VictorJuiz/thesis huggingface dataset:
An ethnomethodologically-informed study of interaction in the MOOC

The massive open online course (MOOC) is an online educational platform that has garnered significant popularity in recent years and is viewed by some as a transformative force in tertiary education. Originally designed to replicate a classroom setting, social interaction should be a fundamental part of using the MOOC. Most research into MOOCs has focused on using quantitative 'big data' to understand social interaction of large cohorts of students over entire courses. However, recently there has been a turn towards understanding qualitative aspects of social interaction in order to really take account of its features.
A substantial gap in existing research on MOOCs is understanding the fine-grained qualitative features of social interaction in terms of the sequential reportable-observable unfolding of activity. In this thesis, these features are explored in detail in order to unpack and enrich the current understanding of social interaction in MOOCs, and to consider how this might inform improved MOOC interface design that better supports it.
This thesis uses mainly video data of social interaction from quasi-naturalistic studies, that is then subject to ethnomethodologically-informed analysis. The studies involve small groups of participants, both co-present and distributed, collaboratively performing open-ended tasks around MOOC educational content. The analyses reveal recurring patterns in interaction that are largely glossed over by many existing 'big data'-based studies.
I pull out a number of conceptual findings that extend current understanding of interaction in MOOCs. Firstly, I show how an act like a ‘click’ may have a diverse and complex role to play in the unfolding of social interaction, at both an individual and group level. Secondly, I explicate some of the key interactional resources that distributed participants may use to transcend boundaries in space and time. I show, for example, how visibility of the immediate context of an act appears to give it a sense of meaning. Thirdly, I discuss how dynamic and complex participation can be; revealing how students can emergently construct and transition between different and multi-faceted modes of participation. Drawing on these findings, I contribute substantively to the MOOC platform by surfacing a number of important issues to inform system requirements.
Methodologically, I reflect on my key learnings taking this approach in terms of advantages and challenges. I find it can be difficult to learn how to undertake an ethnomethodologically-informed study. However, as I show in the thesis, this approach brings to the fore some of the rich seen-but-unnoticed ways participants accomplish social interaction, which other automated methods are not designed to do.

Advisor: Jirotka, M
The economy of empire building: wild ginseng, sable fur, and the multiple trade networks of the early Qing dynasty, 1583-1644

This project examines the multiple trade networks of the early Qing period and argues that the early Manchu rulers accumulated wealth from trade in the process of Qing empire formation. Empires come to mean rule over extensive, far-flung territories, far beyond the original 'homeland' of the rulers. The Qing empire was such a case, as it expanded from a tiny town in Northeast Eurasia to Chinese territory where Ming China ruled. This thesis thus sheds new light on the Qing empire from the economic aspect - describing how the Qing rulers, based on the fusion of steppe and agricultural economies, constructed the Qing empire.
The time frame covered spans from 1583, when Nurhaci started to embark on internal conflicts with other local Jurchen tribes, to 1644, when the Manchus seized control of Beijing, claiming rulership of China. The thesis builds on the archival sources in Manchu, Mongolian, Chinese, and Korean, as well as contributing to the understanding of the remarkable economic transformation over the course of the Qing empire. Previous academic scholarship in Chinese, Japanese, and English focuses on the bilateral trade connections between Nurhaci and Ming China. The primary aim of this thesis, however, is to counter this scholarship by differentiating between the achievements of Hong Taiji and those of Nurhaci over the course of the early Qing empire building. Additionally, it explores wealth accumulation via the establishment of multiple trade networks that developed during Hong Taiji's reign. These multiple trade networks were centred on two prized goods sourced from the Jurchen territory: wild ginseng and sable fur. These valuable items were crucial sources of income for the Qing.
State and parameter estimation of physics-based lithium-ion battery models

