VictorJuiz/thesis huggingface dataset:
Prophecy, history and method: how and why Isaac Newton studied chronology

Isaac Newton spent forty years of his life studying the chronology of ancient civilizations. The manuscript record that bears the fruits of these writings is in significant disarray, which has led to many misinformed conclusions about the nature of his research and his motivations for studying the topic in the first place. By devoting ample attention to Newton’s reading, note-taking, writing, and ordering practices, this thesis makes use both of evidence drawn from Newton's surviving books and of Newton’s digitised manuscripts and transcriptions to reconstruct the evolution of his chronological writings. Originally just an eight-page treatise on the origins of idolatry, ‘Theologiae Gentilis Origines Philosphicae’ (mid-1680s), Newton started expanding and revising it to eventually arrive at the posthumously published Chronology of Ancient Kingdoms Amended (1728). I show that most of the writings he composed in the interval were all part of a single treatise, the ‘Originals’ (1702–06), in which he built on his original research.
In truth, Newton’s chronological studies began even before the ‘Origines’, with his studies of the prophecies in the books of Daniel and Revelation. In order to correctly identify the four monarchies from Daniel and their role in past, present, and future, he needed a reliable timeframe. From Greek and Roman sources he derived a timeline of the kings that reigned over Babylon during the Jewish Exile, which he subsequently collated with the Scriptural record, not shunning to amend the chronological books of Ezra and Nehemiah where necessary. With the ‘‘Origines’’ and ‘Originals’, Newton constructed a timeframe from Greek history using methods from genealogy and astronomy that allowed him to incorporate all of sacred and profane history. Posthumous editorial projects and the scattered manuscript record have obscured much of the connections between Newton’s chronological and prophetic writings, yet for Newton they were part of one and the same project.

Keywords: Chronology
Isaac Newton
Prophecy
Advisor: Iliffe, R
Prediction models for mortality in tuberculous meningitis

Tuberculous meningitis (TBM) is the most severe manifestation of tuberculosis, killing or disabling nearly half of all sufferers despite proper antituberculosis treatment. The British Medical Research Council (MRC) grade, which was first introduced in 1948, is the most widely used grading system for TBM severity. Despite its age and its lack of statistical derivation, improved and robust prediction models for poor outcomes in TBM based on large cohort studies and rigorous statistical methodology are still lacking. In addition, no studies have exploited repeated measurements to update the risk prediction.
The purpose of my DPhil thesis is to develop prognostic models for mortality in adult TBM patients and to address statistical issues that may arise during the modelling process. Firstly, I present prognostic models for 9-month mortality based on patient characteristics at diagnosis. Separate models were constructed for patients with and without HIV coinfection. The models were developed and validated based on a large pooled database of 748 HIV-infected and 951 HIV-uninfected subjects. This is the largest database of prospectively characterized TBM patients to date. The final models showed good performance and are clearly superior to the MRC grading system. However, predictions may be improved and updated once new information on the disease progress becomes available during follow-up. Therefore, in the second part of my thesis, I present prognostic models that dynamically predict death using time-updated Glasgow coma score and plasma sodium measurements, together with patient baseline characteristics. The models were carefully developed and validated based on 518 HIV-infected and 550 HIV-uninfected patients respectively. They outperformed the baseline models. I implemented the baseline models and the dynamic models in web-based calculators to facilitate their application in practice. These prognostic models can be used to assist clinicians in decision-making regarding treatment and patient management. Lastly, I describe and compare strategies for incorporating variable selection with multiply imputed data in the procedure of building a prediction model. I evaluated the performance of the methods on simulated data, and on the same data set of 951 HIV-uninfected patients that I used in the first part. I provide insights on the strengths and weaknesses of the pragmatic approaches that are commonly used.

