VictorJuiz/thesis huggingface dataset:
Mathematical modelling of the Yeast Metabolic Cycle
Keywords: Computational Biochemistry
Yeast Metabolism
Data Analysis
Bioinformatics
Ultradian Rhythms

The Yeast Metabolic Cycle (YMC) is an ultradian rhythm whose precise regulatory mechanism remains elusive. The YMC is a unique system that combines respiratory bursts with oscillations in both transcript levels and hundreds of metabolites in a tightly-controlled manner, creating an effective single-cell behavior that can be studied using sequencing techniques that require large quantities of cells. In this DPhil thesis I present a quantitative mathematical model of the YMC that is able to both describe the yeast synchronized metabolic activity and predict the outcome of several validating experiments.
Histone Modifications (HMs) are intimately related to gene activation and epigenetic changes regulated through chromatin organization. mRNA degradation is related to some HMs accumulation levels, and both are actively involved in the YMC regulatory mechanism. By comparing the RNA and HMs dynamics across the YMC, I have explored the functions of some HMs like H3K4me3 or H3 early-tail lysine acetylations in the yeast metabolism, discovering that H3K18ac abundance is incompatible with mRNA stability.
By clustering the yeast genome according to its expression dynamics during the YMC, I have revealed new insights into the way metabolic processes are compartmentalized at the different phases of the cycle and elucidated potential transcription factors like Met4p, Adr1p, or Thi2p, that may act as regulators of the different clusters, constituting a first attempt of unveiling the YMC regulatory mechanism.
I have employed these clusters as the cornerstone of a mathematical model describing RNA and protein dynamics at an isolated yeast cell using ordinary differential equations, concluding that a transcriptional oscillator guiding the yeast activity is more plausible that a fully metabolic oscillator.
Finally, I have combined a collection of three-component, robust, transcriptional oscillators entrained by a mean-field Hamiltonian to explain the coordination mechanisms underlying the origin and maintenance of the YMC. The resulting mathematical model is able to both replicate the YMC features described by the literature and predict the system behaviour when experimental conditions are changed or perturbations are introduced. In particular, our model explains the shape of the dissolved oxygen trace observed in the chemostat, replicates the spontaneous yeast synchronization obtained after a glucose starvation phase, and predicts the effect that carbon-source perturbations will have on the YMC.
Nonlinear convection in sea ice and other mushy layers
Keywords: fluid dynamics
adaptive mesh refinement
climate
sea ice
mushy layer

The polar regions are changing dramatically. The Arctic ocean has seen an increasing fraction of young seasonal sea ice, which contains a relatively high fraction of liquid brine inclusions, and decreasing fraction of older multi-year ice. The binary mixture of solid ice crystals and liquid brine which forms sea ice is both porous and reactive, and can be classified as a mushy layer. Convection within porous sea ice rejects dense brine into the underlying ocean, where it provides an important buoyancy forcing, and circulates nutrients within the ice with consequences for the local biogeochemistry. In this thesis I aim to build understanding of convective processes within sea ice and other mushy layers. I develop a code for direct numerical simulations in two and three dimensions, which uses adaptive mesh refinement to efficiently resolve the key dynamical features across multiple scales by solving mesoscopic conservation equations. This code is then applied to a variety of settings, whilst focussing on the relatively unexplored far-from eutectic limit which is particularly relevant to sea ice. In this far-from eutectic limit the porosity is small except for a narrow porous layer near the mush-liquid boundary. New scaling laws are found for steady-state growth, where the convection is confined to this porous layer whilst the mush-liquid solute flux scales sublinearly with the Rayleigh number - a dimensionless parameter which characterises the ratio of buoyancy to dissipative forces. Simulations of transient growth from a fixed boundary provide new insights into the dynamics and spacing of brine channels, and I find that flow in 3-D is qualitatively similar to 2-D. Meanwhile, I find evidence that convection within warming sea ice may lead to periods of intense salt fluxes into the ocean. These results have important geophysical implications for the dynamics and biogeochemistry of the polar regions.
Consequences of presynaptic dysfunction in Alzheimer’s Disease models
Keywords: Alzheimer's Disease
Tau
Synaptic plasticity
Amyloid β

