VictorJuiz/thesis huggingface dataset:
Improving scalability of exploratory model checking

As software and hardware systems grow more complex and we begin to rely more on their correctness and reliability, it becomes exceedingly important to formally verify certain properties of these systems. If done naïvely, verifying a system can easily require exponentially more work than running it, in order to account for all possible executions. However, there are often symmetries or other properties of a system that can be exploited to reduce the amount of necessary work. In this thesis, we present a number of approaches that do this in the context of the CSP model checker FDR. CSP is named for Communicating Sequential Processes, or parallel combinations of state machines with synchronised communications. In the FDR model, the component processes are typically converted to explicit state machines while their parallel combination is evaluated lazily during model checking. Our contributions are motivated by this model but applicable to other models as well.
We first address the scalability of the component machines by proposing a lazy compiler for a subset of CSPM selected to model parameterised state machines. This is a typical case where the state space explosion can make model checking impractical, since the size of the state space is exponential in the number and size of the parameters. A lazy approach to evaluating these systems allows only the reachable subset of the state space to be explored. As an example, in studying security protocols, it is common to model an intruder parameterised by knowledge of each of a list of facts; even a relatively small 100 facts results in an intractable 2100 states, but the rest of the system can ensure that only a small number of these states are reachable.
Next, we address the scalability of the overall combination by presenting novel algorithms for bisimulation reduction with respect to strong bisimulation, divergence- respecting delay bisimulation, and divergence-respecting weak bisimulation. Since a parallel composition is related to the Cartesian product of its components, performing a relatively time-consuming bisimulation reduction on the components can reduce its size significantly; an efficient bisimulation algorithm is therefore very desirable.
This thesis is motivated by practical implementations, and we discuss an implementation of each of the proposed algorithms in FDR. We thoroughly evaluate their performance and demonstrate their effectiveness.

Keywords: FDR
Weak bisimulation
CSP
Labelled transition systems
Lazy compilation
Delay bisimulation
Strong bisimulation
Advisor: Roscoe, A
The dynamical systems theory of natural selection

Darwin's (1859) theory of evolution by natural selection accounts for the adaptations of organisms, but, as Fisher (1930) famously said, 'natural selection is not evolution.' Evolutionary theory has two major components: i) natural selection, which involves the underlying dynamics of populations; and ii) adaptive evolutionary change, which involves the optimisation of phenotypes for ﬁtness maximisation. Many of the traditional theoretical frameworks in evolutionary theory have focussed on studying optimisation processes that generate biological adaptations. In recent years, however, a number of evolutionary theorists have turned to using frameworks such as the 'replicator dynamics' or 'eco-evolutionary dynamics', to explore the dynamics of natural selection. There has, however, been little attempt to explore how these dynamical systems frameworks relate to more traditional frameworks in evolutionary theory or how they incorporate the principles that embody the process of evolution by natural selection, namely, phenotypic variation, diﬀerential reproductive success, and heritability. In this thesis, I use these principles to provide the formal foundations of a general framework—a mathematical synthesis—in which the future state of an evolutionary system can be predicted from its present state; what I will call a 'dynamical systems theory of natural selection.' Given the state of an existing biological system, and a set of assumptions about how individuals within the system interact, the job of the dynamical systems theory of natural selection is no less than to predict the future in its entirety.

Keywords: Natural selection
Dynamical systems
Population Genetics
Kin Selection
Quantitative Genetics
Ecology
Evolution
Social evolution
Group selection
Advisor: Preston, G
Foster, K
Yates, K
Hein, J
Villa rustica, villa suburbana: Vernacular Italianate architecture in Britain, 1800-1860

This thesis examines the emergence and evolution of the Vernacular Italianate style of domestic architecture in Britain. The style was introduced in the form of a series of three country houses by John Nash in the first decade of the nineteenth century. It subsequently evolved over the next five decades into a popular template for the modest suburban house, widely disseminated through the medium of the architectural pattern books. The thesis considers the intellectual sources and antecedents which led to the emergence of this style and influenced its characteristics, analyses Nash's particular vision, and explores how the style was able to make a successful transition from villa rustica to villa suburbana, responding to the social and economic pressures which were at play in the expanding towns of the Regency and early Victorian era. It is a style which has been the subject of limited academic study to date, and the extent and significance of its role as a model villa for the new suburb is a theme which has been central to this research. A case is put forward that the style proliferated for two principal reasons: its versatility and adaptability for houses of differing physical scale and location, and its informal charm, inexpensively achieved, which conferred an air of sophistication appropriate to contemporary social aspiration. Nevertheless, as its popularity and accessibility grew over time the intellectual and aesthetic basis which underlay its origins as a product of the Picturesque aesthetic tended to be misunderstood or overlooked entirely, and by the 1860s the style had become diluted, frequently reduced to a matter of exterior detailing, with little reference either to Picturesque composition or to relationship between house and landscape, in contradiction of the tenets of Picturesque architecture propounded in the late eighteenth century, and in complete antithesis to the approach of John Nash in his original and distinctive Italianate interpretation.

