VictorJuiz/thesis huggingface dataset:
Stark deceleration and reactivity of polyatomic molecules and ions at low temperatures
Keywords: ion trapping
cold and ultracold chemistry
angular momentum
reaction dynamics
Stark deceleration

This thesis describes the development of a new experimental technique for studying tunable-collision-energy, quantum state-selected, low-temperature ion-molecule reactions. This has been achieved through the combination of a Stark decelerator for neutral dipolar molecules, and a linear Paul ion trap.
The Stark deceleration process for ND3 was examined in detail, through the analysis of experimental data in combination with newly written molecular dynamics simulation programs. In order to prepare a sample of molecules appropriate for collision studies, additional beamline components were introduced after the decelerator. These components were: two hexapoles, to provide transverse focussing, maximising the molecular density; a molecular buncher, providing increased longitudinal velocity resolution; and a fast-opening shutter, to separate decelerated molecules from undecelerated molecules. The sympathetic-cooling of Xe+ ions and ND+3 ions by laser-cooled, Coulomb crystallised 40Ca+ ions with the ion trap was also studied. In particular, the stable trapping of Xe+ was demonstrated for the first time, and the experimental developments that led to this are discussed.
The work in this thesis represents significant progress towards studying the reaction of tunable-energy ND3 in the |j,mk> = |1,−1> quantum state with cold Xe+ ions. Ion-molecule reactions utilising ND3 molecules electrostatically guided through the Stark decelerator were performed. It was observed that the main source of error in these experiments was in the calculation of the initial number of Xe+ ions that had been sympathetically cooled into the Coulomb crystal. The sensitivity of the crystal morphology to the number of Xe+ ions was evaluated using molecular dynamics simulations. Strategies have been developed to reduce this uncertainty in future studies.
In addition to experimental work, the theory of low temperature ion-molecule reactions has been developed further. The temperature at which classical and quantum mechanical calculations diverge due to purely statistical effects has been investigated using different model intermolecular potentials, for closed-shell and open-shell species, and in the ground and rotationally excited states. From the results of these calculations, several promising candidate reactions have been suggested that might exhibit statistical quantum behaviour at experimentally achievable temperatures.
The art of Platonic love
Keywords: Ancient Greek ethics
love
Plato

This is a study of love (erōs) in Plato’s Symposium. It’s a study undertaken over three chapters, each of which serves as a stepping stone for the following and addresses one of three primary aims. First: to provide an interpretation of Plato’s favored theory of erōs in the Symposium, or as it’s referred to here, a theory of Platonic love. This theory is understood to be ultimately concerned with a practice of living which, if developed correctly, may come to constitute the life most worth living for a human being. On this interpretation, Platonic love is the desire for Beauty, ultimately for the sake of eudaimonic immortality, manifested through productive activity. Second: to offer a reading of the Symposium which attends to the work’s literary elements, especially characterization and narrative structure, as partially constitutive of Plato’s philosophical thought on erōs. Here it’s suggested that Platonic love is concerned with seeking and producing truly virtuous action and true poetry. This reading positions us to see that a correctly progressing and well-practiced Platonic love is illustrated in the character of the philosopher Socrates, who is known and followed for his bizarre displays of virtue and whom Alcibiades crowns over either Aristophanes or Agathon as the wisest and most beautiful poet at the Symposium. Third: to account for how to love a person Platonically. Contra Gregory Vlastos’ influential critical interpretation, it’s here argued that the Platonic lover is able to really love a person: to really love a person Platonically is to seek jointly for Beauty; it is to work together as co-practitioners in the art of love. The art of Platonic love is set up in this way to be explored as a practice potentially constitutive of the life most worth living for a human being.
Oil, conflict and displacement in Sudan
Keywords: Sudan
oil
development
conflict

