VictorJuiz/thesis huggingface dataset:
Sixteenth century printing types and ornaments of Scotland with an introductory survey of the Scottish book trade

This thesis comprises a catalogue of the sixteenth century printing types and ornaments of Scotland, along with an introductory survey of the Scottish book trade. It is divided into two parts, and includes an appendix describing the 337 books discussed in the study.
The first part surveys the Scottish booktrade from its first stirrings in the late fifteenth century until the departure of King James VI to England in 1603. It considers, in particular, the European context of the trade, showing the strong connections Scottish writers and booksellers had with continental printers. Using the typographic evidence presented in the second part of this thesis, it is argued that Scottish printers had neither the resources nor the ability to compete with their continental counterparts in distributing such books, and therefore had to rely almost exclusively on the patronage of the Crown and the Scottish government for the survival of their businesses. The consequent manipulation of the press, by both Catholics and Protestant alike, is considered in this context, as is the increasingly sophisticated efforts of the English to control the trade of printed books in Scotland. The first section concludes by discussing the part that the Scottish booktrade played in the evolution of Scottish literary culture and education.
The second part comprises a catalogue of the sixteenth century printing types and ornaments of Scotland. This section is intended to provide evidence about the supply and distribution of typographical materials throughout the country, discussing the connections earlier printers had with suppliers in France, England, and the Low Countries, as well as the various trends in design that were favoured by an increasingly sophisticated Scottish literary market. The catalogue itself comprises 76 type synopses assembled by the author, as well as reproductions of 35 alphabets, 8 factotums, 12 printers’ devices, 1 title-page border, 6 Coats of Arms, 27 woodcuts, and 31 head and tailpieces, accompanied by extensive notes, covering aspects of provenance, supply, design, and use by other printers.
The appendix describes the 337 books discussed in this thesis, giving short-titles, collations, descriptions of ornamentation, a census of copies, and references for each item. Extended notes are also provided for most books, detailing relevant bibliographical information, much of which is derived from the surviving printers’ inventories. This section assigns new dates and printers to a number of Scottish books based on the evidence presented in part two. Previously unrecorded variants based on a first-hand examination of the books are also included.
Number of words in this thesis: 100,888.

Keywords: sixteenth century
Scotland
type ornaments
16th century
type
printing
type-founding
book trade
Scottish book trade
book industries
book industry
Developing a framework for modelling outcomes in diabetes - A case study with ASCEND

Decision-analytic modelling is used to synthesise clinical and economic data to evaluate health outcomes and costs of novel healthcare interventions. Diabetes is associated with disabling and costly complications which develop over time, and such models are crucial to capture the impact of treatment over a person's lifetime. Most diabetes simulation models to date are based on risk equations estimated using data from the UK Prospective Diabetes Study (UKPDS), a study conducted more than two decades ago, and may not reflect contemporary event rates given changes in treatment and management of diabetes and its complications.
A Study of Cardiovascular Events iN Diabetes (ASCEND) recruited 15,480 participants with diabetes without previous cardiovascular disease, and is one of the largest diabetes trials conducted to date. Using data from the ASCEND study, I found the UKPDS risk equations to overpredict cardiovascular events and mortality, further adding to the evidence base that the UKPDS risk equations are unsuitable for use in contemporary cohorts. I developed a new framework for modelling long-term health outcomes and costs which can be used to assess cost-effectiveness of treatments for people with diabetes without previous cardiovascular disease. New risk equations were estimated using the ASCEND data, and these were integrated into a simulation model which predicts the likelihood of occurrence of cardiovascular, bleeding, cancer, lower-limb amputation, end-stage renal disease and death events over the lifetime of a patient given their baseline characteristics. The simulation model was externally validated in a cohort of 18,250 participants with diabetes without cardiovascular disease identified from the UK Biobank, a longitudinal prospective observational cohort. The simulation model performed well generally. Where discrepancies between model predictions and observed event rates were found, the reasons behind the discrepancies were identified. A novel issue-driven approach was developed to update the risk equations. New estimates of hospital costs and health-related quality of life (QoL) associated with the adverse events in the simulation model were also derived from the ASCEND study and incorporated into the simulation model to quantify the impact of treatments on lifetime cost and QoL.
To demonstrate an application of the framework, I assessed the cost-effectiveness of aspirin for the primary prevention of cardiovascular disease in people with diabetes. In this population, it is still uncertain if the cardiovascular benefits of aspirin use outweigh the bleeding risks. Using the latest evidence available, I demonstrate that aspirin is likely to be cost-effective in the cohort of UK Biobank participants with diabetes without previous cardiovascular disease. However, significant uncertainties in the results warrant further research.

