VictorJuiz/thesis huggingface dataset:
Analytical microscopy of corroded zirconium alloys

Zirconium alloys are widely used as structural and fuel cladding alloys in current nuclear pressurised water reactors. The MUZIC-2 programme, which this project has been part of, is a collaboration between an international team of universities and industry in furthering the understanding of oxidation and hydrogen pickup of these alloys. This project has contributed to the programme by analysing a large number of oxidised zirconium samples by scanning transmission electron microscopy (STEM), scanning electron microscopy (SEM), 3D focused ion beam (FIB) sectioning and secondary ion mass spectrometry (NanoSIMS).
By STEM observations, ZIRLO and Zircaloy-4 have been analysed at different stages of oxidation, comparing oxide thickness, crack content, porosity and second-phase particle content. Utilising state-of-the-art fast low-loss electron energy loss spectroscopy (EELS), the oxygen-saturated metal region has been mapped. The band of oxygen-saturated metal below the metal-oxide interface is found to be thinner for samples that have recently finished the fast stage of oxidation (early pre-transition and early post-transition) than samples in the slower stages of oxidation (late pre-transition). Core-loss EELS has been fitted using a low-loss convolution curve fitting approach and has been used to measure the energy position and intensity of the Zr L edges and white lines across the metal-oxide interface. As the Zr oxidises, the white lines are found to shift to higher energy loss, and the ratio between the L3 and L2 white lines increases. The metastable ZrO suboxide phase is found to follow this trend.
Novel hydrogen and deuterium measurements made using NanoSIMS have been performed on deuterium-traced alloys in both cross-section and as three-dimensional depth profiles to understand the ingress of hydrogen through the oxide barrier. The pre-transition oxide is found to act as an adequate barrier to hydrogen ingress whilst the post-transition oxide is found to be porous and only protective close to the metal-oxide interface. A hydrogen uptake mechanism hypothesis is proposed. Energy-dispersive X-ray spectroscopy suggests that second phase particles may constitute a possible route for hydrogen ingress when close to the metal-oxide interface. Together, these observations contribute to improving the understanding of the corrosion of zirconium alloys.

Keywords: EELS
Zircaloy
Python
Electron Microscopy
Hydrogen Pickup
STEM
NanoSIMS
ZIRLO
Corrosion
Zirconium
Advisor: Lozano-Perez, S
Grovenor, C
A relational analysis of poverty as a social phenomenon

Existing scholarship suggests that despite its material core, poverty is relational and that this relational dimension not only aids its production but its reproduction. Yet, while a plethora of research examines its material aspects, the relational dimensions of poverty remain under-researched and are still not well understood. This research contributes to addressing that gap. Using recognition theory as a theoretical lens, the thesis investigates the question: ‘how do social relationships frame people’s experience of poverty?’ It explores the question through a qualitative case study of people in poverty in a rural district in Eastern Zambia. Zambia’s deep values of community and high levels of poverty provided unique opportunities to examine the role of social relationships in the experience of poverty.
The thesis shows that poverty is experienced as suffering involving psychological pain and ontological insecurity. Feelings and the fear of indignity and shame, based in social interaction, are central to poverty. However, this interaction may also insulate people in poverty from some of its consequences such as social exclusion. The thesis affirms poverty as based in forms of recognition accorded to individuals in various domains of their lives. It highlights how lack of recognition in institutional relationships, including citizenship status, underpins conditions of material deprivation which are then reinforced by insufficient recognition at the level of informal relationships. In this way, the work contributes new and unique insights into how poverty is inherently relational and lies at the intersection of processes of exclusion and subordinate inclusion.
The thesis also furthers current theorising about poverty from a recognition standpoint by drawing attention to state-society relations in the experience of poverty and their effects on the identities and agency of people in poverty outside of high income countries where most previous research on this issue has taken place. This application of recognition theory reveals its potency as an intersubjective theory of poverty. However, the thesis argues for seeing recognition as a continuum which includes both symbolic and material experiences closely entwined.
Broadly, this thesis argues the central importance of the relational dimensions of poverty, showing how they shape the quality of life of people in poverty including the forms of agency and voice that they can possess and enact. The thesis makes a contribution to the small but growing literature on the role of relationality in poverty and raises the question of what social relationships mean for people in poverty in different contexts.

