VictorJuiz/thesis huggingface dataset:
T-cell receptor (TCR) usage in HIV-2 infection
Keywords: cytotoxic T-cells
HIV/AIDS
CD8+ T-cells
HIV-2

Long-term non-progressors (LTPNs) in HIV infection target the structural protein Gag more frequently than individuals who progress to disease. However, the targeting of Gag per se does not always distinguish these two groups. Various factors have been put forth as likely explanations for this discrepancy including differences in the breadth and magnitude of observed responses, the HLA type of the host, the nature of the individual epitopes targeted and the ability of the virus to mutate these antigenic regions.
The purpose of this thesis was to examine, using PBMCs isolated from HIV-2 infected LTNPs and CTL clones established in vitro, the clonotypic architecture and quality of an immunodominant HIV-2 Gag-specific response directed towards the HLA-B*3501-restricted epitope NPVPVGNIY (NY9: Gag245-253). The data presented in this thesis show that in spite of the expression of multiple inhibitory receptors on the surface of NY9-specific CD8+ T-cells, the NY9-response, which is a clonotypically 'private' response, bears a signature characterised by an increased cytotoxic sensitivity and the production of an array of cytokines, most notably IFN-γ and MIP-1β. Moreover, the results of this thesis indicate that the NY9-specific CD8+ T-cells are able to cross-recognise and lyse target B-cells pulsed with the corresponding HIV epitope PY9 and its variants at functional avidities (EC50) that are close to those exhibited by PY9-specific T-cells. However, not all mobilised TCR clonotypes are equally sensitive or equally cross-reactive. When individual CTL clones were studied it emerged that dominant clonotypes within the NY9-specific CD8+ T-cell memory pool possessed a higher avidity for tetramer and sensitivity for antigen than subdominant ones and demonstrated a better cross-reactive potential towards variants of the HIV-2 epitope.
Hence, future HIV vaccine strategies may benefit from the inclusion of epitopes like NY9, the presentation of which appears to mobilise CD8+ T-cells with superior functional profiles.
Decision making, the frontal lobes and foraging behaviour
Keywords: human foraging
decision making
frontal lobes

The aim of this thesis was to understand the function of the frontal lobes during different types of decisions thusfar mostly neglected in cognitive neuroscience. Namely, I sought to understand how decisions are made when comparisons are not about a simple set of concrete options presented, but rather require a comparison with one specific encounter and a sense of the value of the current environment (Chapter 2-3). Additionally, I wanted to understand how decisions between concrete options can be contextualized by the current environment to allow considerations about changing environmental constraints to factor into the decision making process (Chapter 4-5). At last, I wanted to test how the potential for future behaviours within an environment has an effect on peoples decisions (Chapter 6). In other words, how do people construct prospective value when it requires a sense of own future behaviours? All this work was informed by concepts and models originating from optimal foraging theory, which seeks to understand animal behaviours using computational models for different ecological types of choices. Thus, this thesis offers a perspective on the neural mechanisms underlying human decision making capacities that relates them to common problems faced by animals and presumably humans in ecological environments (Chapter 1 and 7). As optimal foraging theory assumes that solving these problems efficiently is highly relevant for survival, it is possible that neural structures evolved in ways to particularly accommodate for the solution of those problems. Therefore, different prefrontal structures might be dedicated to unique ways of solving ecological kinds of decision problems. My thesis as a whole gives some evidence for such a perspective, as dACC and vmPFC were repeatedly identified as constituting unique systems for evaluation according to different reference frames. Their competition within a wider network of areas appeared to ultimately drive decisions under changing contexts. In the future, a better understanding of those changing interactions between these prefrontal areas which generate more complex and adaptive behaviours, will be crucial for understanding more natural choice behaviours. For this temporally resolved neural measurements as well as causal interference will be essential.
The length of conjugators in solvable groups and lattices of semisimple Lie groups
Keywords: solvable groups
geometric group theory
conjugacy problem
semisimple Lie groups
lattices

