VictorJuiz/thesis huggingface dataset:
Detecting the misuse of secrets: foundations, protocols, and verification

Secrets are the basis of most protocol security, enabling authentication and secrecy over untrusted channels even in the presence of active adversaries. The compromise and misuse of secrets can therefore undermine the properties that people and systems rely on for their security. In this thesis, we develop foundations and constructions for security protocols that can automatically detect, without false positives, if a secret such as a key or password has been misused. These constructions allow protocol participants to automatically trigger an appropriate response and minimize the effects of compromise. Our threat model includes malicious agents, (temporarily or permanently) compromised agents, and clones.
Unlike existing approaches to detection, for which designs are interwoven with domain-specific considerations and which usually do not enable fully automatic response (i.e., they need human assessment), our approach makes it clear where automatic action is possible. Our results unify, justify the design of, and suggest improvements for existing domain-specific solutions. For example, we propose an improvement to Cloudflare's Keyless SSL protocol that enables key misuse detection, and a modified ISO-IEC 9798 protocol for use in high-security smart-card applications such as the Common Access Card.
Our results show that protocols which detect misuse must be stateful. Although stateful protocols are becoming more common, formally analyzing them remains a challenge. We develop and implement several improvements to the Tamarin prover to alleviate this difficulty, and use them to formally verify our proposed detection protocols.
We demonstrate the wide applicability of our improvements to Tamarin by analyzing several real-world protocols. Notably, we perform the first full formal analysis of both WireGuard, and the DNP3 Secure Authentication protocol---a complex multi-stage stateful protocol used to authenticate critical monitor and control functionality in SCADA systems.

Advisor: Cremers, C
The effect of in vitro culture conditions on cell metabolism

Because cells have adapted to respond to their extracellular environment, the in vitro conditions under which cells are cultured have the potential to impact on cell metabolism. This study aims to investigate the effect of various components of culture medium on the metabolism of Chinese Hamster Ovary (CHO) cells.
Firstly, the effect of glucose and glutamine, two important carbon sources, was investigated. The impact of these nutrients on cell growth, viability, oxygen consumption rate (OCR) and steady state ATP levels was assessed. Glucose was found to have a suppressive effect on OCR, while under glucose limiting conditions, glutamine was able to enhance OCR. Although commonly considered a waste product, lactate can also act as a source of carbon and can be consumed by CHO cells. The effect of lactate on the above parameters was also measured, but no robust changes were observed.
Serum is added to the majority of cell culture media and is necessary for cell growth. However, since this product is animal derived, batch to batch variability is high and its composition is not well documented. The broad profile of components in serum means it has the potential to exert many effects on cells, but the effect serum of on cell metabolism is poorly understood. For this reason, the metabolic state of CHO cells in reduced serum was investigated using the aforementioned assays. Metabolite profiling was also performed using metabolomics. Cells cultured in 10% foetal bovine serum (FBS) were found to have a higher OCR than those cultured in both 1% and 0.1% FBS. This was supported by metabolite profiling which showed a greater abundance of tricarboxylic acid (TCA) cycle intermediates in these cells. The metabolite data also indicated increased oxidative stress in cells cultured in 10% FBS. Glucose metabolism also appeared to be affected, with a higher abundance of early glycolytic and glycogenesis intermediates in cells cultured in low (0.1%) serum.
This study shows that both the substrates available in culture media and the commonly used supplement, FBS, can influence metabolic pathways within mammalian cells, meaning their effects must be accounted for, particularly in studies of metabolism.

Keywords: Cell culture
Mitochondria
Metabolism
Metabolomics
Glucose
Oxidative stress
Advisor: Morten, K
McCullagh, J
Genotype-phenotype maps for gene networks: from evolution to computation

