VictorJuiz/thesis huggingface dataset:
Reconstructing the timing and location of North-West Saharan rainfall with spatially distributed secondary carbonates

There is significant evidence that the presently hyper-arid Sahara belt stretching across North Africa has experienced periods of increased rainfall and surface moisture coverage at numerous times during the middle to late Pleistocene. During these times, there was increased vegetation coverage, greater mega-fauna distributions and more extensive human occupation. However, our understanding of precisely where and when rainfall increased is currently limited due to a paucity of high-resolution paleoclimate data. Furthermore, present records are over-extrapolated in their interpretations of moisture source and the spatial distribution of rainfall. In this thesis, periods of past in- creased rainfall are assessed in the central and northern Sahara using the formation age, stable isotope compositions and trace element concentrations of radiometrically dated secondary carbonate deposits. Stalagmites from the High- and Anti-Atlas Mountains provide evidence that sub-tropical rainfall occurs in response to increasing North-South inter-hemispheric temperature anomalies during the mid-Holocene African Humid Pe- riod, rather than as the direct result of a northwards extension of the West African Monsoon. Subsequently, older periods of Saharan-, High- and Anti-Atlas speleothem formation throughout the middle to late Pleistocene identifies periods of increased northern Sahara rainfall during a number of major northern hemisphere interglacial and interstadials. In the central Sahara, chronology from flowstone-like secondary cal- cite samples provides the first evidence of carbonate deposition from this region formed from direct, local rainfall rather than as a result of increased surface moisture avail- ability. Calcite formation during Marine Isotope Stage 11 suggests a consistent tropical source of rainfall in the central and northern Sahara. This thesis presents the north- west Sahara as a unique and climatically significant Saharan region, from which the activation of perennial southward flowing river systems was critical for human migration and development. Furthermore, this work better characterises the minimum geographic extent of increased north-west Saharan rainfall and identifies the need to move away from overly-generalised “Green Sahara” interpretations of Saharan climate.

Keywords: Uranium-Thorium
Climate
Rainfall
Stalagmite
Sahara
Paleoclimate
Chronology
Speleothem
Geochemistry
Stable Isotopes
Advisor: Day, C
Henderson, G
The higher lattice gauge theory model for topological phases of matter

Topological phases of matter are characterised by long-range entanglement between their constituent degrees of freedom, which allows them to host excitations with non-trivial exchange statistics. While topological phases in 2+1d are relatively well studied, less is known about their 3+1d counterparts. In this thesis, we examine features of these higher-dimensional phases in a tractable example model, based on a generalisation of lattice gauge theory called higher lattice gauge theory. As well as hosting point-like excitations, the model supports loop-like excitations with non-trivial loop-loop and point-loop braiding statistics. We explicitly construct operators to produce and move these excitations, and use these to find the loop-loop and point-loop braiding relations. These creation operators also reveal that some of the excitations are confined, costing energy to separate, while others are condensed and can be produced locally. This is discussed in the context of condensation-confinement transitions between different cases of this model. We also explain a method for measuring topological charge and use explicit measurement operators to re-derive a relationship between the number of charges measured by a 2-torus and the ground-state degeneracy of the higher lattice gauge theory model on the 3-torus. From these measurement operators, we can see that the ground state degeneracy on the 3-torus is related to the number of types of linked loop-like excitations.

Keywords: Anyon physics
Higher lattice gauge theory
Topological phases of matter
Advisor: Simon, S
Structural patterns in William Faulkner's major novels

