VictorJuiz/thesis huggingface dataset:
A demographic perspective on trait heritability and sex differences in life history

Biologists have long used demographic approaches to answer questions in ecology and evolution. The utility of these approaches has meant a constant development and refinement of methods. A key milestone has been the development of phenotype structured population models that link ecology and evolution. Moreover, biostatistical research steadily improves methods to coax demographic information from scarce data. In this thesis, I build upon some of the recent advances in the field. My first three studies focus on the consequences of sex differences in life history for population dynamics. Firstly, I test whether males matter for the dynamics of African lion (Panthera leo) populations via a previously unquantified mechanism: the inheritance of phenotype from father to offspring. Secondly, I develop a method to estimate age-specific mortality rates for both sexes in species where one of the sexes disperses around the age of maturity. Thirdly, I apply this method to study variation in mortality between the sexes and between two populations of African lions. After these three chapters, which make contributions to the field of sex-structured population dynamics, I focus on the integration of phenotype structured modelling and quantitative genetics. I illustrate how heritability of a quantitative character that develops with age depends on (i) viability selection, (ii) fertility selection, (iii) the development of the phenotype with age, and (iv) phenotype inheritance from parents to offspring. Our results question the adequacy of quantitative genetics methods to obtain unbiased estimates of heritability for wild populations. This thesis advances our understanding of population development over ecological time scales. This knowledge has applications in conservation and population management, but also contributes to untangling evolutionary processes in wild animals.

Keywords: mortality
population models
heritability
sex differences
integral projection models
population ecology
biodemography
Advisor: Coulson, T
Occupational pensions in Germany: an economic geography

By the end of the twentieth century, the generous German public pay-as-you-go pension system had been struggling with a serious deficit due to the country’s ageing population. In 2001, the German government enacted the “Riester” pension reform, named after Mr. Walter Riester, the Labour Minister brokering it, which reduced the level of publicly provided pensions, and strengthened the funded occupational and private pillars in order to replace the loss in retirement income.
This thesis investigates the role and structure of occupational pensions during the Riester-reform and in its aftermath, using an economic geography perspective. In doing so, it discusses the role of trade unions and employer associations (social partners) in moulding the structure of the occupational system, and investigates the geography of occupational pensions both at employer and at employee level. Empirically, the thesis is based on an in-depth interview with Mr. Walter Riester, and a unique, proprietary data-set of a German occupational pension provider, containing information on 332 thousand employees and over 12 thousand employers.
The results show that the internal division of social partners played a critical role in leaving occupational pensions voluntary, but they have been successful in setting standards on the occupational pension market by means of collective bargaining. Employers and employees show systematic spatiotemporal patterns in their pension-related decisions, confirming the importance of local relationships and local contexts in implementing social partners’ measures and in the transformation of the welfare state. It is finally pointed out that the Riester-reform was a part of a gradual transition, which has been reducing employers’ autonomy in order to reinforce the social role of occupational pensions. To achieve that and to catalyse the reform process, employers’ and employees’ risk exposure has been mitigated in the hope that old-age poverty can be avoided.

Keywords: mixed models
pension savings
occupational pensions
individualisation
economic geography
defined contribution
local relationships
Riester reform
defined benefit
behaviour
social pacts
Advisor: Clark, G
Wójcik, D
First investigation on a two-stage CERN PSB collimation system

This thesis investigates the feasibility of a two-stage collimator for the PSB (Proton Synchrotron Booster) at CERN. Simulations of several shapes, sizes and materials were run and the indications from this study are that due to heating concerns either diamond is required for the first stage or a fast kicker would need to be installed to prevent damage in the event of beam loss. Aluminium is also possible with some compromise on performance. The final design would be subject to further simulations on nuclear scattering effects and requires the exact tune to be known; a parameter not yet decided.

Keywords: collimation
particle physics
particle accelerators
physics
Advisor: Peach, K
The Khecarīvidyā of Ādinātha: a critical edition and annotated translation