One of the most fundamental and least understood elements of evolution is the mapping between genotype and phenotype. Recent work on genotype-phenotype (GP) maps suggests that these maps show properties which may have important evolutionary implications. These properties include a skewed distribution of genotypes over phenotypes, linear scaling between phenotype robustness and the logarithm of phenotype frequency, and a positive correlation between phenotype robustness and evolvability. However, most of these properties have only been studied for self-assembling systems, such as protein complexes or RNA folding. In this thesis, we ask ourselves if these properties are more general.
First, we apply tools from algorithmic information theory to a wide class of inputoutput maps, of which GP maps are a subset. We find that these maps show a strong bias towards simple phenotypes, a pattern known as simplicity bias. We also define a matrix map of tunable complexity, with which we can study the conditions under which simplicity bias is present.
Next, we investigate multiple models of GP maps for gene regulatory networks (GRNs). These include Boolean threshold networks, where we fix the strength of gene interactions, while varying the network topology, as well as systems of differential equations, where we fix the network topology while varying interaction strengths. For both modelling frameworks, the GRN GP maps exhibit all the structural properties found in the literature, as well as simplicity bias. We also find that the number of genotypes mapping to the wild-type phenotypes for various GRNs is unusually large, and argue that this is evidence that the structure of the GP map plays an important role in determining evolutionary outcomes.
Finally, we return to more general input-output maps, and show that in addition to simplicity bias these maps also present randomness deficiency, that is, their output spectrum is less complex than expected. We argue that this additional property combines with simplicity bias in GP maps, and more generally, in input-output maps, and suggest a general trend towards simplicity in nature.

Keywords: algorithmic information theory
Advisor: Louis, A
Structural aspects of modelling biopolymer networks

Many biological systems involve intricate, hierarchical networks formed from cross-linked filaments, including the cytoskeleton of eukaryotic cells and the collagen scaffold of the extracellular matrix. Experiments performed on these biopolymer networks have identified exotic and desirable mechanical behaviours that cannot be easily understood without discussing the underlying microstructures and their properties. As such, the theoretical and computational modelling of filament assemblies has increasingly utilized discrete fibre network (DFN) models to investigate their complex local and global mechanical properties. This thesis investigates some of the many structural aspects of these networks, and how details of the network architecture can influence the mechanics of the system. We discuss how the geometry of a fibrous substrate can influence the long-ranged displacement fields generated by contractile resident biological cells, and the extent to which long-ranged mechanical communication between distant cells is plausible. A variety of architecture choices are discussed and compared. Motivated by improvements in electrospinning technologies and recent experiments, we develop a new fibre network model, where cross-link density is allowed to vary while geometry is controlled. The affine-nonaffine transition in this model is discussed and characterized, and theoretical predictions for the scaling of the network shear modulus are presented. As much of the DFN literature focusses on monotypic fibre networks, the mechanics of polymer assemblies formed from two or more filament types, which often arise in Nature, is poorly understood. We seek to address this by extending monotypic fibre network models to incorporate two distinct fibre types. In the low density regime we present extensive theoretical predictions and supporting numerical results for the network response as numerous parameters are varied. The importance of network architecture is discussed in the context of nonaffine fluctuations and their influence on the mechanical response. Finally, dense, random heterotypic networks are studied, in light of experiments and theoretical models that observe `exceptional stiffening' in such systems. We propose a novel explanation for this phenomenon, and provide evidence for our interpretation over others given in the literature. The implications of the research presented here for higher dimensional systems and for finite strains are discussed. Together, this thesis constitutes an argument for the mechanical importance of the detailed structural properties possessed by biopolymer networks, in a variety of systems and at multiple scales.

Advisor: Gaffney, E
The dominant party system in Uganda: Subnational competition and authoritarian survival in the 2016 elections

This thesis studies the authoritarian dominant party system in Uganda during the 2016 general election. It focuses on how subnational competition within the ruling National Resistance Movement (NRM) prolongs the tenure of its leader, 30-year incumbent President Yoweri Kaguta Museveni. In three districts where the NRM has been historically strong – Kyenjojo, Kayunga, and Bugiri – the thesis traces three processes to this end: the decentralisation and localisation of accountability politics away from the regime and toward expendable local politicians (H1); the relationship between local elite rivalry and the NRM’s collective mobilisation for Museveni’s simultaneous re–election (H2); and how competitive electoral pressures on NRM MPs alter the national elite bargain in the president's favour (H3). It concludes that in strong NRM areas, the fractious divisions that characterise intra-party competition are not a by-product of its near monopolistic domination of politics, but the very basis of that dominance. This emphasis on subnational intra-party competition brings a new variable into a literature on non-democratic survival that tends to focus on more narrowly coercive and clientelist regime strategies.
The thesis presents this argument in a qualitative single case study driven by an open and inductive fieldwork component throughout the 2016 election period. Its three hypotheses are built on data from interviews (with voters and elites), ethnographic observations, official data, and secondary sources. This data is used in a process-tracing design before its conclusions are fortified by a subnational comparative analysis of the election results in the three case districts.

