VictorJuiz/thesis huggingface dataset:
Political economy of local and participatory governance

Chapter 2 compares government consultation via an opinion poll and a citizens' jury". In a jury, about fiffteen volunteers spend several days learning about a policy choice before voting. If the public is ill-informed, the government trades-off "information" against participation". Jurors have better information than poll respondents, but constitute a smaller sample. More- over, participation costs may bias the jury sample. Indeed, the literature suggests that costs might induce "neutrality": over-representation of the minority to the extent that the result is uninformative. I show that although the minority will often be over-represented, "neutrality" is a knife-edge result here so juries may be worthwhile. Extensions consider compensating jurors and excluding "special interests".
Chapter 3 uses evidence from the allocation of regeneration funding to motivate a model in which central government may ask councils to compile apparently pointless dossiers to ap- ply for money, because the dossiers provide information about councils' competence. I then consider when the government might prefer a simpler but less flexible auction-type process.
The UK government's ability to "ring-fence" money, obliging councils to spend it on its priority, is central to chapter 3. Chapter 4 develops the analysis of auctions in this context. With variations in competence, ring-fencing effectively imposes type-specific minimum bids. I characterise equilibrium bidding and show that the ring-fencing constraint may not only increase bids, but actually induce councils to contribute resources.
Continuing the themes of participation and competence in the policy process, chapter 5 examines parish councils' use of a general spending power. I find parishes with more well-educated and older citizens (groups with generally higher political participation) are more likely to use their powers. Further investigation suggests that these citizens matter because they are involved in governance, rather than because they exert democratic pressure. This has impli- cations for wider neighbourhood governance policy.

Keywords: auctions
local government
participation
Advisor: Leaver, C
Myatt, D
Molecular modelling of beta-barrel outer membrane proteins

In Gram-negative bacteria, the Outer membrane (OM) acts as a first barrier to screen unwanted compounds whilst enabling ions and very small solutes to diffuse into the cell. Most of nutrients and essential ions are effectively transported across a membrane via the outer membrane proteins (OMPs). The water-filled β- barrel OMPs are called porins. These pores are classified into two groups, non- specific and substrate-specific porins. Each of them has different mechanisms to facilitate its substrate translocation. To reveal the process of substrate permeation and selectivity in microscopic detail, molecular dynamics (MD) simulations and applications were performed in this thesis.
The studies in this thesis focus on a series of classical porins. These proteins share similar feature where extracellular loop(s) (generally loop 3 (L3)) is folded into the middle of the pore and act as a constriction site which is important for substrate specificity and selectivity. The studies firstly concentrate on the structural properties and dynamics of the general trimeric porins, OmpC and OmpF whose sequences share 60% identity. OmpC and OmpF are found to have similar mechanism of latching loop (L2) to maintain trimeric stability. The smaller pore size allows OmpC to be more cation-selective than OmpF. Additionally, the major driving force for cation permeation in both porins is not from electrostatic properties. This differs from the phosphate-selective porin, trimeric OprP, where a phosphate diffusion depends on electrostatic interactions with positively charged pore-lining residues. The charge brush-like behavior of interior Arg and Lys residues plays a major role in phosphate selectivity. Also, the free energy profiles (PMF) reveal two key regions that are important for differentiating phosphate from other anions. The brush-like mechanism of OprP were also implanted to the simplified model pores in order to determine the possibility of transferring phosphate-selective properties of OprP to a model which may be useful for future design of nanopores. It is found that the duplication of functional residues and pore cavity can turn a model into the highly phosphate-selective pore. Importantly, the phosphate-binding affinity is dependent on the ability of the pore to interfere and occupy the hydration shell of a translocating phosphate where such ability can be maximized by an increase in sidechain flexibility. In case of uptake of more complex substrates, OpdK also employs a constriction site to select its substrate, aromatic vanillate (VNL) with total charge of -1. Unlike ion-specific porins, the free VNL is attracted by polar and aromatic interactions and sequentially directed through the periplasmic vestibule by charged residues insides the pore. The correct orientation of VNL on arrival is crucial for OpdK to recognize and enable the permeation process.

