VictorJuiz/thesis huggingface dataset:
Macroevolutionary history of Neotropical vegetation during the Cenozoic: a palynological perspective from Colombia
Keywords: Macroevolution
Neotropics
Palynology
Colombia

The Neotropics are the most plant species-rich realm of the Earth. This surprising megadiversity has been studied since times of Darwin and Humboldt, with different mechanisms proposed, not only to explain how such great diversity was produced but also how it is maintained. This system is not completely understood, and will continue being matter of study for a long time. Knowledge of the deep time patterns of diversity and diversification are central to testing hypothesised mechanisms. But the patterns have received much less attention than have the mechanisms proposed to explain them. In this thesis I used an extensive palynological record of Colombia to study the macroevolutionary history of Neotropical vegetation and its relationship with regional and global process occurring during the Cenozoic. The results show a strong correlation between fluctuations in palynological diversity and global changes in temperature. Contrasting responses of vegetation to temperature between the Palaeocene to Eocene and the Oligocene to Present suggest that different mechanisms operated during greenhouse and icehouse intervals. Throughout the Cenozoic, periods of elevated extinction are followed by periods of high origination. This relationship suggests that in the Neotropics when a species become extinct, it is replaced very fast. In contrast, the lack of correlation between origination and extinction suggest that extinction is not controlled by origination. The examination of the taxonomic rates and the global climatic curve indicate a good correspondence between episodes of global climate change and turnover, suggesting that extinction is exacerbated by these episodes. Finally, the palynological record also indicates that the Neotropics experienced several floods during the Cenozoic. These episodes include marine incursions, the development of extensive lacustrine systems and the establishment of mangrove forests. The relationship between floods and the evolution of Neotropical vegetation is challenging due to the uncertainty related to the temporal and geographic range of the floods. The evidence suggest that the floods had a local rather that a regional effect on the evolution of Neotropical vegetation.
Analytical microscopy of corroded zirconium alloys
Keywords: EELS
Zircaloy
Python
Electron Microscopy
Hydrogen Pickup
STEM
NanoSIMS
ZIRLO
Corrosion
Zirconium

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.
A relational analysis of poverty as a social phenomenon
Keywords: Recognition theory
Social Cash Transfers
Shame and dignity
Relational Dimensions of Poverty

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.
Interlocked and transition metal based halogen bonding host systems for anion recognition and sensing
Keywords: Anion recognition

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.
Role of neuropilin-1 in CD8+ T cells
Keywords: Cancer
Semaphorin
T cell

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.
Characterisation of novel evasins
Keywords: Peptide inhibitor
Chemokine
Biological therapeutic
Cell migration
Evasin

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.
Effective algorithms for inverting the signature of a path
Keywords: Rough paths

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.
Accelerated design and testing of new nickel-based superalloys
Keywords: superalloy
creep
mechanical modelling
miniaturised testing
alloy design

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.
Molecular and physiological consequences of prematurity and blood pressure elevation on the young adult left ventricular stress response
Keywords: hypertension
prematurity
cardiac stress response

Cardiovascular disease is the leading cause of global mortality. Acute disease usually strikes later in life, but risk trajectories are established earlier and are impacted by factors including preterm birth and blood pressure elevation. Prematurity results in increased left ventricular (LV) mass and is a risk factor for hypertensive disorders and heart failure later in life. Blood pressure elevation also contributes to increased LV mass and cardiovascular risk, and is increasingly prevalent in young adults. This thesis used purposive recruitment of young adults with a range of blood pressures and birth histories (preterm-born and term-born) and employed deep baseline cardiovascular phenotyping combined with exercise stress assessments to characterise LV stress response phenotypes in young adults born preterm, or with blood pressure elevation. Those born preterm were found to have impaired, declining exercise ejection fraction with increasing workload. This defect related to shorter LV length, a characteristic structural feature in the preterm-born. Preterm-born young adults also had a lower aerobic capacity than controls, which was commensurate with their exercise systolic impairment. In young adults with elevated blood pressure, it was found that submaximal exercise produced greater fatigue and impaired LV systolic performance vs normotensive controls. Blood pressure elevation was also associated with lower exercise capacity and enjoyment of physical activity and also sub-clinical LV mass increase. Collectively, these findings suggest preterm-born young adults have reduced myocardial functional reserve which likely contributes to risk of future disease including heart failure. Continued research is needed to better understand risk stratification and management for this population. In the blood pressure studies, the dysfunctional exercise stress response and lower aerobic capacity may indicate greater risk, while lower enjoyment of physical activity may confound exercise prescription. Future studies are needed to identify intervention strategies to optimally manage physiological and experiential challenges in this growing population.
Gender segregated labor markets and social inequality between occupations
Keywords: segregation
gender
wage gap
inequality
labor market
United States
Germany
occupations

This thesis is concerned with the link between gender segregation in the labor market and social inequality between occupations. Two topical questions are at the basis of the presented research: First, are female-typed jobs paid less than other jobs? Second, does women’s gender-typed occupational sorting lead to wage inequalities in the female population? In both cases, interest lies in sizes of statistical effects or associations, and in the mechanisms driving observed results. All three of the empirical chapters in this thesis employ a measure of occupations’ gender-type. This way, we classify occupations–either on a continuous or a categorical scale–as rather female-typed, male-typed, or as gender integrated. Confirming broad findings in the extant literature on segregation, this thesis identifies occupational gender-types as a key structural component of past and current wage inequality. Results on the United States suggest that cultural devaluation of female-typed jobs has been confined to the immediate post-war era, and to jobs in the bottom eighty percent of the wage ladder. Effects have strongly declined over time, which we explain by historical trends in society’s adoption of gender-egalitarian views. Analyses of the German case also show a strong link between segregation and wage disparities. This is evidenced by two separate findings: First, occupational gender stereotypes covary negatively with wages in the bottom half of the wage distribution, and in particular for women. Second, gender segregation has recently become a source of emerging wage inequality between women. The most important factor explaining this trend has been the increasing rate at which highly educated women select into male-typed jobs.
'The refugee' reproduced, negotiated, and represented: hierarchies of Malian refugeeness in Burkina Faso
Keywords: Burkina Faso
Intersectionality
Commodification
UNHCR
Refugees
Mali
Inequalities

This dissertation starts from an empirical observation and an intellectual assumption. The former dates from 2013: during a research trip in Burkina Faso I heard and observed humanitarian workers distinguish (in both discourse and practice) between who they thought were 'real refugees' and those who were not, regardless of their legal status. The intellectual assumption is that a category and a label are not only imposed on people designated as such, but are negotiated by the actors themselves and within their interactions with other actors and their social and political economies.
Building on these elements, the questions at the centre of this work are: how are hierarchies of refugeeness (re-)produced? And how, when, and why can this (re-) production create or reinforce inequalities among the refugees? I answer these questions by relying on three empirical chapters which focus on different aspects of the construction of refugeeness and the experiences people have and make of 'the refugee' category in the context of Malian forced migration in urban Burkina Faso. More specifically, I look at the encounter of the refugee regime and the refugees' lives through the study of the reproduction, negotiation, and representation of 'the refugee' status and category.
What I found and show is how hierarchies of refugeeness can create or reinforce inequalities among the refugees, and how refugeeness, and the possibilities to negotiate with it are unequally produced and distributed, locally but also globally. By unpacking refugeeness through the notion of commodification and relying on ethnographic methods and economic anthropology to study humanitarian interventions, I analyse how the encounter between the refugee regime and the refugees' complex, situated, and varied lives can produce inequalities and is experienced unequally by the refugees themselves.