VictorJuiz/thesis huggingface dataset:
Collective decision-making in homing pigeon navigation
Keywords: decision-making
social navigation
animal behaviour
homing pigeon

This thesis focuses on conflict resolution and collective decision-making in co-navigating pigeons, Columba livia. These birds have a remarkable homing ability and frequently fly in flocks. Group navigation demands that group members reach consensus on which path to follow, but the mechanisms by which they do so remain largely unexplored. Pigeons are particularly suitable for studying these mechanisms, due to their sociality and the fact that their possession of information can easily be altered and quantified. I present the results of a series of experiments that manipulated the experience of homing pigeons in various ways so as to observe the effect of information they had previously gathered on their group behaviour. Key findings were:
Previous navigational experience contributes to the establishment of leader-follower relationships. The larger the difference in experience between two co-navigating pigeons, the higher the likelihood the more experienced bird will emerge as leader.
Shared homing experience through repeated joint flights can allow two pigeons to develop into a “behavioural unit”. They form spatial sub-groups when flying with less familiar birds, and perform a similar transition between compromise- and leadership-dominated flights as single birds, although they are more likely to accept compromise routes. Such previous association histories between birds can thus affect collective decision-making in larger flocks.
There is a trade-off between the amount of spatial information handled and the efficiency with which such information can be applied during homing. Leading/following behaviour is influenced by the recency of the route memories.
Leadership hierarchies in pigeon flocks appear resistant to changes in the navigational knowledge of a subset of their members, at least when these changes are relatively small in magnitude. The stability of the hierarchical structure might be beneficial during decision-making.
Mathematical modelling suggests that underlying hierarchical social structures can increase navigational accuracy. Hierarchically organised groups with the smallest number of strong connections achieve highest accuracy. Group leader-follower dynamics resemble the underlying social structure.
Mallarmé Apollinaire Maeterlinck Jarry: Space and Subject in French Poetry and Drama, c.1890-1920
Keywords: embodiment
theatre
reading
subjectivity
spatiality
spectatorship
visual poetry

This study explores the interrelationship between spatiality and subjecthood in the work of Stéphane Mallarmé, Guillaume Apollinaire, Maurice Maeterlinck, and Alfred Jarry. Concerned with various modes of poetry and drama, it also examines the cross-pollination that can occur between these modes, focusing on a relatively narrow corpus of core texts: Mallarmé’s Igitur (c. 1867-70) and Un Coup de dés (1897); Apollinaire’s “Zone” (1912) and various of his calligrammes; Maeterlinck’s early one-act plays—L’Intruse (1890), Les Aveugles (1890), and Intérieur (1894); and Jarry’s Ubu roi (1896) and César-Antechrist (1895). The poetic and dramatic practices of these four authors are assessed against the broader cultural and philosophical contexts of the fin de siècle. The fin de siècle witnessed a profound epistemological shift: the Newtonian-Cartesian paradigm, increasingly challenged throughout the nineteenth century, was largely dismantled, with ramifications beyond physics, philosophy and psychology. Chapter 1 introduces three foundational notions—Newtonian absolute space, the unitary Cartesian subject, and subject-object dualism—that were challenged and ultimately overthrown in turn-of-the-century science and art. Developments in theatre architecture and typographic design are examined against this philosophical backdrop with a view to establishing a diachronic and interdisciplinary framework of the authors in question. Chapter 2 focuses on the spatial dimension of Mallarmé’s Un Coup de dés and Apollinaire’s calligrammes—works which defamiliarise page-space by undermining various (naturalised) conventions of paginal configuration. In Chapter 3, the notion of liminality (the experience or condition of the betwixt and between) is implemented in an analysis of character and diegetic space as constructed in Jarry’s Ubu roi and Maeterlinck’s one-acts. Chapters 4 and Chapter 5 undertake a more abstract investigation of parallel inverse processes—the subjectivisation of space and the spatialisation of the subject —manifest not only in the works of Mallarmé, Maeterlinck, Apollinaire and Jarry, but in the period’s poetry and drama more generally.
Plutarch on Sparta: cultural identities and political models in the Plutarchan macrotext
Keywords: Sparta
Plutarch
Agesilaus
Lysander
Macrotext
Lycurgus
Parallel Lives
De Sera Numinis Vindicta
Seriality