Advisor: Geskus, R
Wolbers, M
Thwaites, G
Enhancing humanity: co-creation and the moral imagination

The prospect of enhancing human characteristics through advancing technologies in genetic engineering, artificial intelligence and nanotechnology is generating interest in academic, commercial and popular spheres. This research focuses on anthropologies of co-creation as a potential theological response to the questions posed by human enhancement. For a theological anthropology to engage in public and cross-disciplinary debates surrounding enhancement concerns, it must first demonstrate scientific and technological literacy and the capacity to incorporate information from these fields. As the strong links between transhumanism and science fiction demonstrate the importance of the imagination for developing, communicating, and evaluating visions of future human being, a theology of co- creation that is able to engage these ideas must also feature a robust account of the imagination in epistemology and the dissemination of knowledge. Philip Hefner’s “created co-creator” incorporates scientific insights into a theological anthropology that is generally positive toward the use of technology to enhance nature. Having inherited an overly rational epistemology from his predecessors in the science and religion field, however, Hefner’s proposal reflects a deficit of imagination. J. R. R. Tolkien’s notion of sub-creation is not as developed as Hefner’s theological anthropology, being primarily a literary theory. Given the high value Tolkien accorded to the imagination and the role of narrative in discerning and conveying ultimate truths, however, his work may offer a corrective to Hefner’s in this respect. Tolkien’s critical stance to technology prevents a fruitful dialogue with human enhancement issues on the basis of his sub-creation proposal alone. A constructive theological anthropology that unites the strengths of Hefner’s and Tolkien’s models is sketched out, drawing on contemporary scholarship in metaphor studies, phenomenology and posthuman discourse, with a view to engaging debates surrounding human enhancement.

Keywords: moral imagination
human enhancement
co-creation
Advisor: McGrath, A
Chinese ceramics in the Islamic world from the 8th to 10th centuries CE

This thesis provides new angles, material and discussion to the topic of Chinese ceramics arriving in the Islamic world from the 8th to 10th centuries CE and their connections with contemporary Samarra Horizon Islamic glazed ceramics. It analyses sites with and without Chinese ceramics during this period and explores the broader question regarding the distribution of early Chinese ceramics in the Islamic world. There are varying patterns related to ceramic finds in these sites. The Persian Gulf region has the highest concentration of sites with Chinese ceramics, especially the Iranian coastal area of the Persian Gulf. There are five main types of Chinese ceramics found in the Islamic world from the 8th to 10th centuries CE. Chinese celadon stoneware is the most widely distributed Chinese ceramics in the Islamic world during this period. This is followed by Chinese white wares, Dusun wares, Changsha wares and Chinese monochrome and polychrome glazed wares. Not all Chinese ceramics in the Islamic world are luxurious traded goods. Different types of Chinese ceramics arrived in different areas and settlements in the Islamic world. They held different values and functions; their amounts in these Islamic sites vary hugely too. The scale of the circulation of Chinese ceramics in the Islamic world during this period may not have always been considerable, as most publications have claimed. It is not precise to describe the relationship between Chinese ceramics and Samarra Horizon ceramics as “imitations”, because there were more dynamic interactions than imitations only. Chinese ceramics influenced Samarra Horizon wares, which also exerted influence on Chinese ceramics.

Keywords: Islamic
Indian Ocean
China
Trade
Ceramic
Advisor: Treadwell, L
Priestman, S
Rawson, J
The role of calcium dependent neurotransmission in axon path finding, myelination and maintenance of specified cortical projection neuron populations

