VictorJuiz/thesis huggingface dataset:
Connectivity driven registration of magnetic resonance images of the human brain

Image registration methods underpin many analysis techniques in neuroimaging. They are essential in group studies when images of different individuals or different modalities need to be brought into a common reference frame. This thesis explores the potential of brain connectivity- driven alignment and develops surface registration techniques for magnetic resonance imaging (MRI), which is a noninvasive neuroimaging tool for probing function and structure of the human brain.
The first part of this work develops a novel surface registration framework, based on free mesh deformations, which aligns cortical and subcortical surfaces by matching structural connectivity patterns derived using probabilistic tractography (diffusion-weighted MRI). Structural, i.e. white matter, connectivity is a good predictor of functional specialisation and structural connectivity-driven registration can therefore be expected to enhance the alignment of functionally homologous areas across subjects.
The second part validates developed methods for cortical surfaces. Resting State Networks are used in an innovative way to delineate several functionally distinct regions, which were then used to quantify connectivity-driven registration performance by measuring the inter- subject overlap before and after registration. Consequently, the proposed method is assessed using an independent imaging modality and the results are compared to results from state-of-the-art cortical geometry-driven surface registration methods.
A connectivity-driven registration pipeline is also developed for, and applied to, the surfaces of subcortical structures such as the thalamus. It is carefully validated on a set of artificial test examples and compared to another novel surface registration paradigm based on spherical wavelets. The proposed registration pipeline is then used to explore the differences in the alignment of two groups of subjects, healthy controls and Alzheimer’s disease patients, to a common template.
Finally, we propose how functional connectivity can be used instead of structural connectivity for driving registrations, as well as how the surface-based framework can be extended to a volumetric one. Apart from providing the benefits such as the improved functional alignment, we hope that the research conducted in this thesis will also represent the basis for the development of templates of structural and functional brain connectivity.

Keywords: brain connectivity
functional connectivity
image analysis
magnetic resonance imaging
MRI
image alignment
brain imaging
image registration
structural connectivity
connectome
Advisor: Smith, S
Jenkinson, M
Plasmonic nanostructures and film crystallization in perovskite solar cells

The aim of this thesis is to develop a deeper understanding and the technology in the nascent field of solid-state organic-inorganic perovskite solar cells.
In recent years, perovskite materials have emerged as a low-cost, thin-film technology with efficiencies exceeding 16% challenging the quasi-paradigm that high efficiency photovoltaics must come at high costs. This thesis investigates perovskite solar cells in more detail with a focus on incorporating plasmonic nanostructures and perovskite film formation.
Chapter 1 motivates the present work further followed by Chapter 2 which offers a brief background for solar cell fabrication and characterisation, perovskites in general, perovskite solar cells in specific, and plasmonics.
Chapter 3 presents the field of plasmonics including simulation methods for various core-shell nanostructures such as gold-silica and silver-titania nanoparticles.
The following Chapters 4 and 5 analyze plasmonic core-shell metal-dielectric nanoparticles embedded in perovskite solar cells. It is shown that using gold@silica or silver@titania NPs results in enhanced photocurrent and thus increased efficiency. After photoluminescence studies, this effect was attributed to an unexpected phenomenon in solar cells in which a lowered exciton binding energy generates a higher fraction of free charge. Embedding thermally unstable silver NPs required a low-temperature fabrication method which would not melt the Ag NPs. This work offers a new general direction for temperature sensitive elements.
In Chapters 6 and 7, perovskite film formation is studied. Chapter 6 shows the existence of a previously unknown crystalline precursor state and an improved surface coverage by introducing a ramped annealing procedure. Based on this, Chapter 7 investigates different perovskite annealing protocols. The main finding was that an additional 130°C flash annealing step changed the film crystallinity dramatically and yielded a higher orientation of the perovskite crystals. The according solar cells showed an increased photocurrent attributed to a decrease in charge carrier recombination at the grain boundaries.
Chapter 8 presents on-going work showing noteworthy first results for silica scaffolds, and layered, 2D perovskite structures for application in solar cells.

