VictorJuiz/thesis huggingface dataset:
The molecular ecology of the Gentoo Penguin (Pygoscelis papua)
Keywords: pathogens
microbiome
wildlife disease
conservation genetics
population genetics
polar front
Antarctica
latitudinal gradient
toll-like receptors; TLRs
seabird
penguin
parasites
viruses
immunogenetics

Gentoo Penguins (Pygoscelis papua) are marine mesopredators facing threats from anthropogenic environmental change, habitat loss, fisheries pressure, pollution, direct disturbance at colonies, and introduced pathogens. These philopatric seabirds breed across the largest geographic and latitudinal range of any penguin taxon. Given the large biophysical range of Gentoo Penguin habitats, evolutionary theory posits that localised biotic and abiotic interactions would place differential pressures on distinct populations of the species, affecting their genotypes and phenotypes. The host-pathogen interface is one such biotic interaction known to shape evolutionary trajectories. This thesis employs molecular techniques to examine the role of geographical variation on the genetic diversity of (I) the penguin as a host and (II) its enteric viruses, bacteria, and eukaryotic parasites. In this work, I uncovered strong host phylogeographic and population genetic structure according to neutral, mitochondrial, and immune gene (Toll-like receptor, TLR) markers. I also present experimentally-supported evidence of positive selection on TLR5, which points to localised pathogen-driven adaptation. Given the limited understanding of the pathogens circulating in modern Gentoo Penguin habitats, I also undertook parallel sequencing-based screening surveys to report novel viral, bacterial, protozoan and helminthic sequences associated with these seabirds and their sympatric species. Alongside undescribed diversity, I found evidence of greater-than-expected connectivity among the enteric microbes of spatially separate and genetically disparate Gentoo Penguins, as well as Pygoscelid-wide microbe commonalities. This research demonstrates the importance of studying species complexes and biotic interaction at the large scale, particularly in the face of emerging threats and the challenges inherent to wildlife disease monitoring in these remote habitats.
Statistics in adjudicative fact-finding
Keywords: statistical inference
fact-finding
statistical evidence
causation
evidence law

Statistics and statistical evidence have been and are an important feature of litigation. Although common, how to appropriately manage and utilise statistical evidence in fact-finding has bedevilled courts across the common law world and led to rampant scholarly and judicial debates. If evidence ought to lead to a greater likelihood that the truth will be uncovered, it should be used in fact-finding. So far, what has been missing from the debates about statistical evidence is how the legal process should come to a view that statistical evidence is ‘good’ for fact-finding. The goal of this thesis is to articulate a framework by which decision-makers can use evidence law to admit, assess the usefulness of, and weigh statistical evidence. This thesis also seeks to address how the objections to statistical evidence may be categorised within the evidentiary processes of relevance, admissibility, weight and proof. First, the thesis describes objections to ‘General Factual Causation’, being the ability of the statistical evidence to be adduced to prove the existence of associations between variables in a state of nature. Second, it addresses the problem of how to infer the existence of a phenomenon in an individual from statistical evidence purporting to show an association between variables in a reference class. This question more than any other has dominated the discussion of statistical evidence, but it often misses how evidence law would and could respond to this issue. Third, this thesis canvasses difficulties arising from the proof of facts by statistical evidence and ‘objective probabilities’ derived from reference classes, including the problem of ‘naked statistical evidence’ and how or whether to use mathematical techniques to calculate the probabilities of individual events.
Parthian Nineveh 
Keywords: Parthian numismatics
ancient Iraq
Nineveh
ancient Near East
ceramic petrography
Roman Empire
Parthian
Mesopotamia

The archaeology and history of the Parthian period (c. 150 B.C. – A.D. 250) in Iraq has received little serious attention from scholars in recent years. This thesis used objects in British museum collections from Nineveh as a focus for the study of this period in Northern Mesopotamia, combining traditional archaeology and numismatic analysis with scientific studies.

Chapter I presents a critical analysis of the excavated evidence for the occupation of Nineveh in the Parthian period with special attention to distinctive artefacts such as figurines, lamps, and molded bowls. Chapter II uses petrographic and chemical analysis of selected ceramics to elucidate the materials and methods of manufacture, with particular attention to identifying local and foreign wares. Special attention is paid to glazed wares. Chapter III is a numismatic study based on the major hoard of Parthian bronze coins of Nineveh. A complete re-classification of the hoard not only identifies a number of new coin types, but also provides a revised list of rulers who issued coins at Nineveh. Chapter IV investigates all aspects of Roman involvement with Nineveh and its place in the stormy relationship between Rome and Parthia. Evidence is advanced for there having been contingents of Roman troops stationed at Nineveh and the site placed within its context in the state of Adiabene.
Transition metal fluorides as lithium ion cathodes
Keywords: transition metal fluoride
nanoparticle
transmission electron microscopy
reaction mechanism
lithium ion battery
conversion cathode
ionic liquid electrolyte

