VictorJuiz/thesis huggingface dataset:
Antecedents of educational attainment: parental involvement, genetics, and non-cognitive skills

Education-driven social inequalities are increasing in the advanced countries. Educational attainment is to large extent driven by one’s early social circumstances and then in turn has a significant impact on one’s later life chances. Sociologists have been successful at documenting many processes relating to educational attainment. However, one important antecedent has not been fully integrated into the sociological toolbox of mechanisms - genetic transmission of educational propensity. My thesis aims to use the methodological advances from the field of social science genetics, namely the educational attainment polygenic score, to better understand how disparities in genetic predispositions, through their interplay with social environments, contribute to the divergence of educational and occupational outcomes.
Over the course of three empirical chapters, I explore the dynamic influence of genetic propensity to education over the life course: from adolescence to early and, eventually, late adulthood. Using the Add Health dataset, I investigate the relationship between parental involvement and child’s genetic potential and how it shapes educational outcomes. The Wisconsin Longitudinal Study helps me to look under the hood of the educational attainment polygenic score by allowing me to investigate the mediating role of non-cognitive skills. I also look into how the complex interconnection of social background, genetics, and education influences occupational attainment.
This thesis makes several contributions to the existing body of research in the fields of social stratification and social science genetics. First of all, I embed the genetic mechanism in the broader sociological framework of attainment. My hypotheses and the construction of variables are theorydriven. I qualify my general findings by exploring their heterogeneity by gender and socio-economic status. Second, I open up the black box of the educational attainment polygenic score, which is widely used in the literature but whose true meaning remains elusive. I study the mediating mechanisms in the form of non-cognitive skills which can help one realise their genetic potential. Third, I show that genetic propensity to education dynamically interacts with social environments and spans the whole life course.

Advisor: Mills, MC
Brazel, DM
The organisation and dynamics of Escherichia coli outer membrane proteins

The outer membrane of E. coli is a component of the cell envelope with significant physiological importance. This multifunctional membrane allows the influx of nutrients and simultaneously excludes toxic compounds, such as antibiotics, which must cross this membrane to elicit their cytotoxic effect. The composition and general structure of this membrane are well known, an asymmetric lipid bilayer containing LPS in the outer leaflet, phospholipids in the inner leaflet, densely populated by integral β-barrel outer membrane proteins and extensively linked to the underlying peptidoglycan through certain lipoylated inner leaflet outer membrane proteins. Little is known, however, about the lateral organisation and dynamics of the proteins in this membrane. In this thesis I investigate the organisation and dynamics of two highly abundant outer membrane proteins: the general porin, OmpF, and the lipoprotein, Pal.
OmpF distribution—visualised with Colicin N fluorescent fusion proteins—could be sorted into distinct categories related to the cell cycle, and these distributions arose due to the biased insertion of OmpF at mid-cell. This biased mid-cell insertion also caused old OmpF to localise to the cell poles during growth. Superresolution investigations showed that at fine resolutions, OmpF displayed a significant degree of clustering in the outer membrane and was highly restricted in its diffusion (Dapp: 0.0018 µm2s−1).
Pal, investigated by PALM-SPT, was shown to accumulate at the septum of dividing cells, revealing a key mechanism by which this protein stabilises the outer membrane during division. Pal diffusion was highly restricted (0.0042 µm2s−1) as a result of peptidoglycan binding, demonstrated by an almost 5 fold increase in diffusion coefficient (0.0205 µm2s−1) upon removal of the PG binding domain.
This work shows that integral β-barrel OMP distribution and dynamics are dictated by the subcellular biased assembly of these proteins into a membrane that does not permit lateral diffusion. In addition, analysis of Pal demonstrates the vastly different diffusive environment of the inner leaflet of the outer membrane and the contribution of underlying cell envelope components on protein diffusion.