Keywords: Recognition theory
Social Cash Transfers
Shame and dignity
Relational Dimensions of Poverty
Advisor: Walker, R
Chase, E
Hydrodynamic limits under pressure

We study the hydrodynamic limit for a one dimensional isothermal anharmonic finite chain in Lagrangian coordinates with hyperbolic space-time scaling. The temperature is kept constant by putting the chain in contact with a heath bath, realised via the addition of a stochastic momentum-preserving noise to the dynamics of the chain. The noise is designed to be large at the microscopic level, but vanishing in the hydrodynamic limit. Boundary conditions are also considered: one end of the chain is kept fixed, while a time-variable tension is applied to the other end. We show that the microscopic deformation and momentum converge (in an appropriate sense) to solutions of a system of hyperbolic conservation laws (isothermal Euler equations in Lagrangian coordinates) with boundary conditions. Since these solutions may develop shocks in a finite time, they are obtained in a weak sense. This is done by adapting the theory of compensated compactness to a stochastic setting. Finally, the external tension allows us to define thermodynamic transformations between equilibrium states. We use this to deduce the first and the second principle of Thermodynamics for our model.

Advisor: Chen, G
Interlocked and transition metal based halogen bonding host systems for anion recognition and sensing

This thesis describes the integration of the halogen bonding iodotriazole motif into a range of interlocked and transition metal based architectures for anion recognition and sensing.
Chapter One introduces the field of anion supramolecular chemistry, describing the non-covalent interactions exploited by host structures. In particular, this chapter reviews hydrogen bonding and halogen bonding acyclic, macrocyclic and mechanically interlocked molecules for anion recognition.
Chapter Two describes the synthesis of acyclic and interlocked tetra-iodotriazole based receptors. In particular, the preparation of a family of [2]catenanes and [2]rotaxanes via a chloride anion template approach is discussed, followed by an investigation of their anion binding properties determined through 1H NMR titration experiments.
Chapter Three presents a new methylene-spaced bis-iodotriazole motif and investigates its ability to complex a range of transition metals for anion recognition and sensing. With the aim of forming a [2]rotaxane via an active metal template method, a range of macrocycles containing the motif are prepared. Towards the construction of a fullerene containing rotaxane, bimetallic C60 fullerene containing halogen bonding and hydrogen bonding anion receptors are prepared and their sensing capabilities investigated via luminescence spectroscopy.
Chapter Four incorporates a novel benzimidazole-iodotriazole motif into a naphthalimide based axle containing dynamic [2]rotaxane. The requirement for both benzimidazole axle protonation and the presence of a chloride coordinating anion is demonstrated to be crucial for facilitating macrocycle shuttling translocation along the axle component of the [2]rotaxane. The ability of the motif to coordinate photoactive transition metals is also reported.
Chapter Five presents a summary of the major conclusions from the research described throughout the thesis.
Chapter Six details the synthetic protocols and characterisation data for each novel compound discussed in the previous chapters. Spectroscopic titration experiment protocols are also outlined.

Keywords: Anion recognition
Advisor: Beer, P
Role of neuropilin-1 in CD8+ T cells

