VictorJuiz/thesis huggingface dataset:
Prototyping the spectrograph mechanisms for harmoni@elt, and the drivers of the main sequence positions of 5muses galaxies

HARMONI (High Angular Resolution Monolithic Optical and Near-infrared Integral field spectrograph) is a planned first light integral field spectrograph (IFS) for the Extremely Large Telescope. Each of the two main mechanical modules within the spectrograph, the Fold Mirror Module (FMM) and the Infrared Grating Module (IGM), used for the folding and dispersion of the beam, respectively, must operate within tight repeatability requirements to ensure that daytime calibration frames (wavelengths and flats) can be taken in the same observational setup following on-sky observations the previous night (to increase the accuracy of the calibration). The first part of this D.Phil thesis involves prototyping and testing the first of the two mirrors of the FMM (the Fold Mirror 1, or FM1) and the entire Infrared Grating Module to ensure they meet the required levels of repeatability. Furthermore, a separate method of achieving the required repeatability is prototyped and tested using detents. This method could be incorporated for use with both the FMM and IGM if their original designs do not meet the required levels of repeatability. A thorough evaluation of the causes of the positional errors is given for each of the three main prototype tests. All tests are conducted at room temperature, as well as initial tests of the detent mechanism and Fold Mirror 1 at 130K, the temperature of the HARMONI cryostat. All three mechanisms achieve warm repeatabilities well within their tolerances.
In the second part of this thesis, data from the Oxford SWIFT Integral Field Spectrograph (IFS) is used to study a statistically significant subset of the 24𝜇m flux-limited 5MUSES galaxies sample. Specifically, the dynamical ratio (rotational velocity 𝑉𝑟𝑜𝑡 divided by the intrinsic disk dispersion σ0, a diagnostic of the galaxy’s evolutionary history) and the Active Galactic Nuclei (AGN) contribution to the Infrared Luminosity (𝐿𝐼𝑅) (AGN fraction, or 𝑓𝐴𝐺𝑁) are investigated to help determine whether the high multiplicative offsets from the expected main sequence of star formation (or the offset from the expected level of star formation given a stellar mass and redshift for each galaxy, and later defined as the ‘Main Sequence Multiple’, or 𝑀𝑆𝑀𝐼𝑅) are due to star formation brought on by interactions, or due to luminosity from an AGN. To do this, the SWIFT subset is kinematically modeled to compute the dynamical ratio, and Spectral Energy Distributions (SEDs) of each galaxy are fit with galaxy and AGN templates to determine 𝑓𝐴𝐺𝑁, which is then used to correct 𝐿𝐼𝑅. It is found that 24% of the SWIFT galaxies are interacting, with 71% isolated, and that galactic interactions are the main cause of the high 𝑀𝑆𝑀𝐼𝑅 observed, rather than AGN. The SWIFT subset of the 5MUSES galaxies serve as a generic representation of the bulk of star forming, main sequence galaxies, making the conclusions of this work applicable to many galaxies in the universe.

Keywords: Instrumentation
Galaxies
Advisor: Thatte, N
Novel applications of bifunctional iminophosphorane superbases in enantioselective catalytic methodology

Chapter 1 introduces enantioselective organocatalysis with a specific focus on bifunctional catalysts and chiral superbases. Subsequently, the discovery and applications of bifunctional iminophosphorane (BIMP) catalysts will be described.
Chapter 2 focuses on the development of a novel enantioselective sulfa-Michael addition employing alkenyl-benzimidazoles as electrophiles. The work in this chapter will showcase a rare example of organocatalysed enantioselective addition to alkenyl heterocycles for the rapid generation of 3-D druglike scaffolds.
Chapter 3 introduces approaches to enantioselective P(V) synthesis, highlighting the strengths and shortcomings of current methods to then focus on the development of an unprecedented enantioselective nucleophilic desymmetrisation of phosphonate esters. The unique ability of a novel ureidopeptide BIMP catalyst to promote this reaction enantioselectively will be demonstrated against a wide array of other BIMPs as well as Chinchona alkaloid and phase transfer catalysts. The downstream utility of the desymmetrised product will be demonstrated in the synthesis of numerous attractive nucleoside derived compounds.
Chapter 4 will disclose an improved enantioselective nucleophilic desymmetrisation of P(V) containing species. Via a superior BIMP catalyst scaffold and a thiazolidinone leaving group on the P(V) electrophiles, higher enantioselectivities, lower catalyst loadings, and improved nucleophile scope were obtained.