The conjugacy length function of a group Γ determines, for a given a pair of conjugate elements u,v ∈ Γ, an upper bound for the shortest γ in Γ such that uγ = γv, relative to the lengths of u and v. This thesis focuses on estimating the conjugacy length function in certain finitely generated groups.
We first look at a collection of solvable groups. We see how the lamplighter groups have a linear conjugacy length function; we find a cubic upper bound for free solvable groups; for solvable Baumslag--Solitar groups it is linear, while for a larger family of abelian-by-cyclic groups we get either a linear or exponential upper bound; also we show that for certain polycyclic metabelian groups it is at most exponential. We also investigate how taking a wreath product effects conjugacy length, as well as other group extensions.
The Magnus embedding is an important tool in the study of free solvable groups. It embeds a free solvable group into a wreath product of a free abelian group and a free solvable group of shorter derived length. Within this thesis we show that the Magnus embedding is a quasi-isometric embedding. This result is not only used for obtaining an upper bound on the conjugacy length function of free solvable groups, but also for giving a lower bound for their Lp compression exponents.
Conjugacy length is also studied between certain types of elements in lattices of higher-rank semisimple real Lie groups. In particular we obtain linear upper bounds for the length of a conjugator from the ambient Lie group within certain families of real hyperbolic elements and unipotent elements. For the former we use the geometry of the associated symmetric space, while for the latter algebraic techniques are employed.
Velocity mapping of elementary bimolecular reactions
Keywords: velocity map ion imaging
molecular dynamics

A new and flexible velocity-map ion imaging apparatus, designed for the study of photodissociation processes and photon-initiated bimolecular reactions in a single molecular beam, has been constructed, developed and characterised. An image Legendre moment fitting analysis was developed to allow recovery of centre-of-mass (CM) angular scattering and kinetic energy release distributions from velocity-map ion images of the products of photon-initiated bimolecular reactions.
The Legendre moment analysis methodology has been applied to images of the HCl(v' = 0,j' = 0-6) products of the reactions of Cl(²P3/2) atoms with ethane and n-butane at collision energies of 0.24 eV and 0.32 eV respectively. The Cl(²P3/2) reactants were generated by polarised laser photodissociation of Cl₂ at 355 nm. For reaction with ethane, the CM angular scattering distributions show a steady trend from forward scattering at low j' to more isotropic, but backward peaking, scattering at high j'. An impact parameter-based mechanism is proposed to account for the observed dynamics. Abstraction of a hydrogen atom from a primary carbon site in n-butane is seen to produce rotationally very cold HCl products that are forward scattered, whereas H atom abstraction from a secondary carbon site in n-butane yields more isotropically scattered HCl products formed with higher rotational excitation. A peripheral mechanism is proposed to operate for the primary abstraction channel, whilst a more rebound type mechanism is seen to account for the dynamics of the secondary abstraction channel. Around 22% and 30% of the available energy is found in internal modes of the alkyl radical co-products of the Cl + C₂H₆ and Cl + n-C₄H₁₀ reactions respectively. Possible sources of alkyl co-product excitation are discussed in each case.
The hydrogen or deuterium atom abstraction reactions of Cl(²P3/2) with CH₄, CD₄ and CH₃D, have been studied at mean collision energies around 0.3 eV. Chlorine atom reactants were generated by polarised laser photodissociation of Cl₂ at 308 nm. The methyl radical products were detected using (2+1) resonance-enhanced multi-photon ionisation, coupled with velocity-map ion imaging. The laboratory frame speed distributions obtained from the images are in excellent agreement with previous work. The interpretation of the experiments is shown to be very sensitive to assumptions made about the reactant velocity distributions. If these are assumed to be narrow, the data are seen to suggest that a significant fraction of the product signal must arise from the reaction of Cl with vibrationally excited methane reactants. This conclusion is in agreement with previous photon-initiated reaction studies. However, by allowing for the spread in collision energies in the molecular beam, it is shown that it is possible to fit the data sensibly assuming reaction with vibrational ground state methane alone. CM angular scattering distributions thereby derived are presented for all three reactions.
What is the nature of authoritarian regimes?: responsive authoritarianism in China
Keywords: public service provision
autocracy
fiscal transfers
China
legitimacy