Keywords: solar cells
thin films
regenerative energy
third generation photovoltaic cell
physics
perovskite
perovskite solar cells
photovoltaics
plasmonics
Advisor: Snaith, H
Exchange rate policy options for Namibia

The thesis assesses the costs and benefits of Namibia's membership of the CMA to determine whether the CMA is an optimal currency area at least from the perspective of Namibia. This issue is examined from two main perspectives: (a) whether real exchange rate (RER) adjustment is frustrated by the inability to use the nominal exchange rate as an instrument of adjustment. Evidence of persistent RER misalignment may be seen as a necessary condition for an independent nominal exchange rate regime, however, it is not sufficient.(b) In this case, we examine whether nominal devaluations will have sustained effects on RER adjustment, given Namibia's structural features, such as the high degree of openness and a small nontradable sector. An equilibrium RER for Namibia is estimated using a single equation model of RER determination. The model is used to compute RER misalignments to determine whether there are sustained long periods of misalignments. To test whether nominal exchange rates can be effective in changing relative prices, a simple model was developed to measure pass-through of foreign price and exchange rate changes to domestic prices and wages. This provides useful information regarding whether nominal devaluations can be sustained. The results show that RER misalignments have been small, while the extent and speed of pass-through is complete and instantaneous for most items, suggesting that nominal devaluations in Namibia are not likely to have real effects.
Even if it was the case that monetary autonomy cannot be supported on grounds of affecting relative prices, it may nevertheless be important for Namibia to pursue an independent exchange rate strategy. To examine this possibility, the analysis was extended by looking at costs and benefits of OCAs which do not rely on the ability to change relative prices. Benefits arising from savings on transactions costs and on foreign exchange reserves amounted to 3.8% and 2.4% of GDP, respectively. Further, we demonstrated that past "shocks" between Namibia and South Africa were highly correlated. The findings of the thesis suggest that the CMA is an optimal exchange regime for Namibia.
Advanced finite element analysis of deep excavation case histories

Deep excavations have been used worldwide for underground construction, but they also alter the ground conditions and induce ground movements which might cause risks to adjacent infrastructure. Field measurements are normally carried out during excavations to ensure their safety, and also provide valuable data to calibrate the results from the numerical analysis which is an effective way to investigate the performance of deep excavations. This thesis is concerned with evaluating the capability of advanced finite element analysis in reproducing various aspects of observed deep excavation behaviour in the field through back analysis of case histories. The finite element model developed considers both geotechnical and structural aspects such as (i) detailed geometry of the excavation and retaining structures, (ii) realistic material models for the soil, structures and the soil-structure interface, and (iii) correct construction sequences. Parametric studies are conducted first based on a simplified square excavation to understand the effect of several important aspects, e.g. (i) the merit of shell or solid elements to model the retaining wall, (ii) the effect of construction joints in the retaining wall, (iii) the effect of the operational stiffness of concrete structural components due to cracks, (iv) the thermal effect of concrete beams and floor slabs during curing process and due to variation of ambient temperature, (v) the effect of soil-structure interface behaviour, and (vi) the effect of stiffness and strength properties of the soil. Two more complex case histories are then investigated through fully 3D analyses to explore the influence of various factors such as (i) neglecting the small-strain stiffness nonlinearity in the soil model, (ii) the selected K_0 value to represent the initial stress state in the ground, (iii) the appropriate anisotropic wall properties to consider the joints in the diaphragm wall, (iv) the parameters governing the settlements of adjacent buildings and buried pipelines, (v) the effectiveness of ground improvement on reducing the building settlement, (vi) the variation of construction sequences, (vii) the effectiveness of earth berms, and (viii) ignoring the openings in the floor slabs. This research has strong practical implications, but cautions should also be taken in applications, e.g. element types and parameter selection.

