VictorJuiz/thesis huggingface dataset:
Confinement of colloidal liquid crystals

The behavior of colloidal liquid crystals in confinement is addressed on the single particle level using laser scanning confocal microscopy. We seek to disentangle how equilibrium director fields are controlled by the complex interplay between confinement, elasticity and surface anchoring.
First, we study the nematic phase confined to wedge structured channels. Varying the wedge opening angle leads to a splay to bend transition mediated by a defect in the bulk of the wedge. Our results are in quantitative agreement with lattice Boltzmann simulations, and we show that comparison between experiments and simulation yields a new method to obtain the splay-to-bend elasticity ratios of colloidal and biological liquid crystals. Next, we extend our study of the wedge structured channels to the cholesteric phase, and measure a splay to twist transition with increasing wedge angle. We directly visualise the 3D nature of the twisted state, and explain how the transition is intricately determined by the anchoring strength and the splay, bend, and twist elasticities. Next, we investigate the effect of rectangular confinement on the nematic phase. The rectangle aspect ratio is systematically varied and we observe five distinct director fields. Comparison with computations of the Frank-Oseen energies yields the extrapolation length, which we find to be of the order of the rod length. Next, we confine the nematic phase to annular geometries of varying dimensions, and observe the novel director fields that are adopted. We approach a level of confinement which is of the order of the particle size. Interpreting our observations with Monte Carlo simulations, which take into account the finite size of the particles, illuminates the applicability of continuum theories down to microscopic lengthscales. We finish with a study of the isotropic-nematic interface in bulk and confinement. We show that parallel anchoring occurs at the interface, and measure the width of the interface to be of the order of the rod length.

Keywords: liquid crystals
colloids
Advisor: Aarts, D
Lettinga, M
Political rationality

This thesis investigates the political scientific implications of the postulate that political actors behave as if they were Rational (i.e., Economic) Men. The basic aim of the theoretical discussion is to explain both the existence and substance of norms of social cooperation. Rational Men would cooperate under special circumstances constituting a "coordination problem." Depending on the details of the situation, they would organize their cooperative efforts through either social processes of mutual adjustment or political-legal processes. The substance of the code of political morality Rational Men would embrace combines an Aggregative Principle that total goods available to society as a whole be maximized and a distributive Works Principle that each individual should prosper according to his own works. The results of this theoretical analysis are subjected to two extended empirical tests. The first is whether the Rational Man code of political morality corresponds in essential respects to the norms of political morality as revealed by linguistic analysis. The second test utilizes both of the theoretical arguments to explain the politics of environmental protection. The Rational Man model can explain the fact of pollution, the demand for governmental intervention, the opposition of some men to such inter- vention, the details of environmental protection laws and the shape of the international dispute.
The emergence of resurrection faith

Exploration of the Easter kerygma reveals the cognitive content of earliest form of post-Easter resurrection faith to be belief in an angelomorphic transformation - the belief that Jesus had been transformed post-mortem into a exalted mediatorial figure who who was Son of God, Lord and Messiah. The conceptual background is that of action proceeding in parallel in heaven and on earth. The Son of Man was not Jesus, but Jesus' heavenly alter ego, Michael-Melchizedek. Under the pressure of threatening external events and eschatological anticipation the always permeable boundary between Jesus and the Son of Man and Jesus own conception of his own identity suffered progressive collapse. Jesus therefore began to speak of his own anticipated suffering and hoped-for vindication in Danielic terms. Thus some at least of the 'suffering' Son of Man sayings may be reflecting underlying sayings in which Jesus spoke as the Son of Man of the Son of Man. Whilst the driving force in the emergence of post-Easter faith was congnitive dissonance, Jesus own understanding of himself as identified with and acting in concert with the heavenly being Michael-Melchizedek may have been communicated to at least some of his followers and may have been reflected in confirmatory visionary experiences during his lifetime. The experience known as the Transfiguration may therefore be the point of origin during Jesus lifetime of the whole edifice of resurrection faith.

