VictorJuiz/thesis huggingface dataset:
The factors affecting reproductive success and breeding density in a rural population of blackbirds, Turdus merula L

The aim of this thesis was to identify the factors determining reproductive success and breeding density in a rural population of blackbirds occupying contiguous woodland and farmland habitats. Once these factors were identified, an attempt was made to assess the quality of the two habitats in terms of reproductive success.
Predation was the major factor affecting reproductive success. There were no significant effects of habitat on predation when habitat was defined as farmland, woodland and woodland edge. When defined in terms of nesting density, high density 'hot-spot' areas had significantly greater nesting cover and lower predation rates than territories in farmland or in the rest of the wood.
Parents could adjust their provisioning rates according to chick demand. Consequently chicks in larger broods were not significantly different in weight to chicks in smaller broods. The seasonal change in clutch size is therefore well adapted to conditions for raising nestlings, although there was indirect evidence that female condition may limit clutch size early in the season. The nestlings were fed two main diet types, earthworms and caterpillars, the availability of the former being related to rainfall and temperature and the latter occurring in a seasonal peak. Nestlings fed on predominantly earthworm diets were significantly heavier, thus caterpillars are probably a lower quality prey. Starvation was a minor cause of nestling mortality. There was some evidence that farmland birds were more dependent on earthworms than woodland birds, and consequently only farmland broods showed a significant relationship between weight and rainfall. This conferred no disadvantage to farmland broods, although this may have implications for reproductive success in very dry years.
Farmland breeders showed some characteristics of a population in a suboptimal habitat. Breeding density was low on farmland compared with woodland. This in part may have been due to lack of suitable nesting cover. An experiment with artificial nests indicated that predation would be proportionately higher on farmland if nesting density was increased. Year-to-year variations in density across the whole study site paralleled the relative harshness of the preceding winter. Food supplementation prior to the breeding season had no effect on subsequent breeding density or clutch size.
It is concluded that farmland is potentially a sub-optimal habitat if subject to different conditions of weather or breeding density than those observed during the three years of this study.

Advisor: Hatchwell, B
The computation of Greeks with multilevel Monte Carlo

In mathematical finance, the sensitivities of option prices to various market parameters, also known as the “Greeks”, reflect the exposure to different sources of risk. Computing these is essential to predict the impact of market moves on portfolios and to hedge them adequately. This is commonly done using Monte Carlo simulations. However, obtaining accurate estimates of the Greeks can be computationally costly.
Multilevel Monte Carlo offers complexity improvements over standard Monte Carlo techniques. However the idea has never been used for the computation of Greeks. In this work we answer the following questions: can multilevel Monte Carlo be useful in this setting? If so, how can we construct efficient estimators? Finally, what computational savings can we expect from these new estimators?
We develop multilevel Monte Carlo estimators for the Greeks of a range of options: European options with Lipschitz payoffs (e.g. call options), European options with discontinuous payoffs (e.g. digital options), Asian options, barrier options and lookback options. Special care is taken to construct efficient estimators for non-smooth and exotic payoffs. We obtain numerical results that demonstrate the computational benefits of our algorithms.
We discuss the issues of convergence of pathwise sensitivities estimators. We show rigorously that the differentiation of common discretisation schemes for Ito processes does result in satisfactory estimators of the the exact solutions’ sensitivities. We also prove that pathwise sensitivities estimators can be used under some regularity conditions to compute the Greeks of options whose underlying asset’s price is modelled as an Ito process.
We present several important results on the moments of the solutions of stochastic differential equations and their discretisations as well as the principles of the so-called “extreme path analysis”. We use these to develop a rigorous analysis of the complexity of the multilevel Monte Carlo Greeks estimators constructed earlier. The resulting complexity bounds appear to be sharp and prove that our multilevel algorithms are more efficient than those derived from standard Monte Carlo.

Keywords: pathwise sensitivities
Financial derivatives
Differentiation of stochastic processes
Barrier options
Computational complexity
multilevel Monte Carlo
Sensitivities of SDE solutions
Binary options
Digital options
simulation
Option pricing
Lookback options
Greeks
European options
Risk
Vibrato Monte Carlo
stochastic differential equations
Monte Carlo simulations
Asian options
Advisor: Giles, M
Applications of DABSO in metal catalysis