Keywords: Health economics
Disease simulation model
Diabetes
Advisor: Leal, J
Bowman, L
Mihaylova, B
Sounding margins : musical representations of white South Africa

White South African culture is not a monolith. Neither was Apartheid. Neither is the pan-Africanist hegemony proclaimed over the New South Africa in the name of the ‘African Renaissance’. It is these highly politicized premises that inform the five case studies undertaken in this thesis — case studies that aim to explore the role music can play as a cultural mediator, acting as a sign-system of difference in the postcolonial sphere in general and in the South African context in particular. Post-Apartheid South Africa presents a time and place where Western musical culture is an uncomfortable, disturbing practice of survival and supplementarity — between art and politics, past and present, the public and the private. Our musicological solutions to political problems, and our attempts to find them, are, I believe, important and exemplary. My reading of art music in South Africa as part of a large and ambitious social and political experiment — the outcome of which hangs in the balance —- makes music a crucial site of imagining more composite, unfinished identities. White South African protest, fears, hopes and strategies are explored in the music of John Joubert, Arnold van Wyk, Stefans Grové, and in the literary texts of N.P. van Wyk Louw, André P. Brink and Breyten Breytenbach. My approach is unashamedly interdisciplinary and intentionally eclectic. Musicology has the chance to show, in the South African context, how difference can be productively engaged with and accepted in a way that does not undermine its significance. By exploring the merits of the postcolonialposition, I also hope to show how South African musicology can contribute to modes of musicological discourse aligned to postmodern thought.

Keywords: white people
South Africa
music
white South Africa
musical representations
intellectual life
Advisor: Parker, R
Deciphering the role of endolysosomal Ca2+ signalling via two-pore channel 2 (TPC2) in cancer: from bench to bedside


Cancer is a major public health problem and one of the leading causes of death worldwide, necessitating the development of innovative cancer biomarkers/targets to improve detection, diagnosis, prognosis, and therapy. Cancer biomarkers have evolved into clinical tools that can improve the efficiency of detection and guide the treatment of cancer patients by providing personalised therapy and information about expected cancer outcomes. There is increasing evidence that links two-pore channel 2 (TPC2, also known as TPCN2) to cancer, revealing the potential applications of TPC2 as a biomarker/ therapeutic target. My thesis studies have underscored the significant role of TPC2 in cancer immunology, biology, and genetics. Monocytes and macrophages are myeloid cells that play a vital role in inflammation, immunity, and cancer. The spleen is an important source of monocytes, which act as direct precursors of haematopoietic stem cell–derived macrophages. Proteins related to the physiological processes involved in the immune system and cancer were significantly altered in TPC1 knockout (KO), TPC2 KO, and TPC1/2 double KO mouse splenocytes, compared to WT controls, suggesting that TPCs may play significant roles in regulating innate immune system functions in various pathophysiological processes. My thesis studies have identified TPC2 as a major regulator of monocyte differentiation and macrophage development. In addition, my studies have revealed, for the first time, an important link between TPC2 and the release of two mediators that are opposed in their functions: IL-8 pro-inflammatory cytokine and IL-10 anti-inflammatory cytokine. Finally, I have discovered variants in the TPCN2 gene that are associated with cancer at the global level or 13 various cancer types at the local level, in the definition of tumour types, susceptibility, and prognosis in the UK-biobank. My thesis gives insights into the pathophysiological significance of TPC2 in cancer immunity and may contribute to the development of new genomics-based guidelines for cancer diagnosis and therapy.

Advisor: Parrington, J
On coalgebras and final semantics

This thesis is concerned with an analysis of the category Coalg(T) of coalgebras of an endofunctor T. The objects of this category can be thought of as transition systems, and the morphisms can be thought of as functional bisimulations. Thus, Coalg(T) is a suitable setting for a category-theoretic account of bisimulation and coinduction. We are particularly interested in final coalgebras, viewing them as strongly-extensional universal transition systems and as recursively defined data types.
One of our main results involves the construction of the final coalgebra of an accessible set functor 7" via an ordinal-indexed sequence of iterates — the so-called final sequence of T. We show that if T is k-accessible, for some regular cardinal k, then this sequence converges to a final coalgebra in k + k steps. Thus, the construction of the final coalgebra can be seen as a two-stage process. In particular, for a finitary (w-accessible) set functor T, the ω-th object in the final sequence of T can be seen, under a natural ultrametric, as the Cauchy completion of the initial T-algebra. It is always a final coalgebra, not necessarily of T', but certainly of a ‘completion’ of T to an endofunctor on the category of complete ultrametric spaces. Beyond ω, in the second stage of the final coalgebra construction, the final sequence becomes a chain of injections until a final coalgebra is eventually obtained after ω + ω steps.
We define a notion of metric bisimulation for coalgebras of endofunctors on the category of metric spaces and non-expansive maps, and we prove that the metric on a final coalgebra is maximum amongst all bisimulations. This result justifies a coinduction proof principle for recursive data types. As suggested by Rutten, and motivated by the idea that metric spaces can be seen as enriched categories, the definition of a metric bisimulation is based on the notion of a bimodule, the enriched categorical counterpart of a relation. Also, we give a condition under which the operational notion of bisimulation agrees with the denotational notion of final semantics. As an application of this theory, we obtain a coinductive characterization of a known metric on the class of probabilistic transitions systems.
We use our analysis of final coalgebras to study more general categorical structure. Given a set functor T, we show that if T preserves wide pullbacks then Coalg(T) is a category of presheaves; if T is accessible and preserves pullbacks then Coalg(T) is a category of sheaves; if T is accessible and preserves weak pullbacks then Coalg(T) is not necessarily a category of sheaves, but its effective completion is a sheaf category. We also characterize products and subobject classifiers in categories of coalgebras, illustrating this characterization in the category of labelled transition systems and functional strong bisimulations.
The compatibility of modified nucleic acids with enzymatic copying and ligand selection