Can we consider Plutarch's Parallel Lives a historical work? Can we read them as a unitary series? These are the initial questions that this thesis poses and that are investigated in the Introduction, five main Chapters, and the Conclusion. In the Introduction, a preliminary status quaestionis about ancient biography is presented before clarifying the methodology adopted for reading the Parallel Lives as a unitary historical work and the reasons for choosing the Lives of Lycurgus, Lysander, and Agesilaus as the case studies to examine in detail. Chapter 1 discusses the historiographical principles that emerge from the De sera numinis vindicta: for Plutarch history is primarily the history of individuals and cities, based on the interpretation of historical events. Chapter 2 tries to verify the hypothesis that the Parallel Lives correspond to the historical project delineated in the De sera numinis vindicta. This Chapter, moreover, reassesses the literary form of the Parallel Lives by employing the concepts of 'open macrotext' and 'cross-complementarity' between the Lives. Chapter 3 analyses the Life of Lycurgus, focusing on the formation of the cultural identity and the political model of Sparta. In the Life of Lycurgus, Plutarch indicates already the intrinsic weaknesses of Sparta and the probable causes of Spartan decline in the fourth century BC. Chapter 4 is devoted to the Life of Lysander, where Plutarch narrates how after the Peloponnesian War Sparta established its hegemony over the Greeks and, simultaneously, began its rapid moral and political decline into decadence. Plutarch also seems to suggest that in this historical period of extraordinary changes not only Sparta and Lysander but all the Greeks were guilty of distorting moral values. Chapter 5 concentrates on Agesilaus, who could have led Sparta and the Greeks to great success against the Persians, but, instead, had to save Sparta from complete destruction after the Battle of Leuctra. The Conclusion recapitulates the main points of the thesis and proposes possible arguments for future research on Plutarch’s Parallel Lives.
The evaluation of the IGF-1R as a proposed biomarker for DNA damaging cancer therapies
Keywords: IGF-1R biomarker DNA damage radiotherapy chemotherapy

Introduction The IGF-1 receptor (IGF-1R) is overexpressed in many cancers, with roles in cell proliferation and survival. IGF-1R inhibition enhances radio- and chemo-sensitivity, potentially influencing DNA damage response, whilst IGF1R SNP rs4966013 has been identified as the SNP in the p53 stress response network most significantly associated with differences in chemosensitivity.
Aims: 1. Test whether IGF-1R protein expression correlates with IGF-1R mRNA, hence indirectly with SNP rs4966013 in high and low IGF-1R mRNA-expressing cell lines and the NCI60 2. Using cytotoxic drugs selected from sensitivity correlations with SNP rs4966013, assess: • whether cell lines expressing high IGF-1R exhibit greater chemo- and radio- resistance • the extent to which IGF-1R inhibition enhances chemo- and radiosensitivity, correlated with IGF-1R expression.
Methods Protein expression was analysed using western blots. Sensitivity to irradiation, chemotherapy and IGF-1R inhibitors, and the effect of IGF-1R inhibition on radiosensitivity were assayed using cell viability assays. Published chemosensitivity and radiosensitivity data were compared with SNP genotype, IGF1R mRNA levels and published IGF-1R protein expression data.
Results IGF-1R protein correlated with mRNA expression in the 8 cell line panel (Spearman’s r=-0.87 p=0.005) and the wider NCI60 (r=-0.71 p<0.0001). Examination of IGF-1R protein and mRNA expression by SNP genotype suggested a dominant phenotype for the A allele.
Examination of public data demonstrated significant correlations between chemosensitivity and any measure of IGF-1R expression for 26 of 113 drugs. In cell viability assays, GI50s for Paclitaxel and Topotecan were higher in cell lines with the GG genotype. However, in the 8 cell lines tested, viability assays showed no correlation between high IGF-1R and paclitaxel resistance, and a non-significant association with topotecan resistance. Viability assays showed non-significantly increased radioresistance in cell lines with higher IGF-1R expression. Published NCI60 radiosensitivity data suggested no relationship with measures of IGF-1R expression.
Significant associations were identified between IGF-1R inhibitor sensitivity and pAKT but not measures of IGF-1R expression in cell viability assays. Public data showed cell lines of the GG genotype to be more sensitive to BMS754807 and possibly to OSI906 IGF-1R inhibitors.
By what right do we own things? A justification of property ownership from an Augustinian tradition
Keywords: St. Augustine
mission
justification of private property
property ownership
rights
calling
justice
John Wycliffe
individual subjective rights
medieval Franciscans
theory of property
St. Thomas Aquinas
St. Bonaventure
private property
natural rights to property
objective moral order
evangelical poverty
ius
dominium
property rights
property

