VictorJuiz/thesis huggingface dataset:
Uncovering the genetic basis of natural variation of leaf form in Cardamine hirsuta
Keywords: Cardamine hirsuta
natural variation
QTL

A major goal in biology is to understand the genetic basis of morphological variation at different evolutionary scales, for example between and within species. Here I investigate this issue by using plant leaves as an example. Previously comparative studies between the simple leaf model plant Arabidopsis thaliana and its dissected leaf relative Cardamine hirsuta have shown that inter-specific differences in leaf shape mostly result from variation in local tissue growth and patterning (Vlad et al., 2014; Hay et al., 2006; Barkoulas et al., 2008). Here, I aim to elucidate the genetic basis of natural variation in leaf form within species, by using divergent strains of C. hirsuta. I present evidence that variation in six strains collected from geographically diverse locations results from different rates of progression of an age-dependent leaf development programme in a phenomenon known as heteroblasty. By using Quantitative trait loci (QTL) mapping with a recombinant inbred line (RIL) population derived from a cross between the Oxford and Azores strains, I detected six QTL that influence leaflet production on multiple leaves. A QTL located on the 4th linkage group was validated and selected for further analysis. Characterisation of QTL effect indicated that the QTL influences leaf form by altering the rate of heteroblastic development. Subsequently I fine mapped this QTL to a DNA segment of 48 kb containing the gene SQUAMOSA PROMOTER PROTEIN BINDING LIKE 9 (ChSPL9), a previously characterised regulator of age dependent development. The parental alleles of ChSPL9 show variation in their sequence and were transformed into A. thaliana to evaluate whether they contribute to the QTL effect. Resultant phenotypes mirrored the QTL effect suggesting that ChSPL9 does indeed contribute to this QTL effect. These results indicate that age-dependent leaf shape progression underlies variation in leaflet number within species and more broadly suggest that in the case of plant leaves different processes might underlie morphological variation between and within species.
Self-assembly and anion recognition with binuclear lanthanide complexes
Keywords: luminescence
self-assembly
macrocycle
lanthanide complex

This work describes an investigation into the solution-phase binding of anionic guests by bimacrocyclic lanthanide complexes. It outlines the preparation of different classes of complexes bearing two metallic domains, and the effects of association on both the complex and the guest. Chapter one provides a cursory introduction to the fundamental properties of the lanthanides with a focus on luminescence. A brief literature review is given on the use of emissive lanthanide probes for the sensing of analytes.
Chapter two concerns the preparation and properties of a series of binuclear complexes in which the two centres are linked with a short spacer group, with the aim of selectively sequestering small anions such as the halides in solution. The concept of luminescence titration will be introduced and then used to assess the binding parameters of a selection of guests.
Chapter three describes a related class of ditopic lanthanide complexes in which the two metal centres are separated by a semi-rigid butyne linking group. Luminescence studies are again used to evaluate the binding constants of homologous series of dianions to ascertain how the size, geometry and functionalization of the anionic guest impacts on binding.
Chapter four explores the coordination of phosphate species and assesses the ability to bind biologically significant phosphates of some of the complexes from Chapter 3.
Chapter five details an investigation into the effects on guest-selectivity of further lengthening the linking unit which separates the two macrocyclic binding domains.
Chapter six summarises the work done throughout the thesis and draws some overarching conclusions, as well as highlighting areas for further study.
Chapter seven describes the experimental procedures.
The use of novel xenografting methods to reveal differential gene expression between breast cancer at primary and metastatic sites 
Keywords: xenograft
gene array
PCR
Microenvironment
Breast
Cancer
matrix-metallo proteinases

In developed countries, breast cancer is the commonest malignancy among women. Understanding the mechanisms involved in breast cancer progression and the influence of the microenvironment on cancer cell proliferation, results in better treatments. This study aimed to optimise breast cancer xenograft rates using a novel chamber developed for tissue engineering purposes. The established tumours were subjected to enzyme digestion, creating a single cell suspension, which was then injected into immunocompromised mice at primary, metastatic and intra-cardiac sites. The resulting tumours in the mammary fat pad (MFP) and bone were compared using species-specific reverse-transcription polymerase chain reaction (RT-PCR) and cDNA microarray, to examine the influence of the microenvironment on gene expression.
The achieved xenograft graft rates of 25% were similar to those previously reported. The matrix metalloproteinase family of enzymes (MMPs) degrade extracellular matrix, influencing invasion and migration of malignant cells. RT-PCR results showed that the majority of the MMPs expressed in the cancers were stromal rather than tumour in origin. MT1-MMP, MMP-2 and MMP-11 had significantly higher expression levels in the MFP than in the bone, but MMP-9 was expressed more in the bone than MFP. There was also an up-regulation of stromal production of MT1-MMP and MMP-13 in the MFP in the presence of tumour. This may have significance when considering which MMPs are the most appropriate targets for inhibition during cancer treatment. The most significant of the differentially expressed genes on microarray analysis were trefoil factor 1 (TFF1) and insulin growth-factor binding protein 3 (IGFBP-3), both expressed significantly more in tumours from the MFP than the bone.
The thesis presented demonstrates some of the complexities of tumour-stromal interactions and supports Paget’s seed-soil theory, confirming in several ways the variation in gene expression in breast cancer between primary and metastatic sites.
'Unregarded age': texts and contexts for elderly characters in English renaissance drama, c.1480-1625
Keywords: early English drama
the elderly
elderly women
ageing
early modern English history

