VictorJuiz/thesis huggingface dataset:
Allee effects: empirical analyses of wild British butterfly populations and theoretical implications for population synchrony

An Allee effect is a density-dependent process that can be responsible for the extinction of small populations. This thesis focuses on the detection of Allee effects, along with other density-dependent processes, and their influence on population synchrony. In chapter 2 I investigate the spatial variation in influential density-dependent processes and density-independent weather factors for the large skipper butterfly Ochlodes sylvanus across its British range. I find both qualitative and quantitative spatial variation in these processes and factors driving population dynamics. In chapter 3, I develop and test a Bayesian methodology, that I then use in chapter 4 to analyse local population level dynamics for 38 British butterfly species. For 35 of these species I found population level Allee effects and also found that phylogeny significant influenced a species’ susceptibility to Allee effects. Finally, in chapter 5 I examine the influence Allee effects have on network population synchrony in a theoretical framework.

Keywords: Allee effects
population dynamics
population synchrony
British butterflies
Advisor: Bonsall, M
Oliver, T
Role pf PPARalpha in the cardiac metabolic adaptation to chronic hypoxia

The principal substrate used by the normal adult human heart is free fatty acids, the remainder being, predominantly,carbohydrate. During failure, the heart becomes less reliant on fatty acid metabolism, possibly as a result of tissue hypoxia. Therefore, understanding hypoxic adaptation may explain the metabolic changes that occur during the development of heart failure.As peroxisome proliferator activated receptor alpha (PPARα) modulates cardiac fatty acid metabolism, the work in this thesis focused on the role of PPARα in cardiac metabolic adaptation to chronic hypoxia. It was found that isolated hearts from chronically hypoxic (11% O2 for 3 weeks)mice were more glycolytic, had reduced PPARα expression and decreased fatty acid metabolism,but had normal function, determined using in vivocine-MRI. 31P MRS of isolated perfused mouse hearts showed a drop in PCr with hypoxia, but ΔGATP was not altered, indicating that metabolic reprogramming was sufficient to maintain ATP production and contractile function. Increased or decreasedPPARα expression, using a high fat diet or PPARα null mice, respectively, prevented metabolic adaptation to hypoxia and caused cardiac dysfunction. Hypoxia with high fat feeding was particularly deleterious, reducing ejection fraction by 9%,possibly due to increased mitochondrial uncoupling. PPARβ/δ and γ were not involved in the adaptation to hypoxia, and none were modified by PPARα stimulation or ablation. Cardiac VEGF and PDK1, prominent hypoxia-inducible factor (HIF) targets, were increased by hypoxia, indicating that HIF may have been involved in metabolic adaption. However, high fat feeding prevented VEGF accumulation during hypoxia, suggesting that impaired HIF signalling may have contributed to the maladaptive response to hypoxia. In order to determine the relationship between HIF and PPARα, HIFwas stabilised pharmacologically using FG2216/BIC in HL-1 cardiomyocytes, to show decreased PPARα expression and caused similar metabolic changes to those seen in the in vivo hypoxic heart. In conclusion, this study demonstrated that HIF downregulation of PPARα is crucial for metabolic adaptation and maintenance of cardiac function during chronic hypoxia. Similar metabolic changes that occur in end-stage heart failure may also be a response to increasing hypoxia.

Keywords: cardiac metabolism
hypoxia
Advisor: Clarke, K
Opal

Parallel processing can provide the huge computational resources that are required to solve todays grand challenges, at a fraction of the cost of developing sequential machines of equal power. However, even with such attractive benefits the parallel software industry is still very small compared to its sequential counterpart. This has been attributed to the lack of an accepted parallel model of computation, therefore leading to software which is architecture dependent with unpredictable performance. The Bulk Synchronous Parallel (BSP) model provides a solution to these problems and can be compared to the Von Neumann model of sequential computation.
In this thesis we investigate the issues involved in providing a modular programming environment based on the BSP model. Using our results we present Opal, a BSP programming language that has been designed for parallel programming-in-the-large. While other BSP languages and libraries have been developed, none of them provide support for libraries of parallel algorithms.
A library mechanism must be introduced into BSP without destroying the existing cost model. We examine such issues and show that the active library mechanism of Opal leads to algorithms which still have predictable performance.
If algorithms are to retain acceptable levels of performance across a range of machines then they must be able to adapt to the architecture that they are executing on. Such adaptive algorithms require support from the programming language, an issue that has been addressed in Opal.
To demonstrate the Opal language and its modular features we present a number of example algorithms. Using an Opal compiler that has been developed we show that we can accurately predict the performance of these algorithms.
The thesis concludes that by using Opal it is possible to program the BSP model in a modular fashion that follows good software engineering principles. This enables large scale parallel software to be developed that is architecture independent, has predictable performance and is adaptive to the target architecture.
Production and trade of Roman and Late Roman African cookwares