Keywords: computer simulations
Advisor: Sansom, M
A functional and structural study of HLA-­B*2705 restricted CTL responses associated with delayed HIV-­1 disease progression

The HIV-1 Gag p24 protein contains the HLA class-1 B*2705 restricted epitope KK10, responses to which are associated with delayed progression. Data from in vitro proteasomal digestion studies from our group has shown the production of a number of C-terminally extended and truncated epitopes containing KK10, produced in far higher quantities during proteasomal digestion than this “optimal epitope” and that the amount of antigen made in proteasomal digestion is instrumental in determining the development of immunodominance. This work aims to characterise the contribution of these naturally processed epitope forms to the cellular immune response to this region.
Further proteasomal digestion studies have shown that the common KK10 intra-epitope escape mutant sequences R132K and L136M have major effects on epitope production by the proteasome and that a range of short peptides containing the N-terminal of the KK10 sequence are produced in large quantities by the proteasome. Recognition of the KK10 epitope forms by HLA B*2705 HIV-1 patients were characterised ex vivo and show recognition of KK10 epitope forms somewhat independent of the presence of KK10 recognition, we also show cross-recognition between KK10 epitope forms by CD8+ T cells, as well as recognition by CD4+ T-cells. TCR from CD8+ T-cells specific for KK10 epitope forms were found to share common features in the HLA binding CDR hyper-variable loops.
Structural studies of the HLA B*2705 molecules in complex with the KK10 epitope forms show a shared binding motif at the N-terminus, and to a lesser extent, the C-terminus of the binding groove which may facilitate cross-recognition of complexes. In addition these studies show a potentially novel binding mode for a 14mer peptide, and refolding of truncated KK10 peptides as short as a 4mer with the HLA B*2705 molecule (crystallisation with a 6mer peptide shown). This demonstrates previously unrecognised flexibility of the HLA class-1 to bind and present peptides of different lengths to T-cells.
We show that these HLA B*2705 binding-capable truncated peptides do not induce a CD8+ T-cell response in HLA B*2705 HIV-1 patients and may be able to block CD8+ T-cell responses to the KK10 epitope. This might represent a novel form of viral CTL escape. In addition we observe the presence of KK10 flanking mutations in patient sequences and significant associations between the presence of intra-epitope escape mutations, KK10 recognition and patterns of escape in flanking sequences.
Finally we note the reduction in binding of KIR3DL1 to KK10 epitope forms relative to the KK10 epitope-HLA B*2705 complex. The presence of HLA B*2705 and KIR3DL1 associate with improved disease course in HIV-1 though the mechanism through which this occurs has yet to be defined.

Keywords: B*27
long-term non-progressor
KK10
HLA
Advisor: Iversen, AKN
Fugger, L
Investigation of the potential of PorA and FetA as meningococcal vaccine components

In the search for a vaccine providing comprehensive protection against meningococcal disease, one vaccine currently under development contains the immunogenic proteins PorA and FetA in meningococcal outer membrane vesicles (OMVs). To achieve high levels of coverage against disease-causing isolates, the antigenic variability of these proteins could be overcome using knowledge of meningococcal epidemiology and population structure. In this study, the possible implications of variable expression levels of PorA and FetA on vaccine efficacy were investigated. Producing OMVs containing consistent amounts of FetA is difficult due to iron-repressed expression; therefore, meningococcal strains were constructed which constitutively expressed FetA at increased levels for OMV vaccine production and analysis. In mice, OMVs from modified strains induced antibodies against both PorA and FetA. These antibodies acted synergistically in a serum bactericidal assay; however, antibodies against FetA were weakly bactericidal alone. The potential to increase levels of PorA- and FetA-specific bactericidal antibodies with a prime-boost strategy, using OMV and protein inoculums, was also tested. While successful for a weakly-immunogenic PorA variant, a similar strategy did not increase bactericidal activity against FetA. Although antibodies against FetA can be induced following OMV immunisation, sufficient antigen expression in target bacteria is also required for bactericidal killing; therefore, the variability and regulation of porA and fetA transcription was investigated in a range of isolates. Despite differences in regulation among clonal complexes, variable expression is unlikely to be an issue for vaccine coverage. In particular, regulation of fetA by iron is reduced in many isolates due to a deletion in the sequence bound by the regulatory protein, Fur. Therefore, a vaccine targeting PorA and FetA may provide high levels of protection against meningococcal disease; however, an alternative formulation or immunisation strategy is required to improve coverage against FetA.

Keywords: vaccine
Neisseria meningitidis
meningococcus
Advisor: Maiden, M
Feavers, I
The potential role of biotic mechanisms in baculovirus dispersal

The role of biotic mechanisms in baculovirus (BV) dispersal was investigated using three Lepidopteran pests; Plodia interpunctella (Hubner), Ephestia cautella Walker and Mamestra brassicae L. and their respective BVs. The first two, pyralid moths, are pests of stored products, and the third is a pest of brassicas.
Detailed host biology and virus mortality studies were undertaken to provide background information for the main investigation of virus dispersal using P.interpunctella.
BV infectionincreased larval activity and thus BV dispersal in all three species until the disease at an advanced stage caused sluggish behaviour and mortality. However, larva to larva virus transmission was limited, especially as the integuments of diseased pylarids did not rupture and cannibalism was rare when a suitable food supply was available.
P.interpunctella adults which received a sub-lethal BV dose in the larval stages appeared normal but the proportion of eggs oviposited, the viability of the eggs and the survival of the progeny were reduced. However, no BV was detected in the adult stage. Transovum transmission occurred if the adults were externally contaminated with BV.
Scavangers, predators and adult parasitoids which fed on diseased prey voided viable BV in their faeces. This contaminated the larval medium and resulted in larval infection. The predators tested readily fed on diseased prey but the parasitoids were less able to compete with BV for hosts, Bracon hebetor Say preferentially avoided diseased hosts. There was little evidence to indicate that BV can be mechanically vectored between host larvae on the ovipositor of a parasitoid or the mouthparts of a predator. The relative potential of the host and other biotic mechanisms to cause BV dispersal is discussed.