More energy dense lithium ion batteries are essential for the production of long-range electric vehicles and all-electric aircraft. These next generation batteries will require high capacity cath- ode materials that move beyond the lithium intercalation chemistry of current electrodes. On paper, transition metal fluorides are among the most promising cathode materials, combining high electrode potentials (2.6 V to 3.5 V vs. Li+/Li) with three to six times the theoretical capacity of conventional cathode materials. However, their commercial application has been hindered by their inability to cycle in a truly energy dense format (i.e. at high active material concentra- tion) and ultimately the inadequate understanding of their electrochemical capabilities and limitations. Both of these issues have been largely resolved as a result of this DPhil project. First I design a materials system that is practically ideal for reversible high-capacity cycling as well as detailed mechanistic study. This is achieved through the development of a new colloidal synthesis method for single-crystalline, monodisperse transition metal fluoride (FeF2, CoF2) nanorods. Size and shape control are demonstrated, and a chemical reaction pathway and nu- cleation and growth mechanism are proposed. Next I present an ionic liquid electrolyte (1 molal lithium bis(fluorosulfonyl)imide in N-methyl-N-propylpyrrolidinium bis(fluorosulfonyl)imide) that forms a stable solid electrolyte interphase, prevents the fusing of particles, and consequently precludes the major failure mechanisms associated with transition metal fluoride cathodes. The use of this electrolyte with the iron(II) fluoride (FeF2) nanorod system results in near theoretical capacity (570 mA h g−1) on discharge and charge, with extraordinarily stable cycling (>90% ca- pacity retention after 100 cycles). This stability is maintained for over 200 cycles at relatively high cycling rates (C/2) and temperatures (50 ◦C). By combining the unique vantage point afforded by this novel materials system with the morphology preserving qualities of our new electrolyte, I am further able to characterize the discharge/charge mechanism with an unprecedented level of detail. High-resolution analytical transmission electron microscopy reveals intricate morphological features, lattice orientation relationships, and oxidation state changes that that provide a new and comprehensive understanding of the discharge/charge (conversion) reaction mechanism. This new mechanistic understanding defines the structural and chemical origins of reversible cycling and cell failure in transition metal fluorides and unearths new concepts such as an inherently high discharge rate capability in FeF2.
Towards the total synthesis of pectenotoxin-4
Keywords: osmium
oxidative cyclisation
natural product synthesis
total synthesis

Chapter 1: Introduction This chapter provides the background of the pectenotoxins (PTX), which includes details of their isolation, structure, and biological activity. Subsequently, the total syntheses of PTX-4 by Evans and of PTX-2 by Fujiwara are discussed. Finally, past efforts of the Donohoe group towards the synthesis of PTX-4 are summarised.

Chapter 2: Synthesis of the ABC fragment This chapter details the retrosynthesis and forward synthesis of the C1–C16 ABC fragment of PTX-4. Moreover, the chapter features extensive discussions on the optimisation efforts for key steps, including the osmium-catalysed double oxidative cyclisation step and the 1,2-hydride shift spiroketalisation cascade. Other major challenges, such as the unexpectedly difficult removal of an Evans oxazolidinone auxiliary, are also discussed.

Chapter 3: Synthesis of the E fragment This chapter describes the retrosynthesis and forward synthesis of the C19–C30 E fragment of PTX-4. Experiments to troubleshoot and develop workarounds for an irreproducible regioselective hydroiodination step to give a vinyl iodide product early in the synthesis are documented. Finally, the synthesis of the C31–C40 F fragment of PTX-4 is briefly covered.

Chapter 4: Uniting the ABC and E fragments This chapter discusses the elaboration of the ABC fragment into its vinyl boronic ester analogue for the planned rhodium-catalysed Hayashi–Miyaura 1,4-addition with the E fragment to unite the two major PTX-4 fragments. Optimisation studies for key reactions arealso discussed and include an allylation reaction, the 1,4-addition, and a dihydroxylation–ketalisation cascade to form the D ring.

