VictorJuiz/thesis huggingface dataset:
The anatomy, taxonomy and systematics of Middle Triassic–Early Jurassic ichthyosaurs (Reptilia: Ichthyopterygia) and the phylogeny of Ichthyopterygia

Ichthyosaurs were a successful group of Mesozoic marine reptiles spanning a time interval of nearly 160 million years, from the Early Triassic to the early Late Cretaceous. Although ichthyosaurs have a long history of research, dating back to the early 18th century, significant controversies still surround their anatomy, taxonomy and evolution.
The revision of the cranial anatomy of the basal ichthyosaur Cymbospondylus from the Middle Triassic (Anisian) resolves a 100-year controversy surrounding the arrangement its skull bones. Comparisons with the recently discovered colossal, predatory ichthyosaur Thalattoarchon result in the identification of shared synapomorphies, which provide evidence for a close relationship between the two taxa. Together with other, recent discoveries from China, this demonstrates the rapid ecomorphological diversification of ichthyosaurs in the early Middle Triassic.
The incompletely sampled Late Triassic marine fossil record hinders our understanding of ichthyosaur evolution across the Triassic-Jurassic boundary. A new genus and species of large-bodied, early parvipelvian (fish-shaped) ichthyosaur from the Late Triassic (upper Norian) of British Columbia, Canada, is described. The new taxon is characterized by the possession of labiolingually flattened, bicarinate tooth crowns. Its co-occurrence with other small- to medium-sized parvipelvians, representing different ecomorphologies, demonstrates that parvipelvian ichthyosaurs were already ecomorphologically diverse at the beginning of their evolutionary history and maintained high ecological diversity throughout the Late Triassic.
The ichthyosaur diversity of the Lower Jurassic (Hettangian–Pliensbachian) of the United Kingdom is still poorly understood, due to the lack of detailed studies of ichthyosaur anatomy. Here, I describe a new genus and species of ichthyosaur, defined by the possession of five autapomorphies and a unique combination of both plesiomorphic and derived characters. Phylogenetic analysis recovers the new taxon as an early-diverging parvipelvian, providing evidence of a temporally staggered, rather than catastrophic, ichthyosaur turnover at the Triassic-Jurassic boundary.

Advisor: Benson, R
Between scripture and human reason: an intellectual biography of Muḥammad ibn Ismāʿīl al-Bukhārī (d.256/870)

By the dawn of the fifth/eleventh century, al-Bukhārī (d. 256/870) was recognized as the most highly regarded hadith scholar and his Ṣaḥīḥ as the most authoritative book, after the Qurʾan. This canonical status promoted a romanticized version of al-Bukhārī that does not reflect the reality that his pre-canonical historical record presents. This study recovers the reality of al-Bukhārī and provides a critical biography of him, tracing the progress of his career and detailing the objectives of his work. It provides a re-assessment of al-Bukhārī’s own juridical, theological, and hadith-criticism principles based on an analysis of his own works, arguing that al-Bukhārī was shaped by the split between hadith and raʾy. It distinguishes three stages in his career: early education under raʾy authorities, conversion to hadith-based school, and his critique of the raʾy-based scholars in Transoxania. Al-Bukhārī was a significant contender of theology and law in his own day and certainly promoted a moderate position in theology and law that proved crucial to his future renown. He appears to have been Medinese in law and Iraqi in hadith criticism. His legal theory adopts some of Mālik ibn Anas’ (d. 179/795) views and al-Shāfiʿī’s (d. 204/820) hermeneutical concepts. His legal method and positive law appear to be systematically anti-raʾy and exhibit a virulent disparage of Abū Ḥanīfa (d. 150/767) and al-Shaybānī (d. 192/804-5). It appears that al-Bukhārī composed the Ṣaḥīḥ over a long period, at least a decade, as the Ṣaḥīḥ itself tends to confirm a chronological progress. This progress, the author contends, was the outcome of al-Bukhārī’s long project in Transoxania, combating raʾy and promoting hadith. Al-Bukhārī achieved prominence within hadith-based circles for his unique transmitter-criticism (rijāl) works, particularly al-Tārīkh, but when he conceded that one’s utterance (lafẓ) of the Qurʾan is created, he was immediately denounced by the hadith-based school. This controversy caused the collapse of al-Bukhārī’s career, leading to his demise in Khartank near Samarqand in 256/870.