Advisor: Evans, H
The path of song

The Path of Song: Semantic Strategies in Iliad VIII is a continuous commentary to Book VIII of the Iliad, applying to this section of the poem a new aesthetic methodology developed primarily by the comparative scholar J. M. Foley. Termed 'traditional referentiality1, this methodology holds that oral traditional poetics is founded upon the duality of 'denotative' and 'connotative' levels of meaning, in which the semantic potential of any given element in the narrative, of any sort, is a result of the audience's experience with that element in previous performances. Thus, the associative qualities of traditional narrative allow the poet during the realisation of the song to manipulate audience expectations as they listen to stories whose general outlines (i.e. who kills who, who must not die at a certain moment in the story, etc.) they know from a lifetime of experience. To recapture this complex of meaning is to recreate the ancient experience of Homeric poetry, giving a modern audience access to the excitement and uncertainty of a narrative designed for a progressive unfolding at the moment of performance.
After a brief introduction, in which a key term within Homeric poetics (οϊμη 'song path') is briefly discussed before we outline the history of the methodology and its place within modern scholarship, the commentary successively summarises and describes the key elements in small sections of the narrative, and then presents for each of these sections the comparative evidence establishing the conclusions reached. A conclusion is followed by two appendices on some of the more contentious speech introduction formulae.

Advisor: Taplin, O
Differential games of exhaustible resource extraction

This thesis is concerned with game-theoretic models of oligopoly resource markets. They revolve around an open market, on which a number of firms sell a common resource. The market price-demand relationship means that the price (demand) that results from the firm’s production (pricing) decisions is a function of the decisions of all firms selling to that market. This means that firms must generally anticipate the actions of competing firms when determining their own strategies, which means that these models often need to be analysed using game theory.
We focus on games in which the resource is exhaustible, with the exception of Chapter 5, in which the majority of the analysis is carried out in an inexhaustible resources setting. Exhaustibility introduces an additional complication into these games; that of allocating the extraction and sale of a limited resource pool over time. We consider several separate areas of extension, which we outline below.
In Chapter 2, we consider a dynamic Stackelberg game. Stackelberg competition is an asymmetric form of competition in which one player (the leader) has the ability to pre-commit to and announce a strategy in advance. The ability to pre-commit to a strategy is almost always highly valuable, and in this case allows the leader to drive down the follower’s production by pre-committing to drive up their own. We follow the framework used in [62] to analyse Cournot competition to derive our results.
In Chapter 3, we compare the two settings in which resource extraction models are usually formulated: Open-Loop, in which the players determine their strategies as functions of time and the initial resource levels of the players only; and Feedback-Loop, in which the players determine their strategies at each point in time as a function of the current resource levels at that time. Our focus is on the investigation of the relationship between the difference in the production or value of a firm under these two models, and the distribution of resources across the firms.
In Chapter 4, we consider a common property resource game. These involve multiple firms which can extract from a common resource pool. We study a widely-used Open- viii Loop model, as formulated in [79]. We examine the result that analysis of the problem by standard methods results in two candidate equilibria, and argue that one of these equilibria can be ruled out by construction of a superior response.
In Chapter 5, we analyse joint constraints on production, namely constraints which are met when the total production is above or below a certain level. It is a well- established result that these constraints can result in multiple equilibria. We provide several brief extensions to existing uniqueness results. We also demonstrate methods by which these results can be utilised to analyse games with piecewise-linear windfall taxes or congestion charges. Finally, we discuss the problems of extending these results to games with resource exhaustibility.

Keywords: Stackelberg
dynamic game
Cournot
Hotelling
resource extraction
Advisor: Howison, S
Partly exchangeable fragmentations

We introduce a simple tree growth process that gives rise to a new two-parameter family of discrete fragmentation trees that extends Ford's alpha model to multifurcating trees and includes the trees obtained by uniform sampling from Duquesne and Le Gall's stable continuum random tree. We call these new trees the alpha-gamma trees. In this thesis, we obtain their splitting rules, dislocation measures both in ranked order and in sized-biased order, and we study their limiting behaviour. We further extend the underlying exchangeable fragmentation processes of such trees into partly exchangeable fragmentation processes by weakening the exchangeability. We obtain the integral representations for the measures associated with partly exchangeable fragmentation processes and subordinator of the tagged fragments. We also embed the trees associated with such processes into continuum random trees and study their limiting behaviour. In the end, we generate a three-parameter family of partly exchangeable trees which contains the family of the alpha-gamma trees and another important two-parameter family based on Poisson-Dirichlet distributions.

