VictorJuiz/thesis huggingface dataset:
Molecular studies of the human x and y chromosomes

The isolation and characterisation of sequences from the X and Y chromosomes will give some insight into the evolutionary relationship between these chromosomes, and may be of use in the study of X-linked disorders.
The availability of cDNA and genomic sequences for the human STS locus (associated with the disorder, X-linked ichthyosis) has allowed a preliminary investigation of this locus in man and other species. The localisation of these sequences to Xp22.3, provides confirmation of the sub-regional assignment of the structural gene for STS. STS homologous sequences have been identified on the long arm of the Y chromosome. These sequences also appear present on the X and Y chromosomes of the chimpanzee. In other higher primates, they appear to be X-, but not Y-, linked, suggesting that the situation in man and chimpanzee is the result of a rearrangement between the X and Y chromosomes during the past 15 million years.
Another region of X Y homology has been analysed. The locus DXYS27 maps to Yp and Xq21. Restriction enzyme analysis and direct sequence comparison has shown the two loci to be «99% homologous. Phylogenetic studies suggest that the locus is X-, but not Y-, linked in the chimpanzee, suggesting an evolutionarily recent transposition of material from the X to the Y chromosome. The mutations resulting in the X-Y differences appear to have occurred on both the X and Y chromosomes. It has been possible to demonstrate that the Y-specific locus is transferred to the X chromosome in many, but not all, aberrant X-Y interchanges resulting in XX maleness.
A sequence has been isolated that detects a hypervariable locus at Xp11.3→Xcen (DXS255) . The hypervariability appears to be due to the presence of a tandemly repeated sequence of variable length. Attempts to clone this repeat have been unsuccessful, as it appears to be unstable in the vector/host systems employed. This sequence will be of value in linkage studies of disease loci known to be present in this region. Hypervariability at this locus has not been identified in other species, suggesting that the repeat sequence is an evolutionarily recent acquisition by the X chromosome.
Taken together, the results obtained suggest that the simple model predicting an ancient origin for the bulk of the Y chromosome will have to be reassessed.
Experiments with a two-dimentional model of the general circulation

Experiments have been conducted with a two-dimensional timedependent, numerical model of the general circulation of the atmosphere up to the mesopause. A scheme for the calculation of cooling rates due to the 15(mu)m band of carbon dioxide is developed. It uses the Curtis matrix approach which incorporates cooling-to-space, transfer of radiation between atmospheric layers and non-equilibrium effects in the upper mesosphere. The sensitivity of the cooling rate calculations to the choice of collisional relaxation time is investigated. An 'almost exact' scheme to calculate heating rates due to the absorption of solar radiation by ozone and molecular oxygen is presented. Use of both new radiation schemes enables the diabatic heating rate to be calculated to the upper boundary of the model. Other heat sources in the region of the mesopause are discussed. Incorporation of the new schemes considerably improves the modelled temperature structure of:the stratosphere and lower mesosphere. The upper mesosphere is not well reproduced with no indication of the observed cold summer mesopause. The heat and momentum budgets of the mesosphere are studied. Eddy momentum fluxes derived from satellite observations of planetary waves are found to be significant for the circulation and transport properties of the stratosphere but incapable of producing the required distribution of angular momentum in the mesosphere. A Rayleigh friction parameterisation is included in the mesosphere to reproduce the observed zonal wind and temperature structure. Momentum deposition by tides and gravity waves is discussed. Curtis matrices are calculated with higher mixing ratios of carbon dioxide and the effects of increased atmospheric CO2 on stratospheric temperatures and ozone is investigated. Temperature decreases of up to about 10K are predicted with increases in ozone concentration in the upper stratosphere. In the lower stratosphere the ozone increases are restricted to high latitudes and a decrease shown in equatorial regions. The latitudinal variations are reflected in the ozone column density. An experiment is conducted in which chlorofluorocarbons are released into the model atmosphere and the effects on stratospheric ozone are in exactly the opposite sense to those predicted for the CO2 case. A run in which CO2 and CFCs are introduced simultaneously shows that the two effects are not linearly additive. A simple photochemical theory is used to investigate the temperature dependence of ozone and to explain the non-linearity of the coupled experiment.

