VictorJuiz/thesis huggingface dataset:
Tuning ultrafast chemical reaction dynamics in photoactive proteins

This dissertation investigates the origins of tunable and efficient photochemistry in three different photoactive proteins, bacteriorhodopsin (BR), rhodopsin (RHO) and green fluorescent protein (GFP). In all cases, significant differences exist between the photoreactivity of model chromophores in solution and in the protein environment, in terms of excited state lifetime and efficiency of the primary photochemical process (opsin proteins) or the type of reaction (excited state proton transfer versus C=C double bond photoisomerisation for GFP).
The work presented here investigates for each case to what extent the protein environment is necessary to alter the photochemistry of model chromophores in solution. For GFP and BR steric and electrostatic interactions between the protein pocket and the chromophore are shown to be likely responsible for shaping the excited state surface along which the photoreactions take place. For RHO it is suggested, contrary to current belief, that selection of a reactive ground state conformer might be the main effect generating the observed differences between solution and protein environment.
The solution photochemistry of structurally modified retinal protonated Schiff bases, taken as model chromophores for the opsin proteins, is studied with continuous wave irradiation experiments and ultrafast transient spectroscopies. Surprisingly large differences are observed for the isomerisation reaction depending on the starting configuration (trans or cis) of the photoactive double bond. The current model for BR based on the tuning of the excited state barrier encountered along the isomerisation coordinate is expanded to include the changes in selectivity, speed and efficiency observed for a series of all-trans derivatives.
For 11-cis, the photoisomerisation in solution is proposed to take place along a barrierless isomerisation coordinate, in contrast with the models currently available in literature. It is suggested that the protein might be discriminating between ground state conformers rather than significantly changing the topography of the reaction coordinate.
For GFP, excited state Raman spectra are recorded for the wild-type protein, two mutants and a model chromophore in solution. It is suggested that the high frequency vibrational modes observed in the excited state spectra of the proteins but not of the model chromophore in DMSO are a sign of a tighter chromophore environment that inhibits the photoisomerisation reaction occurring in solution.

Keywords: Retinal protonated Schiff-base
Ultrafast
Green Fluorescent Protein
Advisor: Kukura, P
Agricultural development in Mid Saxon England

Over the past decade, historians and archaeologists have become increasingly aware that the Mid Saxon period in England (7th-9th centuries AD) witnessed a transformation in agricultural practices. According to the emergent consensus, in contrast to the heavily pastoral, broadly subsistence-based mode of agriculture characteristic of the Early Saxon period (5th-7th centuries), Mid Saxon agriculture was geared towards higher levels of surplus production and placed a greater emphasis upon arable farming. The increased cultivation of bread wheat and the specialist production of sheep’s wool have been identified as particularly important innovations of this period.
This thesis represents the first attempt to explore agricultural development in Mid Saxon England on a systematic archaeological basis. It considers settlement, zooarchaeological, and archaeobotanical evidence in detail, with a special emphasis on charred plant remains. The analyses utilize data gathered from excavation reports, published and unpublished, covering two case study regions: (i) the Upper/Middle Thames valley and environs, and (ii) East Anglia and Essex. In addition, a sub-assemblage of charred plant remains from a Mid Saxon monastic site at Lyminge (Kent) is studied at first hand.
In this way, a series of agricultural innovations is identified in the archaeological record, including in particular: specialized pastoralism, an increased emphasis on sheep in some regions, an expansion of arable production, growth in fibre production, growth in cereal surpluses, a consequent investment in specialist storage and processing facilities, and a general diversification of crop spectra. These innovations were contingent upon, and adapted to, local environmental factors. The process of agricultural development is thought to have begun in the 7th century and continued through the 8th and 9th centuries, facilitated and stimulated by newly consolidated élite landholdings and, probably, a growing population.

Keywords: Anglo-Saxon
archaeology
archaeobotany
zooarchaeology
agriculture
Advisor: Hamerow, H
Bogaard, A
Writing (hi)story : Gascony in Jean Froissart’s chroniques

