VictorJuiz/thesis huggingface dataset:
Oxidation mechanisms in zirconium alloys for nuclear applications

The oxidation of zirconium alloys under aqueous conditions has been studied for more than 50 years in relation to its role as a fuel cladding element in water-cooled nuclear reactors.
The most well-known and interesting phenomenon associated with the corrosion of zirconium alloys is the cyclic oxidation rate. Oxidation initially proceeds rapidly, forming an oxide film. As this film thickens, the rate of oxidation slows before transitioning, and begins oxidising at the higher rate again. This effect has been well studied, although the cause of rate transition is not understood.
Using samples oxidised in conditions very closely matching those of a nuclear reactor, although without radiation, several techniques were used to characterise the oxide before and after the transition in oxidation rate. Comparison of these results allows some insight into the mechanism operating.
Doping samples with isotopic tracers during different points in the oxidation cycle and subsequent analysis with NanoSIMS gave insight into the porosity and protectiveness of the oxide film before and after transition. Before transition, the entire oxide film acts as a barrier, rather than a small sublayer. After transition, the whole layer of previously formed oxide became porous and the oxidising media was admitted directly to the metal/oxide interface. Examining samples of differing oxidation times showed each subsequent transition was a close repeat of the first. Oxide thickness, rather than time under corrosion conditions, was identified as the best predictor of whether a sample would undergo transition. Oxide porosity (and thus rate transition) was demonstrated to be a local process on scales as small &LT; 1μm.
Residual stress in the oxide and underlying metal substrate have been studied for zirconium alloys for some years. Here, a new technique is applied that largely confirms previous measurements made by XRD. Testing pre- and post-transition oxides revealed a large drop in the compressive stress after transition, showing the post-transition oxide is both porous and contains much lower compressive stresses.

Advisor: Lozano-Perez, S
Grovenor, C
An analysis of the relationship between monetary policy, business cycles and financial stability

The thesis sheds light on key policy issues emerging from the recent Global Financial Crisis. The first chapter studies whether expansionary monetary policy contributes to bank risk-taking, in the case of Asia. I rely on panel data analysis covering 432 banks in 9 Asian countries over the year 2000-2011. The ratio of risky assets to total assets serves as a risk-taking indicator. The results support the existence of the bank risk-taking channel, which is more pronounced for banks listed on the stock market. I also report new findings with respect to how banks take more risk following monetary expansion. Importantly, evidence of excessive leverage is not found. The second chapter constructs a model for analyzing bank risk-taking. I embed firm heterogeneity, endogenous default risk and capital adequacy regulation into both RBC and NK DSGE models. A subset of the firms can partially default on their loans obligation but subject to non-pecuniary default penalty. With those financial frictions in place, I find that standard macroeconomic shocks can induce banks to engage in higher risk-taking. The chapter then explores the effectiveness of several macro-prudential tools in mitigating risk-taking. I find countercyclical capital buffers and risky to total asset ratio targeting to be effective. The third chapter emphasises the spillover effects of shocks originating in the housing and financial market on the real economy. I embed endogenous mortgage default into a New Keynesian model that features housing and the banking sector. The latter faces capital regulation. We study two key shocks, namely shocks to the variance of idiosyncratic housing shock and shocks to the penalty on capital regulation. Both are instrumental in causing a surge in mortgage default and loans risk premium, which constrains bank lending activity. The chapter later introduces three macroprudential measures to explore whether they improve economic stability and welfare.

Keywords: Dynamic Stochastic General Equilibrium Model
Mortgage Default
Monetary Policy
Bank Risk-taking
Macroprudential Regulation
Endogenous Default
Advisor: Tsomocos, D
Bowdler, C
Chemical probes for histone lysine demethylases

The primary objective of this DPhil research project was to develop selective and cell-active inhibitors of the histone lysine demethylase KDM2A, which could potentially lead to the discovery of a novel chemical probe. Chapter one of this thesis introduces the role of histone lysine demethylases (KDMs) in the epigenetic regulation of gene expression and discusses the value of chemical probes as tools to study these enzymes. Chapter two describes the synthesis of a library of indoline-based KDM2A inhibitors using a modular synthetic approach to explore key structure-activity relationships and a chiral counterion-mediated strategy to synthesize lead candidates enantioselectively. Chapter three discusses investigations into the cellular activity of lead compounds and explores strategies to address limitations associated with cytotoxicity and promiscuity. Chapter four describes the application of a variety of experimental techniques to identify the mode of target inhibition. Finally, chapter five focuses on the development of an enantioselective C-acylation reaction to access spirocyclic fragments asymmetrically.

