VictorJuiz/thesis huggingface dataset:
The dynamical approach to relativity as a form of regularity relationalism

This thesis investigates the interplay between explanatory issues in special relativity and the theory’s metaphysical foundations. Special attention is given to the ‘dynamical approach’ to relativity, promoted primarily by Harvey Brown and collaborators, according to which the symmetries of dynamical laws are explanatory of relativistic effects, inertial motion, and even the Minkowskian geometrical structure of a specially relativistic world.
The thesis begins with a review of Einstein’s 1905 introduction to special relativity, after which brief historical introductions are given for the standard ‘geometrical’ approach to relativity and the unorthodox ‘dynamical’ approach. After a critical review of recent literature on the topic, the dynamical approach is shown to be in need of a metaphysical package that would undergird the explanatory claims mentioned above. It is argued that the dynamical approach is best understood as a form of relationalism—in particular, as a relativistic form of ‘regularity relationalism’, promoted recently by Nick Huggett. According to this view, some portion of a world’s geometrical structure actually supervenes upon the symmetries of the best-system dynamical laws for a material ontology endowed with a primitive sub-metrical structure.
To explore the plausibility of this construal of the dynamical approach, a case study is carried out on solutions to the Klein–Gordon equation. Examples are found for which the field values, when purged of all spatiotemporal structure but their induced topology, are still arguably best-systematized by the Klein–Gordon equation itself. This bolsters the plausibility of the claim that some system of field values, endowed with mere sub-metrical structure, might have as its best-systems dynamical laws a (set of) Lorentz-covariant equation(s), on which Minkowski geometrical structure would supervene.
The upshot is that the dynamical approach to special relativity can be defended as what might be called an ontologically and ideologically relationalist approach to Minkowski spacetime structure. The chapters refer regularly to three appendices, which include a brief introduction to topological and differentiable spaces.

Keywords: minkowski geometry
explanation
special relativity
space-time
dynamical approach
lorentz covariance
lorentz invariance
spacetime
Advisor: Pooley, O
Timpson, C
Income inequality and political engagement in Eastern Europe

The thesis examines whether income inequality in post-Communist Eastern Europe depresses political engagement or increases the potential for conflict and instability. The thesis finds that while overall income inequality is correlated with lower political engagement and political engagement is stratified by income, income inequality does not appear to depress political engagement among the poor in post-Communist Eastern Europe. I use multilevel modeling to examine mass survey data from the survey done by Professors Whitefield and Evans as part of an ESCR-funded project as well the World Values Surveys.
Interferon regukatory factor 5: a systematic study of macrophage gene regulation

Macrophages are multifaceted innate immune cells, able to adapt their phenotype to respond to a myriad of conditions, engaging in tissue-specific functions and mediating either inflammatory or anti-inflammatory responses depending on the encountered stimuli. They conduct key roles in the orchestration of immune responses; from pathogen recognition through sterilising inflammation to resolution and repair. The Udalova laboratory has previously demonstrated that IRF5 promotes a pro- inflammatory macrophage phenotype, leading to the secretion of TNF, IL-12, and IL-23, enhancing Th1/Th17-mediated immune responses, and described the cooperation between IRF5 and the transcription factor RelA, which mediate the production of pro- inflammatory genes. The aim of this thesis is to further characterise the activity of IRF5 in macrophage inflammatory responses. I demonstrate that IRF5 not only regulates the transcription of cytokines and chemokines in response to bacterial stimuli, but also anti-microbial peptides, whilst simultaneously down-regulating homeostatic and resolving macrophage functions. My data also suggests that IRF5 plays a role in enforcing monocyte to macrophage differentiation by up-regulating the transcription of key macrophages markers and repressing dendritic cell identity genes. To further characterise the mechanisms of the inflammatory response mounted by macrophages I used an unbiased approach; combining twenty-three transcription factor ChIP-seq data sets with chromatin accessibility information from ATAC-seq, uncovering RUNX1 as a novel partner of IRF5 that binds co-operatively to clusters of enhancers, which control the transcription of pro-inflammatory genes in a signal-dependent manner. This is the first study demonstrating a critical role for RUNX1 in activity of inflammatory macrophages.

