VictorJuiz/thesis huggingface dataset:
LD-based SNP and genotype calling from next-generation sequencing reads.

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.

Keywords: SNP-calling
sequencing
phasing
Advisor: Marchini, J
Collective behaviour of model 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.

Keywords: Stokesian dynamics
GPU computing
low Reynolds number
microswimmers
Advisor: Yeomans, J
The validity of theology as an academic discipline

An analysis of relevant aspects of the history of science shows that theology's loss of credibility in an increasingly science-oriented age can be attributed to unresolved disputes from the past over metaphysical, epistemological and methodological issues.
In Chapters 1 and 2, an attempt is made to show that the basic disagreements between science and theology can be traced to the ongoing quest for the principles of knowing shared by all disciplines.
In Chapters 3 to 6, an attempt is made to identify these principles. Firstly, the processes and principles by which science acquires its knowledge and deems it to be objective are examined. Secondly it is argued that these same processes and principles are not the special property of science but are used by the humanities as well. Thirdly, it is contended that these principles are "empirico-critical." They enable us to bridge the gap between thought and reality and gain access to knowledge of the external world. A more comprehensive model for knowing is proposed.
Chapters 7 to 9 examine whether it is possible to apply empirico-critical principles to theology. From a study of relevant aspects of Austin Farrer's thought, it is argued (i) that the processes of knowing in theology are the same as those in the sciences and the humanities, (ii) that, though theology's procedures and techniques are necessarily different from, say, the sciences because of its subject matter, these are capable of adhering to the same principles of objectivity, and (iii) that, in principle, theological decision-making is possible, even in the most controversial debates.
The conclusion is that since the same processes and principles of trustworthy knowing in the sciences and humanities are fully applicable to theology, theology's viability as a source of trustworthy knowing should no longer be held in doubt.
Vibro toxins

Many bacterial toxins are important virulence factors, capable of instigating marked changes in the physiology of susceptible cells and tissues. Mechanisms of membrane attack by Vibrio toxins were examined on target cells, using cell physiological techniques, in particular, assays of haemolysis and radioisotope movement.
Kanagawa haemolysin (KH; commercially available preparation of the thermostable direct haemolysin (TDH)) of V. parahaemolyticus caused lysis of human (but not horse or hagfish) erythrocytes that occurred (a) after colloid osmosis due to raised cation permeability, (b) independently of the KH:red cell ratio, and (c) with a monovalent cation selectivity series (reversed Eisenman VIII with a small K+ anomaly). The binding phase of KH was longer than the 1 - 2 minutes suggested by other workers.
The KH-induced cation leak was (a) rapid in onset, (b) of a magnitude higher in the first ten minutes of treatment than subsequently, (c) of a multi-hit nature, (d) unaffected by a variety of membrane-active agents, and (e) inhibited by Zn2+, Cd2+ or mixing of toxin with dibutyl phthalate. Neuraminidase treatment of HRBC enhanced KH-induced cation influx and haemolysis, suggesting that additional receptors for TDH were unmasked by this treatment. In the presence of subhaemolytic KH, physiological levels of extracellular Ca2+ increased K+ influx by the Gardos channel, and Mg2+ (1.5 mM) decreased flux by the Na+/K+/2Cl cotransporter. There were no significant changes to sodium pump activity.
TDH and El Tor haemolysin (ETH) were purified from culture supernatants of V. parahaemolyticus and non-Ol V. cholerae, respectively. Highly purified TDH was derived from KH and used to confirm that the identified features of KH action were attributable to TDH. Although ETH also caused haemolysis by colloid osmosis secondary to increased cation permeability, it differed from TDH in its lability to air/vibration, relative magnitude of induced influx with respect to time, and selectivity series of induced lesion. Concentrated supernatants, from V. cholerae strains deleted of known virulence factors, caused morphological changes of Chinese hamster ovary cells, suggesting the presence of unidentified factors capable of perturbing cell physiology.
Confirming its potential as an enterotoxin, KH (albeit at a high dose) increased the efflux rate constant for 86Rb+ from rabbit jejunocytes. These findings are discussed in the context of a possible pathogenic role for TDH in the gastrointestinal tract.

Advisor: Hall, A
Wages, family background, on-campus performance and gender: an investigation of Chinese graduates’ first job salaries

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.

