VictorJuiz/thesis huggingface dataset:
The utility of merging mechanistic and geospatial models for malaria intervention planning and policy guidance

This thesis describes the development and refinement of two frameworks for usefully combining mechanistic and geospatial models in malaria research. The first framework, focused on malaria transmission, uses machine learning tools and spatial data to identify key features for a mechanistic transmission model, then utilizes spatial data again to place mechanistic model results in a global context. This strategy is novel, flexible, customizable, and computationally efficient. The second, focused on insecticide-treated net coverage, uses a mechanistic commodity tracking model as the backbone for a spatiotemporal regression model in order to appropriately capture different countries' unique histories of net procurement, distribution, and retention. Examples of the on-the-ground policy impact of this work are included for stakeholders such as the World Health Organization, the Clinton Health Access Initiative, and the Bill and Melinda Gates Foundation. Both of these modeling frameworks showcase the value of combining the flexibility and versatility of mechanistic modeling with the statistical rigor and geographical tools of geospatial modeling.

Keywords: geospatial
model
malaria
epidemiology
statistics
Advisor: Gething, P
Hollingsworth, T
On termination and divergence of linear programs

The objective of this thesis is to shed some light on the boundaries of decidability by answering some of the central problems in the study of linear programs, and to provide an up-to-date survey of the latest results in this field.
In particular, we review some of the classical decision problems in the theory of linear recurrence sequences. Namely, we revisit the Skolem Problem, Positivity Problem, Ultimate Positivity Problem, and Absolute Divergence Problem. We then show that the Divergence Problem, the problem of deciding whether a given linear recurrence sequence diverges to infinity, is decidable for all linear recurrence sequences of order at most 5, and when the linear recurrence sequence is simple it is decidable up to order 8. Our results hold for both homogeneous and inhomogeneous linear recurrence sequences. As a by-product of our approach, we extend existing results on the Positivity Problem and Ultimate Positivity Problem for homogeneous linear recurrence sequences to inhomogeneous linear recurrence sequences. We further demonstrate why it is unlikely to improve these decidability boundaries to higher order linear recurrence sequences, by establishing reductions from long-lasting open problems in Diophantine Approximation.
Next, we answer a 15-year-old problem of Tiwari, which asks whether a given linear loop program with integer coefficients terminates over all its integer initial values. We use novel techniques to evade the obstacles in answering the Positivity and Ultimate Positivity Problems. In more detail, we exploit the freedom to choose the initial value to circumvent the need to solve “hard instances” of the Positivity Problem. Our algorithm decides, in double exponential space, whether a linear loop program with integer coefficients terminates over all integer initial values.
Finally, we summarise the state-of-the-art results in the field, and provide the reader with a landscape of some of the new and classical open problems in the field. We also discuss some of the shortcomings of the current approaches, and provide direction for further research.

Keywords: algebraic numbers
Skolem problem
divergence
program verification
positivity
linear recurrence sequences
integer affine programs
integer linear programs
loop termination
Advisor: Ouaknine, J
Worrell, JB
On what matters in defining concepts

Defining concepts has become an integral part of philosophical methodology. However, it isn’t clear what the primary purpose of this activity is. There are two competing models answering this question: according to the Conservative Model, the primary purpose of defining concepts is to accurately report their actual meaning. According to the Revisionary Model, the primary purpose of defining concepts is to make a normative judgement about what they should mean, and, if necessary, revise their actual meaning accordingly. The objective of this thesis is to argue that the Conservative Model doesn’t give us a satisfactory picture of what is at stake in defining concepts and that we should therefore rely more upon the Revisionary Model when working with concepts in philosophy.

Advisor: Magidor, O
The spatial dynamics of microbiota-immune interactions

In recent years, the modulating role of the microbiota on host health has become increasingly apparent. The composition of this diverse community is intrinsic to the host-associated benefits of a microbiota and is regulated by the host’s immune system. Understanding the dynamics of microbiota-immune interactions is therefore necessary before modulating microbiota community composition for therapeutic purposes is viable. Ecological theory holds that the scale at which a community is considered changes the forces by which it is shaped. However, to date, microbiota-immune interactions have been assessed predominantly at large scales.
Within this thesis the selective pressures which control microbiota community composition are explored. An individual-based model of biofilm growth is initially used to interrogate the role of adhesion in maintaining microbiota diversity. A fine-scale method is then developed to investigate the model’s predictions of spatial heterogeneity within the microbiota, allowing consideration of whether the scale at which the microbiota and adaptive immune populations are sampled changes the apparent dynamics of these communities.
At small scales species interactions are important in community dynamics. To investigate species interactions within the microbiota, a method of estimating species interactions across space is developed. By grouping species according to their relative abundance, the role of rare individuals in community stability is investigated.
Finally, an avian B-cell knockout is used to assess the role of immunoglobulin A (IgA) in modulating microbiota composition. By comparing the effect of IgA absence upon the microbiota at large and fine scales, the importance of sampling scale in elucidating immune and microbiota interactions is highlighted.