This thesis investigates novel algorithms for enabling the use of first-principle electrochemical models for battery monitoring and control in advanced battery management systems (BMSs). Specifically, the fast solution and state estimation of a high-fidelity spatially resolved thermal-electrochemical lithium-ion battery model commonly referred to as the pseudo two-dimensional (P2D) model are investigated. The partial-differential algebraic equations (PDAEs) constituting the model are spatially discretised using Chebyshev orthogonal collocation enabling fast and accurate simulations up to high C-rates. This implementation of the P2D model is then used in combination with an extended Kalman filter (EKF) algorithm modified for differential-algebraic equations (DAEs) to estimate the states of the model, e.g. lithium concentrations, overpotential. The state estimation algorithm is able to rapidly recover the model states from current, voltage and temperature measurements. Results show that the error on the state estimate falls below 1% in less than 200s despite a 30% error on battery initial state-of-charge (SoC) and additive measurement noise with 10mV and 0.5°C standard deviations.
The parameter accuracy of such first-principle models is of utmost importance for the trustworthy estimation of internal battery electrochemical states. Therefore, the identifiability of the simpler single particle (SP) electrochemical model is investigated both in principle and in practice. Grouping parameters and partially non-dimensionalising the SP model equations in order to understand the maximum expected degrees of freedom in the problem reveals that there are only six unique parameters in the SP model. The structural identifiability is then examined by asking whether the transfer function of the linearised SP model is unique. It is found that the model is unique provided that the electrode open circuit voltage curves have a non-zero gradient, the parameters are ordered, and that the behaviour of the kinetics of each electrode is lumped together into a single parameter which is the charge transfer resistance. The practical estimation of the SP model parameters from frequency-domain experimental data obtained by electrochemical impedance spectroscopy (EIS) is then investigated and shows that estimation at a single SoC is insufficient to obtain satisfactory results and EIS data at multiple SoCs must be combined.

Keywords: identifiabilility
state estimation
extended Kalman filter
parameter estimation
Chebyshev orthogonal collocation
electrochemical modelling
lithium-ion battery
single particle model
pseudo-two dimensional model
Advisor: Howey, D
Duncan, S
Improving sensitivity and specificity in diffusion MRI group studies

Diffusion MRI provides a unique opportunity to study the brain tissue architecture at a microscopic level. More specifically, it allows to infer biophysical properties of the axons in the white matter in-vivo. Microstructural parameters are widely used in multi-subject studies to track pathological processes, follow normal development and aging, or investigate behaviour. This thesis aims to identify and potentially address the limitations and pitfalls in voxelwise comparison of diffusion MRI parameters across subjects.
To allow for accurate matching of brain structures across subjects, non-linear transformation that spatially aligns the data is required. We demonstrate that using advanced registration methods, we can outperform the standard registration-projection approach both in terms of sensitivity and specificity.
The coarse resolution of the data typically causes partial volume effects that bias the diffusion parameters and potentially mislead the interpretation of a group study outcome. We provide evidence that these effects can be addressed by constraining the diffusion model parameter space, which leads to marginally lower sensitivity, but allows an accurate interpretation of the results. Additionally, we suggest that additional information inferred with a data driven approach might mitigate the loss in sensitivity.
Finally, we design an original tract-specific modelling framework that enables to estimate microstructural parameters unbiased by the presence of foreign fibre populations or tissues. We demonstrate the sensitivity of our method in a study relating microstructure and behaviour.

Keywords: diffusion mri
computational neurology
group studies
machine learning
Advisor: Smith, S
Jbabdi, S
Germline determinants of colorectal cancer risk and outcome

Colorectal cancer (CRC) is the third most common global cancer. Approximately one fifth of phenotypic variance in CRC is attributable to additive genetic inputs: the disease risk is heritable. The nature and location of these genetic inputs has been the preoccupation of association studies over the last decade. Variation at some 30 genomic loci influences sporadic CRC risk. However, in Mendelian disorders this risk is almost absolute. Such cancer syndromes include Lynch syndrome, caused by defective DNA mismatch repair, and serrated polyposis syndrome, which has no confirmed genetic cause.
The aim of this thesis was to continue exploring how common and rare germline genetics influence CRC liability. A reexamination of the chromosome 15 GREM1 locus in seven imputed UK case-control cohorts revealed a new, genome-wide significant risk polymorphism at rs17816465, independent of previously reported associations. This polymorphism lies near to conserved regulatory elements within the FMN1 gene and had allele-specific luciferase activity.
Similar fine-mapping at the POLD3 locus showed a large haplotype carrying CRC risk, making further refinement of the signal difficult. A risk score incorporating a correlate of this haplotype and all other independently CRC-associated polymorphisms was significantly higher in cases than in controls, but did not predict patient survival. Instead, the risk score anticorrelated with tumour driver mutation burden in publically available colorectal cancer data.
This thesis also reports the mapping and calling of the whole-genome sequences of 299 UK CRC and adenoma patients. Rare variants within this cohort were shown to be shared beyond expectation in geographic clines not visible to principal component analysis. Future rare variant association studies will need to correct for cryptic population structure using other statistical tools.
In contravention of recruitment criteria, known polyposis syndrome genes were often deleteriously mutant within the genomes. Also, filtering on phenotype or gene subsets revealed potentially pathogenic variants in either whole-genome or whole-exome sequences in EXO1, RPA4, and LNX1. One individual displayed homozygous mutation of the mismatch repair gene MSH3. This was the second account of a germline MSH3 change causing tetranucleotide-unstable CRC. Lastly, a family suffering serrated polyposis was shown to carry a heterozygous RNF43 frameshift that segregated with the disease.
This thesis improves our account of both sporadic and Mendelian CRC risk. It identifies a new genome-wide significant association with sporadic CRC at the GREM1 locus and provides a haplotypic account of risk at POLD3. It also describes two rare germline causes of Mendelian CRC: MSH3 and RNF43 loss of function.

