VictorJuiz/thesis huggingface dataset:
Structural studies of icosahedral viruses

Described as “organisms at the edge of life”, viruses are the most abundant type of biological entity that can infect all types of life forms and are found in almost every ecosystem on Earth. Although virus capsids can be found with a wide range of shapes, around half of the virus families have an icosahedral arrangement. This thesis mainly focuses on structural studies of proteins from two types of viruses: the VP5 protein of Bluetongue Virus (BTV) serotype 15, and the capsid protein (CP) of Maize Streak Virus (MSV) (the Nigerian strain).
Bluetongue (BT) disease in ruminates is caused by BTV and is of important agricultural and economic impact. As one of the two proteins that comprise the outer capsid of the virus, VP5 has been shown to play an important role in membrane penetration. I describe structures of BTV VP5, at both high and low pH, both solved by X-ray crystallography to atomic resolution. These provide insights into the membrane penetration process for a non-enveloped virus at the molecular level. An atomic level mechanism of pH dependant conformation changes was revealed, including a re-arrangement of 3 bent helices into one long straight helix protruding out of the molecule, and a transformation from a β-sheet to an α-helix. The significant change due to the movement of the helix of the so-called unfurling domain could be caused by a conformation change of H386 pushing the conserved E316 residue in the so-called beam helix, α12, which contacts the anchoring domain. Our low pH structure fits well into the low pH cryo-EM image, clarifying the observed protruding density.
Geminiviruses cause diseases in various plants, leading to great economic loss. MSV is the type member of genus Mastrevirus of the family Geminiviridae. The MSV capsid is composed of a single protein, termed, CP. Infectious virus particle capsids are generally constructed from two incomplete T=1 icosahedra, joined to form a so-called geminated viral particle of dimensions 220 x 380 Å with a fivefold symmetry axis coincident with the long axis, so that the CPs are arranged with quasi-icosahedral symmetry. The MSV VLP (single icosahedral particles) and the geminated MSV virion structures were solved to resolutions of 9.5 Å and 7.4 Å, respectively, by cryo-EM. A localized reconstruction method was used in the processing procedure in the geminated MSV virion structure by treating each half of the geminated particle (one incomplete icosahedral half) as a new single particle. These structures revealed structural information about the virus and help our understanding of the assembly of geminiviruses. The MSV geminated virus particles are characterized by a twinned icosahedral capsid with distorted peripentonal pentamers and equatorial pentamers observed by us, and a 12˚ offset between the two halves of the particle.

Keywords: Protein Structure
Geminivirus
Cell Penetration
Maize Streak Virus
Icosahedral VIruses
Bluetongue Virus
Advisor: Stuart, D
Essays on mobile money services, microenterprises and role models in developing countries

Mobile money services have rapidly expanded across East Africa, with 66% of people using an account actively. Understanding the impact of these services is therefore an important area of research, which the first two chapters of my thesis contribute to.
Chapter One of my thesis uses survey data from Tanzania to understand how mobile money services affect the risk sharing capabilities of households. I look at the aftermath of rainfall shocks at the village level, and examine how consumption has been affected for users of mobile money services, non-users who reside in villages with other users, and households that live in villages without access to mobile money services. I find that after a village-based rainfall shock, only users of mobile money services are able to smooth their consumption. Non-users, regardless of whether they have access to mobile money or not, experience a 6% fall in their consumption. This raises questions of who benefits from the introduction of new financial services.
Chapter Two looks at integrating mobile money services into a microfinance loan product and the impact this has on the businesses of women in Uganda. In a field experiment, I randomly assigned women applying for a microfinance loan to receive the loan on a mobile money account or as cash. I find that women who receive their loan on a mobile money account invest 11% more of the loan into their business and experience 15% higher profits. These impacts are greatest for women who experienced high pressure to share money with family and friends at baseline. This study suggests that the manner in which a loan is disbursed has important implications for whether women are able to control how the loan is used.
The third chapter of my thesis looks at a different topic: role models and how they impact behaviour. I study the impact of being randomly assigned to see a movie featuring a potential role model, Queen of Katwe, or a placebo movie, on the exam results of secondary school students in Uganda. Seeing Queen of Katwe results in lower secondary school students scoring 0.11 standard deviations higher in their maths exam, mainly because they are less likely to fail maths, and upper secondary school students scoring 0.13 standard deviations higher in their finishing exams. Impacts are largest for female students. Further research is needed to uncover the mechanisms by which a role model can raise exam performance, with both changing beliefs and raising aspirations potential channels.