This thesis is a comprehensive investigation of Roman African cookwares that examines their contribution to studies on the consequences of the incorporation of Africa into the Roman imperial economy. It aims to synthesise and analyse the most significant evidence and examines how the flow of capital, technical knowledge and people, between provinces and regions, affected production, trade and distribution trends.
The technology and organisation of Roman African cookware production are examined first, in order to create a solid foundation for the following distribution study. Scientific analyses of African cookware samples from production and consumption sites offer important additions to our knowledge of the fabric composition, technical superiority, provenance and movement of these wares around the Mediterranean. The key discussion focuses on the commercial dynamics of Roman African cookwares from local, regional and Mediterranean-wide perspectives. Beginning at the production sites, the research investigates the management and transportation of these wares from major ports in Africa Proconsularis to Mediterranean ports, and beyond. A chronological assessment of the evolution of cookware production and trade in relation to periods of political and economic change reveals the significant contribution these wares can make towards tracing and even anticipating major stages in the evolution and eventual decline of Roman economic systems. Other key achievements include the creation of a new illustrated typology with profile drawings of all the cookware forms; a gazetteer of all known African cookware production sites and the forms they produced; and a synthesis and catalogue of African cookware fabrics.
The importance of this research lies in the fact that although the abundance of Roman African cookwares on Mediterranean sites is well recognised, a catalogue and analysis of production and trade has never previously been attempted.

Keywords: economy
trade
production
cooking wares
ceramics
Advisor: Wilson, A
Myopia, retirement planning and commitment

Decisions made by individuals planning for retirement may be myopic. One way of capturing this myopia is with quasi-hyperbolic discounting. It is well known that such preferences may explain why individuals fail to provide an adequate retirement income for themselves. In this thesis, the quasi-hyperbolic discounting model is applied to a number of other decisions and outcomes related to planning for retirement. There are three main focuses. Firstly, the thesis considers a model where individuals are quasi-hyperbolic discounters over both retirement and saving, and extends the results of Diamond and Köszegi (2003). It argues that mechanisms designed to overcome myopic saving decisions may lead to unplanned early retirement. This may depend on the form of income in retirement -- regular income options such as annuities offer commitment over overconsuming early in retirement, which makes early retirement less desirable to myopic retirees.
Secondly, it tests these predictions using a new laboratory experiment. Over a two-month period, participants were asked to attend weekly sessions, and could leave the experiment (or "retire") in any week of their choosing. Part of their payment for attending these sessions was put aside and paid only after they had left. The results indicated that more impulsive individuals left the experiment earlier, both overall and relative to plans made in the first week of the experiment.
Finally, this thesis presents a model of rising wages as a forced saving mechanism. Assuming individuals face some borrowing constraints, deferred wages implicitly place some earnings aside until much closer to retirement, when quasi-hyperbolic discounters save a greater fraction of their income, increasing total retirement wealth. It also shows that demand for rising wages should disappear for people with access to more direct saving commitment mechanisms, although when these schemes offer less commitment (due to early withdrawal or early retirement options), a combination of both mechanisms is preferred.

Keywords: behavioural economics
discounting
time preferences
retirement
commitment mechanisms
experimental economics
time inconsistency
Advisor: O'Shaughnessy, T
Cyclodextrin-based rotaxanes

