VictorJuiz/thesis huggingface dataset:
Statistical models for social network dynamics

The study of social network dynamics has become an increasingly important component of many disciplines in the social sciences. In the past decade, statistical models and methods have been proposed which permit researchers to draw statistical inference on these dynamics. This thesis builds on one such family of models, the stochastic actor oriented model (SAOM) proposed by Snijders [2001]. Goodness of fit for SAOMs is an area that is only just beginning to be filled in with appropriate methods. This thesis proposes a Mahalanobis distance based, Monte Carlo goodness of fit test that can depend on arbitrary features of the observed network data and covariates. As remediating poor fit can be a difficult process, a modified model distance (MMD) estimator is devised that can help researchers to choose among a set of model elaborations. In practice, panel data is typically used to draw SAOM-based inference. This thesis also proposes a score-type test for time heterogeneity between the waves in the panel that is computationally cheap and fits into a convenient, forward model selecting workflow. Next, this thesis proposes a rigorous method for aggregating so-called relational event data (e.g. emails and phone calls) by extending the SAOM family to a family of hidden Markov models that suppose a latent social network is driving the observed relational events. Finally, this thesis proposes a measurement model for SAOMs inspired by error-in-variables (EiV) models employed in an array of disciplines. Like the relational event aggregation model, the measurement model is a hidden Markov model extension to the SAOM family. These models allow the researcher to specify the form of the mesurement error and buffer against potential attenuating biases and other problems that can arise if the errors are ignored.

Keywords: social network analysis
statistical modeling
Advisor: Snijders, T
Early Israelite wisdom

The thesis is an examination of the wisdom literature preserved in the book of Proverbs, and of evidence pertinent to the nature and historical setting of this material. The first section examines the arrangement of sayings in the sentence literature, reviews the comparative Near Eastern material and its significance for the exegesis of Proverbs, and discusses the claims that early wisdom was secular, rejecting them. The second section concentrates upon the setting of the literature, with studies of 'wisdom' and 'wise men' in the Old Testament, the internal evidence for associating Proverbs with the royal court, the nature of the Joseph Narrative, Solomon's wisdom and the influence of Egypt on his administration, and, finally, the biblical and epigraphic evidence for formal education in Israel. On the basis of these studies, it is concluded that conventional views of the wisdom literature as scribal and pedagogical are ill-founded and in need of revision. It is suggested that indications within Proverbs itself are a better guide to the nature of the material, and that early wisdom literature should be viewed as an integral part of the literary culture within Israel, not as the product of an international movement or specific professional group.
Germline determinants of 5-fluorouracil drug toxicity and patient survival in colorectal cancer

Despite a decade of publications investigating the effect of germline polymorphisms on both toxicity related to treatment with 5-fluorouracil-based (5-FU) chemotherapy and prognosis following diagnosis with colorectal cancer (CRC), few genetic biomarkers have been identified convincingly. For 5-FU toxicity and CRC prognosis, in four results chapters, this thesis aims to validate previously-reported genetic biomarkers, identify new markers, determine the mechanistic basis of associated polymorphisms, and expand upon methods in the field.
The first three results chapters investigate genetic biomarkers for the prediction of toxicity caused by 5-FU-based treatment, particularly for the 5-FU prodrug capecitabine (Xeloda®, Roche). In the first, a systematic review and meta-analysis is performed for all variants that have been previously studied for an association with toxicity caused by any 5-FU-based drug regimen. 16 studies are analysed, including 36 previously-studied variants. Four variants show strong evidence of affecting a patient’s risk of global (any) 5-FU-related toxicity upon analysis of both the existing data and over 900 patients from the QUASAR2 trial of capecitabine +/- bevacizumab (Avastin®, Roche/Genentech): DPYD 2846, DPYD *2A, TYMS 5’VNTR and TYMS 3’UTR. Next, 1,456 polymorphisms in 25 genes involved in the activation, action or degradation of 5-FU are investigated in 1,046 patients from QUASAR2. At a Bonferroni-corrected p-value threshold of 3.43e-05, three novel associations with capecitabine-related toxicity are identified in DPYD (rs12132152, rs7548189, A551T) and the previously-identified TYMS 5’VNTR and 3’UTR toxicity polymorphisms are refined to a tagging SNP (rs2612091) downstream of TYMS and intronic to the adjacent ENOSF1, the latter of which appears to be functional. Finally, a genome-wide investigation of 4.77 million directly genotyped or imputed SNPs identifies one variant (rs2093152 on chr20) as significantly associated with capecitabine-related diarrhoea (p<5e-08), though no associations meet this threshold for global toxicity.
In the study of CRC prognosis, a severe left truncation to the VICTOR trial is defined and shown to probably reduce statistical power but not bias effect estimates. Applying standard and novel genome-wide analysis approaches, a set of 43 SNPs are prioritised for future work.
With over one million new CRC cases annually, this work helps define biomarkers that could become broadly applicable in the clinical setting.