The justification of property ownership based on individual subjective rights is tightly bound to humanist moral perspectives. God is left out as irrelevant to the just grounds of ownership, which is established primarily on the basis of human self-referential, moral capacity. This thesis aims at developing an alternative justification, both for property as an institution and as a private holding, with a view to bringing God back into the centre stage and thereby placing property ownership on the objective concept of right. A tradition hitherto generally left unnoticed, yet uncovered here as the source of inspiration, vests the whole project with a moral-teleological tone. The tradition, enunciated by St. Augustine and developed by St. Bonaventure and John Wyclif, invites us to see property from the perspective of a moral end: it ought to be used for the love of God and neighbours, and as such it can be owned only by the just. In spite of important insights into the moral nature of property, the Augustinian thesis not only fails to spell out what ‘use for love’ means but also suffers from elitism. Nor does it offer an adequate justification of private property. Such weaknesses call for revision. When we reinterpret the Augustinian thesis through the concept of the divine imperative of service coupled with a proper understanding of human work, property acquires a distinctive justification. Property, as an institution, is justified as a requisite for carrying out God’s redemptive work towards the world. From this general justification ensues the particular justification. We hold property as specifically ‘mine,’ since each person’s ordained mission to participate in God’s work requires a uniquely personal material means, although the recognition and fulfilment of individual mission still demands communal efforts. The duty to carry out the God-commanded mission at first allows us to possess private property only in a non-proprietorial and non-exclusive manner. Yet in the prevailing condition of economic scarcity and human greed, civil jurisdiction must provide a structure of rights to enforce property institution. As God’s invitation for the transformation of the world is a universal command, everybody should have a minimum of property, and yet in differentiation of the scope and kinds commensurate with the particularities of individual mission.
Writing and publishing music theory in early seventeenth-century Italy: Adriano Banchieri and his contemporaries
Keywords: Cataloguing
Patronage
Music theory
Seventeenth century
Publishing
Catalogue
Printing
Adriano Banchieri

Why write music theory and publish it? In the thesis I investigate the reasons for a seeming over-abundance of practically oriented music treatises in early seventeenth-century Italy. Throughout I challenge our conventional assessment of the study of music theory: I suggest that we can define a music-theoretical text in terms of its material form in addition to its content. Adriano Banchieri (1568-1634) was the most prolific theorist in early seventeenth-century Italy. His music-theory books exemplify contemporary printing patterns, an overt practical focus, and a synthesis of contemporary theoretical innovations.
In Chapter 1, after considering the meaning of 'music theory' and how it is typically classified, I discuss the process of and purposes for writing and publishing music theory. In Chapter 2 I explore Banchieri's practical and philosophical motives for writing music theory, and thus introduce the reader to his music-theoretical corpus. The focus of the thesis then broadens: in Chapter 3 I survey the typical authors, publishing houses, content, material form, function and readers of the various kinds of theoretical texts printed in Italy between 1600 and 1630. In Chapter 4 I examine the widespread practice of publishing second and revised editions of music-theory books in order to establish the extent to which a new edition corresponds to a seeming demand for a particular text. The case study of the paratext of Banchieri's Conclusiones de musica (Bologna, 1627) in Chapter 5 demonstrates the great extent to which the preliminary matter of an early Seicento music-theory book is embedded in its socio-cultural context and how a paratext projects ideas contained in the text proper. Lastly, in Chapter 6 I explore to whom and in which particular forums theoretical writings circulated. Here I focus principally on Banchieri's printed letters, which provide evidence of how an author circulated his music books.
Challenges in the relationship between the protection of internally displaced persons and international refugee law
Keywords: refugee law
refugees
internally displaced persons

Internally Displaced Persons ('IDPs') outnumber refugees by two to one and often have the same fears, needs and wants as refugees recognised as such under international law. However, refugee status entails international protection, while IDPs are left to the protection of their own state, which may, but by no means necessarily, be the very entity that has forced them to flee in the first place.
In recent years, there have been significant developments in the realm of IDP protection. This includes the conclusion of two regional treaties on the protection of IDPs, the development of relevant soft law instruments, and the reformed 'Cluster Approach' of humanitarian response. Although the increased focus on IDP protection is a welcome development, the UNHCR has expressed the fear that 'activities for the internally displaced may be (mis)interpreted as obviating the need for international protection and asylum.'
This thesis represents the first legal analysis of the relationship between the protection of IDPs and International Refugee Law. It will discuss five key challenges in this respect. First, the challenge of drawing the attention of the international community to the plight of IDPs; second, the challenge of developing an appropriate framework for the protection of IDPs; third, the challenge of ensuring that internal protection is not interpreted as a substitute for asylum; fourth; the challenge of determining the relationship between complementary protection and internal displacement; and fifth, the challenge of ensuring that IDP protection in an inter-agency context does not trigger the application of Article 1D of the Refugee Convention, rendering the Convention inapplicable to the recipients of that protection.
This thesis will conclude by setting out the future challenges in the relationship between IDP protection and International Refugee Law, by identifying questions left open for further research, and by illustrating the overall impact and importance of this thesis' findings.
Construction and performance of the ATLAS SCT barrels and cosmic tests
Keywords: ATLAS
silicon detectors
cosmic rays