Keywords: Epigenetics
Chemical Probes
Lysine Demethylases
Advisor: Smith, M
Brennan, P
The oocyte activation factor, phospholipase C zeta (PLCζ): potential mechanisms of action and scope for human infertility treatment

It is widely believed that the sperm-specific protein phospholipase C zeta (PLCζ) is released into the oocyte upon fusion and initiates calcium (Ca2+) oscillations which regulate oocyte activation. Reduced amounts, abnormal localisation patterns, and aberrant forms of PLCζ underlie certain types of male-factor infertility, prompting significant interest in the use of this fundamental protein as a clinical therapeutic agent or diagnostic marker. This thesis systematically addressed a range of outstanding questions relating to the expression, localisation, and therapeutic/diagnostic application of PLCζ. Using immunohistochemical and quantitative immunofluorescence techniques, the current study investigated the effect of paternal age and epididymal maturation upon PLCζ expression and localisation in mouse sperm. Neither age nor epididymal maturity exhibited significant effect upon the total level of PLCζ in mouse sperm, although there was a significant trend towards post-acrosomal localisation as sperm matured during transit in the epididymis. Immunohistochemical analysis of mouse testis showed that the expression of PLCζ first appeared at the roundspermatid stage of spermatogenesis. Paternal age did not influence total levels of PLCζ expression or localisation pattern in human sperm samples (n=29), with PLCζ being predominantly localised to the post-acrosomal region. A significant reduction (34%) was detected in the proportion of sperm exhibiting PLCζ from an oocyte-activation deficient patient compared with fertile controls. Novel immunohistochemical analyses suggested, for the first time, that PLCζ is first expressed from the round spermatid stage in humans, and that the analysis of PLCζ expression in human testicular biopsies (n=29) may provide credible indication of the oocyte activation ability of surgically-retrieved sperm samples from infertile patients. Initial data also suggest that flow cytometry may serve as a useful prognostic/diagnostic tool for the quantitative analyses of PLCζ expression in human sperm samples. Mammalian and bacterial expression systems were utilised to generate recombinant human PLCζ protein as a therapeutic agent and for the generation of a novel monoclonal anti-PLCζ antibody respectively. Expression studies using HEK293T cells demonstrated that human PLCζ appeared to localise to the endoplasmic reticulum and that the EF hand domain appeared to be involved in regulating this pattern of localisation. Collectively, these studies extend our fundamental knowledge of how PLCζ is expressed in developing sperm and assist in the translation of PLCζ as a clinical therapeutic and diagnostic biomarker for oocyte activation ability.

Advisor: Coward, K
Synthesis and characterization of monolayer molybdenum disulphide

Monolayer molybdenum disulphide (MoS2) is a semiconductor with a direct bandgap of &Tilde;1.9 eV. Much research attention has been attracted to its potential applications in nanoelectronics and optoelectronics recently, all of which are based upon a scalable production of high-quality monolayer MoS2 and the in-depth comprehension of its fundamental properties. The PhD project focused on developing chemical vapour deposition (CVD) methods to grow monolayer MoS2 and its related two-dimensional (2D) vertical heterostructures with an understanding of the growth mechanism. Subsequently, a range of characterizations were conducted to investigate the structural, vibrational, optical and mechanical properties of as-grown samples.
An atmospheric-pressure CVD (APCVD) approach was first developed to grow monolayer MoS2 crystals on silicon substrates with a 300 nm oxide layer (SiO2/Si) by using molybdenum trioxide (MoO3) and sulphur (S) as precursors. A sharp gradient of MoO3 was intentionally created, which induced a location-dependent shape evolution of MoS2 domains. A qualitative explanation was proposed, attributing this phenomenon to local changes in the Mo:S ratio of precursors and its influence on the kinetic growth dynamics of edges. Subsequently, the CVD setup was improved in both the precursor loading manner and the substrate orientation to achieve centimetre-scale monolayer MoS2 films with large domain sizes of 10-20μm. Finally, 2D MoS2/hexagonal boron nitride (h-BN) vertical heterostructures were fabricated via an all-CVD method. Raman and photoluminescence (PL) spectroscopy were applied to show its merits of smaller lattice strain, lower doping level and better interlayer contact compared with CVD-grown MoS2 on SiO2/Si substrates and mechanically stacked samples.
Aberration-corrected transmission electron microscopy (AC-TEM) was carried out to study the defect structure and fracture mechanics of monolayer MoS2 at a single atom level. Subtle lattice reconstructions of line defects in various lengths and widths were resolved. Density functional theory (DFT) predicted a reduction of the bandgap as the line defects broaden, which eventually makes them behave as metallic channels embedded in the semiconducting MoS2. Another joint experimental and theoretical study was conducted to track the real-time crack propagation in monolayer MoS2. The atomically sharp crack tip went through the preferential lattice direction with least energy release. Increasing defect density was found to induce an enhanced fracture toughness and a fracture mechanism transition from brittle to ductile.

