
Advisor: Blair, J
Multiparameter persistent homology of data

We explore two distinct topics in the field of topological data analysis: invariants and metrics for multiparameter persistence modules, and the homology of random geometric simplicial complexes.
We define a computable, stable invariant for multiparameter persistence modules, the multiparameter persistence landscape, and exemplify this invariant to be sensitive to the topology and geometry of multifiltered data sets. We prove a local bi-Lipschitz equivalence between two well-studied metrics for multiparameter persistence modules: the interleaving distance and the matching distance. A consequence of this equivalence result is that the multiparameter persistence landscape is a locally complete invariant for finitely presented multiparameter persistence modules.
Finally, we explore the asymptotic properties of Čech complexes built on compact Riemannian manifolds with non-empty boundary. We attain homological connectivity thresholds with identical leading terms. An upper threshold above which the Čech complex has homology isomorphic to the homology of the underlying manifold with high probability, and a lower threshold beneath which with high probability it does not.

Keywords: random geometric simplicial complex
persistent homology
Advisor: Nanda, V
Tillmann, U
Reducing mobile bearing dislocations in the Oxford Domed Lateral unicompartmental knee replacement implant

The Oxford Domed Lateral (ODL) mobile bearing Unicompartmental Knee Replacement (UKR) provides good clinical results, but the bearing dislocation rate is unacceptably high.
A systematic review and meta-analysis found that changing the articulating surface on the tibial component from a flat to a domed shape reduced the overall bearing dislocation rate from 17% to 3.7%. The risk of anterior/posterior (AP) dislocations was reduced substantially. Most dislocations were found to occur medially and with the knee in a flexed position.
Dislocations occur in flexion because when the knee is flexed, the lateral ligaments are lax. Therefore a mechanical rig, which allowed the relative position of components to be adjusted and the joint to be distracted, was used to determine the minimum Distraction required for a Dislocation (DD), which is related to the risk of dislocation. However, as testing with the rig was inefficient, a computational dislocation analysis tool based on the mechanical rig was developed and validated against results from the rig. The tool uses path planning algorithms from the field of robotics to allow the bearing to find a viable dislocation pathway. It was found that medial dislocations required a much lower DD than AP dislocations, which explains why medial dislocations are more common than AP dislocations. Further, changing the tibial surface from a flat to a dome increased the DD for AP dislocations substantially, which explains why this change primarily decreased AP dislocations.
A series of potential implant design changes were studied to see if they would decrease the DD for medial dislocations to that of AP dislocations as the risk of AP dislocation was considered acceptable. The simplest change to achieve this was to increase the tibial wall height by 2 mm, but to avoid the femoral and tibial components hitting if there is bearing wear, the minimum bearing thickness would have to be 5 mm. Alternatively if the centre of the femoral component sphere was moved laterally, the bearing made wider laterally and the wall height increased, then an acceptable dislocation rate would be achieved with a minimum bearing thickness of 4 mm. For both these modifications to be successful, surgeons must ensure that the bearing is not more than 4 mm from the tibial wall.
Cadaveric and clinical studies are required to assess the viability of the proposed changes. If the risk of dislocation can be minimised or reduced, more patients may benefit from the advantages of lateral mobile bearing UKRs.

Keywords: Osteoarthritis
Lateral knee
Oxford Knee
Bearing dislocation
Knee arthroplasty
Advisor: Murray, D
Mellon, S
Aspects of Hrusso Aka phonology and morphology

This thesis is part of a collective effort to support the Hrusso Aka language in its struggle for survival and revival. At a critical juncture in the history of this endangered language, this thesis addresses the pressing need for a systematic study of its phonology and morphology, necessary to lay the sound, scientific foundation, required by the newly emerging culture of written literature. It is also part of a larger scientific endeavour, paving the way for a future reference grammar and providing primary data and coherent phonological analysis for a diachronic study. As the title suggests, this work has two distinct parts. The first (Chapters 2-7) focusing on phonology, analyses the segmental structure of Hrusso Aka and, using the Featurally Underspecified Lexicon (FUL) model (Lahiri & Reetz 2010; Lahiri 2018), offers a detailed analysis of Hrusso Aka's sound system, explaining its "bewildering" complexity. In a chapter dedicated to tone, this thesis gives an account of the underlying tonal system and tone-stress interaction of the language. The second part (Chapters 8-9) deals with morphology, describing the word classes and word-building strategies of Hrusso Aka.