This work proposes a new theory of authoritarian regimes: responsive authoritarianism. Most existing theories of autocracies take as their point of departure elite politics or the state’s repressive apparatus to explain the rise and fall of regimes. I argue that, for many states, regimes also have to consider the consent of the governed when designing policies.
Specifically, when regime legitimacy is low but the central leadership maintains a long time horizon, autocratic regimes are predicted to become more responsive to the needs of citizens. This theory is tested against a number of aspects of the Chinese fiscal system dealing with public goods provision during the period of 2002-2011 and generally finds in favor of the theory. Chapter 4 tests the fiscal transfer system, Chapter 5 tests the fiscal expenditure data, and Chapter 6 tests data on the results of the transfer and expenditure data: actual public goods provision.
This theory has a number of implications that suggest that scholars begin to rethink how they conceptualize power dynamics within an authoritarian regime, in particular paying closer attention to the relationship between the ruler(s) and the ruled. It suggests that, at least in the political science literature, power be returned to the people.
Usability and security of human-interactive security protocols
Keywords: human-computer interaction
security protocols
mobile device interactions
usable security

We investigate the security and usability of Human-Interactive Security Protocols (HISPs); specifically, how digests of 4 or more digits can be compared between two or more sys- tems as conveniently as possible while ensuring that issues such as user complacency do not compromise security. We address the research question: given different association scenarios and modes of authentication in HISPs, how can we improve on existing, or design new, empirical channels that suit human and contextual needs to achieve acceptable effective security? We review the literature of HISPs, proposed empirical channels,and usability studies of HISPs; we follow by presenting the methodology of the research reported in this thesis. We then make a number of contributions discussing the effectiveness of empirical channels and address the design, analysis, and evaluation of these channels. In Chapter 4 we present a user study of pairwise device associations and discuss the factors affecting effective security of empirical channels in single-user scenarios. In Chapter 5 we present a user study of group device associations and discuss the factors affecting effective security of empirical channels in multi-user scenarios. In Chapter 7 we present a framework designed for researchers and system designers to reason about empirical channels in HISPs. The framework is grounded in experimental data, related research, and validated by experts. In Chapter 8 we present a methodology for analysing and evaluating the security and usability of HISPs. We validate the methodology by applying it in laboratory experiments of HISPs. Finally, in Chapter 6 we present a set of principles for designing secure and usable empirical channels. We demonstrate the effectiveness of these principles by proposing new empirical channels.
The role of primary auditory cortex in sound localisation
Keywords: sound localisation
primary auditory cortex