Keywords: 5FU
association study
SNP
diarrhoea
TYMS
genetics
TS
drug personalisation
cancer
survival
ENOSF1
chemotherapy
drug personalization
colorectal cancer
5-fluorouracil
toxgnostics
DPYD
toxicity
neutropaenia
metabolism
thrombocytopaenia
DPD
GWAS
5-FU
Advisor: Tomlinson, I
Johnstone, E
Midgley, R
East African rainfall: classification of rain producing systems - a modelling and observation study

The study of anthropogenic climate change is a research area of vital importance for the coming decades, with rainfall change and variability expected to be keenly felt in vulnerable regions of the world, including Africa. The focus of this study is daily rainfall during the short rains season over East Africa from October to December, which has one of the most coherent increasing rainfall projections in the Coupled Model Intercomparison Project (CMIP) dataset. This thesis aims to examine the fidelity of coupled climate models over an East African domain, with the question approached through focus on the daily (rather than monthly) rainfall field.
The self-organising map is used as a clustering tool to establish contemporary characteristics of daily rainfall events in reanalysis (ERA-40) and satellite (TRMM) rainfall datasets between 1971-2000 and 1998-2010 respectively for the East African short rains. Moisture flux divergence is found to be the circulation parameter that is most closely related to the presence of rainfall events or dry conditions over East Africa. Coupled climate models are poor at replicating the daily rainfall field over the domain. A key result of the analysis is the consistent overestimation of daily rainfall by climate models for days where dry conditions of suppressed convection should prevail. In contrast, the moisture flux divergence field maps well to dry nodes for days of the self-organising map array for the models. Dry days are associated with widespread anomalous moisture flux divergence and rainfall events with co-located anomalous moisture flux convergence. This is in agreement with the moisture flux divergence field in the ERA-40 dataset; it is the rainfall field where there is disagreement for days of suppressed convection.
Twenty to thirty-five percent of the projected rainfall increase towards the end of the twenty-first century results from an increase in the proportion of days assigned to nodes of suppressed convection in six of the seven models and the ensemble mean. There is an accompanying projected rainfall increase associated with days assigned to these nodes. Such days in the 2090s are characterised by projected increased strength moisture flux divergence over East Africa. Given that the moisture flux field was more successfully simulated in the coupled models under contemporary conditions than the daily rainfall field, this suggests that rainfall projections under a high emissions scenario at the end of the twenty-first century are overestimated and that an important part of the key increase in the projected rainfall may not be real.

Keywords: rainfall
geography
climate change
East Africa
climate
Advisor: Washington, R
Computational studies of signalling at the cell membrane

In order to associate with the cytoplasmic leaflet of the plasma membrane, many cytosolic signalling proteins possess a distinct lipid binding domain as part of their overall fold. Here, a multiscale simulation approach has been used to investigate three membrane-binding proteins involved in cellular processes such as growth and proliferation. The pleckstrin homology (PH) domain from the general receptor for phosphoinositides 1 (GRP1-PH) binds phosphatidylinositol (3,4,5)-trisphosphate (PI(3,4,5)P₃) with high affinity and specificity. To investigate how this peripheral protein is able to locate its target lipid in the complex membrane environment, Brownian dynamics (BD) simulations were employed to explore association pathways for GRP1-PH binding to PI(3,4,5)P₃ embedded in membranes with different surface charge densities and distributions. The results indicated that non-PI(3,4,5)P₃ lipids can act as decoys to disrupt PI(3,4,5)P₃ binding, but that at approximately physiological anionic lipid concentrations steering towards PI(3,4,5)P₃ is actually enhanced. Atomistic molecular dynamics (MD) simulations revealed substantial membrane penetration of membrane-bound GRP1-PH, evident when non-equilibrium, steered MD simulations were used to forcibly dissociate the protein from the membrane surface. Atomistic and coarse grained (CG) MD simulations of the phosphatase and tensin homologue deleted on chromosome ten (PTEN) tumour suppressor, which also binds PI(3,4,5)P₃, detected numerous non-specific protein-lipid contacts and anionic lipid clustering around PTEN that can be modulated by selective in silico mutagenesis. These results suggested a dual recognition model of membrane binding, with non-specific membrane interactions complementing the protein-ligand interaction. Molecular docking and MD simulations were used to characterise the lipid binding properties of kindlin-1 PH. Simulations demonstrated that a dynamic salt bridge was responsible for controlling the accessibility of the binding site. Electrostatics calculations applied to a variety of PH domains suggested that their molecular dipole moments are typically aligned with their ligand binding sites, which has implications for steering and ligand electrostatic funnelling.