The thesis examines the mechanisms involved in regulation of myelination during mammalian cortical development and the subsequent maintenance of the myelin in cortical projection neurons during adult life. Myelin in the central nervous system is produced by oligodendrocytes to ensure fast saltatory conduction of action potentials at the nodes of Ranvier, the gaps left by myelin. Myelination in the central nervous system is among others dependent on neuronal activity but the underlying mechanism is not yet completely understood. Because myelination plays an important role in many neuronal diseases, such as multiple sclerosis and schizophrenia, it is important to understand the molecular and cellular mechanisms. To do so, I examined the effects of genetically suppressing the neuronal activity in two separate ways in deep cortical layers of the mouse.
One way to reduce neuronal activity was to abolish regulated vesicular release by removing Snap25 (synaptosome-associated protein of 25 kDA), member of the SNARE ((N-ethylmaleimide-sensitive factor) Attachment Protein Receptor) complex in a Snap25-flox mouse in which the essential exon 5a/b is flanked by LoxP sites and therefore truncated in the presence of Cre-recombinase. Since the fusion of neurotransmitter containing vesicles is mediated amongst others by the SNAP25 protein, removal of the functional SNAP25 protein prevented calciumdependent regulated vesicle exocytosis in a cell-type specific manner. Nrsr1 (for Layer VI) and Rbp4 (for Layer V) conditional Snap25 KO mice were bred on a floxed-stop-tdTomato background such that all affected cells were tdTomatolabelled within the subpopulation of layer V or VI projection neurons. My results for layer VI and Layer V demonstrated that preventing neurotransmitter release in Snap25 cKO mice does not affect the onset of myelination, density of oligodendroglia, nodal structure or thalamic fibre targeting but it has the effect of premature fibre degeneration causing myelin degeneration and decreasing the gratio in the dorsal corticospinal tract. The time course of degeneration occurs in a cell type specific manner, layer V being the most sensitive for silencing.
The second way to influence neuronal activity was by introducing the inwardly rectifying potassium channel (Kir2.1) by in utero electroporation at the time of the cortical projection neuron generation. The overexpression of Kir2.1 lowers the probability of action potential formation through hyperpolarization of the neurons which leads to a decrease of the membrane resistance so that they are less excitable. Examining this model at various stages did not reveal differences in targeting of projections or myelin in the corpus callosum when assessed by MBP immunohistochemistry at P14.
Together, the results indicate that neuronal activity has little effect on the onset of myelination but has effects on the g-ratio in deep cortical layer projection neurons in mice.

Advisor: Molnár, Z
Hoerder-Suabedissen, A
What social movements ask for, and how they ask for it: Strategic claiming and framing, and the successes and failures of indigenous movements in Latin America

Whether social movements can make a difference remains a perennial question of social movement scholarship. This thesis aims to make a contribution to this debate by examining the contentious collective action of indigenous people(s) in Latin America. This has the potential to enrich both the Latin American scholarship on indigenous politics, which often takes the impact of indigenous movements for granted, and the social movement scholarship on outcomes, which seems to increasingly question whether protest can have any direct impact at all. This thesis suggests that neither approach is adequate and that factors under the control of indigenous movements themselves can lead to positive outcomes. The choice of tactics, the nature of claims and the way in which they are framed, play a role, both directly and in interaction with contextual variables. Taking into account movements’ strategic claiming and framing is thus crucial for understanding social movement outcomes. Few studies have been able to show the effect of framing on movement outcomes; partially at least this is because the claiming (what) and framing (how) of social movements have not been distinguished well within framing theories. To have an impact, movements need to be able to impose material and symbolic costs on their targets that exceed the cost that meeting their demand would present. This can be done through creating enough materially costly disruption—such as by using roadblocks or sustaining mobilisation—and imposing enough symbolic costs—such as making claims framed in a way that resonates with the agendas and discourses of their targets, as well as the public. Overall, this work thus suggests that despite the empirical support for the thesis that social movements tend to rely on political opportunities for securing desired outcomes, this is not inconsistent with the fact that social movements can succeed even in unfavourable political conditions. In the latter situation, if protest can impose a high enough combination of both material and symbolic costs, it can indeed matter.