This study seeks to provide historical and literary contexts for elderly characters from English play-texts c.1580 to 1625. Its primary aim, from a literary perspective, is to draw attention to the ways that a better understanding of elderly characterisation can enrich the appreciation of much-studied play-texts, and to indicate some interesting features of more obscure ones. Its secondary aim is to suggest the value, for social historians of old age in early modern England, of play-texts as social evidence.
I have examined most of the published extant play-texts of the period, and have found approximately 150 of these to be relevant (the most important of these are listed in the Appendix). Because of the problems of handling all aspects of such a large amount of material, I have chosen to consider the plays chiefly as texts to be read, with little reference to their performative aspects. However, I analyse the dramas as literary as well as social documents. Specific plays provide illustrations for observations and support for various hypotheses about dramatic representations of the elderly. In some instances, I address plays which have received little critical attention.
The thesis falls into two parts. In the first three chapters, I discuss the socio-historical, cultural and non-dramatic literary contexts for representations of elderly men and women in play-texts. In chapters four through seven, I examine elderly characters in specific role or relationship categories: as sovereigns and magistrates, in sexual and marital relationships, and as parents. In the final chapter, I offer a detailed analysis of The Old Law by Thomas Middleton and William Rowley.
Partially-drained loading of shallow foundations on sand
Keywords: offshore
foundation
sand

Wave loading on offshore structures founded on sand can result in partially drained response of the foundation soil. The characteristics of the rate of loading, the permeability of the soil, and the size of the foundation affect the degree of partial drainage. Partial drainage refers to situations where pore pressures develop in the soil, and the response of the soil is neither fully drained nor undrained. This thesis is concerned with the effects of loading rate, and consequent drainage, on the behaviour of a flat footing that is founded on the surface of a saturated sand base. The results of physical tests performed in the laboratory on a model-sized footing are reported. The footing was founded on oil-saturated fine sand and was subjected to combined loading. The effect of the vertical, horizontal, and rotational displacements are reported. The response of the footing is analysed in the context of existing drained foundation models that are based on work hardening plasticity theory. The rate dependency of the vertical load:deformation behaviour and the combined yield surfaces are described.
Large-scale layered systems and synthetic biology: model reduction and decomposition
Keywords: Timescale Separation
Layering
Biochemical Reaction Networks
Model decomposition
Model reduction
Dissipativity
Storage Functions
Singular Perturbation

This thesis is concerned with large-scale systems of Ordinary Differential Equations that model Biomolecular Reaction Networks (BRNs) in Systems and Synthetic Biology. It addresses the strategies of model reduction and decomposition used to overcome the challenges posed by the high dimension and stiffness typical of these models. A number of developments of these strategies are identified, and their implementation on various BRN models is demonstrated.
The goal of model reduction is to construct a simplified ODE system to closely approximate a large-scale system. The error estimation problem seeks to quantify the approximation error; this is an example of the trajectory comparison problem. The first part of this thesis applies semi-definite programming (SDP) and dissipativity theory to this problem, producing a single a priori upper bound on the difference between two models in the presence of parameter uncertainty and for a range of initial conditions, for which exhaustive simulation is impractical.
The second part of this thesis is concerned with the BRN decomposition problem of expressing a network as an interconnection of subnetworks. A novel framework, called layered decomposition, is introduced and compared with established modular techniques. Fundamental properties of layered decompositions are investigated, providing basic criteria for choosing an appropriate layered decomposition. Further aspects of the layering framework are considered: we illustrate the relationship between decomposition and scale separation by constructing singularly perturbed BRN models using layered decomposition; and we reveal the inter-layer signal propagation structure by decomposing the steady state response to parametric perturbations.
Finally, we consider the large-scale SDP problem, where large scale SDP techniques fail to certify a system’s dissipativity. We describe the framework of Structured Storage Functions (SSF), defined where systems admit a cascaded decomposition, and demonstrate a significant resulting speed-up of large-scale dissipativity problems, with applications to the trajectory comparison technique discussed above.
LD-based SNP and genotype calling from next-generation sequencing reads.
Keywords: SNP-calling
sequencing
phasing

