VictorJuiz/thesis huggingface dataset:
Formal methods for the analysis of wireless network protocols

In this thesis, we present novel software technology for the analysis of wireless networks, an emerging area of computer science. To address the widely acknowledged lack of formal foundations in this field, probabilistic model checking, a formal method for verification and performance analysis, is used. Contrary to test and simulation, it systematically explores the full state space and therefore allows reasoning about all possible behaviours of a system.
This thesis contributes to design, modelling, and analysis of ad-hoc networks and randomised distributed coordination protocols.
First, we present a new hybrid approach that effectively combines probabilistic model checking and state-of-the-art models from the simulation community in order to improve the reliability of design and analysis of wireless sensor networks and their protocols. We describe algorithms for the automated generation of models for both analysis methods and their implementation in a tool.
Second, we study spatial properties of wireless sensor networks, mainly with respect to Quality of Service and energy properties.
Third, we investigate the contention resolution protocol of the networking standard ZigBee. We build a generic stochastic model for this protocol and analyse Quality of Service and energy properties of it. Furthermore, we assess the applicability of different interference models.
Fourth, we explore slot allocation protocols, which serve as a bandwidth allocation mechanism for ad-hoc networks. We build a generic model for this class of protocols, study real-world protocols, and optimise protocol parameters with respect to Quality of Service and energy constraints. We combine this with the novel formalisms for wireless communication and interference models, and finally we optimise local (node) and global (network) routing policies.
This is the first application of probabilistic model checking both to protocols of the ZigBee standard and protocols for slot allocation.

Keywords: quantitative analysis
formal methods
wireless network protocols
probabilistic model checking
Advisor: Kwiatkowska, MZ
Genome mapping of malaria resistance genes: the host ligands of PfEMP1

Erythrocytes infected by mature forms of the Plasmodium falciparum parasite adhere to other components of the vascular space, a behavior considered critical to the pathogenesis of severe malaria. Adhesion is mediated by the P. falciparum erythrocyte membrane protein 1 (PfEMP1), a highly variant antigen expressed by the parasite and subject to switching during the course of an infection. The host ligands of PfEMP1 include CD36, ICAM-1 and the ABO antigens. By employing a series of population- and family-based association studies from multiple African populations, we examined whether variation in the genes underlying these molecules affects susceptibility to severe malaria. Our results suggest that a common frameshift mutation in the ABO glycosyltransferase, responsible for blood group O, is associated with protection from severe malarial phenotypes (P=2x10⁻⁷), particularly severe malarial anaemia. However, we found no significant disease associations with variation in either the ICAM1 or CD36 genes. We focused on two particular functional polymorphisms, the missense ICAM-1Kilifi and the CD36 nonsense mutation T1264G. We genotyped both markers in around 10,000 individuals, but neither demonstrated an association with severe malarial phenotypes. Malaria has been a profound selection pressure shaping human genetic diversity. The last decade has seen the development of several haplotype-based methods to detect signatures of recent positive evolutionary selection. These techniques are potentially invaluable tools in our hunt for genetic variants that protect from life threatening malaria. We used simulations and empirical data from the International HapMap Project to demonstrate the validity of searching for long regions of haplotype homozygosity, as an approach to finding alleles undergoing selective sweeps. We analysed genetic data from a range of populations, particularly those utilized by HapMap, to investigate whether our candidate genes were associated with signals of recent positive selection. We characterized the distribution of a selection event associated with the CD36 1264G allele, focused in Central-West Africa, and demonstrated a novel signal of low population differentiation at the ABO gene, suggestive of longstanding balancing selection. Our work confirms that variation in the host ligands of PfEMP1 modulates severe malaria susceptibility, and highlights the value of using signals of selection, along with functional experiments and genetic association studies, to dissect the biology of severe malaria.

Keywords: cytoadherence
candidate gene
genetic epidemiology
positive selection
human evolution
PfEMP1
ABO
extended haplotype homozygosity
CD36
genetic association
severe malaria
ICAM1
linkage disequilibrium
Advisor: Kwiatkowski, D
Impulsivity, the orbitofrontal cortex and borderline personality disorder

