VictorJuiz/thesis huggingface dataset:
Soft X-ray contact microscopy using laser generated plasma sources

The ultimate objective of this project was to develop a small, transportable X-ray microscope which would be able to view a wide range of biological specimens without the need for any type of sample preparation at a resolution greater than that obtainable by conventional light microscopy (ie. about 250nm). Of the various possible implementations of X-ray microscopy currently being investigated, contact microscopy was chosen as being the most suitable for the development of such a small-scale instrument, while at the same time minimizing the effects on image quality of radiation damage to the biological specimen.
The requirement for a high brightness pulsed X-ray source of less than 50ns duration for illumination of the specimen was met by the production of laser generated plasmas. These were formed by focusing a 2.2J KrF laser beam, of wavelength 248nm and duration 20ns, onto the surface of one of a number of different target materials. In order to obtain the large intensities required for the production of a sufficiently high temperature plasma, a doubly pre-ionized, discharge-pumped amplifier KrF laser was developed. This was seeded by a smaller oscillator laser by means of a coupled unstable resonator configuration. A number of different cavity arrangements were investigated and an output beam divergence of 2.5 times the diffraction limit was achieved.
The plasmas generated by focusing the laser beam to an intensity of 1014W/cm2 onto carbon, titanium, molybdenum and tungsten targets were characterized as fully as was necessary for their use in the X-ray microscope. Preliminary investigations on the use of a grazing incidence ellipsoidal mirror to focus the emitted X-rays onto the specimen of the microscope were made and such an optical component was manufactured and tested.
Finally, numerous images of a number of different biological specimens were made and resolutions of better than 100nm were achieved. Images were read out using a Park Scientific Instruments atomic force microscope, which enabled the entire microscopy process to be carried out in a single working day. The system is now in routine use and can produce more than ten images per session.
Measurement of the through-thickness strength of composites

This research deals with the mechanical characterisation of thick composite laminates in the through-thickness direction. Three independent glass fibre/epoxy laminate configurations, namely cross, quasi-isotropic, and woven, plies were investigated. Six specimen configurations, of which two were developed herein, were employed in order to determine the strength behaviour of these three laminate configurations when subjected to interlaminar shear and interlaminar tensile stresses in isolation and in combination. The stress and strain distributions were estimated using the ABAQUS FEA package. The strain distribution obtained thereby was verified experimentally via Moirandeacute; interferometry which records the exact strain field at the test section. A two dimensional failure envelope is defined for each laminate configuration using the experimentally obtained data. All three independent laminate configurations exhibited almost identical failure envelopes. The woven laminate exhibited superior interlaminar shear strength when subjected to combined interlaminar shear and interlaminar tensile stresses, whereas the cross-ply laminate exhibited superior interlaminar tensile strength when subjected to the same combination of stress. The characteristics of the quasi-isotropic laminate were similar to that of the cross-ply laminate. A partial three dimensional failure envelope was also defined for the materials tested.
Design of a ratiometric reporter to improve the dynamic range and sensitivity of a bacterial biosensor

For applications from biosensor generation to synthetic biology, the ability to accurately and quantitatively generate input-output data from biological systems over a wide dynamic range is becoming increasingly important. This study has demonstrated that a simple approach utilising multiple promoters, recognising the same transcriptional activator but with differing affinities, linked to compatible reporter genes can achieve this goal. This simple system highlights that even for complex promoters with multiple binding sites we can use the ratio of two reporters to obtain accurate and reproducible input-output data for reporters contained on a high copy number plasmid without the need for any background subtraction or accurate determination of cell number. It has also demonstrated that the precise promoter strengths are not too crucial to the design, provided they are significantly different, as taking the ratio of either the high affinity/low affinity or medium affinity/low affinity channels give similar improvements over any single channel alone.
The modularity of this system means that it should be possible to exchange the IPTG inducible promoter and hence place the ntrC* gene under the regulation of any environmentally important promoter.
It should also be possible to simply construct different strength promoters for the same transcriptional activator by standard DNA synthesis techniques, therefore allowing direct ratiometric detection of specific active transcription factors. Finally, there is considerable interest in the biosensor field in the use of immobilised cells for field based applications. In these cases, determining the exact number of viable cells present at the time of use may be problematic and obtaining high signal levels may also be essential. In this regard, the use of ratiometric reporters from constructs on high copy number plasmids could alleviate many of these potential problems and significantly simplify the required biosensor detection equipment.