Next-generation sequencing is revolutionising in genetics, where base-by base information for the whole genome is available for a large sample of individuals. This type of data is becoming commonly used and will continue to be in the near future. One of the first questions arising is the identification of novel variants and subsequently genotype calling of the individuals in the sample. However, given the cost of sequencing, so far most projects are sequencing individuals in low to medium coverage.
In this thesis, we present two distinct methods for SNP and genotype calling from low-coverage sequencing data, TreeCall and MVNcall, that combine sequencing and Linkage Disequilibrium (LD) information. We begin by describing the pipeline for next-generation sequencing analysis and existing methods for SNP and genotype calling using low-coverage sequencing information. Subsequently, we present the two novel LD-based methods for SNP and genotype calling. The two methods developed assume a study design where the individuals are both genotyped and sequenced at low-coverage. The genotypes are used to construct a haplotype scaffold, where the LD information is extracted, either by the construction of genealogical trees (TreeCall), or the approximation of a windows of contiguous SNPs of the scaffold by a multivariate normal distribution (MVNcall).
Both methods have been applied on real datasets from the 1000 Genomes project and compared to other LD-based methods applied on the same datasets, mainly in terms of genotype calling and phasing. Whereas TreeCall gives lower genotype concordance rates than the other methods, MVNcall provides the highest genotype concordance rates for a dataset with a small sample size (Lowcoverage pilot of the 1000 Genomes project).
Applying the MVNcall on a larger dataset (Phase 1 of the 1000 Genomes project), it achieves an overall genotype discordance rate of 0.58%, whereas SNPTools achieves an overall genotype discordance rate of 0.57%, Thunder 0.56%, and BEAGLE 0.61% (comparison based on Axiom chip). The main advantage of MVNcall is in terms of phasing accuracy, where by using a haplotype scaffold, and especially in the case where the haplotype scaffold is phased using pedigree information, it provides accurate haplotypes. MVNcall is also extended to incorporate trio information for genotype calling. Experiment on a deeply sequenced trio leads to an accurate set of haplotypes of the trio with switch error rates as low as ~0.28 for the parents and ~0.12 for the offspring.
Collective behaviour of model microswimmers
Keywords: Stokesian dynamics
GPU computing
low Reynolds number
microswimmers

At small length scales, low velocities, and high viscosity, the effects of inertia on motion through fluid become insignificant and viscous forces dominate. Microswimmer propulsion, of necessity, is achieved through different means than that achieved by macroscopic organisms. We describe in detail the hydrodynamics of microswimmers consisting of colloidal particles and their interactions. In particular we focus on two-bead swimmers and the effects of asymmetry on collective motion, calculating analytical formulae for time-averaged pair interactions and verifying them with microscopic time-resolved numerical simulation, finding good agreement.
We then examine the long-term effects of a swimmer's passing on a passive tracer particle, finding that the force-free nature of these microswimmers leads to loop-shaped tracer trajectories. Even in the presence of Brownian motion, the loop-shaped structures of these trajectories can be recovered by averaging over a large enough sample size.
Finally, we explore the phenomenon of synchronisation between microswimmers through hydrodynamic interactions, using the method of constraint forces on a force-based swimmer. We find that the hydrodynamic interactions between swimmers can alter the relative phase between them such that phase-locking can occur over the long term, altering their collective motion.
Wages, family background, on-campus performance and gender: an investigation of Chinese graduates’ first job salaries
Keywords: investigation
first job
on-campus performance

The last five decades have witnessed an increasing interest in the education-employment transition. In China, millions of university students graduate each year. Their employment has important impact on various aspects of the Chinese society. Additionally, university-work transition is related to the well-being of university graduates and their families. Therefore the university-work transition in China deserves more attention from scholars and practitioners.
This thesis examines the determination of Chinese university graduates’ first job salaries. It investigates whether and how university graduates’ family background, on-campus performance (OCP) and gender are linked with their first job salaries. The thesis distinguishes three dimensions of graduates’ family background: Hukou status, parental CCP membership and income. It distinguishes three dimensions of graduates’ OCP: academic achievements, professional capability and political/ideological attainment. Information collected through interviews is used to interpret the statistical results. The results show that graduates’ first job salaries are significantly affected by their professional skills, political/ideological attainments and family income. Graduates’ gender, academic performance and family Hukou status have little impact on their first job salaries.
Compared with the widely observed wage disparities among less educated workers caused by gender and Hukou status, this thesis provides evidence that higher education helps reduce the gender wage gap and rural-urban disparity in China. Analyses in the thesis are consistent with ‘state as equalizer’ and ‘market as equalizer’ theories. This thesis provides little evidence to support the marketized transition theory, as we find graduates’ first job salaries are still largely affected by their political/ideological attainments in university. Considering the unique context, the results suggest that some widely used human capital indicators and productivity signals are not applicable in the Chinese labour market. Practical implications are derived from the thesis.
Does prenatal maternal depression predict foetal and infant development? A study of mothers and infants in rural South India
Keywords: prenatal depression
foetal heart rate
HPA Axis
temperament
infant cortisol
child development
maternal depression