Keywords: resurrection
transfiguration
Jesus
angelomorphic transformation
exaltation
Advisor: Morgan, R
Cation ordered and anion-vacancy ordered perovskite materials

The investigation in this thesis focuses on the synthesis of cation-ordered perovskite phases by introducing anion vacancies into the structure.
Complex cation-ordered phases Ba2YMO5 and Ba3YM2O7.5 (M = Fe, Co) have been synthesized using ceramic or citrate gel methods under flowing argon. Close inspection reveals that the structures are constructed from Y2M2O10 2 basic units which consist of two YO6 octahedra and two MO4 tetrahedra in a rock-salt type arrangement. In the structure of Ba2YMO5 (M = Fe, Co), the neighbouring Y2M2O10 2 units are connected with an equivalent one in the yz-plane with YO6 octahedra sharing an apex. In the structure of Ba3YM2O7.5 (M = Fe, Co), the basic units are connected to each other by the M2O7 dimers via a chain of Y – O – M – O – M – O – Y bonds. Complex cation ordering can be achieved by carefully controlling the anion vacancies and selecting the cations with different ionic radii.
The anion vacancies present in Ba2YMO5 (M = Fe, Co) (space group P21/n) allow the intercalation of anions like O2- and F- into the lattice. The fluorination of Ba2YCoO5 leads to the formation of a new orthorhombic phase Ba2YCoO5F0.42 (space group Pbnm) in which the inserted fluoride ions are distributed in a disordered manner. In contrast, the topochemical oxidation of Ba2YFeO5 leads to the formation of a new orthorhombic phase Ba2YFeO5.5 (space group Pb21m), in which Fe4+ centres are located in 4-coordinate tetrahedral sites and 5-coordinate pyramidal sites, respectively. The polar structure of Ba2YFeO5.5 is confirmed by the observation of second-harmonic generation activity and pyroelectric behaviour. Ba2YFeO5.5 also exhibits a combination of ferromagnetic and antiferromagnetic behaviours at low temperature.
LaCa2Fe2GaO8 adopts a six-layer structure consisting of an OOTLOOTR stacking sequence of layers of (Fe/Ga)O6 octahedra (O) and (Fe/Ga)O4 tetrahedra (T), related to that of the four-layer brownmillerite structure (space group Pbma). The chains of tetrahedra in the structure of LaCa2Fe2GaO8 exhibit a cooperative twisting distortion in which the twisting direction of the chains of tetrahedra alternates in adjacent tetrahedral layers.
LaxSr2-xCoGaO5+δ (0.5 < x < 1) adopts brownmillerite structures which consist of octahedral and tetrahedral layers with mixed valence of Co2+/Co3+. The members with x = 0.5, 0.6 and 0.7 adopt structures with I2mb space group symmetry, in which all the tetrahedra twist in the same direction. The members with x = 0.8, 0.9 and 1.0 adopt structures with Imma space group symmetry, in which the chains of the tetrahedra twist in a disordered manner. A change in the Co3+ spin state from high spin (HS) to low spin (LS) is observed as the La/Sr ratio increases. The change of the Co3+ spin state can be rationalized on the basis of internal chemical pressure.

Keywords: perovskite
tranistion metal oxides
Advisor: Hayward, M
Essays in occupational social class and status in post-Soviet Russia

The aim of this thesis is to explore several aspects of occupation-based inequality in post-Soviet Russia that have previously been given little attention in the literature. The data sources for statistical analysis are the Russian Longitudinal Monitoring Survey (RLMS) and the International Social Survey Programme (ISSP). Various statistical techniques have been used, such as regression models with random and fixed effects, nonparametric and semiparametric regression models, survival models and log-multiplicative models for contingency tables.
First, the thesis looks at the validity of the application of the European Socio-Economic Classiffcation (ESeC) in Russia. The results show that ESeC classes in Russia are different in respect to several aspects of their employment contract, such as the probability of informal employment, the index of fringe benefits and unemployment risks. This confirms the validity of the ESeC for Russia.
Second, the association between earnings and age is analyzed. The shape of cross-sectional age-earnings profiles in Russia is different from the shape in Western countries, especially for men. There is little variation in earnings across age groups, and younger men have higher average earnings than older men. The thesis suggests and discusses several explanations for this, such as age segregation in the labour market and the effect of class structure.
Third, the thesis explores the class gap in mortality. Non-manual classes have lower mortality risks than manual classes, both for men and women. The size of the class gap in mortality in Russia is larger than in Western European countries.
Fourth, the thesis constructs an occupational status scale and analyzes its properties. The scale is based on the information about intermarriages between occupational groups. The Russian scale is similar to the scales previously constructed for European countries and the USA.
Overall, the thesis demonstrates similarity in the patterns of occupation-based inequality in Russia and in Western industrial countries. It also discusses some technical aspects of class analysis and suggests a more clear separation between the descriptive and causal logic within it.