Keywords: fluorescence
Microbial
bacteria
microbiology
ratiometric
Biosensor
Advisor: Wadhams, G
Biggin, P
The energetics of nucleotide binding to RAS proteins

Ras proteins are a special class of proteins that mediate cell growth signals. Their importance lies in the fact that they are products of a proto-oncogene. This means that under certain conditions the gene that determines its structure is altered and a mutant protein results that is involved in the transformation of normal cells to cancer cells.
The actual function by which the protein acts in the signal pathway is not known. However it is known that they act as a switch, undergoing a cycle involving the exchange of guaninosine nucleotides in the binding site. This thesis uses computer simulations to study the energetics of this binding, with the long term aim of developing a drug to inhibit the transforming activity of the oncogenic protein.
To begin with, a model of the protein based on a crystal structure is built. Using Molecular dynamics the motion of this model is studied. A possible mechanism by which one half of the nucleotide cycle could be induced is investigated, with the result that phosphorylation of the protein may be involved.
The main part of the thesis is then devoted to using the free energy perturbation (FEP) method to calculate the difference in Gibbs binding free energy between the nucleotides in the protein.
Using histamine as a model, a method of dealing with charged, flexible molecules is developed; namely the inclusion of a reaction field and comprehensive conformational analysis. The results from the associated calculations are seen to be very close to experimental data. The same procedures are then applied to the much more complex ras: nucleotide system with less successful results, the reason for which is mostly due to the restriction of limited computer resources to tackle such a problem.
The conclusion is that given the resources and by using the techniques developed in this thesis, this type of calculation is a feasible way to study such systems.

Advisor: Richards, W
Richards, G
Genetic control of the olive fruit fly, Bactrocera oleae

The olive fruit fly, Bactrocera oleae, (Rossi) (Diptera:Tephritidae), is a key pest of olive crops. The sterile insect technique (SIT) is an environmentally benign and species-specific method of pest control, aiming to reduce the reproductive potential of a wild population through the mass-release of sterile insects. Previous olive fly SIT trials, involving the release of gamma-ray sterilised mixed-sex populations, achieved limited success. Key problems included altered diurnal mating rhythms of the laboratory-reared insects, leading to assortative mating between released and wild populations, and low competitiveness of the radiation sterilised mass-reared flies. Consequently, the production of competitive, male-only release cohorts is seen as essential.
The RIDL (Release of Insects carrying a Dominant Lethal) system is a transgene-based derivative of SIT, one version of which involves the mass release of insects carrying a female specific lethal transgene (fsRIDL). This thesis describes: 1) the development of fsRIDL olive fly strains and the molecular analysis of transgene insertion and function; 2) the analysis of strain life-history parameters; 3) studies into sexual selection and mating compatibility; 4) a caged proof-of-principle population suppression trial; and, 5) selection dynamics on the fsRIDL trait in caged populations.
Olive fly fsRIDL strains were developed with full female-lethal penetrance and repressibility. The lead strain displayed similar life-history and sexual competitiveness traits to those of the wild-type strain from which they were derived. In addition, transgenic males showed photoperiod compatibility and strong sexual competitiveness with field-collected wild olive flies. The feasibility of the fsRIDL approach was demonstrated when repeated male releases caused eradication of caged olive fly populations. Although needing field confirmation, these results suggest that fsRIDL olive fly strains may help to mitigate key problems experienced in previous olive fly SIT trials, and could help form the basis of a renewed effort towards olive fly SIT control.

Keywords: tephritid
olive fly
autocidal
sterile insect technique
transgenic
RIDL
Advisor: Alphey, L
Shimeld, S
Social sharing of emotions on individual, dyadic, and group levels

People turn to others for help and advice during hard times. Early psychologists suggested a ‘talking cure’ as a remedy for emotional turmoil (e.g., Freud, 1916–7/1963; Rogers, 1942). Likewise, folk psychology often sees heart-to-heart conversations as a win-win proposition that brings relief to the afflicted person and reinforces social bonds at the time of need. However, talking about problems does not always help (e.g., Rimé, 2009; Rimé, Mesquita, Boca, & Philppot, 1991; Rimé, Philippot, Boca, & Mesquita, 1992; Rose, 2002). In some cases, problem-talk can be a lose-lose proposition that drags both discussants into depression (Rose, 2002; Rose, Carlson, & Waller, 2007). This thesis examines co-rumination (Rose, 2002), a case of emotional sharing that hurts people instead of helping them, on three levels of analysis (individuals, dyads, and groups).
At the individual level, I sketch the life course of co-rumination and replicate earlier findings of gender differences. Furthermore, online survey data (N = 464) links co-rumination with agreeableness and neuroticism. I also demonstrate that co-rumination can be assessed with a brief measure that is 66% shorter than the original. At the dyadic level, data from recorded conversations between romantic couples show that face-to-face co-rumination influences people’s real-time emotional trajectories in complex ways. Furthermore, observer-ratings of the conversations suggest that third-parties can detect co-rumination, even from silent videos. Finally, I study how people react to others’ negative mood and co-rumination in a real social context by longitudinally following two cohorts of students and modelling their interactions with social network analysis tools. These models show that co-rumination appears to elicit social rejection from others, implying a possible pathway to depression via loneliness imposed on the co-ruminators.