Introduction: Prenatal maternal depression is associated with an increased risk of psychopathology in childhood. The understanding of the mechanisms underlying this association is limited. Further, despite high rates of prenatal depression in the developing world, no research investigating this issue exists from these settings.
Objectives: The primary objectives of this thesis are to study the association between prenatal maternal depression and the following early offspring outcomes in a non-smoking, non-alcohol consuming prenatal sample from rural, South India:
i. Foetal stress responsivity, measured through foetal heart rate (FHR)
ii. Infant stress responsivity, measured through infant cortisol response to immunisation
iii. Infant temperament.
Methods: 194 pregnant women from Solur, India were assessed for depression. The first 67 mothers with elevated symptoms of prenatal depression and the first 66 controls underwent FHR monitoring to study foetal stress responsivity. 58 mother-infant dyads returned at 1.5-3 months post birth. Infant salivary cortisol was measured before and after immunisation. Information on infant temperament and maternal postnatal depression (PND) was also collected.
Results: Twenty nine mothers (14.9%) met a diagnosis of major depression during pregnancy while 67 (34.5%) had elevated symptoms of prenatal depression.
Whilst there were no linear association between prenatal depression and foetal responsivity, a curvilinear (U shaped) association existed with the foetuses of mothers with very high and very low levels of prenatal depression having elevated stress responses compared to those with moderate levels of prenatal depression.
Prenatal depression predicted infant cortisol responsivity independent of PND (B=13.08, p=0.02).The relationship between infant cortisol responsivity and prenatal depression was also U shaped.
There was no association between prenatal depression and infant temperament.
Conclusions: This is the first study from the developing world investigating the relationship between prenatal depression and offspring outcomes. It provides evidence suggestive of the programming influence of prenatal depression on the developing offspring.
'The King's Irishmen': the roles, impact and experiences of the Irish in the exiled court of Charles II, 1649-1660
Keywords: Richard Talbot
John Bramhall,Bishop of Derry
allegiance
Peter Talbot (SJ)
James Butler,Marquis of Ormond
Theobald,Lord Taaffe
identity
Western Europe (Seventeenth Century)
Ireland (Seventeenth Century)
Murrough O'Brien,1st Earl of Inchiquin
Gilbert Talbot
Britain (Seventeenth Century)
Daniel O'Neill
Thomas Talbot (OFM)

This thesis represents an important investigation into the much-neglected period of exile endured by many Royalists as a consequence of the violence and alienation of the Wars of the Three Kingdoms (1639-1651).Drawing from extensive archival research conducted in Britain, Ireland and Europe, this study expands upon existing literature on royalism, British and Irish interaction with Continental Europe and seventeenth-century mentalities more generally in order to illumine the unique issues faced by these exiles. Central to this study are the roles and experiences of the Irish element within Charles II’s exiled court. Recent studies focussed upon the place of Ireland within Europe and the North Atlantic are employed to assess such issues as confessional division, court culture, the impact of memory and the influence of conflicting European ideas upon the survival of the exiles and the course of the restoration cause. A thematic, rather than chronological structure is employed in order to develop these interpretations, allowing for an approach which emphasizes the place of individuals in relation to broader Royalist mentalities. Dominant figures include Murrough O’Brien, Lord Inchiquin (c. 1614-1674), Theobald, Lord Taaffe (d. 1677), John Bramhall (1594-1663), Church of Ireland bishop of Derry, Daniel O’Neill (c. 1612-1664), Father Peter Talbot (SJ) (c. 1618/20 – 1680) and James Butler, marquis of Ormond (1610-1688). Through investigation of Irish strands of royalism and the wider issues in which they were set in the course of civil war and exile, this thesis makes a powerful argument for the need to consider seventeenth-century ideas of allegiance and identity not only within a ‘Three Kingdoms’ approach, but Europe more generally. It also makes a compelling case for the centrality of Irish Royalists in the formation and implementation of policy during the exile period through their familiarity with and access to European centres of power and influence.