ATLAS is a multi-purpose detector for the LHC and will detect proton-proton collisions with center of mass energy of 14 TeV. Part of the central inner detector, the Semi-Conductor Tracker (SCT) barrels, were assembled and tested at Oxford University and later integrated at CERN with the TRT (Transition Radiation Tracker) barrel. The barrel SCT is composed of 4 layers of silicon strip modules with two sensor layers with 80 micro m channel width. The design of the modules and the barrels has been optimized for low radiation length while maintaining mechanical stability, bringing services to the detector, and ensuring a cold and dry environment. The high granularity, high detector efficiency and low noise occupancy (< 5*10^-4) of the SCT will enable ATLAS to have an efficient pattern recognition capability. Due to the binary nature of the SCT read-out, a stable read-out system and the calibration system is of critical importance. SctRodDaq is the online software framework for the calibration and also the physics running of the SCT and has been developed and tested during construction and commissioning of the detector with cosmics. It reliably measures the SCT performance parameters for each of the 6.3*10^6 channels in the SCT, identifies defects and problematic modules and writes them to an offline database for access from Athena, the ATLAS offline software framework. This dataflow chain has been exercised during the cosmics run at CERN, where a 5*10^5 cosmics sample for the combined SCT and TRT detectors was collected with a scintillator based trigger. It is now being commissioned in the ATLAS pit.
Aquaporins in magnaporthe oryzae
Keywords: aquaporins
magnaporthe
plant disease

The Ascomycete fungus Magnaporthe oryzae is the causative agent of Rice Blast, and has become the predominant model organism for study of fungal phytopathogens and other appressorium-forming fungi. I identified and attempted to elucidate the function of the six aquaporin genes in the M. oryzae genome. These small membrane channels have been implicated in the transport of water, glycerol, and a variety of other small molecules. We speculated that these functions might be important in the formation of the appressorium – a specialised infection structure that relies on the generation of turgor. The role of these proteins in general fungal biology is poorly understood, and this project endeavoured to correct this gap.
A phylogenetic analysis of aquaporins in extant fungi revealed the significant expansion of this gene family in Pezizomycete and Basidiomycete fungi, with up to 17 genes in some species. I characterised the expression pattern of the six identified aquaporins in the M. oryzae genome during pathogenic development and found there to be substantial up-regulation co-incident with appressorial turgor generation. Single knock-outs of each aquaporin gene were fully pathogenic, with normal infection-related development and axenic growth. I speculated that the absence of a strong phenotype may have been caused by functional redundancy, and used qRT-PCR investigate the incidence of transcriptional up-regulation of remaining family members in the knock-out backgrounds. This uncovered a putative reciprocal relationship between two genes MoAQP1 and MoAQP2, suggesting that deletion of one results in up-regulation of the other. I subsequently tested the substrate permeability of this gene pair and found them to be permeable to hydrogen peroxide. However, deletion of one of these genes did not appear to affect the rate of flux of hydrogen peroxide across the plasma membrane. My attempt to characterise the cellular localisation of these proteins using GFP fusions was largely unsuccessful with the exception of a single gene, MoAGP2, which appears to be located on the endoplasmic reticulum.
High-fidelity microwave-driven quantum logic in intermediate-field 43Ca+
Keywords: Ion trapping
fidelity
microwaves
quantum computing

This thesis is concerned with the development of an intermediate magnetic field "clock-qubit" in 43Ca+ at 146G and techniques to manipulate this qubit using microwaves and lasers. While 43Ca+ has previously been used as a qubit, its relatively complicated level structure - with a nuclear spin of 7/2 and low-lying D-states -- makes cooling it in the intermediate field an intimidating prospect. As a result, previous experiments have used small magnetic fields of a few gauss where coherence times are limited and off-resonant excitation is a significant source of experimental error.
We demonstrate a simple scheme that allows 43Ca+ to be cooled in the intermediate field without any additional experimental complexity compared with low fields. Using the clock-qubit, we achieve a coherence time of T*2 = 50 (10)s - the longest demonstrated in any single qubit. We also demonstrate a combined state preparation and measurement error of 6.8(6)x 10-4 - the lowest achieved for a hyperfine trapped ion qubit [NVG+13] - and single-qubit logic gates with average errors of 1.0(3) x 10-6 - more than an order of magnitude better than the previous record [BWC+11]. These results represent the state-of-the-art in the field of single-qubit control. Moreover, we achieve them all in a single scalable room-temperature ion trap using experimentally robust techniques and without relying on the use of narrow-linewidth lasers, magnetic field screening or dynamical decoupling techniques.
We also present work on a recent scheme [OWC+11] to drive two-qubit gates using microwaves. We have constructed an ion trap with integrated microwave circuitry to perform these gates. Using this trap, we have driven motional sideband transitions, demonstrating the spin-motion coupling that underlies the two-qubit gate. We present an analysis of likely sources of experimental error during a future two-qubit gate and the design and preliminary characterisation of apparatus to minimise the main error contributions. Using this apparatus, we hope to perform a two-qubit gate in the near future.