VictorJuiz/thesis huggingface dataset:
Reading for pleasure in Britain: trends, patterns, and associations

This thesis investigates reading for pleasure in Britain from a variety of perspectives, in the context of popular concerns surrounding levels of readership, particularly among young people, and consists of four substantive chapters.
The first chapter reports how book sales and library circulation have changed, and what predicts readership in the Taking Part survey. I show that claims surrounding changes in reading in Britain may be overstated, although the number of issues from British libraries has fallen, and that while the predictors of readership are largely as expected, there are some important results surrounding social status, and ethnic differences in children.
The second chapter investigates changes in young people’s reading behaviour, using the Longitudinal Study of Young People in England. I show that changes in young people’s reading cannot be explained through a displacement effects account, and that socioeconomic differences in readership do not increase as panel members get older.
In the third chapter, I investigate whether the relationship between reading for pleasure and educational attainment can be explained through cultural capital, and extend this with occupational attainment, using the 1970 British Cohort Study. I show a relationship between reading for pleasure and occupational attainment net of education, and I show that this relationship seems to have a cultural dimension beyond a cognitive effect account.
In the fourth chapter, I show that the relationship between leisure in adoles- cence and educational and occupational attainment is not driven purely by highbrow activities, as on a certain understanding of Bourdieu: in particular, I show a relationship between occupational attainment and middlebrow activities.

Keywords: sociology of culture
lsype
taking part
reading for pleasure
bcs70
Advisor: Chan, T
Religion in Tacitus' Annals

I examine how religion is presented in the Annals of Tacitus, and how it resonates with and adds complexity to the larger themes of the historian’s narrative. Memory is essential to understanding the place of religion in the narrative, for Tacitus constructs a picture of a Rome with ‘religious amnesia.’ The Annals are populated with characters, both emperors and their subjects, who fail to maintain the traditional religious practices of their forebears by neglecting prodigies and omens, committing impious murders, and even participating in the destruction of Rome’s sacred buildings. Alongside this forgetfulness of traditional religious practice runs the construction of a new memory – that of the deified Augustus – which leads to the veneration of living emperors in terms appropriate to gods. This religious narrative resonates with and illuminates Tacitean observations on the nature of power in imperial Rome. Furthermore, tracing the prominence of religious memory in the text improves our understanding of how Tacitus thinks about the past, and particularly how he thinks about the role of the historian in shaping memory for his readers.
I consider various religious categories and their function in Tacitus’ writings, and how his characters interact with them: calendars (do Tacitus’ Romans preserve or change the traditional scheduling of festivals?), architecture (what determines the building of or alterations to temples and other religious monuments?), liturgy (do they worship in the same ways their ancestors did?), and images (how do they treat cult statues?). I analyze the patterns of behaviour, both in terms of ritual practice and in how Tacitus’ characters think about and interpret the supernatural, and consider how Rome’s religious past features in these patterns. The thesis is structured according to the reigns of individual emperors. Four chapters chart Tiberius’ accession, Germanicus’ death, its aftermath, and Sejanus’ rise to power; one chapter examines the religious antiquarian Claudius; and the final chapter analyzes Nero’s impieties and their consequences.

Keywords: Tacitus
Roman historiography
Roman religion
Annals
cultural memory
Advisor: Ash, R
Control and observation of DNA nanodevices

The uniquely predictable and controllable binding mechanism of DNA strands has been exploited to construct a vast range of synthetic nanodevices, capable of autonomous motion and computation. This thesis proposes novel ideas for the control and observation of such devices. The first of these proposals hinges on introducing mismatched base pairs into toehold-mediated strand displacement – a fundamental primitive in most dynamic DNA devices and reaction networks. Previous findings that such mismatches can impede strand displacement are extended insofar as it is shown that this impediment is highly dependent on mismatch position. This discovery is examined in detail, both experimentally and through simulations created with a coarse-grained model of DNA. It is shown that this effect allows for kinetic control of strand displacement decoupled from reaction thermodynamics.
The second proposal improves upon a previously presented strand displacement scheme, in which two strands perform displacement cooperatively. This scheme is extended to be cascadable, so that the output of one such reaction serves as input to the next. This scheme is implemented in reaction networks capable of performing fundamental calculations on directed graphs.
The third proposal is exclusively concerned with a novel observation methodology. This method is based on single-molecule fluorescence microscopy, and uses quantum dots, a fluorescent type of semiconductor nanocrystal, as a label. These quantum dots display a set of characteristics particularly promising for single-molecule studies on the time- and length scales most commonly encountered in DNA nanotechnology. This method is shown to allow for highly precise measurements on static DNA devices. Preliminary data for the observation of a complex dynamic device is also presented.