Keywords: mobile money
uganda
secondary school
microenterprise
microfinance
role models
risk-sharing
Advisor: Dercon, S
Quintana-Domeque, C
Progressive ideals and the promotion of ‘high’ culture: classical music in British adult education, c.1945-1965

This thesis examines the promotion of classical music through adult education in Britain during the first two decades following the Second World War. In doing so, it illuminates the relationship between progressive political ideals (namely, democratisation and egalitarianism) and ideas about ‘high’ culture in Britain during the immediate post-war era. A number of prominent musical figures were associated with adult education institutions during this period. This thesis focuses on their activities at university ‘extramural’ departments and adult colleges.
In addition to possessing generally left-leaning political outlooks, these figures contributed to a common musical project. This sought to reorient the culture of classical music in Britain, and thus elevate British culture more broadly, by reforming music education in general and adult musical education in particular. Ultimately, it sought to place classical music in Britain on more secure intellectual, aesthetic, and social foundations.
Encouraged by developments within the expanding post-war adult education sector, reformist approaches to adult musical education circulated increasingly widely from the late 1940s onwards. The results draw attention to the ways in which both ‘high’ culture and middle-class identity were being re-thought in the immediate postwar era. They also present a picture of gradual cultural change during this period, with visions of cultural reform which centred on ‘high’ culture being guided by, and applying, progressive ideals throughout.
Both democratisation and egalitarianism, however, were defined in particular ways within adult musical education, and they were realised unevenly in practice. Examining adult musical education in the immediate post-war era also shows how progressive ideals, in shaping ideas about ‘high’ culture, were interacting with ideals of voluntarism and individualism. The degree to which both individualism and authenticity were emphasised within adult education’s promotion of ‘high’ culture, meanwhile, suggests that these ideals were shaping post-war British culture from the outset.

Keywords: music
Hans Redlich
Northern Ireland
Shropshire
high culture
Great Britain
college
the left
Geoffrey Bush
University of Birmingham
Belfast
extension
culture
Liverpool
Gerald Abraham
SAEC
Birmingham
musicology
extramural
adult education
classical music
twentieth century
progressive
WEA
universities
class identity
London
Iain Hamilton
Workers’ Educational Association
authenticity
Walter Bergmann
social change
reconstruction
Morley College
Michael Tippett
Walter Goehr
history
education
Queen’s University Belfast
William Glock
Thea Musgrave
democratisation
Denis Arnold
England
music education
music administration
individualism
political ideals
egalitarianism
cultural reform
Shropshire Adult Education College
Peter Racine Fricker
voluntarism
middle class
Anthony Milner
Wilfrid Mellers
University of Liverpool
intellectual culture
Mátyás Seiber
post-war
University of London
Advisor: Grimley, M
Cold reactive collisions between neutral molecules and trapped ions

This thesis describes the development and demonstration of techniques for the study of ion-neutral reactive collisions at low temperatures conducted using two unique experimental apparatuses comprising radio-frequency Paul traps. One apparatus combines a Stark decelerator with a Paul trap; the other apparatus features a buffer gas cell interfaced with a Paul trap through an electrostatic quadrupole guide.
A novel ion trap time-of-flight mass spectrometer has been introduced and characterised. This apparatus is designed to detect the ion products of reactive collisions at low temperatures (< 10 K). This detection approach affords excellent detection efficiency and is broadly applicable to all ion-molecule reactions that one could study within a linear Paul ion trap. A proof-of-principle reaction between xenon ions and neutral ammonia isotopologues is examined to test the performance of the new detection set-up.
With the goal of achieving full control over the reaction parameters, the amount of alignment retained by rotationally and translationally cold ammonia molecules exiting the electrostatic guide has been examined using (2 + 1) REMPI detection of the molecules with varying linear polarisation. Simulations suggests how modifications to the current setup will enable full orientation of the cooled molecules reaching the detection region to be achieved.
Experiments on cold charge exchange reactions between sympathetically-cooled Xe+ and room temperature ammonia (NH3 and ND3) have been conducted within lasercooled Ca+ Coulomb crystals in a linear Paul ion trap. There is ongoing work to ascertain any difference in reactivity between NH3 and ND3 as the neutral reactant species. Preliminary data are discussed at a qualitative level, with the prospect of observing any isotope effect in this charge transfer process. Charge exchange reaction experiments using cold state-selected ammonia are discussed with the goal of establishing reaction rate constants at different collision energies.