Soluble oligomeric assemblies of amyloid β (Aβo) drive much of Alzheimer’s disease (AD) pathology. Among these, changes in synaptic plasticity including attenuated long-term potentiation (LTP), and facilitated long-term depression (LTD), accompanied by postsynaptic weakening, are believed to be significant contributors to disease progression. Much work has been directed at characterising the postsynaptic effects of oligomers, with little or conflicting evidence of their impact at the presynaptic bouton. Some studies investigating presynaptic boutons directly, have suggested that Aβo elevate presynaptic transmitter release. Given that transmitter release precedes postsynaptic processes, an alteration in presynaptic biology could drive postsynaptic pathology. One important downstream process of AD pathology is tau hyperphosphorylation. The relationship between Aβo and tau phosphorylation is unknown. Recent evidence that tau plays a physiological role in AMPAR endocytosis as a result of LTD induction might provide a link between tau phosphorylation and Aβo-induced synaptic changes. Here I probe the presynaptic effects of Aβo and how they impact AD pathogenesis. I confirm that Aβo can enhance both evoked, and non-evoked spontaneous miniature presynaptic release using direct, optical techniques in rat hippocampal cultures. Furthermore, I show that partial reduction in presynaptic function can restore Aβo-induced plasticity deficits in adult mouse acute hippocampal slices. I also demonstrate that these plasticity deficits might underly tau pathology; In rat organotypic slices I show that chronic NMDAR-dependent LTD can cause pathological tau phosphorylation, mimicking the effects of chronic Aβo incubation, which also requires NMDARs. In addition, I show that reduction in presynaptic function prevents Aβo-induced pathological tau phosphorylation, suggesting that the pathological tau phosphorylation that occurs in AD could be a result of repeated LTD-inducing conditions driven by an enhancement of presynaptic release probability. Previously, little work has been done to establish a role for presynaptic changes in AD. I have developed this area within the thesis and have established a link between aberrant Aβo aggregation and pathological tau phosphorylation that could have an important impact on AD therapy.
Theory of specialisations
Keywords: Model Theroy
Valued fields
Specialisations
Zariski geometries
Zariski structures

This thesis aims to develop a theory of specialisations for Zariski structures. The main question this thesis is centred around is when is a specialisation is κ-universal?
In Chapter 3 we look at the case of algebraically closed fields and Zariski structures definable in these. We show that any specialisation of an algebraically closed field defines a residue map of a valuation ring, and moreover we show that any residue map induces a κ-universal specialisation whenever the algebraically closed field is κ-saturated over the residue field.
In Chapters 4 and 5 we look at the κ-universal specialisations of finite and infinite covers of Zariski structures. Under some natural assumptions we show that a specialisation of a cover of a Zariski structure is κ-universal if and only if it extends a κ-universal specialisation of a base Zariski structures and satisfies a simple axiom.
Searching for Beyond the Standard Model resonances in the HH → bb̄bb̄ final state using the ATLAS detector
Keywords: HH-&gt;4b
HH
HH4b
di-Higgs
ATLAS
Scalar resonance
Exotics
Higgs
Scalar
4b
HDBS

An ATLAS analysis searching for Beyond the Standard Model resonances, X, that are produced and decay through the pp → X → HH → bb̄bb̄ process is presented. These events are studied in the phase space region where the four b-quarks produce four well-separated jets.
A significantly stronger upper-limit is set on the pp → X → HH cross-section for these resonances than was set by the Early Run 2 ATLAS analysis. Above 350 GeV these limits are also stronger than those of the combination of all ATLAS di-Higgs searches with 27.5 fb-1 to 36.1 fb-1 of data. No statistically significant excesses are found, with the largest excess having a global significance of 1.2+0.4−0.3 σ. In particular, with an improved pairing algorithm and more sophisticated background modelling, the 2.8σ excess found at 280 GeV by the Early Run 2 analysis is not confirmed. The results of this analysis suggest the upcoming version, which uses an evolution of the same technique on the same data to look for Standard Model di-Higgs production, will be able to set stringent limits on that process.
Information theory and banking
Keywords: banking
imperfect competition
stress tests
strategic communication
insurance
tying contracts
selection markets
central bank design

This thesis uses information theory to study policy questions in banking, finance, and industrial organization. It consists of four independent papers.
The first paper, “Time Inconsistency in Stress Test Design”, shows that central banks face a time inconsistency problem when publishing bank stress test results. Before a stress test, they want to appear tough as the threat of letting banks fail the stress test incentivizes prudent behaviour. After the stress test, they want to act soft by releasing only partial information in order to reassure financial markets about bank health. The paper characterises an institutional design solution to this commitment problem: a social planner sets the framework within which the central bank communicates. We find that a hurdle rate framework, where all banks are judged to pass or fail relative to a common threshold, is optimal in many settings as it generates intermediate levels of both incentives and reassurance. We show that, in such a hurdle rate framework, stress tests become an informational contagion channel.
The second paper proposes a model of imperfect competition in markets with selection and investigates whether imperfect competition mitigates the inefficiency which, in these markets, arises under perfect competition. Focusing on markets with advantageous selection, such as consumer credit markets, we find that no degree of competition can restore the first best efficient allocation. We discuss policy alternatives.
The third paper shows that, in markets with adverse selection, tying contracts can prevent unravelling and thus have a substantial positive effect on welfare. We illustrate this effect for two insurance markets. When one characteristic (such as life-expectancy) is hidden information and causes agents to have high expected cost for one product (life insurance) but low expected cost for another (pension annuity), then for tying contracts cost differences partially cancel out. This can prevent unravelling.
In the fourth paper, which is joined work, we build on a field experiment, find that some agents increase effort when it becomes more costly, and rationalize this in a signalling model. In the field setting, agents also choose whether to truthfully disclose their effort. The data on this form of strategic communication adds further support to the interpretation that effort choices are driven by signalling motives.
A case study of the Late Bronze and Early Iron Age cemeteries of Tell el-Far'ah (South)
Keywords: West Bank
Bronze Age
Tombs
Canaanites
Palestine