Keywords: strand displacement
synthetic reaction networks
DNA nanotechnology
Advisor: Turberfield, A
Protein structures from NMR data

This thesis describes the use of nuclear magnetic resonance techniques to determine the structures of two proteins in solution, hen egg-white lysozyme and human interleukin-4.
Using 2D 1H methods an extensive set of structural data has been collected for hen lysozyme (1158 NOE distance restraints, 68 o and 24 ?1 dihedral angle restraints) and these data have been used in distance geometry-dynamical simulated annealing calculations to determine an ensemble of NMR structures for the protein. The overall Ca RMSD from the average for a set of 16 calculated structures is 1.8 ± 0.2 A but, excluding 14 residues in exposed disordered regions, this value reduces to 1.3 ± 0.2 Å. Regions of secondary structure, and particularly the four a helices, are well defined (Ca RMSD 0.8 ± 0.3 Å for helices). Detailed comparisons of the NMR structures with crystal structures of the protein have shown the close similarity of the main chain fold and the conformation of interior side chains in solution and in crystals. 3Jaß coupling constant measurement have indicated, however, that the conformational mobility of the side chains of many surface residues is significantly more pronounced than an individual crystal structure would suggest.
For human interleukin-4, a strategy involving 15N and 13C labelled recombinant protein together with heteronuclear 3D NMR techniques has been employed to determine the structure of the protein. The work has provided the first structure for this protein, a left-handed four helix bundle with an up-up-down-down connectivity. For an ensemble of 10 final calculated NMR structures there is a Ca RMSD from the average of 1.6 ± 0.4 Å, the definition of the helical core of the protein being particularly good (0.8 ± 0.2 Å). There is, however, some disorder in the long overhand loops of the structure; this reflects the unusually high conformational mobility of these regions. Comparison of the interleukin-4 structure with proteins with related folds, particularly members of the haemopoietic cytokine superfamily, suggests that the fold found here for interleukin-4 may be the adopted structure throughout this cytokine superfamily.
In a postscript to this thesis the NMR structure of human interleukin-4 is shown to have a very similar conformation to a crystal structure of the protein which has been solved very recently.

Advisor: Dobson, C
The role of the Zic genes in mouse neural crest development

The neural crest is an embryonic population of migratory, multipotent cells that are formed at the boundary of the neural and non-neural ectoderm around the time of neural tube closure. After migrating to locations throughout the embryo the neural crest cells differentiate into many different cell types including osteoblasts and chondrocytes of the cranio-facial skeleton and neurones and glia of the peripheral nervous system. Gain of function experiments demonstrate that many genes, including the Zic gene family, are involved in neural crest formation. In order to determine whether they have a role in endogenous neural crest development, loss of function studies are required. The ability to perform genetic analysis in the mouse makes it an ideal organism in which to do this.
When this study commenced Zic1, Zic2 and Zic3 were assigned as members of the mammalian Zic gene family. A comparison of their expression patterns during mouse neural crest development reveals Zic2 and Zic3 to be the most likely to have roles in neural crest formation. Analysis of neural crest induction and migration in loss of function alleles of Zic2 and Zic3 reveals that loss of either gene function alone causes both a delay in the onset of trunk neural crest production and a reduction in the number of neural crest progenitor cells. Additionally, loss of Zic2 gene function results in a heightened response to BMP signalling by the neural tube. A more severe neural crest depletion occurs in embryos lacking Zic3 and heterozygous for a mutation in Zic2. These results indicate that Zic2 and Zic3 cooperate in the formation of the neural crest by mediating the competence of the dorsal neural tube to respond to inductive signals. This work provides the first genetic evidence that Zic2 and Zic3 are involved in neural crest development and that they function together during mouse development.