Keywords: cell signalling
membrane-binding proteins
Pleckstrin homology domains
inositol phosphates
phosphoinositides
Brownian dynamics simulations
PTEN tumour suppressor
molecular dynamics simulations
Advisor: Sansom, MSP
Human capital, informality and labour market outcomes in sub-Saharan Africa

In this thesis I explore three topics in labour economics, using micro data from South Africa and Tanzania.
South Africa suffers from extremely high income inequality, in part as a result of comprehensive Apartheid-era racial discrimination. The first topic explores possible explanations for the extremely large earnings differences across different types of employment for black South Africans, using the KwaZulu-Natal Income Dynamics Study data. I analyse the relative importance of individual ability and institutions, including public sector wage setting and trade unions, in determining earnings. My results suggest that human capital explains much of the earnings differentials within the private sector, including union premiums, but cannot explain the large premiums for public sector workers.
Self-employment is very common in urban Tanzania but, unlike South Africa, survey data show that there are large overlaps in the distribution of earnings in private wage employment and self-employment. This suggests that self-employment represents a viable alternative to wage employment in small, low productivity firms for the majority of urban Tanzanians. In chapter three I build an equilibrium search model of the urban Tanzanian labour market to explain the choice of wage and self-employment and the variation in earnings across and within these sectors.
In the final topic I explore the effect of education on earnings in Tanzania. Estimating the returns to education has stimulated much recent work in applied econometrics as researchers advance their understanding of the effect of individual heterogeneity on the possibility of estimating the returns to education. In my attempt to purge estimates of the return to education of the influence of individual heterogeneity, I use an education reform in Tanzania as a natural experiment that provides exogenous variation in education. When using Ordinary Least Squares (OLS) I find high and strongly convex, increasing returns to education. My best attempt at separating out the effect of individual heterogeneity suggests that returns are still high but that they may actually be concave.

Keywords: Tanzania
human capital
South Africa
informality
Advisor: Teal, F
Health and responsibility: the relationship between parental illness and children's work in South Africa

South Africa faces a high disease burden and a limited public capacity to provide care to the ill. Research from the UK and sub-Saharan Africa suggests the burden often falls to children, who also take over domestic responsibilities necessary for household survival. To date, there is limited research exploring the relationship between parental illness and children’ responsibilities, or the moderating effect of socio-demographic variables.
The thesis is comprised of three research phases. The first is a literature review to summarise existing research and identify substantial gaps, which included limited amounts of quantitative evidence on this topic and a lack of a tool to as-sess child responsibility that had both been adapted to the South African context and included caring responsibilities. The second research phase consists of an exploratory study of n = 349 children living with ill adults in urban and rural communities in the Western Cape province of South Africa to investigate their range of responsibility, which included caring for an ill parent, household chores, childcare, and income-generation. The resulting data were used to create the Child Responsibility Measure, which assesses the range and time burden of re-sponsibilities among South African children.
The third research phase is a cross-sectional quantitative survey of n = 2,476 pairs of children and parents from urban and rural communities in KwaZulu-Natal province, South Africa. Resulting data on parental health, socio-demographics, and child responsibilities were analysed with multiple regres-sions to determine drivers of children’s responsibility. Among the findings were that parental illnesses increase the likelihood children provide care and have larger responsibility workloads, and girls are more likely to take on all types of responsibility excluding income-generating activities, which were more common in boys. Additionally, while urban children were more likely to provide personal care, rural children had greater responsibility workloads.

Keywords: child caregivers
young carers
children and youth
Africa
parentification
orphaned and vulnerable children
Advisor: Cluver, L
A fictitious domain approach for hybrid simulations of eukaryotic chemotaxis

Chemotaxis, the phenomenon through which cells respond to external chemical signals, is one of the most important and universally observable in nature. It has been the object of considerable modelling effort in the last decades. The models for chemotaxis available in the literature cannot reconcile the dynamics of external chemical signals and the intracellular signalling pathways leading to the response of the cells. The reason is that models used for cells do not contain the distinction between the extracellular and intracellular domains.
The work presented in this dissertation intends to resolve this issue. We set up a numerical hybrid simulation framework containing such description and enabling the coupling of models for phenomena occurring at extracellular and intracellular levels. Mathematically, this is achieved by the use of the fictitious domain method for finite elements, allowing the simulation of partial differential equations on evolving domains. In order to make the modelling of the membrane binding of chemical signals possible, we derive a suitable fictitious domain method for Robin boundary elliptic problems. We also display ways to minimise the computational cost of such simulation by deriving a suitable preconditioner for the linear systems resulting from the Robin fictitious domain method, as well as an efficient algorithm to compute fictitious domain specific linear operators. Lastly, we discuss the use of a simpler cell model from the literature and match it with our own model. Our numerical experiments show the relevance of the matching, as well as the stability and accuracy of the numerical scheme presented in the thesis.

