VictorJuiz/thesis huggingface dataset:
Fourier transform ion cyclotron resonance mass spectrometry for petroleomics

The past two decades have witnessed tremendous advances in the field of high accuracy, high mass resolution data acquisition of complex samples such as crude oils and the human proteome. With the development of Fourier transform ion cyclotron resonance mass spectrometry, the rapidly growing field of petroleomics has emerged, whose goal is to process and analyse the large volumes of complex and often poorly understood data on crude oils generated by mass spectrometry.
As global oil resources deplete, oil companies are increasingly moving towards the extraction and refining of the still plentiful reserves of heavy, carbon rich and highly contaminated crude oil. It is essential that the oil industry gather the maximum possible amount of information about the crude oil prior to setting up the drilling infrastructure, in order to reduce processing costs.
This project describes how machine learning can be used as a novel way to extract critical information from complex mass spectra which will aid in the processing of crude oils.
The thesis discusses the experimental methods involved in acquiring high accuracy mass spectral data for a large and key industry-standard set of crude oil samples. These data are subsequently analysed to identify possible links between the raw mass spectra and certain physical properties of the oils, such as pour point and sulphur content.
Methods including artificial neural networks and self organising maps are described and the use of spectral clustering and pattern recognition to classify crude oils is investigated. The main focus of the research, the creation of an original simulated annealing genetic algorithm hybrid technique (SAGA), is discussed in detail and the successes of modelling a number of different datasets using all described methods are outlined.
Despite the complexity of the underlying mass spectrometry data, which reflects the considerable chemical diversity of the samples themselves, the results show that physical properties can be modelled with varying degrees of success. When modelling pour point temperatures, the artificial neural network achieved an average prediction error of less than 10% while SAGA predicted the same values with an average accuracy of more than 85%. It did not prove possible to model any of the other properties with such statistical significance; however improvements to feature extraction and pre-processing of the spectral data as well as enhancement of the modelling techniques should yield more consistent and statistically reliable results.
These should in due course lead to a comprehensive model which the oil industry can use to process crude oil data using rapid and cost effective analytical methods.

Keywords: artificial neural networks
mass spectrometry
machine learning
FT-ICR-MS
data modelling
genetic algorithms
petroleomics
Advisor: Cartwright, H
Indian death rituals

This work provides a survey of Indian funeral rites, concentrating on ceremonies performed by rural mainland Hindus, who have been divided into the broad social categories of brahmins, caste Hindus and outcastes/tribes. The primary intention is to identify a core of ritual, which can be used as a baseline against which particular funeral performances can be checked. This work also examines the variation of brahminical ritual over time through a survey of ethnographic material taken from Gazetteers and Government Ethnographic Surveys; the Purāṇas, represented by a version of the Garuḍa Purāṇa and a work known as the Garuḍa Purāṇa Sāroddāra; and Caland's summary of Vedic ritual in Die altindischen Todten- und Bestattungsgebräuche.
In each of these three sections the funeral rituals have been divided into six stages and these stages have been further divided into sub-sections containing specific rituals or groups of rituals. Sections on untimely death and the role of the widow in her husband's funeral are also included.
Particular emphasis is placed throughout the historical survey on the recurrent theme of ambivalence towards death as reflected both in ritual and its interpretation: the relative is loved and honoured but the corpse is frightening and quickly becomes disgusting. The survey examines the relationship between the primary emotional response to death and secondary ideological constructs, and it reveals that while ritual reflects the emotional response to death it does not always reflect secondary ideology.
In addition this work includes a summary, in table form, of the variation of funeral ritual according to geographical area for all three social groups; again taken from the ethnographic material of the Gazetteers and Government Surveys.
Control of cardiac metabolism and efficiency