Keywords: Macrophage
IRF5
Transcription
Advisor: Udalova, I
Proudfoot, N
Copper-mediated nucleophilic 18F-radiolabelling of (hetero)arenes for applications in positron emission tomography

This thesis focuses on the development of a novel nucleophilic 18F-fluorination of (hetero)arenes and of a rapid screening experiment to facilitate the application of this reaction to complex heterocyclic targets of medicinal importance.
Chapter 1 introduces the use of molecules labelled with fluorine-18 as tracers in positron emission tomography and reviews methods for the preparation of [18F]fluoroarenes published prior to the start of the work in this thesis.
Chapter 2 describes the development of a novel method for the preparation of electronically-diverse [18F]fluoroarenes from aryl boronic esters and [18F]fluoride, mediated by a copper complex. Application of this 18F-fluorodeboronation to electron-rich radiotracers is demonstrated. Methods for the preparation of [18F]fluoroarenes published after the start of the work in this thesis are reviewed.
Chapter 3 outlines a rapid screening experiment for assessing the tolerance of the 18F-fluorodeboronation towards heterocycles, and the use of this method to guide the retro-radiosynthesis of heterocycle-rich, medicinally relevant molecules.
Chapter 4 contains synthetic procedures and characterisation data for compounds in Chapters 2 and 3.

Keywords: PET
Positron Emission Tomogrphy
18F-Fluorination
Copper
[18F]Fluoroarenes
18F-Radiolabelling
Advisor: Gouverneur, V
The agrarian question in Iraq

The first part of the thesis is concerned with questions arising from the dual society of "tribesmen and townsmen,"as the distinction is often briefly but inaccurately described. Nearly two thirds of the rural population and more than half of the total population may be regarded as having their social centre of gravity still in some form or other of tribal organisation.
1. British policy towards the tribes, as it shaped at first after the occupation of the country during the last war, stood in contradiction to the axiom which had been common to all the changing patterns of Turkish tribal policy. Far from being intent on destroying tribalism, it favoured its preservation. But the experiment in indirect administration of tribal areas came to an end in 1920. In some districts conditions forbade its introduction, in others its introduction courted failure.
With the establishment of the provisional Arab Government the emphasis shifted back towards the bureaucratic administration of tribal areas. With the assistance of the British Royal Air Force, the establishment of direct administration in the outlying districts proceeded steadily. After the release from the Mandate, the Iraqi army proved its ability to act efficiently in face of serious tribal opposition.
The ascendancy of the central Government faces tribalism with difficult problems of re-adjustment.
From Introduction. Continued in thesis ... .

Keywords: land
tribes
nomads
agriculture
Iraq
agrarian
reform
state
Coptic interference in the syntax of Greek letters from Egypt

Egypt in the early Byzantine period was a bilingual country where Greek and Egyptian (Coptic) were used alongside each other. Historical studies as well as linguistic studies of the phonology and lexicon of early Byzantine Greek in Egypt testify to this situation. In order to describe the linguistic traces the language-contact situation left behind in individuals’ linguistic output, this thesis analyses the syntax of early Byzantine Greek texts from Egypt. The primary object of interest is bilingual interference in the syntax of verbs, adverbial phrases, discourse organising devices and formulaic sections.
The thesis is based on a corpus of Greek and Coptic private letters on papyrus, all of which date from the fourth to mid-seventh centuries, originate from Egypt and belong to bilingual, Greek-Coptic, papyrus archives. The data is analysed with a particular focus on three interrelated questions:
(1) What kinds of deviations from the standard pattern appear and to what extent can language-internal confusion account for them?
(2) How are instances of language-internal confusion and bilingual interference distributed over the selected syntactic domains?
(3) Do deviations from the standard accumulate in certain letters or archives belonging to the corpus and do they correlate with additional indicators of bilingualism such as code-switching or circumstantial information about writers?
In addition to answering these questions, the thesis seeks to explain the observed distributions.
The results obtained from this study suggest that bilingual interference is linked to the way writers assimilated structures. In fact, there is a marked difference between deviating syntactic structures in non-formulaic and formulaic contexts. The study further suggests that bilingual interference does not affect every domain of syntax to the same degree. The degree of complexity of the syntactic structure in question as well as the degree of divergence from the corresponding Coptic structure seem to play a role.

Keywords: bilingual interference
learning methods
Coptic
language contact
usage-based model
post-classical Greek
Advisor: Willi, A
Palaeodietary reconstruction in late antique Spain and assessing means of inter-site comparison

Dentine and bone samples from thirty-six individuals from Sanisera and thirty-five individuals from Mérida, as well as dentine and bone samples from twenty-five faunal samples from Sanisera and two from Mérida (all dating from the between the 3rd - 9th centuries AD) were analyzed for stable carbon and nitrogen isotopes. The remains from Sanisera originated from the Late Antique Period (5th - 7th centuries AD) and were taken from tombs containing multiple disarticulated inhumations. The remains from Mérida dated from the Late Roman to Islamic Periods (3rd - 9th centuries AD), were mostly single inhumations with multiple burial styles. The isotopic analysis showed primarily a terrestrially-based C3 diet, which in the case of individuals from Sanisera was occasionally supplemented by marine sources. These isotopic data were compared to human and faunal results from twenty-seven published studies of fifty-three contemporary sites in Europe and North Africa to see how these two Spanish sites fit within the larger Late Antique world using a more analytical comparison. Integration of this multi-site dataset was discussed in terms of the raw data. Direct comparison of isotopic data from different sites suffers from the effects of a number factors extraneous to diet such as climate, time period, and local geography. Previous attempts to minimize these effects have proven insightful, but lack interpretive power in terms of overall dietary reconstruction. Based on the multi-site dataset, an alternative, Faunal Correction, model was proposed. This model adjusts both nitrogen and carbon isotopic values using a faunal standard developed from faunal isotopic data. Not only did this new model have the advantage of relying solely on isotopic data, it successfully reduced overall variability of both carbon and nitrogen isotope data between the sites and, because of its structure, it can easily accommodate additional factors whose impact on isotope values may be better understood in the future.