Keywords: John Nash
Villa
Picturesque Architecture
Italianate Architecture
Suburbs
Advisor: Tyack, G
Defining the optimal management of Plasmodium falciparum malaria on a background of emerging artemisinin combination therapy resistance

Drug resistant falciparum malaria has emerged twice from the Thai-Cambodian border and spread to the rest of the globe with disastrous consequences. The deployment of artemisinin-based combination therapy (ACT) as first-line treatment for P. falciparum malaria has reduced the burden of malaria dramatically worldwide and reignited the interest in the goal of malaria elimination. However, slow-clearing parasites resistant to artemisinin are emerging across the Greater Mekong Sub-region eventually leading to the failure of the ACTs.
One objective of this thesis was to determine the association between therapeutic efficacy of one of the first line ACTs (mefloquine-artesunate) and the drug-resistant molecular markers for the constituent drugs (Pfmdr-1 and K-13 mutations). Between 2003 and 2013, the adequate clinical and parasitological response to mefloquine-artesunate declined from 100% to 81.1% as the proportions of isolates with multiple Pfmdr-1 copies doubled from 32.4% to 64.7% and those with K-13 mutations increased from 6.7% to 83.4%. Detailed investigations of the various K-13 polymorphisms revealed that along the Thailand–Myanmar border, the fittest alleles (C580Y) are taking over from less resistant or less fit ones.
The second objective of this thesis was to evaluate new antimalarials (OZ439, a synthetic peroxide structurally related to artemisinin; KAE609, a spironindolone; and KAF156, an imidazolopiperazine, both are structurally novel molecules) in Phase 2a proof-of-concept studies. Parasitological efficacy was evaluated by measuring parasite clearance half-life. In all trialled doses of OZ439, KAE609 and KAF156 parasite clearance half-lives were not different in patients with artemisinin-sensitive and artemisinin-resistant parasites. No serious drug-related adverse effects were reported and these compounds will move into Phase 2b studies in late 2016.

Advisor: White, N
Nosten, F
Straight from the Heartland: New Sincerity and the American Midwest

As more and more critics now write about postmodernism in the past tense, the “New Sincerity” of a group of late twentieth-century American writers, led by David Foster Wallace, Jonathan Franzen, and Richard Powers, has been championed as one of its successors. In response to these increasingly widespread views, this dissertation argues that much more can be learned about these three writers when we stop thinking of their work within this “end of postmodernism” discourse. Instead of attempting to make claims about its novelty, this thesis conducts a literary-historical inquiry into the New Sincerity, arguing that its roots extend across postmodernism and reach back to regionalism, in particular from the midwestern provinces that all three authors grew up in and that occupy a central place in their work. Though regionalism’s subject matter, small-town America, is commonly believed to have died in the postwar period, it is this “death of the prairie town” and its symbolic afterlife that have opened up new literary possibilities outside the realm of conventional regionalism. The powerful feelings of loss and nostalgia that its death has engendered are precisely those of which Wallace, Franzen, Powers, and the New Sincerity in general make creative use. The thesis examines how they do so in a series of three extended chapters, each of which focuses on one author. The first chapter pays careful attention to Wallace’s re-imagining of the Midwest over the course of his career and reveals how he constantly deviated from the literary trajectory he had outlined in his essay “E Unibus Pluram,” a key text in the “end of postmodernism” discourse. The second chapter explores what role the Midwest plays in Franzen’s authorial self-presentation and his contradictory attempts to balance “high-art” status with an anti-elitist image. The third and final chapter gets to the root of Powers’s problems with flat characters by examining how he all too readily relies on the Midwest and its stereotypical associations with all-American goodness in his attempts to create endearing characters. Here, as well as in the other two chapters, it is the construction of a symbolic “heartland” that plays a central role in the creative process behind the author’s New Sincerity writing.

Keywords: the prairie town
David Foster Wallace
Richard Powers
the Midwest
Jonathan Franzen
Advisor: Hayes, P
Moderate Alcohol Consumption and the Brain: Friend or Foe?