A major limiting factor in anti-tumour immunity is the ability of T cells to infiltrate and function in the suppressive tumour microenvironment.
Semaphorins are a family of secreted and membrane-bound proteins that act as guidance cues in neurons and endothelial cells during development. By multimerizing heterodimers of neuropilin-1 (NRP1):plexin A receptors semaphorins strongly affect the F-actin cytoskeleton. Since many developmental programs are up-regulated in cancer cells, we hypothesized that tumours would hijack this physiological process to hamper immune responses.
In tumour-specific T cells, we found that NRP1 was up-regulated in vitro and in vivo upon activation. To directly interrogate the role of Semaphorin 3A (Sema3A) in modulating T cell functions, we performed two complementary lines of research:
1. In vivo, we evaluated the role of NRP1 in T cell—tumour immunity by generating a T cell conditional knockout of NRP1
2. In vitro, we assessed the ability of Sema3A to modulate T cell survival, migration, adhesion and immunological synapse formation.
We demonstrated that mice lacking expression of NRP1 on T cells control the growth of transplantable tumours cell-lines. We showed that addition of Sema3A affects T cell migration and adhesion. Additionally, we showed an inhibitory effect of Sema3A on peptide MHC:TCR synapse formation. Experiments suggested that these effects were mediated through Myosin IIA hyper-activation.
Finally, we extended these findings to humans, demonstrating that in renal cell cancer a subset of tumour-infiltrating T cells express NRP1. These T cells are most likely newly activated T cells, in the sense that they were more clonal and expressed T cell antigen receptors (TCRs) specific for cancer testis (CT)-antigens. They were also found in close proximity to Sema3Arich areas.
Taken together, our results provide novel insights into the NRP1/Plexin/Sema3A axis as an important tumour evasion mechanism.

Keywords: Cancer
Semaphorin
T cell
Advisor: Cerundolo, V
Three essays on frictions of trade

By examining the case of the West Austria retail fuel market, Chapter 1 investigates the nature of price competition in a spatially differentiated, but otherwise homogeneous product market. A spatial model is utilised for estimating the spatial dependence relationship among various locations. With the aid of statistical and machine learning tools, no prior knowledge is required regarding the structure of spatial dependence. This feature distinguishes this paper from the precedent works in the field. The results indicate that competition is highly localised but differs greatly in terms of market concentration. In addition, while location centrality affects firms pricing strategies, distance (or closeness) between competitors is not an adequate proxy for measuring the strength of competitive interactions.
The absence or poor quality of transport infrastructure can make it difficult for certain regions to access international markets. However, there is little empirical evidence on how improvements in domestic transport infrastructure stimulate international trade. Chapter 2 examines the relationship between China’s regional trade patterns and national road infrastructure in the early 2000s. The analysis is based on an adapted gravity model with several alternative specifications for robustness checks. The result suggests that improvements on the road network lead to trade expansion on both intensive and extensive margins, but the effects vary across the regions. At the same time, sectors producing time-sensitive products benefit more from road construction and improvement. These findings support the claim that intranational trade costs, which have the same impact as international trade costs, are a determinant of comparative advantage and affect international trade patterns.
Chapter 3 evaluates the potential economic costs of China’s pronounced unilateral trade sanctions on Japan in the early 2000s and provides an interpretation of the strategies used by both countries. A two-type goods version of Eaton–Kortum model of trade is used. The model captures the basic features of the China–Japan trade relations. I experiment with counterfactual simulations and explore the economic costs on China, Japan and other countries with respect to the unilateral Chinese boycotts, embargoes, two-way blockages, import tariffs and export taxes. The results show that were China to implement trade sanctions against Japan, it would have lost more than Japan in terms of welfare change. Neighbours of both countries would have been impacted due to the spillover effects.

