VictorJuiz/thesis huggingface dataset:
Model-driven design and uncertainty quantification for cardiac electrophysiology experiments

The goal of systems biology is to provide a predictive and quantitative understanding of complex biological systems and their experimental data using mathematical and computational models. Mathematical modelling and computational simulation has been a crucial tool for basic research in cardiac electrophysiology for decades, and has provided remarkable insights into many physiological mechanisms. More recently these quantitative cardiac models have begun to transition into safety-critical clinical and pharmaceutical development applications. Using cardiac mathematical models in such applications requires high levels of credibility as well as an accurate quantification of the uncertainty in the model predictions. In this thesis, we develop a suite of Bayesian inference and uncertainty quantification techniques and software tools to study cardiac cellular electrophysiology. We then design and perform high-throughput experiments to construct and validate cell-specific mathematical models for human Ether-à-go-go-Related Gene (hERG) channel dynamics, and to study its temperature dependence, which is important for cardiac safety pharmacology and cardiac action potential models. Using the Bayesian statistical framework together with the high-throughput measurements allows us to quantify the uncertainty and variability of the model parameters. We also model and analyse how experimental artefacts contribute to the observed variability of these recordings, allowing us to separate the effects of these artefacts from physiological behaviour. A similar approach for uncertainty characterisation and experimental design will have to be adapted for other ion currents to create better predictive models, as accurate ion channel models are essential for constructing trustworthy cardiac action potential models.

Keywords: hiPSC-CM
high-throughput
variability
model discrepancy
ion channel
hERG
patch clamp
temperature dependence
Bayesian inference
uncertainty
experimental design
cardiac drug safety
cardiac model
Advisor: Gavaghan, DJ
Mirams, GR
Clerx, M
Polonchuk, L
Wang, K
Renewing left-wing ideas in late twentieth-century Britain: Marxism Today, c. 1977-1994

This thesis explores how the political thought of left-wing authors based around the journal Marxism Today transformed between the late 1970s and the 1990s. Under the editorship of Martin Jacques, the journal became a site of major debates on the British left over the course of the period and its contributors came from a wide variety of intellectual, social and political backgrounds. I trace their changing approaches to a number of themes, assessing whether their revisionism was characterised by ideological capitulation to their political opponents on the right. Their reception of the Italian Marxist Antonio Gramsci; attitudes to the boundaries of the state; debates about class, identity and new social movements; shifting perspectives on European integration; and the communitarian political thought of Geoff Mulgan are all charted and analysed in this thesis. Notwithstanding the preoccupation with ‘Thatcherism’ among the journal’s authors, this thesis complements recent revisionist historical scholarship which seeks to de-centre Thatcher’s government from histories of the 1980s and which complicates descriptions of the final decades of the twentieth century as an age of neo-liberal revolution. I illustrate the specific dynamics that shaped left-wing debate in the 1980s, arguing that these years were consequential to the revision of left-wing ideas and that the authors of Marxism Today departed significantly from dominant forms of twentieth-century British socialism. In examining the interventions made within the journal, in addition to a wide range of contemporary publications and archival material, I place the more famous essays and debates in their historical context where other historians and commentators have failed to pay due regard to the status of the journal’s articles as primary sources. Through the systematic treatment of Marxism Today from a history of political thought perspective, I demonstrate that the left was not a passive, defeated force in the period.