Advisor: Arkell, R
A study of atom and radical kinetics

This thesis describes the measurement of rate constants for gas phase reactions as a function of temperature (285 ≤ T/K ≤ 850) and pressure (48 ≤ P/Torr ≤ 700). One or both reactants was monitored directly in real time, using time–resolved resonance fluorescence (for atoms) and u.v. absorption (for radicals). Reactants were produced by exciplex laser flash photolysis. The technique was used to measure rate constants to high precision for the following reactions under the stated conditions: • H+O2+He->HO2+He and H+O2−→OH+O, for 800 ≤ T/K ≤ 850 and 100 ≤ P/Torr ≤ 259. A time–resolved study was performed at conditions close to criticality in the H2–O2 system. The competition between the two reactions affected the behaviour of the system after photolysis, and the rate constants were inferred from this behaviour. • H+C2H4+He<-->C2H5+He (T = 800 K, 97 ≤ P/Torr ≤ 600). The reactions were well into the fall–off region at all conditions studied. At 800 K, the system was studied under equilibrating conditions. The study provided values of the forward and reverse rate constants at high temperatures and enabled a test of a new theory of reversible unimolecular reactions. The controversial standard enthalpy of formation of ethyl, DH0f,298 (C2H5), was determined to be 120.2±0.8 kJ mol−1. Master Equation calculations showed that reversible and irreversible treatments of an equilibrating system should yield the same value for both thermal rate constants. • H+C3H5+He->C3H6+He (T = 291 K, 98 ≤ P/Torr ≤ 600) and O+C3H5 −→ products (286 ≤ T/K ≤ 500, 48 ≤ P/Torr ≤ 348). Both reactions were pressure–independent, and the latter was also independent of temperature with a value of (2.0±0.2) ×10−10 cm3 molecule−1 s−1. • H+C2H2+He<-->C2H3+He (298 ≤ T/K ≤ 845, 50 ≤ P/Torr ≤ 600). At 845 K, both reactions were in the fall–off region; rate constants were used to determine the standard enthalpy of formation of vinyl, ¢H0f,298 (C2H3), as 293±7 kJ mol−1. The value of this quantity has until recently been very controversial. • H+CH4 <--> CH3+H2. The standard enthalpy of formation of methyl, DH0 f,298 (CH3), was determined by re–analysing existing kinetic data at T = 825 K and 875 K. A value of 144.7±1.1 kJ mol−1 was determined. Preliminary models were examined to describe the loss of reactants from the observation region by diffusion and pump–out. Such models, including diffusion and drift, should prove useful in describing the loss of reactive species in many slow–flow systems, enabling more accurate rate constants to be determined.

Keywords: master equation
equilibration
dissociation
rate constants
vinyl
sensitivity analysis
equilibrium
radicals
hydrogen
combustion
diffusion
association
atoms
oxygen
FACSIMILE
ethyl
allyl
methyl
CHEMKIN
enthalpy
density of states
kinetics
nonlinear
Advisor: Pilling, M
Enantiorecognition phenomena in asymmetric synthesis

This thesis is concerned with investigations into applications of double asymmetric induction and parallel kinetic resolution in asymmetric synthesis.
Chapter 1 introduces enantiorecognition phenomena as a significant field in asymmetric synthesis. The main approaches in this field are described: double asymmetric induction, kinetic resolution, parallel kinetic resolution and dynamic kinetic resolution.
Chapter 2 describes investigations into the use of double asymmetric induction as a mechanistic probe to elucidate the reactive conformation of enantiopure α,β-unsaturated esters (derived from Corey’s 8-phenylmenthol auxiliary) and hydroxamates [derived from (S)-N-1-(1'-naphthyl)ethyl-O-tert-butylhydroxylamine] upon conjugate addition.
Chapter 3 describes investigations into the doubly diastereoselective organocatalytic intramolecular Michael cyclization of enantiopure enamides (derived from a 4-substituted-5,5-dimethyl-oxazolidin-2-one auxiliary) and α,β-unsaturated esters (derived from Corey’s 8-phenylmenthol auxiliary) using α-methylbenzylamine and its derivatives as the chiral catalysts.
Chapter 4 describes investigations into parallel kinetic resolution of acyclic γ-amino-α,β-unsaturated esters utilising a 50:50 pseudoenantiomeric mixture of lithium amides. To highlight the synthetic utility of the resultant β,γ-diamino esters, their elaboration to a range of 5-substituted-4-amino-pyrrolidin-2-ones is demonstrated and a concise synthesis of natural product (±)-absouline is performed.
Chapter 5 contains full experimental procedures and characterisation data for all compounds synthesised in chapters 2, 3 and 4.