Advisor: Schulting, R
Constructing RNA based genetic circuits for the detection of endogenous microRNAs

Synthetic biology is a rapidly evolving field enabling the rational design of new biological functionality. RNA is particularly amenable to this rational design processes due to relatively straightforward structural modelling principles and its ability to perform diverse roles, from that of simple messenger RNAs to complex catalytic ribozymes. Consequently, the synthetic design and assembly of RNA building blocks into functional circuits and networks can far exceed the complexity of what could be achieved using protein components. MicroRNAs (miRNAs) are fascinating short non-coding RNA molecules (~22nt long) which have the capacity to bind and tune the expression of thousands of mRNAs, functioning as molecular rheostats during development, physiology and disease. The ability to detect miRNAs, via synthetic biosensor circuits would therefore offer a unique insight into cellular behavior in addition to the ability to link miRNA expression signatures to an output expression programme of choice.
In this thesis, I have developed novel synthetic circuit architectures for the detection of miRNA activity. Firstly, protein and RNA modules were used in concert to develop a biosensor circuit consisting of two serially linked NOT gates that could activate output expression in response to a specific input miRNA. Secondly, methods were devised for the construction of a single molecule biosensor device, built entirely using RNA. At the heart of this device were novel miRNA responsive allosteric ribozymes which have been created through two independent in vitro selection methodologies devised for this study. Such engineered modules now constitute part of the synthetic biology toolbox, increasing the versatility with which miRNAs can serve as inputs to artificial genetic circuits.

Advisor: Fulga, T
Cardiac consequences of epileptic seizures in the tetanus neurotoxin model of temporal lobe epilepsy

Death is the most destructive outcome of epilepsy. Around 18% of deaths in those with epilepsy cannot be attributed to the disease itself; these deaths are collectively categorised as Sudden Unexplained Deaths in Epilepsy (SUDEP). Currently, the cause of SUDEP is hypothesised to involve seizure-induced respiratory or cardiac failure. Ictal (during seizure) central and obstructive apnoea, decreases in ictal oxygen saturation, changes in blood pressure, heart rate, autonomic control and cardiac conductivity in both patients and animal models have all been observed. In order to explore the effects of seizures on the autonomic control and cardiac conductivity, tetanus neurotoxin was injected into the ventral hippocampus of male Wistar rats; previously implanted with biopotential radiotelemeters.
Continuous recordings of electrocardiogram, electrocorticogram, and video were made for six to eight weeks post induction of epilepsy. The conductivity of the heart was analysed by calculating the PR, QT, corrected QT (QTc) intervals and QRS width. The central control of the heart was explored by analysing the interictal heart rate and calculating various time-based Heart rate variability measures. Statistical analysis was performed using One-Way ANOVA with Bonferroni post-hoc comparisons.
Increases in the PR interval, QRS width, RR interval, QT and QTc intervals were observed between preinduction and 150th seizure. The change in PR interval, RR interval, and QT interval persisted into the Post Seizure State. Significant differences were not observed for any of the Heart Rate Variability measures. The increase in QT and QTc intervals indicate a pathological change in the time taken for cardiac ventricular depolarisation and repolarisation to occur. The changes in PR and RR intervals and QRS width are not physiologically significant. Due to large variation between animals, meaningful conclusions about changes in central control of the heart could not be drawn. This study ultimately shows that the tetanus neurotoxin model of temporal lobe epilepsy induces changes in cardiac conductivity, and could aid in investigating the mechanisms through which SUDEP occurs.