Advisor: Jackson, B
Development of new generation receivers for experimental cosmology with the cosmic microwave background and systematic effect studies

Most of current and future Cosmic Microwave Background (CMB) Radiation experiments are targeting the polarized B-mode signal. The small amplitude of this signal makes a successful measurement challenging for current technologies. Therefore, very accurate studies to mitigate and control possible systematic effects are vital to achieve a successful observation. An additional challenge is coming from the presence of polarized Galactic foreground signals that contaminate the cosmological signal. When they are combined, the foreground signals dominate the polarized CMB signal at almost every relevant frequency. Future experiments, like the LiteBIRD space-borne mission, aim at measuring the CMB B-mode signal with high accuracy to measure the tensor-to-scalar ratio r at the 10−3 level.
In this thesis, after briefly introducing the science case, the LiteBIRD mission and some of its key technologies, we focus on a few systematic effects concerning mostly the band-pass response. In this context we present novel studies to determine the impact of band-pass uncertainties on the data.
Good control over the response of the superconductive detector is another key ingredient for the success of the mission. We present our modelling of the detector response and a framework to study non-linearity effects due to thermal and optical loading fluctuations.
Lastly, we present results of detector characterization using a test-bed under development that will be used to further our understanding of the interaction between various telescope sub-systems.

Advisor: Hazumi, M
Matsumura, T
Taylor, A
Jones, M
Ludovico Ariosto's lyric poetry in the literary context of his time

This thesis is conceived as a monograph on the vernacular lyric poetry by Ludovico Ariosto (1474-1533). It aims to show that, although the rime belong to the ‘minor works’ of the author of the Orlando furioso, they nevertheless testify to Ariosto’s search for a personal poetics also in the lyric genre.
The thesis is divided into four chapters (with an introduction and a conclusion), each of which focuses on a different leitmotif in the lyrics. Chapter I centres on the self-fashioning of the lyric ‘I’ in some poems adopting the terza rima and dealing with a typically elegiac theme: the speaker’s sorrow at being parted from his beloved. Chapter II looks at the way Ariosto fashions the love relationship; in particular, I highlight (once again) his debts towards the Latin elegy, and the way these debts are intertwined with motifs belonging to the tradition of Petrarchism. Chapter III is concerned with Ariosto’s treatment of the descriptio puellae; it examines Ariosto’s tendency to feature details clearly drawn from life (eschewing the mere repetition of topoi) and to praise his beloved’s intellectual qualities, not merely her beauty. In the fourth and last chapter, I investigate the treatment of political themes, showing how they coincide with a set of references to members of the Medici family, Ariosto’s opinion of whom I try to reappraise.
The purpose of the thesis is to understand the relationship (both stylistic and thematic) between the rime and the context of lyric vernacular poetry of Ariosto’s time: I show how they are poised between fifteenth-century courtly Petrarchism and a more modern fashion, and furthermore bear the marks of a strong classical inspiration. I provide, where relevant, some comparisons with the Furioso and the Satire, in order to investigate how the same themes are treated by Ariosto in different poetic genres.

Keywords: Renaissance Poetry
Renaissance Self-Fashioning
Italian Literature
Lyric Poetry
Ariosto
Ludovico Ariosto
Courtly Poetry
Love Poetry
Duchy of Ferrara
Medici Dynasty
Advisor: Dorigatti, M
McKean-Vlasov diffusion and the well-posedness of the Hookean bead-spring-chain model for dilute polymeric fluids

We reformulate a general class of classical bead-spring-chain models for dilute polymeric fluids, with Hookean spring potentials, as McKean–Vlasov diffusion. This results in a coupled system of partial differential equations involving the unsteady incompressible linearized Navier–Stokes equations, referred to as the Oseen system, for the velocity and the pressure of the fluid, with a source term which is a nonlinear function of the probability density function, and a second-order degenerate parabolic Fokker–Planck equation, whose transport terms depend on the velocity field, for the probability density function. We show that this coupled Oseen–Fokker– Planck system has a large-data global weak solution. We then perform a rigorous passage to the limit as the masses of the beads in the bead- spring-chain converge to zero, which is shown in particular to result in equilibration in momentum space. The limiting problem is then used to perform a rigorous derivation of the Hookean bead-spring-chain model for dilute polymeric fluids, which has the interesting feature that, if the flow domain is bounded, then so is the associated configuration space domain, and the associated Kramers stress tensor is defined by integration over this bounded configuration domain. We close by establishing the short-time existence of strong solutions to the corresponding Navier–Stokes–Fokker– Planck system.