Keywords: exchangeability
continuum random tree
Markov branching model
Poisson-Dirichlet distribution
alpha-gamma tree
self-similar fragmentation
R-tree
dislocation measure
splitting rule
sampling consistency
part exchangeability
Advisor: Winkel, M
The North Helvetic Flysch of eastern Switzerland

The North Alpine Foreland Basin (NAFB) comprises sediments of late Eocene to middle Miocene age. The earliest deposits are the North Helvetic Flysch which are exposed in the regions of Glarus and Graubunden, eastern Switzerland. The Taveyannaz sandstones are the first thrust wedge (southerly) derived sediments of the North Helvetic Flysch. The Taveyannaz basin was divided into two sub-basins by a thrust ramp palaeohigh running ENE/WSW (parallel to the thrust front). Palaeocurrent directions were trench parallel towards the ENE. Sedimentation in the Inner basin (140m thick) is characterised by very thick bedded turbidite sands generated by thrust induced seismic events confined within the thrust-top basin. The Outer basin (240m min. thickness) comprises 10-15 sand packages (5-100m thick) formed by turbidite sands which are commonly amalgamated. Sedimentation in the Outer basin is considered to have been controlled by thrust-induced relative sea-level variations. The Inner basin underwent intense deformation at the sediment/water interface prior to the emplacement of a mud sheet over the basin whilst the sediments were partially lithified. Later tectonic deformation involved fold and thrust structures detaching in the underlying Globigerina marls.
The stratigraphy of the NAFB can be considered as two shallowing upward megasequences separated by the base Burdigalian unconformity. This stratigraphy can be simulated by computer by simplifying the foreland basin/thrust wedge system into 4 parameters: 1) the effective elastic thickness of the foreland plate, 2) a transport coefficient to describe the erosion, transport and deposition of sediment, 3) the surface slope angle of the thrust wedge, 4) the thrust wedge advance rate. The Alpine thrust wedge underwent thickening during the underplating of the External Massifs at about 24-18Ma. This event is simulated numerically by slowing the thrust wedge advance rate, and increasing the slope angle and keeping all other parameters constant. This event causes rejuvenation of the forebulge, and erosion of the underlying stratigraphy, so simulating the base Burdigalian unconformity without recourse to eustasy or anelastic rheologies to the foreland plate.

Advisor: Watts, A
Platt, J
Tony Watts, J
Dams of Damocles

Theories of transboundary water politics have failed to explain the status quo in many river basins: fragile political relations between riparian states and nationalist domestic politics, as well as weak regional institutions and huge economic inefficiencies – but also an absence of wars over water. This is due to an uncritical approach to scale, power, and geopolitics. It is the purpose of this thesis to address these conceptual gaps by critically evaluating the multiple relationships between the logic of large dams and the politics of international rivers.
The meaning of dams, the politics of their operation and construction, and their impact on international relations are much more ambiguous, opaque and complex than existing explanations have suggested so far. In turn, their logic influences, competes with, and contradicts the logic of river basin governance. Dams produce alternative spaces of development, energy, and state power that complement or are superimposed on existing spaces of riparian cooperation. This thesis argues that the contradictions between these spaces explains the geopolitical limbo of many international rivers in the developing world.
Drawing from Foucault’s governmentality theory, the literature of critical geopolitics, and post-structural approaches to spatial scale the case-oriented research design of this thesis evaluates two geopolitical processes in contentious transboundary river basins: the construction of the Grand Ethiopian Renaissance Dam on the Nile and the operation of the Toktogul Dam in the Kyrgyz stretch of the Syr Darya River.
By unpacking these processes, this thesis makes three substantial contributions to existing scholarship. Firstly, it is argued that regional river basin management is essentially a geopolitical project that contradicts the geo-economic imperatives of the dam. Secondly, power and agency in water politics is diffused far beyond the nation-state and can be understood in terms of “network effects”. Thirdly, to marry the concerns of the geopolitical and the geo-economic, I propose that the contrasting logics give rise to “geopolitical entrepreneurs” – actors who use geopolitics for wealth accumulation, legitimacy, nation-building, and other ends. While dams may provide power, wealth, and authority an allegorical Sword of Damocles is let down on the riparians.

Keywords: Syr Darya
dams
Nile
geopolitics
transboundary water politics
Advisor: Pallot, J
Daley, P