VictorJuiz/thesis huggingface dataset:
Of friendship and hospitality: Victorian women’s travel writing on Meiji Japan

This thesis explores the possibility and challenges of international/interracial female friendship and anti-communitarian hospitality through writings of Victorian female travellers to Meiji Japan between 1854 and 1918. It features three travellers, viz. Isabella Bird, Mary Crawford Fraser, and Marie Stopes.
The introduction delineates the context of key events in the Anglo-Japanese relationship and explores the representation of Japan in Victorian travelogues and literary works.
Chapter I considers the philosophical dialogue between Jean-Luc Nancy, Maurice Blanchot, and Jacques Derrida on community, friendship, and hospitality. It demonstrates the potential of applying their thinking, notwithstanding its occasional complicity, to an analysis of the place of hitherto marginalised groups, women and foreigners, in Western philosophical models.
Chapter II examines relationships between Bird and Japanese natives, especially her interpreter, Ito in Unbeaten Tracks in Japan (1880) in terms of questions of stable identity and translation. It further undertakes a comparative study between the travelogue and Itō no koi (2005) by Nakajima Kyōko. I explore the afterlife of Bird in Japanese literature.
Chapter III investigates friendships in Fraser’s A Diplomatist’s Wife in Japan (1898). It uncovers her connection with Japanese female writers in oblivion, Yei Theodra Ozaki and Wakamatsu Shizuko. I discuss the influence her friendships had on Fraser’s fictional works such as The Stolen Emperor (1903), especially on the fair portrayals of Japanese women.
Chapter IV explores friendships between the sexes in Stopes’ A Journal from Japan (1910) and articulates its relationship with Love-Letters of a Japanese (1911) and Plays of Old Japan (1913). I examine Stopes’ romantic relationship with Fujī Kenjirō and its influence on her career in sexology. It also investigates Stopes’ collaboration with Sakurai Jōji on Nō translation and exposes complex gender, racial, and linguistic politics.
The conclusion explores three Japanese female travellers to Victorian Britain, focusing on their contact with local women. It considers Tsuda Umeko’s Journal in London, Yasui Tetsu’s Wakakihi no ato, and Yosano Akiko’s Pari yori (1914).

Keywords: Postcolonialism
Victorian Literature
Travel Writing
Victorian Female Travellers
Politics of Friendship
Japonisme in Victorian Britain
Representation of Japan
Advisor: Mukherjee, A
Nuclear structure, nuclear reaction

In this thesis, particle- particle angular correlations for reactions in non-zero degree geometry and with non-zero spin nuclei are performed and found to be a valuable tool for spin determination, (d-α) angular correlations in the reaction process 14N(6Li,d)18F* (α)14N are measured for three high excited states in 18F with a 6Li beam of 36MeV. Spins and parities for two of the observed states are determined, and in agreement with theoretical predictions, these states are suggested as members of the Kπ=1+ α-rotational band. The three analysed 9.58MeV 6+, 11.2MeV, 14.1MeV 8+ states are found to undergo a predominant α-particle decay to the ground state of 14N. Gamow unbound formalism is carried out for the state descriptions. Angular distributions are measured and analysed under Hauser Feshbach and exact finite range DWBA formalisms. Spectroscopic factors are extracted and compared to shell model predictions, showing a reasonable agreement.
(3He-α) and (t-α) angular correlations for the reaction processes 14N(6Li,3He)170* (α)13C and 14N(6Li,t)17F* (α)13N respectively are measured at 36MeV of 6Li. High selectivity is observed for the three particle transfer processes and percentages of the different particle decays for the high populated states are presented. Structureless angular correlations hinder definite spin and parity assignements, but the displacement of the preferred direction observed in the pattern decay gives some information on the range of plausible angular momenta. Shell model calculations are performed for comparison with the experimental data, and this allows tentative spin identifications. EFR EWEA calculations are carried out, providing some confirmation on the spin suggestions. Useful nuclear structure information is obtained for the mass 17 and 18 nuclear states.
The particle-particle angular correlation expression for a process where a direct reaction mechanism is involved is reviewed, programmed and used for obtaining the theoretical predictions to be compared to the experimental results.