Keywords: McKean–Vlasov diffusion
equilibration in momentum space
Fokker–Planck equation
Oseen equation
Hookean bead-spring-chain model
global weak solution
small-mass limit
Advisor: Suli, E
Exploring the impact of TGF-β superfamily cytokines on HIV-1 replication

The transforming growth factor (TGF)-β superfamily comprises evolutionarily conserved cytokines including TGF-β isoforms, activins and bone morphogenetic proteins (BMPs). Recent work has shown that TGF-β superfamily cytokines elicit transcriptional changes overlapping with those of type I interferons (IFNs) in hepatoma and epithelial cells and control the replication of several viruses by IFN-dependent and -independent mechanisms. Type I IFNs play a complex role in HIV-1 infection, restricting virus replication and transmission but also driving immune activation and apoptosis. However, the roles of TGF-β superfamily cytokines in HIV-1 infection are less well understood. In this thesis, both the induction of TGF-β superfamily cytokines during HIV-1 infection and their putative roles in HIV-1 control and pathogenesis were explored.
TGF-β1 was found to be systemically induced very early in acute HIV-1 infection (prior to the innate cytokine “storm”), likely due to release from platelets; remaining upregulated throughout infection. In contrast, activins A and B, and BMP-2 were not found to be significantly perturbed during acute or chronic infection. TGF-β1 inhibited HIV-1 replication in primary, activated CD4+ T cells in vitro, but had no effect on HIV-1 replication in less activated cells or in macrophages. Other TGF-β superfamily cytokines did not inhibit HIV-1 replication in any of the cell types tested. Neither TGF-β1, activin A nor BMP-2 upregulated antiviral genes or modulated type I IFN signalling genes in activated CD4+ T cells. Further investigation of how TGF-β1 restricts HIV-1 replication suggested that TGF-β1 may reduce the proportion of Th17 cells in activated PBMC cultures. Most notably, TGF-β1 reduced cell activation status and proliferation; and diminished transcriptional activity from the HIV-1 promoter. This study gives insight into the utility of harnessing TGF-β1 activity for HIV-1 prophylaxis or therapy, and provides broader insight into an apparent cell type-dependent nature of innate antiviral activity of TGF-β superfamily cytokines.

Keywords: innate immunity
BMP
transforming growth factor beta
TGF beta
HIV
cytokine
activin
bone morphogenetic protein
Advisor: Drakesmith, A
Borrow, P
Topics in combinatorics and additive number theory

In this thesis, we will consider five problems with an additive combinatorial flavour.
In Chapter 2, we will consider bounds for the arithmetic removal lemma in abelian groups, and show that good bounds would hold as a consequence of good bounds on a related problem.
In Chapter 3, we will discuss sets of integers with many solutions to a linear equation, and prove various results about the maximal number of solutions for various equations.
In Chapter 4, we will consider special subspaces of a finite vector space called Cyclically Covering Subspaces, and discuss bounds for the smallest such subspaces. The work in this chapter answers a question asked by Cameron, and is joint with Carla Groenland and Tom Johnston.
In Chapter 5, we will prove that, among functions supported on a Hamming Sphere with a fixed ℓ2 norm, the one which maximises the additive energy is constant, proving a conjecture of Kirshner and Samorodnitsky.
In Chapter 6, we will present a possible strengthening of the celebrated Polynomial Freiman-Ruzsa conjecture, and show why such a strengthening cannot hold.