Keywords: Finite Element Analysis
Deep Excavations
Soil Models
Case Histories
Field Measurement
Site Investigations
Advisor: Burd, H
Houlsby, G
Molecular mechanisms of ARF regulation in response to DNA damage

DNA is a highly unstable molecule. Endogenous souces of DNA damage, such as reactive oxygen species (ROS), can cause DNA damage and it has been estimated that 20000 lesions occur in a cell per day. BER is the major pathway for the repair of these lesions and therefore maintains genome stability, thus preventing the development of human diseases such as neurodegenerative diseases and cancer. Therefore, if BER cannot accomplish the repair, accumulation of DNA damage occurs, triggering different cellular responses, such as cell cycle delay and senescence.
The ARF tumour suppressor protein, the gene of which is frequently mutated in many human cancers, plays an important role in the cellular stress response by orchestrating upregulation of p53 protein. Moreover, ARF expression is upregulated in senescent cells, suggesting that ARF induction might be triggerred in response to persistent DNA damage. Although ARF has been reported to be important in the regulation of proteins involved in the DNA damage response, its role is still controversial.
Here, it has been shown that ARF gene transcription is induced by DNA strand breaks (SBs) and that ARF protein accumulates in response to persistent DNA damage generated by disabling BER. These data suggest that PARP1-dependent poly(ADP-ribose) synthesis at the sites of SBs initiates DNA damage signal transduction by reducing the cellular concentration of NAD+, thus inhibiting SIRT1 activity and consequently activating E2F1-dependent ARF transcription. These findings suggest a vital role for ARF in DNA damage signalling, and furthermore explain the critical requirement for ARF inactivation in cancer cells, which are frequently deficient in DNA repair and accumulate DNA damage.

Keywords: PARP1
DNA
ARF
SSBs
Advisor: Dianov, G
Electrochemical detection of gases

This thesis discusses diverse electrochemical strategies for the determination of the concentration of the gases hydrogen sulfide, ammonia and halothane.
The chemical tagging of sulfide by a variety of structurally diverse substituted benzoquinone species was studied over a wide range of pH (22
S in the range 20-200 μM. More sensitive (LoD= 1 (μM) amperometric detection of sulfide was obtained at modified nickel electrodes in acidic media in which sulfide was stripped from the nickel oxide layer. This approach was exploited further by using nickel modified screen printed carbon (Ni-SPC) electrodes as economical and disposable sensors for sulfide.
Next, two different strategies for determining gaseous ammonia in the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluromethylsulfonyl)imide, [EMIM][N(Tf)2], and in DMF are described. The first approach exploits the effect of ammonia as a proton acceptor species on the anodic oxidation of hydroquinone, resulting in a linear detection range from 10 to 95 ppm ammonia (LoD= 4.2 ppm). The second approach is based on the direct oxidation of ammonia in either DMF or [EMIM][N(Tf)2].
The possibility of photochemically induced electrocatalytic processes within microdroplets containing p-chloranil (2,3,5,6-tetrachloro-1,4-benzoquinone, TCBQ) was examined as a means of detecting the anaesthetic gas halothane.
Finally, two of the more promising routes for sulfide detection were studied at elevated temperatures (up to 70 °C) with a view to developing H2S sensors capable of meeting the demands of oilfield applications.

Advisor: Compton, R
Dysfunction as a function of authority: understanding the power and performance of international non-governmental organizations

In this work, I present a conceptual framework for understanding how international non-governmental organizations (INGOs) become powerful international organizations (IOs), and how their pursuit of legitimacy leads to the formation of specific kinds of organizational cultural proclivities and dysfunctional tendencies that shape how these groups behave as international actors. Despite their increasing prominence in international affairs, INGOs remain largely understudied by International Relations (IR) scholars; my work provides a theoretically driven and empirically supported analysis of the power and performance of these actors, thus filling the existing gap in the IR literature. Relying on the basic tenets of sociological institutionalism, I argue that there is an indissoluble relationship between the ways in which an INGO becomes powerful and its ultimate performance outcomes.