Keywords: Russia
occupational status
social inequality
occupational class
Advisor: Chan, T
Impact of TMPRSS2-ERG fusion gene on prostate cancer cell response to chemotherapy, radiotherapy and androgen deprivation therapy

Many aspects of the mechanisms by which prostate cancer (PCa) progresses from being a confined tumour to advanced metastatic and castration-resistant disease remain unclear. The aim of this study is to evaluate in vitro the potential role of the fusion gene TMPRSS2-ERG in the response of PCa cells to ionising radiation (IR) and androgen deprivation therapy (ADT). This research focused on assessing the presence of the TMPRSS2-ERG transcript across various PCa cell lines and identifying any correlation between the TMPRSS2-ERG transcript and other genes, particularly genes related to DNA damage repair pathways. Several genes involved in cell metabolism and development were found to correlate with TMPRSS2-ERG but not genes involved in DNA repair. In accordance with previous reports, this research confirmed a proliferative advantage for cells expressing ERG. However this project also tested the role of ERG-status in response to chemotherapy, radiation and ADT. The data showed that VCaP and DuCaP cells exposed to low-dose radiation demonstrated decreased viability irrespective of their ERG-status. Similarly ADT decreased the viability of VCaP cells and seemed to neutralise the proliferative advantage of TMPRSS2-ERG positive cells. Stimulation with dihydrotestosterone caused increased radioresistance of TMPRSS2-ERG positive cells. Treatment with taxanes showed stronger effect on cells with lower ERG expression. This work suggests that the proliferative advantage conferred by ERG overexpression in in vitro models can be neutralised by castration and IR.

Keywords: fusion gene
prostate cancer
TMPRSS2-ERG
Advisor: Hamdy, F
Studies in historical living standards and health: integrating the household and children into historical measures of living standards and health

This dissertation attempts to integrate the household and children more fluidly into measures of well-being in the past. In part one, I develop a Monte Carlo simulation to test some of the assumptions of Allen’s welfare ratio methodology. These included his assumptions that family size was constant over time, that there were no female-headed households and that women and children did not participate in the labour force. After all of the adjustments, it appears that Allen’s welfare ratios underestimate the welfare ratios of a demographically representative group of families, especially if women and children’s labour force participation is included. However, the predicted distributions also highlight the struggles of agricultural labourers, who are given separate consideration. Even the average agricultural labourers’ family with women and children working would have had to rely of self- provisioning, gleaning, poor relief or the extension of the working year to make ends meet at the poorest point in their family life cycle. Part two adjusts Floud et al.’s estimates of calorie availability in the English economy from 1700 to 1909 for the costs of digestion, pregnancy and lactation. Taken together, these three additional costs reduced the amount calories available by around 15 per cent in 1700 but only by 5 per cent in 1909 because of the changing composition of the English diet. Part three presents a new adaptive framework for studying changes in children’s growth patterns over time and a new methodology, longitudinal growth studies, for measuring gender disparities in health in the past. An adaptive framework for understanding growth provides a more parsimonious explanation for the vast catch-up growth achieved by slave children in the antebellum American South. The slave children were only able to achieve this catch-up growth because they were programmed for a tall height trajectory by relatively good conditions in utero. Finally, impoverished girls experienced greater catch-up growth than boys in two schools in late-nineteenth century Boston, USA and early-twentieth century London, suggesting that girls were deprived relative to boys before entering these institutions.

Keywords: American Slaves
Real Wages
Family Income
Monte Carlo Simulation
Children's Growth
Energy Cost Accounting
Health History
Living Standards
Advisor: Allen, RC
Oxley, D
Object functions and the syntax of double object constructions in lexical functional grammar 

It has long been observed that, in a double object constructions (DOC), the two objects exhibit different syntactic behaviour. In Lexical Functional Grammar (LFG), these two objects are characterized as two distinct grammatical functions. The object that syntactically patterns with the monotransitive object is the unrestricted object OBJ. The one that does not is the restricted object OBJθ. The goals of this dissertation are to investigate the syntax of DOCs, and to explore the two object functions in LFG.
When thinking about DOCs, the verb that almost invariably comes to mind is GIVE. This verb, however, may not be as prototypical as is commonly assumed. In Cantonese, it is the only verb whose objects are in an anomalous order, with the object that bears the theme role preceding the object which expresses the recipient role. Cantonese as a language does not uniformly have the direct (theme) object preceding the indirect (recipient) object. Other than the difference in their linear order, the objects in the GIVE-construction pattern with those in all other DOCs in the language.
In some languages, there is a possibility of having more objects than is required by the underived form of a verb. An additional object can be licensed by the affixation of an applicative morpheme to the verb root. The syntax of the objects in an applicative construction is directly related to the type of semantic role that is applied. This has posed challenges for previous accounts of applicative constructions, as a change in the morphological structure of a verb is accompanied by a change in its argument structure. A new proposal is offered to account for this.
A study of the syntax of DOCs involves much more than merely acknowledging the presence of two object functions in the construction. The morphology of the verb, the semantic roles that are required by the verb and the linear order of the arguments that express these roles are all relevant. Assuming various parallel but inter-related levels of representation, the theory of LFG has the suitable tools to take all these into consideration. Reference can be made straight-forwardly to the information at the different levels of representation, including the a-structure, the c-structure, the f-structure and the m-structure.