Advisor: Green, B
Late Quaternary dune activity in the Thar Desert and its implications for palaeoenvironmental reconstructions: an insight from optically stimulated luminescence dating

Sand dunes in the Thar Desert, owing to their location in the Indian summer monsoonal (ISM) regime, are rich archives of past geomorphological and palaeoenvironmental changes. However, existing dune records are not robust enough to allow their assessment and integration with a growing multiproxy framework of palaeoenvironmental change. Therefore, with an aim to investigate the timing of dune activity in the Thar, three research questions are answered in this thesis: (i) what are the key phases of dune activity; (ii) what is the effect of anthropogenic influences on the landscape; and (iii) how can dune chronologies be interpreted most effectively to reconstruct late Quaternary environmental changes? To answer these, systematic sampling of multiple dunes was carried out in the dunefields in the central and northern Thar, and luminescence dating was used to provide a detailed chronological framework.
Results demonstrate that the Thar dunes are >58 ka old, with preserved accumulation phases throughout the Holocene at ~11.6-8.5, 4-3, 2-1, 0.6-0.2 and 0.07 ka. First records of modern net accumulation are presented, with rates varying between 2-5 m/year, attributable to anthropogenic disturbances. Dune accumulation intensity methodology, in conjunction with available highly-resolved marine and terrestrial datasets, is used to infer palaeoenvironmental changes in the Thar. Whilst the strengthening of the ISM has been evidently shown to have a significant influence on widespread dune accumulation in the early Holocene, equivocal relationships between both lake levels/dune accumulation and monsoon variability during later Holocene suggest a complex interplay of regional and more local drivers like sediment supply, lowered sea levels etc. The study concludes with emphasis on the importance of recognising external and local controls on dune systems, and demonstrates that diverse responses to same environmental stimuli should be expected in palaeoenvironmental reconstructions.

Keywords: Thar Desert
OSL dating
Sand dunes
palaeoenvironmental change
aeolian geomorphology
Advisor: Thomas, DSG
Durcan, JA
Preparing and characterizing quantum states of light using photon-number-resolving detectors

A longstanding goal in quantum optics has been to realize a photon-number-resolving detector that efficiently counts the number of photons in an optical field. This goal has been largely met with the development of transition edge sensors which can count up to roughly 20 photons with efficiencies over 95%. This thesis presents three experiments that employ these detectors to characterize and prepare quantum states of light.
Firstly, we develop a weak-field homodyne detector. By replacing the photodiodes conventionally used in homodyne detection with transition edge sensors, we experimentally implement a versatile measurement device that can tune between photon counting and quadrature measurements. We study the transition between these complementary measurement regimes and determine the minimum local oscillator strength needed to perform quadrature measurements.
Secondly, we use the weak-field homodyne detector as a quantum state engineering tool. We propose a scheme to prepare a wide range of definite parity states, including two- and four-component Schrödinger cat states of arbitrary size with nearly perfect fidelity.
Thirdly, we perform optical interferometry using quantum states of light with the aim of surpassing the maximal precision achievable with classical light, i.e. the shot-noise limit. We propose and experimentally implement a scheme that uses high-gain squeezed vacuum sources and transition edge sensors to prepare loss-tolerant entangled states containing up to 8 photons. While our achieved precision does not unconditionally (i.e. without post-selecting on certain measurement trials) surpass the shot-noise limit, our results do demonstrate the robustness of these entangled states to loss despite their size.

Keywords: quantum optics
quantum metrology
Advisor: Lvovsky, A
Patel, R
Walmsley, I
The effect of H₂O on O₂ reduction in Li-O₂ batteries