For many years high levels of plasma non-esterified fatty acids (NEFAs) have been associated with a decreased cardiac energy stores, though the mechanism for this has been elusive. The aim of this thesis was to investigate the possible detrimental effects of the elevated plasma NEFA levels that have been reported in heart failure.
In the chronically ligated rat heart, a model of heart failure post-myocardial infarction, levels of UCP2 and UCP3 were increased, correlating with increased plasma NEFAs, and were associated with increased mitochondrial uncoupling. The cardiac mitochondria isolated from these rats were less abundant and had a reduced maximal respiratory capacity, possibly due to mitochondrial DNA damage mediated by reactive oxygen species.
Patients with heart failure have insulin resistance, here it was found that the chronically ligated heart had reduced uptake of D[2-3H] glucose after stimulation with insulin. This was associated with decreased cardiac levels of the insulin-responsive glucose transporter, GLUT4, the levels of which correlated negatively with plasma NEFAs. D[2-3H] glucose uptake was also reduced during cardiac ischaemia, leading to greater loss of ATP and lower contractile recovery upon reperfusion.
In human heart, levels of UCP2 and UCP3 correlated positively with plasma NEFA concentrations, and may explain the decrease in phosphocreatine that is reported in heart failure patients. Also, levels of GLUT4 in heart and skeletal muscle correlated negatively with plasma NEFA concentrations, and could result in myocardial insulin resistance in heart failure patients.
In conclusion, increased levels of circulating NEFAs in rats post-myocardial infarction, increased cardiac levels of UCP2 and UCP3, which were associated with increased mitochondrial uncoupling, and decreased cardiac levels of GLUT4, which were associated with insulin resistance and impaired energy metabolism. Similarly, in patients, high levels of NEFAs were associated with increased cardiac UCP levels and decreased GLUT4 levels in heart and skeletal muscle. This could explain the reduction in myocardial energy stores in heart failure patients which have high plasma NEFA levels.

Advisor: Clarke, K
Diamond politics in the Angolan periphery: colonial and postcolonial Lunda 1917–2002

Angola is currently the fifth-largest diamond producer in the world. Yet neither the politics nor the history of Angola's diamond trade receives much attention either in the Angolan scholarship or the thematic literature on the mining sector more generally. The gap in the literature is significant, for diamond companies produce far more than revenue and profits: for some one hundred years, the diamond sector has governed, policed, defended, and controlled the strategic, diamond-rich provinces of Lunda Sul and Lunda Norte.
This thesis explores the historical trajectory of the diamond sector in the Lundas. It concentrates on the powerfully symbiotic relationship between the diamond sector and the state from the colonial period to the present time. Drawing on a wide range of untapped official documents as well as interviews, it argues that the diamond sector has functioned historically as the conduit through which the state projects its power and secures its interests in a strategic but hostile territory. The thesis further shows how the politics of resource control both define the state’s strategies towards the diamond sector and perpetuate the entrenched system of privatised governance that has existed in the Lundas for more than a century.
The thesis builds upon both the historical and contemporary literature on the mining sector and the literature on state formation. It challenges the conventional notion that the persistent power of private companies in Africa is the result of state weakness or state absence, underlining instead how state leaders instrumentalise and empower companies according to their changing priorities. It also considers the implications of this case study more broadly through a cross-case analysis of mining politics elsewhere in Africa. In the process, this study provides an original approach to state–mining sector relations that is of relevance to scholars working on the politics and political economy of state-making and of resources extraction in Africa.

Keywords: Lunda
diamond sector
DIAMANG
Angola
Lunda Sul
Lunda Norte
Advisor: Soares de Oliveira, R
Functional genetic analysis of motor neuron disease

Amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA) are the commonest motor neuron diseases of adult- and childhood onset. Alterations of the RNA binding protein TDP-43 are associated with most cases of ALS, while SMA is caused by deletion of the Survival Motor Neuron (SMN1) gene. SMN has been well characterised in its role in the assembly of the cellular machinery that carries out splicing of pre-mRNA, but is thought to have other functions in RNA metabolism unrelated to pre-mRNA splicing. It is conceivable that specific aspects of RNA handling are disrupted in both SMA and ALS. A variety of genetic, molecular and neuropathological approaches were applied to investigate a potential common pathway in these diseases. The spectrum of genetic mutations underlying motor neuron disorders were explored by screening patient DNA. Cell culture and mouse models were used to test the hypothesis that altered pre-mRNA splicing causes motor neuron death. Human neuropathological specimens were examined for changes in proteins involved in RNA metabolism. The results indicate that altered pre-mRNA splicing is a late occurrence in disease and more likely to be a consequence rather than the cause of motor neuron degeneration. However, the notion that RNA metabolism is highly relevant to motor neuron diseases was strengthened by the discovery of mutations in another RNA binding protein, FUS, in cases of ALS without TDP-43 pathology. Overall the findings highlight the need to consider disruption of mRNA transport and regulation of mRNA translation in future motor neuron disease research.