This thesis explores the political dimensions of development-induced displacement and resettlement (DIDR) in the context of oil extraction in Sudan. It provides a detailed perspective on the experience of displacement of the local people in the oil-rich areas of Southern Sudan. It also offers an important insight into the local politics of this much-publicized dimension of Sudan’s political crises. The analytical frameworks common to the field of DIDR, mostly developed through studies of the impact of dams, mainly deal with economic and social aspects of displacement. These frameworks are inadequate for explaining oil-induced displacement, because they largely ignore the political contexts of DIDR: the focus of this thesis. Sudan’s oil project is carried out in the name of the “national interest.” But in reality, it serves the interests of the main beneficiaries: Sudan’s Northern “Arab” and Muslim elites and their supporters. Many Southern Sudanese have had to resort to arms, partly to protect their interests in oil development, and in order to contest the purported “national interest” championed by the government. This thesis problematizes the idea of a “national interest” in Sudan in order to question who benefits from development projects that cause human displacement. It argues that conflicts of interests between central government elites and local peoples best explain why displacement connected to natural resource development occurs in weak states, such as Sudan. As a result, ethnic, religious, linguistic, regional and other identities are often exploited by elites in such states in an “instrumentalist” way so as to gain, or retain, power and access to resources. This is, at the expense of local people adversely affected by development projects.
Intersecting doublesex neurons underlying sexual behaviours in Drosophila melanogaster
Keywords: doublesex
neural circuitry
male courtship
female behaviour
drosophila

In Drosophila, the functionally conserved transcription factor, doublesex (dsx), is pivotal to the specification of sexual identity in both males and females. One of its key dedicated roles involves regulating the development of a sexually dimorphic nervous system (NS) that underlies both male and female reproductive behaviours. Specific inhibition of the function of dsx-expressing neurons in males and females results in a global disruption of these sex-specific behavioural outputs. However, little is known about the functional organisation of this dsx circuit that encodes the potential to display these behaviours.
Such investigations require the generation of a novel transgenic tool, capable of separating the function of dsx in the NS from that of the body. To achieve this, I generated a novel split-GAL4 dsxGAL4-DBD hemidriver by ends in homologous recombination. Coupling the novel tool with the pan-neuronal elavVP16-AD hemidriver, revealed spatial restriction of dsxGAL4-DBD/elavVP16-AD expression to dsx neurons only; enabling the realisation of novel patterns of dsx-expression in the peripheral NS.
Next, the ability to elicit male-specific behavioural outputs upon activation of all dsx neurons formed the basis of a large behavioural screen aimed at parsing dsx circuitry into functionally distinct clusters. I utilised the novel dsxGAL4-DBD hemidriver to screen a large collection of extant enhancer trap lines (ETVP16-AD), for the elicitation of distinct sub-behaviours of male courtship. Here, I show that the activity of dsx-expressing clusters in:
i) the brain (dsx-pC1, -pC2 and -pC3 collectively) regulate the early steps of male courtship (initiation, orientation and wing extension),
ii) the pro- and mesothoracic ganglia (dsx-TN1 and -TN2) regulate the middle steps of male courtship (wing extension and possibly courtship song) and
iii) the abdominal ganglia (dsx-Abg) regulate the late steps of male courtship (abdominal curling, attempted copulation and copulation).
These data establish functional correlations between dsx clusters in distinct neuroanatomical foci and specific sub-behaviours of the courtship repertoire.
Furthermore, the novel intersectional tool primed a collaborative study on female post-copulatory behaviours. We identified key sensory neurons in the female reproductive tract involved in initiating post-mating behaviours. Subsequent functional interrogations of dsx circuitry in the central NS revealed a subset of dsx-expressing neurons in the Abg that mediate changes in the female behavioural repertoire after mating.
Characterisation of this relatively simple neural circuitry sheds light on the organisation of the fly brain. Ultimately, future studies will define principles of neural circuit operation, which may be similarly conserved in the nervous systems of higher animals.
Lambda-Fleming-Viot processes and their spatial extensions
Keywords: Mathematical genetics
Lambda Fleming Viot
genealogies
Lambda coalescent
Bayesien statistics