Keywords: Hadith criticism
Bukhari
early kalam
Islamic law
Advisor: Melchert, C
Three-dimensional modelling of coral reefs for structural complexity analysis

Coral reefs are some of Earth’s most biodiverse and economically valuable ecosystems. Simultaneously they are among the most threatened by anthropogenic factors including global climate change. Their unique three-dimensional (3D) structural complexity is part of what enables them to provide their ecosystem services. It strongly affects species richness, abundance, and other indicators of ecosystem health.
This thesis explores the relationship between coral reef 3D structural complexity and ecosystem features. It has developed a new, low-cost method for creating and analysing photogrammetric 3D models of shallow reefs from diver-held camera footage. 3D models are analysed at scales 1-175 cm in terms of point-to-point distances, linear rugosity (R), fractal dimension (D), and vector dispersion (1/k). The 3D models’ accuracy and precision were determined by comparisons with ground truths. The 3D models have root mean square errors of 1.35-1.48 cm in the X, Y and Z dimensions. Values of R from the 3D models were 86.8% accurate compared to in-situ chain-and-tape measurements. Values of D and 1/k were 86.9-99.6% accurate compared with ground truths from 3D printed objects modelled underwater. Data collected around Utila, Bay Islands, Honduras in the Caribbean showed that 3D metrics automatically calculated from the 3D models had the same predictive power for fish abundance and diversity as the more traditional Habitat Assessment Score (HAS). Like HAS, the 3D metrics explained 12-34% of variation in the fish data. A controlled experiment furthermore tested how 1/k affected sessile epibenthic organism settlement around Utila after one year. Results from approximately 200 3D printed recruitment tiles showed that 1/k significantly affected algae settlement, but not coral spat, polychaete, sponge, or bryozoan settlement. The results suggested that the surfaces of artificial reefs can be designed to minimise algal recruitment and that the availability of sheltered, reef-facing area influences epibenthic settlement more strongly than 1/k at the 1 cm scale. Finally, a convolutional neural network (CNN) learned patterns between the 3D models and fish data with just 85 data points. The CNN is a promising approach for analysing larger data sets without 3D metrics.
We suggest 3D models become a standard approach for measuring reef structural complexity. Not only can they explain as much variation in fish abundance and diversity as traditional measurements, but also they can nondestructively produce a variety of 3D metrics at numerous spatial scales and keep a permanent record of reef structure over time.

Advisor: Rogers, A
Exton, D
Prisacariu, V
The Armenians in the Ottoman Empire after the First World War (1918-1923)

This thesis is a historical study of the Ottoman Armenians in the Ottoman Empire from 1918-1923. It seeks to delineate how the Ottoman Armenians reorganised their political position against the massive socio-political crises that led to the collapse of the Ottoman Empire. The thesis analyses the transformation of the Armenian political position by examining the Ottoman Turkish and Armenian press. The study contends that the Ottoman Armenians struggled to reorganise their political and social life after the First World War and established alliances with the Allied Powers to create an independent ‘Western Armenia’, which would ultimately unite with the Armenian state in the Caucasus. The Ottoman Armenians developed a patriotic approach that sought unification with their compatriots in the Caucasus. However, after the defeat of the Greek army by the Nationalist troops in Anatolia in 1922, the collective approach among the Ottoman Armenians changed significantly. After the Nationalist victory had become inevitable, the Ottoman Armenians sought reconciliation and peace with the Turks. This reconciliation was only possible through the acceptance of 'Turkish supremacy' by the Ottoman Armenians. In other words, the Armenians who chose to remain within the boundaries of Turkey preferred to pledge loyalty to the newly established Nationalist government in Ankara. The establishment of the Türk-Ermeni Teali Cemiyeti (Turkish Armenian Ascent Association) and the reconciliation attempts of the Ottoman Armenians with the Muslim Turks is an example of the transformation of the Armenian collective position among the Ottoman Armenians. This study employs Armenian and Ottoman Turkish media sources published in Istanbul and Anatolia during the Armistice years (1918-1923) to track the post-war interrelationship of Ottoman society in general and the Armenian community in particular, the social and political reorganisations of the Armenian community and the transformation of the Armenian political position in the last years of the Ottoman Empire. By doing so, the thesis challenges both Ottoman/Turkish and Armenian historiographies, and attempts to bring these two historiographic approaches together with a new approach to understand this historical period.

Keywords: Armenians
Ottoman Empire
Armistice years
First World War
Advisor: Van Lint, T
Tchilingirian, H
Questioning neutrality: Sino-Portuguese relations during the war and the post-war periods, 1937-1949

This thesis is a study of neutrality and collaboration during the Second World War in East Asia. It analyses the relations between China and Portugal during the conflict and the immediate post-war period, with a particular focus on the enclave of Macau, the only foreign-administered territory in China not to be occupied by Japan. It argues that the practice of Portuguese neutrality in East Asia was marked by great ambivalence and used by different actors for their own, often conflicting, ends. In social history terms, Macau was part of the war, with comparable experiences to other cities in China, including a massive refugee influx, as well as everyday experiences of hunger, popular mobilisation for relief, and urban crime. Wartime Macau was marked by multiple layers of collaboration involving Chinese, Portuguese, British, Japanese, and others. This thesis also argues that wartime issues left unsolved had an impact on Sino-Portuguese relations after the war. Its dealings with a small European imperial power reveal China’s attempts and difficulties to exercise its regained sovereignty and new international status.