William Faulkner wrote nineteen novels. Continually experimenting with the structure of the narrative, he produced a few superbly successful technical achievements, an intermediate body of works that are fascinating for what they attempt and the ways they attempt it, and more than several outright failures. With an experimenter, even a failure is usually of some interest.
"(I)t was simply because to me that seemed the most effective way to tell that story,"! Faulkner would answer to questions about his use of a particular unorthodox structure. But in spite of that disavowal, and in spite of the fact that it is undoubtedly true, that the novels were certainly first and foremost independent units, with structures selected as purely as possible to present most effectively the given story and theme; still, there are connections to be made among the various novels. At least eight of the major works, in fact, are built on the pattern of two types of structure, which might be given the labels contrapuntal and centripetal.
"To what extent does Faulkner work in terms of polarities, oppositions, paradoxes, inversions of roles?" Robert Penn Warren asked, reviewing Malcolm Cowley's compilation of The Portable Faulkner, in August, 1946. "How much does he employ a line of concealed (or open) dialectic progression as a principle for his fiction? The study of these questions may lead to the discovery of principles of organization in his work not yet defined by criticism."! Such a study has yet to be systematically done.
Continued in thesis ...

Keywords: Literary style
20th century
William Faulkner
novels
twentieth century
American literature
Faulkner
Structural patterns
The life and times of the Empress Wu Tse-t'ien of the T'ang dynasty

The Life and Times of the Empress Wu Tse-t'ien of the T'ang Dynasty is an attempt to describe and place in perspective the régime of perhaps the most controversial ruler in the history of medieval China. It is an attempt also, to define an imperial vision, to show the shifting priorities and stages of policy by which the Empress Wu set out to achieve certain aims; and it offers comment on the successes and failures of her career. Within this context, the Empress herself emerges as a woman whose consistency of character and virtuosity of mind is reflected only palely in previous studies.
Emphasis is placed in several areas. The first of these is the question of her position and her power. How did she win recognition as the legitimate sovereign of a state and a culture which had never before been ruled by a woman? And why, after this unique achievement, did she fail to preserve her position until her death? What influence did her unorthodox governmental role have upon the T'ang dynasty? And did her half-century of power leave any enduring marks upon China?
Out of these considerations grows a second emphasis-- the tension between Confucian state-theory and the anomaly of a female ruler. In this clash, the tradition proved to be of greater flexibility than is generally recognized, but at the same time, proved to be so durable and so resilient that in the Chou, the Empress found herself increasingly frustrated and finally defeated by it. This study suggests that while husband or son occupied the throne, she was able to borrow their legitimacy and make great strides in the achievement of her two principal goals: the creation of a viable centralization, and of an imperial institution which would be free, secure, and supreme in its relationship with a new bureaucracy. In the Chou, however, the contemporary power structure came increasingly to resist innovation and with increasing success. As a result, the dynasty is best regarded as it was at the restoration, as a "caretaker" régime, a period of consolidation and continuity of policies initiated in the preceding quarter century. The Empress Wu seized the throne to preserve rather than to innovate.
Continued in thesis ...

Keywords: Biography
Republicanism and the state between Brazil and the River Plate: Rio Grande do Sul, 1808-1845

The Rio Grandense Republic rose and fell between 1836 and 1845 in Brazil’s southernmost province, Rio Grande do Sul. Its founders, known as ‘farroupilhas’, first rebelled in 1835, decrying the Brazilian Empire’s centralisation and taxation, but they soon turned to separatism. Their decade-long attempt to establish an independent state remains Brazil’s longest armed conflict, as well as its last separatist uprising. This thesis is centred on an analysis of this separatist republic, contextualising it against Brazilian and River Plate developments, while contending that the farroupilhas consciously embarked on a state-building experiment after their separatist turn. An emphasis on the farroupilha state and its administration sets this dissertation apart from much of the scholarship on the so-called ‘Farroupilha Revolution’, whose scholars have most often focused on particular aspects of the conflict, like military engagements, individuals’ trajectories, or the immediate causes of the conflict.
The Rio Grandense Republic also serves as a window to state-building processes beyond Brazil, as well as to the transnational entanglements underpinning River Plate frontier politics. The development of the Brazilian state (especially its province-metropole relations) is thus discussed here as the immediate context to the Farroupilha Revolution, including a series of provincial revolts whose non-separatism serve as a foil to the farroupilhas. But River Plate republicanism, too, influenced the farroupilhas, even though the Rio Grandense Republic was not recognised by its republican neighbours. Rio Grande do Sul’s ‘frontier’ society was deeply enmeshed with those of Argentina and Uruguay, providing avenues for commercial, political, and even family linkages, which predated and survived the revolutionary conflicts of the early nineteenth century. These connections facilitated mobility across the River Plate-Rio Grandense borderlands, allowing various political exiles, including Giuseppe Garibaldi, to participate in movements like the Farroupilha Revolution, acting as both soldiers and propagandists.

