VictorJuiz/thesis huggingface dataset:
Transcriptomic approach to understanding and characterising disease pathogenesis in sarcoidosis
Keywords: Sarcoidosis

Sarcoidosis is a multisystem immunological disorder, centred on the dysregulation of T cell activity, macrophage activation and granuloma formation. Most pulmonary sarcoidosis patients have a good prognosis, but up to 20% can go on to develop lung fibrosis. Previous research in sarcoidosis has generally focused on sarcoidosis as a single disease entity, whereas this thesis has focused on the importance of phenotypical characterisation, in particular active fibrotic pulmonary disease, and the standardisation of measuring disease activity.
I first developed a scoring system to measure disease activity based on typical findings on high resolution CT scanning (CTAS). I then identified a set of readily available blood markers and a chest radiographic score as a surrogate for the CT activity score, which enables the physician to easily assess the level of disease activity in the clinic setting (SCAS).
Using a transcriptomic approach, I used the activity score to identify the immunological pathways and individual genes correlating directly with increasing activity, both at the site of disease and in the periphery. Enrichment of immune response and defense response gene sets, particularly in BAL cell samples, were observed as disease activity increased, with CCR2, TREM2, and CCL18 featuring as prominent genes involved in the propagation of activity. CXCL9 and CXCL10 were identified as peripheral markers of active disease reflecting the activity in various compartments. In addition, after phenotyping patients with active disease into those with and without fibrosis, differential gene expression showed enrichment of immune related gene sets in the fibrotic cohort, and highlighted the roles of several significantly upregulated genes including CCL19, CCR7, CXCR3, CCR2, ADAMDEC1 and MMP12 in the pathogenesis of fibrotic sarcoidosis. Finally, enrichment of an IPF signature derived from differential expression to sarcoidosis, was observed in the fibrotic sarcoidosis cohort. This information may lend itself to further therapeutic treatments options already used in other fibrotic lung conditions in this interesting and understudied phenotype.
Domesticating Winckelmann: His critical legacy in Italian art scholarship, 1755-1834
Keywords: Giambattista Gherardo D'Arco
Giovanni Battista Piranesi
Journals
Italy
Carlo Amoretti
Luigi Lanzi
Foreignization
Art History
Domestication
Nationalism
Translation
Carlo Fea
Winckelmann
Periodicals
Lawrence Venuti
Leopoldo Cicognara
Francesco Milizia

This thesis explores the reception of Johann Joachim Winckelmann in Italian art scholarship, 1755-1834. Winckelmann posed a problem: he was a presence in Italy that could not be ignored, yet the views he expounded were Italophobic and contentious to an Italian readership. In light of this dilemma, the research question asked is how did Italian art scholarship respond to Winckelmann in this period and why did it respond in that way.
The core argument advanced is that there were two opposing reactions to Winckelmann, both of which were motivated by nationalism. On the one hand, Italian art scholars presented Winckelmann, his works, and his views as less attractive to an Italian readership than they would otherwise have appeared and, on the other hand, they presented him as more attractive. Through these reactions – termed foreignization and domestication respectively – art scholarship either defended against and ostracized Winckelmann or, when presented as less offensive, welcomed and embraced him amongst Italians. Thus this thesis argues that both reactions demonstrate a nationalistic attempt to portray Winckelmann in the manner most auspicious to the yet-to-be-united peninsula.
In order to explore this response to the German scholar, the thesis centres on three media: translations, art literature, and artistic journalism. Both foreignization and domestication are evident throughout the sources analysed, yet there is a predominance of domestication, achieved through a variety of methods.
This investigation adds to existing literature by examining the previously overlooked dilemma that Winckelmann posed. Moreover, employing the original conceptual framework of foreignization and domestication allows for a re-evaluation of how the art scholarship of the period engaged with the German scholar. Finally, demonstrating the infiltration of nationalistic sentiment in this period, even extending to Italian art scholarship, this thesis is the first to posit that nationalism played a significant role in Winckelmann’s critical legacy.
Investigation of ASPPs as regulators of pancreatic inflammation and tumorigenesis
Keywords: iASPP
ASPP2
Pancreatic cancer
Kras
p53