Keywords: social sharing
co-rumination
social networks
Advisor: Parkinson, B
Computational studies of transmembrane helix insertion and association

Membrane proteins perform a variety of functions essential for the viability of the cell, including transport and signalling across the membrane. Most membrane proteins are formed from bundles of transmembrane helices. In this thesis molecular dynamics simulations have been used to investigate helix insertion into bilayers and helix association within bilayers. The potentials of mean force for the insertion of helices derived from the cystic ﬁbrosis transmembrane conductance regulator into lipid bilayers were calculated using coarse-grained molecular dynamics simulations. The results showed that the insertion free energy increased with helix length and bilayer hydrophobic width. The insertion free energies obtained were signiﬁcantly larger than comparable quantities obtained from translocon- mediated insertion experiments, consistent with a variety of previous studies. The implications of this observation for the interpretation of in vivo translocon-mediated insertion experiments, and the function of the translocon, are discussed.
Coarse-grained and atomistic molecular dynamics simulations of the transmembrane region of the receptor tyrosine kinase EphA1 suggested that the transmembrane helix dimer was most stable when interacting via the glycine zipper motif, in agreement with a structure obtained by NMR spectroscopy. Coarse-grained simulations of the transmembrane region of EphA2 suggested that the dimer has two stable orientations, interacting via a glycine zipper or a heptad motif. Both structures showed right-handed dimers, although an NMR structure of the transmembrane region of EphA2 shows a left-handed dimer interacting via the heptad motif. Both structures obtained from coarse-grained simulations proved unstable when simulated at an atomistic level of detail.
The potentials of mean force for dissociating the EphA1 and EphA2 dimers were calcu- lated using coarse-grained molecular dynamics calculations. Convergence of the detailed structure of the proﬁles was not conclusively shown, although association free energies cal- culated from the proﬁles were consistent over a variety of simulation times. The association free energies were slightly larger than experimental values obtained for comparable sys- tems, but consistent with similar computational calculations previously reported. However, direct comparisons are difﬁcult owing to the inﬂuence of environmental factors on reported association free energies. The potential of mean force proﬁles showed that the interaction via the glycine zipper motif for EphA1 was signiﬁcantly more stable than any other confor- mation. For EphA2 the potential of mean force proﬁles suggested that interaction via the glycine zipper and heptad motifs both provided stable or metastable conformations, with the interaction via the glycine zipper motif probably at least as stable as that via the heptad motif.

Keywords: potential of mean force
transmembrane helix insertion
membrane proteins
molecular dynamics
Advisor: Sansom, M
Classical lyricism in Italian and North American 20th-century poetry

This thesis defines ‘classical lyricism’ as any mode of appropriation of Greek and Latin monodic lyric whereby a poet may develop a wider discourse on poetry. Assuming classical lyricism as an internal category of enquiry, my thesis investigates the presence of Sappho and Catullus as lyric archetypes in Italian and North American poetry of the 20th century.
The analysis concentrates on translations and appropriations of Sappho and Catullus in four case studies: Giovanni Pascoli (1855-1912) and Salvatore Quasimodo (1901-1968) in Italy; Ezra Pound (1885-1972) and Anne Carson (b. 1950) in North America. I first trace the poetic reception of Sappho and Catullus in the oeuvres of the four authors separately. I define and evaluate the role of the respective appropriations within each author’s work and poetics. I then contextualise the four case studies within the Italian and North American literary histories. Finally, through the new outlook afforded by the comparative angle of this thesis, I uncover some of the hidden threads connecting the different types of classical lyricism transnationally.
The thesis shows that the course of classical lyricism takes two opposite aesthetic directions in Italy and in North America. Moreover, despite the two aesthetic trajectories diverging, I demonstrate that the four poets’ appropriations of Sappho and Catullus share certain topical characteristics. Three out of four types of classical lyricism are defined by a preference for Sappho’s and Catullus’ lyrics which deal with marriage rituals and defloration, patterns of death and rebirth, and solar myths. They stand out as the epiphenomena of the poets’ interest in the anthropological foundations of the lyric, which is grounded in a philosophical function associated with poetry as a quest for knowledge. I therefore ultimately propose that ‘classical lyricism’ may be considered as an independent historical and interpretative category of the classical legacy.