Keywords: spinal muscular atrophy
motor neuron disease
Amyotrophic lateral sclerosis
Advisor: Talbot, K
Carrier dynamics within semiconductor nanocrystals

This thesis explores how the carrier dynamics within semiconductor nanocrystals can be directly engineered through specific core-shell design. Emphasis is placed on how material characteristics, such as strain or alloying at a core-shell interface, can influence the exciton energies and the recombination dynamics within semiconductor nanocrystals.
This study synthesises type-II heterojunction ZnTe/ZnSe core-shell nanocrystals via a diethyl zinc-free synthesis method, producing small size distributions and quantum yields as high as 12%. It was found that the 7% lattice mismatch between the core and shell materials places limitations on the range of structures in which coherent growth is achieved.
By developing compositional and strained atomistic core-shell models a variety of physical and optical properties could be simulated and has led to a clear picture of the core-shell architecture to be built. This characterisation provides evidence that the low bulk modulus ZnTe cores are compressed by the higher bulk modulus smaller lattice constant ZnSe shells. Further studies show how strain is manifested in structures with 'sharp' core-shell interfaces and how intentional alloying the interface can influence the growth and exciton energies. A (2-6)-band effective mass model was able to distinguish between the as-grown 'sharp' and 'alloyed' interfaces which indicated that strain accentuates the redshift of the excitonic state whilst reduced strain within an alloyed interface sees a reduced redshift.
Single nanocrystal spectroscopy investigations of brightly emitting single graded alloyed nanocrystals and of a size series of commercially available CdSe/ZnS nanocrystals showed almost no fluorescence intermittency (nearly 'non-blinking'). These investigations also identified trion recombination as the main mechanism within the blinking 'off' state.
Ultimately this thesis adds to the growing understanding of how specific core-shell architectures manipulate the electronic structure and develops techniques to identify specific material characteristics and how these characteristics influence the physical and optical properties within semiconductor nanocrystals.

Keywords: blinking
nanocrystals
alloy
type-II heterojunction
semiconductor nanocrystals
core-shell nanoparticles
strain
nanoparticle
quantum dots
Advisor: Smith, JM
The career and works of Samuel Harsnett, Archbishop of York, 1561-1631

This thesis provides a study of the career and works of Samuel Harsnett, one of the most senior members of the early Stuart Church. Harsnett enjoyed a distinguished career as bishop of Chichester and Norwich, and finally as archbishop of York, but earned notoriety much earlier, by virtue of preaching a controversial sermon against the then orthodox Calvinist position on predestined grace. It was this early expression of anti-Calvinism (or Arminianism as it later became termed), together with a predisposition towards tradition on the liturgy and ceremony of the Church, which has earned Harsnett, as Conrad Russell put it, a place among "the cream of the English Arminians".
As the first future bishop to express openly anti-Calvinist views Harsnett's career is contemporaneous with the first forty years of what Nicholas Tyacke described as the 'Rise of Arminianism'. For that reason he is deserving of a biographical study, both to determine the nature of Arminianism in practice and his particular contribution to its 'Rise'. In seeking to determine Harsnett's contribution to the Arminian phenomenon this thesis suggests that Harsnett was, in a number of respects, hardly the archetypal Arminian that Professor Russell and most other modern historians have assumed. This raises important questions as to the actual significance of the theology of predestination to developments in the early Stuart Church.
The significant areas of Harsnett's career considered in the thesis are: his formative years as a scholar and then fellow at Pembroke College, Cambridge; his early career as chaplain to Richard Bancroft when Harsnett probably developed his lifelong dislike of Puritan non-conformity; his episcopal career at Chichester and then Norwich; his parliamentary career, which was marked by major ideological differences with fellow Arminians; his final appointment as archbishop of York, senior religious adviser to the king and Privy Councillor.

Advisor: Heal, F
Lead free solders for aerospace applications

The factors controlling the reliability of Pb-free solders when subject to thermomechanical regimes relevant to the harsh aerospace environment have been studied. Ball grid array (BGAs) typical of microelectronic devices have been manufactured in-house and subjected to isothermal ageing and thermal cycling. The BGAs comprised both Cu and Ni-Au metallizations, Pb-free Sn-Ag-Cu 400 and 600μm solder balls, FR4 and Al2O3 boards, and included circuits to measure resistance changes due to damage in the joints during thermal cycling. Microstructural evolution within the solders balls and complex interfacial reactions were studied in all configurations using various types of electron microscopy. The mechanical properties of the different phases formed within solder joints were studied using nanoindentation at room and elevated temperatures up to 175°C for the first time. Intermetallic compounds (IMCs) were stiff, hard and brittle with very low creep rates, while the softer primary Sn, eutectic regions and Cu metallization readily underwent creep. Two-dimensional finite element analysis (FEA) of nanoindentation was used to understand better the physical meaning of nanoindentation creep data. Reliability experiments comprised both thermal cycling and FEA of BGAs. The difference in coefficient of thermal expansion (CTE) in the BGA materials caused interfacial fatigue damage in the solder joints, which was detected primarily at the solder/metallization interface of the outermost, most strained solder joint. Accumulated creep strain per cycle at this interface was evaluated using 3D FEA of the stress-strain state of the BGA and results calibrated against experimental BGA mean lifetimes using the Coffin-Mason relationship. Nanoindentation combined with FEA has been shown to be a viable route for the rapid assessment of creep performance and lifetime in lead-free solders under aerospace thermal cycles.