This thesis investigates the involvement of primary auditory cortex (A1) in sound localisation. Experiments were carried out both to assess the effect of A1 inactivation on sound localisation, and to measure the sensitivity of single A1 neurons to sound source location.
Ferrets were trained to localise bursts of broadband noise, of varying intensity and duration, from an array of loudspeakers that spanned 360 degrees in azimuth. Bilateral A1 inactivation caused an impairment on this task, but only for short-duration stimuli. Unilateral A1 inactivation also resulted in an impairment for short-duration stimuli, but this was limited to the side of space contralateral to the inactivation, and was only seen in animals which had been highly trained prior to surgery. A feature of the impairment in all animals was the increased number of "front-back confusions", where the animal's response was on the correct side of the midline but the wrong side of the interaural axis.
Recordings from ferret A1 showed that the firing rate of individual neurons varied little as sound source location was changed. Further, the neurons' location sensitivity was affected by changes in stimulus intensity and duration. However, mathematical techniques were used to measure the information these neurons provided about sound source location, and it was found that this information was not sensitive to intensity or duration changes. The analysis also showed that the amount of information provided by response latency was greater than that carried by firing rate. Similar mathematical treatment tentatively suggested that the information from different neurons was only slightly redundant, so it may be possible to account for whole-animal localisation performance by assuming that the output of large numbers of neurons is considered.
It is concluded that A1 is involved in processing the location of sound sources, but it seems unlikely that sound localisation is A1's primary or only role within the auditory system.
The influence of anxiety: re-presentations of identity in Antiguan literature from 1890 to the present
Keywords: Caribbean calypso
Caribbean protest literature
Jamaica Kincaid
gender
race
Caribbean oral traditions
small-island literature
Antigua
Antiguan literature
class relations
Caribbean literary traditions
Caribbean literature

This thesis examines Antiguan narratives’ peculiar engagements with the national question. It draws largely upon the works of four writers—Jamaica Kincaid, Joanne C. Hillhouse, Marie-Elena John and Frieda Cassin—and selected calypsonians including Antigua’s leading female and male calypsonians, Queen Ivena and King Short Shirt. It reads anxiety as the chief organising principle of the singular deconstructions of gender, ‘racial’, ethnic, and class identities undertaken by these texts. I offer a retooled account of anxiety that elaborates the local/regional concept of bad-mindedness informing the core of the narratives’ deconstructive and recuperative projects.
Chapter one probes the bad-minded delimiting of Antiguan literary production. It interrogates the singular cohesive Caribbean canon typically suggested by critical readings, which obscure the narratives/ literary traditions of smaller territories such as Antigua. It also highlights locally produced canons’ intervention into the dominant canons/maps of Caribbean literary traditions. Its discussion is underpinned by the concept of bad-mindedness which I use to frame the evils that locate the smaller territory and its inhabitants at the cultural periphery
.
Chapter two examines the texts’ enunciations of the bad-mindedness inherent in the construction of the composite gendered identities of 19th century Creole women, 20th century working-class Afro-Antiguan women and men, and 20th century proletarian Carib women. It refashions Erna Brodber’s kumbla trope, Kenneth Ramchand’s notion of terrified consciousness, and Jamaica Kincaid’s line trope to elaborate these enunciations.
Chapter three examines Antiguan calypsos’ record of the peculiar responses of small-islanders to their subordinate position within the ‘global village’ and continuing entanglement in British colonialism and neo-colonial relationships and processes. It draws upon Charles Mill’s theory of smadditization/ smadditizin’ or the Afro-Caribbean struggle for recognition of personhood and Paget Henry’s account of the dependency theory to analyse the calypsos’ anxious insistence upon Afro-Antiguan personhood.
The primary conclusion of my thesis is that an engagement with the neglected literary traditions of the smaller territories and national literatures on the whole, is likely to excavate a cornucopia of currently sidelined experiences, issues, and transnational relationships which can only serve to enrich our postcolonial conversations.
Logical aspects of quantum computation
Keywords: coalgebra
string diagram
logic
category theory
quantum computation