Pancreatic ductal adenocarcinoma (PDAC) is a cancer of unmet need with a 5-year survival following diagnosis of 3% with limited surgical, radiotherapy and chemotherapy treatment options. Central to PDAC tumorigenesis is acquisition of an oncogenic Kras mutation to drive acinar-to-ductal metaplasia and progression to PDAC that is potentiated by NF-kB deregulation. However, PDAC requires the additional loss of tumour suppressors such as p53, SMAD4 or p16. ASPP family members ASPP2 and iASPP regulate both p53 and NF-kB, and are classified as a tumour suppressor and oncogene respectively. However, the precise roles of ASPP2 and iASPP in pancreatic cancer are unknown. In this thesis I demonstrate that ASPP2 suppresses metastasis and iASPP suppresses the pro-inflammatory tumour microenvironment. In a mouse model of PDAC development, ASPP2-deficiency does not alter metaplasia, PanIN progression or primary PDAC onset. However, median survival due to metastasis is significantly reduced in an ASPP2-deficient PDAC model. I demonstrate ASPP2-deficient PDAC can result in increased squamous differentiation defined histologically or via increased p63 expression. I propose ASPP2 is a key suppressor ΔNp63 and the squamous PDAC subtype in vivo. Conversely, iASPP is a putative oncogene and high expression in cancer associates with poor prognosis. However, in a mouse model of PDAC, loss of iASPP accelerates PDAC onset and metastasis. I demonstrate that iASPP is a functional tumour suppressor of a pro-inflammatory phenotype in response to oncogenic Kras and pancreatitis. I propose ASPP2- and iASPP-deficient mouse models of PDAC represent in vivo the squamous and immunogenic subtypes of PDAC respectively; and are relevant tools to study mechanisms of metastasis and inflammation-driven carcinogenesis.
Bushmeat hunting, retaliatory killing, habitat degradation and exotic species as threats to Fosa (Cryptoprocta ferox) conservation
Keywords: Fossa
Deforestation
Madagascar
Invasive species
Human-wildlife conflict
Hunting
Eupleridae
Poaching

Large carnivores are in global decline, chiefly resultant of anthropogenic persecution, habitat reduction and disturbance. Fosas represent Madagascar’s largest carnivore, occupying much of the island's forest. This thesis examines the threats of bushmeat hunting, retaliatory killing, habitat alteration and exotic species using sociological and remote-sensing methodologies.
Habitat degradation was not associated with reduced fosa occupancy, indicating some resilience within large, contiguous forests. However, competition with exotic species (cats, dogs) was associated with reduced fosa occupancy and potential temporal shifts towards greater nocturnality.
Poor households were more likely to consume protected species. Conversely, wealthier households consumed more fish and eel. This pattern is reflected in Malagasy reported taste preference to consume domesticated animals and certain legally hunted wild species. Protected areas were not associated with reduced protected species consumption.
Fosas' predation was a major cause of rural poultry mortality. Predation was more likely to occur in deciduous forests, in the dry season, during the evening. Fosa predation, and lower education was associated with negative Malagasy attitudes. Wealthy households, and those that had experienced fosa predation were most likely to retaliatory kill a fosa.
Strategies to safeguard fosas' long-term persistence should seek to improve domestic husbandry, build robust coops with the use of watchdogs, promote education, and reduce exotic species abundance.
Mediators of transdiagnostic psychological treatments for eating disorders
Keywords: treatment personalisation
structural equation modelling
interpersonal psychotherapy
statistical mediation
treatment personalization
cognitive behavior therapy
multilevel modelling
eating disorder
cognitive behaviour therapy