Background
Alcohol consumption is widespread and increasing in some sectors of society. Whilst adverse effects on the brain of chronic heavy use are well characterised, the effects of more moderate use are poorly understood. Previous work has lacked prospectively gathered data on alcohol use. Robust evidence of harm would have important public health implications.
Methods
Associations between self-reported alcohol consumption data gathered over a thirty-year period (1985-2015), neuroimaging markers of brain structure and function, and cognition were examined in community dwelling older adults in the Whitehall II cohort (n=550). Structural, diffusion tensor, and resting state functional magnetic resonance imaging was performed in 2012 to 2015. Cognitive performance was determined cross-sectionally across multiple domains at the time of scanning and longitudinally throughout the study.
Results
No participants scored as alcohol dependent on the CAGE screening questionnaire. Higher alcohol consumption throughout the study was associated with hippocampal atrophy (even in those drinking 14-21 units (112-<168g) weekly), lower white matter integrity of the corpus callosum, increased functional connectivity within the Default Mode Network, and faster decline of lexical fluency. No protective effects of light drinking were found. Age, sex, premorbid IQ and white matter integrity predicted better verbal memory performance in the presence of small hippocampi.
Discussion
This thesis describes three novel neuroimaging associations with moderate alcohol consumption. Alcohol, even in small quantities, may represent a modifiable risk factor for adverse brain outcomes and faster cognitive decline. Learning effects or confounding by higher premorbid intelligence or social class may explain previous findings of a protective effect of moderate alcohol consumption.

Advisor: Ebmeier, K
The interest of 'North Britain': Scottish lobbying, the Westminster Parliament, and the British Union-state, c.1760-c.1830

This thesis is a study of the role of Scots and Scottish society in the politics of the Westminster Parliament and the British Union-state during the later Georgian period. Specifically, it analyses the lobbying activity of certain Scottish interests at Parliament and the central agencies of the British state in London during the period c.1760-c.1830. In doing so, this thesis is concerned with the developing efficacy of Scottish lobbies, as well as the extent to which they represented identifiably Scottish interests at Westminster and within the British Union-state over the course of this period. It aims to expand our understanding of how important elements within Scottish society gradually came to play an active role in the British political centre and argues that Scottish lobbying changed over this period from a position of nurturing and defending a separately constructed Scottish 'national' interest to becoming part of an integrated set of interests operating within a broader and more comprehensive British framework. This change was brought about by the need to represent Scottish interests more effectively within the British Union-state, particularly as the politics of Westminster became more important to certain parts of Scottish society from the 1780s onwards during the early industrial revolution. This process was, at times, uneven, and there was often tension between ongoing convergence and persistent distinction. Nevertheless, Scottish interests became more closely integrated within the British political system over the course of this period through their lobbying activities at the Westminster Parliament and of ministers in Whitehall. They increasingly operated more effectively as part of the British political and legislative process, and did so in ways which no longer presented them as separate or different in what was becoming a more authentically 'British' political culture.

Keywords: British Union-state
Scotland
Westminster Parliament
Advisor: Harris, B
Structural and functional study of MACPF/CDC superfamily proteins

The thesis mainly focuses on structural study of proteins in membrane attack complex- perforin/cholesterol-dependent cytolysins (MACPF/CDC) superfamily, in particular, Astrotactins from human and perforin-like proteins (PLPs) from Toxoplasma and Plasmodium. Both of these subfamily proteins are implicated in human diseases and structurally uncharacterised before.
Astrotactins (ASTNs) have been shown to play a crucial role in enabling neural migration along glial fibres. While ASTN1 directly forms contacts between the neuron and the fibre, ASTN2 is responsible for extracting ASTN1 from contacts at the lagging edge of the cell and recycling them to the leading edge. ASTN2 is associated with endosomes, with the majority of its structure (at the C-terminus) projecting into their lumen, anchored by a pair of transmembrane –-helices. Here we present the structure of this "endodomain" region of ASTN2, and find it to consist of a unique combination of polypeptide folds comprising a membrane attack com- plex/perforin (MACPF) domain, an EGF-like domain, a previously-unobserved form of fibronectin type III (Fn(III)) domain and an annexin-like domain. Taken together, the structural characterisation provides a framework for better understanding the mechanism of the ASTNs and related proteins in neural and other forms of vertebrate development.
Perforin-like proteins from Toxoplasma and Plasmodium (TgPLP1 and PPLPs) are critical for normal life cycle progression of these parasites, and knockout out of any of them results in significant defects in their life cycle, entrapping the parasites within the host cells and thus limiting their ability to egress. Here we present the crystal structures of TgPLP1 MACPF domain and C-terminal domain at 2.0 Å and 1.1 Å, respectively. We also presents the MACPF domain assembled in helical and hexameric ring form, which indicates the possibility of pore-formation by 6 subunits. This is the first structure of perforin-like protein from Apicomplexan parasites and provides a structural basis to elucidate the function of PLPs in toxoplasmosis and malaria pathogenesis.
The final section is a continuation of a previous study in our lab on pleckstrin homology (PH) domain of kindlins. We determined the crystal structure of kindlin-3 PH domain and characterised its lipid and membrane binding properties. Using nanodiscs incorporated with different lipids as model membrane system to study the interaction between inositol phosphate lipids and kindlin-3 PH domain, together ￼with molecular dynamic simulation studies (in collaboration with Mark Sansom’s group, University of Oxford), we propose that a subset of PH domains is able to bind to multiple inositol phosphates simultaneously and so via an avidity effect have its interaction with target membranes strengthened.