Keywords: Superbase
Organic Synthesis
Catalysis
Enantioselective
Advisor: Dixon, DJ
Classifying spaces of low-dimensional bordism categories

The truncated bordism category Cob_d is the symmetric monoidal category whose objects are closed oriented (d-1)-manifolds and whose morphisms are diffeomorphism classes of compact oriented d-dimensional bordisms. In this thesis we study the classifying spaces of Cob1, Cob2, and several related categories.
In the first part we show that the conditions in Steimle’s "additivity theorem for cobordism categories" can be weakened to only require locally (co)Cartesian fibrations, making it applicable to a larger class of functors. As an application, we construct a fiber sequence that relates the classifying space of the (2,1)-category Csp of cospans of finite sets to the classifying space of its homotopy category Csp = h(Csp), where isomorphic cospans are identified.
In the second part we compute the classifying space of Cob1 by exhibiting it as a circle bundle over Ω∞−2 CP-1∞. As part of our proof we construct a quotient Cob1 → Cob1red where circles are deleted and we show that its classifying space is Ω∞−2 CP-1∞. Based on this we construct a bordism model for the topological cyclic homology of simply connected spaces. We also explicitly describe an infinite loop space map B(Cob1red) → Q(Σ2 CP∞+) and use it to derive combinatorial formulas for rational cocycles on Cob1red representing shifted Miller-Morita-Mumford classes κi ϵ H2i+2(B(Cob1); Q)
The third part concerns the classifying space of the surface category Cob2 and its subcategory Cob2χ≤0 subset of Cob2 that contains all bordisms without disks or spheres. We show that, after passing to a refinement Cob2 → Cob2 , the classifying space of the surface category is BCob2 ≃ S1 - proving that a conjecture of Tillmann becomes true in this setting. We also compute the classifying space of Cob2χ≤0 and show that its rational homotopy groups contain the homology of the tropical moduli spaces ∆g, which is known to grow exponentially. The tools we develop can be applied to a large class of symmetric monoidal categories, which we call labelled cospan categories. In particular, we show that B(Csp) is contractible, whereas the classifying space of its homotopy category is B(Csp) ≃ τ≥3Q(S2).

Keywords: Bordism categories
Topological cyclic homology
Miller-Morita-Mumford classes
Tropical moduli spaces
Category theory
Quillen's theorem B
Advisor: Tillmann, U
Re-thinking smartness: designing more ethical connected devices for the home

Modern smart devices are capable of incredible things: making life easier, more enjoyable, and more secure. But this 'smartness' often comes at the cost of devices harvesting data from the home, constraining how we use them, and changing the ways we relate to each other. This thesis explores what it means for a device to be smart, the ethical concerns that smartness causes, and ways that we might re-think smartness to better support people's needs and values. It does so using four lenses of smartness, privacy, social actors, and respect.
In order to better understand the problem, we begin by presenting the results of surveys and interviews investigating perceptions of what smartness is, and how it manifests across a variety of contexts. In doing so we identify concomitant ethical concerns, such as privacy and autonomy, and discuss the similarities and differences in how they operate across devices. We then follow up by addressing two of the identified problems in greater detail. We present the results of a six-week technology probe deployment designed to give people control over their connected devices by visualising and constraining their data flows. We show how participants preferences shifted over the course of the study and how, when given the right resources, people can learn and come together to solve privacy problems in the home. Secondly, we explore social concerns around voice interfaces, with a survey exploring correlations between trust, anthropomorphism, and relationship development with voice assistants. We show how people develop relationships with social devices in a similar manner to those between people, raising questions about the potential for social interaction modalities to be used to manipulate. The thesis then brings these lines of enquiry together by proposing the concept of respect as a lens for using standards of interpersonal interaction to evaluate interactions with smart devices. Practical and theoretical perspectives on respectful behaviour from a variety of disciplines are used to link the behaviours of intelligent systems to previous work on moral theory, agency, social hierarchies, and oppression.
Drawing on each of these four lenses, the thesis closes by discussing potential ways to re-think smartness, reaping its benefits whilst mitigating its problems. From rejecting smartness altogether, giving people greater control over their devices, making devices more respectful, and using different conceptual models of devices, the thesis lays the foundations for more socially aware systems that use their smartness to support users in managing and enjoying life in the connected home.