This thesis contains a critical edition and annotated translation of the Khecarīvidyā of Ādinātha, an early haṭhayogic text which describes the physical practice of khecarīmudrā. 31 witnesses have been collated to establish the critical edition. The notes to the translation adduce parallels in other works and draw on Ballāla's Bṛhatkhecarīprakāśa commentary and ethnographic data to explain the text.
The first introductory chapter examines the relationships between the different sources used to establish the critical edition. An analysis of the development of the text concludes that its compiler(s) took a chapter describing the vidyā (mantra) of the deity Khecarī from a larger text to form the framework for the verses describing the physical practice. At this stage the text preserved the Kaula orientation of the original work and included verses in praise of madirā, alcohol. By the time that the text achieved its greatest fame as an authority on the haṭhayogic practice of khecarīmudrā most of its Kaula features had been expunged so as not to offend orthodox practitioners of haṭhayoga and a short fourth chapter on magical herbs had been added.
The second introductory chapter concerns the physical practice. It starts by examining textual evidence in the Pali canon and Sanskrit works for practices similar to the haṭhayogic khecarīmudrā before the time of composition of the Khecarīvidyā and then discusses the non-physical khecarīmudrās described in tantric works. There follows a discussion of how these different features combined in the khecarīmudrā of the Khecarīvidyā. Then a survey of descriptions of khecarīmudrā in other haṭhayogic works shows how the haṭhayogic corpus encompasses various differnt approaches to yogic practice. After an examination of the practice of khecarīmudrā in India today the chapter concludes by showing the haṭhayogic khecarīmudrā has generally been the preserve of unorthodox ascetics.
In the third introductory chapter are described the 27 manuscripts used to establish the critical edition, the citations and borrowings of the text in other works, and the ethnographic sources.
The appendices include a full collation of all the witnesses of the Khecarīvidyā, critical editions of chapters from the Matsyendrasaṃhitā and Haṭharatnāvalī helpful in understanding the Khecarīvidyā, and a list of all the works cited in the Bṛhatkhecarīprakāśa.

Keywords: ethnography
Sanskrit
philology
Hinduism
yoga
tantra
Advisor: Sanderson, A
Structural studies of chemotaxis in prokaryotes and higher eukaryotes

Chemotaxis, the ability of a cell to change its motility as a response to environmental stimuli, belongs to the most important signal transduction mechanisms in life. Evolution has created a plethora of different molecular mechanisms to enable cells to react appropriately to extracellular changes. In this thesis, chemotactic signal transduction pathways in bacteria, in particular two component signalling in R. sphaeroides, and eukaryotes, in particular human axon guidance, are studied by means of X-ray crystallography complemented with biophysical, biochemical and cellular studies.
Two-component signal transduction in bacteria is one of the most abundant signalling pathways in biology. Here the determinants for specificity for a crucial sensor kinase-response regulator interaction are presented and used to design novel, synthetic two-component pairs. The activation mechanism of response regulators has been extensively studied and a model for activation that crucially involves a Thr and a Tyr residue has been widely accepted in the field. In this thesis, two structures of a response regulator from R. sphaeroides are presented and together with biophysical and cellular assays suggest a novel paradigm for response regulator activation.
Axon guidance is an essential process in human development and relies crucially on chemotaxis. Two signalling pathways, the plexin-semaphorin and the Rgm-Neogenin pathway are studied extensively in this work. Structures of the intracellular region of Plexin-B1 provide an elegant mechanism explaining how ligand binding events on the extracellular and intracellular side can be integrated into a single signalling output. The study of RgmB in complex with its receptor Neogenin provides the first structural insight into the important family of repulsive guidance molecules and explains their role in the disease juvenile hemachromatosis.
In summary, this work provides insights into a plethora of chemotactic pathways and extends our current knowledge of these important mechanisms significantly.

Keywords: rgm
plexin
chey
crystallography
chemotaxis
structural biology
Advisor: Armitage, J
Jones, E
Surface attachment behaviour in Rhodobacter sphaeroides

Motility and chemotaxis have been implicated in the process of biofilm formation in a wide range of species. Using a combination of microscopy and image analysis, genetics, microbiology and biochemistry, the initial approach of Rhodobacter sphaeroides cells to a solid surface has been characterised. Interestingly, these data suggest that for R. sphaeroides alterations in motility and swimming behaviour may result in differences in biofilm formation simply by changing the number of cells which reach the surface. This is in contrast to a few other well-studied species where the motility apparatus, the flagellum, has been shown to play an active role in surface sensing and the transition to biofilm growth.
Tracking swimming cells and measuring surface attachment revealed that changes in motility affect the ability of cells to attach to a surface, with non-motile cells attaching least and mutants with frequent stops attaching less than smooth swimming cells with few stops. Tracking attaching cells and classifying their method of attachment revealed that flagellar tethering is not essential for R. sphaeroides attachment.
Competition assays with fluorescently labelled strains showed that the initial imbalance between motile and non-motile cells remains as microcolonies develop over 48 hours,and the proportion of non-motile cells remains fairly constant. Development on a surface over 48 hours was similar for motile and non-motile strains, including aflagellate strains, once attached.
Using parameters calculated by tracking swimming cells to calculate the effective diffusion coefficient in a simple model of cell movement suggested that motion alone could explain the differences in attachment without assuming different cell properties. In particular, aflagellate strains might be hindered from surface attachment by their reduced motility alone. This is interesting since some other bacterial species use the flagellum as a surface sensor.

