VictorJuiz/thesis huggingface dataset:
Insights into the emergence of novel infectious diseases to humans

Novel infectious diseases in humans are of great concern to public health authorities and researchers in epidemiology. Zoonotic pathogens in particular have the potential to cause epidemics without any or little warning. In this thesis, I investigate evolutionary and environmental conditions, and the interactions between both, which facilitate the zoonotic emergence of novel pathogens. I start with a list of the mechanisms and processes which might influence a zoonotic emergence, and identify some unsolved problems. I address these with multiple, theoretical models. First, I use a village-city model with different adaptation scenarios to examine the influence of spatial heterogeneity on the emergence process. I derive general analytical results for the statistical properties of emergence events, including the probability distribution of outbreak sizes. My results suggest that, for typical connection strengths between communities, spatial heterogeneity has only a weak effect on outbreak size distributions, and on the risk of emergence per introduction. Next, I extend the research on environmental conditions by looking at pathogen specialisation in multi-host systems. I derive threshold connectivities for which generalist pathogens, which infect multiple species and might therefore be more dangerous to cross into the human species, can sustain transmission and are not dominated by specialists, which can only cause sustained transmission chains in a single host species, but are able to cause emergences with little warning. My third research chapter is interested in the effect of the loss of biodiversity. I analytically derive expected prevalences for fast growing and slow growing species. If fast growing species tend to perform better in degraded environments, my analytical results suggest that the overall prevalence level of infectious diseases will rise as environments degrade, which facilitates the chance of zoonotic jumps. In my last research chapter, I examine the actual impact of a novel, emerging infectious disease. I use data from the recent `Swine flu' epidemic in England to estimate epidemiological parameters of the infectious agent. My results suggest that the majority of infected cases showed no or only mild symptoms. This reveals that more data than just the estimated number of cases are necessary to fully evaluate the danger of a possible zoonotic, emerging infectious disease. I conclude by discussing my results and the implications which these might have.

Keywords: ecology
zoonotic emergence
mathematical modeling
infectious diseases
environment
Advisor: McLean, A
Phenomenological studies of top quark production in the forward region of phase space at the LHC

This thesis contains phenomenological studies of top quark production in the forward region of phase space at the Large Hadron Collider (LHC). The production of highly forward top quarks has so far not been observed in nature. As the LHCb detector at the LHC is instrumented in the forward region, this opens the possibility of studying top quark properties in this yet unexplored region of phase space. This feasibility of performing cross section and charge asymmetry measurements of top quark pairs with available and future LHCb data is studied in detail. In both cases, potential analysis strategies are proposed, and sophisticated theoretical predictions are provided for both signal and background. By studying the expected experimental sensitivity of cross section measurements, the potential constraints on parton distribution functions is quantified. The sensitivity of the proposed charge asymmetry measurements with the full Run II LHCb data is also considered.

Keywords: QCD
top quark physics
forward physics
Advisor: Haisch, U
John, M
Edition and study of Teive’s Epithalamium: The Epodon libri tres (1565) and Neo-Latin kiterature in Counter-Reformation Portugal

This dissertation comprises the first study of the poetry of the Portuguese humanist Diogo de Teive (1513-14 – c. 1569). It examines and presents a scholarly edition of the Epithalamium which Teive composed on the occasion of the marriage of Princess Maria of Portugal to Alessandro Farnese in 1565. It also critically explores the work in which the poem was published, the Epodon libri tres (Lisbon, 1565).
Because both this and the Epithalamium bring together different strands of Teive’s literary work, Chapter One analyses the development of his literary career, linking it to the ideological and cultural transformations which took place in Portugal from the 1540s to the 1560s, and the author’s attempt to carve his identity and space in the Portuguese literary scene. Chapter Two explores the concepts of ‘imitatio’ and ‘mimesis’ in the Epodon libri tres, shedding light on specific aspects of the Epithalamium. In the eyes of his readers, Teive emerges as a Catholic Horace. This is achieved by means of formal imitation, ‘aemulatio’, and allusion to Horace, a process whereby Teive introduces significant and ideologically motivated differences representative of the impact of Counter-Reformation upon literary writing. The ‘aemulatio’ of Prudentius’s Peristephanon in book II is to be understood in this light. Part Two engages with Teive’s comments on questions of verbal representation in the Epodon libri tres. Chapter Three analyses the Epithalamium from a generic perspective, arguing that it presents instances of generic enrichment, and that these are an example of the appropriation of occasional poetry for the purpose of authorial self-representation. One of the instances of generic enrichment is the incorporation of a didactic passage indebted to the tradition of the ‘speculum principum’, which is analysed in Chapter Four. Part One interprets the rewriting and appropriation of Plutarch and Erasmus as authorising strategies whereby Teive represents himself as an advisor of kings in the Epodon libri tres. Part Two discusses the author’s political thought and opinions, drawing from an analysis of the Epithalamium. Finally, Chapter Five comprises the study of the transmission of the poem, its metrical analysis, edition, translation, and commentary.