Keywords: immunology
evolutionary immunology
microbiota
Advisor: Smith, AL
Foster, K
Microscale and ultrafast high cycle fatigue testing of titanium

The fatigue properties and crack growth behaviour in Grade 2 commercially pure titanium (CP Ti) was investigated using a miniature ultrafast testing method. Using finite element modelling (FEM) a dogbone type mesoscale cantilever specimen was designed, that facilitated the shift of stress concentrations from sharp corners in a simple initial cantilever design to the centre of a beam. This ensured that failure was more dependent on microstructure than sample geometry.
Monotonic single crystal microscale cantilever tests were performed that isolated <a> prism, <a> basal and <c+a> first order pyramidal planes. The bulk critically resolved shear stress (CRSS) for these slip systems were 130 MPa, 298 MPa and 795 MPa respectively. These experiments showed that slip is most likely to occur on <a> prism planes. In addition, using von Mises cri- terion to determine the yield stress from the CRSS of <a> prism (225 MPa) was comparable to the mean bulk 0.2􏰡 yield stress measured by monotonic tensile tests (243 MPa). The mono- tonic bulk tensile tests on typical dogbone samples also demonstrated that the elastic modulus along the length axis of a microcantilever as measured from the microscale tests of <a> prism had good agreement with bulk data (~105 GPa). It has also been shown that in ultrafast mesoscale tests there is good agreement with both microscale and macroscale tests as it has been shown that failure is extremely unlikely to occur below ~240 MPa.
By comparing both single-step and multi-step testing approaches to ultrasonic fatigue test- ing it has been shown that there is little/no coaxing effect in Grade 2 CP Ti. By fitting a Basquin power law fit to the fatigue data generated, a fatigue coefficient (S) of 675 MPa and fatigue expo- nent (b) of -0.048 was achieved. In-situ ultrasonic mesoscale testing has also shown the ability to track crack growth and demonstrate the importance of fatigue crack initiation resistance when designing for high cycle fatigue resistance. In addition, the testing method has been able to distin- guish between sample surface conditions and calculate the fatigue performance deficit as a result. Fractography data has also informed that fatigue cracks in these specimens initiate primarily from the surface and the edges of the beam. Furthermore, fractography has allowed for the observation of the steady-state nature of crack growth as the crack extends into the centre of the beam.
A significant correlation was established between increased local GND density as revealed by HR-EBSD, and local surface slip features imaged in SEM, with grain boundaries at which the slip systems available in the two grains were misaligned. Increased plastic work and poor stress transfer between the misaligned shear planes lead to slowing of the fatigue crack and/or a change in crack path generally increasing resistance to short fatigue crack growth at these features.

Keywords: ultrasonic fatigue
fatigue
aerospace
titanium
micromechanics
Advisor: Wilkinson, A
Gong, J
Structural and functional studies of the antiviral target proteins HCV p7 and ER alpha-glucosidase II