Keywords: object
syntax
double object constructions
Lexical-functional grammar
Advisor: Dalrymple, M
Antimicrobial resistance and gallbladder carriage of Salmonella Typhi and Salmonella Paratyphi A in Kathmandu, Nepal

Enteric fever remains the most common febrile illness in urban Nepal. Some individuals may have recurrent infection and some may even progress to become long term chronic carriers. The aim of this thesis was to investigate the rate and factors leading to relapse with typhoid fever in patients who were enrolled in clinical treatment trials for acute enteric fever. The results show that relapses in enteric fever is a common complication and is more likely to be associated with the treatment antimicrobial, cefixime. Gallbladder carriage of invasive Salmonella is considered fundamental in sustaining enteric fever transmission as humans are the only known natural host. This thesis, therefore, also aimed to investigate the prevalence, characteristics, immunological responses, and mechanism of carriage of invasive Salmonella in the gallbladder by examining bile and tissue obtained from individuals who underwent cholecystectomy in Kathmandu. Data presented here demonstrate that S. Paratyphi A is almost as prevalent as S. Typhi in the gallbladder and that carriage may not be driven by antimicrobial resistance. Gallbladders that contained Salmonella were more likely to show evidence of acute inflammation with extensive neutrophil infiltrate. Chronic carriers were found to have dramatically elevated levels of IgG to O:2 and Vi antigens with high bactericidal activity yet low pro-inflammatory cytokine levels suggesting that Salmonella are stimulating a constant immunological response, in the form of antibody. S. Typhi may be controlling the inflammatory process through the expression of the Vi capsule in the gallbladder. Genome sequencing of S. Typhi isolated from chronic carriers were different from those S. Typhi causing acute disease. These data question the current dogmas surrounding the carriage of S. Typhi in gallbladder and predict a pivotal role of Vi capsule and gallstones in maintaining carriage. Therefore, prospectively identifying these individuals is paramount for rapid local and regional elimination. Furthermore, combining cytokine profiles and antibody levels may be a method of prospectively detecting carriers in the general population.

Keywords: chronic biliary carriage
enteric fever
Advisor: Baker, S
Dolecek, C
Antenatal mood disturbance and infant development: investigating neurobiological mechanisms of risk

Introduction: Maternal antenatal depression is associated with increased risk of adverse offspring outcomes, which manifest in approximately 20% of infants. However, the mechanisms by which risk is transferred from mother to infant, and the factors determining susceptibility to antenatal mood disturbance, remain poorly understood.
Objectives: The primary objectives of this thesis are to investigate whether:
Antenatal depression is associated with alterations of the maternal and infant Hypothalamic-Pituitary-Adrenal (HPA) axis.
The infant serotonin transporter genotype (5-HTTLPR) confers susceptibility to antenatal mood disturbance.
Methods: This thesis is an analysis of two different cohorts. First, 103 pregnant women were recruited in Oxford, UK. Participants’ self-reported antenatal mood, and salivary cortisol was assessed in response to a stressor and diurnally. 88 participants were visited two months post-birth. Mothers reported postnatal mood and infant temperament. Infant cortisol responses to inoculation were assessed, as was infant DNA methylation. Analysis of this cohort addresses the first objective of this thesis. Next, data from the ALSPAC cohort was analysed to address the second objective. Maternal-reported antenatal mood and infant behaviour up to 7 years was available, as was 5-HTTLPR genotype data for over 4,000 infants.
Results: Antenatal depression was not associated with increased maternal cortisol during pregnancy. Neither antenatal depression nor cortisol was associated with infant cortisol reactivity or temperament. Antenatal depression predicted increased NR3C1 DNA methylation in males, and decreased BDNF DNA methylation in male and female infants. Infant 5-HTTLPR genotype did not moderate associations between antenatal mood disturbance and behavioural difficulties.
Conclusions: This thesis does not support the theory that antenatal depression exerts influence on infant development via increased activity of the maternal and infant HPA axis; however, changes in infant DNA methylation may be a mediating mechanism. Further, susceptibility to antenatal mood may be more complex than previously thought.

Keywords: prenatal depression
infant development
Advisor: Ramchandani, P
Murphy, S