VictorJuiz/thesis huggingface dataset:
Knowledge games: the achievement of ignorance in managing Olympic and Commonwealth mega-events
Keywords: project management
Commonwealth Games
megaprojects
ignorance
Olympic Games
knowledge

The concept of ignorance has been unfairly stigmatised in research and practice, and consequently has not received the attention it deserves as a powerful motivator of behaviour in organisations. To understand the role of ignorance, it must be examined as a productive force rather than a shameful weakness, an achievement instead of a failure.
This thesis develops an understanding of how ignorance is achieved and why it is perpetuated in the context of managing the Olympic and Commonwealth Games, a series of worldwide mega-events that are popular with proponents of urban development, but which have experienced persistent organisational problems in the form of cost overruns, schedule delays, and scope creep.
To do so, this research draws on literature about ignorance from the disciplines of philosophy, anthropology, sociology, and organisational theory, to motivate an embedded case study of Games Organising Committees (OCs) in six host cities around the world. These OCs, which were actively planning the Games during the research, are studied through qualitative research, to develop a dynamic understanding of the role of ignorance in planning the Games. The findings and analysis are presented from two perspectives: the structure of the ‘Games system’ and of the OC; and, the substance of Games planning in the areas of cost, time and scope.
While other studies have focused on ignorance as necessary, strategic, and inadvertent, the original contribution to knowledge of this thesis is the proposal of a theoretical framework that focuses on the functional and detrimental outcomes of ignorance. This framework is also shown to be useful in understanding why ignorance persists between organisations, and suggests three basic principles for further research: ignorance as a productive force in management; structure as a scaffold for ignorance; and budget, time and scope as catalysts for ignorance.
High jet multiplicity physics at the Large Hadron Collider
Keywords: jets
QCD
particle physics
CERN
Physics
ATLAS
LHC
supersymmetry

The Large Hadron Collider at CERN completed its first data-taking phase in 2013, after three years of remarkable performance. The high-energy proton-proton collisions recorded by the ATLAS experiment provide a gateway to the world of subatomic particles. This thesis presents two analyses of the full 8 TeV dataset taken by ATLAS, inspired by two of the major physics goals of the experiment. The first analysis is a search for new phenomena that could explain the nature of Dark Matter and solve the hierarchy problem. In particular, the search is optimised to look for heavy supersymmetric particles decaying to large numbers (7 to ≥10) of jets. The events are further classified according to the number of jets identified as originating from a b quark. No evidence is found for physics beyond the Standard Model, so the results are interpreted in terms of exclusion limits on various simplified supersymmetry-inspired models where gluinos are pair produced, as well as a mSUGRA/CMSSM model. The main background to the search is due to multi-jet production via the strong force. This motivates the second analysis presented in this thesis, which is a measurement of the cross section of four-jet events. The measurement is performed differentially in a series of variables which describe the kinematics and spatial configuration of the events. The results are compared to existing theoretical predictions.
Investigating the role of APOE-ε4, a risk gene for Alzheimer's disease, on functional brain networks using magnetoencephalography
Keywords: APOE
functional connectivity
resting-state networks
magnetoencephalography
independent component analysis

Alzheimer's disease (AD) is developing into the single greatest healthcare challenge in the coming decades. The development of early and effective treatments that can prevent the pathological damage responsible for AD-related dementia is of utmost priority for healthcare authorities. The role of the APOE-ε4 genotype, which has been shown to increase an individual's risk of developing AD, is of central interest to this goal. Understanding the mechanism by which possession of this gene modulates brain function, leading to a predisposition towards AD is an active area of research. Functional connectivity (FC) is an excellent candidate for linking APOE-related differences in brain function to sites of AD pathology. Magnetoencephalography (MEG) is a neuroimaging tool that can provide a unique insight into the electrophysiology underpinning resting-state networks (RSNs) - whose dysfunction is postulated to lead to a predisposition to AD.
This thesis presents a range of methods for measuring functional connectivity in MEG data. We first develop a set of novel adaptations for preprocessing MEG data and performing source reconstruction using a beamformer (chapter 3). We then develop a range of analyses for measuring FC through correlations in the slow envelope oscillations of band-limited source-space MEG data (chapter 4). We investigate the optimum time scales for detecting FC. We then develop methods for extracting single networks (using seed-based correlation) and multiple networks (using ICA). We proceed to develop a group-statistical framework for detecting spatial differences in RSNs and present a preliminary finding for APOE-genotype-dependent differences in RSNs (chapter 5). We also develop a statistical framework for quantifying task-locked temporal differences in functional networks during task-positive experiments (chapter 6). Finally, we demonstrate a data-driven parcellation and network analysis pipeline that includes a novel correction for signal leakage between parcels. We use this framework to show evidence of stationary cross-frequency FC (chapter 7).
Conservation and land use planning applications in Gabon, Central Africa
Keywords: land use
conservation planning
Spatial prioritization