Damage to the orbitofrontal cortex (OFC) has been associated with disinhibited or socially inappropriate behaviour and emotional irregularities in both humans and monkeys. Prominent characteristics of several personality disorder syndromes, in particular Borderline Personality Disorder (BPD), are impulsivity and affective instability.
This investigation aimed to determine if certain aspects of the Borderline Personality syndrome, in particular impulsivity, are associated with OFC dysfunction. Basic questionnaires of personality, emotion, and impulsivity together with tasks sensitive to frontal lobe dysfunction that assess possible factors related to impulsivity, including time perception, sensitivity to reinforcers, and spatial working memory (SWM), were administered to OFC lesion, BPD, non-OFC prefrontal cortex lesion control, and normal control participants.
OFC and BPD patients performed similarly, in that they were more impulsive, reported more inappropriate behaviours, BPD traits, anger, and less happiness than both control groups. They were also less open to experience and had a faster perception of time (in terms of time production) than normal controls. They performed differently on other tasks: BPD patients were less extraverted and conscientious and more neurotic and emotional than all other groups. OFC patients had more severe deficits in reversing stimulus-reinforcer associations compared to all other groups and had a faster perception of time (in terms of time estimation) than normal controls.
Both OFC and non-OFC lesion patients had mixed lesions that included dorsolateral prefrontal cortex (DLFC) damage. Accordingly, they both had SWM deficits, a task used to control for DLFC damage, compared to normal and BPD participants. Since BPD participants were not impaired on this task and non-OFC patients did not perform poorly on the same tests that OFC patients did, the neuropsychological deficits of BPD and OFC patients could not be attributed to SWM deficits or DLFC dysfunction.
The findings suggest that some of the cognitive/behavioural deficits commonly found in BPD patients are related to OFC dysfunction while others are unrelated and are perhaps related to other brain systems. The possibility of amygdala dysfunction is discussed. The similarities and dissociations found between BPD and OFC patients on certain tasks may lead to a better understanding of the aetiology of BPD and the functions of the OFC. Theoretical and therapeutic implications of the findings are discussed.

Advisor: Edmund Rolls, S
Causal inference with instruments and other supplementary variables

Instrumental variables have been used for a long time in the econometrics literature for the identification of the causal effect of one random variable, B, on another, C, in the presence of unobserved confounders. In the classical continuous linear model, the causal effect can be point identified by studying the regression of C on A and B on A, where A is the instrument. An instrument is an instance of a supplementary variable which is not of interest in itself but aids identification of causal effects. The method of instrumental variables is extended here to generalised linear models, for which only bounds on the causal effect can be computed. For the discrete instrumental variable model, bounds have been derived in the literature for the causal effect of B on C in terms of the joint distribution of (A,B,C). Using an approach based on convex polytopes, bounds are computed here in terms of the pairwise (A,B) and (A,C) distributions, in direct analogy to the classic use but without the linearity assumption. The bounding technique is also adapted to instrumental models with stronger and weaker assumptions. The computation produces constraints which can be used to invalidate the model. In the literature, constraints of this type are usually tested by checking whether the relative frequencies satisfy them. This is unsatisfactory from a statistical point of view as it ignores the sampling uncertainty of the data. Given the constraints for a model, a proper likelihood analysis is conducted to develop a significance test for the validity of the instrumental model and a bootstrap algorithm for computing confidence intervals for the causal effect. Applications are presented to illustrate the methods and the advantage of a rigorous statistical approach. The use of covariates and intermediate variables for improving the efficiency of causal estimators is also discussed.

Keywords: causal bounds
instrumental variables
Advisor: Lauritzen, S
Extensional thin layer flows

In this thesis we derive and solve equations governing the flow of slender threads and sheets of viscous fluid. Our method is to solve the Navier-Stokes equations and free surface conditions in the form of asymptotic expansions in powers of the inverse aspect ratio of the fluid, i.e. the ratio of a typical thickness to a typical length. In the first chapter we describe some of the many industrial processes in which such flows are important, and summarise some of the related work which has been carried out by other authors. We introduce the basic asymptotic methods which are employed throughout this thesis in the second chapter, while deriving models for two-dimensional viscous sheets and axisymmetric viscous fibres. In chapter 3 we show that when these equations govern the straightening or buckling of a curved viscous sheet, simplification may be made via the use of a suitable short timescale. In the following four chapters, we derive models for nonaxisymmetric viscous fibres and fully three-dimensional viscous sheets; for each we consider separately the cases where the dimensionless curvature is small and where the dimensionless curvature is of order one. We find that the models which result bear a marked similarity to the theories of elastic rods, plates and shells. In chapter 8 we explain in some detail why the Trouton ratio - the ratio between the extensional viscosity and the shear viscosity - is 3 for a slender viscous fibre and 4 for a slender viscous sheet. We draw our conclusions and suggest further work in the final chapter.
The place of lead in an Egyptian port city in the late period