Keywords: biofilm
bacterial motility
Advisor: Wadhams, G
Measurement of the invisible width of the Z boson using the ATLAS detector

The invisible width of the Z boson is its partial width to neutrinos and is a well known Standard Model quantity. A direct measurement of the Z boson’s invisible width has been performed using the ATLAS detector. The width was measured to be Γ(Z → inv) = 481 ± 5(stat.) ± 22(syst.), which rivals the precision of the direct measurements performed by the LEP experiments. Such a precise was measurement performed by measuring the ratio of Z → νν to Z → ee events and correcting for the differences between the neutrino and electron selections. The measurement is sensitive to any non Standard Model interactions with a jet(s) + undetected particle final state. No evidence was found for a deviation from the Standard Model, however improvements have been suggested to allow more sensitivity to new phenomena at high energies.

Keywords: LHC
ATLAS
Z boson
Invisible width
Advisor: Weidberg, T
Understanding the mechanisms of stress corrosion cracking

Austenitic stainless steels are frequently used in the cooling circuits of nuclear reactors. It has been found that cold-worked 304 stainless steels can be particularly susceptible to stress corrosion cracking at the operating conditions of such reactors. Despite more than 130 years of research underlying mechanisms are still not properly understood. For this reason, the effects of cold-work and applied stress on the oxidation behaviour of 304SS have been studied in this thesis.
A set of samples with/without prior cold-work, and with/without stress applied during oxidation, were oxidized in autoclaves under simulated pressurised water reactor primary circuit conditions. Atom-probe tomography and analytical transmission electron microscopy were used to investigate the local chemistry and microstructure in the different samples tested. Regions containing grain boundaries, deformation bands, and matrix material in contact with the environment, were extracted from the coupon specimens with a focused ion beam machine. Cross-sections of crack tips were studied with secondary ion mass spectrometry and electron backscatter diffraction. The compositions of oxides grown along the surface and the different microstructural features were analysed. Fe-rich spinels were found at the surface and Cr-rich spinels were observed along fast diffusion paths. Ni-enrichment was found at the metal/oxide interfaces and a Ni-rich phase was detected in precipitates ahead of grain boundary oxides. Li was observed in all oxidised regions and B segregation, originating from impurities in the alloy, was observed in grain boundaries and crack tip oxides. Cavities and hydrogen associated with Ni-rich regions were found ahead of the bulk Cr-rich oxide in some of the samples.
The implications of these findings for the understanding of SCC mechanisms are discussed. It is suggested that Ni precipitation as well as the presence of deformation bands may play an important role in controlling SCC susceptibility in 304 stainless steel. A modification of the film-rupture model including internal oxidation and fast diffusion along H-stabilised vacancies in strain fields at the crack front is proposed.

Keywords: grain boundary
APT
stress corrosion cracking
HELP
stainless steel
TEM
PWR
hydrogen
corrosion
atom probe
3D-FIB-slicing
oxidation
Advisor: Lozano-Perez, S
Saxey, D
Smith, G
Mechanistic studies on transition metal complex catalysed homogeneous hydrogenation

The development of systems capable of catalysing the reduction of unsaturated bonds with very high selectivities is one of the greatest successes of asymmetric catalysis. The mechanism by which rhodium complexes catalyse alkene hydrogenation has been effectively established through a combination of kinetic studies and isolation and characterisation of the intermediates in solution. It was hoped to elucidate the corresponding ruthenium catalysed mechanism using similar techniques.
Following the synthesis of a selection of ruthenium catalysts, their activity towards the reduction of a selection of dehydroamino acid derivatives at ambient temperature and pressure was investigated. Having successfully tested out the activity of these catalysts, NMR studies were initiated in order to observe and characterise intermediates in the catalytic cycle.
Considerable effort was put into the NMR studies, the systems were looked at under both argon and hydrogen, but although some substrate containing species were observed, it was found to be effectively impossible to break into the catalytic cycle and observe intermediate species using NMR techniques. Electrospray mass spectrometry investigations yielded more successful results, though still no hydrogen containing intermediates were observed.
However, it was possible to make a detailed kinetic study of several ruthenium catalyst / substrate systems by looking at the dependence of reaction rate on classic variables such as hydrogen pressure, catalyst concentration and substrate concentration. The combined results of electrospray experiments, kinetic analyses and kinetic modelling using computer packages enabled a possible mechanistic pathway to be proposed.
Imaging membrane potential