Spatial prioritization and systematic conservation planning methods are designed to improve land use decisions and conservation outcomes, yet remain underutilized in many biologically-rich places that need them most. This thesis applies the theory and methods developed in the discipline of spatial prioritization to conservation and land use decisions in the Central African country of Gabon. Creating a spatial information base of priority species, habitats and land uses in a region that is notoriously data-poor, I reveal that many features important for both conservation and natural resource production are highly localized; their coincidence has important implications for management. Setting conservation targets for species and habitats, I find that representation in existing protected areas is relatively low, and identify a number of near-optimal solutions that meet all targets, with minimal impact on land used for local livelihoods. I distill these solutions down to a handful of critical biodiversity sites that are top priority to protect, and make management actions explicit for the species and habitats they contain. To make the work more widely applicable, I also develop a novel method to identify where field surveys are most likely to improve decisions about protected area expansion, providing decision-makers with more options of places that could be protected to achieve conservation goals. This study contributes to the research, development and practice of conservation prioritization and spatial planning, particularly in data-poor contexts like Gabon, which still have a wealth of biodiversity, and need to carefully plan for its conservation alongside development.
Subplate populations in  normal and pathological cortical development
Keywords: cortical layers
thalamocortical connectivity
gene expression
neocortex
cortex
thalamus
laser capture microdissection
microarray
cortical development
brain development
subplate

The subplate layer of the cerebral cortex is comprised of a heterogeneous population of cells and contains some of the earliest-generated neurons. Subplate plays a fundamental role in cortical development. In the embryonic brain, subplate cells contribute to the guidance and areal targeting of corticofugal and thalamic axons. At later stages, these cells are involved in the maturation and plasticity of the cortical circuitry and the establishment of functional modules. In my thesis, I aimed to further characterize the embryonic murine subplate by establishing a gene expression profile of this population at embryonic day 15.5 (E15.5) using laser capture microdissection combined with microarrays. I found over 250 transcripts with presumed higher expression in the subplate at E15.5. Using quantitative RT-PCR, in situ hybridization and immunohistochemistry, I have confirmed specific expression in the E15.5 subplate for 13 selected genes which have not been previously associated with this compartment. In the reeler mutant, the expression pattern of a majority of these genes was shifted in accordance with the altered position of subplate cells. These genes belong to several functional groups and likely contribute to the maturation and electrophysiological properties of subplate cells and to axonal growth and guidance. The roles of two selected genes - cadherin 10 (Cdh10) and Unc5 homologue c (Unc5c) - were explored in more detail. Preliminary results suggest an involvement of Cdh10 in subplate layer organization while Unc5c could mediate the waiting period of subplate corticothalamic axons in the internal capsule. Finally, I compared the expression of a selection of subplate-specific genes (subplate markers) between mouse and rat and found some surprising species differences. Confirmed subplate markers were used to monitor subplate injury in a rat model of preterm hypoxiaischemia and it appeared that deep cortical layers including subplate showed an increased vulnerability over upper layers. Further characterization of subplate-specific genes will allow us to broaden our understanding of molecular mechanisms underlying subplate properties and functions in normal and pathological development.
Theoretical limits to tidal stream energy extraction
Keywords: Tidal Stream Turbines
Tidal Energy
Linear Momentum Acutator Disc Theory

Tidal stream energy has gained attention as a source of predictable and renewable energy. Devices resembling underwater wind turbines, placed in fast tidal streams, have been proposed to extract this energy. Arrays of many such devices will need to be deployed to deliver a significant amount of energy to the electricity grid. One consequence of energy extraction is that the array provides a resistance to the tidal stream, which may change the local and far field hydrodynamics, which in turn affects the power available to the array. Array-scale hydrodynamic changes affect the flow presented to the devices, which in turn affects the total resistance the array provides to the flow. This thesis is concerned with the interactions between device, array, and the tidal stream resource, to better understand the power potential of turbine arrays.
Linear momentum actuator disc theory is employed to describe the operation of an idealised turbine array partially spanning a wide channel. The model is comprised of two quasi-independent sub-models, an array-scale model, describing flow phenomena around the array, which provides the upstream boundary condition to the device-scale model, describing the flow around a device. The thrust applied by the array is the sum of the thrust applied by the devices, completing the sub-model coupling.
The numerical simulation of arrays in depth-averaged simulations is then investigated using the two-scale concept developed in the analytic partial-array model. It is shown that the device-scale flow must be modelled with a sub-grid scale model in order to correctly describe the unresolved device-scale flow and hence estimate the power available to an idealised array. Turbulence modelling in depth-averaged simulations of turbine arrays is also discussed.
Temporal variations in tidal amplitude and strength mean that generator capacity will need to be economically matched to the available resource. As device performance may consequently depart from the relationship derived in idealised models when power capping is employed, blade element momentum theory is modified to parameterise tidal turbine performance during power capping. The array-scale effect of power capping is studied in depth-averaged simulations, in which it is shown that a significant reduction in device thrust may occur during power capping, reducing the impact of energy extraction from the tidal stream.
Sonic properties of silks
Keywords: silk
vibration
biomechanics
web