Keywords: Organic synthesis
Advisor: Davies, S
Robust &amp; stochastic model predictive control

In the thesis, two different model predictive control (MPC) strategies are investigated for linear systems with uncertainty in the presence of constraints: namely robust MPC and stochastic MPC. Firstly, a Youla Parameter is integrated into an efficient robust MPC algorithm. It is demonstrated that even in the constrained cases, the use of the Youla Parameter can desensitize the costs to the effect of uncertainty while not affecting the nominal performance, and hence it strengthens the robustness of the MPC strategy. Since the controller u = K x + c can offer many advantages and is used across the thesis, the work provides two solutions to the problem when the unconstrained nominal LQ-optimal feedback K cannot stabilise the whole class of system models.
The work develops two stochastic tube approaches to account for probabilistic constraints. By using a semi closed-loop paradigm, the nominal and the error dynamics are analyzed separately, and this makes it possible to compute the tube scalings offline. First, ellipsoidal tubes are considered. The evolution for the tube scalings is simplified to be affine and using Markov Chain model, the probabilistic tube scalings can be calculated to tighten the constraints on the nominal. The online algorithm can be formulated into a quadratic programming (QP) problem and the MPC strategy is closed-loop stable. Following that, a direct way to compute the tube scalings is studied. It makes use of the information on the distribution of the uncertainty explicitly. The tubes do not take a particular shape but are defined implicitly by tightened constraints. This stochastic MPC strategy leads to a non-conservative performance in the sense that the probability of constraint violation can be as large as is allowed. It also ensures the recursive feasibility and closed-loop stability, and is extended to the output feedback case.

Keywords: stochastic uncertainty
model predictive control
robust control
recursive feasibility
probabilistic constraint
Advisor: Kouvaritakis, B
Cannon, M
The identification and characterisation of germline genetic variants that affect human cancer

Single nucleotide polymorphisms (SNPs) have great potential to serve as important biomarkers in the clinic to identify those at increased risk for developing cancer, progressing more rapidly, and not responding to therapies. However, the clinical application of cancer-associated SNPs has proven to be more complicated than expected. One of the necessary steps will certainly be the description of the molecular and cellular mechanisms behind the observed associations. The p53 tumour suppressor pathway harbours well-described SNPs that affect p53 signalling and cancer. The aim of the work presented in this thesis was to utilise this knowledge to more efficiently characterise cancer-associated SNPs. Firstly, cancer-associated SNPs in a p53 network gene, CD44, were studied. Specifically, based on CD44’s known roles in both p53-dependent and independent signalling, it was predicted that the cancer-associated SNPs could function as biomarkers for chronic lymphocytic leukaemia progression, and for the response to anti-EGFR therapy for colorectal cancer. Indeed, supportive data is presented. Next, a methodology is presented that aims to identify cancer-associated SNPs in functional p53 binding sites using genome-wide datasets. Interestingly, a SNP is identified that dramatically influences the ability of p53 to regulate transcription of the KITLG oncogene and that associates with one of the largest risks of cancer identified to date. Intriguingly, the SNP is also shown to have undergone positive selection throughout human evolution, signifying a selective advantage, but similar SNPs are demonstrated to be rare in the genome due to negative selection, indicating that polymorphisms in p53 binding sites have been primarily detrimental to humans. Lastly, and in order to begin to explore if other polymorphic transcription factor binding motifs could be found in cancer-associated SNPs, a methodology was designed to identify SNPs in E-box transcription factor binding motifs, as they are sensitive to single base pair changes and affect cancer. Taken together, the work presented in this thesis shows how the study of how SNPs associate with, and impact upon, cancer has great potential to improve both biological knowledge and clinical outcomes.