Advisor: Tomlinson, I
Dancing on the devil’s staircase: the synchronization of the quasi-biennial oscillation in the tropical stratosphere

In this thesis we investigate the variability of the Quasi-Biennial Oscillation (QBO), which is the dominant mode of variability in the tropical stratosphere. In particular, we study the susceptibility of the QBO to the phenomenon of synchronization; that is, the adjustment of the rhythms of the QBO under the influence of a periodic external force. We approach the problem using a combination of theoretical analysis, numerical modelling, and observational study. The dynamics of the QBO are studied in detail using the Holton-Lindzen partial differential equation. We introduce various forcing terms to this equation, to simulate the effects of the Brewer-Dobson circulation, the Semi-Annual Oscillation, the Inter-Tropical Convergence Zone, and tropical wave forcing variations on the QBO. We find that the QBO enters a state of synchronization in its interactions with all of the above forcing terms, with the exception of the Semi-Annual Oscillation. The general structure of QBO synchronization takes the form of either exact frequency locking, discrete multi-cycle periods, or quasiperiodic behaviour. By recasting the Holton-Lindzen equation into the form of a descent rate model, we demonstrate that the dynamics of the QBO period can be described using a simple one-dimensional ordinary differential equation, which is shown to be closely related to the circle map. This simplification greatly reduces the complexity of the model, whilst retaining all the key observed features of synchronization.
We study the dynamics of the QBO in reanalysis and general circulation model datasets, using a combination of Extended Empirical Orthogonal Function analysis and analytic phase techniques. We show that the descent rate of the QBO correlates with the strength of tropical upwelling. Further, by defining a statistical measure for QBO synchronization based on the evolution of QBO periods, we demonstrate that both the observed and modelled QBOs behave in a way that is consistent with synchronization to the annual cycle. The observed QBO is found to be phase synchronized with the Brewer-Dobson circulation, and we find that it jumps irregularly between the 2 : 1, 5 : 2, and 3 : 1 synchronization ratios. We find evidence that the phase slips of the observed QBO tend to occur during periods when the El Niño Southern Oscillation is in a strong positive phase.
Our results make a robust case in favour of the proposition that the QBO is synchronized to the annual cycle via seasonal and inter-annual variations in tropical upwelling strength and tropical wave activity.

Keywords: Synchronization
Stratosphere
Quasi-Biennial Oscillation
Advisor: Read, P
Moroz, I
Osprey, S
Ecological and evolutionary significance of crassulacean acid metabolism in the montane genus puya (Bromeliaceae)

Little is known about the evolution and ecology of crassulacean acid metabolism (CAM) in the genus Puya Molina. CAM is a photosynthetic pathway typified by nocturnal CO2 fixation and is regarded as a water-saving mechanism. Puya is one of the largest genera in the pineapple family (Bromeliaceae), with 226 species distributed across the Andes to Costa Rica and the Guiana Shield, and from sea level to 5000 m. About 21% of Puya species are CAM and at least 10 of these CAM species occur above 3000 m. The main aim of this thesis was to uncover new evidence to understand the ecophysiology and evolution of CAM in the montane genus Puya. The prevalence of CAM and C3 species in Puya was estimated from carbon isotope values of 161 species. The climatic niche of constitutive CAM species and C3 species of Puya was modelled using georeferenced herbarium records and climatic variables to evaluate the differences between their niches.
The evolution of CAM in Puya was investigated by reconstructing the ancestral photosynthetic pathway on an AFLP phylogeny and by studying positive selection in the genes encoding the key enzyme phosphoenolpyruvate carboxylase (PEPC). The coldresistance and the thermal lability of PEPC was investigated for high- and low- elevation CAM species of Puya to explore the potential molecular adaptations of CAM plants in high-elevation environments. The present study concludes that the common ancestor of Puya was a cold-resistant plant. This is suggested to explain the prevalence of Puya at highelevations.
The evolution of CAM was correlated with changes in the climatic niche, and occurred multiple times in Puya. These multiple origins were not independent because the common ancestor of Puya was likely to be a weak CAM plant (based on a diagnostic Arg679 residue in the PEPC sequence). It is likely that populations of P. chilensis gained CAM by introgression with P. alpestris ssp. zoellneri. Weak CAM photosynthesis and coldxv resistance allowed Puya to colonise the Andes from the south to the north; and, in the process, constitutive CAM and C3 evolved. The later-evolving species in the genus are suggested to have lost their capacity for CAM as they radiated into more mesic habitats during their colonisation of the northern Andes.