Silks are biomaterials made by spiders and silkworms, evolved for natural functions ranging from protection to predation. The research presented in this Thesis combines principles and methods from engineering, physics and biology to study the material properties of single silk fibres from a biological perspective. In particular, the factors that contribute to the variation in properties of single silk fibres are investigated. The first part of the Thesis focuses on silks made by silkworms. Whether naturally spun or forced reeled, the mechanical properties of these silks are sensitive to a range of environmental and processing conditions, such as humidity, stretching and reeling speed. The research presented in this section contributes to the understanding of how these applied conditions affect silk mechanical properties, which can be understood in terms of silk’s protein structure and biological context. The second section compares both silkworm and spider silk single fibres to other materials in terms of their sonic properties – how the materials propagate sound waves, whether following impact, or propagating vibrations. The results are discussed in the context of the silk’s natural function for impact resistance (silkworm cocoon or spider web) and vibrational signalling (spider silks). The Thesis ends with a discussion of how the presented techniques can be applied to help further our understanding of orb web function through studying spider silks. Overall, this interdisciplinary Thesis contributes to our understanding of the structure-property-function links of these fascinating biomaterials.
Town, crown, and urban system: the position of towns in the English polity, 1413-71
Keywords: political culture
urban history
Wars of the Roses
networks

In this thesis, a collective urban sector-consisting, in various different guises, of civic governments, urban merchants, and townspeople-is presented as a vital and distinctive component of later medieval English political society. The dynamics of this urban political sector are reconstructed through the use of a modified version of the 'urban systems' approach found in historical geography and economic history, positing that towns are defined by their evolving relationship with one another. Drawing from the municipal records of twenty-two towns, this thesis charts the composition of the later medieval English 'urban system' and the manner in which urban groups belonging to this 'system' participated in a broader national political sphere over four chronological periods-1413-35, 1435-50, 1450-61, and 1461-71. In 1413-35, the highly authoritative and institutionalised governments of Henry V and the child Henry VI fostered vertical relationships between the Crown and a variety of individual civic governments, leading both national and urban political actors to operate within a shared political culture, but not necessarily encouraging inter-urban political communication. This would change in the periods that followed, as the absence of strong royal authority after 1435 renewed the strength of lateral mercantile networks and facilitated the re-emergence of a semi-autonomous inter-urban political community, which saw little reason to participate in the civil wars of the early 1450s that now seemed divorced from its own interests. In the 1460s, however, the financially extractive policies of Edward IV once again gave civic governments and ordinary townspeople a greater stake in royal government, which was reflected in the high level of urban participation in the dynastic conflicts of 1469-71. The developments occurring in these four phases illustrate both the interdependence of urban and national politics in the later medieval period, and the mutability of their relationship with one another.
Cultivating the heart: suffering and language in Ancrene Wisse, the Wooing Group, and the Katherine Group
Keywords: literature
medieval spirituality

This thesis examines the language of pain/suffering in Ancrene Wisse, the Wooing Group, and the Katherine Group, arguing that the anchoress nourishes an acute but discriminating sensitivity to pain. It seeks to demonstrate that the anchoress uses these early Middle English texts to cultivate sophisticated affective stirrings. Chapter 1 foregrounds the multidimensional penitence in Ancrene Wisse, situated in the context of Latin and vernacular penitential and homiletic material. The anchoress’ penitential processes demand not only physical pain, but also affective pain and intensive cognitive processes of self-examination. Chapter 2 argues that the Wooing Group meditations are tools of pain-cultivation, which the anchoress uses to nurture her affective pain as she develops her intimacy with the Spousal Lamb and his Mother. Chapter 3 assesses imagery of physical and affective woundedness. This chapter examines the anchoress’ use of imagery of Christ’s wounds, sin-wounds, and penitential wounding in Ancrene Wisse and the Wooing Group, and then studies her use of the saints’ wounding in the Katherine Group. Chapter 4 contends that spectatorship and performance of suffering are not separable acts for the anchoress. The chapter assesses: the anchoress’ spectatorship in the Katherine Group hagiographies, a spectatorship based on defamiliarization; the anchoress’ participation with the pain of Christ in Ancrene Wisse and the Wooing Group, including an examination of her potential use of church wall paintings; and the female reader of Hali Meiðhad, who immerses herself in the suffering of a married and child-bearing woman. Chapter 5 examines the crucial affective phenomenon of compassion, arguing that compassion in Ancrene Wisse and the Wooing Group is not a distanced ‘pity’, but a complex ‘co-feeling’ (using Milan Kundera’s (1984) term). The thesis concludes by underscoring the fact that the anchoress’ painful existence is not pathological; it is an existence characterized by agency and emancipation.
Quantatitive analysis of type Ia supernova spectra and implications for cosmology
Keywords: cosmology
supernovae