Keywords: Superresolution Microscopy
Colicins
Microbiology
OmpF
OMPs
Membrane Biology
Microscopy
Bacteriocins
Outer Membrane Protein
Advisor: Kleanthous, K
Mohammed, S
Rhyme in Shakespeare's theatre

This thesis analyses, contextualises, and celebrates rhyme in Shakespeare’s plays. Taking a historical formalist methodology, it reads rhyme’s local and structural functions both in aesthetic terms and within the network of cultural, textual, and theatrical associations that nourish them. The audiences’ varied horizons of expectation regarding rhyme – from literary reading, earlier forms of theatre, previous encounters with Shakespeare and other early modern dramatists, and wider performance culture – provide a basis for examining rhyme’s effects and allusions. The thesis explores the fully rhyming drama that preceded and influenced Shakespeare’s theatre; the productive tension in early modern dramatic rhyme between the classical and the English; the self-reflexive humour of Shakespeare’s early comedies; the different ways in which two Henriads invoke the register of the Mirror for Magistrates; the development of the rhyming lover; the influence of clowns, fools, and their improvised rhyme performances on Shakespeare’s work, specifically King Lear; the ways in which Othello, Hamlet, and Macbeth subvert different established conventions of the early modern dramatic couplet; Shakespeare’s negotiation of the line and the line ending in his late work, and its relation to the human and the wild in Cymbeline; and finally the legacy of Shakespearean dramatic rhyme, with brief discussions of post-Restoration adaptations and contemporary hip-hop Shakespeare productions. The thesis aims to be holistic not only in its approach to the various agents of theatre experience, but also in the way it views rhyme within a play. Rather than focusing solely on specific instances in their local contexts, it considers these moments as parts of broader structural and tonal principles. The argument of this thesis is that Shakespeare’s dramatic rhyme is worthy of study, not only for its powerful place in individual moments, but as a device with far-reaching associations and engagements: structural, allusive, and cultural.

Keywords: Rhyme
Form
Shakespeare
Renaissance
Theatre
Advisor: van Es, B
Mapping tissue magnetic susceptibility and its biological correlates in the human brain

Magnetic resonance imaging (MRI) of the brain visualises anatomical structures on the scale of millimetres, but is nevertheless sensitive to microscopic tissue features. One of the features that is intrinsically important to MRI is magnetic susceptibility (χ). In brain imaging, χ contrast between structures primarily arises from tissue iron, calcium and myelin content, all of which are important tissue constituents related to a variety of brain functions and diseases.
Interest in quantification of tissue χ distribution has thus led to quantitative susceptibility mapping (QSM), a technique that quantifies tissue χ distributions through sophisticated postprocessing of phase images. The past decade has witnessed great progress in QSM. The histological correlates of χ estimates have been established including an approximately linear relationship with iron concentration validated using post-mortem brain tissue, and in vivo studies have demonstrated QSM’s ability to detect disease-relevant changes, particularly iron accumulation in neurodegeneration.
The work presented in this thesis seeks to further investigate the biological correlates of tissue χ measures in previously unexplored settings. The first experimental chapter discusses the development of a QSM processing pipeline for fixed post-mortem, whole-brain data. Using this pipeline, we compared the resulting χ maps in brains from patients with amyotrophic lateral sclerosis and controls, with validation against iron and myelin histology. The second and third research chapters discuss implementing QSM in a large-cohort study. We developed a robust QSM processing pipeline to produce χ estimates in 35,885 subjects from the UK Biobank imaging study. We carried out phenotypic association studies and the first genome-wide association studies of χ estimates in the brain, identifying a broad range of associated phenotypes and genetic variants.
The results presented in this thesis demonstrate the richness of information provided by QSM and hopefully promote greater clinical take-up of QSM in the future.