Keywords: borderland
Latin America
Age of Revolutions
farrapo
River Plate
Brazil
state
Garibaldi
frontier
state-building
Rio Grande do Sul
republicanism
farroupilha
Advisor: Posada-Carbó, E
Investigation of haematopoietic cell growth and the impact of common mutations in myeloid malignancies

The myelodysplastic syndromes (MDS) are disorders of the haematopoietic stem cell and are characterised by ineffective haematopoiesis. The TET2 and ASXL1 genes have been implicated to be important in the pathology of MDS, but their function has not yet been characterised as co-mutations in erythroid and myeloid human cell lines. In this light using the CRISPR/Cas9 system, we engineered erythroid and myeloid models of myeloid malignancy in HUDEP2 and KBM5 cells respectively, with homozygous TET2 or heterozygous ASXL1 singular or co-mutations. Here, HUDEP2 and KBM5 cell models were robustly generated to express mutations in the TET2 and/or ASXL1 gene(s). Our cellular models demonstrate decreased mRNA expression of TET2 in the homozygous TET2 cell variants and physiological mRNA expression of ASXL1 in the heterozygous ASXL1 cell variants. We found zero unintended off-targets of our TET2 and ASXL1 targeted sgRNAs in our HUDEP2 and KBM5 cell models. We next aimed to functionally characterise the effect of these mutations on key cellular function, such as proliferation, the cell cycle, apoptosis and differentiation. We demonstrate that cells exhibiting co-mutations of TET2 and ASXL1 gained a proliferative advantage. Studies on the cell cycle revealed that cells exhibiting co-mutations of TET2 and ASXL1 demonstrated an increase in cell cycle progression. We subsequently investigated apoptosis and differentiation in our cellular models. In our HUDEP2 cell model, the TET2 mutants demonstrated a decrease in apoptosis and our ASXL1 mutants demonstrated an increase in apoptosis. Next, we investigated differentiation; our HUDEP2 cell mutants demonstrated a block in erythroid differentiation. Finally, we expanded CD133+ cells using novel combinations of cytokines and small molecules, as a prelude to their gene editing.

Keywords: CRISPR
Advisor: Boultwood, J
Watt, S
Investigating and modelling early upper gastro-intestinal neoplasia

In recent years, gastro-oesophageal cancers have increased in incidence in the western world with no known cause. Barrett’s oesophagus (BO) is a premalignant lesion induced by chronic biliary reflux. The cell of origin of BO has been greatly contested yet elusive. Non-dysplastic BO is a poorly understood but highly heterogeneous metaplastic tissue with deranged differentiation and a high incidence of early P53 mutations. Intestinal metaplasia (IM) is an internationally accepted defining criterion for BO diagnosis. In this thesis, I have examined the role of early P53 mutation in the development of gastro-oesophageal cancers by using a combined P53 mutant transgenic mouse in combination with a biliary reflux model. Although gastric cancers did not consistently occur, I found evidence that P53 mutations may potentiate inflammation in non-dysplastic BO. Further investigation of BO cellular complexity using sc-RNA-seq also found that BO shared transcriptional similarity with a subset of oesophageal cells, but not with gastric or duodenal cells, and identified a number of potential biomarkers. Lastly, I have developed organoid models for BO, and demonstrated their ability to differentiate into cell populations see in the scRNA-seq data. In conclusion, my findings reveal a striking similarity between normal OSG cells and BO cells with the high expression of LEFTY1 and TFF3. I identify potential early markers for goblet cell differentiation, SPINK4 and ITLN1 and OLFM4 expression as a marker of BO progenitor cells, which may have clinical implications.