This thesis presents the spectroscopic observations of the Supernova Legacy Survey (SNLS) from the Gemini-North telescope from May 2006 – May 2008. During this time 68 of 95 targets were confirmed as Type Ia supernovae (SNe Ia) or classified as probable SNe Ia events. We use these objects and reanalyse other high-z spectra obtained as part of SNLS to search for signs of evolution in SNe Ia properties. To do this we use a multicolour method to remove host galaxy contamination from the high-z spectra and measure the equivalent widths of three spectral features in the rest-frame blue part of the spectrum: CaII H&K, SiII and Mg II. These are compared to a sample of low-z objects drawn from the literature. No evidence for evolution is found, but a change in the properties of the SiII feature is observed. This can be explained by changing supernova demographics, an outcome of the two-component progenitor model for SNe Ia.
The utility of SNe Ia supernovae for cosmology is confirmed and the possible use of spectral features as alternative calibrators is investigated. The equivalenth width of the SiII feature is anticorrelated with light curve stretch and this is used to define a "spectral stretch" from the low-z sample, which is used to reduce the scatter in the low-z sample. This holds promise for improving the calibration of high-z SNe Ia, particularly if new facilities are used to provide higher-quality spectra.
Neural mechanisms of suboptimal decisions
Keywords: Decision Making
Reinforcement Learning

Making good decisions and adapting flexibly to environmental change are critical to the survival of animals. In this thesis, I investigated neural mechanisms underlying suboptimal decision making in humans and underlying behavioural adaptation in monkeys with the use of functional magnetic resonance imaging (fMRI) in both species.
In recent decades, in the neuroscience of decision making, there has been a prominent focus on binary decisions. Whether the presence of an additional third option could have an impact on behaviour and neural signals has been largely overlooked. I designed an experiment in which decisions were made between two options in the presence of a third option. A biophysical model simulation made surprising predictions that more suboptimal decisions were made in the presence of a very poor third alternative. Subsequent human behavioural testing showed consistent results with these predictions. In the ventromedial prefrontal cortex (vmPFC), I found that a value comparison signal that is critical for decision making became weaker in the presence of a poor value third option. The effect contrasts with another prominent potential mechanism during multi-alternative decision making – divisive normalization – the signatures of which were observed in the posterior parietal cortex.
It has long been thought that the orbitofrontal cortex (OFC) and amygdala mediate reward-guided behavioural adaptation. However, this viewpoint has been recently challenged. I recorded whole brain activity in macaques using fMRI while they performed an object discrimination reversal task over multiple testing sessions. I identified a lateral OFC (lOFC) region in which activity predicted adaptive win-stay/lose-shift behaviour. In contrast, anterior cingulate cortex (ACC) activity predicted future exploratory decisions regardless of reward outcome. Amygdala and lOFC activity was more strongly coupled for adaptive choice shifting and decoupled for task irrelevant reward memory. Day-to-day fluctuations in signals and signal coupling were correlated with day-to-day fluctuations in performance. These data demonstrate OFC, ACC, and amygdala each make unique contributions to flexible behaviour and credit assignment.
Structural studies of cell surface signalling molecules for neuronal guidance and connectivity
Keywords: Crystallography
Neurobiology

Signal transduction is critical during the lifetime of a neuron as it navigates to reach its targets, forms functional synaptic connections and adjusts the molecular architecture of these connections in an activity-dependent manner. Understanding the molecular organisation of components required for neuronal signalling will provide novel biological insight and can contribute to the design of therapeutics for neurodevelopmental and neurodegenerative disorders.
The focus of the thesis is on determining mechanistic molecular details of a number of distinct cell surface systems implicated in neuronal signalling. Crystallographic studies on the cell surface complex between Eph receptor A4 and ephrinA5 contributed to understanding how the modes of higher order arrangements of receptors involved in guidance affect signal transduction across the membrane. A set of structural and biophysical studies addressed the proteoglycan regulation of RPTPσ-TrkCtrans-synaptic interaction and contributed to deciphering the principles of the switch from axonal growth to synapse establishment and formation. A crystallographic and biochemical analysis of the neuronal C1q-like family, enabled mapping their interactions with potential synaptic partners, and guided functional studies aimed at elucidating their roles in the maintenance of synaptic integrity. Preliminary work on the neuronal Sigma-1 receptor chaperone laid the foundations for the structural determination of this receptor.