Keywords: Voice Assistants
Respect
HCI
Smart homes
Advisor: Van kleek, M
Neutron scattering studies of some unconventional magnets

The identification and characterisation of low-dimensional and frustrated magnetic systems is an area of great importance in the field of solid-state chemistry. If we intend to design and control the magnetic properties of frustrated magnets, we must first understand the microscopic interactions responsible for the formation of these disordered magnetic phases. This is of fundamental interest due to the potential for frustrated magnets to form e.g. quantum spin liquid materials. Frustrated and low-dimensional phases are not solely of fundamental interest; a number of properties have been identified as stemming directly, or indirectly, from disordered magnetic states. Correlated magnetic disorder has been implicated in the formation of, for example, high-temperature superconducting, multiferroic, and magnetocaloric systems. The analysis of neutron scattering is of pivotal importance in understanding such systems. In disordered phases, we cannot rely on Bragg peaks in neutron scattering patterns, since the long-range order is suppressed by frustration. Instead we must turn to the diffuse magnetic neutron scattering created by local, short-range, correlations. In this thesis I present investigations of several frustrated and low-dimensional magnetic systems using a variety of neutron scattering techniques. In Chapters 3 and 4 I explore the structures of two triangular lattice antiferromagnets, CsCoCl₃ and the metal-organic framework Tb(HCO₂)₃. In Chapter 5 I present the first neutron scattering investigation of Gd₂Pt₂O₇; a recently reported magnetic pyrochlore system. I have employed both polarised diffuse neutron scattering and inelastic neutron scattering measurements in order to quantify the microscopic interactions which serve to relieve the frustration, relative to other gadolinium pyrochlores. Finally, in Chapter 6, I have investigated the spin-chain compound Er₂BaNiO₅ using a combination of single-crystal neutron diffraction, and bulk magnetic and electrical property measurements.

Advisor: Goodwin, A
Stewart, R
Finite element approximation of elliptic homogenization problems in nondivergence-form

This thesis focuses on the construction of finite element numerical homogenization schemes for both linear and selected fully-nonlinear elliptic partial differential equations in nondivergence-form.
In the first part of the thesis, we study periodic homogenization problems of the form A(x/ε):D2 uε = f subject to a homogeneous Dirichlet boundary condition. We provide a qualitative W2,p theory and obtain optimal gradient and Hessian bounds with correction terms taken into account in the Lp-norm. Consequently, we find that (uε)ε>0 converges strongly in the W1,p-norm to the solution of the corresponding effective problem, and that the optimal rate for this convergence is O(ε). Based on these quantitative homogenization results, we propose and rigorously analyze a finite element-type numerical homogenization scheme for the approximation of the solution to the effective problem and the solution uε to the original problem in the H1 and H2 Sobolev-norms. We extend the scheme to the framework of nonuniformly oscillating coefficients and provide a variety of numerical experiments illustrating the theoretical results.
In the second part of the thesis, we propose and rigorously analyze numerical homogenization schemes for the fully-nonlinear Hamilton--Jacobi--Bellman (HJB) and HJB--Isaacs (HJBI) equations. More precisely, we are interested in the approximation of the effective Hamiltonian which determines the effective equation. Our numerical schemes are based on finite element approximations for suitable corrector problems arising in the periodic homogenization of these equations. We present a mixed finite element scheme as well as discontinuous Galerkin and C0 interior penalty finite element approaches. Several numerical experiments accompany the theoretical results and illustrate the performance of the numerical schemes.