Advisor: Rauch, F
Characterisation of novel evasins

Chemokines are a family of chemotactic cytokines that recruit innate and adaptive immune cells to sites of inflammation. Whilst these signalling proteins are vital for ensuring an effective immune response, several chemokines have been shown to be associated with the pathophysiology of a number of inflammatory diseases. Despite their relevance to disease there remain no treatments that target chemokines for inflammatory disorders. This may be due, in part, to the chemokines signalling through a robust network, driven through “one-to-many” interactions between the chemokine ligands and their receptors. This renders the “one-drug- one-target” mechanism of action that is associated with most drugs ineffective in this context. Evasins are the family of proteins found in tick saliva that bind to chemokines with a “one-to many” binding mechanism, possibly to neutralise the chemokine network to allow the tick to feed on the host for several days without eliciting an immune response. As a consequence of this novel mechanism, evasins present a possible route to a new anti-chemokine therapeutic. This thesis describes the identification and characterisation of a new evasin, P672, which can bind to and neutralise multiple CC-class chemokines. P672 was found to possess a chemokine binding domain where this domain and its functional properties can be transferred to another evasin. This domain can also be synthesized as a peptide that possesses the “one-to-many” binding mechanism observed in the P672 protein. This work has identified a novel evasin and provides proof of concept that peptides with the “one- to-many” binding mechanism that has evolved in the tick evasins can be rationally designed through the study of an evasin/chemokine interaction.

Keywords: Peptide inhibitor
Chemokine
Biological therapeutic
Cell migration
Evasin
Advisor: Bhattacharya, S
Kawamura, A
Understanding and exploiting naïve human pluripotency

Naïve human pluripotent stem cells (hPSC) represent an earlier stage in human development compared to conventional “primed” hPSC. They resemble the inner cell mass of an embryonic day (E) 5 human blastocyst and are considered developmentally equivalent to mouse embryonic stem cells (mESC). Access to this new cell type facilitates interrogation of early human development. In this thesis, I have shown that the Theunissen et al. protocol for generating naïve hPSC yields cells that most closely approximate the human E5 inner cell mass and is robustly reproducible across several induced pluripotent stem cell lines. miRNAs are essential in mouse embryogenesis for differentiation from the naïve to the primed state, but the miRNAome of the human E5 inner cell mass has yet to be determined. I have established the naïve to primed differentiation and identified the miRNAome of naïve, differentiating and primed human pluripotent stem cells by miRNAseq. This novel dataset has revealed that the largest difference in the miRNAome between mouse and the human is due to cell state rather than species. The mouse miR-290 family are the most highly expressed miRNAs in mESC and the absence of the human equivalent homologs miR- 371-373 in conventional hPSC was thought to be a difference in species. Using the miRNAseq dataset, I have shown that miR-371-373 are highly upregulated in naïve hPSC, confirming that naïve hPSC more closely resemble mESC. I also observed high expression of miR-182-5p, which downregulates the homology directed repair (HDR) pathway. This surprising finding contrasts with previous publications which suggest that naïve hPSC genomes are more efficiently manipulated by HDR. In support of this finding, I show that naïve hPSC repair Cas9 induced double strand breaks less often by HDR than primed hPSC and demonstrate that a higher proportion of naïve hPSC are in G1 phase of the cell cycle which is likely a contributor to the lower rates of HDR.

Advisor: Flynn, R
Meyer, C
Cowley, S
The roles of CD38 and NAADP in cardiac tissue

Nicotinic acid adenine dinucleotide phosphate (NAADP) is an endogenous molecule that releases calcium ions (Ca2+) from acidic endolysosomal stores. This Ca2+-mobilising molecule is known to play a role in modulating cardiac excitation-contraction coupling and pathophysiology.
The first part of the thesis focuses on understanding the mechanistic details of NAADP actions, particularly during the flight and fight response of the heart. Paced ventricular myocytes, which had genetically- (Tpcn2-/-) or pharmacologically-impaired (bafilomycin-A1 treatment) NAADP signalling pathways, had blunted responses to isoprenaline. Further investigations revealed that NAADP actions are dependent of functional CaMKII proteins but independent of L-type Ca2+ channels.
The main part of the thesis focuses on understanding the enzymatic production of NAADP in the heart. Although CD38, which belongs to the ADP-ribosyl cyclase (ARC) family, has been shown to catalyse the synthesis of NAADP in other mammalian tissue, whether CD38 is responsible for the production of NAADP in the heart remains debatable. Membrane fractions from CD38-/- mouse hearts were not able to generate NAADP through catalysing the base-exchange reaction. Experiments involving the permeabilisation of cardiac myocytes also revealed the intracellular expression of CD38 on the sarcoplasmic reticulum (SR). The SR-enriched membrane preparation (SRMP) from sheep heart is also capable of catalysing NAADP production and showed properties associated with those of CD38. Upon isoprenaline addition, paced CD38-/- myocytes had smaller Ca2+ transients and contraction amplitudes, compared to those of wild type animals. In addition, impairing NAADP signalling using bafilomycin-A1 did not affect the effect of isoprenaline on CD38-/- myocytes. highlighting the role of CD38 in coupling NAADP action to beta-adrenoceptor signalling.
Lastly, a novel ARC inhibitor, SAN4825, was also shown to inhibit NAADP synthesis in both mouse and sheep cardiac preparations, through targeting CD38. CD38-/- hearts or SAN 4825-treated hearts were resistant to isoprenaline-induced arrhythmias. These observations support the hypothesis that NAADP is generated by intracellular CD38 in the heart, which contributes to the positive inotropic and pro-arrhythmic effects of the beta-adrenoceptor activation.