Advisor: Sinclair, D
The Structural Basis of the Disabling of the Actin Polymerization Machinery by Yersinia

Yersinia pestis is a human pathogen and the causative agent of bubonic plague, responsible for causing three massive pandemics, resulting in hundreds of millions of deaths in the 14th century alone. Yersinia’s virulence stems from its ability to overcome host immune defences by the injection of six Yersinia outer proteins (Yops) into the host cells via its Type III secretion system. One of these Yops, YopO specifically disables the actin polymerization machinery, leading to the crippling of phagocytosis. YopO consists of a GDI domain which sequesters Rac and Rho, and a kinase domain, the activity of which is dependent on host actin. Little is known about the targets of the kinase domain and the mechanism of function of YopO remains incomplete.
In this work, YopO was crystallized in complex with actin, revealing that YopO binds to actin on subdomain 4, away from the 'hotspot’ between subdomains 1 and 3 which is involved in binding most actin-binding proteins. The structure reveals how recruitment of YopO-bound actin monomers stalls actin polymerization by steric hindrance. The structure also demonstrates how YopO uses actin for self-activation and suggests that actin is being used by YopO as bait for recruitment into actin machineries. Using SILAC mass spectrometry, actin cytoskeletal machineries within macrophages that recruit YopO are identified and these include, amongst others: VASP family proteins, gelsolin family proteins, formins and WASP. Of these, VASP, EVL, diaphanous1, WASP and gelsolin have been identified to be phosphorylated by YopO and were validated by in vitro phosphorylation. This work demonstrates that YopO uses actin as a scaffold for selection of kinase substrates, enabling targeted phosphorylation of the actin machinery and provides insight into the regulation of the actin cytoskeleton by phosphorylation under non-pathogenic conditions.

Keywords: actin cytoskeleton
plague
Yersinia
Structural biology
actin
Advisor: Grimes, J
Robinson, R
Cytotoxic T-Cells in HIV-1: "The Good" and "The Bad"

CD8+ T-cell antigen sensitivity is critical for optimal control of persistent viral infections, including HIV-1. The devastating HIV-1 pandemic may be countered by development of a cytotoxic T lymphocyte based vaccine if qualities associated with protection can be defined at the molecular level. However, the heterogeneity of the total viral-specific CTL response confounds identification of protective correlates and T-cell sensitivity is no exception and remains controversial. To address this issue we reduced the heterogeneity of the HIV-1 CTL response to single units, generating 19 CTL clones that recognise the same HIV-1 derived epitope restricted by HLA B*08. Correlation of functional assays directly with the ability of each clone to control HIV-1 replication in vitro, the “viral suppression assay,” identified antigen sensitivity as a key quality for anti-viral efficacy. Remarkably, four clones from this panel, isolated from one individual, a long-term non-progressor, all used an identical TCR yet had distinct antigen sensitivity and suppressive activity. Two of these clones were characterised in detail, and had distinct cytokine profiles, regulated by epigenetic mechanisms, and differential expression of a group of cell surface receptors with the potential to modulate the signalling threshold to antigen. Expression of the TNFα locus of the high sensitivity clone with “Good” suppression was repressed by DNA methylation. Understanding how CTL qualities required for optimal control of HIV-1 replication differentiate and are then enriched in the total CTL response, and if repression of TNFα contributes to this process, will contribute to rational vaccine design. This is the first evidence that avidity maturation in CD8+ T cells with the same TCR affinity occurs in viral infections in humans as reported in the mouse. This suggests the induction of high sensitivity CTL will be critical for an effective HIV-1 vaccine, but offers hope that this can be achieved even in individuals without protective HLA alleles, by further exploration of peripheral avidity maturation and epigenetic regulation of the HIV-1 specific CD8+ T-cell response.

Keywords: antigen sensitivity
HIV
cytotoxic T-cells
Advisor: McMichael, A
Dong, T
Bubbles: sensors for the micro world

It has been proposed that coated gas microbubbles, currently used as ultrasound contrast agents could also be used as microscale sensors due to the sensitivity of their acoustic response to changes in their environment. However, their behaviour is not fully understood and there remains considerable scope for improving their characterisation. The aim of this thesis is to improve the theoretical description of microbubble dynamics under ultrasound excitation with the ultimate aim of assessing the regimes in which they could be exploited most effectively as sensors.
Previous theoretical and experimental work relating to the confinement and acoustic excitation of microbubbles is reviewed. Specifically, optical trapping as a method for the isolation and manipulation of individual bubbles is studied for use in developing a sensor. An assessment of the existing models’ validity is undertaken. This is followed by the development of models for optical trapping of single microbubbles, and the coupled radial and translational motion of a microbubble under ultrasound excitation, which includes time dependent phenomena. The latter model is used to perform a sensitivity analysis to determine the uncertainty associated with using microbubbles as sensors. The potential for uniquely characterising the shell of the microbubble from experimental data is also assessed.
Subsequent chapters present the results from a combination of computer simulations and experimental data, used to develop and assess the validity of the new models for describing microbubble behaviour. Particularly, the model is used to simulate the response of a dilute suspension of microbubbles undergoing large amplitude oscillations and single microbubbles undergoing lipid shedding. The optimal regimes in which microbubbles may be utilised as sensors for liquid physical properties and local pressure variations are then assessed. Finally, a summary of the conclusions and areas for further work is presented.