Keywords: aerospace
Pb free solders
nanoindentation
reliability
microstructure
Advisor: Grant, P
Johnston, C
Between accommodation and resistance: political elites in post-conflict Bosnia and Macedonia

This thesis explores why political elites in post-conflict ethnically divided states accommodate or resist each other across ethnic lines. The geographic focus of research is on post-conflict Bosnia and Herzegovina, and Macedonia. In both countries the track record of post-conflict politics has been uneven and on some issues political elites still resist agreement and co-operation across ethnic lines. This thesis explores the reasons behind this mixed pattern of ethnic accommodation and resistance.
Based on the post-conflict literature in social science, the thesis examines the impact that the following explanatory variables have on ethnic accommodation and resistance: power-sharing mechanisms, political party dynamics, informal practices, policy legacies, and external actors. The analysis is situated at the policy level. Two policy areas, highly sensitive for ethnic relations in the post-conflict context, are analysed and compared in each of the two countries. In Bosnia, the focus is on military and police reforms; in Macedonia, on minority education and decentralisation.
Within the wider institutionalist approach, the empirical chapters present the findings of process tracing in each of the four policy fields. Based on these findings, the thesis demonstrates that although power sharing arrangements tend to lead to greater ethnic accommodation, they are not always sufficient to produce accommodating outcomes. Informal practices often supplement the work of formal institutions in providing incentives and means towards greater accommodation. External actors tend to enable greater accommodation when perceived as neutral and credible by domestic political elites. Ethnic divisions in both countries remain and require regular management by a flexible set of institutions, which can accommodate challenges unforeseen by peace agreements.

Keywords: Macedonia
Bosnia
power-sharing
ethnic accommodation
Advisor: Anastasakis, O
Predicting Greek Cypriot children's reading and spelling from morphological and dialect awareness

The aim of this longitudinal study was to examine the contribution of phonological, morphological and dialect awareness to the prediction of reading and spelling in a Greek bi-dialectal setting. The target group (N=404) consisted of children, aged 6 to 9 years at the start of the project, who learn literacy in Cyprus, where a dialect is spoken in certain contexts but where Standard Modern Greek is also widely used. At present there are few studies with Greek Cypriot children on how phonological, morphological and dialect awareness relates to reading and spelling.
Because there are no standardised measures of phonological, morphological and dialect awareness with Greek Cypriot children, measures of these factors were developed during the pilot study and their internal consistency was assessed. With the larger sample the measures were validated by examining their construct validity. The first wave of data collection showed that morphological and dialect awareness make unique contribution to the prediction of reading and spelling in Greek.
The second wave of data collection showed that the measures of morphological and dialect awareness predicted performance in reading and spelling eight months later, even partialling out grade level, estimation of verbal intelligence and initial scores in reading and spelling. A model with dialect awareness as a mediator between phonological and morphological awareness and reading and spelling fitted the data better than a model with phonological or morphological awareness as mediators, and hence, phonological awareness and morphological awareness help children to become aware of the differences between their dialect and the standard variety, and dialect awareness in turn facilitates reading and spelling. Cross-lagged correlations showed that the more experience children have with reading and spelling, the more likely they are to develop morphological and dialect awareness.
This study makes theoretical, empirical and practical educational contributions. The established mediational model contributes to the theoretical knowledge of the connection between dialect awareness and phonological and morphological awareness and reading and spelling while the longitudinal study contributes to theory the long term relation of morphological and dialect awareness with reading and spelling in Greek. Empirically, the study established the plausibility of a causal link between morphological and dialect awareness and reading and spelling, which must be tested in further research using intervention methods. In practice, this study contributes valid measures for assessing morphological and dialect awareness in the Greek Cypriot setting.

Keywords: standard modern Greek
language awareness
dialect awareness
morphological awareness
spelling
Greek Cypriot
reading
Advisor: Nunes, T
Loukina, A