Keywords: Diogo de Teive/ Iacobus Tevius (c.1514 - c. 1569)
Counter-Reformation
Reception of Horace - Epodon liber
Reception of Erasmus - Institutio Principis Christiani
Neo-Latin literature in Portugal
Epithalamium (genre)
Generic Enrichment
imitatio and mimesis
Reception of Prudentius - Peristephanon
career criticism
Advisor: Earle, T
The effect of Ottoman rule on fin de siècle Beirut

The proposed thesis deals with Beirut's urban development from a maritime town to a provincial capital in the 19. and early 20. centuries. It does so in the context of physical, politico-administrative and socio-cultural inscriptions on the city by a centralizing Ottoman state. The center-periphery relations in the Ottoman Empire are examined in terms of the forces of political integration and social cohesion as well as challenges to them. The empire-city nexus that is maintained throughout this thesis posits Beirut both as the site of Ottoman imperial discourses and practices and as the site of local appropriation of- and resistance to - them. Local power was articulated in arenas of negotiation between Istanbul and Beirut (e.g. municipal councils, bureaucratic and personal networks, production of space, practices of urban management). At the same time, the quality of the city's growth and wealth created discontent and resistance among these sectors of society that were excluded from, or threatened by, Beirut's development as a port city and provincial capital (e.g. strikes, boycotts, demonstrations, riots). The condition of Beirut at the turn of the century was commented and reflected upon in contemporary Arabic journal editorials, newspaper articles, poems and speeches whose transformative power, it will be argued, affected the very physical form of Beirut's urban fabric.

Advisor: Rogan, E
Some problems in the theory of groups

This work is divided into three parts, all of which are concerned with the characterisation of certain families of classical groups as doubly transitive permutation groups satisfying certain extra hypotheses.
The first part is purely expository. It culminates in the characterisation andndash; due to Marggraf andndash; of the affine groups over GF(2).
The second part deals with a characterisation of certain collineation groups of protective spaces as Jordan groups which admit a Jordan set of prime power cardinality and which have extra restrictions on some Sylow subgroups.
The third part consists of results obtained while attempting to establish that insoluble groups of prime degree p (andgt;7), whose Sylow p-subgroups have index 3 in their normalisers, are of the form PSL(3,q), for suitable prime powers q.
Star-forming galaxies in the epoch of reionization

This work presents a search for galaxies at 6.5 < z < 9.8 based on the Lyman-break technique, using the latest HST WFC3 near-infrared data covering ∼ 150 arcmin^2 of the GOODS-South field. With these data, it is possible to find sufficient z ≈ 7−9 galaxies to fit both φ∗ and M∗ of the UV Schechter luminosity function. There is evidence for evolution in this luminosity function from z = 6−7 to z = 8−9, in the sense that there are fewer UV-bright galaxies at z ≈ 8 − 9, consistent with an evolution mainly in M∗. The candidate z ≈ 7 − 9 galaxies detected have insufficient ionizing flux to reionize the Universe, and it is probable that galaxies below our detection limit provide a significant UV contribution. The faint-end slope, α, is not well constrained. Adopting a similar faint-end slope to that determined at z = 3 − 6 (α = −1.7), and a Salpeter initial mass function, reionization could be achieved at z ≈ 7 for an escape fraction of ionizing photons fesc = 0.5 integrating the luminosity function down to M_UV= −15, while at z ≈ 8, for the same fesc, the ionizing photon budget still falls short even integrating down to M_UV = −8. A steeper faint end slope or a low-metallicity population (or a top-heavy IMF) might still provide sufficient photons for star-forming galaxies to reionize the Universe, but confirmation of this might have to await the James Webb Space Telescope.