Keywords: leadership
legitimacy
IO
moral
culture
organization
INGO
authority
international
bureaucracy
charismatic
non-governmental
behavior
Advisor: Mattli, W
The manuscript and print contexts of older Scots romance

This thesis is a study of the fifteenth- and sixteenth-century manuscript and print contexts of Older Scots romance. Building on recent developments in Middle English romance scholarship and Older Scots book history, it seeks to contextualise the surviving corpus of Older Scots romances in light of their unique material witnesses and contemporary cultural milieu.
Chapters 1 to 8 focus respectively on the following Older Scots romances: the Octosyllabic Alexander, the Buik of King Alexander the Conquerour, Florimond, Lancelot of the Laik, King Orphius and Sir Colling, Golagros and Gawane and Rauf Coilȝear, the Scottish Troy Book, and Clariodus. The conclusion assesses and evaluates the most significant and recurring features of these chapters and reveals how they cumulatively deepen our understanding of the book-producing and book-owning culture of fifteenth- and sixteenth-century Scotland. The conclusion also looks forward to new witness- conscious editions of Older Scots romance that endeavour to represent as far as possible a text’s unique and idiosyncratic manuscript and print contexts.
  In each chapter I examine the set romance’s primary contexts of composition, including authorship, date, and first audience, as well as its secondary publication contexts. A full palaeographical, codicological and bibliographical description of each manuscript and print is provided, with details of when, where and by whom each witness was produced. Information about when and where that witness was read is also given, with details of the owners and readers where known. Significant attention is paid to the use of titles, rubrication and mise-en-page to reveal the trends and bibliographical codes in copying and presentation. Where appropriate, the compilation choices made by scribes and readers are also analysed. Careful assessments of these are shown to aid modern thematic and comparative literary interpretation.
Most notably, each chapter of this thesis also provides much-needed new information about fifteenth- and sixteenth-century Scottish literary communities. Several significant and often-overlapping circles of scribes, readers and owners are revealed. The familial, professional and geographical associations between these groups of producers and consumers are traced and consequently new book- publishing and book-owning networks are documented. In further original work, a number of hitherto unknown texts, scribes and readers are also successfully identified.

Keywords: manuscript and print contexts
Older Scots literature
Older Scots and Middle English romance
Advisor: Mapstone, S
CD161+ Gamma Delta T-cells in health and liver disease

CD161 γδ T-cells have been implicated in the pathogenesis of Multiple Sclerosis however their role in health and chronic liver disease requires further exploration.
In health, the majority of γδ T-cells expressed CD161 – a C-type lectin, and predominantly expressed the Vδ2 chain. The CD161+ γδ T-cells demonstrated a Th1-like pattern, expressing IFN-γ, TNF-α and Granzymes/Perforin when compared to the CD161- subset. The CD161+ γδ T-cells also expressed CCR6 and IL-18R thus also displaying a Th17-like pattern. These cells were also found in the lamina propria in the gut and rapidly expanded in the 1st few weeks of life in the periphery.
On gene array analysis, there were 409 genes expressed on the CD161+ γδ T-cells when compared to their CD161-ve counterparts including those coding for β2 receptors, CCL20, Acetycholinesterase, CCR1 and IL-18R. A potential clinical correlation to cardiac diseases was found when the upregulated genes were analysed. When the CD161+ γδ and CD161+ αβ T-cell populations were compared via gene-array, an association with a risk variant for coeliac disease was found. Thus in health, CD161+ γδ T-cells are not only a distinct subset of T-cells (confirmed by a FACS approach and gene array methods), but also the expression of CD161 may be linked to common genetic signals downstream in cell processes and disease pathogenesis, irrespective of T-cell subset population.
In chronic liver disease there was a significant reduction in the periphery of CD161+ γδ T-cells in patients with chronic Hepatitis C (HCV) and an increase in patients with Primary Biliary Cirrhosis and Primary Sclerosing Cholangitis when compared with healthy individuals. The CD161+ γδ T-cells appeared to be of a different phenotype in HCV infection. There was no overall significant localisation into of CD161+ γδ T-cells patients with chronic liver disease or specifically in HCV infection. There was however a CD161+ γδ T-cell enrichment in the liver in patients with Non-Alcoholic Fatty Liver disease. The CD161+ γδ T-cells were also found in Hepatocellular Carcinoma tissue.
Overall it appears the CD161+ γδ T-cells are indeed a unique subset, playing a distinct role in health, as part of an early innate response, but also potentially involved in disease pathogenesis.