Advisor: Walshaw, C
Investigations of open-shell open-shell Van der Waals complexes

The question posed in this work is how one would model and predict the rotational spectrum of open-shell open-shell van der Waals complexes. There are two secondary questions that arise: the nature of radical-radical interactions in such systems and the modelling of the large amplitude motion of the constituent molecules. Four different systems were studied in this work, each providing part of the answer to the main question.
Starting with the large amplitude motion, there are two theoretical approaches that may be adopted: to either model the whole complex as a semi-rigid molecule, or to perform quantum dynamical calculations. We recorded and analysed the rotational spectrum (using Fourier transform microwave spectroscopy) of the molecule of tertiary butyl acetate (TBAc) which exhibits a high degree of internal rotation; and of the weakly-bound complex between a neon atom and a nitrogen dioxide molecule (Ne-NO2). We used the semi-rigid approach for TBAc and the quantum dynamical approach for Ne-NO2. We also explored the compatibility of these two approaches. Moreover, we were able to predict and analyse the fine and hyperfine structure of the Ne-NO2 spectrum using spherical tensor operator algebra and the results of our dynamics calculations.
To explore the nature of the interactions in an radical-radical van der Waals complex we calculated the PESs of the possible states that the complex may be formed in, when an oxygen and a nitrogen monoxide molecule meet on a plane using a number of high level ab initio methods. Finally, our conclusions were tested and applied when we performed the angular quantum dynamics to predict the rotational spectrum of the complex between an oxygen and a nitrogen dioxide molecule, and account for the effect of nuclear spin statistics in that system.

Keywords: microwave spectroscopy
open-shell
ab initio
radicals
Van der Waals complexes
Advisor: Howard, B
Nutrient limitation of marine phytoplankton

Phytoplankton across the majority of the world’s oceans are thought to be limited by the availability of either nitrate or iron (Fe). However, the spatial resolution of experiments confirming this is low. Two thesis chapters present the results of bottle enrichment experiments at high spatial resolution across (i) the South Subtropical Convergence (SSTC) in the South Atlantic, and (ii) the Scotia Sea-Drake Passage sector of the Southern Ocean. These studies have added detail to the boundaries of limiting nutrients in these regions. Patterns of Fast Repetition Rate fluorometry (FRRf) derived parameters, physiological regulation of these parameters including influences of community structure, and the environmental controls driving them are analysed. Given its role as an essential micronutrient, there has been much effort in constraining potential sources of bioavailable Fe to the ocean, with one such source receiving recent interest: erupted ash from volcanoes. Bottle-scale ash-incubation experiments alongside conventional iron additions and laboratory ash-leaching experiments were conducted, the results of which suggest phytoplankton would respond strongly to ash deposition in the High Nitrate, Low Chlorophyll (HNLC) areas of the Southern Ocean. Particularly notable was the evidence these experiments provided for potential (co-)limitation of phytoplankton in these waters by the micronutrient manganese. The first three chapters of this thesis highlight a number of biogeochemical implications of trace metal stress, particularly that of Fe stress. Therefore, the ability to map the oceanographic extent of Fe-stressed regions using remote sensing would represent a particularly useful advance in marine biogeochemistry. Theoretically it could be possible to map Fe stress from space using satellite images of chlorophyll fluorescence, yet there are important uncertainties that need to be addressed before this can be carried out. In particular, a better understanding of the midday non-photochemical quenching driven reductions in chlorophyll fluorescence occurring at the time satellite images are captured is required. Analysis of over 200 non-photochemical quenching experiments collected over three research cruises, has allowed us to explore non-photochemical quenching and its relevance for using sunlight induced chlorophyll fluorescence to assess broad patterns of Fe stress. Our results have confirmed that satellite fluorescence quantum yields have the potential to reveal broad regions of Fe stress, however a dynamic non-photochemical quenching correction derived from our experiments and analysis was necessary to achieve this.

Keywords: Biogeochemistry
Physiology
Phytoplankton
nutrients
Advisor: Bouman, H
Henderson, G
Moore, M
Studies of the chemistry of plasmas used for semiconductor etching

Optical diagnostic techniques have been developed and then used to investigate the chemistry of reactive species formed in CF4 / O2 rf parallel plate discharges, similar to those employed in semiconductor material processing.
Oxygen atoms were detected by two photon laser induced fluorescence (LIF), and the technique was found to have a number of experimental caveats owing mainly to the high laser intensities required. In particular, amplified spontaneous emission (ASE), was observed from laser excitation of oxygen, and was found to influence the spontaneous fluorescence signal and thus question the use of LIF for ground state concentration measurements in these systems. The spin orbit states of the 3p 3P level were resolved for the first time, both in using high resolution excitation experiments and also as a consequence of detecting ASE. Spin orbit temperatures of less than 50° above ambient were observed. The absolute concentration of oxygen has been found to be 7.4 ± 1.4 x 1013 cm-3 in a 50 mTorr, 100 W, 85% O2 / CF4 plasma.
Optical emission was also used to study fluorine atoms and to examine the use of the actinometered emission technique as a measure of ground state concentrations. The latter was investigated directly by comparison with LIF measurements of O and CF2, and in many cases shown to be a poor representation of the ground state concentration.
To investigate the chemical and physical processes in the plasma, time resolved methods are required and a new technique, time resolved actinometry, has been developed, tested by comparison with LIF measurements and then used to study the kinetics of fluorine atoms. Results have shown the importance of wall reaction rates on the magnitude of the fluorine atom concentrations, and the sensitivity of these concentrations to the nature of the surface, particularly in the presence of oxygen and silicon. Oxygen has also been shown to be removed predominantly at the surface but the influence of gas phase reactions with CFx radicals is apparent in discharges containing low percentages of O2.
Studies on an afterglow type, electron cyclotron resonance reactor have been carried out as a comparison to the parallel plate system, and high excitation and dissociation levels have been observed from differences in the emission intensities and from measured values of the absolute CF and CF2 concentrations.
The use of LIF as a diagnostic for CF has been investigated by probing the predissociation of the A2Σ+ state. Emission from the A2Σ+ (v = 2) level has been seen for the first time, and a J independent predissociation mechanism, with a rate of 3 x 109 s-1 has been observed.