Keywords: nondivergence-form elliptic PDE
finite element methods
Homogenization
Advisor: Süli, E
Capdeboscq, Y
A Spinozist approach to affective patterns in revolutionary springs

This thesis is about revolutionary springs, defined as fast transnational diffusion of revolutionary uprisings in the absence of any financial or military collaboration. Due to their speed, their international nature, and their spontaneity, I argue that these phenomena cannot be satisfactorily explained by material or ideological factors alone, hence the need for original analytical tools. To analyse the structures of affects, I offer to look at three affective patterns, namely repressive fear, revolutionary fraternity, and revolutionary martyrdom. The first part of this thesis draws from Baruch Spinoza’s philosophy to understand how collective affects emerge and circulate transnationally within and across multitudes, and briefly distinguishes this perspective from the one developed by Antonio Negri and Michael Hardt. The second part describes how affective patterns interplay in revolutionary dynamics in two empirical cases, namely the Springtime of the Peoples and the Arab Spring. It first connects Spinoza’s ontological foundations with methodology by presenting the textual, visual, and sound materials and respective methods that are handled to investigate affective patterns in revolutionary times. Then, I examine these affective patterns at the national level during the Springtime of the Peoples and the Arab Spring to show how they contribute to the emergence of the revolutionary multitude. The last two chapters offer an international theory of affective patterns in revolutionary springs by showing how a transnational multitude may emerge and be set in motion through affective patterns. This part also uses affective patterns to investigate negative cases, that is, countries that could have joined the revolutionary movement and did not. This work has implications for the understanding of both revolutions, especially but not exclusively revolutionary springs, and transnational affective circulations.

Keywords: International Relations
Spinoza
Affects
International Relations Theory
Indignation
Emotions
Revolution Theory
Advisor: Keene, E
The use of deuterium in reaction kinetics in solution

The difference in chemical and physical properties of the isotopes of the heavier elements is very small. The isotopes of hydrogen differ greatly in mass and hence the thermodynamic properties such as vapour pressure, solubility and chemical equilibrium of its isotopic compounds differ considerably. It was the difference in vapour proasure of U2 and HD that permitted Urey, Brickwedee and Murphy (1) to prove the existence of deuterium. The propertios of the oxide of deuterium, heavy eater, have been studied extensively.
[Introduction continued in thesis]
Use of stem cell-derived macrophages and gene editing to investigate viral pathology and innate immunity

Induced Pluripotent Stem Cell (iPSC)-derived macrophages are a rapidly emerging model of tissue resident macrophages for investigating human disease. As potentially infinitely replicating cells, iPSC lend themselves for genetic manipulation by CRISPR-Cas9 editing before terminal differentiation into a vast array of cell types. As such, long standing challenges in exploration of macrophage gene functions during inflammatory diseases and infections, such as HIV-1, caused by donor variability and immortalised cell line deficiencies can finally be overcome. With over 30 different protocols for macrophage differentiation from iPSC now described, culturing of these cells is gradually becoming more accessible to researchers, and essential processes for differentiation better understood. However, with this progress comes the ever-greater need for clear definition of culturing conditions of these cells, so that we can compare results between methodologies, and eliminate undesirable sources of variability.
This thesis sought to capitalise on this new system to explore the complicated and often contradictory role of TRIM5α in HIV-1 infection, and to explore with a precision only achievable through CRISPR-Cas9 genome editing the function of the cyclophilin family of peptidyl-prolyl isomerases. I demonstrate protection of HIV-1 from TRIM5α restriction by cyclophilin A, as well as regulation of the innate immune inflammatory response more generally by the cyclophilin family. However, prior to exploring this, this thesis sets out to address some of current issues in iPSC-derived macrophage culture and the ill-defined components of growth media and cellular environment. I describe a new macrophage differentiation medium using serum free, defined, and open-sourced components to bring needed transparency into the field. I also address the variability in macrophage phenotype and function brought about by the fundamental, but largely overlooked, impact of cell crowding in ex vivo culture. This revealed evidence for a potential plating density-dependent anti-inflammatory feedback loop relevant for human diseases like Alzheimer’s disease.