To accomplish the correct folding of N-glycosylated proteins eukaryotes rely on their endoplasmic reticulum quality control pathway. This pathway which consists of glycosyl- hydrolases and -transferases, lectins and chaperones, assists the folding of immature glycoproteins post their translation into the ER lumen. Glycoproteins are processed based on glycan and protein misfold recognition. While correctly matured glycoproteins proceed through the secretory pathway to their final destination, immature glycoproteins are discarded eventually by the ER associated degradation pathway.
Many viruses hijack the glycoprotein quality control pathway after host cell infection in order to produce their own viral glycoproteins, which makes them vulnerable to the interference with the correct performance of the cycle.
Iminosugars which are glucose mimetics inhibit N-linked glycan processing enzymes such as alpha-glucosidase I and II of the glycoprotein quality control pathway, resulting in decreased virion secretion from infected cells and/or virus infectivity.
Presented in this thesis is the protein X-ray crystallography work carried out on ER alpha- glucosidase II in combination with a new class of N-alkyloxy iminosugars revealing binding motifs of the latter within the active site of the enzyme. Furthermore, the study demonstrates a new approach of potential alpha-glucosidase II inhibition and the development and use of a fluorescence energy resonance transfer-based high-throughput screen for new drug discovery. The findings enable future studies aimed at improving alpha-glucosidase II inhibition both by developing more specific active site inhibitors as well as via a novel strategy that aims to prevent or disrupt GluII heterodimerisation by targeting the enzyme’s 𝛼-/𝛽- subunit interface. Long alkyl chain iminosugars do not only inhibit certain host cell enzymes such as ER alpha- glucosidase II but also the hepatitis C virus p7 ion channel, but it is not yet known how this inhibition is achieved. The analysis of how iminosugars interact with their target protein p7 is hindered by the lack of knowledge of the protein channel’s oligomeric structure and its location in the ER membrane. Work in this thesis uses electron paramagnetic resonance spectroscopy in combination with spin labelled HCV p7 to analyse the oligomerisation behaviour of the p7 protomer in lipid bilayers. The structural information gained provides the basis for future experiments to better understand drug inhibition of the p7 ion channel and contributes to the still very limited information about viral ion channels in lipid environments.

Keywords: DEER
Lipid
EPR
Ion channel
HCV p7
Advisor: Zitzmann, N
Leveraging the left: examining Russian left-leaning provocation on Instagram in 2020

Pursuing a strategy of provocation, the Russian government has leveraged proxy media accounts on social media to disseminate strong, often-fringe political stances within a broader left-leaning ecosystem. While these proxy voices, termed “the Fringenet,” author such narratives, their posts are spread by “fellow travellers,” accounts that wittingly or unwittingly amplify Russian provocation efforts. Beyond their symbolic importance, it remains unclear whether reposts have any significance, such as generating follower growth for Fringenet accounts.
This thesis seeks to tackle this question with a series of theoretical and methodological contributions to the literature. By drawing together a novel dataset of Instagram reposts and posts by Russian provocation accounts, social network theory, and time-series modelling, I examine how three Fringenet media channels built their amplification network of followers. To determine whether reposts influence follower growth, I use vector autoregression models paired with Granger causality tests and impulse response functions to explore the time-ordered relationship between reposts and follower growth. Further, to examine who is reposting Russian provocation content and on what topics, I conduct an intensive manual coding process of account types (N = 1,870) and posts and reposts (N = 4,050).
My results reveal both a top-down broadcast model – where influential users like private companies and influencers generated follower growth for Fringenet accounts by signalling to their followers that these accounts were authentic and credible – and a bottom-up social contagion model – where the sheer number of users reposting Fringenet accounts led to follower growth by building a critical mass. Furthermore, my descriptive analyses highlight that reposts were frequently shared by fellow independent and alternative news accounts as well as authentic private companies and activists and civil society groups. Finally, I find reposts and posts converging around topics such as Black Lives Matter, climate change, and COVID-19.
Given recent decisions to label Russian media accounts as state-run, the substantive and methodological contributions of this thesis are relevant for the academic community and for policymakers. For the academic community, this thesis demonstrates the need for a multiplayer analysis when studying Russian information operations. For policymakers, this thesis highlights the drawbacks of a focus solely on countering disinformation through fact-checking, which overlooks the way Russian accounts are not merely passive purveyors of false information but rather active participants fanning the flames of ongoing political discourse.

Advisor: Bright, J
Mathematical modelling, scenario simulation and policy analysis

Scenario simulation and stress testing have become indispensable tools for policy makers for the monitoring and management of risk in complex socio-economic systems with heterogeneous, interrelated components. This thesis contains several methodological contributions to this increasingly important field at the intersection of mathematical modelling and policy, with applications focusing on three specific areas: the stress testing of large financial institutions, the financial stability of the UK reinsurance sector and the analysis of control policies for the COVID-19 pandemic in England.
Chapter 2 proposes a new framework for the joint stress testing of liquidity and solvency risk for financial institutions. Rather than being specified independently from solvency shocks and applied in parallel to them, liquidity shocks are instead endogenously generated through mechanisms that model the liquidity-solvency nexus. The framework is applied to balance sheets of large financial institutions and provides interesting insights into the links between solvency and liquidity risk.
Chapter 3 proposes a network model for counterparty credit risk in the UK reinsurance market. A multi-layered network approach is used to incorporate information on reinsurance contract risk types and ownership structure for life and non-life insurers. The UK reinsurance sector is found to exhibit a 'small-world' property with a scale-free, core-periphery structure and topological characteristics common to other financial networks, making it 'robust-yet-fragile' to financial shocks. A stress simulation exercise shows the network to be robust to a shock to the value of total investments, and to idiosyncratic shocks to large, highly interconnected reinsurers.
Chapter 4 proposes a spatial epidemic model with demographic and geographic heterogeneity to study the regional dynamics of COVID-19 in England. The model provides a framework for assessing the impact of policies targeted towards sub-populations or regions. We define a concept of efficiency for comparative analysis of epidemic control policies and show targeted mitigation policies based on local monitoring to be more efficient than country-level or non-targeted measures.