Advisor: Hancock, G
Analysis of a bipartite network of movie ratings and catalogue network growth models

Network science is a rapidly growing field that draws important results from mathematics, physics, computer science, sociology, and many other disciplines. There are many problems in nature and man made systems that involve interactions between large number of agents which take place over a non-trivial topology. These problems lend themselves naturally and successfully to a network representation. Of particular interest are the models that deal with growth and evolution of networks because the vast majority of the systems represented by them are not static. This work is concerned about systems with two different types of interacting constituents known as bipartite networks. This thesis is structured as follows: In Chapter 1 a network is defined as a graph and a brief introduction to the concepts used throughout this work is given. We describe the well-known network growth model of Preferential Attachment [2] and a model of the evolution of a bipartite network whose agent quantities are fixed [9]. In Chapter 2 we study data from Netflix, an online movie rental service whereby users can give ratings to movies they rent. We show how this system can be represented as a network and analyse some of its properties. The probability distribution of the number of ratings of users and movies follows a power-law distribution with an exponential cutoff, which indicates saturation in the number of ratings that a movie can receive or a user give. We also found that movies and users in the system form densely connected neighbourhoods. Chapter 3 is concerned with the development of network growth and evolution models which attempt to explain the growth and evolution of networks with saturation and a limited number of agents. We develop a network growth model in which the agents are drawn from fixed catalogues. An exact analytical solution to the model can sometimes be found, an approximate one using asymptotics in other cases and numerically in general. The results given by this model describe what is observed in simulated networks and show some of the characteristics observed in the Netflix network.
A Bayesian chromosome painting approach to detect signals of incomplete positive selection in sequence data : applications to 1000 genomes

Methods to detect patterns of variation associated with ongoing positive selection often focus on identifying regions of the genome with extended haplotype homozygosity - indicative of recently shared ancestry. Whilst these have been shown to be powerful they have two major challenges.
First, these methods are constructed to detect variation associated with a classical selective sweep; a single haplotype background gets swept up to a higher than expected frequency given its age. Recently studies have shown that other forms of positive selection, e.g. selection on standing variation, may be more prevalent than previous thought. Under such evolution, a mutation that is already segregating in the population becomes beneficial, possibly as a result of an environmental change. The second challenge with these methods is that they base their inference on non-parametric tests of significance which can result in uncontrolled false positive rates.
We tackle these problems using two approaches. First, by exploiting a widely used model in population genomics we construct a new approach to detect regions where a subset of the chromosomes are much more related than expected genome-wide. Using this metric we show that it is sensitive to both classical selective sweeps, and to soft selective sweeps, e.g. selection on standing variation. Second, building on existing methods, we construct a Bayesian test which bi-partitions chromosomes at every position based on their allelic type and tests for association between chromosomes carrying one allele and significantly reduced time to common ancestor.
Using simulated data we show that this approach results in a powerful, fast, and robust approach to detect signals of positive selection in sequence data. Moreover by comparing our model to existing techniques we show that we have similar power to detect recent classical selective sweeps, and considerably greater power to detect soft selective sweeps.
We apply our method, ABACUS, to three human populations using data from the 1000 Genome Project. Using existing and novel candidates of positive selection, we show that the results between ABACUS and existing methods are comparable in regions of classical selection, and are arguably superior in regions that show evidence for recent selection on standing variation.