Advisor: Warner, J
Social norms and learning in games

Duelling
The norm of duelling endured for hundreds of years in Europe. In the United Kingdom it disappeared abruptly in the mid-nineteenth century, whereas in France it declined slowly. I present a simple model of social norms that explains these phenomena. The model predicts that the evolution of norms is characterised by tipping, whereby norms can shift suddenly due to shocks, and by a ratchet effect, whereby changes in parameters can cause norms to decline gradually. I show that the model can be supported by an equilibrium of a repeated game, with no special assumptions about preferences.
Community enforcement using modal actions
I prove two folk theorems for repeated games with random matching. A large group of players is rematched at random each period, so that players who deviate must be sanctioned by third parties. Previous analyses have either relied on strong assumptions about information transmission, or have been limited to equilibria that are not robust to noise or in which players are indifferent. I use a simple construction based on modal actions to obtain results for strict and robust equilibria.
Learning repeated-game strategies
The literature on boundedly rational learning has tended to focus on stagegame actions. I present a stochastic learning rule for repeated-game strategies. Players form beliefs about their opponent’s strategy based on past actions and best-respond. Occasionally, they make mistakes and experiment, and I show that the equilibrium selected depends on exactly how players make mistakes. Simple specifications of the learning rule yield intuitive selection results: the maxmin, or Rawlsian, outcome; the Nash bargaining solution; the maximum of the sum of payoffs; and a generalisation of risk dominance.

Keywords: Social norms
Learning
Advisor: Young, P
Norman, T
The genetic regulation of Kranz anatomy in maize

The C4 photosynthetic pathway acts to concentrate CO2 around the enzyme Ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco), ensuring that it catalyses a carboxylation rather than oxygenation reaction, which in turn suppresses photorespiration. In nearly all cases C4 photosynthesis is underpinned by characteristic Kranz anatomy, with concentric wreaths of bundle sheath (BS) and mesophyll (M) cells surrounding closely spaced veins. The increased yields associated with the C4 pathway have lead to the suggestion that C3 crops such as rice should be engineered to undertake C4 photosynthesis, however, this goal is currently held back by a lack of understanding about how the development of Kranz anatomy is regulated.
Recently, a number of candidate Kranz regulators have been identified in an RNA-seq study that compared leaf development in maize foliar (Kranz) and husk (non-Kranz) leaves. However, this study did not consider the impact of a recent whole genome duplication in the maize lineage on the gene expression patterns analysed. Therefore, in this thesis maize homeolog gene-pair divergence during early leaf development was assessed. This revealed that expression divergence of homeolog gene-pairs is a significant evolutionary phenomenon.
Functional validation of a subset of Kranz candidates revealed that a Zmscr1-1; Zmscr1h-1 double mutant exhibited defects in Kranz patterning, including increased formation of extra BS cells and veins with no separating M cells. Furthermore, Zmnkd1; Zmnkd2 double mutants exhibited a subtle increase in extra BS cell formation. Taken together, this indicates that both ZmSCR1/ZmSCR1h and ZmNKD1/ZmNKD2 function redundantly during Kranz development. No evidence was obtained that two additional genes, ZmSHR2 and ZmRVN1, play a role in Kranz development, and expression of candidate Kranz regulators in rice did not alter leaf anatomy. Together, this work has confirmed roles for a number of genes in Kranz regulation, and has provided insight into the complex regulation underpinning Kranz development in maize.

Keywords: Kranz
Gene duplication
IDD genes
Scarecrow/ shortroot genes
Rice
Maize
Advisor: Langdale, J
The Rose playhouse in context

This thesis conducts the first book-length study on the operation of the Rose playhouse as a key theatrical presence whose operational history spanned over a transitional period for early modern English theatre. Inspired by the current increasing awareness of the playing company as an organising unit in additional to the author-based perspectives for studying early modern English drama, this project undertakes the task of examining the Rose playhouse as a unit for theatrical production and a nexus where various strands of the material, cultural-geographical, political, financial, as well as literary forces converged and interacted with each other.