Keywords: Local politics
Museveni
Uganda
Authoritarian elections
African politics
NRM
elections
Advisor: de Oliveira, R
Stochastic analysis and stochastic PDEs on fractals

Stochastic analysis on fractals is, as one might expect, a subfield of analysis on fractals. An intuitive starting point is to observe that on many fractals, one can define diffusion processes whose law is in some sense invariant with respect to the symmetries and self-similarities of the fractal. These can be interpreted as fractal-valued counterparts of standard Brownian motion on Rd. One can study these diffusions directly, for example by computing heat kernel and hitting time estimates. On the other hand, by associating the infinitesimal generator of the fractal-valued diffusion with the Laplacian on Rd, it is possible to pose stochastic partial differential equations on the fractal such as the stochastic heat equation and stochastic wave equation. In this thesis we investigate a variety of questions concerning the properties of diffusions on fractals and the parabolic and hyperbolic SPDEs associated with them. Key results include an extension of Kolmogorov's continuity theorem to stochastic processes indexed by fractals, and existence and uniqueness of solutions to parabolic SPDEs on fractals with Lipschitz data.

Keywords: Partial Differential Equations
Calculus
Fractals
Probability
Geometry
Stochastic Analysis
Advisor: Hambly, B
Encouraging providence: uncertainty, wellbeing, and the making of new American futures in the home

THIS THESIS CONSIDERS how households in Providence, Rhode Island in the United States negotiate uncertainty and sustain wellbeing in their everyday lives. Drawing on twelve months of participant observation and interviews in eighteen middle class households in recent states of transition, the thesis introduces the concept of 'everyday uncertainty,' which encapsulates embodied senses of not knowing and conditions with unknown outcomes. Everyday uncertainty emerges as relational and productive, mediated through social, material, and individual means, and as entangled in the desire to cultivate wellbeing or the good life. Adapting an everyday material culture approach to the home, the ethnography attends to material culture and everyday practice, participant narratives, the atmosphere of space, and the home as a part of the nation and city. For the middle class homes described,ontological security, aspiration, improvisation and creativity, and the material environment of the city emerge as core facets of everyday uncertainty and the making of the good life. I draw their experiences together to argue that the 'frontier' of new American futures can be found in the home. This study of 'everyday uncertainty' sheds light on what people have to negotiate in conditions that are not particularly precarious or insecure. The ordinariness of everyday domestic lives helps begin to untangle the nuances between innate human improvisation and the neoliberal expectation of individual adaptability, particularly in the United States context.

Advisor: Ulijaszek, S
Daniels, I
Proﬁnite properties of 3-manifold groups

In this thesis we study the finite quotients of 3-manifold groups, concerning both residual properties of the groups and the properties of the 3-manifolds that can be detected using finite quotients of the fundamental group.
A key theme is the analysis of when two 3-manifold groups can have the same families of finite quotients. We make a detailed study of this 'profinite rigidity' problem for Seifert fibre spaces and prove complete classification results for these manifolds.
From Seifert fibre spaces we continue on this trajectory and extend our classification results to all graph manifolds. We illustrate this classification with examples and several consequences, including for graph knots and for mapping class groups.
The third part of the thesis concerns the behaviour of the finite p-group quotients of 3-manifold groups. In general these quotients may be scarce and poorly behaved. We give results showing that some of these issues may be resolved by passing to finite-sheeted covers of the manifold involved. We also prove theorems concerning the p-conjugacy separability of certain graph manifold groups.
The concluding chapter of the thesis collects other results linking low-dimensional topology and finite quotients of groups. In particular we prove that finite quotients of a right-angled Artin group distinguish it from other right-angled Artin groups, and we give an argument detecting the prime decomposition of certain 3-manifold groups from the finite p-group quotients.