Modified nucleic acids have important applications in molecular biology, genetics and genomics. Here I report a series of modified 5-aminomethyl-deoxyuridine (5-AM-dU) analogues with different functional groups on the 5-position of the pyrimidine ring. These modified 5-AM-dU nucleotides were evaluated in primer extension and polymerase chain reaction (PCR) amplification assays and were shown to be compatible with the polymerase enzymes. In total, six 5-AM-dU analogues with either stabilising or destabilising functional groups were prepared and efficiently incorporated by polymerases. Another modified nucleoside, the fluorescent quadracyclic adenine analogue qAN1 (qAN1) is incorporated with low efficiency in PCR. I was able to show that when this highly duplex stabilising modification is paired with the complementary duplex-destabilising 5-AM-dU, PCR amplification becomes possible. This is because the stabilising effects of one analogue offsets the destabilising properties of the other. Two destabilising thymidine analogues with hydrophobic functional groups at the 5′ position of the nucleobase enabled the use of qAN1 in place of deoxyadenosine at full substitution. In combination, these artificial qAN1-5-AM-dU base pairs allow the preparation chemically modified DNA in which all the A and T nucleobases are modified. These chemically modified 5-AM-dU analogues were used into SELEX to generate a series of aptamers through in vitro selection. In parallel, similar approaches were used to construct modified nucleic acid libraries with aminoethyl glycine (AEG) substituents on thymidine.

Keywords: PCR/qPCR
SELEX
DNA encoded library
aptamers
modified nucleic acids
Advisor: Brown, T
Quantitative rational verification

Rational verification asks whether certain temporal properties hold within the equilibria of multi-agent systems. Typically, the literature considers games where the agents traverse some concurrent game structure (or some succinct representation of it), with player goals and specifications given by LTL formulae. Whilst this is an effective framework for reasoning about a variety of different systems, it has two clear shortcomings --- it assumes that agents are unrestricted in choosing their actions, and it only allows two possible player preferences over outcomes: a satisfied temporal goal and an unsatisfied one. Whilst this is sufficient for verifying binary properties (such as safety, fairness and liveness) of a system where agents can act arbitrarily, this framework lacks the ability to differentiate between non-functional behaviours of resource-constrained systems.
For an agent in a system, there may be multiple ways of having it achieve its goal, but these may have different resource requirements (such as energy usage or time expended). As such, it is natural to ask questions like \enquote{does this fleet of autonomous cars have enough power to safely get from point A to point B?} or \enquote{how can these industrial robots perform their respective functions, whilst collectively expending the least amount of battery power?}. These are real world problems which also invoke rich questions in theoretical computer science.
In this thesis, we introduce quantitative aspects to the framework of rational verification. We build on the existing literature by extending the traditional temporal goals of players with mean-payoff rewards; we constrain our agents by making their available actions contingent on resources they possess; and we will look at how quantitative aspects can introduce non-determinism to the rational verification setting.
As such, this will give us games with a greater strategic interest than previously analysed, bringing the theory closer to understanding real-world systems.
Readers of Erasmus: humanism and the English Reformation, 1500-1550