Jean Froissart’s Chroniques, composed of four Books, relate the first stages of the Anglo-French conflict later known as the Hundred Years’ War (1337–1453).
This thesis explores Froissart’s textual journey(s) to Gascon lands (south-west of modern-day France) and history/stories. Relying on Gérard Genette’s and Mikhail Bakhtin’s narrative theories, it uses literary and narratological tools to analyse three passages from Book I and III concerned with Gascony: the Earl of Derby’s Gascon campaigns (Chapter 1); the Black Prince’s Gascon campaigns and the principality of Aquitaine (Chapter 2); Froissart’s personal journey to and stay at the court of Gaston Fébus, count of Foix-Béarn (Chapter 3).
One aim of the study is to investigate the representation of the region but it also argues that the Gascon passages have wider implications for the Chroniques, Froissart’s work as a whole, and the writing of history in the fourteenth century. At the turn of the twentieth century, Froissart’s ‘history’ was often disparagingly discussed by scholars due to factual inaccuracy and literary embellishments: such a ‘historical narrative’, it was felt, fell short of history and was nothing more than an entertaining story presenting outdated chivalric ideals. Although this approach has been partly revised, some critics still view the Chroniques’ earlier Books as being a narratively straightforward reflection of such a chivalric ideology, lacking critical hindsight on fourteenth-century events and society, and thus presenting paradoxical and irreconcilable tensions with later Books to the extent that they are occasionally deemed to be an entirely different kind of work than their later counterparts.
The narrative thread of Froissart’s Gascon (hi)story explored here allows the revision of such views and shows that Froissart’s narrative is far from narratively and ideologically straightforward. This complexity is present as early as the first versions of the Book I, which should be envisaged in parallel, not in opposition, with the ‘later’ Chroniques. Similarly, the various tensions (e.g. fiction/history; ideal/real) underpinning the whole work, manifested in the portrayal of Gascony/the Gascons, are best approached in terms of co-existence, not antagonism. Such a multi-faceted work (a mirror and/or product of the fourteenth century?), à mi-chemin between history and fiction, between conflicting yet co-existing perspectives, is precisely what makes Froissart’s Chroniques valuable to literary critics, philologists, and historians alike.

Keywords: Gascony
historiography
France
medieval chronicles
narratology
polyphony
late medieval ideology
Jean Froissart
fourteenth century
Aquitaine
Advisor: Marnette, S
The epic fragment in mid sixteenth-century French poetry

This study aims to produce a positive assessment of the Franciade, by viewing Ronsard's epic venture in the context of works by Ronsard himself and by poets such as Baïf and Belleau. The com- positions considered extract single episodes from an epic whole, and are united by their structural and rhetorical techniques, forming a group dominated by the Franciade.
The first chapter examines the question of genre raised by the fragments, and reviews classical models utilized by the French poets, placing particular emphasis upon the Alexandrians. It re- veals how the sixteenth-century poets long to produce a full-scale epic .
Chapter 2 groups the fragments according to theme, highlighting Argonautic poems, notably Ronsard's Hymne de Calais, et de Zetes, Hymne de Pollux et de Castor, and Hylas.
Chapter 3 examines the structure of the fragments in terms of contraction and expansion. Some poets circumscribe their material with a prelude and conclusion; others extend its temporal and spatial perspectives, by such means as retrospection, prophecy, and descriptions of ornate objects.
The rhetoric of the fragments is seen in Chapter 4 to reflect the expansive urge: simile, circumlocution, and preterition all widen the poetic vistas.
Chapter 5 studies Ronsard's approach to the problem of inven- ting an original framework for his epic, how he tries to lend it coherence by structural and rhetorical means. Yet the techniques Ronsard practised in the fragments finally prevail: the Franciade breaks up into a series of vivid miniatures: Ronsard repeatedly returns to material made familiar by classical epics.
The conclusion emphasizes that the 'accidental' fragmentation of the Franciade should be viewed alongside the voluntary frag- mentation of the sixteenth-century heroic miniatures. The Franciade should, especially, be considered in conjunction with other Ron- sardian productions, such as the Argonautic hymns. Together with these, it forms an intricate fretwork of epic motifs.
The social biography of ethnomusicological field recordings: eliciting responses to Hugh Tracey's 'the sound of Africa' series

This thesis is an ethnographic analysis of a collection of field recordings of music from sub-Saharan Africa: The Sound of Africa series made and published by Hugh Tracey between 1933 and 1973. I analyse the aims, methods, value and potential use of this collection, now held at the International Library of African Music (ILAM), in order to address a gap in the ethnomusicological literature and to begin to develop a critical framework for an evaluation of field recording and aural ethnography.
An archival analysis of the collection enables me to trace the scope and intended uses of Tracey’s recordings. Identifying a primary intended audience that has not to date been engaged, I argue for the need to develop a new way to circulate recordings among a source community that has never before been reached through institutional archival practice.
I use a small sample of Tracey’s archival Xhosa recordings and develop a method of sound elicitation designed to take the recordings back to urban Xhosa communities in the townships located near ILAM. By circulating archival recordings using local mechanisms in township communities, rather than institutional archival methods, I assess the potential relevance of historical recordings to an urban source community more than fifty years after the recordings were made.
Having collected and analysed contemporary Xhosa responses, I consider the limitations and the potential for the recordings to connect with indigenous audiences and generate value. I argue that non-analytical responses to historical recordings may contribute to ethnographic understanding, to people’s own sense of Xhosa identity, and to archiving practice in future. Such responses may help increase our understanding of the relationships between music collectors in the field and the people recorded, whether fifty years ago, today or in future.