Keywords: Astrophysics
Advisor: Bunker, A
Probing the effect of oxygen vacancies in strontium titanate single crystals

This thesis describes investigations into the role of non-stoichiometry in the surface and bulk properties of SrTiO3 single crystals. A family of (n×n) reconstructions, where n = 2, 3, 4, 5, 6 are produced by argon ion sputtering of the SrTiO3 (111) single crystals and subsequent annealing in UHV or in an oxygen rich environment. The sputtering process introduces defects or oxygen vacancies in the surface region of the sample, whilst the annealing gives rise to surface reconstructions. The surface preparation conditions such as sputtering time, annealing temperature and environment are optimized to obtain various reconstructions in a controlled and reproducible manner. High resolution STM images of these reconstructions are also obtained and utilized in the investigation of the surface reactivity. Fullerene molecules are deposited on the reconstructed surfaces to elucidate the surface reactivity through template assisted growth. Fullerene molecules are first deposited with substrate surfaces held at room temperature. Being the most highly reduced among the (n×n) family, the 5×5 reconstruction significantly influenced the growth of fullerenes. Both C60 and C70 adsorb as individual molecules and produce clusters with magic numbers. The 4×4 and 6×6 reconstructed surfaces encourage the formation of close-packed structures upon the deposition at room temperature. When the surface covered with fullerenes is heated to a temperature of around 200 °C, epitaxial islands are observed. The 6×6 reconstructed surface appeared to be less reactive than the 4×4.
Electrical transport, cathodoluminescence (CL) and electron spin resonance (ESR) experiments are also carried out to investigate the effect of oxygen vacancies on the bulk properties of UHV annealed SrTiO3 single crystals. Thermal reduction leads to carrier doping of the material, which not only gives rise to electrical conduction but also induces room temperature luminescence. Both the electrical conductivity and CL intensity increases with annealing time. The work presented in this thesis provides insight into the defect driven properties in both the surface and bulk of SrTiO3 single crystals, which could play an important role in the development of oxide-based electronic devices.

Keywords: Molecular self-assembly
Electron spin resonance spectroscopy
Surface reconstructions
Strontium Titanate
Scanning tunnelling microscopy
Cathodoluminescence spectroscopy
Advisor: Castell, M
Oceanic cycling of rare earth elements and the application of Nd isotopes to assess changes in Mesozoic ocean circulation

Rare earth elements (REEs) and their isotopes (such as Nd isotopes) can be potentially used to trace a wide range of oceanic processes in both modern and ancient oceans, but their successful application as tracers requires a comprehensive understanding of REE cycling in the modern ocean.
Previous studies of REEs in seawater were largely constrained by analytical difficulties in generating accurate and precise REE data from seawater, which typically contain REE concentrations at a sub-ppt to ppt level. A new, and relatively simple, analytical method for precise and accurate determination of all dissolved REE concentrations in reasonably small (&Tilde;100 ml) seawater samples is presented in this thesis.
With the application of the new method, this thesis reports the first full-depth, zonal ocean section of all dissolved REE concentrations, collected during the CoFeMUG cruise along &Tilde;12°S in the South Atlantic. The section approach of this study places the distribution of dissolved REE concentrations in a well-constrained hydrographic context, allowing the first quantitative assessment (by an inverse model) of the relative importance of hydrographic controls resulting from advection/mixing of ocean circulation, together with non-conservative controls resulting from local particle scavenging and remineralization, in controlling the distribution of dissolved REEs in this region. A noteworthy decoupling of Ce and Mn with respect to their cycling in the water column was also observed in this study.
The application of Nd isotopes as a tracer to reconstruct changes in ocean circulation in the NW European chalk shelf sea during rapid climatic events, including the mid-Cenomanian Event and oceanic anoxic event 2 (OAE 2), suggests a tight coupling between ocean circulation and transient climatic cooling during the general warm Late Cretaceous. An advected volcanic signal during OAE 2 was registered in the seawater Nd-isotope record from the English Chalk, probably suggesting a period of enhanced ocean ventilation/mixing at this time.

Keywords: REEs
OAEs
rare earth elements
trace metal cycling
anoxic events
ocean circulation
Cretaceous
Nd isotopes
ICP-MS
Atlantic
Advisor: Henderson, G
Jenkyns, H
A molecular, anatomical and developmental account of copine-6 protein expression in the rodent brain

This thesis describes the developmental expression and anatomical distribution of Copine-6, a neuron specific member of the Copine family of calcium-dependent phospholipid-binding proteins, in rodent brain. A polyclonal antibody targeting the full Copine-6 sequence has been characterised prior to its employment for the immunohistochemical analysis of rodent embryonic and adult brain tissue. Several different Copine-6 labelled neuron populations in the neocortex, hippocampus and olfactory bulbs were discovered, and one of these with an unusual ‘spiny’ morphology in the adult rodent corpus callosum, bordering the neurogenic subventricular zone and rostral migratory stream, was studied in detail. A full molecular characterisation of these Copine-6 ‘spiny’ neurons showed that these cells are mature, GABAergic, axonless interneurons with putative synaptic communication, unusual for their location in the white matter close to the region of adult neurogenesis. A full bromodeoxyuridine (BrdU) birth-dating analysis was performed, which indicated an early embryonic birthdate for the Copine-6 spiny cells. This timeframe is typical of cortical GABAergic interneurons suggesting that their unusual positioning is programmed from embryogenesis. Furthermore, electron microscopic analysis of these Copine-6 interneurons in Chapter 5 confirms that indeed these cells contain vesicles and are synaptically integrated as postsynaptic recipients. The presence of vesicles in the architecturally dendritic processes is suggestive of dendro-dendritic signalling by these cells. Observations from electron microscopic nanoparticle labelling also showed that the Copine-6 protein is restricted to the plasma membrane, smooth endoplasmic reticulum, and multi-vesicular bodies.
These embryonically generated Copine-6 labelled axonless interneurons are a novel neuron population in the corpus callosum, and the presence of vesicles in the dendritic processes of these cells suggests that they might have a novel communication mechanism.