Chapter 1 discusses the importance of the sulfonyl moiety in biological compounds and the developments in the use of sulfur dioxide and sulfur dioxide donors in metal catalysis and organic synthesis.
Chapter 2 focuses on the serendipitous discovery, optimisation and exploration of a route towards the synthesis of sulfones via an N-aminosulfonamide intermediate exploiting both palladium-catalysed aminosulfonylation and the predisposition of N aminosulfonamides to decompose to the sulfinate salt (Scheme 1).
Scheme 1
Chapter 3 investigates the synthesis of benzosultams with an aryl-N-SO2 linkage. A range of benzosultams and its derivatives were prepared after optimisation of a synthetic sequence involving palladium-catalysed aminosulfonylation and a subsequent Buchwald– Hartwig coupling (Scheme 2).
Scheme 2
Chapter 4 describes efforts towards the synthesis of a benzosultam with an aryl-SO2-N linkage through various precursors and metal-catalysed routes using DABSO as the sulfur dioxide source (Figure 1).
Figure 1
Chapter 5 provides a summary of this thesis and outlines possibilities for future work.
Chapter 6 provides experimental details and data for compounds discussed in this thesis.
Appendix A details a brief investigation into the synthesis of N aminosulfonamides from heteroaryl iodides as an extension of the Willis group palladium-catalysed aminosulfonylation reaction (Scheme 3).
Scheme 3
Appendix B presents 1H and 13C NMR spectra as well as X-ray crystallographic data of key compounds.

Keywords: chemistry
Advisor: Willis, M
The performance of jacked pipes

Pipejacking is a tunnel construction technique which is increasing in popularity, but fundamental research is necessary to fully understand the extent of its possible uses and limitations. This dissertation reports on laboratory research into the performance of reinforced concrete pipes, assessment of pipe joints and the use of joint packing materials. The research has addressed specific problems which the tunnelling fraternity have raised. Model pipes have been constructed at scales of 1:6 and 1:10.5 using reinforced microconcrete and they have been tested in either a sand filled chamber or between supporting yokes. Current British Standard tests have been used as a control on the quality of pipe manufacture. Data have been recorded of changes in soil pressures, pipe geometry and strains induced in the pipes. The tests have investigated deformation of pipes, deflection angles between consecutive pipes, distribution of stress concentrations and the effects of the use of joint packing materials on allowable jacking loads and induced stress magnitudes in the pipes. A review of current pipejacking practice is presented and recommendations for the control and supervision of pipejacking operations are made. The conclusions include recommendations for fieldwork monitoring and implications of this stage of the research to industry. Recommendations are made for maximum installation jacking loads for any given deflection angle between pipes. The prediction of friction angles at the pipe soil interface have been assessed at different soil stress levels and new recommendations are made. The effects of cyclic loading on the pipejacking system and transfer from jacking load to ground loading once the pipes are installed are presented. The criteria used in the selection of a recommended joint packing material for use in jacking operations have been included. Failure modes of pipes are stated and recommendations are made for pipe design, installation and monitoring to predict and prevent such failures. This dissertation is the report on the first stage of an overall programme of research which is now set to progress with monitoring of pipejacking operations on several construction sites.

Keywords: pipe jacking
Advisor: Milligan, G
Growth factors and lipid transport in early mammalian development

The insulin-like growth factors (IGFs) are broadly distributed in the human conceptus and are thought to play a role in the growth and differentiation of tissues during development. The addition of IGF-I and IGF-II to early cleavage stage mouse embryos in vitro did not influence their growth rate to the blastocyst stage; they neither affected cell numbers nor cell doubling. The addition of basic fibroblast growth factor (bFGF) marginally increased blastocyst hatching, and in serum-free conditions the addition of IGF-I plus bFGF to postimplantation embryos partially compensated for the absence of serum.
Using in situ hybridization it has been demonstrated that human blastocysts produced by in vitro fertilization show no IGF-II expression, thus bracketing the time of first accumulation of IGF-II mRNA to between 5 and 18 days postfertilization. The pattern of IGF-II expression shows specific age-related differences in different tissues. In the first trimester kidney, for example, expression is found in the cells of the metanephric blastema and this is dramatically reduced as the blastema differentiates. The reverse pattern of expression is also seen in that there is an increase in expression of IGF-II in the cytotrophoblast layer of the placenta with gestational age. IGF-II expression is most frequently, but not exclusively, associated with areas of high mitotic activity and it is possible that IGF-II functions in an autocrine/paracrine fashion during human development.
Apolipoprotein B (apo B) is thought to be involved in mediating the transport of lipids to the growing human conceptus. Apo B expression is detected in the hepatocytes of the fetal liver, in the large endodermal cells of the secondary yolk sac, and in the lining epithelium of the intestine from 6-12 week post-fertilization human conceptuses. The fetal brain shows no detectable hybridization. The cellular distribution of apo B transcripts emphasizes the similar functions of these cells. Unlike the situation seen in the adult, immunoprecipitation experiments demonstrate that only apo B-100 is synthesized and secreted by the liver, yolk sac and intestine in the early stage of human development.