Advisor: Heazlewood, B
Softley, T
The social world of hunter-gatherers in early Holocene Lesotho: integrating method and theory

This thesis presents new early Holocene excavations at Ntloana Tšoana in western Lesotho and makes the case for reintegrating method and theory in southern African Later Stone Age archaeology. It is argued that the distancing of method and theory relates to discipline-wide economic and material culture biases. An alternative is proposed which focuses on the everyday residues and temporal relations of hunter-gatherer life in order to build an understanding of attachment to place. This approach, which is more accepting of the multi- temporal qualities of complex stratigraphies, is ideally suited to the abundant and well- stratified rockshelters of southern Africa. Importantly, tracing sequence in the construction of stratigraphic diagrams, the modelling of radiocarbon dates, as well as in studies of artefact production use and discard, remain central to the work presented here. At the same time, however, equal weight is placed on the durational and imbricated qualities of the archaeological record, which, it is argued, deserve to be repositioned as positive attributes. In this way of thinking sedimentation and erosion are vital to the human story and provide much of the movement and depth to the history-writing process. These insights are brought to bear on the 600–1700 calendar years of early Holocene stratigraphy at Ntloana Tšoana, during which time a complex history of social fragmentation and coalescence is traceable, sandwiched between, and partly overlapping with, two major flooding events. The site also becomes associated with a specific set of practices over many centuries involving the construction of large hearth features and the working of animal hides. Discussion revolves around the manner in which rockshelter residues may have acted as a stabilising force within the fluid socio-material world of hunter-gatherer groups and how this may have operated over an inter-generational timeframe.

Keywords: Rockshelter
Stone Age
Archaeology
Africa
Advisor: Mitchell, P
Baptismal art and identity construction in the Western Mediterranean in the fifth and sixth centuries

This thesis interrogates material sources from the fifth and sixth centuries to come to a nuanced understanding of what implications the association of Christianity and Romanness had for the conduct of late antique Christians’. I argue that Christian art and material culture shows us that in their lived religious practices, Christians treated Roman cultural techniques and Roman spaces, which high-ranking church representatives considered un-Christian or even pagan, as parts of Christian culture. The thesis demonstrates that very diverse Christian groups, some located on the rural edges of the Western Mediterranean and others in one of its imperial centres, Ravenna, allowed Roman visual culture, and even pre-Christian cult spaces, to shape baptismal art and architecture. Whether these manifestations of Romanness had an impact on Christian beliefs, i.e. their orthodoxy, can be shown by analyzing material culture only with great difficulty. Roman-Christian material culture does provide evidence, however, that late antique Christians privileged keeping Roman traditions alive over contemporary scholarship considers correct Christian conduct. Roman cultural techniques, officially deemed un-Christian, appear in the material record, and suggest that individual communities’ understandings of permissible and orthodox ways of performing Christianity were influenced by the cultural landscapes that surrounded them.

Keywords: Late Antiquity
Romanness
Baptism
Spain
Romanitas
Art
Ravenna
Archaeology
Identity
Western Mediterranean
Afterlife of Antiquity
Portugal
North Africa
Advisor: Elsner, J
Rosser, G
Molecular pathogenesis of pain in osteoarthritis

Over half of the UK population over 75 suffers from osteoarthritis (OA). It is the most common musculoskeletal disorder, with pain presenting as the most prevalent symptom. Three quarters of patients with OA complain of pain on a daily basis, often severely affecting quality of life. Understanding the mechanism behind the generation of pain in OA, with a view to abrogate this symptom, is of utmost clinical importance.
The results of this thesis explore unchartered territory of pain research in OA. It provides further insights into the pathogenesis of pain in this disease, and is likely to have translational benefits into clinical medicine in the future.

Advisor: Vincent, T
The Architecture of Nanoparticle Surfaces and Interfaces

Heterogeneous catalysts are vital for many industrial processes, however the high compositions of platinum group metals mean that the catalysts are often expensive and are not always cost efficient. In many cases, although platinum is a good catalyst, an enhancement in activity can be seen when alloying with a secondary metal. In order to increase the cost efficiency of these catalysts, an improvement in activity and reduction in expensive metal mass is needed. One method of combining these factors is the production of core-shell nanoparticles, removing the highly expensive metal from the inactive particle core while maintaining the close contact of the active metal with the secondary metal.
This thesis provides an insight into two synthetic methods to produce designed bimetallic nanoparticles with tailored active sites for improving catalysis. The first method explored uses the polymer polyvinylpyrrolidone as a capping agent while subsequent deposition techniques are employed to tailor the surface layer. The second method uses a mesoporous silica (SBA-15) which induces the surface segregation of some secondary metals. These two synthetic methods are evaluated through extensive characterisation to better understand the metallic interfaces and through the use of the formic acid decomposition reaction to understand the changes in the active sites at the surfaces. The SBA-15 method was also used to produce a series of catalysts with enhanced activity for the oxygen reduction reaction. The research presented is a step towards highly designed nanoparticle catalysts, with the tailoring of active sites made possible through degree of interaction of a secondary metal.