Keywords: Finite Elements
Fictitious domain method
PDEs
Chemotaxis
Advisor: Burrage, K
Erban, R
Kay, D
Properties of foam/sand mixtures for tunnelling applications

This thesis presents experimental work on foam/sand mixtures carried out in the Civil Engineering Laboratory at Oxford University, as well as the findings associated with it. This research represents the preliminary stage of a research project on Soil Conditioning Agents in Pipe Jacking and Mechanised Tunnelling, sponsored by the Pipe Jacking Association (PJA) and three water companies. The experimental work was carried out in order to evaluate the fundamental soil properties of foamed sand, in particular its compressibility, permeability and shear strength. The first chapter deals with the basic aspects of soil conditioning agents and their application to tunnelling, and provides an understanding of the fundamentals of foam behaviour. An introduction to the problems encountered in tunnelling is given. A brief study of foams and their properties is presented and the role of foams as soil conditioning agents is described. In the second chapter, a description of the foam generator used is provided. Two types of sand (fine and coarse), four types of foaming agents and a specific polymer mixture were employed for the testing. In some cases, sodium bentonite was used alone or in combination with foam and polymer. The sample preparation method, together with the results from measuring the reduction of the power input required to mix sand with foam, are presented. The third chapter presents the compression tests performed in a 75 mm Rowe cell. Results are presented as volume changed variation with the applied vertical stress. Quality control was carried out on the test results in order to evaluate the likely inconsistencies during the preparation and measurements. The most notable outcome was that for fine sand even at high pressure the final voids ratio of foam/sand mixtures after the compression remained higher than the maximum voids ratio of dry sand. Some measurements of the foam/sand mixtures permeability were also performed in the Rowe cell. Tests were carried out using the constant head principle with a "Marriotte bottle". Permeability values determined from testing are compared with indirect evaluation from the compression tests. In the fourth chapter direst shear tests in a standard shear-box are presented. Fine and coarse sand mixed with foam were test in shear under seven different vertical loads. Results are presented as plots of shear strength against horizontal deformation. Very low values of shear strength for foamed sand tests are recorded. The shear strength is plotted against the relative density index along with the experimental results from Bolton's correlation. Foamed sand shear strength values are scattered within a range below that of Bolton's Correlation. Finally, the conclusions form the test results are discussed.

Keywords: tunnelling
pipejacking
Advisor: Houlsby, G
Radiogenic isotope studies of crust-forming processes in the Lofoten-Vesterålen province of north Norway

The Lofoten-Vesterålen province of North Norway consists almost exclusively of Precambrian granulite-facies rocks. The oldest rocks in the province are monzonitic and dioritic migmatitic gneisses, the protoliths of which were formed at 2.7 Ga.
The migmatites are overlain by a series of supracrustal gneisses, from 2.1 Ga, largely volcanogenic in origin, but with interbedded marbles and banded ironstones. The first occurrence of marble in western Lofoten is reported. Deposition in a subsiding back-arc basin or in an Andean- type environment on a thin continental margin is inferred.
Both gneiss sequences were intruded by basic rocks at 1.8 Ga. The basic rocks could not have been formed simply by extraction from the mantle at 1.8 Ga. The required contribution from 2.7 Ga migmatites could be as much as 37%, but less if contamination took place via anatectic melts. The first report of eclogitic rocks from the Lofoten-Vesterålen province is made in this study; their formation is associated with shear deformation
Both gneiss sequences and the basic rocks were intruded by mangeritic rocks at 1.8 - 1.7 Ga. Their chemical compositions can be explained by fractional crystallization from magmas formed from 2.7 Ga and 2.1 Ga gneisses and 1.8 Ga mantle-derived magmas. Parameters derived from Rb-Sr, Sm-Nd and U-Pb systems to express the relative proportions of crust and mantle contributions to the mangerites mutually correlate, supporting the crust-mantle source model for the mangerites. Mixing calculations suggest that the late Archaean contributes in excess of 50% by mass for almost all mangerites.
Anatectic veins present, especially in the Moskenesøy supracrustal gneisses, are inferred to represent partial melts which coalesced to form the mangerites at higher structural levels. Anatexis was caused by basaltic underplating associated with limited crustal extension.
Later rock-forming events were the emplacement of dolerite dykes; the 1.65 Ga Lødingen Granite; the Leknes Group metasediments and the Caledonian granite pegmatites.

Advisor: Taylor, P