Chapter 5: Experimental This chapter lists all experimental procedures for the reactions described in this thesis, as well as the characterisation data for the compounds synthesised.
Job search and migration
Keywords: job search
regional economic differences
internal migration

Standard models of within-country mobility assume that all migration is speculative: workers move to search for jobs in other labour markets. I establish a new stylised fact showing that the majority of cross-regional migration in the US is in fact with a job in hand, as a result of a job offer from another region. The fact that a significant fraction of migration is a result of cross-regional hiring, and that this hiring is subject to search and matching frictions, has important implications for the level of regional mobility and hence regional differences within a country. In the first two chapters, I show empirically that the availability of cross-regional employment opportunities does matter for workers’ migration behaviour. Using US panel data, I demonstrate that the observed gap in migration propensity between the more and less educated workers can be partly explained by differences in labour market frictions. The less educated workers find job search in more distant regions much more difficult, which limits their options to move for a specific job and reduces their overall mobility. This result opens a new policy channel in addressing regional differences and those left behind: the importance of the ability to find a job before moving suggests a large social return to improving regional search and matching for less educated groups. In the third chapter, I explore the theoretical implications of an imperfect search and matching process on the existence and persistence of regional disparities. First, I show that if the efficiency of the search and matching process increases in the size of the labour market, migration will serve to exacerbate, not equilibrate, the differences in regional economies. A bigger labour market will experience higher wages and lower unemployment rates, attracting migrants from other regions and thus accelerating the process of regional divergence. At the same time, larger labour market frictions in the smaller regions reduce firms’ incentives to hire there, curtailing cross-regional hiring and hence the opportunity to move for a specific job. The interaction of these two forces give rise to multiple equilibria and explain how, in the presence of labour market frictions, regional disparities can be large and persistent at the same time.
Computational framework for multiscale investigation of pro-arrhythmic mechanisms in the human cardiac Purkinje system
Keywords: computer modeling
arrhythmias
cardiac Purkinje
in silico trials
human cardiac electrophysiology

Ventricular arrhythmias are a major cause of sudden cardiac death, which accounts for about 50% of cardiovascular mortality worldwide. Understanding the mechanisms underlying arrhythmias generations is crucial to improve its diagnosis and treatment. Cardiac Purkinje cells constitute the peripheral conduction system of the electrical stimulation in ventricles and are responsible for the correct contraction pattern of the heart. Experimental studies on animal models pointed out that drug actions, mutations or cardiac diseases might alter the electrical activity of Purkinje cells and lead to arrhythmia onsets. However, the pro-arrhythmic mechanisms in Purkinje cells are not entirely understood, and results obtained in animal studies do not always translate to humans, due to inter-species differences.

The aim of this thesis is to develop an experimentally-informed computational framework to mechanistically investigate the role of human Purkinje cells in arrhythmia onset, and predict Purkinje cells electrophysiological response to pharmacological therapy. Multiscale simulations are used to identify the mechanisms underlying electrical abnormalities in human Purkinje cell and tissue models, as well as to evaluate drug safety and efficacy on cardiac Purkinje electrophysiology in humans, also accounting for biological variability.
Right atrial deformation through speckle tracking echocardiography and feature tracking CMR
Keywords: speckle tracking echocardiography
feature tracking Cardiac Magnetic resonance

The right atrium (RA) plays a vital role in the electromechanical regulation of the heart. Various invasive and non-invasive techniques have been used to elucidate right atrial structure and function. One such novel technique is speckle-tracking echocardiography (STE). Speckle tracking-derived deformation is a relatively new parameter, which is less dependent on loading conditions. STE tracks acoustic scatters (speckles) of myocardium, frame by frame, to calculate the strain or deformation indices of the myocardium. The right atrium is a relatively neglected chamber as it is mostly studied for assessment of atrial mass lesions, congenital and acquired valve lesions and for electro physiological studies. However, its role in the systolic and diastolic function of the right ventricle of the heart has been less explored. I have adapted the STE technique, designed for left ventricular analysis, for use in the right atrial analysis. I undertook a reproducibility study for right atrial deformation parameters and defined normal reference ranges for longitudinal deformation parameters. I have found the analysis approach used generates similar values to those reported in the limited number of previous studies on right atrial STE. I then compared STE derived strain with cardiovascular magnetic resonance feature tracking derived measures of right atrial strain and found moderate agreement between the two techniques. Finally, I investigated whether there are differences in right atrial longitudinal deformation parameters in different patient disease groups. I studied those with Heart Failure with Normal Ejection Fraction (HFNEF) and found a decrease in right atrial function. Whereas, in another cohort of patients with Rheumatoid Arthritis (RhA) there was no statistical difference compared to healthy controls. This thesis therefore demonstrates the feasibility of using STE to measure right atrial strain and provides evidence that right atrial strain does vary in certain disease conditions.
The rationality and normativity of intention
Keywords: agency
intention
rationality
normativity

This thesis develops a Neo-Humean, functionalist account of practical rationality and normativity. On this view, principles of practical rationality are grounded in the proper function of our agency, while the normative force of a normative reason in calling for a certain response on our part consists in its capacity to engage the function of that response. This functionalist picture, I contend, undermines three long-held and widely-accepted views about practical rationality and normativity. Contra orthodox Humeanism about practical rationality, the functionalist account shows that the rational principles governing our intention are not limited to instrumental and formal coherence principles. Contra rationalists about the nature of rationality, the functionalist account supports an environmentally-embedded conception of practical rationality and demonstrates that the requirements of practical rationality are not necessary, a priori requirements. Finally, contra externalists about normative reasons for action, the functionalist account reveals that the normative force involved in normative reasons for action is best captured not by externalist considerations, but instead by our intentions or volitional states.
Effects of conflict on resistance and cooperation in hierarchical groups
Keywords: hierarchy
egalitarianism
resistance
evolution
game theory
cooperation
public goods games
contest games