This thesis analyses a range of lead objects discovered in Thonis-Heracleion, an Egyptian port city, and offers a new perspective on the use of metals in antiquity. It advances two central arguments: firstly, that the large quantity of lead artefacts in Thonis-Heracleion is not exceptional but rather a more accurate reflection of the metallisation of ancient societies and secondly, that the corpus of lead objects sheds light on aspects of ancient communities that normally remain invisible due to the ease of recycling and low cost of lead.
The first chapter reviews the presence of lead in the archaeological record in Egypt, the factors affecting its deposition and preservation, and the corpus as a whole from Thonis-Heracleion. A comparison between the two puts the lead from the site in a new Egyptian perspective. The second, third, and fourth chapters offer substantial analyses of lead ingots, weights, and containers found at Thonis-Heracleion with parallels from around the Mediterranean. The chapters show the potential of this corpus to shed light on activities in the Egyptian town despite the notable lack of direct parallels. It becomes clear for example that large lead objects appear earlier in the archaeological record and that the range of objects is wider than previously suspected. The analysis in these chapters offers a robust dating framework for lead objects previously unavailable.
Together the lead artefacts illustrate local mercantile activities, the economic role of the port city, and, through the identification of the first Athenian weights found in Egypt, trade connections between Egypt, Athens, and the rest of the Eastern Mediterranean. The result is an overview of lead in Egypt and its place in Thonis- Heracleion, demonstrating the significance of metals for understanding ancient societies.

Keywords: metal containers
ancient metrology
Egyptian archaeology
maritime archaeology
Late Period
lead (metal)
ingots
Advisor: Robinson, D
Britain's withdrawal from the Persian Gulf, 1964-1971

This thesis is about British disengagement from the southern coast of the Persian Gulf. Britain never had colonies in the region, but had held significant imperial sway over nine Protected States since the nineteenth century. The informal empire remained intact until the Labour government (1964-70) announced its intention to leave, in consequence of which Bahrain, Qatar and the United Arab Emirates became independent in 1971.
This thesis attempts three things. First, it draws on extensive archival research to provide the fullest possible account of British withdrawal: why it had to leave, how it did and what followed. The Gulf rulers wanted to maintain British protection for their own security, but Britain decided nonetheless on military retreat, because it needed to placate the domestic constituency in order to push forward the reversal of social reforms due to economic retrenchment. The Gulf rulers responded quickly, yet unsuccessfully, in deciding how many states would be formed as they achieve independence. It was only after the Gulf rulers and the British diplomats on the ground made late and mutually acceptable compromises about coming together that the nine Protected States became three new independent sovereign states. In the end, Britain was able to leave the Gulf peacefully, and the new states retained close relations with Britain.
Second, the study of an informal empire illuminates the enduring collaborative relationship between Britain and the Gulf rulers, characterised by the nominal sovereignty given to the Protected States. This relationship not only helped Britain maintain its imperial sway at little cost, but also made possible a peaceful withdrawal and the orderly emergence of the new states.
Third, this informal empire characterised by collaboration and nominal sovereignty laid the structural foundations for the later international society in the region – a point more generally telling for the study of international relations.

Keywords: sovereignty
map-making
Bahrain
United Arab Emirates
informal empire
collaboration
catography
Qatar
Persian Gulf
Advisor: Shlaim, A
Structural biology of IgG Fc glycoforms

The conserved N-linked glycosylation site on the Fc domain of IgG1 antibodies is essential for maintaining a functionally active conformation of the antibody. Different glycoforms of the Fc exhibit widely different effector functions. Similarly, therapeutic antibodies, with engineered glycosylation, exhibit altered binding to cellular Fc receptors (FcRs). Here, X-ray crystallographic structures were obtained for biosynthetic intermediate glycoforms of human IgG1 Fc bearing: unprocessed oligomannose-type, intermediate hybrid-type, and mature complex-type glycans. The fully processed Fc protein crystallised in an “open” conformation with glycans forming canonical stabilising interactions on the protein surface. Analysis of the biosynthetic intermediates revealed that these stabilising hydrophobic protein-glycan interactions are formed only after processing by Golgi -mannosidase II. Mutagenesis of hydrophobic residues on Fc disrupted crucial protein-glycan interactions resulting in the selective destabilization of the 3-arm of the glycan chain with the 6-arm closely matching that seen for the native structure. However, carbohydrate analysis of released glycans shows increased processing on both arms indicating a more accessible and flexible glycan in the mutant structure suggesting that the crystallographic structure of these antibody glycans represents a minor low-energy conformation. The importance of Fc glycosylation is highlighted by endoglycosidases which eliminate Fc effector function. The crystallographic structure of enzymatically deglycosylated IgG Fc revealed a significant collapse of the of Cγ2 domains resulting in a ‘closed’ quaternary conformation, incompatible with Fc receptor binding. This provides a structural explanation for immune deactivating properties of endoglycosidases including those under preclinical development for the treatment of antibody-mediated immune pathology. One such bacterial endoglycosidase, Endo S, was studied further and revealed a specificity for complex-type glycans of the type found on IgG but no hydrolytic activity towards an engineered IgG Fc with oligomannose-type glycans. Introduction of both the engineered monoclonal IgG and endoglycosidase in serum led to a dramatic increase in FcR binding as the competitive binding of serum IgG for FcRs was selectively eliminated. This approach is a general technique for boosting the effector signal of therapeutic antibodies.