Advisor: Graham, C
Genetic variation and sexual system evolution in the annual mercuries

The Mercurialis annua L. (Euphorbiaceae) species complex comprises a group of closely related lineages that present a wide range of sexual-systems, making it a valuable model for the study of plant sexual-system evolution. Within this polyploid complex, diploid populations are dioecious, and polyploid populations either monoecious or androdioecious (males coexist with functional hermaphrodites). The primary aim of this thesis was to use patterns of genetic diversity to elucidate the evolutionary origin and maintenance of the sexual-system diversity in M. annua. The phylogeny of the M. annua complex was reconstructed using chloroplast and ITS DNA sequence. This, in conjunction with morphometric analysis, showed that both hexaploid M. annua, and a novel species from the Canary Islands (newly described here as Mercurialis canariensis), were allopolyploid in origin. Such an origin for hexaploid M. annua suggests that androdioecy may have been able to arise in this group as a consequence of hybridisation between a monoecious lineage, tetraploid M. annua, and a dioecious lineage, M. huetii. Artificial crosses were used to show that hexaploid M. annua has disomic marker inheritance, and a statistical approach was developed to quantify genetic diversity and differentiation in polyploids with disomic inheritance. Strong gradients in genetic (allozyme) diversity at a pan-European scale were used to infer the existence of separate glacial refugia for dioecious and monoecious races of M. annua, at the eastern and western ends of the Mediterranean basin, respectively. A metapopulation model had previously been proposed to explain the ecological maintenance of androdioecy in M. annua. Here, population-level patterns of genetic diversity were used as an indirect test of this model. The discovery of lower within-population diversity, and of greater genetic differentiation between populations, for monoecious populations than for androdioecious populations was consistent with the metapopulation model, and suggests that androdioecy is maintained by the occurrence of regular local extinction.

Keywords: phylogeny
population genetics
mating-system
Mercurialis annua
androdioecy
Advisor: Pannell, J
Harris, S
Formal relationships in sequential object systems

Formal specifications describe the behaviour of object-oriented systems precisely, with the intent to capture all properties necessary for correctness. Relationships between objects, and in a broader sense the relationship between whole components, may not be adequately captured by specifications. One critical component of specifications having a role in relationships are invariants which define a constraint between multiple objects. If an object's invariant relies on external objects for its conditions, correct operations which abide by their specifications modifying these external objects may violate the constraint. Such an invariant defines a relationship between multiple objects which is unsound since it does not adequately describe the responsibilities which the objects in the relationship have to each other.
The root cause of this correctness loophole is the failure of specifications to capture such relationships adequately as well as their correctness requirements. This thesis addresses this shortcoming in a number of ways, both for individual objects in a sequential environment, and between concurrent components which are defined as specialized object types. The proposed Colleague Technique [29] defines sound invariants between two object types using classical Design-by-Contract [35] methodologies. Additional invariant conditions introduced through the technique ensure that no correct operation may produce a post-state which does not satisfy all invariants satisfied by the pre-state.
Relationships between objects, as well as their correct specification and management, are the subjects of this thesis. Those relationships between objects which can be described by invariants are made sound with the Colleague Technique, or the lightweight ownership type system that accompanies it. Behavioural correctness beyond these can be addressed with specifications in a similar manner to sequential systems without concurrency, in particular with the use of runtime assertion checking [11].

Keywords: JML
object oriented
design-by-contract
Java
computing
specification
formal methods
DbC
type system
Advisor: McKeever, S
Control of cell growth in root hairs

During development plant cells acquire different shapes and often these shapes are correlated with their function. To understand how these cell shapes and forms develop, it is necessary to understand the underlying regulatory mechanisms of cell growth. The growth of root hair cells is a good example of cells undergoing localized cell expansion to acquire their final form. In Arabidopsis two bHLH transcription factors RHD6 and its target RSL4 have been identified as key regulators of the initiation and elongation phases of root hair (H) cell development. However in order to obtain a better understanding of this RHD6-RSL4 transcriptional pathway controlling root hair growth, the characterization of the immediate targets of RSL4 is necessary. Here I describe the use of a glucocorticoid inducible expression system coupled with the microarray analysis to identify the direct targets of RSL4. Thirty four putative direct target genes of RSL4 were identified. I assessed the requirement of nine of these genes by characterising the phenotypes of plants homozygous for the loss of function alleles. Plants homozygous for loss of function mutations in AT1G22620/SAC1, AT1G35670/CPK11/CDPK2, AT1G30870/PRX7 and AT5G03540/EXO70A1 (44% of the genes analysed) exhibited defects in root hair growth. Taken together my results not only identified potential RSL4 target genes but also demonstrated that RSL4 controls root hair growth by regulating genes that encode proteins involved in cell signalling, vesicle trafficking and cell wall modification.