Cognitive behaviour therapy and interpersonal psychotherapy are the leading treatments for eating disorders. Little is understood regarding their mechanisms of action. The research described in this thesis investigated the purported mechanisms of action of two transdiagnostic versions of these treatments; enhanced cognitive behaviour therapy (CBT-E) and interpersonal psychotherapy for eating disorders (IPT-ED). A series of mediation studies were embedded within a randomised controlled trial comparing CBT-E and IPT-ED in a transdiagnostic sample of patients with eating disorders. An analytic strategy using multilevel and structural equation modelling was used to assess for statistical mediation. Three of the key purported mediators of action of CBT-E (regularity of eating, frequency of weighing, and frequency of shape checking) and the key purported mediator of IPT-ED (interpersonal problem severity) were studied. Only regularity of eating demonstrated a strong case for being a mediator of the effect of CBT-E (on frequency of binge eating). The findings were inconclusive regarding other putative mediators of the effect of CBT-E, and for interpersonal problem severity being a mediator of the effect of IPT-ED. Limitations of the research included the non-optimal choice of measures and non-optimal timing of measurements for establishing temporal precedence. Future research should investigate the mediating role of both cognitive (e.g. interpretation of weight) and behavioural processes (e.g. frequency of weighing) in CBT-E, and the role of interpersonal functioning in CBT-E and IPT-ED. Research should use daily, or session by session measurement to better assess the temporal relationship between the purported mediator/s and the outcome/s. Experimental designs comparing dismantled versions of treatment would also help determine the relative effects that different treatment procedures have on treatment outcome/s.
Semantic refactorings
Keywords: refactoring
software verification
software synthesis

Refactorings are structured changes to existing software that leave its externally observable behaviour unchanged. The intent is to improve readability, performance or other non-behavioural properties of a program. Agile software engineering processes stress the importance of refactoring to keep program code extensible and maintainable. Despite their apparent beneﬁts, manual refactorings are time-consuming and prone to introducing unintended side eﬀects. Research eﬀorts seek to support and automate refactoring tasks to overcome these limitations.
Current research in automatic refactoring, as well as state-of-the-art automated refactoring tools, frequently rely on syntax-driven approaches. They focus on transformations which can be safely performed using only syntactic information about a program or act overly conservative when knowledge about program semantics is required. In this thesis we explore semantics-driven refactoring, which enables much more sophisticated refactoring schemata. Our semantics-driven refactorings rely on formal veriﬁcation algorithms to reason over a program’s behaviour, and we conjecture they are more precise and can handle more complex code scenarios than syntax-driven ones.
For this purpose, we present and implement a program synthesis algorithm based on the CEGIS paradigm and demonstrate that it can be applied to a diverse set of applications. Our synthesiser relies on the bounded model checker CBMC as an oracle and is based on an earlier research prototype called Kalashnikov. We further deﬁne our Java Stream Theory (JST) which allows us to reason over a set of interesting semantic refactorings. Both solutions are combined into an automated semantic refactoring decision procedure, reasoning over program behaviours, and searching the space of possible refactorings using program synthesis. We provide experimental evidence to support our conjecture that semanticsdriven refactorings exceed syntax-driven approaches in precision and scope.
Aristocracy, politics and power in Byzantium, 1025-1081
Keywords: Peira
Middle Byzantine Empire
Kekaumenos
Consilia et Narrationes
Michael Psellos
Networks
Aristocracy
Political History
Byzantine History