The subject of this thesis is the study of the Late Bronze and Early Iron Age tombs of the site of Tell el-Far'ah (South) in southern Palestine, excavated in 1928 and 1929 by W. M. F. Petrie. Because contextual information on the tombs is particularly scant, this work essentially concentrates on the analysis of the material furnishings which were found in association with the burials. It is primarily concerned with the pottery assemblages, but the rich variety of small finds discovered in the tombs is also discussed.
The prime interest of the tombs of Tell el-Far'ah, which cover the important transition period going from the 13th to the early 10th centuries B.C., does not only reside in the diversity of the nature of their furnishings, which, besides pottery also include beads, scarabs, amulets, metal and stone vessels, worked ivory, weapons and tools, but also in the variety of the foreign influences which they reflect. Although none of the tombs considered here does contain foreign imports in significant quantities (whether from the Aegean, Cyprus, Egypt or Syria), the majority of them, for example through the presence of local imitations of foreign pottery types, suggest that relationships between the various regions of the eastern Mediterranean were still alive during the period under consideration. Instead of ascribing the diverse innovations, changes and apparent disturbances of the Early Iron Age Levant to the activities of migrating populations from the Aegean (the “Sea Peoples”) this research proposes an alternative explanation to the question. It notably argues that the furnishings of the tombs of Tell el-Far'ah provide an important insight into the emergence of new patterns of trade and exchanges in the Mediterranean, accompanied by new forms of socio-economic organization.
Amongst the shadows of mineralized mountains: resource-making and social becoming in the Peruvian Andes
Keywords: Anthropology of mining
Peru
Extraction

Since the 1990s, the adoption of the extractive imperative in Peru, while leading to unprecedented economic growth, has simultaneously entailed the proliferation of local contestation at the point source of mineral exploitation. To date, academic attention on ‘conflictos mineros’ (mining conflicts) has been dominated by interpretations of political economy which shroud local realities amongst the implicit assumptions of ‘isolation’ and ‘alterity’. Ethnographic interventions on contemporary mining in Peru have lagged behind the explanatory rush. This dissertation, based on 15 months of fieldwork in the communities which surround the Bambas copper mine, attempts to shift and destabilize scholastic presumption. Grounding its theoretical trajectory in progressive imaginaries of social mobility (the ‘search for a better life’), the thesis attempts to dissolve the dominant prisms of ‘peasant’ and ‘indigenous’ communities to elucidate the complex and, at times, contradictory outcomes of mining as practiced in southern Peru. Resource-making, it is argued, interjects upon fraught histories of marginalization, activating latent desires for social becoming. Over time, however, the maturation of mining, from exploration to eventual low-labor production, unfurls stark discordances between development’s image and reality. Communities and individuals are forced to navigate this shifting social terrain, interpreting millennial moral orders, developing alternative projects for the ‘better life’, and, ultimately, ‘waiting’ for imagined futures that are increasingly threatened by precarity. These crises in social becoming produce unintended outcomes, even amongst the ‘responsible’ precepts of ‘modern mining’. Accordingly, CSR works to govern expectation and corporate entanglements with shadowed communities. Environmental regulation creates complex and insecure relations between toxic legacies and endurance. While indigenous legal precepts transform through the friction of travel and contact to eventually assemble artisanal mining ventures. The overarching empirics move with and beyond conventional conceptions of Andean peoples and corporate interventions to demonstrate festering frustrations with development trajectories and continuous maneuvering within them.
‘Hospitality, chantries, and other works of piety’: a select study of the functions and longevity of hospitals in small towns and villages in medieval England, c. 1150-c. 1450
Keywords: charity
poor
hospitality
urban
hospital
patronage
medieval
chantry
Mortmain
parish
welfare