Keywords: Quantitative Susceptibility Mapping
Magnetic Resonance Imaging
Advisor: Tendler, B
Miller, K
Connecting the pathways of retinal ganglion cell survival and death in glaucoma: new tools to diagnose, repair and regenerate

A recent analysis of blindness and vision impairment trends over the past 30 years by the Vision Loss Expert Group for the Global Burden of Disease Study revealed that glaucoma remains the leading cause of irreversible blindness worldwide in an ageing population. The mechanisms underlying retinal ganglion cell degeneration in glaucoma are not fully understood.
This thesis examines two key features of glaucomatous neurodegeneration, namely impairment of optic nerve axonal transport and dysregulation of aqueous outflow.
First we demonstrate the continued need to develop new diagnostic and therapeutic approaches for glaucoma by assessing rates of glaucoma progression in the local Cambridge population. We show there is still a clear rate of progression despite tertiary level access to the best treatments currently available.
We describe a new non-invasive tool to assess and quantify the dysregulation of aqueous outflow. Despite being a key therapeutic target in current clinical practice, our understanding of this system is derived largely from post-mortem studies, indirect estimates or, more recently, invasive techniques that alter the physiology of aqueous outflow and are limited in the information they provide. There are currently no non-invasive techniques available that directly visualise detailed aqueous outflow in vivo. We use a non-invasive imaging modality developed to image the anterior microcirculation of the human eye – haemoglobin video imaging – to examine aqueous outflow into the episcleral venous circulation in detail, and to observe and quantify alterations in aqueous outflow following treatments that aim to selectively target this pathway.
We then evaluate a combined receptor-ligand gene therapy onstruct which overexpresses brain derived neurotrophic factor and its receptor tropomyosin kinase B on optic nerve axonal transport and retinal ganglion cell function. We use a rat glaucoma model and a humanised tauopathy model of reduced axonal transport and showed combined overexpression is more effective in stimulating axonal transport than either receptor administration or ligand administration alone. We also demonstrate functional recovery in the glaucoma model.
Furthermore, we offer promising evidence there may be an improvement in short term memory loss in the tauopathy model, suggesting that this strategy to target intrinsic mechanisms to improve neuronal function and facilitate repair may be relevant to multiple neurodegenerative diseases.
We then assess whether manipulating the degenerative process could also be associated with optic nerve regeneration in experimental glaucoma. We demonstrate for the first time the glaucomatous optic nerve also has the potential to regenerate using strategies previously only used after traumatic injury.

Advisor: Martin, K
Osborne, N
Form unfollows function: subversions of functionality

This practice-led doctoral thesis explores what happens when we consider works of art as designed objects (i.e., their process of production as a process of design) through two discrete yet mutually informing components: a series of original objects and a written dissertation.
This practice-led doctoral thesis explores what happens when we consider works of art as designed objects The objects, which play with the language of industrial design yet are presented in a traditional fine art exhibition setting, are intended to oscillate between a sense of utility and a sense of futility, thereby destabilising the ground on which they are presented and received. By straddling both registers, the objects resist neat subsumption either into the category of “art” or that of “design,” consequently urging their re-evaluation.
The dissertation, which draws on Donald Norman’s theory of the design of everyday things on the one hand and Wolfgang Kemp’s theory of reception aesthetics in the visual arts on the other, sets up a theoretical framework for considering the products of artistic production in design terms (namely, affordances, constraints, signifiers, feedback, mapping, and conceptual model). Through a close focus on three works of modern art—Claes Oldenburg’s "Saw," Joseph Beuys’s "Capri Battery," and Lygia Clark’s "Critter"—the dissertation offers keyhole comparisons of everyday products and the canonical sculptures, whereby the analyses of the former enable unexpected “functional” readings of the latter.
Through these two complementary forms of enquiry (the object-making and the writing), the thesis aims to challenge traditional distinctions between different modes of creative production, and it argues for a consideration of artistic production as a rational mode of visual and material production that does not follow means-end rationality.