Keywords: Profinite groups
3-Manifolds
Advisor: Lackenby, M
The grounds of unity: substantial and sub-substantial being in Aristotle

Strawson famously classified Aristotle as a descriptive metaphysician, alongside himself, and in contrast to more revisionary philosophers like Plato. The extent to which Aristotle was merely concerned to describe our conceptual scheme has, however, been over-estimated by some. Although common-sense beliefs are among the starting-points from which Aristotle pursues his metaphysical inquiries, the conclusions of those inquiries are in fact quite radical.
In chapter one, we identify three interpretative questions about Aristotle’s notion of substance:
(1) does Aristotle change his mind about what things are the substances between writing the Categories and the Metaphysics?
(2) are matter, form and the compound of the two all substances, albeit to different extents, or are only forms substances?
(3) however we resolve these questions about hylomorphism, what range of forms count as substantial, and why?
In chapter two, we examine the criteria of being a substance. These provide evidence for Aristotle’s changing his mind between the Categories and Metaphysics. An examination of the ‘χωριστόν’ criterion also supports the view that only forms are substances: Aristotle claims that compounds are separate simpliciter, since they can exist without items in other categories, and not vice versa, but this claim cannot be supported. Only forms are separate in definition, and so, on the assumption that being separate is necessary for being a substance, only forms are substances.
If we are to understand the claim that only forms are substances, we should acquire a better understanding of what is meant by ‘form’, and why Aristotle thinks there are such things. Chapters three to five undertake this task. Chapter three discusses Aristotle’s introduction of matter and form in the Physics to account for substantial generation, and his argument in Z.17 that form is substance, since it is what makes some matter one thing. In chapter four, this unificatory role is distinguished from the role of a principle of individuation, and it is argued that only individual forms are suitable to play the latter role. In chapter five, we examine some recent attempts to blur the distinction between matter and form, by maintaining that form is essentially matter-involving. We argue that the view according to which form is defined independently of matter is preferable.
In chapters six and seven, we address the third interpretative question. Chapter six argues that artefacts are not substances (and not merely substances to a lesser degree than organisms) because they are not separate, since they depend on the intentional activity of their creators or users. Chapter seven considers Aristotle’s views about mixtures. These are also compounds of matter and form, but fail to be substances because, like matter, they depend on a higher form to make them one thing.

Keywords: Aristotle
metaphysics
matter
form
hylomorphism
Advisor: Shields, C
When value chains go south: governance and upgrading of the Kenyan leather sector

In the last three decades, the global economy has witnessed an ambivalent phenomenon of integration through disintegration. Whilst the amount of regional and global trade dramatically increased, vertical specialisation prompted the outsourcing of manufacturing, assembling, and other business functions regionally and globally. The slicing up of value chains and the consequent surge in trade of intermediate goods drew the attention of scholars interested in the economic, social, and environmental consequences of this phenomenon. Yet, most of the literature on value chains has concentrated on the institutional and market linkages between firms in developed economies and delocalised suppliers in the global South. Conversely, less attention has been paid to the rise in South-South trade that accompanied the development of South- South and regional value chains.
The following chapters provide new evidence on the opportunities and constraints that participation in value chains across North-South, South-South, and regional trajectories entails for local suppliers in developing countries. This is achieved by means of a mixed-methods approach that combines firm-level export data with over 100 semi-structured interviews across the Kenyan leather sector.
On the one hand, results show how North-South value chains are characterised by more profitable and stable relationships between buyers and local suppliers. Nonetheless, whilst defined by higher product and process standards, linkages with developed economies appear to prevent rather than encourage local value addition. On the other hand, South-South value chains are governed by instability and distrust underpinned by pressures to reduce prices and lack of upgrading opportunities.
Like the global South, regional value chains are characterised by fierce competition and low profitability. Even so, they often constitute an alternative for small suppliers willing to venture into new products and functions. Particularly, the local and regional markets represent an upgrading platform for innovative firms whose low capital endowments prevent them from accessing premium North-South value chains. In this case, industrial policy and entrepreneurship play a crucial role in enabling smallholders to upgrade in a competitive environment.

Keywords: Entrepreneurship
Global Value Chains
Upgrading
Governance
South-South trade
Africa
Kenya
Advisor: Sanchez-Ancochea, D
Fu, X