Keywords: Portugal
Second Sino-Japanese War
Second World War
China
Macau
Advisor: Mitter, R
The politics of performance in Viking Age skaldic poetry

This thesis examines the political functions of the performance of skaldic poetry during the Viking Age. It aims to establish the vital role that skaldic verse plays in the establishment and maintenance of power, as well as the importance of skaldic performance in the negotiation of that power in the inter-community relations between various courts both within and outside of Viking Age Scandinavia. The first chapter provides a contextual understanding of Viking Age power structures by considering the central ideological constructs surrounding the concept of óðal (ancestral property). Óðal-derived power, it will be shown, is based on ruler-presence (which extends to ancestral presence) in the landscape, which is perceived as a crucial element in the legitimisation of authority and power. My second chapter will consider the political significance of skaldic performance within the context of ruler itinerancy, which develops in response to political practices based on the importance of óðal-derived legitimacy. Of particular importance in this respect, will be the use of ‘presencing’ proper- and praise-names in skaldic poetry that effect both spatial and temporal itinerancies in a highly distributable format. My third chapter will establish the representational features of skaldic performance and elaborate on the definition of Performance not only as action (in the Austinian sense), but also as a type of action that is defined by its artifice, its temporal continuity and its emergent dialogism. This will provide the theoretical context for my fourth and final chapter which will aim to examine the employment of skaldic Performance in Viking Age diplomatic praxes. Here the phenomenologically perceived ‘binding’ of the Self through the dialogic rhythmicity that arises out of skaldic ambiguity and crypticism will be of central importance.

Keywords: Dialogic
Skaldic
Old Norse
Performance
Diplomacy
Óðal
Viking Age
Politics
Advisor: O'Donoghue, H
‘The world created anew’: Land, religion and revolution in the Gran Nayar region of Mexico

The Mexican Revolution – the first of the great revolutions of the twentieth century – is today recognised by scholars as the cumulative result of ‘many Revolutions,’ occurring in multiple locations, for multiple reasons, over a thirty year period from Madero’s rebellion against the Díaz dictatorship in 1911, to the consolidation of the Mexican state in the late 1930s. No region remained untouched by the rebellions and reforms that transformed the country over these years: not least ‘el Gran Nayar’, a 20,000 km2 expanse of mountains and canyons spanning parts of four different states, which constitutes one of Mexico’s most ethnically diverse areas, and is home to one of the country’s most prominent indigenous groups – the Huichols – along with their Cora, Tepehuano, and Mexicanero Indian neighbours. However, despite a boom in regionally-grounded studies of Mexican history, and the long-standing popularity of the Gran Nayar as a site for anthropological research, my book is the first study of the participation of the Gran Nayar’s inhabitants – among the least ‘assimilated’ indigenous groups in the Americas – in the Mexican Revolution.
Over the course of this thesis, I show that the Revolution in the Gran Nayar entailed a violent confrontation between an expansionist state and the region’s highly autonomous Indian peasant communities: a clash between practitioners of subsistence agriculture and promoters of capitalist development, rival Indian generations and political factions, and rival visions of the world, of religion, and of daily life. These clashes produced some of the most severe defeats that the Mexican government’s state- and nation-building programmes suffered during this period, with sometimes counter-intuitive consequences. Thus members of ‘traditionalist’ Indian factions, who upheld a resolutely pagan religious tradition and defined themselves in opposition to local mestizos, became an important force within the Catholic-inspired, mestizo-dominated Cristero rebel movements of the 1920s and 30s. Similarly, the Federal educational programmes so often lauded for bringing literacy and ‘progress’ to rural Mexico, instead precipitated violent opposition in the Gran Nayar, which involved the burning of schools, and even the murder of several teachers. And the radical land reforms of left-leaning President Lázaro Cárdenas (1934-40), which proclaimed the liberation of the Mexican peasantry from social and economic oppression, caused violent territorial conflicts between local communities, some of which continue to define life in the region today.