A series of novel [2]rotaxanes of general formula 1 has been synthesised, exploiting the hydrophobic effect to cause binding inside α- or β-cyclodextrin cavities, and making use of Suzuki coupling to stopper the rotaxane.
The size complementarity of the dumbbell and cyclodextrin units was investigated. The rotaxanes were characterised by use of 2D NMR techniques and, in one case, by X-ray crystallography.
The reactivity of one such rotaxane (α-cyclodextrin, stilbene core and carboxylic acid stoppered) was investigated by comparison with the corresponding dumbbell. The presence of the cyclodextrin was shown to have a protective influence towards some reactants.
The absorption and emission properties of these rotaxanes were compared. We have demonstrated an increase in the fluorescence quantum yield by up to a factor of three.
The photo-induced isomerisation of all the stilbene-based rotaxanes and dumbbells synthesised was surveyed; in one case it was found that encapsulation had completely prevented this isomerisation. A quantitative investigation of the proportions and extinction coefficients of the trans and cis isomers of one rotaxane in the photostationary state was undertaken, and the quantum yields of switching deduced. The rate of photodegradation and the ultimate products of this were investigated. The major photoproduct in both cases arose through photo-induced hydration of the stilbene double bond.
The final chapter is concerned with attempts to synthesise rotaxanes by reaction of a 1,3,5-triazine with an azo dye (2).
Related rotaxanes have been successfully prepared in the past1-3 , however in this instance the attempts did not result in significant amounts of rotaxane formation. This was rationalised by the shorter length of the dye.
The thesis as a whole illustrates the stabilisation of chromophores that is possible through the formation of rotaxanes.

Advisor: Anderson, H
Mathematical modelling of mitotic exit control in budding yeast cell cycle

The operating principles of complex regulatory networks are more easily understood with mathematical modelling than by intuitive reasoning. In this thesis, I study the dynamics of the mitotic exit control system in budding yeast. I present a comprehensive mathematical model, which provides a system’s-level understanding of the mitotic exit process. This model captures the dynamics of classic experimental situations reported in the literature, and overcomes a number of limitations present in previous models.
Analysis of the model led to a number of breakthroughs in the understanding of mitotic exit control. Firstly, numerical analysis of the model quantified the dependence of mitotic exit on the proteolytic and non-proteolytic functions of separase. It was shown that the requirement for the non-proteolytic function of separase depends on cyclin-dependent kinase activity. Secondly, APC/Cdc20 is a critical node that controls the phosphatase (Cdc14) branch and both cyclin (Clb2 and Clb5) branches of the cell cycle regulatory network. Thirdly, the model proved to be a useful tool for the systematic analysis of the recently discovered phenomenon of Cdc14 endocycles.
Most proteins belonging to the cell cycle control network are regulated at the level of synthesis, degradation and activity. Presumably, these multiple layers of regulation facilitate robust cell cycle behaviour in the face of genetic and environmental perturbations. To falsify this hypothesis, I subjected the model to global parameter perturbations and tested viability against pre-defined criteria. According to these analyses, the regulated transcription and degradation of proteins make different contributions to cell cycle control. Regulated degradation confers cell cycle oscillations with robustness against perturbations, while regulated transcription plays a major role in controlling the period of these oscillations. Both regulated transcription and degradation are part of important feedback loops, that combined promote robust behaviour in the face of parametric variations.

Keywords: mathematical model
cell cycle
mitotic exit
budding yeast
Advisor: Novak, B
Plato and Lucretius as philosophical literature

This thesis compares the interaction of philosophy and literature in Plato and Lucretius. It argues that Plato influenced Lucretius directly, and that this connection increases the interest in comparing them.
In the Introduction, I propose that a work of philosophical literature, such as the De Rerum Natura or a Platonic dialogue, cannot be fully understood or appreciated unless both the literary and the philosophical elements are taken into account.
In Chapter 1, I examine the tradition of literature and philosophy in which Plato and Lucretius were writing. I argue that the historical evidence increases the likelihood that Lucretius read Plato. Through consideration of parallels between the DRN and the dialogues, I argue that Plato discernibly influenced the DRN. In Chapter 2, I extract a theory of philosophical literature from the Phaedrus, which prompts us to appreciate it as a work of literary art inspired by philosophical knowledge of the Forms. I then analyse Socrates’ ‘prelude’ at Republic IV.432 as an example of how the dialogue’s philosophical and literary teaching works in practice.
In Chapters 3 and 4, I consider the treatment of natural philosophy in the Timaeus and DRN II. The ending of the Timaeus is arguably an Aristophanically inspired parody of the zoogonies of the early natural philosophers. This links it to other instances of parody in Plato’s dialogues. DRN II.333-380 involves an argument about atomic variety based on Epicurus, but also, through the image of the world ‘made by hand’, alludes polemically to the intelligently designed world of the Timaeus. Through an examination of Plato’s and Lucretius’ polemical adaptation of their predecessors, I argue that even the most seemingly technical passages of the DRN and the Timaeus still depend upon literary techniques for their full effect.
The Conclusion reflects briefly on future paths of investigation.