Keywords: Hruso
Underspecification
Aka (Hruso)
Complex consonants
Sentence-final particles
Tibeto-Burman languages
Featurally Underspecified Lexicon (FUL)
Advisor: Lahiri, A
Dalrymple, M
Characterisation of emergent and emerging human-infective RNA viruses

Improved understanding of the early adaptation of zoonotic, human-infective RNA viruses and the genetic factors leading to spillover will inform public health approaches attempting to limit the morbidity and mortality associated with these events. In this thesis, I use clinical microbiological methods to characterize the intra-host replicative and evolutionary dynamics of SARS-CoV-2 and bioinformatic approaches to investigate genetic factors associated with spillover of arboviruses.
Chapter one broadly reviews the field of virology.
Chapter two reviews the apolipoprotein B mRNA-editing enzyme, catalytic polypeptide (APOBEC) family of proteins, focusing on their emergence, diversification, and function, and summarizes the bioinformatic and functional evidence of their role in SARS-CoV-2 evolution.
Chapter three details the methods underlying the subsequent results chapters.
Chapter four describes the development and validation of single nucleotide polymorphism-based genotyping assays for identifying variants of concern in COVID-19 clinical samples. Their performance is compared to next-generation sequencing, demonstrating the superiority of the genotyping assays at a wide range of viral loads.
Chapter five uses amplification data generated from two COVID-19 clinical trials to explore factors associated with viral load and within-patient viral load dynamics, uses a novel polymerase chain reaction approach to quantify subgenomic RNA transcripts, and investigates the emergence and spread of the Alpha variant in the United Kingdom and the Zeta, Gamma, and Delta variants in Brazil.
Chapter six investigates the interaction between SARS-CoV-2 virological features and COVID-19 clinical outcomes leveraging patients admitted to intensive care within the REMAP-CAP convalescent plasma clinical trial. The null results in this chapter support severe COVID-19 pathology being primarily immune-mediated.
Chapter seven quantitatively tests the hypothesis that convalescent plasma treatment was responsible for the emergence of SARS-CoV-2 variants of concern using an intensively sampled cohort within the REMAP-CAP convalescent plasma trial. Using a variety of approaches, no evidence in support of convalescent plasma therapy as a general driver of immune-escape substitutions was found.
Chapter eight probes the genetic factors associated with human-human transmissibility of arboviruses, finding strong evidence for the role of CpG suppression in the host optimization of flaviviruses. The strong genetic barriers to spillover enable more focused surveillance of this informal classification of viruses.

Keywords: SARS-CoV-2
zoonoses
clinical virology
arboviruses
virus evolution
molecular diagnostics
Advisor: Simmonds, P
Smith, A
Harvala, H
Virtual court hearings: judicial perspective from Ontario judgments

The onset of the Covid-19 pandemic has sparked a phenomenal rise in virtual hearings in Ontario (Canada), much like in many other jurisdictions around the world. While video court participation has been available for decades, hearings have, until recently, remained courtroom-centric events and the possibility of dematerialized courts had seemed far off, if not far-fetched. Inspired by the latest evolution of justice delivery, this thesis explores the views of Ontario judges on the implications of virtual justice. What judges have to say about video-enabled testimony and adjudication matters enormously given their role in the administration of justice. Through a systematic content analysis of reported judicial decisions from the superior trial court and appellate court in Ontario between 16 March 2017 and 17 December 2021, this thesis tackles the question: To what extent do reported decisions by Ontario judges confirm or challenge concerns about virtual hearings expressed in scholarly debates about the topic? The analysis suggests that judges share many of the concerns articulated by scholars about proceeding virtually, such as the loss of solemnity and the expanded opportunity it lends to remote participants to behave in ways that undermine the integrity of the trial. At the same time, judges agree that proceeding virtually can be effective, fair, and in some cases, a more efficient alternative to the in-person format. The findings further reveal how judges have adapted their hearing management practices to accommodate the virtual court environment and assert control over remote sites. Overall, judicial conceptions of the modern trial appear to have evolved to the point that it is no longer seen as inevitably a courtroom affair.