Keywords: low-index optical trapping
microbubble
ultrasound
Advisor: Stride, E
Calix[4]arene transition metal and crown ether based anion and ion-pair receptors

The aim of this thesis is to develop novel receptors for the recognition of anions and ion-pairs. The guest binding and sensing properties of the receptors are studied by spectroscopic and electrochemical techniques. The ion-pair receptors described herein incorporate amide or urea functionalities for anion binding and crown ether moieties for alkali metal cation complexation. In addition, many receptors contain redox- and/or photo-active groups capable of sensing guest binding events.
Chapter One introduces the field of supramolecular chemistry. A review of synthetic cation, anion and ion-pair receptors reported in the literature is undertaken, and the formation of selfassembled architectures is discussed.
Chapter Two details the synthesis and study of a range of new upper-rim functionalised calix[4]arene anion and ion-pair receptors. The anion and ion-pair binding and sensing properties of the receptors are investigated by ¹H NMR spectroscopy, electrochemistry and luminescence spectroscopy. Two ion-pair receptors display a positive cooperative ion-pair effect, whereby the presence of potassium cations causes an enhancement in the strength of anion binding via electrostatic interactions and conformational effects.
Chapter Three centres on ion-pair receptors incorporating an azacrown group for alkali metal cation complexation together with amide functionalities for anion binding. Receptors containing either ferrocene or transition metal dithiocarbamate groups are capable of electrochemically and/or optically sensing the binding of anionic guests.
Chapter Four describes disulphide-appended receptors designed for self-assembly onto gold surfaces. A ferrocene- and disulphide-appended calix[4]arene receptor incorporating hydrogen bonding moieties forms self-assembled monolayers on gold electrodes which exhibit a surface sensing amplification in the electrochemical recognition of anions. In addition, the assembly of receptors onto gold nanoparticles is explored with the aim of producing UV-VIS spectroscopic sensors for guest binding.
Chapter Five reports the experimental procedures and characterisation for all products. The Appendices provide information on experimental techniques, list the crystallographic data and summarise all the receptors studied.

Advisor: Beer, P
Trees and graphs: congestion, polynomials and reconstruction

Spanning tree congestion was defined by Ostrovskii (2004) as a measure of how well a network can perform if only minimal connection can be maintained. We compute the parameter for several families of graphs. In particular, by partitioning a hypercube into pieces with almost optimal edge-boundaries, we give tight estimates of the parameter thereby disproving a conjecture of Hruska (2008). For a typical random graph, the parameter exhibits a zigzag behaviour reflecting the feature that it is not monotone in the number of edges. This motivates the study of the most congested graphs where we show that any graph is close to a graph with small congestion.
Next, we enumerate independent sets. Using the independent set polynomial, we compute the extrema of averages in trees and graphs. Furthermore, we consider inverse problems among trees and resolve a conjecture of Wagner (2009). A result in a more general setting is also proved which answers a question of Alon, Haber and Krivelevich (2011).
After briefly considering polynomial invariants of general graphs, we specialize into trees. Three levels of tree distinguishing power are exhibited. We show that polynomials which do not distinguish rooted trees define typically exponentially large equivalence classes. On the other hand, we prove that the rooted Ising polynomial distinguishes rooted trees and that the Negami polynomial determines the subtree polynomial, strengthening results of Bollobás and Riordan (2000) and Martin, Morin and Wagner (2008). The top level consists of the chromatic symmetric function and it is proved to be a complete invariant for caterpillars.

Keywords: partition function
spanning tree congestion
reconstruction
regularity lemma
random graphs
inverse problems
Advisor: Scott, A
Genetic analyses of MAP kinase signalling in mouse gonad development