Advisor: van Es, B
Adoptive families: working with parent and child

The literature on parenting emphasises that, not only does parental behaviour influence child development, emotions and behaviour, but child behaviour influences parents’ behaviour and well-being. Such dyadic interactions may be particularly important in the case of adoption, where research has shown that children are likely to have had difficult early attachments or separations and where parents are likely to experience unique stressors. Therefore, understanding the effects of parenting stress and understanding how to best work with early trauma are important in adoptive families.
Paper A provides a systematic review of quantitative research on parenting stress in adoptive parents. Results showed adoptive parents to have parenting stress scores within the normal range. However, adoptive parents tended to have higher scores than non-adoptive parents, particularly if their child had lengthier exposure to adverse pre-adoptive environments, special needs or if parents perceived child difficulties.
Paper B aimed to gather the experiences of adoptive parents who had undergone dyadic developmental psychotherapy (DDP), an attachment-focused therapy for families where the child has experienced complex trauma or attachment difficulties. Interpretative Phenomenological Analysis revealed four superordinate themes: increased understanding, "it's a different method of parenting generally", the DDP journey and "it's a shared kind of experience you go through and come out together". Discussion of implications for clinical practice, policy and research is provided.

Advisor: Gurney-Smith, B
Remnant in koinonia: towards an Adventist version of communio ecclesiology

In the last two decades, Seventh-day Adventist scholars have been attempting to articulate a balanced and distinct ecclesiology, aimed at helping the denomination to retain its global unity, maintain its relevance and enable a more fruitful and meaningful interaction with others. No comprehensive account of the church has been developed yet, however.
This thesis is intended to facilitate a more rounded and systematically articulated concept of church from an Adventist perspective. Part I presents a thumbnail history of the denomination and considers the advantages and limitations of its standard claim to be the 'remnant', awaiting a pre-millennial parousia. Part II engages with the ideas of some of the ablest communio ecclesiologists of the twentieth and twenty-first centuries and considers their ecclesiological system, built around the concept of koinonia, while Part III examines ways in which their theoretical framework can assist the Adventist community to deal with practical ecclesial issues.
Four major proposals are made for deepening Adventist understanding of the nature of church. Whereas the formal structure of communio framework can help Adventists move beyond one-sided, single-metaphor communal self-descriptions, the idea of the church as essentially a koinonia of believers in God can supplement their predominantly functionalist portrayal of the church as herald or messenger. Thirdly, the Adventist notion of truth can be enriched by viewing the community of believers not only as a messenger, but also as an organic part of divine revelation. This makes ecclesiology central to the theological enterprise, intrinsic to the grounding of theological claims and the interpretation of biblical texts. Finally, the development of a richer interpretation of the Spirit’s activity in the church is seen as one of the key prerequisites for a fuller, more nuanced account of the church’s participation in the life of the triune God. The highlighting of these four aspects, hitherto neglected or underdeveloped in Adventism, and the presentation of tentative solutions to its ongoing ecclesiological problems, form the principal contribution of this monograph.

Keywords: communio ecclesiology
ecclesiology
identity
remnant
theology
communion
community
adventism
fellowship
adventist
seventh-day adventism
church
Holy Spirit
Advisor: Endean, P
Hindu-Muslim violence in Gujarat, 2002: political logic, spatial configuration, and communal cooperation

This thesis uses a mixed methods approach to investigate the different levels of Hindu-Muslim violence in Gujarat (western India) in 2002 when at least a thousand Muslims were killed. An original dataset of killings is compiled to analyse macrospatial variation in the violence across towns and rural areas of Gujarat. Data collected from 21 months of ethnographic fieldwork in Ahmedabad city is used to investigate microspatial variation across three neighbourhoods with varying levels of violence.
Macrospatial analysis discusses the link between political authority and its capacity to instigate ethnic violence as a response to electoral calculations and identifies the mechanisms by which violence against Muslims was orchestrated by the Hindu nationalist Bharatiya Janata Party (BJP). Ethnographic findings demonstrate the importance of ecological strategies adopted by attackers and targets during the course of attack and urge a re-examination of the intuitive association of spatial proximity with greater interethnic contact. Findings also reveal methods of enforcement used by legitimate and illegitimate institutions of a peaceful slum neighbourhood in resolving commitment problems of cooperation. Finally, the thesis examines the aftermath of the violence, more specifically a political phenomenon of Muslims of Gujarat supporting the BJP nine years after the brutal violence.
Methodologically, the main contribution of this thesis is in bridging the quantitative and ethnographic traditions in the sociology of ethnic violence to make possible the linking, and disentangling, of macrolevel risk factors associated with violence from microlevel factors. Findings of the thesis hopefully provide a better understanding of ethnic violence in multi-ethnic democracies and a roadmap of policy-making for India as it continues to struggle with ethnic strife.

Keywords: conflict
India
Gujarat
Hindu-Muslim
ethnic violence
Advisor: Biggs, M
Heath, A