Keywords: sound archiving
Ethnomusicology
Xhosa music
Hugh Tracey
field recording
Advisor: Morton, C
Stokes, M
Human frontal eye fields and visual search

This thesis tested whether the human frontal eye fields (FEFs) have visuospatial functions that are dissociable from FEF oculomotor functions. Functional magnetic resonance imaging (fMRI) was used to localize the FEFs, and transcranial magnetic stimulation (TMS) was applied in a series of experiments to transiently disrupt information processing in the FEFs.
It was shown that TMS applied over the right FEFs degrades subjects' performance on a visual conjunction search task in which eye movements were not required and were not made. A TMS timing protocol subsequently showed that computations in the FEFs that occur between 40 and 80ms after the onset of a visual search array are critical for accurate performance. This suggests that, as in the monkey, the human FEFs may accumulate and use visual evidence from extrastriate cortex, which forms the basis for accurate visuospatial discrimination.
A training protocol showed that the right FEFs are no longer critical for accurate visuospatial discrimination performance once a search task has been extensively practised. This study further suggested that the FEFs may have a previously unknown role in the perception of left-right rotated shapes.
A study on feature and spatial priming indicated that these two phenomena have distinct causal mechanisms. The left FEFs appear to access a spatial memory signal during the process of saccade programming. When TMS is applied during this period, the spatial priming benefit is abolished.
Altogether, this thesis presents evidence that visuospatial and oculomotor functions can be dissociated in the human FEFs. The data on timing and the effects of learning correspond well with results reported in monkeys. The priming experiment offers the first evidence that the left FEFs are crucial for spatial priming, while the learning study suggests the novel hypothesis that the FEFs are crucial for left-right rotated shape perception.

Advisor: Walsh, V
Cowey, A
Crystallographic studies on 2-oxoglutarate dependent oxygenases

The Fe(II) and 2-oxoglutarate dependent oxygenases (2OG oxygenases) catalyse a broad range of oxidative reactions in various organisms. 2OG oxygenases use 2OG and molecular oxygen to catalyse the oxidation of a variety of substrates including small molecules, fatty acids, nucleic acids and proteins. Several human 2OG oxygenases are implicated in diseases. The fat mass and obesity associated protein (FTO) is linked to obesity, whilst collagen prolyl-4-hydroxylases (CPHs), the procollagen lysyl hydroxylases (PLODs), and the hypoxia inducible factor hydroxylases (PHDs) are linked to cancer. Therefore, structure-based inhibition studies on FTO, CPH and related 2OG oxygenases are of significant therapeutic interest.
The obesity-associated FTO is an mRNA N6-methyladenine (m6A) demethylase and a homologue of E. coli alkylated DNA repair protein (AlkB), a DNA repair enzyme that demethylates N1-methyladenine (m1A) and N3-methylcytosine (m3C) bases. Human AlkB homologue 5 (ALKBH5) has a similar substrate profile as FTO, i.e. ALKBH5 is another mRNA m6A demethylase, making it a target for structural and inhibition studies to improve inhibitor selectivity for FTO. The CPH and PLODs catalyse hydroxylation of collagen prolyl- and lysyl-residues; the resultant 4-hydroxyprolyl- and 4-hydroxylysyl-residues are important for the formation of the collagen triple helix and intermolecular crosslinks, respectively. Another 2OG oxygenase, the 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 2 (OGFOD2), is related by sequence similarity to the PLODs but its biological role is unknown.
This thesis describes crystallographic, biochemical and inhibition studies on five 2OG oxygenases: AlkB, FTO, ALKBH5, OGFOD2 and CPH. Three AlkB-inhibitor complexes were determined; taken together, these structures serve as proof-of-principle that the AlkB subfamily 2OG oxygenases are amenable to structure-based inhibition studies. Several classes of inhibitors of FTO were then identified and their binding modes were investigated through the determination of 7 crystal structures of FTO-inhibitor complexes. Subsequently, a crystal structure of ALKBH5 was determined, which provided insights into its substrate recognition mechanisms. The ALKBH5 structure also serves as a template for inhibitor design. Preliminary structural and biochemical data were also obtained for OGFOD2 and CPH.
Overall, these results contribute to the development of a biophysical understanding of human 2OG oxygenases, and will help to enable the development of selective inhibitors of 2OG oxygenases involved in nucleic acid and collagen modifications.