Advisor: Jefferys, J
Serotonin transporter function and emotional behaviour

The serotonin transporter (5-HTT) is a key regulator of synaptic serotonin (5-HT), a monoamine that is significantly involved in the regulation of fear and anxiety processes. Importantly, low or null 5-HTT expression levels have also been associated with anxious and depressive phenotypes in several species. This remains controversial, however, with different research groups reporting conflicting results with most of the methodologies used so far to investigate whether such an association exists. An emerging 'neuroplasticity theory of 5-HT function' argues that low 5-HTT-expressing individuals, who are thought to have increased 5-HT availability, are not more vulnerable to anxious and depressive phenotypes per se but more sensitive to aversive and non-aversive life events. Subsequently, this increased sensitivity could lead to facilitated emotional learning in a 'for-better-or-for-worse' manner depending on their experiences in a given environment.
This thesis aimed to investigate this further by testing knockout mice for the 5-HTT (5-HTTKO mice) in approach–avoidance conflict tests, social assays and discrimination learning tasks with negative and positive emotional stimuli. Additionally, in a subset of mice, altered basolateral amygdala (BLA) function during an aversive learning task was also investigated via recordings of neuronal and haemodynamic responses to emotional cues.
The experiments reported here have shown that 5-HTTKO mice exhibit altered sensitivity towards emotionally-relevant negative and positive events and towards social influences. Moreover, 5-HTTKO mice exhibited superior aversive learning via augmented BLA function. However, the nature of the stimuli used in the experiments was crucial for the observation of such facilitated learning, given that learning about reward-predicting cues was not facilitated in 5-HTTKO mice.
Overall, the results obtained in this thesis provide evidence for the neuroplasticity theory of 5-HT function at the behavioural and neurophysiological level. However, further studies are warranted to clarify the boundaries of this theory.

Advisor: Bannerman, D
McHugh, S
The constitution of illicit orders

Within the context of a modern globalizing world, this thesis investigates governance in fragile areas where unconsolidated territorial-sovereign statehood offers niches for ‘illicit’ forms of social order to develop. Through recursive theoretical and empirical research rooted in the 'abductive' method of Pragmatism, the analysis has three overarching objectives: First, it offers a different conceptual approach by moving away from negative categorization of the phenomena, e.g. failed states, ungoverned spaces, limited statehood etc., towards a positive conceptualization, i.e. illicit orders. By casting off the legal-rational, sovereign-territorial lens, the pursuant conceptual reconfiguration of territory, authority, and institutions recognizes and more directly conveys the existence of local social organization apart from the modern state via the agency of social groups acting in violation of domestic and/or international legal norms, rules, and institutions. Second, it seeks to explain the constitution of ‘illicit orders’ by offering a sociologically-cognizant analytical framework capable of elucidating the ‘micro’ processes inherent to governance in territories where state institutions remain nominal and ineffective. Based on insights from theoretically-informed empirical fieldwork in Rio de Janeiro, Brazil’s favelas, I maintain that inter-subjective relations of authority can be produced when a given actor asserts predominance in three co-constitutive domains; namely, organized violence, socioeconomic security, and social legitimacy. Resultant authority then gives rise to the ‘structuration’ of norms, rules, and institutions, which also recursively reinforces the institutionalization of authority – a process inherent to the constitution of social order in these circumscribed territories. Third, it provides an understanding of how inherently local ‘illicit orders’ at once form part of a diffuse mosaic of social, political, and economic structures that collectively constitute ‘global society’, while simultaneously existing in dramatic juxtaposition to the Western-led ‘international order’ of states within it. Such an understanding purports to further challenge ‘neoutilitarian’ and 'macro-structural' theoretical approaches predominant in contemporary International Relations discourses.

Keywords: Sovereignty
Rio de Janeiro, Brazil
Institutions
Authority
Organized Crime
Social Order
Non-State Actors
Advisor: Hall, R
Gledhill, J
Towards efficient Bayesian inference: Cox processes and probabilistic integration

In this thesis we present a variety of new, continuous, Bayesian Gaussian-process-driven Cox process models. These are used to model sparse event data distributed on a continuous domain, where the events may have a tendency to cluster. These find direct use in application areas ranging from disease incidence modelling through to statistical cosmology, where the distribution of galaxies in the universe is weakly clustered due to the effects of dark matter. They may also be deployed in a more abstract sense, for example as a structured prior for network communications.
In previous work, the difficulty of performing inference in Gaussian-process-driven Cox processes has hindered their application to large, high-dimensional datasets. We develop novel and computationally efficient inference schemes for these models as well as our own extensions to them, demonstrating an improvement on the existing state of the art using real data. In particular, we present the first known variational inference scheme for such models, which scales linearly with the size of the dataset.
Spurred on to consider the problem of computationally efficient Bayesian inference in general, we tackle model evidence estimation. Arriving at an accurate measure of model evidence quickly allows for the objective measure of model fit, and ensures we select a set of assumptions which most closely embody the data-generating process.
We deviate from the traditional core Monte Carlo estimator, and instead present a computationally efficient general Bayesian quadrature scheme for model evidence computation. This is the first such scheme which can be shown to be demonstrably wall-clock competitive with state of the art Monte Carlo approaches.

Advisor: Roberts, S
Osborne, M