Keywords: literature
Phaedrus
Timaeus
Lucretius
De Rerum Natura
philosophy
Plato
influence
Republic
Epicurus
Advisor: Reinhardt, T
Fowler, P
The mechanical properties of tendon

Although the tensile mechanical properties of tendon have been well characterised, the viscoelastic and anisotropic properties remain uncertain. This thesis addresses the anisotropic and viscoelastic material properties of tendon. A method to characterise the three-dimensional shape of tendon is reported and experiments to characterise the fibre-aligned and fibre-transverse viscoelastic properties of tendon are presented.
The cross-sectional profiles of bovine digital extensor tendons were determined by a laser-slice method. Linear dimensions were measured within 0.15 mm and cross-sectional areas within 1.7 mm². Tendons were compressed between two glass plates in creep loading at multiple loads. Compression was then modelled in a finite element environment. Tendon was found to be nearly incompressible and reproduction of its isochronal load-displacement curve was achieved with a neo-Hookean material model (E ≃ 0.3 MPa). The fibre-aligned tensile mechanical properties were described using a Quasi-Linear Viscoelastic model. The model was effective at reproducing cyclic loading; however, it was ineffective at predicting stress relaxation outside the scope of data used to fit the model.
When all experimental results are considered together, two significant conclusions are made: (1) tendon is much stiffer in fibre-aligned tension than in fibre-transverse compression and (2) the fibre-aligned tensile response is strain dependant, while the transverse response is not.

Keywords: tension
compression
anisotropic
viscoelastic
measurement
tendon
Advisor: Zavatsky, A
Buckley, C
Living under different laws: the Babatha and Salome Komaise archives

The Babatha and Salome Komaise archives contain the legal documents of two Jewish women and their families, dating mostly from c. 94 C.E. to 132 C.E. The community that they attest lived in a small village which was first part of the Nabataean Kingdom but was later incorporated into the province of Roman Arabia in 106 C.E. The documents consequently provide invaluable information about a community’s experience before and after the creation of the province.
The laws and traditions in evidence in the two archives are remarkable for their diversity, exhibiting elements of Jewish, Nabataean, Roman and Hellenistic law. This thesis examines this complex legal situation and considers the ways in which people coped with the array of legal options available to them. A ‘ground-up’ approach is adopted, focusing on the people involved in the documents’ creation and use in order to detail how different parties affected the working of law in the area.
An overview of the individual documents is provided in The Survey of the Documents. The rest of the thesis is then structured according to the various groups that influenced their formulation and use: The Scribes, Legal Advisors, The Parties, The Alternatives to the Assizes and The Roman Officials. These various contributions are then brought together in the Conclusion to model how law operated in this particular community. The primary contributions of this study are therefore to Roman provincial and legal history, as well as the history of the Jewish people in the inter-revolt period.

Keywords: Roman provinces
Roman Law
Roman Arabia
Judaean Desert Documents
Jewish History
Legal Pluralism
Advisor: Goodman, M
Image processing techniques for Doppler global velocimetry

There is a demand for a whole field velocimetry technique which offers the capability of rapid characterisation of complex engineering flow fields. This thesis describes a research programme aimed at the development of a reliable Doppler global velocimeter, suited to the measurement of such flows. The programme of work undertaken is discussed with reference both to research undertaken elsewhere and to previous work on the system at Oxford. While much of the underlying technology required for the construction of an accurate and reliable velocimeter has already been studied in Oxford and elsewhere, little attention has been paid by previous workers to the examination of the impact of data processing techniques on attainable flow measurement accuracy. In the present work, a number of image processing methods have been utilised for Doppler global velocimetry data processing. Those methods are described here, together with a theoretical analysis of their expected performance when applied to Doppler global velocimetry data. The expected error resulting from image processing considerations and also from the physical characteristics of the Doppler global velocimetry hardware are quantified in such a way that error estimates may be computed for real measured data frames. The results of the application of the velocimeter to the simple test case of measuring a velocity component of a rotating disc are presented. The velocimeter was subsequently applied to the measurement of a free jet flow and to a transonic flow field in a convergent-divergent nozzle. Correlations with accepted velocity field values were undertaken, and compared to the expected error previously determined. The choice of image processing algorithms was found to be of great importance in terms of Doppler global velocimetry measurement accuracy.

Keywords: Doppler Velocimetry Image-Processing
Advisor: Ainsworth, R