Keywords: network analysis
policy analysis
solvency-liquidity nexus
COVID-19
risk management
scenario simulation
mathematical modelling
Advisor: Rama, C
Holography, hydrodynamics and the transseries expansion

The transseries is an ansatz for generating solutions to classical problems which are both perturbative and non-perturbative in some limit of parameter space. In this thesis we apply this technique to three systems described by classical gravity with relevance to holographic plasmas of strongly coupled gauge theories.
To begin we compute the gradient expansion to arbitrarily high orders for an N=4 Super Yang-Mills (SYM) plasma at infinite 't Hooft coupling undergoing Bjorken evolution, later finding the full transseries by including non-perturbative (in gradient) terms. Mathematical relations exist between these transseries sectors, which we verify by calculating the leading terms of the first non-hydrodynamic series solution entirely through the coefficients of the gradient expansion. Relaxing the limit of infinite 't Hooft coupling we compute the leading transseries solution for a family of finitely coupled gauge theories, and estimate the typical path of Bjorken evolution a far-from-equilibrium system might take while evolving to the hydrodynamic regime.
Next we consider a holographic Bjorken expanding system in arbitrary spacetime dimensions D, now instead using the number of dimensions as our large parameter. Due to a greater degree of analytic control we can compute combinations of transport coefficients relevant for Bjorken flow up to 6-th order in gradients to 3rd order in 1/D, finding that our perturbative solution recovers the same dynamics controlled by the hydrodynamic gradient expansion. Computing the non-perturbative (in 1/D) contributions of this set up we demonstrate an identification between these terms and the non-hydrodynamic solutions of the small gradient transseries.
Lastly we apply the transseries to study the near equilibrium dynamics of blackbranes. Due to the simplicity of this system we can analytically find the time-evolving divergence of the entropy current to second order in the transseries, determined entirely the blackbrane's quasinormal modes frequencies and equilibrium temperature. This pedogogical example demonstrates the power of the expansion which can be easily applied to wider contexts.

Keywords: heavy ions
hydrodynamics
transseries
black holes
holography
AdS/CFT correspondence
resurgence
Aristotle's Metaphysics Book K

From the peculiar catalogue of aporiai in the opening to the extracts from books Β, Γ, and E of the Physics at the end, book K has always been a puzzling text inside the Metaphysics. The present research aims at clarifying our understanding of the whole book and its implications on Aristotle’s Metaphysics and doctrine by confirming whether K is a dependable Aristotelian source. It comprises three main parts: an introduction to the main problems, a translation with notes, and a commentary that follows the order of the chapters. In doing so, particular focus is given to a comparison with other Aristotelian works and Aristotle’s legacy in the ancient Peripatos, linking K’s oddities to equivalent situations in other Aristotle’s treatises (particularly the Ethics). The interpretation of the book across the centuries to date will be examined in the course of the study to outline the debate over the authenticity and the athetesis of the book. New evidence is found on certain unique expressions that date to a later Greek than the one of Aristotle and are attributed to a late editor who intervened on parts of the book. Plausible connections are drawn with Theophrastus’ Metaphysics and the work of Eudemus of Rhodes. Despite being a hotchpotch, K carries a meaning and it is not just a perfunctory repetition of something else better explained elsewhere in the corpus. Therefore, this research sheds light on the potential for new understanding derived from K, if not about Aristotle himself, at least on the school of thought he built and the first philosophy he was trying to define by conversing with his pupils and colleagues.

Keywords: Book K
Authenticity
Eudemus
Theophrastus
Peripatos
Aristotle
Lyceum
Metaphysics
Authorship
Advisor: Judson, L
Irwin, T