Keywords: Gamma delta T-cells
CD161
Advisor: Klenerman, P
Suspense in the English novel from Jane Austen to Joseph Conrad

Because of critical neglect, there is no established terminology to describe techniques of suspense. Borrowing from Aristotle, Koestler, and others, a new body of concepts is suggested and importantly, a distinction of tense is established, between types of suspense which relate to the narrative past, present, and future. The classical world's intuition of a connection between mental uncertainty and the physical state of hanging has conditioned Western man's notion of narrative suspense until a comparatively recent date. Eighteenth-century theories of the sublime helped to create an understanding that suspense was not necessarily painful. Through an analysis of novels by Jane Austen, George Eliot, Dickens, Hardy, and Conrad, an attempt is made to identify and evaluate the most common suspense strategies in the period's popular genres, notably the Austenian romance, mystery, and tragedy. The Austenian romance is compared to the detective story in that narrative presentation is determined by the need to control the reader's expectations, and to achieve an ending which is both satisfactory and surprising. The latter requirement may have contributed to the gradual disappearance of the authorial "voice" in the course of the nineteenth century, and a consequent reduction in the pleasures of irony and comedy. During the Victorian period, many genres are combined in the long novel, but mystery gradually advances in popularity and sophistication, to the point where narrative events are often inappropriately exploited as secrets. Tragedy involves a creative conflict between the reader's hopes and expectations, so he is permitted to glimpse the overall tragic process, and suspense is generated on the levels of theme and causaliy. The problems incurred by an inability or unwillingness to conclude structures of theme suspense are considered finally.

Keywords: detective
structuralism
Dickens
suspense
Victorian
narrative
whodunit
recognition
anagnorisis
romance
Austen
Hardy
Aristotle
mystery
Conrad
Barthes
novel
Advisor: Bayley, J
Essays in econometrics and forecasting

Whether we would like to model imports and exports, or forecast inflation, structural variation in an economy frequently causes problems. This thesis examines such variation in two dimensions: first, in a cross-section of individuals, and secondly, over time. A panel of manufacturing industries in several developed countries reveals that there is substantial variation across sectors, in the response of trade to changes in prices and incomes. Ignoring this heterogeneity can render conventional results biased and inconsistent, so a number of robust methods are used to obtain reliable estimates of long-run and short-run trade relationships. The findings point to common behaviour across sectors, which could be due to similarities in technology.
The impact of structural breaks over time is examined in the second part of the thesis. Unpredictable shifts in deterministic terms such as the mean of a process are shown to generate significant forecast failure, and even the methods used to evaluated forecast accuracy are affected. Using the Kullback-Leibler discrepancy to measure the size of forecast errors, various robust mechanisms are discussed, that do not fail systematically after a break. Although they can provide a degree of insurance if a shift does occur, this comes at a cost if there is no change, and in the presence of measurement error they can exacerbate the uncertainty surrounding a forecast. An empirical illustration with a model of UK money demand provides some support for the automatic correction mechanisms, although there does seem to be a role for direct modeling of a break process.

Keywords: Econometrics
Panel Data
Panel Cointegration
Trade elasticities
Forecasting
Advisor: Hendry, D
Bond, S