In the high to late Middle Ages, hospitals were ubiquitous. It has been estimated that by the fourteenth century more than 500 hospitals were scattered across the English landscape. Yet to date, hospitals located in small towns and villages in England have received little scholarly attention. This study seeks to contribute to the field by offering a wide-ranging assessment of 72 lesser-known hospitals. It considers whether these houses can be defined by the functions they performed as opposed to the guests they served. And it seeks to establish the extent to which they were reliant on patronal support throughout the core period of the study. The project combined the results generated from its bespoke database with an in-depth appraisal of the hospitals in Aynho and Brackley, Northamptonshire. In addition, it incorporated material concerning obscure hospitals into its analysis.
The results found that the hospitals can be defined by their core functions of hospitality, chantries, and other works of piety which were offered to a variety of guests. Such was the importance of the provision of hospitality, it was implicit within their most commonly-used name. A main finding was that hospitals were remarkably resilient: at least 50% were viable in the sixteenth century. The minimum average lifespan of these houses was 238 years, and the evidence revealed a degree of specialisation in their functions in the later Middle Ages. During this time, many successfully mitigated both internal and external threats through a wide-ranging network of support. This included monarchs and bishops in their role as temporary patrons and reformers. However, the study concludes that it was in the gift of the legal patron to ultimately seal their fate.
All about politics: the American electoral cycle and decision-making in war
Keywords: Elections
Decision-making
US foreign policy
War

How does electoral politics affect presidential decision-making in war? As both Commanders-in-Chief and elected officeholders, American presidents must balance the national interest with their often competing interest in political survival when assessing alternative strategies in war. Yet despite the increasing attention paid to domestic political explanations of international relations, surprisingly little has been written on the electoral connection. It can still seem as if the politicians are left out of international politics. Grounded in the field of foreign policy analysis and drawing on the logic of democratic constraint, this thesis argues that electoral pressures in fact play a profound role in wartime decision-making, systematically pushing and pulling the president away from courses of action he perceives to be strategically optimal. Going beyond the existing literature’s focus on cases of conflict initiation, it outlines five mechanisms – delay, dampening, spur, hangover and spoiler – which capture the ways in which electoral considerations shape both decisions to escalate an ongoing conflict and efforts to bring it to a satisfactory conclusion. Rich historical case studies of the wars in Korea, Vietnam and Iraq illustrate how these pressures conform to a rhythm dictated by the electoral cycle. Using a qualitative methodological approach, employing material from extensive archival research and a series of interviews with senior officials, this thesis offers an in-depth look at exactly how electoral constraints have materially affected past decisions. The findings of this thesis carry broader implications for the literature on democracy and war, enriching our understanding of electoral accountability, and provides a new conceptual lens through which scholars can analyse presidential decision-making.
The politics of quotation: Charlotte Smith’s radical fictions and their allusions to the works of Milton, Rousseau, and Voltaire
Keywords: radicalism
politics
quotation
Rousseau
Charlotte Smith
John Milton
eighteenth century
romantic literature
Voltaire

Charlotte Smith is both a known radical sympathizer and an allusive writer. This thesis investigates the political meanings embedded through the selection and treatment of allusion in each of Charlotte Smith’s novels published between the outbreak of the French Revolution and the end of the Reign of Terror. Specifically, it investigates how Smith utilizes quotations from authors connected with political radicalism—John Milton, Voltaire, and Jean-Jacques Rousseau—to work through the nuances of her own political thought. I argue that these specific authors feature significantly in her work because of their known republican sympathies. Yet, Smith frequently deploys these quotations in a context far from that which was originally intended by her source, capitalizing on their republican significations but making the actual polemical content all her own. Both the frequency and diversity of her allusive engagement increases during the period of the Revolution, which marks the Revolutionary period as one essential to the development of Smith as both a novelist and as a radical. Through tracking the presence of quotation in each novel, one published each year between 1791 and 1794, the thesis traces the evolution in Smith’s political thought and, specifically, her changing attitudes toward the French Revolution as it moves through its early utopian stages to the violence and excess of the Reign of Terror. Not only does this study contribute to recent scholarship on the use of quotation in eighteenth-century writing, but it also provides an in-depth study of Smith’s evolving radicalism. In this way, the project demands reassessment of critical studies of Smith’s work which have failed to recognize the extent of the polemical content within the first work in the sequence, Celestina, and the continuing commitment to republican sympathies despite burgeoning conservatism in the last, The Banished Man.
A systematic review of research on listening strategies in second language lecture comprehension
Keywords: a systematic review
second language
lecture comprehension
listening strategies

This study adopted a systematic research methodology to synthesize previous literature on listening strategies in second language lecture comprehension. After identifying 21 eligible studies, the review mapped out the current state of empirical research related to the topic. It also synthesized and assessed the quality of evidence pertaining to the three in-depth review questions:
1. What evidence is available on the deployment of listening strategies in second language lecture comprehension?
2. What evidence is available on the effectiveness of listening strategies in second language lecture comprehension?
3. What evidence is available on the development of listening strategies in second language lecture comprehension?
The results of this review revealed several research gaps in terms of research focus (e.g., participants, contexts) and methodology (e.g., study design, data collection, data analysis) and were discussed in relation to the above questions to make suggestions for future research.