VictorJuiz/thesis huggingface dataset:
Multi-level modelling and spatial inference for large-scale neuroimaging data
Keywords: linear mixed model
statistics
fMRI
neuroimaging
confidence regions
spatial statistics
functional magnetic resonance imaging

Recent developments in data sharing and availability provide a vast new window of opportunity for large-sample fMRI analysis. The increased statistical power resulting from larger sample sizes allows researchers to model previously inaccessible phenomena such as the complex grouping structures present in large multi-level datasets (e.g. genetic, familial, geographical) and the spatial variation present in shape, size and locale of excursion sets (identified regions of activation). This thesis is comprised of two halves, which investigate each of these features in turn.
In the first half, we employ the Linear Mixed Model (LMM) to detect and account for grouping and covariance structure present in large experimental designs. At present, the existing fMRI LMM tools are neither scalable nor fully exploit the computational speed-ups afforded by vectorisation of operations over voxels. For this reason, such tools cannot be employed in the large-sample setting. To address this issue, we derive new expressions for LMM estimation and inference and illustrate their usage to perform computationally efficient large-scale fMRI LMM analyses. Our methods are validated empirically via simulations and illustrated using data drawn from the UK Biobank (Allen et al. 2012).
In the second half, we extend a method proposed by Sommerfeld et al. (2018) to provide confidence bounds for the intersection or ‘conjunction’ of excursion sets that have been acquired across the same spatial region but under different study conditions. Such 'conjunctions’ are of natural interest as they correspond to the question “Where was activation observed under all study conditions?". Our method provides, with a desired confidence, sub- and super-sets of the 'conjunction set' without any assumptions on the dependence between the different conditions. Extensive simulations are provided assessing the method’s performance, and a demonstration of the method is given using data drawn from the Human Connectome Project dataset (Van Essen et al. (2013)).
Johann Friedrich Agricola (1720–1774): a critical study and catalogue of the musical sources
Keywords: Musical analysis
Johann Friedrich Agricola (1720-1774)
Classical
Critical edition
Eighteenth century
Material culture
Musical exchange
Source studies
Palaeography
Manuscripts
Galant
Thematic catalogue
Baroque

The Berlin Hofkomponist Johann Friedrich Agricola (1720–1774) is today still perhaps best known as a pupil and copyist of Johann Sebastian Bach. Together with Carl Philipp Emanuel Bach, he co-authored Bach’s 1754 obituary, and later received acclaim for his translation and revision of Pier Francesco Tosi’s singing treatise, published in German as 'Anleitung zur Singkunst' (1757). However, Agricola’s own musical legacy has received very little attention, despite the fact that he composed a substantial quantity of music across a range of genres and was also a prolific copyist of works by many major composers of his day. These sources demand attention as both the legacy of an important Berlin composer schooled in the Bach tradition, and, more broadly, as case studies in the rich and complex networks of musical exchange that occurred between composers and musicians during this period.
This thesis presents the first critical study of all the known sources of music, both manuscript and printed, connected to Agricola. It is divided into three sections. Volume I opens with a biographical profile of Agricola, before considering some of the theoretical and historiographical challenges associated with approaching galant music and the materiality of eighteenth-century sources as evidence for musical networks and exchange. This is followed by an overview of the development of musical life at the Dresden and Berlin courts, which enjoyed a close relationship in the first half of the eighteenth century, and the major Berlin collections where most of the Agricola sources are found. A detailed re-examination of Agricola’s handwriting in light of newly uncovered manuscripts, together with watermark and ink analyses, provides the basis for a refined chronology of the sources. These findings then inform my discussion of two areas where the autograph manuscript tradition is particularly rich: the genre of sacred music, and Agricola’s role as a copyist, where I consider selected manuscripts in more detail. In Volume II, I present a critical edition of two hitherto unpublished cantatas by Agricola, the Easter Day cantata 'Die Auferstehung des Erlösers' and the funeral cantata 'Wallet ihr Seelen voll Schwermut'. The edition supplements the discussions of these works in Chapter 4 and makes them available in a scholarly text for the first time. Volume III comprises the first thematic catalogue of Agricola’s works, the Agricola-Werke-Verzeichnis (AgWV), and a descriptive catalogue of the manuscript copies that are wholly or partially in Agricola’s hand. The thesis is intended to provide the fundamental groundwork for future source studies on Agricola, the Berlin School and the legacy of the Bach tradition after 1750.
Inventing Slavonic: cultures of writing between Rome and Constantinople 
Keywords: medieval
byzantine
written
nationalism
history
culture
hagiography
slavonic

This thesis offers a study of changing ideas about and attitudes toward writing, as they are expressed in the earliest texts concerned with the invention of the Slavonic alphabet and its legendary ninth-century inventor, the Byzantine diplomat, Constantine-Cyril. It is divided into three case studies, each focusing on the three major texts narrating the invention of Slavonic and dating to the late ninth and early tenth centuries: the Life of Constantine-Cyril, the Life of Methodios, Cyril’s brother, and On Letters, a treatise written in defence of the new alphabet.
In contrast with existing scholarship which largely accepts these texts as telling a unified, monolithic story of the birth of Slavonic culture, the thesis approaches each text as an intellectual monument, that sought to make an intervention into a specific set of socio-political circumstances. In so doing it reveals the intricate ways in which early medieval authors in Central and Eastern Europe navigated through Greek and Latin language intellectual culture, in order to compose and compile texts and thus propagate specific agendas. Moreover, it demonstrates the complex and profound ways in which the Slavonic alphabet was invented and reinvented in this process, and how this multitude of ideas about writing, albeit present in the medieval sources, has been flattened by modern historiography.
The biogeography of giant kelp submarine forests at the sub-Antarctic latitudes of South America
Keywords: South America
Macrocystis pyrifera
persistent ecosystems
marine ecosystems
Giant Kelp
sub-Antarctic
Patagonia