Keywords: investigation
first job
on-campus performance
Advisor: Mills, C
Murphy, R
The preparation and characterisation of novel organo-ruthenium Langmuir-Blodgett films

In recent years, there has been considerable interest in media which exhibit significant non-linear physical properties. The non-linear optical response of many materials has attracted a great deal of attention from the telecommunications industry owing to their possible use for signal processing applications. Also, applications such as thermal imaging depend ultimately upon the proficient operation of the active material within the device structure. Traditionally, inorganic materials such as lithium niobate and strontium barium niobate have been used for non-linear optics and infra-red detection. However, the last decade or so has exposed the potentially high efficiency offered by organic materials which, coupled to the ability to engineer their physical properties by subtle modifications at the molecular level, suggests an exciting and productive future.
In order to maintain compatibility with existing integrated optics and display technologies, it is often useful to process the active compound in thin film form. The stringent symmetry requirements imposed upon the molecules and their organisation in the macroscopic structure necessitates the existence of non-centrosymmetric molecular structures for second-order non-linear applications such as those mentioned above. The Langmuirandndash;Blodgett deposition technique enables such assemblies to be constructed by the sequential transfer of organic monomolecular layers from a liquid-air interface onto a solid substrate. The precise control of film thickness and molecular architecture afforded by the technique allow polar multilayer structures to be produced which possess the properties required for highly efficient second-order non-linear physical operation.
This thesis describes the development of a series of novel organo-metallic complexes which possess the necessary molecular properties for LB deposition in addition to those required for the observation of a large non-linear response. The complexes offer substantially improved thermal stability over other LB materials, and are thus appealing to the industrial device engineer. Their physical properties have been systematically studied and related to their detailed molecular structure. In particular, optical second-harmonic generation studies have shown that they possess high molecular coefficients and have provided a launching stage for further development. Their high pyroelectric response has attracted much enthusiasm from both industry and academia because of their potential commercial exploitation in thermal imaging devices.

Advisor: Roberts, G
Witchcraft prosecutions in Essex, 1560-1680

The purpose of this thesis is to consider the connections between witchcraft prosecutions and other social phenomena. A single county and a limited period of time have been chosen so that a study in depth can be made. W.Notestein's History of Witchcraft in England 1558-1718 (Washington, 1911) had already surveyed English witchcraft beliefs at a general level and the various works by C.L. Ewen, particularly his Witch Hunting and Witch Trials (1929), had shown that there was still a consid- erable amount of legal material relating to the prosecution of witches in the archives. Ewen's abstracts from Assize indictments suggested that Essex would be a suitable county for intensive study since it produced an over- whelming proportion of his witchcraft cases. The first part of the thesis is therefore an extension of the work of Ewen and Notestein. It discusses the various sources which may be used to analyse witchcraft beliefs. The cases which result from the investigation of these sources are presented in an appendix of prosecutions.
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Advisor: Thomas, K
Does prenatal maternal depression predict foetal and infant development? A study of mothers and infants in rural South India

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.

Keywords: prenatal depression
foetal heart rate
HPA Axis
temperament
infant cortisol
child development
maternal depression
Advisor: Ramchandani, P
Stein, A
'The King's Irishmen': the roles, impact and experiences of the Irish in the exiled court of Charles II, 1649-1660

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.

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)
Advisor: Barnard, T
Determining indeterminacy

This thesis investigates the role of Boulez's writings in encouraging a divergent reading of the music of the post-war avant-garde. Taking Nattiez's 1990 assertion that Boulez and Cage 'embody two radically opposed streams of post-war music history' as a point of departure, it examines Boulez's claim to a serially derived, intentional independent musical aesthetic and contrasts it with his ongoing evaluation of the chance procedures of Cage.
Concentrating throughout on Boulez's writings as primary source material, this study traces the composer's account of his independent indeterminate musical work from 1949 through three principal stages. Stage one extends from his meeting with Cage in 1949 to his rejection of Cage's method of tossing dice in 1951. Stage two begins in 1952 and continues to 1957, when Boulez wrote 'Alea' and outlined his conception for the Third Piano Sonata. Stage three extends from 1957 through his 'open-form' compositions and 'works in progress' of the 1960s and 1970s to the premiere of Répons in 1981. It also incorporates commentaries written in the 1980s and 1990s by Boulez, Nattiez and others in light of the claim that Répons 'redeemed' Boulez's troubled post-war project.
Against this background, each of the chapters addresses a key assumption about the independence of Boulez's indeterminate aesthetic. Chapter One investigates the role of electronic music in Boulez's dissociation from Cage's work after 1952. Chapter Two addresses the claim that the open-form aesthetic of the Third Piano Sonata was a response to the inspiration of the writers James Joyce and Stéphane Mallarmé. Chapter Three examines the status of the Third Piano Sonata as an 'unfinished' composition and studies its aesthetic goals in light of Boulez's compositions in the 1960s and 1970s. Chapter Four explores the claim that Répons represented the culmination of Boulez's independent indeterminate aesthetic, and that its structural goals had been unique to Boulez since 1949.
This study is framed by questions about the wider implications of a belief in Boulez's independent indeterminate aesthetic for divergent trends such as Europeanism vs. Americanism, modernism vs. postmodernism and serial structure vs. non-serial structure. In conclusion it suggests that an ongoing tendency toward historical revisionism in Boulez's texts may be a function of the difficulty in articulating an intentional indeterminate aesthetic in light of the serial inheritance.

Advisor: Franklin, P