VictorJuiz/thesis huggingface dataset:
Structural studies of chemotaxis in prokaryotes and higher eukaryotes
Keywords: rgm
plexin
chey
crystallography
chemotaxis
structural biology

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.
Surface attachment behaviour in Rhodobacter sphaeroides
Keywords: biofilm
bacterial motility

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.
Measurement of the invisible width of the Z boson using the ATLAS detector
Keywords: LHC
ATLAS
Z boson
Invisible width

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.
Understanding the mechanisms of stress corrosion cracking
Keywords: grain boundary
APT
stress corrosion cracking
HELP
stainless steel
TEM
PWR
hydrogen
corrosion
atom probe
3D-FIB-slicing
oxidation

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.
Imaging membrane potential
Keywords: Voltage Sensitive Dyes

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).
Envisioning Byzantium: materiality and visuality in Procopius of Caesarea
Keywords: Procopius
ancient rhetoric
ancient historiography
Greek literature - history and criticism

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.
Pipe-jacked tunnelling: jacking loads and ground movements
Keywords: pipe jacking

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.
Effects of real and imagined contact under conditions of socially acceptable prejudice
Keywords: contact
homosexuality
imagined contact
social norms
schizophrenia
prejudice

The objective of this thesis was to examine the effectiveness of contact and imagined contact (a derivative of direct contact) in reducing intergroup prejudice when the prejudice in question is deemed socially acceptable. Studies focused on two populations that are targets of socially acceptable, prejudice – people suffering from schizophrenia in the U.K., and homosexual men in Jamaica. These target groups were selected because they are similar in that they are both targets of socially acceptable prejudice, but also because of their differences in that the stereotypes associated with them are quite dissimilar. The first part of the thesis empirically tested the assumption that the aforementioned populations are targets of socially acceptable prejudice. Two cross-sectional studies, one of which was also cross-cultural, measured motivation to control prejudice against these target groups, and compared it to motivation to control prejudice against targets of socially unacceptable prejudice. I found that motivation to control prejudice against people with schizophrenia in the U.K. was lower than motivation to control prejudice against Black people in the U.K. Also, motivation to control prejudice against homosexual men was higher in the U.K. and the U.S.A. than in Jamaica, and differences in motivation to control unspecified prejudice were significantly smaller. The second part examined the association between actual contact and prejudice for both populations. Two cross-sectional studies, one of which was also cross-cultural, found that contact was associated with less prejudice. This effect was mediated by intergroup anxiety in all cases, and also by fear in the case of people with schizophrenia. Furthermore, I found that contact was more strongly negatively associated with anti-homosexual prejudice in Jamaica, where the prejudice is socially acceptable, than it was in Britain, where the prejudice is not socially acceptable. The third part tested the effect of imagined contact, a form of extended contact, on prejudice against people with schizophrenia. Four experimental studies demonstrated that imagined contact can be an effective means of reducing prejudice against this group. However imagined contact must be conducted in very specific ways, otherwise it has the potential to increase prejudice against people with schizophrenia.
The development of a novel technique for characterizing the MICE muon beam and demonstrating its suitability for a muon cooling measurement
Keywords: MICE
muon
emittance
betatron function
ionization cooling
neutrino
ionisation cooling
momentum spectrum
muon collider
neutrino factory
Twiss parameters
time of flight
emittance measurement

The International Muon Ionization Cooling Experiment (MICE) is designed to demonstrate the currently untested technique of ionization cooling. Theoretically, this process can condition the high quality muon beams required to build a neutrino factory or muon collider which will be the next generation of machines for the study of Particle Physics. The beam line to transport muons into the MICE cooling channel lattice cell was installed in December 2009. Step I of the experimental programme, whose goal was to demonstrate that the beam line can generate beams similar to those expected in a neutrino factory cooling channel, was completed in August 2010.
Methods were developed to use time difference measurements in the MICE time of flight counters (TOFs) to obtain a transverse spatial resolution of approximately 10 mm and to track muons through the focusing elements of the beam line, thus allowing the trace space vectors of individual muons to be reconstructed and their integrated path length to be calculated. The TOFs were used to make an absolute measurement of the momentum of muons with zero bias and a systematic error of less than 3 MeV/c.
The measured trace space vectors of single muons were used to estimate the emittances and approximate optical parameters of eighteen muon beams. The results of beam line simulations were compared with the measurements and, once the effects of experimental resolution had had been included, found to be in good agreement.
A sample of individual muons whose phase space vectors had been measured was injected into a simulation of the full MICE cooling channel; the beam was found to be suitable for demonstrating muon cooling, although some fine tuning of the cooling channel optics will eventually be required.
Facing climate change in the Marshall Islands
Keywords: climate change
Marshall Islands
risk perception
small island states

The Marshall Islands may be rendered uninhabitable by sea level rise and other consequences of global climate change within 50 years, a threat with which locals are increasingly familiar via educational events, firsthand environmental observation, and Biblical exegesis. This thesis explores Marshallese attitudes towards this spectre, in particular explaining why ‘ordinary’ Marshall Islanders (if not their government) have strongly favoured a response strategy based on self-blame and local mitigation, rather than other-blame and protest of industrial nations. I argue that this strategy does not stem from ignorance or disempowered pragmatism, but from a moral reading of climate change consonant with Marshallese values. Bringing together literature on traditionalism, entropy, and the cultural cognition of risk, I demonstrate that Marshallese reactions to climate change are intelligible in light of a vigorous pre-existing narrative of self-inflicted cultural decline. Climate change becomes framed as both a cause and a consequence of weakening custom, the over-reliance on foreign things, transforming global warming into a locally resonant, and indeed ideologically appealing, risk. Based upon this case study, I sketch a ‘trajectorial theory of risk perception’ and accompanying research agenda.
Symbolic and ideological representation in national parliaments
Keywords: gender
issue positions
parliament
political representation
ethnic groups

Using a cross-national perspective covering all free and partly free countries, this thesis addresses two questions: What factors are associated with levels of gender representation, ethnic group representation, and ideological representation? And what are the relationships between levels of gender, ethnic group, and ideological representation? Ideological representation regards policy positions in different issue domains, whilst gender and ethnic group representation are concerned with the inclusion of women and ethnic groups in parliament. The representation of ethnic groups is approached in a multivariate cross-national analysis for the first time. Cultural rather than institutional factors seem to be the best predictors for the different levels of gender representation and ethnic group representation. Cultural attitudes are measured with survey questions on attitudes to women as political leaders, and tolerance of marginalized groups in society. The thesis finds that on average quotas for women and ethnic groups are not associated with higher levels of representation, perhaps because of issues regarding how quotas are implemented. Broadly speaking, little effect of the electoral system on any form of representation could be observed. Looking at levels of ideological representation, in line with some recent studies, the thesis suggests that the electoral system is not associated with different levels of ideological representation. I show that this is the case across various policy domains. Furthermore, the thesis finds no evidence for a direct relationship between levels of gender representation and levels of ethnic group representation, but levels of gender representation may be associated with levels of left–right representation. The relationship between different forms of representation might be shaped by the salience of ideological domains and awareness of under-representation of ethnic minority groups. Overall, the thesis argues that cultural attitudes are central to understanding levels of political representation, a factor often neglected in the literature.