Keywords: Covid-19
administration of justice
online hearings
online courts
remote hearings
online justice
judges
courts
pandemic
hybrid hearings
court technology
Ontario
virtual hearings
Canada
virtual justice
Advisor: Mulcahy, L
Tsalapatanis, A
Investigating large-scale change in volcanic time series data using machine learning analysis

Volcanic eruptions are characterised by large-scale transitions in behaviour, which include the transitions governing repose to unrest, unrest to eruption, and eruption to quiescence. Identification of these transitions is a fundamental goal in volcanology. This thesis aims to explore the use of machine learning approaches which are established for the monitoring of critical systems, such as healthcare or jet engine monitoring, to better understand the timing of large-scale transitions in volcanic activity. The first research chapter is an application of machine learning approaches to better understand the timing of eruption end, which has no systematic definition. Multi-class machine learning methods were applied to time series derived from volcano-seismic data from two volcanoes with contrasting eruption styles: Nevado del Ruiz, Colombia and Telica, Nicaragua. The resulting eruption end-dates agreed with previous, generic definitions of eruption end and provide an independent constraint on the timescale of eruption cessation processes. The second research chapter is an extension of this methodology to multi-parameter datasets from the 2005 – 2006 unrest and eruption of Augustine, Alaska. Both multi-class and novelty detection approaches, in which models are trained only on non- eruptive data, are applied. The resulting transition from non-eruptive to eruptive identified from the modelling agrees with previous estimates of the timing of dike initiation prior to eruption. Additionally, I explored the use of different types of data and different seismic catalogues for distinguishing between eruptive and non-eruptive activity. The final research chapter is an application of deep active learning to automated volcano-seismic event classification. Active learning is the process by which a machine learning model actively selects the training data which it learns from. This approach has the potential to reduce the quantity of labelled data required to train a successful model. The deep active learning approach is applied to two datasets from Nevado del Ruiz, Colombia and Llaima, Chile. Active learning models performed better on unseen testing data for both datasets and achieved better performance during training for the Nevado del Ruiz dataset.

Keywords: Volcano-seismology
Machine learning
Active learning
Novelty detection
Volcanology
Advisor: Mather, T
Pyle, D
Clifton, D
Rodgers, M
Bismash products and group algebras

We give a fully detailed and expanded version of the proof given in [5] that the bismash product arising from the standard factorization of the symmetric group on p + 1 letters, where p is a prime greater than 3, does not have the structure of a group algebra. We also obtain the same conclusion for several other bismash products constructed from small groups, namely A5, S5 and GL(3, 2). The methods used involve results from group theory, the representation theory of algebras, and the theory of blocks of finite groups.

Advisor: Erdmann, K
Rising powers, subordinate monopolization, and major interstate war

This dissertation argues that the association of rising powers with major interstate war is dependent on competition over subordinates. It develops the theory of subordinate monopolization, arguing that when rising powers seek to close and monopolize subordinates, this increases the probability of conflict with other major powers. By contrast, when rising powers pursue openness and common-pool approaches to subordinates, conflict is much less likely. This theory addresses two omissions in the field. Firstly, the failure to treat peaceful rises seriously, which problematizes the pathway between the existence of a rising power and revisionist approaches to the international order. Secondly, the absence of subordinates from accounts of major power politics, despite their value. Subordinate monopolization is compared and contrasted with three alternative approaches: the realist focus on relative power between major powers, the need for status recognition and reform of distributional and institutional structures, and locating foreign policy within a domestic political context. Through quantitative examination of rising power disputes between 1816 and 2010, and two pairs of case studies of rising power disputes in the long nineteenth century and early Cold War, robust evidence for the theory is found which is more consistent than for any of the alternatives. This leads to the conclusion that rising powers should be understood in terms of their interactions with subordinates, as well as with the major powers.

Keywords: revisionism
subordinate monopolization
rising powers
major power relations
norms
war
Advisor: Hurrell, A