The subject of this thesis is the study of certain stochastic models arising in Population Genetics. The study of biological evolution naturally motivates the construction and use of sometimes sophisticated mathematical models.
We contribute to the study of the so-called Lambda models. Our work is divided into two parts. In Part I, we study non-spatial models, introduced in 1999. Although there is a very rich literature concerning the description of genetic diversity thanks to the genealogies arising in these models, we obtain new results by considering the dynamics of the full population. We also contribute by presenting the first Bayesian method that allows us to reconstruct the genealogies generated by these models from data.
In Part II, we study a recent extension of these models to the spatial setting. In particular, we prove a non trivial result concerning the geographical dispersal of a new mutant under this model.
Aspects of beyond the Standard Model string phenomenology
Keywords: branonium
black hole superradiance
string excitations
string phenomenology

String theory is currently the best-known candidate for a theory of quantum gravity, having the necessary ingredients to describe all known elementary particles and interactions. It also includes several novel features, arising, for instance, from the additional six compact dimensions required for its internal consistency, making it the natural arena to construct extensions of the Standard Model. In this thesis, we analyze some of the new phenomenological aspects introduced by string theory within the framework of low energy effective theories, focusing on their applications to cosmology, astrophysics and collider experiments. We first consider a particular realization of the brane-world scenario in branonium bound states, showing that the orbital motion of a probe antibrane about a central brane stack leads to a resonant amplification of its world-volume scalar modes. We analyze the cosmological development of this process and also its potential relevance for either dark or baryonic matter generation in the early universe. We then focus on the spectrum of quark and lepton string excitations in warped compactifications, modeled by an effective 5-dimensional Randall- Sundrum throat. Motivated by the observed fermion mass hierarchy, we show that the spin-3/2 Regge excitation of the right-handed top quark is the lightest of such resonances in a significant region of parameter space, possibly lying below the TeV scale, and discuss its potential signatures at the Tevatron and at the LHC. Finally, we study the emission of sub-eV scalar particles by maximally rotating Kerr black holes, motivated by the recent string axiverse proposal. We focus on the spectrum of unstable scalar bound states in the superradiant regime, leading to an exponentially large axion cloud around astrophysical black holes, and analyze two semi-analytical methods for computing the growth rate of this instability, comparing the obtained results with previous analytical and numerical analyses.
A study of the cone-pressuremeter test in sand
Keywords: cone pressuremeter
sand

The cone-pressuremeter is a new site investigation device which incorporates a pressuremeter behind a standard cone penetrometer tip. This dissertation is concerned with an understanding of the new device, and in particular the establishment of a detailed procedure to allow the test to be used to determine the engineering properties of cohesionless soils. A series of 34 calibration tests was performed, in which three cone-pressuremeter prototypes with cross-sectional areas corresponding to 15cm², 10cm² and 5cm² were used. The tests were carried out on cylindrical samples, enclosed in a chamber 1.0 m in diameter and 1.5 m in height. Stress controlled boundaries allowed independent control of vertical and horizontal stress in the range of 50 kPa to 300 kPa. A raining deposition technique was used to produce three sand densities, corresponding to loose, medium and dense samples. A programme of calibration was designed to provide an examination of the influence of relative density, stress level and stress ratio on cone-pressuremeter test data. Soil properties were related to the values of the limit pressure obtained from the pressuremeter test and the cone resistance values from the cone test. Empirical relationships were proposed for deriving density, friction angle and horizontal stress. Cone-pressuremeter tests were used for assessing directly the shear stiffness of the soil. A series of calibrations was needed to obtain the best possible estimation of the unload-reload shear modulus. Interpretation of the measured modulus was made by examining appropriate methods of calculating the modulus from unload-reload loops. Strain arm measurements and volume change measurements were compared. A method has been presented that allows the shear modulus values to be correlated to the relevant stress level acting around the pressuremeter during the test. The values of shear modulus obtained with the cone- pressuremeter were compatible with those obtained from the self-boring pressuremeter. An assessment of chamber size effects yielded useful information regarding the applicability of test correlations derived from calibration chambers to field problems. An additional study identified experimentally the influence of length to diameter ratio on the pressuremeter pressure-expansion curve.
Consequence-based reasoning for ontology classification
Keywords: description logics
classification
algorithms and optimization