There is significant interest in aprotic lithium-air batteries due to their high theoretical specific energy. During discharge, O2 is reduced at the positive electrode and forms Li2O2. Cells are typically discharged in O2, not air, because CO2 and H2O can interfere with the discharge reaction. However, lithium-air batteries will need to use atmospheric O2 if they are to supplant state-of-the-art lithium-ion cells. Therefore, it is important to establish how detrimental CO2 and H2O are to the battery. The former is well-known to induce the formation of Li2CO3 in Li-O2 batteries, but the recent work has suggested that H2O appears to be beneficial at low concentrations in some solvents (e.g. glyme ethers), increasing discharge capacities and still forming Li2O2, while in other solvents, such as acetonitrile (CH3CN), LiOH is the discharge product. Several mechanisms have been proposed to rationalise these findings, but as yet, there is no consensus on the role of H2O on O2 reduction.
The purpose of this work was to understand how H2O affects O2 reduction in electrolytes using acetonitrile (CH3CN), dimethyl sulfoxide (DMSO) and tetraethylene glycol dimethyl ether (TEGDME) solvents, and, why the 4e- reduction appears to be unfavourable at low H2O concentrations. Electrochemical and spectroscopic analysis found that, in CH3CN, 4e- reduction occurred at lower H2O concentrations than in DMSO and TEGDME. A mechanism based on the ability of the H2O/solvent mixture to stabilise OH- was proposed, with mixtures that stabilise OH- promoting 4e- O2 reduction. The mechanism was confirmed by using pressure cells to identify the electrochemical reaction occurring during discharge. Cells using DMSO and TEGDME solvents underwent 2e- O2 reduction, even with 1 M H2O concentrations. Finally, TEGDME cells were discharged in a 13% RH at 25 °C O2 atmosphere, corresponding to 1 M H2O in solution, and Li2O2 was confirmed as the discharge product, demonstrating that it is possible for electrolytes to withstand a near-atmospheric humidity.

Keywords: lithium-air battery
water
oxygen reduction
Advisor: Bruce, P
Learning to become and belong: a study of participation in sociocultural activity in Gunayala

This study sets as its central problem the question of whether, and how, participation in shared sociocultural activity enables and mediates the learning of girls and women in Gunayala. In line with the existing literature on anthropological approaches to learning, the study primarily uses interviews and observation to examine how Guna girls and women learn and develop through the shared practice of making Molas, which is rooted in the broader cultural traditions of the community. It argues that through participation in shared sociocultural activity, women in Gunayala learn to become independent and interdependent as well as to belong within their community and wider world. Failing to draw on this understanding of learning as situated and a process resulting from participation has far-reaching implications with regards to the way Guna children are educated and thence how the community is able to reproduce itself.

Keywords: Mola
situated learning
mediated learning
sociocultural learning
community of practice
shared activity
Gunayala
Advisor: Johnson, D
The religious policy of the Cecils, 1588-1598

The thesis examines the Cecils contribution to three areas of religious policy during 1588-98: the control of protestant non-conformity; the loyalty of lay catholics; and the political and financial management of the episcopate.
Lord Burghley (William Cecil) supported strong measures against protestant separatists, but opposed Archbishop Whitgift's suppression of moderate puritanism. His criticism of the authoritarian claims of the church hierarchy won limited support from Elizabeth I, but when Whitgift pressed for the exemplary execution of leading separatists - against Burghley's will - the archbishop prevailed. The thesis argues, however, that at this same moment (April 1593) Burghley outmanoeuvred Whitgift in parliament by securing an anti-separatist statute that protected moderate puritans.
Burghley's central role in anti-catholic policy is shown to have reached a peak during 1590-93, to be replaced by a climate from 1594 in which councillors resisted his calls for the creation of ever-harsher sanctions against recusants. Burghley's justifications of this policies were rejected by Sir Thomas Tresham, and it is suggested that, increasingly, councillors began to re-assess the coherence and effectiveness of Burghley's measures.
The period also saw widespread changes among bishops in the established church: almost half the bench was replaced during 1594-98. Robert Cecil is shown - with Whitgift - to have been the main political patron in this process, and on occasion to have outwitted Burghley in pursuit of his own ends. Moreover, Cecil is also revealed as the crown's main agent (with Burghley's cooperation) in the diversion of church wealth to the county gentry, despite the resistance offered by some bishops.
It is concluded that the religious policies of Burghley, Cecil and Whitgift were held in a balance, and that this reflected the tensions of a decade which saw the beginnings of significant change in later Reformation politics.

Keywords: Salisbury
religious
Cecil
Britain
century
Church
policy
state
Burghley
16th
Advisor: White, BR
Williams, P