Advisor: Terrar, D
Galione, A
Effective algorithms for inverting the signature of a path

The signature of a path is an important concept in rough paths theory. It has been proved in the literature that the terms in the signature of a path are bounded above, and it would then be interesting to consider whether a lower bound exists for the signature of a bounded-variation path. It has also been proved that the signature of a bounded-variation path is unique up to some modifications, then a natural question is reconstructing the path from its signature, i.e. inverting the signature of a path.
We show the connection between the two questions above, and provide practical methods for signature inversion. First we prove a result about the super-multiplicativity and the decay of the signature of a path with bounded variation, then we describe the method of symmetrisation, which was first introduced by Lyons and Xu, and demonstrate an algorithm to invert the signature of a monotone path. Moreover we introduce the method of inverting the signature by insertion, and provide examples using the insertion method to invert the signature of a path. We compare these two methods of signature inversion, and illustrate the differences with computational results.

Keywords: Rough paths
Advisor: Lyons, T
Ni, H
Accelerated design and testing of new nickel-based superalloys

Nickel-based superalloys have emerged as the materials of choice for high-temperature jet propulsion and industrial gas turbine applications due to their unique combination of resistance to loading under static, fatigue, and creep conditions, as well as to environmental degradation. The specific fuel consumption and CO2 emissions of turbines can be significantly reduced by increasing the operating temperature, thus providing a continued drive within the materials research community to develop new alloy grades with improved properties.
However, design and qualification activities are difficult and costly, which explains why the time needed to insert novel materials into industrial applications can be notoriously long. The research of the present work was carried out with the aim of accelerating the overall design—make—test—analyse development cycle for new superalloys, with a focus on the design and testing of single-crystal compositions with improved creep properties.
First, a novel mechanical testing system using miniaturised testpieces is introduced. Rapid testing methods involving temperature ramping and stress relaxation are employed to extract key high-temperature strength parameters, with the quantitative data measured then compared to conventional tests.
Second, operating creep damage mechanisms during such tests are investigated with cutting-edge electron microscopy characterisation techniques and dislocation dynamics modelling. This combination of experiments and simulations yields an improved understanding of damage evolution and of the roles played by alloy composition and microstructure in imparting creep strength.
Third, these new insights into damage mechanisms inform a novel physically based model for the creep resistance of single-crystal superalloys. A comprehensive critical assessment of previous modelling methods is carried out in an effort to approach best practice. Predictions are tested against a large experimental data set and it emerges that the present model is more accurate for alloy design purposes than existing merit indices from the literature.
Last, a set of trial alloys with carefully controlled chemistries is extensively analysed to reveal the complex influence of composition on physical properties. Experimental results provide an important benchmark for thermodynamic calculations and help derive a set of guidelines for alloy design within this particular compositional space.

Keywords: superalloy
creep
mechanical modelling
miniaturised testing
alloy design
Advisor: Reed, R
Wilkinson, A