Description logics (DLs) are knowledge representation languages that provide the theoretical underpinning for modern ontology languages such as OWL and serve as the basis for the development of ontology reasoners and tools.
Most modern ontology reasoners are based on optimized tableau algorithms, which perform reasoning by trying to build counter-models. More recently, another kind of reasoning algorithms has been introduced that, instead of building counter-models, directly derive logical consequences of axioms in the ontology using inference rules. Such consequence-based algorithms were first introduced for the EL family of DLs, and later extended to more expressive Horn DLs. However, up until now, consequence-based algorithms could not handle non-Horn features such as disjunctions.
We consider several complementary aspects of consequence-based reasoning in this thesis. Firstly, we describe the parallelized consequence-based reasoner ELK, which is currently the fastest reasoner for EL ontologies. Secondly, we demonstrate how consequence-based algorithms can be extended to handle disjunctions using inference rules reminiscent of ordered resolution. Finally, we combine our consequence-based framework with methods based on tree decompositions, and thus obtain what we believe are the first fixed-parameter tractability results for subsumption reasoning in DLs.
A model-independent theory of computational complexity: from patience to precision and beyond
Keywords: theoretical computer science
computational complexity
unconventional computing

The field of computational complexity theory--which chiefly aims to quantify the difficulty encountered when performing calculations--is, in the case of conventional computers, correctly practised and well understood (some important and fundamental open questions notwithstanding); however, such understanding is, we argue, lacking when unconventional paradigms are considered. As an illustration, we present here an analogue computer that performs the task of natural-number factorization using only polynomial time and space; the system's true, exponential complexity, which arises from requirements concerning precision, is overlooked by a traditional, `time-and-space' approach to complexity theory. Hence, we formulate the thesis that unconventional computers warrant unconventional complexity analysis; the crucial omission from traditional analysis, we suggest, is consideration of relevant resources, these being not only time and space, but also precision, energy, etc.
In the presence of this multitude of resources, however, the task of comparing computers' efficiency (formerly a case merely of comparing time complexity) becomes difficult. We resolve this by introducing a notion of overall complexity, though this transpires to be incompatible with an unrestricted formulation of resource; accordingly, we define normality of resource, and stipulate that considered resources be normal, so as to rectify certain undesirable complexity behaviour. Our concept of overall complexity induces corresponding complexity classes, and we prove theorems concerning, for example, the inclusions therebetween.
Our notions of resource, overall complexity, normality, etc. form a model-independent framework of computational complexity theory, which allows: insightful complexity analysis of unconventional computers; comparison of large, model-heterogeneous sets of computers, and correspondingly improved bounds upon the complexity of problems; assessment of novel, unconventional systems against existing, Turing-machine benchmarks; increased confidence in the difficulty of problems; etc. We apply notions of the framework to existing disputes in the literature, and consider in the context of the framework various fundamental questions concerning the nature of computation.
Studies on HIF hydroxylases
Keywords: Oxygen sensing
Factor Inhibiting HIF
MYPT1
2OG-dependent dioxygenases
Prolyl Hydroxylase Domain-containing 3
FIH
Hypoxia
Myosin phosphatase
HIF
Ankyrin repeat proteins
Proteomics
Mass spectrometry
Notch
PHD3
Hydroxylation