Keywords: modern art
design of everyday things
art and design
design
contemporary art
Lygia Clark
modern sculpture
reader-response theory
reception aesthetics
Claes Oldenburg
Donald Norman
Wolfgang Kemp
Joseph Beuys
Advisor: Gaiger, J
Martin, D
Supersymmetric geometries in string theory

Supersymmetric vacua of string theory endow the internal space with a special geometric structure. We refer to these structures collectively as supersymmetric geometries. The objective of this thesis is to study two classes of supersymmetric geometries and their associated quantum field theories arising from string compactifications.
In the first part of this thesis, we study M-theory compactifications on G2- manifolds. We focus on the gauge sector of such compactifications by studying the Higgs bundle, characterizing a local ALE-fibration over a supersymmetric three-cycle M3, obtained from a partially twisted 7d super Yang-Mills theory on M3. We derive the BPS equations and find the massless spectrum for both abelian and non-abelian gauge groups in 4d. The mathematical tool that allows us to determine the spectrum is Morse theory, and more generally Morse-Bott theory. We make contact with twisted connected sum (TCS) G2- manifolds, which form the largest class of examples of compact G2-manifolds. M-theory on TCS G2-manifolds is known to result in a non-chiral 4d spectrum. We determine the Higgs bundle for this class of G2-manifolds and provide a prescription for how to engineer singular transitions to models with chiral matter.
In the second part, we consider GK geometries that arise in AdS compactifications of IIB string theory and M-theory and play a key role in the geometric dual to c-extremization. We provide a mathematically oriented exposition of GK geometries in general dimension. We study the extension of the geometric dual of c-extremization for 2d (0, 2) superconformal field theories (SCFTs) that have an AdS3 dual realized in Type IIB with varying axio-dilaton, i.e. F- theory. M/F-duality implies that such AdS3 solutions can be mapped to AdS2 solutions in M-theory, which are holographically dual to superconformal quantum mechanics (SCQM), obtained by dimensional reduction of the 2d SCFTs. We analyze the corresponding map between holographic c-extremization in F- theory and I-extremization in M-theory, where in general the latter receives corrections relative to the F-theory result.

Advisor: Schafer-Nameki, S
Sparks, J
Experimental and analytical investigations of non-skeletal carbonate production

The overriding aim of this research is concerned with understanding the chemical controls on carbonate sedimentation in naturally occurring highly alkaline systems that produce enigmatic mineral assemblages. The main approach taken here is to characterize the kinetic pathways of Ca-Mg-carbonate precipitation and mineralization in systems lacking a biological carbonate factory and to understand the relationship between fluid chemistry and mineralogy in non-classical nucleation regimes. The first line of research explores the kinetics of Ca-Mg-carbonate nucleation and recrystallization in the presence of phosphate (PO4) as an inhibitor in high-alkalinity experiments. We identify and constrain new crystallization pathways to Mg-rich carbonates magnesite and disordered dolomite from amorphous precursors that overcome energy barriers under Earth surface conditions. The second line of research explores CaCO3 nucleation under Neoproterozoic seawater conditions. We identify and constrain saturation state thresholds required for nucleation in these settings that are influenced by micromolar concentrations of PO4. The third line of research explores geological carbonates to test our hypotheses that PO4 may have influenced the mid-Neoproterozoic CaCO3 factory. We reveal new P records that identify abundant and widespread P distribution at significantly elevated PO4 concentrations in Neoproterozoic Tonian-aged carbonate rocks. Together, this research indicates enhanced P-cycling in the Tonian that influenced the CaCO3 factory and may have resulted in enhanced concentrations of bioavailable P that was crucial for biological evolution.