Advisor: Knight, A
Rethinking the role of sleep dysfunction in psychosis

Sleep dysfunction – including sleep disorder symptoms, dissatisfaction with sleep, and other sleep abnormalities - has long been linked with psychosis, but the traditional view has been that sleep dysfunction is a consequence of psychosis. This thesis reconceptualises this relationship by testing a causal role of sleep dysfunction in psychosis. The first step was a systematic review (Chapter 1), in which correlational, but no causal, evidence is found for an association between sleep dysfunction and psychosis. This was addressed in Chapter 2 with a non-clinical manipulation study (n=68) which found that sleep loss caused increases in psychotic experiences, mediated by increases in negative affect. Chapter 3 explored the longitudinal relationship between short sleep duration and psychotic experiences in an at-risk group (n=160), finding that short sleep duration predicted later severity of psychotic experiences (although this prediction was not robust against conservative controls). In Chapter 4 the first detailed assessment of sleep disorders in a clinical group of individuals with psychosis (n=60) was reported, finding that sleep disorders were common, untreated, and often complex. A subgroup (n=29) were assessed twice more over the subsequent three months, allowing statistical modelling of the influence of insomnia on psychotic experiences over time (Chapter 5). The results again supported a significant predictive role of insomnia on psychotic experiences in this clinical group, mediated by negative affect. Finally, a novel exploratory study into hypersomnia in psychosis (n=26; Chapter 6) was carried out. The results suggested that hypersomnia is not associated with sedation or longer sleep duration, but is associated with increased fatigue, sedentary behaviour and depression. Overall, this thesis demonstrates that sleep dysfunction is not just a consequence of psychosis, but appears to have a causal role in the onset and maintenance of psychosis. The clinical implications are that sleep might be a novel therapeutic target in treating psychosis.

Advisor: Freeman, D
Sheaves, B
Investigation of the dose and temporal effects of intravenous iron on human cardiopulmonary physiology

Sustained hypoxia induces a progressive rise in pulmonary artery systolic pressure (PASP). Intravenous (IV) iron administered immediately prior to the hypoxic exposure attenuates this effect, suggesting that manipulation of iron stores may modify hypoxia-induced pulmonary hypertension. Not yet understood is the duration of effect of IV iron, or the dose-response relationship between clinical indices of iron status and modest loading of iron in non-iron deficient individuals. To address this, two placebo-controlled, double-blind, sustained isocapnic hypoxia studies were conducted in healthy iron-replete participants.
In Study A, 22 participants were randomised to a single intravenous bolus dose of iron as ferric carboxymaltose (FCM), or saline on day 1 and exposed to six hours of hypoxia on days 0, 1, 8 and 43. Following the administration of FCM the concentrations of ferritin and hepcidin plus transferrin saturation rose significantly (p &LT; 0.001, p &LT; 0.005, p &LT; 0.001 respectively), and transferrin concentration decreased significantly (p &LT; 0.001); changes that persisted for the study. FCM significantly attenuated the rise in PASP in response to hypoxia (p &LT; 0.001), an effect that persisted at day 43.
In Study B, 18 participants were randomised to saline or 250 mg FCM, administered monthly for six months. To avoid iron overload, FCM was only administered to participants who had a ferritin &LT; 300 μg/L and transferrin saturation &LT; 45%. PASP was measured during eight hours of hypoxia, before and after the six month period. Serum ferritin concentration was robustly elevated by FCM by 0.21 µg/L/mg of iron delivered (95% CI: 0.15-0.26 µg/L/mg). Both iron dose and increase in ferritin concentration correlated with an attenuation in PASP rise with hypoxia (p &LT; 0.05 and p &LT; 0.01, respectively).
In summary, a bolus dose of iron resulted in an increase in iron indices and altered the cardiorespiratory response to hypoxia for at least 43 days. This was also achieved by incremental doses of iron that did not cause iron overload. The persistent effect of intravenous iron suggests that it may be of therapeutic benefit in some forms of pulmonary hypertension and other hypoxic cardiorespiratory diseases.

Advisor: Robbins, P
Dorrington, K
Mathematical modelling of cerebral ischaemia-reperfusion injury

Restoring cerebral blood flow using reperfusion treatment is a common method in treating ischaemic stroke. Reperfusion treatment should be given within 4.5 hours from stroke onset. However, reperfusion beyond this time window poses the risk of reperfusion injuries such as intracranial haemorrhage and cerebral tissue swelling. The focus of this thesis is to study the effect of cerebral tissue swelling after reperfusion as it can occur in a few hours after the treatment. Cerebral tissue swelling may cause brain structure movement and cerebral microvessel compression; the latter may then lead to secondary ischaemia occurrence.
In this thesis, two mathematical models are presented. The first model investigates the effect of ischaemia-reperfusion in the formation of cerebral tissue swelling. This model provides the understanding of suitable reperfusion conditions to reduce the effect of tissue swelling and also becomes the basis for the subsequent model. Meanwhile, the second model studies the role of a water-transporting protein, aquaporin-4 in ischaemia-reperfusion and its potential as part of treatments for cerebral tissue swelling. In addition, the ionic concentration may change during ischaemia which may be a factor contributing to cerebral tissue swelling. Thus, the effect of ionic concentration on the swelling formation is also investigated.
Finally, validations of these models are achieved by developing patient-specific geometries from available ischaemic stroke patient MRI data and utilising finite element analysis. Comparison between the simulation results and the MRI data is done by quantifying the brain ventricles movement during cerebral tissue swelling.

Advisor: Payne, S