Keywords: Heterogeneous catalyst
interfaces
Electronic modification
surfaces
Oxygen reduction reaction
Formic acid dehydrogenation
nanoparticles
Geometric modification
Advisor: Tsang, S
Estimation and reliability of myocardial blood flow with dynamic PET

Dynamic Positron Emission Tomography (PET) enables the estimation of Myocardial Blood Flow (MBF), by modeling the temporal evolution of a radio-labeled pharmaceutical over multiple PET images acquired over time. Despite its advantages, the absolute quantification of MBF is not used routinely in the clinic due to a lack of clinical standardization. MBF estimates can be affected by patient motion, among other factors, which creates displacements between different PET frames and leads to errors in MBF calculation. Automated motion correction techniques are difficult to perform, due to the rapid change of the tracer spatial distribution throughout the PET images series, and the low resolution of PET image series. Furthermore, it is challenging to quantitatively evaluate the success of motion correction techniques, and their impact on MBF reliability is not fully understood.
In this thesis, we developed a framework for estimating MBF along with the uncertainty on the estimate. The framework relies on Bayes theory, which represents the kinetic parameters as a probability distribution, from which uncertainty measures can be extracted. If the uncertainty extracted is high the parameter studied is considered to have high variability - or low confidence - and vice versa. A Bayesian model inference technique, called Variational Bayes, was chosen due to its relatively inexpensive computations compared to other Bayesian techniques.
The reliability of parameter and uncertainty estimates were first evaluated through simulations and compared with another Bayesian model inference technique considered the "gold standard". It was found that the uncertainty metric was estimated robustly across multiple noise levels, which was necessary as motion can be seen as an additional source of noise. The uncertainty metric was then used to assess motion correction, performed manually by experienced observers. The uncertainty, calculated before and after motion correction, reduced significantly in moderate and high motion cases, demonstrating the usefulness of the method. The uncertainty was subsequently used to evaluate a motion correction algorithm, showing comparable performance to manual realignment provided by experienced users, with regards to the uncertainty metric. Finally, we investigated different situations where the use of the uncertainty metric may convey clinical information, besides assessing motion correction.

Advisor: Chappell, M
Jenkinson, M
Innovative scripts and spellings in Roman Egypt: investigations into script conventions, domains, shift, and obsolescence as evidenced by hieroglyphic, hieratic, demotic, and Old Coptic manuscripts

Innovative Scripts and Spellings in Roman Egypt studies the hieroglyphic, hieratic, Demotic/demotic, and Old Coptic manuscripts which evidence the conventions governing script use, the domains of writing those scripts inhabited, and the shift of scripts and their domains, before the obsolescence of Egyptian writing during the Roman Period. Utilising macro-level frameworks from sociolinguistics, the textual culture from four case study sites of the 1st and 2nd centuries CE are contextualised within the communities of speech, script, and practice constituting the priesthoods that produced them. Utilising micro-level frameworks from linguistics, both the scripts of the Egyptian writing system written, and the way the orthographic methods fundamental to those scripts changed, are typologised. Additionally, this study treats the way in which logographic vs alphabetic orthographies are deciphered and understood by the reading brain, and the rationales behind (ortho)graphic shift, such as where conventional as opposed to innovative spellings sit along continua of orthographic depth. By analogy to language death in speech communities, current scholarship on script obsolescence in Mesoamerica, Mesopotamia, and Egypt is appraised, and by problematising generalised synoptic narratives of obsolescence, the phenomenon of domain-by-domain language and script shift is then compared directly to that of domain-by-domain obsolescence of the scripts of the Egyptian writing system. “Innovative scripts and spellings” are analysed at Oxyrhynchus, Tebtunis, Soknopaiou Nesos, and Narmouthis, and a synthesis of the evidence these provide for script conventions, domains, shift, and obsolescence is undertaken. In doing so, this study draws conclusions on how the unprecedented pressures on priestly populations during the 2nd century CE are evidenced in, and a cause of, the (ortho)graphic innovations attested, and how this informs upon the domain-by-domain shift in conventions and scripts, and eventual tip of hieratic towards obsolescence during the 2nd century CE.

Keywords: Language Shift
Ostraca
Hieratic
Papyri
Script Shift
Egyptian Hieroglyphs
Bilingualism
Language Death
Demotic
Script Obsolescence
Coptic
Multigraphia
Advisor: Smith, M