Imaging membrane potential is a promising technique in the elucidation of the interactions of large networks of neurons. The membrane potential in a neuron varies as an action potential, the basic electrical signal of neuronal communication, travels along the length of the cell. Voltage sensitive dyes play a key role by providing an optical readout of the electric field generated across a neuron membrane by the action potential. However, none of the dyes reviewed in Chapter 1 generate sufficient signal change with changes in membrane potential; this sensitivity problem limits the ability of the imaging membrane potential technique to allow the high spatial and temporal resolution necessary for neuronal networks to be better understood. This thesis features two avenues of research that are expected to result in the necessary enhancements to voltage sensitive dyes to improve the signal change.
The first avenue is based on the effect of an electric field upon the non-linear optical properties of a porphyrin macromolecule. The encouraging field sensitivity of a previous porphyrin monomer voltage sensor inspired an investigation which identified optimisations to enhance the voltage sensitivity (Chapter 2). The design, synthesis and initial characterisation of optimised porphyrin voltage sensors is detailed in Chapter 3.
The second avenue is based on the effect of an electric field upon the rate of intermolecular electron transfer. In a suitably designed dye, the competition between electron transfer and fluorescence, following excitation by incoming light, allows the fluorescence intensity to act as an optical indicator of the electron transfer rate. New dyes were rationally designed and synthesised, as this effect had not been applied to voltage sensitive imaging before the research detailed in Chapter 4. The challenging purification of the new amphiphilic dyes synthesised also inspired research into a novel testing method which does not require amphiphilic dyes (Chapter 5).

Keywords: Voltage Sensitive Dyes
Advisor: Anderson, H
Envisioning Byzantium: materiality and visuality in Procopius of Caesarea

The three works of Procopius of Caesarea, the History of the Wars, the Buildings and the Secret History, form a corpus which can be profitably studied as a whole. My thesis is a typology of the visual in Procopius’ corpus, which is embedded in a study of narrative technique. It concerns itself with the representation of material reality and the complex relationship between materiality and the text. It utilises the digressive and the descriptive as an indirect entry point to expose Procopius’ literary finesse and his use of poikilia.
In the first half of this thesis, the main object of my study is the representation of the material world in Procopius. The first chapter is devoted to the first book of the Buildings as it depicts the city of Constantinople. The second chapter moves to the representation of space and the third chapter to that of objects of all sizes and kinds. From these three different angles, I demonstrate how the visual is deeply charged with both ideological and meta-textual intentions.
The second half of the thesis goes beyond materiality to examine what I discuss as the imaginaire of Procopius. The fourth chapter examines the way violence is depicted in a material and spectacular manner as well as its meta-textual implications, and the fifth and final chapter addresses the omnipresence of the supernatural in the corpus as well as Procopius’ self-representation as narrator and character.
While preoccupied to some extent with ideological and political concerns, this thesis is first and foremost centred on the text itself and how its relationship to the description of material culture throws light on a crucial author on the cusp between the classical and the medieval imaginaire, one of the most significant authors in Byzantine literary culture.

Keywords: Procopius
ancient rhetoric
ancient historiography
Greek literature - history and criticism
Advisor: Elsner, J
Whitmarsh, T
Pipe-jacked tunnelling: jacking loads and ground movements

The reported work constituted the third phase of a programme of research into the performance of concrete pipes during installation by the pipe-jacked tunnelling technique. This third stage was a continuation of the on-site monitoring of full-scale pipe jacks during construction. Four schemes were monitored in different ground conditions: London clay, dense fine sand below the water table, stiff glacial till and soft alluvial clay. Pipe sizes ranged from 1000mm to 1800mm internal diameter and excavation methods included hand tools, slurry machines and an open face tunnel boring machine. The main objective was to collect information on jacking loads and stresses at the pipe-soil interface to provide a better basis for future designs. This was achieved by building twelve stress cells -capable of measuring total normal stresses, shear stresses and pore pressures - into the wall of a standard concrete jacking pipe that could be inserted anywhere in the pipe string. Jacking loads and forward movement of the pipe string were simultaneously recorded and the results were correlated against site activities, including lubrication operations, and tunnel alignment surveys. Another objective was to monitor the ground response by measuring displacements around the tunnel and ground pressures above the perpendicular to the intended line. Ground movements were measured using conventional surveying techniques for surface settlements, and inclinometer access tubes for sub-surface deformation. On one scheme, electro-levels were employed in a near-horizontal tube to measure centre line settlement as the tunnel bore advanced. Push-in spade cells and pneumatic piezometers were installed on two schemes to measure the change in horizontal pressures with the passage of the shield. Because of the myriad data collected, it has only been possible to present a summary of the results obtained. Jacking force records from all the monitored schemes - including the previous fieldwork stage - are presented. The pattern of jacking load build up and the magnitude of frictional resistance can differ significantly according to the type of ground and use of lubricants. Stress measurements at the pipe-soil interface show that the interaction between jacking loads, pipeline misalignment, stoppages, lubrication, excavation technique etc, is highly complex. Ground movement measurements compared to well established empirical predictive methods show that short-term displacements are related to ground losses caused by closure of the overbreak void between shield and pipe.

Keywords: pipe jacking
Advisor: Milligan, G