Hypoxia-inducible factor (HIF) is the master regulator of genes involved in adaptation to hypoxia. The stability and transcriptional activity of HIF are regulated by post-translational hydroxylations: prolyl hydroxylation by the prolyl hydroxylase domain-containing enzymes PHD1 – 3 earmarks HIF for proteasomal degradation, whilst asparaginyl hydroxylation by factor inhibiting HIF (FIH) blocks the interaction of HIF with the transcriptional coactivators p300/CBP. The PHDs and FIH hydroxylate HIF directly from molecular oxygen and are therefore oxygen sensors.
Recent literature shows that FIH also hydroxylates a number of proteins containing an ankyrin-repeat domain (ARD). Together with reports suggesting that the PHDs are involved in HIF-independent pathways, this suggests that the HIF hydroxylases may have a wide range of non-HIF targets. This thesis describes my investigations into novel substrates of the HIF hydroxylases.
This work has characterized the FIH-dependent hydroxylation of the ARD-containing protein Notch1, and defined a consensus sequence for hydroxylation that corresponds to the ankyrin-repeat consensus. Using this consensus potential sites of hydroxylation in a novel ARD FIH substrate, myosin phosphatase targeting subunit 1 (MYPT1), were identified then subsequently confirmed and characterized.
Notch1 competes with HIF for FIH hydroxylation. My experiments show that this occurs because Notch1 is a more efficient substrate than HIF, whilst studies on MYPT1 and other proteins indicate that competitive inhibition of FIH may be a general property of ARDs.
There are more than 300 ARD proteins in the human genome, and this thesis demonstrates that FIH may hydroxylate a significant percentage of these. In addition to the analysis of ARD hydroxylation a proteomic investigation into novel PHD3 substrates has identified two candidate proteins, suggesting that the PHDs may also have multiple targets. These results have important implications for oxygen sensing, and indicate that post-translational hydroxylation is likely to be a widespread modification in cell biology.
Foragers on the frontiers: the |Xam Bushmen of the Northern Cape, South Africa, in the nineteenth century
Keywords: hunter-gatherer
animism
colonial history
shamanism
San
Bushmen
Khoisan

This thesis constructs an ethnography for the nineteenth century ǀXam Bushmen of the Northern Cape Province of South Africa, known primarily through a nineteenth century manuscript collection of oral narrative (the Bleek-Lloyd archive), which has, over the past twenty-five years, increasingly become the focus of scholarly attention, mined for insights about the cultural world of southern Bushman societies. It draws on the Bleek-Lloyd archive to produce a detailed ethnographic case study, focusing on the ideological and ontological concepts that underpinned the differentiation of ǀXam society. Firstly, the thesis situates the archive and ǀXam society within their particular environmental and historical contexts, providing valuable supplementary information that informs readings of the narratives. By producing a fully searchable transcription of the entirety of the archive, paying close attention to emic terminology, and examining the recurrence of thematic associations of this phraseology throughout the narratives, the analysis explores the constitution of ǀXam ‘personhood’ and examines the extent to which the ‘hunter-gatherer’ category forms a useful heuristic for understanding ǀXam society, with a particular focus on models of the ‘animic ontology’. The ǀXam deployed a series of positively and negatively evaluated traits in the creation of dimensions of authority, obligation, and social responsibility, embedded in particular social identities; central to these constructions and to the differentiation of these identities were the techniques and resources of ǀXam subsistence practices, salient in the production of admirable (socially-responsible hunters), reprehensible (antagonistic ‘beasts of prey’), and more ambiguous (ǃgi:tǝn ritual specialists) identities. Recognising this internal differentiation, the thesis outlines ǀXam ‘subsistence strategies’ and suggests they should be defined broadly to include their contacts and interactions with non-ǀXam groups, with domesticated animals, and with the novel material culture of the colonial period; these interactions were a consequence of their ‘hunter-gatherer’ strategies rather than a negation of them. Such strategies generated experiences that reinforced and reconstituted ǀXam ideological frameworks, incorporating the dynamics of the nineteenth century ‘frontier’ scenario and provided avenues for social change that ultimately led to the collapse of independent hunter-gatherer lifeways, and to the adoption of strategies that incorporated ǀXam individuals within rural and urban ‘Coloured’ populations of the Northern Cape; placing the ǀXam in a comparative colonial context, the thesis stresses the wider relevance of this particular ethnography for understanding hunter-gatherer engagements with food-producing, state-level societies.