Sexual development begins with the process by which the bipotential gonads of the embryonic urogenital ridge develop into either testes or ovaries. In the mouse, sex determination occurs at around 11.5 dpc and depends on the presence or absence of the Y chromosome and the associated activity of the testis-determining gene, Sry, in supporting cell precursors. The mutually antagonistic male and female developmental pathways are regulated by many cellular and molecular processes, disruption of which can lead to disorders of sex development (DSDs). However, many of the molecular mechanisms regulating the differentiation of the two gonads are still unknown.
The boygirl (byg) mutant was identified in an ENU-based forward genetic screen for embryos with gonadal abnormalities. On the C57BL/6J background, XY byg/byg homozygotes exhibited complete embryonic gonadal sex reversal. The defective gene in byg, Map3k4, is a component of the mitogen-activated protein (MAP) kinase signalling pathway and provides the first evidence for a function of this pathway in sex determination.
This thesis describes experiments aimed at investigating the cellular and molecular basis of the sex reversal phenotype associated with the XY Map3k4byg/byg mutant. Cellular characterisations revealed a defect in male-specific proliferation at 11.5 dpc, which was attributed to a defect in Sry up-regulation. Elucidation of the downstream kinases activated by MAP3K4 during sex determination was attempted, with particular focus on identifying a role for p38α MAP kinase (MAPK). Using a conditional knockout approach, the function of p38α in Steroidogenic factor-1 (Sf1)-positive somatic cells was assessed. However, specific inactivation in these cells did not affect gonad development. Conditional inactivation of Map3k4 itself in these Sf1¬-positive cells also did not disrupt gonad development, suggesting that this pathway is either initiated in a different cell lineage or at an earlier stage than deletion driven by Sf1-Cre can disrupt. Conditional inactivation of p38α in the Müllerian duct mesenchyme and ovarian granulosa cells using Amhr2-Cre did reveal a function for p38α in female fertility, but did not disrupt embryonic sexual development. Gene knockdown in organ culture was attempted to determine a role for multiple p38 MAPKs in all cell types of the gonad. Therefore, this thesis details further characterisations of a novel signalling pathway important for the expression of Sry, focussing on the role of the p38 MAPKs.

Keywords: testis determination
mouse
sexual development
mammalian sex determination
p38 MAPK
MAPK signalling
Advisor: Greenfield, A
Pears, C
Topological phases of matter, symmetries, and K-theory

This thesis contains a study of topological phases of matter, with a strong emphasis on symmetry as a unifying theme. We take the point of view that the "topology" in many examples of what is loosely termed "topological matter", has its origin in the symmetry data of the system in question. From the fundamental work of Wigner, we know that topology resides not only in the group of symmetries, but also in the cohomological data of projective unitary-antiunitary representations. Furthermore, recent ideas from condensed matter physics highlight the fundamental role of charge-conjugation symmetry. With these as physical motivation, we propose to study the topological features of gapped phases of free fermions through a Ζ2-graded C*-algebra encoding the symmetry data of their dynamics.
In particular, each combination of time reversal and charge conjugation symmetries can be associated with a Clifford algebra. K-theory is intimately related to topology, representation theory, Clifford algebras, and Ζ2-gradings, so it presents itself as a powerful tool for studying gapped topological phases. Our basic strategy is to use various K-theoretic invariants of the symmetry algebra to classify symmetry-compatible gapped phases. The super-representation group of the algebra classifies such gapped phases, while its K-theoretic difference-group classifies the obstructions in passing between two such phases. Our approach is a noncommutative version of the twisted K-theory approach of Freed--Moore, and generalises the K-theoretic classification first suggested by Kitaev. It has the advantage of conceptual simplicity in its uniform treatment of all symmetries. Physically, it encompasses phenomena which require noncommutative algebras in their description; mathematically, it clarifies and provides rigour to the meaning of "homotopic phases", and easily explains the salient features of Kitaev's Periodic Table.

Keywords: K-theory
Topological matter
Advisor: Hannabuss, K
On the bridge between constraint satisfaction and Boolean satisfiability

A wide range of problems can be formalized as a set of constraints that need to be satisfied. In fact, such a model is called a constraint satisfaction problem (CSP). Another way to represent a problem is to express it as a formula in propositional logic, or, in other words, a Boolean satisfiability problem (SAT). In the quest to find efficient algorithms for solving instances of CSP and SAT specialised software has been developed. It is, however, not clear when should we choose a SAT-solver over a constraint solver (and vice versa). CSP-solvers are known for their domain-specific reasoning, whereas SAT-solvers are considered to be remarkably fast on Boolean instances. In this thesis we tackle these issues by investigating the connections between CSP and SAT.
In order to answer the question why SAT-solvers are so efficient on certain classes of CSP instances, we first present the various ways one can encode a CSP instance into SAT. Next, we show that with some encodings SAT-solvers simulate the effects of enforcing a form of local consistency, called k-consistency, in expected polynomial-time. Thus SAT-solvers are able to solve CSP instances of bounded-width structure efficiently in contrast to conventional constraint solvers. By considering the various ways one can encode CSP domains into SAT, we give theoretical reasons for choosing a particular SAT encoding for several important classes of CSP instances. In particular, we show that with this encoding many problem instances that can be solved in polynomial-time will still be easily solvable once they are translated into SAT. Furthermore, we show that this is not true for several other encodings.
Finally, we compare the various ways one can use a SAT-solver to solve the classical problem of the pigeonhole principle. We perform both theoretical and empirical comparison of the various encodings. We conclude that none of the known encodings for the classical representation of the problem will result in an efficiently-solvable SAT instance. Thus in this case constraint solvers are a much better choice.

Keywords: constraint satisfaction
Boolean satisfiability
Advisor: Jeavons, P