Keywords: Latin America
Bolivia
indigenous politics
social movements
mixed methods
Advisor: Payne, L
Early fourteenth century physics of the Merton school

Until early in this century it had been customary (and in certain writings it still is) for histories of science to speak of Galileo as the father of modern physics as though nothing preceded him, except the downfall of Aristotle. During the first two decades of this century Pierre Duhem devoted untiring energy to the study or "les précurseurs parisiens de Galilée". Among other significant discoveries, he thought that he had found in the theory of 'impetus' defended by Jean Buridan and his 'school' in the early and mid-fourteenth century the modern principle of inertia, which Galileo expressed by impeto, or momento. Constantine Michalski's studies on the theological movements of scepticism and criticism during the fourteenth century did not affect Duhem’s thesis, but Michalski did point out that the Franciscan, Francis de Marchia, proposed the theory some years before Buridan. The acceptance of Duhem’s thesis encouraged historians of science, a growing group, to see other points of similarity, and even identity, between the ‘school' of Jean Buridan in the Parisian Faculty of Arts and the seventeenth century founders of classical physics.
Continued in thesis …

Keywords: century
physics
Heytesbury
Merton
medieval
Dumbleton
14th
fourteenth
Remotely actuated polymeric nanocomposites for biomedical applications

The present work describes the synthesis, structural and mechanical characterisation of soft polymeric materials used for biomedical purposes.
This thesis is separated in two parts: the first one pays special attention to natural polymeric hydrogels for Tissue Engineering (TE) described in chapter 3 and chapter 4 describes the synthesis of magnetically responsive nanocomposite hydrogels for TE.
In this first part, I mainly focus on the mechanical characterisation of the synthesised materials. I use AFM microindentations to characterise them locally and oscillatory shear rheometry to characterise the bulk responses of the material, obtaining the reduced Young’s modulus (E*), the storage G′ and the loss G′′ modulus respectively. Furthermore, in chapter 3, the assessment of the stability of microbeads made of alginate for modular TE is described, followed by a novel magneto-mechanical coupling observed for the first time in chitosan hydrogels. In the 4th chapter, I characterise the mechanical response of a chitosan-Fe3O4 nanocomposite with an enhanced magneto-mechanical coupling.
The second part of this work (chapter 5) describes a simple synthesis of polymeric micro-ellipsoidal particles for torque generation assays in biomedicine. I characterise the rotation of these particles in comparison to commercially available spherical microparticles and their enhanced ability to follow low magnetic rotating fields.

Advisor: Contera, S
Experimental and theoretical studies in quantum metrology with optomechanical and multi-parameter-estimation applications

This thesis explores the field of optomechanics and the theory of multi-parameter estimation for quantum metrology applications.
An optomechanical state inside a microresonator-taper system is studied experimentally, where the optical and mechanical modes interact by means of Brillouin anti-Stokes scattering. The scattering leads to sideband cooling of the mechanical (acoustic) mode and the underlying optomechanical coupling takes the form of a beam-splitter interaction Hamiltonian. The mechanical mode is further cooled by continuously monitoring the optical anti-Stokes mode by a heterodyne detector. The resulting time-domain data is input offline to a stochastic master equation model for Gaussian states to optimally estimate the mechanical phase space trajectories and subsequently reduce the observer’s uncertainty associated with the phase space coordinates. It is shown that more information about the mechanical mode can be obtained by heterodyne monitoring than by the commonly used in optomechanics homodyne detection for the beam-splitter type interaction Hamiltonians.
The second part of this thesis theoretically considers the problem of simultaneous estimation of phase and phase diffusion using fixed-particle number states in the framework of quantum Cramér-Rao bound. Quantum Fisher information matrices are derived analytically in the limits of large and small diffusive noise to quantify the maximum amount of information available in the individual estimation of the parameters. The former is for a general fixed-particle number state and the latter for Holland-Burnett states for which quantum-enhanced estimation of phase as well as diffusion can be obtained. The precision limits given by quantum Fisher information may not be achievable in the joint estimation of the parameters due to the possible non-commutativity of the optimal measurements and this can be quantified in terms of a trade-off relation. This trade-off relation can reach the maximum of 2 in the large diffusion regime, whereas in the small diffusion regime a numerical evidence is shown that the optimal trade-off relation approaches 1 for Holland-Burnett states. These numerical results are valid in the small particle number regime. Finally, numerical results showing behaviour of the trade-off for a general value of phase diffusion when using Holland-Burnett states are provided.