Keywords: intestinal metaplasia
Barrett's Oesophagus
single cell sequencing
Gastric neoplasia
Advisor: Middleton, M
Lu, X
Impact of grey literature on systematic reviews of randomized trials

Systematic reviews are increasingly important in evidence-based medicine. Their validity is dependent on the underlying data, thus any decisions about the eligibility of trials based on where they are published, for example excluding trials from the grey literature, could _bias their results and conclusions. However, the identification and inclusion of trials published in the grey literature can be time consuming and difficult. This thesis assesses the actual and potential impact of including trials reported in the grey literature in systematic reviews of healthcare interventions. A review of existing knowledge in this area was first carried out. Four substantial projects were then conducted.
The first of these projects assessed the actual impact of grey literature in meta-analyses published in the Cochrane Database of Systematic Reviews. This showed that published trials may produce larger treatment effects than trials identified in the grey literature (grey trials). There was no difference in methodological quality between published and grey trials; this was often unclear or not reported in both sources. The second project assessed the potential impact of grey literature in systematic reviews. Practical issues in locating and including grey trials were identified, namely the quantity and quality of information available. The third project built on these findings, assessing the quality of trials reported in conference proceedings and whether this improved over time. Important limitations were identified including a lack of numerical data and the preliminary nature of the results presented; these appear to be worse in recent years. The final project assessed how trial information reported in a conference abstract differs from its full publication. Major changes between abstract and full publication were identified, in particular details of trial results and participants included and analysed in the trial. It reinforces the preliminary nature of some trials reported in conference proceedings.
This thesis confirms that the exclusion of trials reported only in the grey literature remains a threat to the validity and reliability of systematic reviews. Systematic reviewers must, therefore, search for and include trials from the published and grey literature. Failure to do so may result in the results and conclusions of that review being biased and unreliable.

Advisor: Clarke, M
The reception of the work of Nicole Bozon via William Herebert: an analysis of London, British Library Additional MS 46919

Nicole Bozon, a Franciscan friar active in England at the turn of the fourteenth century, is the author of a number of Anglo-Norman texts ranging from saints’ lives to passion poems. Despite his large and varied corpus, his output remains critically neglected, and the scant scholarship devoted to him is often outdated. The picture which has emerged of Bozon focuses on his texts and use of Anglo-Norman as emblematic of Franciscan spiritual instruction, and pays little attention to manuscript context in responding to questions of audience or reception.
This thesis contends that a new approach is necessary in order to re-evaluate Bozon’s work in line with recent developments in manuscript studies and Anglo- Norman language and literature. This project therefore centres around the transmission of Bozon’s work in London, British Library Additional MS 46919, which forms the basis of his corpus, and its reception in this codex by William Herebert, another Franciscan author of the early fourteenth century. A close reading of texts in their manuscript context addresses the following research questions: i) what can Herebert’s compilation of, and interaction with this manuscript tell us about the composition of Bozon’s audience?, ii) how did Herebert use these texts, or envisage that they might be used?, and iii) how did Herebert understand Bozon’s language choice in the trilingual context of medieval England?
To answer these questions, Chapter I will outline and re-assess the conclusions of previous scholarship on Bozon. Chapter II will provide a detailed description of the of BL Add. 46919, which will be considered further in Chapter III which will discuss a number of views of the codex as a whole. Chapter IV will turn to the question of authorship, asking how the figure of Bozon is constructed by this manuscript and its compiler, William Herebert. The final two chapters of the manuscript will focus on language choice, in Chapter V through a reading of Bozon’s multilingual work, the Contes moralisés, and finally in Chapter VI with an analysis of Herebert’s translations of his work in this codex.