Keywords: protein structure
structural biology
inhibition
Advisor: Schofield, C
Performing barbers, surgeons and barber-surgeons in early modern English literature

This study addresses the problem critics have faced in identifying contemporary perceptions of the barber, surgeon and barber-surgeon in early modernity by examining the literature, predominantly the drama, from the period. The name ‘barber-surgeon’ is not given formally to any character in extant early modern plays; only within the dialogue or during stage business is a character labelled the barber-surgeon. Barbers and surgeons are simultaneously separate and doubled-up characters. The differences and cross-pollinations between their practices play out across the literature and tell us not just about their cultural, civic and occupational histories but also about how we interpret patterns in language, onomastics, dramaturgy, materiality, acoustics and semiology. Accordingly, the argument in this study is structured thematically and focuses on the elements of performance, moving from discussions of names to discussions of settings and props, disguises, stage directions and semiotics, and from sound effects and music, to voices and rhetorical turns. In doing so, it questions what it means in early modernity to have a developed literary identity, or be deprived of one. The barber-surgeon is a trope in early modern literature because he has a tangible social impact and an historical meaning derived from his barbery and surgery roots, and consequently a richly allusive idiom which exerted attraction for audiences. But the figure of the barber-surgeon can also be a trope in investigating how representation works. An aesthetic of doubleness, which this study finds to be diversely constructed, prevails in barbers, surgeons’ and barber-surgeons’ literary conception, and the barber-surgeon in the popular imagination is created from opposing cultural stereotypes. The literature from the period demonstrates why a guild union of barbers and surgeons was never harmonious: they are opposing dramaturgical as well as medical figures. This study has a wide-ranging literary corpus, including early modern play texts, ballads, pamphlets, guild records, dictionaries, inventories, medical treatises and archaeological material, and contributes to the critical endeavours of the medical humanities, cultural materialists, theatre historians and linguists.

Keywords: Shakespeare
early modern theatre
early modern literature
English literature
medicine and literature
Advisor: Maguire, L
Topologically close-packed phase prediction in Ni-based superalloys: phenomenological structure maps and bond-order potential theory

Single crystal nickel-based superalloys are used in modern gas turbines because of their remarkable resistance to creep deformation at elevated temperatures, which is ensured by the addition of significant amounts of refractory elements. Too high concentrations of refractory elements can lead to the formation of topologically-close packed (TCP) phases during exposure to conditions of high temperature and stress which result in the degradation of the creep properties. The traditional methods for predicting the occurrence of TCP phases in Ni-based superalloys have been based on the PHACOMP and newPHACOMP methodologies which are well-known to fail with respect to new generations of alloys. In this work a novel two-dimensional structure map (Nbar, deltaV/V) for TCP phases where Nbar is the valence-electron count and deltaV/V is a compositional dependent size factor. This map is found to separate the experimental data on the TCP phases of binary, ternary and multi-component TCP phases into well-defined regions corresponding to different structure types such as A15, sigma, chi, delta, P, R, mu, and Laves. In particular, increasing size factor separates the A15, sigma and chi phases from the delta, P, R, mu phases. The structure map is then also used in conjunction with CALPHAD computations of sigma phase stability to show that the predictive power of newPHACOMP for the seven component Ni–Co–Cr–Ta–W–Re–Al system is indeed poor.
In order to gain a microscopic understanding of the observed structural trends, namely the differences between the two groups of TCP structures with increasing deltaV/V and the trend from A15 to sigma to chi with increasing Nbar, the electronic structure is coarse-grained from density functional theory (DFT) to tight-binding to bond-order potentials (BOPs). First, DFT is used to calculate the structural energy differences across the elemental 4d and 5d transition metal series and the heats of formation of the binary alloys Mo-Re, Mo-Ru, Nb-Re, and Nb-Ru. These calculations show that the valence electron concentration stabilizes A15, sigma and chi but destablizes mu and Laves phases. The latter are shown to be stabilized instead by relative size difference. Second, a simple canonical TB model and in combination with the structural energy difference theorem is found to qualitatively reproduce the energy differences predicted by the elemental DFT calculations. The structural energy difference theorem rationalizes the importance of the size factor for the stability of the mu and Laves binary phases as observed in the structure map and DFT heats of formation. Finally, analytic BOP theory, is employed to identify the structural origins of the energetic differences between TCP structure-types that lead to the trends found within the two-dimensional structure map.

Keywords: Ni-base superalloys
Bond-order potentials
topologically close-packed phases
Tight-binding
Advisor: Pettifor, D
Drautz, R
Kolmogorov, A