Keywords: SNPs
germline
oncology
cancer
Advisor: Bond, G
Toward an integrated methodology

The thesis is a demonstration of an integrated methodology in the investigation of Chinese paintings.
Section I outlines methods of analysis used by specialists in China, Japan and the West, and proposes their integration.
Section II implements the Integrated Methodology in the identification of prime objects in a group of works attributed to Wu Zhen now in the National Palace Museum, Taipei.
Section III presents a systematic method of investigating the non-genuine works, and charts their respective relationships to the prime objects and/or to each other.
The findings clarify fundamental issues regarding period styles in the fourteenth and fifteenth centuries and challenge, by implication, long held assumptions of authenticity of a great many works labelled with Yuan dates. They invite a reconsideration of our methodology as well as our basic assumptions of style-images associated with particular masters.
Structural and mechanistic studies on prolyl hydroxylases

Oxygen dependent prolyl-4-hydroxylation of the alpha-subunit of the hypoxia inducible transcription factor (HIF-alpha) plays an essential role in the hypoxic response. Hydroxylation of proline residues in the N- or C-terminal oxygen dependent degradation domains (NODD or CODD) increases the affinity of HIF-alpha to the von Hippel-Lindau protein (pVHL) by approx. 1000 fold so signalling for HIF-alpha degradation. With limiting oxygen, HIF-alpha hydroxylation slows, it dimerises with HIF-beta and activates the transcription of a gene array. Prolyl-4-hydroxylation also stabilises the triple helix structure of collagen, the most abundant human protein. Both the collagen and the HIF prolyl hydroxylases (PHDs) are Fe(II) and 2-oxoglutarate (2OG) dependent oxygenases.
Crystal structures of PHD2 in complex with CODD were determined in the current study. Together with biochemical analyses, the results demonstrate that catalysis involves a mobile region of PHD2 that encloses the hydroxylation site and stabilises the PHD2.Fe(II).2OG complex. When bound to PHD2 the pyrrolidine ring of the non-hydroxylated proline-residue adopts a C⁴-endo conformation. Evidence is provided that 4R-hydroxylation enables a stereoelectronic effect that changes the proline conformation to the C⁴-exo state, as observed when hydroxylated HIF-alpha is bound to pVHL and in collagen. The results help to rationalise NODD/CODD selectivity data for PHD isoforms and the effects of clinically observed mutations on PHD2 catalysis. Analyses on the interaction of nitric oxide with PHD2 are described and discussed with respect to regulation of the hypoxic response by nitric oxide.

Keywords: nitric oxide
double-stranded-beta helix
2-oxoglutarate
prolyl hydroxylase
hypoxia inducible factor
transcription
crystallography
Advisor: Schofield, C
The patristic concept of the deification of man examined in the light of contemporary notions of the transcendence of man

This thesis examines the proposition that there is a correspondence between the concept of human self-transcendence and the concept of the deification of man in that both are concerned with the bringing of human nature to its fulfilment by a process of 'redemption'.
The first issue addressed is what it means to speak of man participating in divinity, and this notion is then traced through the religion and philosophy of the ancient classical world and the later Graeco-Roman world as the background against which early Christian doctrine emerged. Some modern interpretations of the notion of transcendence as it relates to the human existent are then reviewed, with particular attention being given to the suggestion that it is legitimate to speak of man rather than God as the 'locus' of transcendence by virtue of the inherent openness of human nature to the transcendence of being that meets it in its ex-sisting in being.
The second, third and fourth chapters examine the development of the concept of deification as a way of speaking of humanity being brought to a resemblance to God, partaking of the divine nature, and thereby being enabled to realize the image of God in which man was originally created.
The fifth chapter investigates the contributions of a selection of contemporary thinkers on the notion of man's quest for fulfilment by the process of self-transcendence, that process of overcoming the aspects of being human which compromise and threaten actual human existence. The final chapter shows how the insights of contemporary thought on the concept of self-transcendence can illuminate for us the patristic concept of deification as a way of speaking about the nature and destiny of human existence and the thesis concludes with a suggestion of three areas of contemporary investigation to which this study might be related.