Keywords: manuscripts
Anglo-Norman
medieval
Nicole Bozon William Herebert
Advisor: Burrows, D
The behaviour and charging dynamics of concentrated electrolytes in confinement under potential control

The current understanding of intermolecular and interfacial forces in concentrated electrolytes is limited. Their importance to fields such as medicine, biology, ecology and the energy industry means that the pursuit of better knowledge has a wide-ranging impact on other areas of science and technology. In particular, the ubiquitous nature of batteries and energy-storing devices makes the behaviour of concentrated electrolytes near charged surfaces of special interest. This thesis presents two novel surface force balance (SFB) methods to measure surface forces across electrolytes confined between charged surfaces, where one or both of the surfaces are under electrochemical control. The first method combines a muscovite mica surface and an ultra-smooth gold surface (gold/mica SFB), and the second uses two ultra-smooth gold surfaces. A large part of this work is concerned with the use of gold to fulfil the triple role of confining surface, working electrode and interferometric mirror. Improvements to surface fabrication methods yielded unique high-resolution (∼ 0.1 nm) force measurements in the gold/mica setups and electrochemical measurements where the gold surfaces were under potential control. These setups were used to measure force profiles in an ionic liquid (IL), 1-butyl-1-methylpyrrolidinium bis(trifluoromethanesulfonyl)imide (C4C1pyrr TFSI), and in a dilute electrolyte, potassium chloride in water (KCl (aq)) at 1.5 mM and 0.6 mM concentrations. In the gold/mica setup, unprecedented resolution was achieved, as evidenced by the presence of molecular layering in the force profiles.
Force measurements reported in this work show that underscreening, a long-range electrostatic force that has been observed in concentrated electrolytes, is independent of surface potential. It was also observed that the magnitude of the force does not scale with that of the applied potential. Potential step methods were used to show that the current decay in IL has three characteristic timescales corresponding to three different charge transport modes.

Keywords: ionic liquids
surface force balance
surface force measurements
underscreening
charging dynamics
concentrated electrolytes
Advisor: Perkin, S
Investigation into early interneuron circuits of the mouse visual cortex

GABAergic interneurons play critical roles during cortical development in mammals, by maintaining excitatory-inhibitory balance and controlling emergent activity. In the mouse barrel cortex (S1BF), somatostatin-expressing (SST+) interneurons establish early, transient synaptic connections with thalamo-recipient excitatory neurons in cortical layer (L)4, while they receive transient thalamic inputs. This immature feed-forward inhibitory motif by SST+ cells acts as a scaffold for the mature S1BF neuronal networks and regulates developmental plasticity mechanisms. Given this critical role, it is conceivable transient networks by SST+ interneurons are a general feature of the developing mammalian cortex; however, there is limited knowledge on early networks and functions of SST+ interneurons in other brain regions. To explore this issue, the current thesis explores the primary visual cortex (V1) of the mouse, to study the degree of similarity between GABAergic interneuron networks and functions across sensory areas over early postnatal development. In vitro electrophysiology and optical techniques were used to map input/output connectivity patterns of SST+ interneurons in V1 to show they are only engaged in feedback inhibitory motifs with local excitatory neurons. Differences at the neuronal network level between V1 and S1BF relates to distinct functions played by SST+ interneurons across the developing brain. In vivo electrophysiology, together with optogenetics and chemogenetics, revealed SST+ interneurons in V1 regulate spontaneous activity but have minor impacts on early sensory activity before the onset of active perception. Circuit mapping experiments onto L6 excitatory neurons extended the concept of different early GABAergic networks between V1 and S1BF to the output layer of the cerebral cortex. Although canonical cortical circuits permeate the adult mammalian cortex, their developmental trajectories differ between similar primary sensory areas. GABAergic interneurons have been associated with neurodevelopmental disorders; it is, hence, pivotal to consider their developmental networks and functions to gain an understanding of the mechanisms underlying these disorders.

Advisor: Butt, S