The purpose of this thesis is to further our understanding of the period between the death of Basil II in 1025 and the accession of Alexios I Komnenos in 1081. Modern scholarship has often portrayed these 56 years as an important, transformative period, viewing the empire as standing at the height of its power at its beginning, only to be brought to the brink of collapse by civil wars and foreign invasions following the battle of Manzikert in 1071. Based on three unique and underexploited sources of evidence, namely the letters of Michael Psellos, the judicial handbook commonly known as the Peira and the so-called Consilia et Narrationes of Kekaumenos, it argues that the Byzantine state to a large extent relied on private networks to carry out public administration throughout the empire. Public and private power were thus intimately intertwined and by conveying information, orders and requests, but also by reproducing and enforcing norms of acceptable political behaviour, these networks served to compensate to some extent for the institutional shortcomings of the premodern state. It also challenges the idea that the political dynamic of the eleventh century was centred around the power struggles of ‘great families’ or clans that effectively functioned as political parties, as well as the idea that the emperors and their officials were apathetic about governing the provinces beyond what was necessary to pacify and extract resources from them. Taken together, the evidence examined consequently appears to suggest that, by the standards of the pre-modern world, the Byzantine empire had a reasonably well-functioning state and a fairly coherent society during the period in question, suggesting that the focus of the scholarly debate on the eleventh-century Byzantine collapse should, to some extent, be shifted from internal to external factors.
Negotiating Norms
Keywords: Norm contestation

This thesis examines the practice of normative contestation in the African Union (AU) and Association of Southeast Asian Nations (ASEAN). Dissatisfied with existing liberal, realist, and rationalist accounts of normative change, the thesis develops a new theoretical approach involving competing 'norm circles,' actors committed to endorsing or enforcing a norm, whose perceived utility of a norm determines their stance. The model suggests that under conditions of contestation involving at least two norm circles, actors compete according to the terms of their domain, the regional organization. The differences involve actors' competencies in controlling the initiative, their mastery of other shared norms, and their ability to seek other opportunities of influence, termed 'metis.'
Empirically, the thesis examines six case studies, three each from the AU and ASEAN, in which significant new norms testing member state sovereignty were proposed, after which the norms were either accepted, rejected, or qualified, according to how the contest unfolded. Each case reviews the historical origins of the norm and the proposal, followed by analysing how each norm circle used the factors mentioned above to seek approval for their proposals. It then assesses the relative importance of the factors, alternative explanations, and future implications for the norms in each case. In the AU, the three cases were the proposals for the United States of Africa, the Conference on Security, Stability, Development and Cooperation in Africa, and the Pan-African Parliament. In ASEAN, the thesis examines the question of human rights in the ASEAN Charter, the attempt to formalize the 'ASEAN minus X' principle, also during the charter drafting, and the contestation over the creation of a regional human rights mechanism, which eventually became the ASEAN Intergovernmental Commission on Human Rights.
Hellenistic and Roman bronze statuettes in the Ashmolean Museum
Keywords: Reception of Antiquity
Ashmolean Museum
Greek and Roman statuettes

This thesis is an aetiological investigation of the Hellenistic and Roman figural bronze statuettes in the round that form part of the Ashmolean Museum’s antiquities collection. The collection serves as a lens through which to study aspects of ancient and modern receptions of Classical sculptural forms. This approach is based on the premise that the collection’s composition has been historically determined not only by how the modern parties responsible for its creation and growth responded to the sculptural forms and images recovered from antiquity, but also by how sculptural forms developed in Greece during the Classical and early Hellenistic periods were received by makers and users of bronze statuettes in antiquity.
The thesis has three primary objectives: firstly, to produce a useful and informative catalogue of the Ashmolean Museum’s collection of Hellenistic and Roman figural anthropomorphic bronze statuettes in the round; secondly, to determine not only how that collection came to have the characteristics that it does, but also how the reception of ancient sculpture has historically affected the formation of collections of bronze statuettes and their compositions; thirdly, to use archaeological evidence of bronze statuettes to reconstruct possible contexts and to determine in greater detail the reception of canonical sculptural figure types in the form of small bronzes during the Hellenistic and Roman periods.
Part I of the thesis deals with the modern contexts for the statuettes, investigating the collection history, pulling out its salient characteristics and then comparing these to other major collections to make informed observations about how and why specific types of statuettes have survived from antiquity and the roles that modern reception of antiquity has played in shaping collections. This leads to Part II, which attempts to reconstruct possible ancient contexts for the Ashmolean bronzes by looking at the archaeological evidence for their production, movement use and display. Part III uses some of the figures of dwarfs, Herakles and Hermes in the collection to develop case studies that examine aspects of the visual relationships that existed between small bronzes and classical sculpture from the Classical and early Hellenistic periods.
Intellectuals and the Eastern question: 'historical-mindedness' and 'kin beyond sea', c. 1875-1880
Keywords: historiography
race
religion