Advisor: Gilbert, R
The rise and fall of the middle class: technology, skills, and inequality

Over the twentieth century advanced economies have seen an economic and social development process which was build upon the consolidation of a strong middle class. Yet, recent decades have seen an increase in wealth and income inequality, reaching levels not seen since before the Second World War. This thesis explore some of the these issues in two parts. The focus of the first part of the thesis is on the role of education and technology in the rise of the middle class. By means of an overlapping generations model with endogenous growth, I study the conditions that enable a society to transit from underdevelopment to development. The model in place reproduces a Kuznets curve, which is deemed an important empirical feature of the history of advanced economies. The second part focuses on the fall of the middle class, by studying the effect of technology and skills in job polarisation – i.e. the fall in employment in middle-skill occupations. The approach is both theoretical and empirical. A sorting model based on tasks is developed and adapted to study polarisation. Central to this model are the distributions of skills that workers have. Thus, a complete chapter is dedicated to characterise these ability distributions, using longitudinal data from the UK for 1991-2008 in an econometric model based on the so-called Mincer equation. The estimated distributions – positive skewed – are used to calibrate the sorting model. Then, this model is used to identify the nature of the technological process affecting the UK economy over the selected period of study. Simple counterfactual exercises shed light on the strong effect of technical progress on both polarisation and inequality. In contrast, the role of change in skills is negligible. The overall conclusion is that the nature of technological change is essential in defining distributional outcomes: whilst technology can enable the rise to a strong middle class, it can also undermine it.

Keywords: inequality
technological change
skills
job polarisation
middle class
education
Advisor: Vines, D
Do morphological awareness and language status predict vocabulary knowledge?

This study explored the within and cross-language contributions of English and French morphological awareness to English and French vocabulary in pupils learning French as a modern foreign language (MFL) in England. Approximately half of the learners were English native speakers (EL1) acquiring French as a second language whilst half were pupils with English as an Additional Language (EAL) who were acquiring at least a third language. Whilst morphological awareness has been shown to have a positive relationship with vocabulary knowledge both in the native language and in an additional language, this relationship had not been measured while controlling for important covariates. Furthermore, the relationship between morphological awareness and vocabulary knowledge in a taught foreign language at secondary school level had not been investigated. Finally, there are few empirical studies that compare the relative contributions of morphological awareness to vocabulary for EL1 and EAL speakers.
Consequently, this thesis adopted a cross-sectional 2x2 between-subjects factorial design with between-participant factors of language status (EL1 vs EAL) and year group (year 8 vs year 10). The results of this study reinforced the importance of morphological awareness to native and additional language receptive vocabulary, whilst extending its importance to foreign language vocabulary for older pupils. With regard to cross-language effects, the contribution of English morphological awareness to French receptive vocabulary was replicated. Additionally, the contribution of English and French morphological awareness to English and French vocabulary were found to be similar for EL1 and EAL pupils. This suggested that morphological awareness played a similar role in vocabulary acquisition for EL1 and EAL pupils.
The implications of these results were threefold. Firstly, the study suggested the usefulness of a morphology-based approach to vocabulary instruction in the MFL context for older pupils. Secondly, this study indicated the need for a new theoretical model as the basis for investigating predictions of morphological awareness to vocabulary. Lastly, it was demonstrated that EAL pupils learn similar amounts of modern foreign language vocabulary to their EL1 peers. Considering this finding, it was suggested that EAL pupils with a variety of language backgrounds may reasonably benefit from the same foreign language instruction as their EL1 peers.

Advisor: Murphy, V
Sylva, K