A fundamental component of theoretical computer science is the application of logic. Logic provides the formalisms by which we can model and reason about computational questions, and novel computational features provide new directions for the development of logic. From this perspective, the unusual features of quantum computation present both challenges and opportunities for computer science. Our existing logical techniques must be extended and adapted to appropriately model quantum phenomena, stimulating many new theoretical developments. At the same time, tools developed with quantum applications in mind often prove effective in other areas of logic and computer science. In this thesis we explore logical aspects of this fruitful source of ideas, with category theory as our unifying framework.
Inspired by the success of diagrammatic techniques in quantum foundations, we begin by demonstrating the effectiveness of string diagrams for practical calculations in category theory. We proceed by example, developing graphical formulations of the definitions and proofs of many topics in elementary category theory, such as adjunctions, monads, distributive laws, representable functors and limits and colimits. We contend that these tools are particularly suitable for calculations in the field of coalgebra, and continue to demonstrate the use of string diagrams in the remainder of the thesis.
Our coalgebraic studies commence in chapter 3, in which we present an elementary formulation of a representation result for the unitary transformations, following work developed in a fibrational setting in [Abramsky, 2010]. That paper raises the question of what a suitable "fibred coalgebraic logic" would be. This question is the starting point for our work in chapter 5, in which we introduce a parameterized, duality based frame- work for coalgebraic logic. We show sufficient conditions under which dual adjunctions and equivalences can be lifted to fibrations of (co)algebras. We also prove that the semantics of these logics satisfy certain "institution conditions" providing harmony between syntactic and semantic transformations.
We conclude by studying the impact of parameterization on another logical aspect of coalgebras, in which certain fibrations of predicates can be seen as generalized invariants. Our focus is on the lifting of coalgebra structure along a fibration from the base category to an associated total category of predicates. We show that given a suitable parameterized generalization of the usual liftings of signature functors, this induces a "fibration of fibrations" capturing the relationship between the two different axes of variation.
The impact of implied constitutional principles on fundamental rights adjudication in common law jurisdictions
Keywords: common law
constitutional principles
human rights
implied principles
constitutional law

This thesis explores the roles played by implied constitutional principles in fundamental rights cases in the common law jurisdictions of Canada, Australia, the Commonwealth Caribbean, and the United Kingdom. The two principles selected for this research are the separation of powers and the rule of law, both of which are relied upon in courts in common law states. The thesis examines the types of cases in which such principles are used, the possible reasons for the appeal of these principles, and the functions that they play in fundamental rights adjudication.
The thesis begins with a brief discussion of the applications of the rule of law and the separation of powers, outlining the content of these principles as applied by the courts. However, the bulk of the analysis throughout the thesis is concerned with a thematic study of the functions played by the principles. It is argued that the principles are used as interpretative aids, as independent grounds for invalidating legislation, and as gateways to comparative legal analysis. The thesis ends by showing the necessary preliminary work that must be undertaken in order to engage in a thorough normative analysis of the use of implied principles in rights adjudication.
Throughout the thesis, several themes are identified as key to our understanding of the functions played by implied principles in the cases discussed. One such theme is legitimization, specifically the role the principles play in the attempt to legitimize arguments, state institutions (particularly the courts), and the state itself. The theme of institutional self-protection also arises; it is evident in the use of principles to protect the jurisdictional sphere of the courts. The analysis of the operation of implied constitutional principles also highlights the legacy of Empire and the deployment of traditional principles to signal the maintenance of democratic traditions and institutions.
Background rejection for the neutrinoless double beta decay experiment SNO+
Keywords: SNO+ Neutrino

The SNO+ experiment will use a liquid scintillator based detector to study solar, geo, and reactor neutrinos and double beta decay. This thesis discusses the effect of backgrounds on the measurement of neutrinoless double beta decay and describes analysis techniques developed to reduce their impact.
Details of the modeling of the photomultiplier tubes in the SNO+ Monte Carlo RAT are first described and comparisons are made with the SNO Monte Carlo SNOMAN. SNOMAN has been extensively verified with calibration sources and RAT is shown to be in good agreement. The event reconstruction techniques are then presented and predict an achievable 15cm position and 7% energy resolution.
The backgrounds are discussed and pileup backgrounds identified, including many previous unknown pileup backgrounds. Techniques to reject the pileup background are presented and shown to give over 99% rejection in the region of the double beta decay end point (3-4MeV), below the irreducible background from solar neutrinos. Finally the resulting limit on the effective Majorana neutrino mass SNO+ could achieve in 2015 is predicted to be 270meV and this is compared with other experiments that are underway.