Keywords: Andes
Puya
CAM
Crassulacean acid metabolism
South America
Advisor: Smith, J
Harris, S
The theme of conspiracy in fifteenth-century Italian humanist literature

This study investigates fifteenth-century Italian humanist literature that deals with the topic of conspiracy, focusing on the most important texts that contain accounts of political plots. This thesis identifies for the first time a 'thematic genre' of monographic works devoted to this specific political theme: an output that consists of texts belonging to different literary genres and that enjoyed widespread diffusion in the second half of the Quattrocento, when the development of this strand of literature proves to be closely connected with the emergence of a centralized political ideology in Italian states.
The first chapter of the thesis provides a general introduction to the theme of conspiracy in humanist literature, defining this 'thematic' genre and contextualizing it in the historical background of 1400s. Then, the following chapters focus on the most significant works on fifteenth-century political plots which are examined as case studies: Orazio Romano's epic poem Porcaria (ch. 2) and Leon Battista Alberti's epistle Porcaria coniuratio (1453) (ch. 3); Giovanni Pontano's historical work De bello Neapolitano (1465-1503) (ch. 4); and Angelo Poliziano's Coniurationis commentarium (1478) (ch. 5). The four main chapters provide an in-depth examination of each work, from a historical, stylistic, and critical perspective, illustrating the circumstances of compositions, the influence of the classical legacy on the texts and the process of imitation performed by the authors. This textual analysis shows the political perspectives that inform these works and the narrative strategies adopted by the humanists to represent the historical events and deal with the burning issue of conspiracies.
The final chapter (Conclusions), as a comparative study, traces the overall evolution of the issue of conspiracies in humanist literature and points out the recurring patterns, narrative approaches and political angles that characterize the literary transfiguration of this topic. These texts reveal the growth of a new princely ideology in that period and unveil the significant interplay between historiographical, political, and literary elements in shaping this aspect of political thought, allowing us to trace the development of a blossoming theory of statecraft that had a significant influence also on the idea of modern state. The texts are published in the Appendix of the thesis and are followed by apparatuses which illustrate thoroughly the classical models used by the authors. The texts and apparatuses act as a support for the critical study in the preceding chapters.

Advisor: McLaughlin, M
Novel phosphasalen ligands for the ring-opening polymerisation of lactones

Bio-derived polymers offer a sustainable alternative to petroleum-derived polymers. One such polymer, polylactide (PLA) is synthesised from the ring-opening polymerisation (ROP) of rac-lactide (rac-LA). The monomer contains two stereocentres which gives a range of tacticities. The isotactic ROP of rac-LA yields the most desirable polymer properties (physical and mechanical properties) and is quantified using a Pi (probability of isotactic enchainment) value. This thesis investigates tri- and tetradentate ligands coordinated to zinc(II), aluminium(III) and indium(III) to understand the ligand effects on both rate and isoselectivity.
The first results chapter, Chapter 3, outlines the synthesis of a tetradentate salen ligand, its analogous phosphasalen ligand, where the imine bonds are replaced with iminophosphorane bonds and a hybrid ligand containing a mixture of both imine and iminophosphorane bonds. The salen, phosphasalen and hybrid ligands are coordinated to both aluminium and indium and used as initiators for the ROP. The indium hybrid initiator yields the highest isoselectivity (Pi = 0.71) which is significantly higher than its salen and phosphasalen analogues (Pi = 0.51 - 0.52)
Chapter 4 investigates structure-activity relationships of the indium hybrid initiator, by modification of the ligand scaffold. Bulkier ortho-phenolate substituents do not affect rate or isoselectivity. Electron-withdrawing chloride substituents increase rate but decrease isoselectivity (Pi = 0.61). Modification of the phosphorus substituents yields the highest isoselectivity value (Pi = 0.75). It may be hypothesised that isoselectivity depends upon steric hindrance at both ortho-substituents and at phosphorus. Furthermore, the synthesis of a ferrocene containing indium hybrid complex is developed for future use in redox-switch catalysis.
Chapter 5 describes the synthesis of two tridentate half-phosphasalen ligands and their coordination chemistry with zinc(II) and indium(III). Zinc initiators are active but display poor polymerisation control and low isoselectivity values (Pi = 0.67). Zinc complexes, with a less sterically encumbered ligand, preferentially form a homoleptic complex, which cannot be used in ROP. Indium initiators are slower than analogous half Schiff base initiators reported in the literature but show an improved isoselectivity value (Pi = 0.72).

Advisor: Williams, C