Keywords: Ezra Pound
Sappho
Classics
Catullus
20th-Century
Salvatore Quasimodo
Anne Carson
lyric
American poetry
translation
Classical Tradition
Giovanni Pascoli
Italian poetry
Greek
Latin
Advisor: Gardini, N
“One of the Most Penetrating Minds in England:” Gerald Heard and the British Intelligentsia of the Interwar Period

Gerald Heard (1889-1971) was an influential figure among the intelligentsia of the 1930s, once described by E. M. Forster as “one of the most penetrating minds in England.” However, he remains an ill-defined footnote, a marginal figure whose influence and reputation, although acknowledged, remains unexamined. This dissertation examines his life and work, and considers the role which Heard, as a generaliser and public intellectual, played in the intellectual landscape of the 1930s.
Central to Heard’s philosophy was a belief that society was in need of a spiritual and psychological force which could allow isolated individuals to participate in community with one another. Heard’s solution to bring about this evolution of consciousness would prove to be partly psychological, partly mystical and partly down to the product of a particular way of living. The first chapter outlines Heard’s philosophy in detail. Subsequent chapters are structured so as to provide a loose biographical chronology, each focussing on a different phase of Heard’s career and examining the development of his thought. Running throughout the dissertation is a consideration of Heard’s role as a public intellectual. It was as a popular ‘generaliser’ of thought that Heard found his public, and the limited degree of success he found as a man of action could be seen to be a natural limitation of the role he had constructed for himself.
Chapter II focuses on Heard’s time as personal secretary to Sir Horace Plunkett, father of the Irish Co-Operative Movement, and how the ideals of this movement can be seen to inform his developing ideas of human community. Chapter III looks at Heard’s role as a broadcaster with the B.B.C., where he became a noted populariser of science, firmly establishing himself as a public figure and cultural authority. It is arguably this increased public profile which provided Heard with a ‘public’ to whom he could address his ideas. Chapter IV, drawing on archival material from Dartington Hall, considers Heard’s role as a lecturer at Dartington School, and more importantly his first experiment to establish a small ‘group’ for meditation in an attempt to discover the mystical and psychological basis for a co-operative society. Chapter V examines his career as an outspoken pacifist, where he would advance his arguments for a radical reorganisation of society as a practical solution to the question of peace and further attempt to become a man of action.

Keywords: Pacifism
Aldous Huxley
1930s
Henry FitzGerald Heard
Dartington Hall
Gerald Heard
Advisor: Bradshaw, D
Whitworth, M
One world and the many sciences

The subject of this thesis is physicalism, understood not as some particular doctrine pertaining narrowly to the philosophy of mind, but rather as a quite general metaphysical claim to the effect that everything is, or is fundamentally, physical. Thus physicalism explicates the thought that in some sense physics is the basic science. The aim of the thesis is to defend a particular brand of physicalism, which I call eliminative type physicalism. It claims, roughly, that every property is a physical property – a property mentioned in the laws of physics, and hence that any putative property not identifiable with a physical property must be eliminated from our ontology.
Eliminative type physicalism is apt to face three objections, and so my thesis, like Caesar's Gaul, falls into three parts. In the first, I argue against the idea that there are tenable positions, both physicalist and non-physicalist, alternative to eliminative type physicalism. I argue that each of these positions – token physicalism (Fodor, middle Putnam), supervenience physicalism (Lewis, Horgan) and and a non-physicalist view I call pluralism (Goodman, late Putnam) – is defective. In the second part, responding to the objection that there is just no reason to be a physicalist, I develop a positive argument for eliminative type physicalism, an argument resting upon a strong version of the explanatory test for reality according to which only explanatorily indispensable properties can justifiably be said to exist. In the third and final part, I argue, against the charge that eliminative type physicalism cannot accommodate what I call phenomenal properties (qualia, raw feels etc.), that there is no good reason to deny, and one good reason to affirm, that phenomenal properties just are physical properties.
Centralisers and amalgams of saturated fusion systems

In this thesis, we mainly address two contrasting topics in the area of saturated fusion systems. The first concerns the notion of a centraliser of a subsystem E of a fusion system F, and we give new proofs of the existence of such an object in the case where E is normal in F. The second concerns the development of the theory of `trees of fusion systems', an analogue for fusion systems of Bass-Serre theory for finite groups. A major theorem finds conditions on a tree of fusion systems for there to exist a saturated completion, and this is applied to construct and classify certain fusion systems over p-groups with an abelian subgroup of index p. Results which do not fall into either of the above categories include a new proof of Thompson's normal p-complement Theorem for saturated fusion systems and characterisations of certain quotients of fusion systems which possess a normal subgroup.

Keywords: saturated fusion systems
finite group theory
Advisor: Collins, MJ
Craven, DA