Many social organisms engage in collective actions in which there is a mismatch between individual and common interest. Such problems may include competition with other groups or collaborative efforts to secure resources from the environment. In this thesis I test novel theoretical predictions which see hierarchy as one potential solution to the collective action problem at hand. More specifically, models have shown that high-rank individuals in hierarchical groups are expected to contribute more toward the group’s success than low-rank individuals during inter-group conflict. This pattern of contribution by the high-rank group members is expected to increase the group effort of hierarchical groups in comparison to egalitarian groups. However, the increased individual effort of high-rank individuals is expected to reduce their net benefits in comparison to individuals with lower rank.
To study these effects, I devised eight behavioural experiments with more than 2300 participants from three national cultures which operationalized hierarchy in both political and economic terms. In these experiments, I utilized a behavioural game theory paradigm called the contest game, which simulates an inter-group collective action problem in experimental settings. Results from the thesis suggest that in economic hierarchy high-rank players may contribute more than low-rank players, while in political hierarchy this may not be the case. Groups with economic hierarchy exerted less effort than groups without such hierarchy (e.g. egalitarian), mainly due to a reduced contribution of the low-rank players. However, groups with political hierarchy usually exerted more effort than politically egalitarian groups. These findings suggest that the type of hierarchy is important, as it leads to different results in terms of contribution both at the individual and at the group level.
Further to the these questions, I studied the effect of the collective action problem type, gender, and cognitive processing on the contribution preferences of players. Results suggest that usually inter-group conflict is not important for the contribution preferences of players. Furthermore, the gender of participants and the decision making speed were not important factors for their relative contribution as well, neither under political, nor under economic hierarchy.
Athenian power in the fifth century B.C.
Keywords: Greek history
Athens
Epigraphy
Empire

The aim of this thesis is to provide a distinctive study of fifth-century BC Athenian power. I argue that Athenian power was composed of multi-directional and heterogenous interactions between the Athenians and allied communities, including assertions of allied agency and negotiation.
Studies of other ancient Mediterranean empires have benefitted from the fresh perspectives provided by awareness of scholarship on imperial and hegemonic powers of other periods and geographies. Approaches to the fifth century, however, are to a significant extent dominated by diachronic, narrative historiography, and hierarchical and centralised examinations of Athenian power, both rooted in close study of Thucydides. Understanding of the ancient economy has not been sufficiently integrated into analysis of political development. Some recent scholarly contributions have begun to break with these approaches, but there is scope for a new examination of Athenian power.
This thesis differs from previous contributions in three key ways: through engagement with a comparative framework; through new analysis of Athenian sources, inscribed documents and Old Comedy in particular; and through comparison of Athenian power in the context of regional dynamics. After demonstrating in the first half of the thesis that Athenian power, particularly its fiscal aspect, was flexible and negotiated - but that this negotiation was increasingly controlled in the final decades of the fifth century - I consider in the second half how local conditions determined the operation of Athenian power in three contested and peripheral Aegean regions, resulting in similar but opportunistically differentiated strategies.
Exhibiting archaeology: constructing knowledge of Egypt at temporary exhibitions in London, 1884-1939
Keywords: Egypt Exploration Fund
Egypt
Archaeological representation
Egypt Exploration Society
History of Archaeology
Temporary exhibition
Ancient Egypt
Annual exhibition
Museum
Reception
Exhibition
British School of Archaeology in Egypt
History of Egyptology

Between 1884 and 1939 the Egypt Exploration Fund (later Society) and the British School of Archaeology in Egypt held a series of annual exhibitions in London to showcase the finds of each archaeological season. Displaying artefacts excavated just weeks before, alongside new archaeological interpretations and interpretive devices, and in varying locations across the capital, these temporary exhibitions functioned as network hubs for the circulation of disciplinary objects and knowledge. Established at a time when archaeology was emerging as a new, professional scientific discipline and the British occupation of Egypt was altering political dynamics, the practice reflected a period of considerable change in the display and reception of ancient Egyptian collections. The aim of this thesis is to centre the exhibitions in the theoretical framework of archaeological representation, addressing how the practice contributed to the construction and communication of knowledge about ancient and contemporary Egypt in the imperial metropole. The following discussion will argue that the annual exhibitions utilised their temporary, transient, and transitional nature to experiment with new ways of displaying Egypt and of shaping the visual culture and material products of Egyptian archaeology.