Keywords: RSL4 gene targets
Advisor: Dolan, L
‘Every Age is a Canterbury Pilgrimage’: art and the sacred journey in Britain, c. 1790 – 1850

This thesis examines the intersections of the concept of pilgrimage and the visual imagination in Britain from the years 1790 to 1850. Historically, distinctions between understandings of pilgrimage as motif, metaphor, artistic process, and actual journey have been blurred to varying degrees, resulting in the creation of images that were at once narratives, memorials, and stimuli for contemplative journeys from pictorial space to imagination. In the first half of the nineteenth century, religious architecture, sacred landscapes, and the emblematic figure of the pilgrim with coat, hat, and scrip functioned as temporal reminders of a promised land to come, as mediated through artistic practice. Through a close analysis of a range of interrelated visual sources, I contend that pilgrimage, both in practice and as a form of mental contemplation, helped to shape the religious, literary, and artistic imagination of the period and beyond. This study draws out the various levels at which pilgrimage engaged the visual imagination. In doing so it offers a detailed perspective on the conjunction of content, form, meaning, and process for artists and theorists, as notions of the transfer of ‘spirit’ from sacred space to represented space re-emerged as a key aspect of the theological and artistic discourse of the period. Chapter 1 outlines the antiquarian dissemination of medieval pilgrimage texts and images. I suggest that an awareness of pilgrimage as embodying the real and imagined emerged with the recovery of allegorical texts, histories of actual pilgrimages, and an interest in pilgrimage souvenirs. The discussion moves on to intersections between pilgrimage and religious art in Chapters 2 - 4, including the idea of painting as pilgrimage, as demonstrated through specific case studies, and the refashioning of relics and religious ruins as contemporary sites of pilgrimage (Chapter 5).

Keywords: art history
material and visual culture
religion
nineteenth century
pilgrimage
Britain
Advisor: Garnett, J
Kemp, M
The complexity and expressive power of valued constraints

This thesis is a detailed examination of the expressive power of valued constraints and related complexity questions. The valued constraint satisfaction problem (VCSP) is a generalisation of the constraint satisfaction problem which allows to describe a variety of combinatorial optimisation problems. Although most results are stated in this framework, they can be interpreted equivalently in the framework of, for instance, pseudo-Boolean polynomials, Gibbs energy minimisation, or Markov Random Fields. We take a result of Cohen, Cooper and Jeavons that characterises the expressive power of valued constraint in terms of certain algebraic properties, and extend this result by showing yet another connection between the expressive power of valued constraints and linear programming. We prove a decidability result for fractional clones. We consider various classes of valued constraints and the associated cost functions with respect to the question of which of these classes can be expressed using only cost functions of bounded arities. We identify the first known example of an infinite chain of classes of constraints with strictly increasing expressive power. We present a full classification of various classes of constraints with respect to this problem. We study submodular constraints and cost functions. Submodular functions play a key role in combinatorial optimisation and are often considered to be a discrete analogue of convex functions. It has previously been an open problem whether all Boolean submodular cost functions can be decomposed into a sum of binary submodular cost functions over a possibly larger set of variables. This problem has been considered within several different contexts in computer science, including computer vision, artificial intelligence, and pseudo-Boolean optimisation. Using a connection between the expressive power of valued constraints and certain algebraic properties of cost functions, we answer this question negatively. Our results have several corollaries. First, we characterise precisely which submodular polynomials of degree 4 can be expressed by quadratic submodular polynomials. Next, we identify a novel class of submodular functions of arbitrary arities that can be expressed by binary submodular functions, and therefore minimised efficiently using a so-called expressibility reduction to the (s,t)-Min-Cut problem. More importantly, our results imply limitations on this kind of reduction and establish for the first time that it cannot be used in general to minimise arbitrary submodular functions. Finally, we refute a conjecture of Promislow and Young on the structure of the extreme rays of the cone of Boolean submodular functions.

Keywords: valued constraints
pseudo-Boolean optimisation
min-cut
submodularity
complexity
CSP
MRF
expressive power
Advisor: Jeavons, P