Keywords: antibody glycoforms
antibody glycosylation
endoglycosidase S
monoclonal antibodies
Advisor: Scanlan, C
Wentworth, P
Magnetic transport and Bose-Einstein condensation of rubidium atoms

This thesis describes the design, construction and optimisation of a new apparatus to produce Bose-Einstein condensates (BECs) of 87Rb atoms. The main aim in building this system was to include a high resolution imaging system capable of resolving single atoms. Optical access for the imaging system was created by including a stage of atom transport in which the atoms are magnetically transferred ~50 cm from a magneto-optical trap (MOT), where they are initially collected, to a glass science cell where experiments are carried out and imaging takes place. Two magnetic transport schemes have been demonstrated, based on approaches first used in other laboratories. First, a scheme in which the atoms are transferred in a moving pair of magnetic trapping coils. Second, a hybrid scheme where the atoms are translated part of the distance in the moving coils, and the rest of the way by switching the current in a chain of fixed coils. This second scheme was designed to allow optical access for a high numerical aperture microscope objective to be placed immediately next to the science cell for high resolution imaging.
The atoms were first collected in a large pyramid MOT which can be loaded with 3 × 10^9 atoms in a time of 20 s. Around half of these atoms – those in the |F = 1, mF = −1> magnetic substate – were then magnetically trapped prior to transport. The typical fraction of the trapped atoms transferred to the science cell was ~30% and ~18% for the moving coils and hybrid schemes respectively.
Evaporative cooling was carried out on the atom cloud following transport with the moving coils and loading into a time-orbiting potential trap. The optimised cooling sequence lasted for 28 s and consistently produced a pure condensate with 5 × 10^5 atoms. A BEC has also been produced by evaporative cooling following hybrid transport. The next experimental steps will be to optimise the hybrid transfer approach further and install the high resolution imaging system.
The system is well-placed to continue an ongoing series of experiments in which ultracold atoms are trapped in RF-dressed potentials. These potentials will be used to study low-dimensional quantum gases as well as in experiments where small atom number BECs are rapidly rotated to enter the fractional quantum Hall regime.

Keywords: Bose-Einstein Condensation
Magnetic transport
RF-dressed potentials
Rubidium
Advisor: Foot, C
Electronic structure of TiO2-based photocatalysts active under visible light

This thesis is concerned with furthering our understanding of the basis of visible region photocatalytic activity exhibited by doped TiO2-based materials. A range of experimental techniques including high resolution X-ray photoemission spectroscopy and diffuse reflectance spectroscopy are used to investigate electronic structure and an attempt is made to link these results to the observed photocatalytic activity. Both anionic (N) and cationic (Rh and Sn) dopants are investigated. [See pdf file for full abstract].

Keywords: photocatalysis
doping
x-ray photoelectron spectroscopy
Advisor: Egdell, R
Some topics in the theory of finite groups

A regular 2-graph consists of a set andOmega; together with a (non-empty) set t of three-element subsets of andOmega; such that any two-element subset of andOmega; is contained in the same number of elements of t, any four-element subset of andOmega; contains an even number of elements of t and not every three-element subset of andOmega; is in t. These objects were introduced by G.andnbsp;Higman who used a regular 2-graph with 276 points to provide a combinatorial setting for the doubly transitive representation of Conway's sporadic simple group C3.
In this thesis it is shown that regular 2-graphs are in one-one correspondence with equivalence classes of strong graphs (as defined by J.J.andnbsp;Seidel). Moreover, for each point of a regular 2-graph there is a natural way of defining a strongly regular graph on the remaining points. These graphical representations are used to obtain restrictions on the structure and on the parameters of a regular 2-graph. It is also possible, via the strong graphs, to represent a regular 2-graph as a configuration of equiangular lines in Euclidean space. Conversely, results about regular 2-graphs obtained in this thesis extend the results of J.J.andnbsp;Seidel on equiangular lines.
Regular 2-graphs are constructed which admit the PSL(2,q) , qandequiv;l (mod 4), Sp(2m,2), in both doubly transitive representations; PSU(3,q2), q odd; all groups of Ree type together with 2G2(3) = Aut(PSL(2,8)); the sporadic simple groups C3 and HiS; the group V.Sp(2m,2) which is the semi-direct product of the group V of translations of a vector space of dimension 2m over the field GF(2) by Sp(2m,2). By studying the centraliser ring of a monomial representation associated with the doubly transitive representation it is shown that (with the possible exception of some groups with a regular normal subgroup) the above groups are the only known groups which can act as doubly transitive groups of automorphisms of a regular 2-graph.

Advisor: Higman, G