Advisor: Vanner, M
Datta, A
A.Walmsley, I
Cultural property in practice: the role of French museum professionals

There has recently been a proliferation of cultural property rules and standards at both international and national levels. This thesis examines the relevance, significance, and influence of these norms on the ground. I study them from a ‘law in action’ perspective by focusing on a rarely-seen aspect of museum practice: curators engaging with cultural property law and ethics. What is the application of legal and ethical rules in curatorial practice? What significance do they have in museum work beyond their practical application? How have they shaped different aspects of curatorial practice?
To address these questions, the thesis uses three Parisian museums as case studies and field sites: Musée du Quai Branly, Musée du Louvre, and Muséum National de l’Histoire Naturelle. It takes an empirical and informant-driven approach, and describes how French curators refer to and follow various legal and ethical norms relating to the protection and administration of museum collections.
The thesis shows that the way in which cultural property norms and standards are applied in museum practice is not homogenous. Rather, there is variation in how the actors involved in using them on a daily basis – in this case, curators – understand and appeal to them in their practice. Certain norms acquire a status akin to moral principles, whilst others prescribe the correct or accepted way of conducting different museum tasks. The thesis also shows that the use and interpretation of cultural property is influenced by factors that do not directly relate to these norms. In the French case, the most important such factor relates to the close relationship that exists between museums and the state.

Advisor: Pirie, F
Replication fork collapse and recombination-dependent replication restart at replication fork barriers

In order for the genome of any organism to be successfully replicated its replication machinery has to overcome barriers in the template DNA. These so-called replication fork barriers (RFBs) can sometimes cause the replication fork to collapse. Replication fork collapse is a poorly understood process that is thought to involve either replisome remodelling and/or disassembly paving the way for homologous recombination (HR) proteins to act and restart replication, by a process known as recombination dependent replication restart (RDR), which is essential for completing DNA synthesis. In this thesis I present my work identifying factors that are instrumental in the replication restart process, with a particular focus on those factors that are needed to aid the transition from collapsed fork to one that is receptive to HR proteins. I have used the RTS1 site-specific RFB in fission yeast for this study as it acts as a potent polar RFB that triggers fork collapse and recombination protein recruitment. By screening candidate factors, I identified the PCNA unloader Elg1 as being strongly required for RTS1-induced recombination. By genetic experiments and live cell imaging, I show that unloading of PCNA by Elg1 promotes RDR by allowing efficient recruitment of Rad52 to the blocked replication fork and by limiting the anti-recombinogenic activity of Fbh1. I also provide evidence that Ctf18 acts in opposition to Elg1 to limit RTS1-induced recombination. Finally, I investigate the importance of Rad51, the central HR protein, and its mediators (Rad55-Rad57, Swi5-Sfr1, and Rdl1-Rlp1-Sws1) in RDR. By genetic analysis of RTS1-induced recombination, I discover that neither Rad51 nor its aforementioned mediators are essential for RDR. These findings indicate the existence of a robust Rad51-independent pathway of RDR in fission yeast.

Advisor: Whitby, M
Using smart contracts to attract conservation investment

The conservation sector is facing a financial crisis. It is underfunded by billions of dollars, motivating conservationists to find alternate funding sources. It has been suggested that attracting private capital in the form of investment could solve this problem. This dissertation explores the question: can smart contracts (computer programmes that automate the transfer of funds and digital representations of objects) be used to attract conservation investment? Exploratory research into what smart contracts can afford to conservation and the creation of a model smart contract using the European Wildlife Bank as a case study were used to answer this question. It is concluded that although technologically possible to attract investment, this application is limited in scale and will not solve the financial crisis. It is recommended that the conservation sector continue to explore emerging technologies to identify more feasible solutions.

Keywords: blockchain
conservation investment
smart contracts
Advisor: Jepson, P