The intractable problems posed by the decline of the Ottoman Empire were a defining feature of the nineteenth-century British experience. Events such as the Greek War of Independence (1821-32), the Crimean War (1853-5), and the Bulgarian Agitation (1876-8) were merely prominent denouements in the protracted history of what contemporaries called 'the Eastern Question'. The Eastern Question could be construed in many ways and admitted many answers. But by the 1870s, many Victorians had come to construe the Eastern Question as primarily an historical question.
This thesis explores the ways in which Victorian public intellectuals brought 'historical-mindedness' to bear on the Eastern Question. Nineteenth-century historiography, it is suggested, may often be understood as a variety of contemporary political thought. Part One takes the historian E. A. Freeman, one of the Bulgarian Agitation's leaders, as its subject. Studied in depth, Freeman becomes a window onto how nineteenth-century intellectuals could experience and understand the Eastern Question.
Part Two turns to the remarkable efflorescence of historical writing elicited by the so-called Eastern Crisis of 1875-80, investigating how historical arguments were invoked not merely in history books but also in newspaper reports, politically-freighted travel writing, and above all in periodical articles, over two-hundred of which are studied here.
When Gladstone invoked the authority of 'the historical school of England' to criticise Lord Beaconsfield during this period, he did so advisedly, for historians both lay and professional were remarkably unanimous in their interpretation of events in south-eastern Europe. Drawing on the insights of comparative philology and often sympathetic to Eastern Orthodoxy for reasons of religion, these historians tended to emphasise the Balkan Christians' European identity, situating them within teleological narratives of progress which evoke contemporaneous Whig histories of England.
Militancy, moderation, & Mau Mau: A reconsideration of Koinange wa Mbiyu and Peter Mbiyu Koinange
Keywords: colonial Kenya
African politics
Mau Mau
African chiefs
Kenya
decolonization

This thesis examines the lives of Senior Chief Koinange wa Mbiyu and his eldest son, Peter Mbiyu Koinange. It joins with the growing rise of biographical work within African Studies. It challenges the historical understanding of late colonial rule in Kenya and the role of official myth in pre- and post-independence historical narratives. Koinange wa Mbiyu was the patriarch of one of the most respected, wealthy, and politically influential Kikuyu families of Kenya’s colonial and post-colonial period. His eldest son, Peter Mbiyu, received a prestigious education abroad and returned to Kenya where he became a prominent leader for African independent education African political action. Koinange and Peter bear frequent mention in academic discussions of collaboration, discontent, nationalism, and militancy in Kenya’s colonial era.
This thesis challenges the widely held narrative that Koinange and Peter embraced militant politics opposing colonial rule during the 1940s. While fitting larger understandings of decolonisation, it is not an honest depiction of the Koinange’s political actions. As a result, this thesis is intentionally a work of revisionist history that looks to the profound changes in the culture and nature of colinal rule during the 1940s, rather than a political shift in the Koinanges. In addition to challenging the prevalent understanding of Koinange and Peter’s political action, this thesis raises a number of areas – gender, wealth, elite and family dynamics, to name a few – where the Koinange family history would further illuminate the historical understanding of the colonial era.
This thesis is a dual biography, crafted as a work of narrative history. It challenges a breadth of current scholarship, utilizing the largest collection of pre-Mau Mau archival records to date. This thesis engages with a number of historiographical challenges related to biography, the individual, the family, and the challenges of oral history shaped in the crucible of cultural crisis.