This dissertation is a study of the reception of Desiderius Erasmus (d.1536) in England in the first half of the sixteenth century, spanning the period between his first visit to the country (1499-1500) and the landmark publication of the English Paraphrases (1548-52). In these years, Erasmus was transformed from an obscure Augustinian canon into Europe’s most celebrated writer. Yet his rise to fame occurred just as the continent descended into religious turmoil. As a result, Erasmus’ reputation, scholarly methods and faith came under increasing scrutiny. In few regions was this process as complex as in England, where the Dutchman had long been in contact with the royal family, patrons and scholarly community. This thesis thus explores Erasmus’ changing place in English intellectual life in the sixteenth century, asking how his status as a humanist and theologian shifted against the backdrop of the English reformation.
This thesis primarily investigates these transformations from the perspective of Erasmus’ readers. The heart of this study is an analysis of several hundred surviving editions of the scholar’s works in repositories across the UK and elsewhere, tracing the ownership, circulation and annotation of his writings by English men and women in the early sixteenth century. Erasmus’ readership was extremely varied and this survey looks at a wide cross-section of readers, from kings, queens and courtiers, to scholars, clerics and members of the religious orders.
This thesis argues that readers took a far more critical approach to Erasmus’ writings than usually supposed. Challenges emerged from both within and outside the humanist community. Working from the margins, they sought to improve the scholar’s books, often reworking his ideas in the light of different scholarly and confessional agendas. These processes led to the fragmentation of his writings and the application of ever more sophisticated historical and scholarly techniques for understanding his work.

Keywords: Desiderius Erasmus
English Reformation
Renaissance humanism
readers
Advisor: Brigden, S
Gunn, S
Seeing beyond seeing: the idea of figurative exposition in the High Middle Ages

Medieval exegetes composed figurative expositions on animals and the created world that were shaped and informed by the authority of scripture and the Fathers (‘auctoritas scipturae et auctoritas patrum’). Despite this observation, the historiographical framing of works such as Isidore of Seville’s Etymologiae, Alexander Neckam’s De naturis rerum, and second- and transitional-family bestiary manuscripts, have often been misrepresented as either proto-scientific, pseudo-scientific, or encyclopaedic. Whilst it is generally acknowledged that each of these works (and related medieval literature) had a strong moral element and figurative connotations, persistent scientific and encyclopaedic framing in historiography inhibits more creative and sympathetic engagements with the expositions they contain.
In response to scientific framings of medieval figurative expositions, especially ones that feature animals, this thesis proposes a re-evaluation of significant texts produced in the High Middle Ages according to proper theological context. Noting the inheritance of patristic exegetical practice, and considering the moral and material dimensions of the created world medieval theologians inhabited, such a re-evaluation recognises seemingly absurd or bizarre ideas about animals as significant contributions to medieval religious practice. Conforming to an established and authoritative mode of writing that used the created world to expose a deeper intention of meaning, figurative expositions on animals became a way of articulating the hidden things of God. This was especially the case through expositions on fish and birds. In this sense, medieval ideas about animals and the created world were closely connected to the idea of scripture as sound, and the communicative ability of the sacraments (‘sacramenta’) to transform the believer through faithful engagement with corporeal things. Through five chapters, this thesis not only demonstrates the religious sophistication underpinning figurative expositions on animals, but it also reveals the interconnected nature of religious devotion and medieval life through what is termed a ‘deeper sense of seeing’, or a ‘seeing beyond seeing’.

Advisor: Harrison, C
Gasper, G
Numerical simulations of waves passing over a slope

Extreme waves have been studied for decades in terms of the problems such as the formation of the extreme waves and the underestimate of the probability of extreme waves by the standard models in the open ocean. There are different mechanisms exist to explain extreme waves and one of the possible mechanisms is waves propagation over an abrupt depth transition. It is found that the statistical distribution of waves can be modified when they propagate over sharp discontinuities in the bathymetry. According to the experimental results, the statistics of the waves in the experiments and the Gaussian model contradict considerably, and the distribution of surface elevation significantly deviates from the Gaussian distribution when waves propagate over sharp discontinuities. After lots of studies on this problem, it is found that this mismatch is contributed by strong nonlinear effects, which can result in errors when only using the law of superposition and Gaussian model to evaluate the waves. Thus, investigation on how the abrupt depth transition provokes extreme waves becomes important to understand the extreme waves for the safety design of offshore infrastructures.
One mechanism to explain the relationship between the extreme waves and the abrupt depth transition is the interaction between second-order bound waves and free waves released due to the abrupt depth transitions. Another mechanism is that sea-states are pushed out of equilibrium. In our work, we not only analyze the progress of wave propagation over an abrupt depth transition, but also study the wave kinematics after the top of the slope. We emphasize that all of the slopes or abrupt depth transitions mentioned in this thesis are rising slopes (i.e. waves propagate from deeper water side to shallower water side). Because the wave kinematics is also important as the wave loading on offshore structures is mainly determined by the wave kinematics as well as the dynamics. For practical engineering purposes, wave loading is closely related to the safety of engineering design.
In this study, a thorough convergence test and validation for the numerical code (OceanWave3D) is conducted. The wave propagation over the abrupt depth transitions is analyzed for unidirectional wave groups, unidirectional random waves, and directional spreading wave groups. The wave kinematics after the top of the slope is investigated, and the wave loading on the offshore structures is evaluated. In addition, we analyze the angle of the second-order released waves when directional spreading waves propagating over the abrupt depth transitions.

Advisor: Thomas, A
Ton, vdB