Keywords: Natural Selection
Bayesian
Hidden Markov Models
Sequence Analysis
Advisor: Holmes, C
Spencer, C
Characterization of RNA aptamers that bind to HIV-1 gp120

RNA aptamers with 2'-fluoro-pyrimidine chemistry were previously selected by in vitro evolution to bind to monomeric HIV-1 gp120 from the R5 strain BaL. A group of 36 novel aptamers were cloned and sequenced from the heterogeneous pool and were tested for their ability to bind to gp120. The diversity of the RNA secondary structure of these, and 27 aptamers isolated previously, was analysed using a bioinformatics approach. This showed that eight aptamers contain a common branched motif, and RNA mutagenesis indicated that this structure is probably required for gp120 binding. Chemically synthesised derivatives of one such aptamer, B40, were designed and tested for binding to gp120. Truncation was found to decrease their binding, but the introduction of point mutations to stabilise the branched conformation and 2'-O-dimethylallyl-modified residues to stabilise helices increased binding to levels greater than that of the parental aptamer. The aptamer epitope on gp120 was mapped by testing aptamer binding to alanine-scanning mutants and deletion mutants of gp120 using a novel plate-based assay. This study showed that the aptamer binding site overlaps with the CCR5 epitope and is confined to four key residues at the base of the V3 loop, one of which is highly conserved. This finding may account for the observation that a number of aptamers were shown previously to neutralise a range of HIV-1 R5 clinical isolates in PBMC cultures. Interestingly however, the aptamer was unable to neutralise HIV-1 pseudovirus in a cell line, which is most likely due to the increased levels of cell-surface CCR5 in cell lines compared to PBMC. Future work should focus on identifying the structure and epitopes of other anti-gp120 aptamers as well as testing neutralisation of HIV-1, HIV-2 and SIV by the B40-derived aptamers. These aptamers can be used as tools to investigate the HIV-1 entry pathway and also have the potential to be developed as anti-HIV-1 microbicides.

Keywords: gp120
HIV-1
aptamer
Advisor: James, W
Cyberattacks in international relations

New methods of conflict and coercion can prompt tectonic shifts in the international system, reconfiguring power, institutions, and norms of state behavior. Cyberattacks, coercive acts that disrupt or destroy the digital infrastructure on which states increasingly rely, have the potential to be such a tool — but only if put into practice. This study examines which forces in the international system might restrain state use of cyberattacks, even when they are militarily advantageous. To do so I place this novel technology in the context of existing international regimes, employing an analogical approach that identifies the salient aspects of cyberattacks, and compares them to prior weapons and tactics that share those attributes. Specifically, this study considers three possible restraints on state behavior: rationalist deterrence, the jus ad bellum regime governing the resort to force, and incompatibility with the jus in bello canon of law defining just conduct in war. First, I demonstrate that cyberattacks frustrate conventional deterrence models, and invite, instead, a novel form of proto-competition I call ‘structural deterrence.’ Recognizing that states have not yet grounded their sweeping claims about the acceptability of cyberattacks in any formal analysis, I consider evidence from other prohibited uses of force or types of weaponry to defining whether cyberattacks are ‘legal’ in peacetime or ‘usable’ in wartime. Whereas previous studies of cyberattacks have focused primarily on policy guidance for a single state or limited analysis of the letter of international law, this study explicitly relates international law to state decision-making and precedent. It draws together previously disparate literature across strategic studies, international law, and diplomatic history to offer conclusions applicable beyond any single technology, and of increasing importance as states’ dependence on technology grows.

Keywords: international law
norms
cyberwar
international relations
cyberdeterrence
deterrence
cyber
cybersecurity
cyberattacks
Advisor: Khong, Y
Percy, S
Closure games: the politics of clubs in international society

This thesis develops a theory of international social closure to examine (i) the politics of membership in status groups – or, clubs – in international society and (ii) the persistence of clubs in international society. This thesis offers new concepts to improve the English School’s understanding of international society, its expansion, and its reproduction. In so doing it also addresses limitations and gaps in the IR status literature and the global governance and diplomacy literatures concerned with clubs and networks. This thesis analyses strategies of exclusion, entry, and incorporation used by actors to deny, attempt, or grant inclusion into clubs as well as the institutional contexts underpinning those clubs. Specifically, this research undertakes a study of instances of exclusion, entry, and incorporation in the context of three clubs: the Family of Civilised Nations, the Great Powers club, and G-summitry. In the first two cases, this research relies primarily on secondary sources while in the case of G-summitry it presents original empirical research gathered through archival research, interviews, and ethnographic participant observation. This thesis presents four main conclusions about the operation of closure: (i) the logics of different closure games are defined by overarching normative institutions of international society; (ii) despite a collectivist closure rule, closure in international society is predominantly individualistic; (iii) actors seeking entry tend to employ deferential entry strategies that reproduce a stratified status quo order; and (iv) incorporation promotes stratification along both functional and cultural lines. This thesis also draws three specific conclusions that run counter to much current scholarship: (i) contemporary international society is neither more open nor less hierarchical than nineteenth century international society; (ii) hierarchy is reproduced to a large degree by entry and incorporation strategies rather than exclusion strategies; and (iii) closure does not run along a ‘west versus the rest’ fault line.

Keywords: Mobility Dampeners
G20
G8
G7
Family of Civilised Nations
Standard of Civilisation
Status
Closure Theory
International Society
Great Powers
Entry
Exclusion
Credentialism.
G-Summitry
Inclusion
Social Closure
Incorporation
Advisor: Keene, E