Keywords: HIV
RNA sequencing
differentiation
toll-like receptors
macrophages
cyclophilins
innate immunity
CRISPR
stem cells
TRIM5
Advisor: James, W
A genealogy of reasons

I will attempt to answer three questions about reasons: what kinds of entities they are, why we should care about responding to them, and how they are related to motivation. In Chapter One, I argue that the debate in the theory of reasons is stagnant and that we would be better off adopting a radically new approach— pragmatic genealogy. In Chapter Two, I discuss the nature of pragmatic genealogy. In Chapter Three, I develop a pragmatic genealogy of reasons based on the need to reconcile conflicting beliefs and desires in both individual and communal settings. In Chapter Four, I respond to possible objections. In Chapter Five, I apply the information gained from our genealogy to address our three central questions and argue that it turns out that pragmatic genealogy is a methodology uniquely suited to doing so.

Keywords: Reasons
Genealogy
Pragmatic Genealogy
Philosophy of Action
Adaptive therapy for cancer: Integrated modelling of tumoral competition for controlling drug resistance

Treatment in advanced cancers often provides only temporary improvements due to the emergence of drug-resistant tumour subpopulations. Standard-of-care regimens seek to maximise cell kill in order to achieve a cure, but thereby inadvertently also free resistant cells from the intra-tumoral competition which usually constrains their growth. An emerging alternative strategy, called adaptive therapy (AT), aims to tackle this problem by prioritising tumour control over cure. The idea is to leverage intra-tumoral competition to slow, or even avoid, the expansion of resistance.
In this thesis we present an integration of mathematical modelling, clinical data analysis, and biological experiments in order to investigate: i) the factors which determine whether a patient will benefit from AT, and ii) how to best adjust treatment to control resistance. We begin by studying a simple two-population model, which we formulate first as an ordinary differential equation (ODE), and subsequently as an agent-based, model. We dissect the impact of various model parameters on the benefit of AT, and identify cell turnover as an important, but previously overlooked, factor. Furthermore, we find that the tumour’s spatial organisation reflects, as well as modulates, intra-tumoral competition, and we discuss implications for intermittent androgen deprivation treatment in prostate cancer.
In the second part of this thesis, we investigate whether adaptive scheduling of poly-adenosine di-phosphate ribose polymerase inhibitors (PARPis) can improve the treatment of ovarian cancer. We develop a framework which uses an ensemble of six ODE models to dynamically guide AT decision-making. In collaboration with an experimentalist, we test our framework in an in vitro spheroid model, and find that it compares favourably to other adaptive dosing algorithms. However, this work also shows that high-dose, continuous treatment achieves the best overall outcome. To conclude we therefore develop an ODE model of PARPi treatment, and discuss implications for PARPi scheduling. Overall, this thesis provides novel insights into the eco-evolutionary underpinnings of AT, and highlights some of the challenges involved in translating AT to a new cancer type.

Keywords: mathematical oncology
tumour evolution
prostate cancer
cancer drug resistance
ovarian cancer
adaptive cancer therapy
mathematical biology
Advisor: Maini, P
Anderson, A
Cyprus betwixt Greeks and Saracens, A.D. 647-965

A re-examination of the documentary evidence in conjunction with, and in the light of, available archaeological evidence indicates that:
For some sixty years after Muawiya's first Arab raid against Cyprus, in 649, the Island was under the control of whichever of the two powers contesting it - Byzantium and Islam - was the stronger.
After the second Arab raid of 653/4 an Arab garrison may have been established in Cyprus, as the Arab chronicler Baladhuri states. But numismatic and other archaeological evidence is cited to show that such an Arab garrison must have been withdrawn from the Island, soon after it is reported to have been stationed there, by Muawiya himself. An Arab garrison reported, by Baladhuri, to have been withdrawn from Cyprus by Muawiya's successor, Yezid, may have been re-established in the Island during the siege of Constantinople in the seventies of the seventh century.
Extensive repair works to various public buildings, the erection and decoration of others and the fortification of the central part of the capital, Constantia, which was renamed Nea Justinianopolis after Justinian II, are cited as evidence for Byzantine control of Cyprus between 680 and 688. The view of modern historians that Nea Justinianopolis of the 39th Canon of the Council-in-Trullo was in the Hellespont is examined and shown to be untenable.
… Continued in thesis.

Keywords: Byzantine Empire
Islamic Empire
Foreign relations
Islamic
Cyprus
Greeks
Saracens
Advisor: Hussey, JM