Keywords: neurogenesis
dendrodendritic
corpus callosum
interneuron
synapse
Copine-6
Advisor: McIlhinney, R
The redefined centre, periphery and margin: the long-term interaction sphere of southern China 3000 – 221 BC

This thesis investigates southern China as a part of dynamic and extensive interregional networks from the third to the first millennium BC and explores the changing roles of different southern regions within the interregional relationships. This was an important transitional period for southern China as it was the time when several prominent and farreaching innovations of technologies and material culture were made or adopted in the area. Four key sets of materials – rice, bronze, ceramics and jade – are examined with a World-system perspective to reveal interregional contacts in different directions and of different nature between southern China and a number of neighbouring regions.
By stressing on local responses towards different technologies and material culture in different period, an alternative narrative to that stemmed from Chinese historiography is, therefore, suggested. Instead of being a passive and 'backward' periphery in the traditional sense, southern China presents diversification of material culture over time. Many of the mechanisms of transmission and circulation in the south are characterised by 'leaked' technologies and designs, as well as 'selective adoption' and local redevelopment of material culture.

Keywords: Chinese Archaeology
Marin
High-fired ceramics
Bronze
Periphery
Southern China
Core
Rice cultivation
World-system
Jade
Advisor: Rawson, J
Multiplicative robust and stochastic MPC with application to wind turbine control

A robust model predictive control algorithm is presented that explicitly handles multiplicative, or parametric, uncertainty in linear discrete models over a finite horizon. The uncertainty in the predicted future states and inputs is bounded by polytopes. The computational cost of running the controller is reduced by calculating matrices offline that provide a means to construct outer approximations to robust constraints to be applied online. The robust algorithm is extended to problems of uncertain models with an allowed probability of violation of constraints. The probabilistic degrees of satisfaction are approximated by one-step ahead sampling, with a greedy solution to the resulting mixed integer problem. An algorithm is given to enlarge a robustly invariant terminal set to exploit the probabilistic constraints.
Exponential basis functions are used to create a Robust MPC algorithm for which the predictions are defined over the infinite horizon. The control degrees of freedom are weights that define the bounds on the state and input uncertainty when multiplied by the basis functions. The controller handles multiplicative and additive uncertainty.
Robust MPC is applied to the problem of wind turbine control. Rotor speed and tower oscillations are controlled by a low sample rate robust predictive controller. The prediction model has multiplicative and additive uncertainty due to the uncertainty in short-term future wind speeds and in model linearisation. Robust MPC is compared to nominal MPC by means of a high-fidelity numerical simulation of a wind turbine under the two controllers in a wide range of simulated wind conditions.

Keywords: predictive control
stochastic MPC
control theory
wind turbine control
model predictive control
wind power
MPC
robust control
probabilistic control
Advisor: Cannon, M
Kouvaritakis, B
The rebellion in Awadh, 1857-58

This thesis studies the popular character of the revolt of 1857 in Awadh. It argues that in the pre-annexation rural world of Awadh talukdars and peasants had a symbiotic relationship which was destroyed by the first British revenue settlement of 1856-57. The sudden annexation together with the removal of the King from Lucknow and the dispossession and overassessment resulting from the revenue settlement created the basis for disaffection. The sepoys of the army - largely recruited from Awadh - sparked off the revolt but it quickly spread through the countryside. Certain similarities in the way the sepoys sought destruction are emphasized. A detailed study is attempted of the extent of mass participation, especially of talukdars and peasants. Lists are provided of all talukdars of southern Awadh who joined in the rebellion. As distinct from the extant literature on the subject, which emphasize British movements and forms of fighting, the present thesis studies how the rebels fought. It seeks to explore the ways in which the rebellion was organized, of the use that was made of religion as the rallying cry and of the attempts made to restore the traditional world.