Keywords: Limestone
Mg-calcite
Experimental
Geochemistry
Precamabrian
Carbonate
Magnesite
Neoproterozoic
Tonian
Phosphate
Advisor: Tosca, N
Robinson, S
Holocaust memory and its mediation by teachers: a study of England and France (1987 - 2018)

Holocaust education has expanded in its purpose and status between 1987 and 2018, reflecting increasing practices and rituals of remembrance in Holocaust memory. Whilst changes in policy, museums, memorials, cultural productions and school textbooks have all been examined by Holocaust scholars, the practice of Holocaust education in classrooms has avoided scrutiny in memory studies and history of education despite becoming a primary place of memory transmission. This thesis considers the role of the secondary school history teacher, as a consumer, producer and mediator of Holocaust memories. It argues teachers do not simply present the ‘official’ textbook narrative of history to school pupils, but construct a historical memory based on their beliefs about the purpose of history education, the needs of society and the needs of their pupils. Their lessons and pedagogies are informed and challenged by the cultural memory of the Holocaust, memories of their own family histories of the Second World War, and also current affairs and politics. Accordingly, their mnemonic nexus articulates the dynamics of collective memory.
Using oral semi-structured ‘life history’ interviews with history teachers, this thesis explores the mnemonic influences on individual teachers’ understanding of the Holocaust in four localities across England and France. Combined with a review of professional teaching magazines and journals, and local newspapers, this thesis charts the trajectory of Holocaust education across Aix-en-Provence, Leeds/Bradford, Lincolnshire and Marseille. By doing so, it looks for moments when family memory enriched or subverted dominant narratives of the Holocaust, as well as the relationship between Holocaust education and other ‘difficult histories’ of genocide and empire. As teachers engage emotionally with the Holocaust, this thesis argues that teachers also aimed to produce emotion in classrooms as a tool to shape ‘future citizens’ and to develop local, national and European identities.

Keywords: Holocaust
genocide
memory
teachers
oral history
Holocaust education
Advisor: Gildea, R
Tisdall, L
Inferring dated genealogies from modern and ancient genomes

Tree sequences encode the ancestral history of a sample of genomes, reflecting the sum total of what is theoretically knowable about the sample’s evolutionary history. However, to realise the promise of this structure, scalable methods that infer time-resolved tree sequences from both modern and ancient samples are needed. In this thesis, I address this challenge and thus realise the power of tree sequences for population genetic analysis. First, I investigate a key assumption of the tree sequence inference algorithm tsinfer: that allele frequency reflects relative allele age. I derive an exact iterative formula for the expected accuracy of frequency in assigning the relative age of pairs of alleles at unlinked loci under the coalescent. Using coalescent simulations approximating human demographic history, I further show that allele frequency correctly orders 91.6% of the mutation pairs that are relevant for topological inference.
Second, I introduce new statistics to summarise genetic relationships between individuals and populations. Genealogical Nearest Neighbours quantifies topological relationships in a tree sequence and is applied to population sequencing datasets. The related Genomic Descent statistic quantifies descent from ancient individuals. I use this statistic to reveal links between Neolithic Britons and modern Sardinian individuals, as well as between an Afanasievo family of four and UK Biobank participants from traditionally Celtic regions of Britain and Ireland.
Third, I introduce tsdate, an approximate Bayesian method for inferring the age of ancestral haplotypes conditional on a tree sequence topology. I validate the algorithm using simulations and empirical analyses, the latter indicating that 96.3% of tsdate-estimated derived allele ages from Chromosome 20 of the 1000 Genomes Project are consistent with radiocarbon-dated ancient samples.
Finally, I use an iterative approach combining tsinfer and tsdate to infer the largest time-resolved genealogy constructed to date with 3,719 ancient and modern samples from eight datasets. The genealogy provides estimates of the distribution of time to most recent common ancestor for the 215 populations in the datasets, recovers patterns of descent from Archaics, and suggests that up to 17.5% of variant sites could be the result of more than one ancestral mutation. I also introduce a simple, non-parametric estimator of the spatiotemporal properties of inferred ancestors that recapitulates key events in hominin history. These results demonstrate that tree sequences are a powerful means of synthesising genetic data and provide rich insights into human evolution.

Keywords: population genetics
ancient DNA
tree sequence
Advisor: Gil, M
Jerome, K
Yan, W