This doctoral thesis presents the first work on the extent, spatial dynamics, and long-term trends of the giant kelp (Macrocystis pyrifera) ecosystem in southern South America and sub-Antarctic latitudes. This work was based on an interdisciplinary approach of remote sensing using satellite images, unmanned aerial vehicles (UAV), geographical information systems, underwater exploration, and a collection of historical sources and secondary information from international collaborations.
The first research paper of this thesis (Chapter 3) presents a mapping methodology of giant kelp derived from filtering values from the satellite Sentinel-2. This method was validated with secondary sources (previous kelp surveys) and primary sources of data, such as detailed orthomosaics made with UAV. Because of the high overall accuracy of this method, it was possible to map and measure the surface of the complete distribution of the giant kelp ecosystem by ecoregion and province.
The second paper (Chapter 4) is based on the mapping methodology from Chapter 3, developing a spatial analysis of the sub-Antarctic kelp from South America, Falkland Islands (Malvinas) and South Georgia to understand the abiotic patterns that could predict the typical size of a giant kelp forest. Additionally, these patterns were compared in a temporal analysis stretching as far back as the 19th century to assess the persistence of this ecosystem. The results of this paper indicate that sub-Antarctic giant kelp is one of the least modified and most persistent marine ecosystems on Earth.
Chapter 5 analyses the spatial distribution of marine sea surface temperature (SST) heatwaves and marine cold spells in the Channels and Fjords ecoregion in past decades, with a focus on understanding the climatological trends as they can affect giant kelp ecosystems. This paper established that, in contrast to the main global trend pointing towards SST warming, the frequency of marine cold spells in the nearshore coastlines of southernmost South America has in fact increased in the decade of 2010. We identified two main mechanisms as possible causes for this trend: increased frequency of storms driven by the Antarctic Circumpolar Current and glacier melting in the Patagonian fjords. Cold waters favour the persistence of giant kelp and associated biodiversity, hence the lack of SST warming highlights the region as a potential refugium for the ecosystem. However, more studies are needed to understand these new dynamics, and we conclude the paper with a summary of potential stressors to giant kelp ecosystems in the study area.
Finally, Chapter 6 provides an overview of the main findings of this thesis and recommendations for future research, highlighting the need for further interdisciplinary studies on the Magellanic marine province as a climatic refugium for the giant kelp ecosystem.
Nanoscale mechanical and transport properties of multilayers and energy materials
Keywords: Residual Stress
Operando battery
Li-ion battery
Energy Materials
Mechanics of Materials

Thermal and mechanical properties of thin films and nano-multilayer coatings are governed by a multitude of interlinked material properties that arise as a consequence of deposition technique and parameters. Understanding the origin of these properties including residual stress, fracture toughness, thermal diffusivity and thermal degradation activation temperature enables the careful design and control of material properties, tailored to technological applications.
The key objective of this thesis is to expand the current knowledge of the origins and controllability of thin film properties, by understanding the link between deposition parameters, film microstructure, mechanical properties and thermal properties. Starting with the mechanical properties, advanced residual stress measurement techniques are used to show how magnetron chamber pressure variation can be used to control residual stress distributions within thin films, and how this stress is linked to microstructural properties. To develop further mechanical insights directly applicable to technological applications of thin films on polymer substrates, a model for the mechanical degradation under uniaxial tension is presented, in addition to a new method for the determination of the Mode I fracture toughness.
Based on the obtained findings, thermal properties including thermal diffusivity and thermal degradation onset temperature are linked to deposition-induced microstructural properties. A model for the residual-stress driven thermal diffusion activation is presented, combining insights gained from both mechanical and thermal property analysis.
To apply the findings to cutting-edge technology, interlinked diffusion and mechanical degradation phenomena in next-generation Li-ion battery cathode material are analysed. Based on the identified mechanisms and using novel experimental techniques, a deep understanding of the relation between Li-ion transport, stress and microstructural degradation in thin film, solid state multilayer batteries is developed.
The investigations presented in this thesis open new perspectives for the precise optimisation of high-technology thin film and nano-multilayer properties and performance.
Development of the ionisation signal analysis and the thermometry system for the LUX-ZEPLIN direct dark matter detection experiment
Keywords: experiment
dark matter
LUX ZEPLIN

There is substantiated astrophysical evidence for a substance known as Dark Matter within the universe, at both galactic and cosmological scales. Despite this evidence, the true nature of Dark Matter remains one of the most profound questions in modern physics. One viable candidate is the Weakly Interacting Massive Particle (WIMP), which could nicely explain the observed measurements. The LUX-ZEPLIN (LZ) detector is searching for WIMP interactions with xenon nuclei, through both scintillation and ionisation signals. It comprises a time-projection chamber filled with 7 tonnes of liquid xenon, situated at the Sanford Underground Research Facility in South Dakota.
The experiment operates at low temperatures (about 175
Kelvin). During the cool-down of the experiment from room temperature and to ensure stability during running, the temperature needs to be monitored closely to ensure the detector is not damaged and that high-quality data can be collected. The unique implementation of the thermometry system within LZ necessitates bespoke solutions to overcome challenges related to the radiopurity and cleanliness. This thesis examines how these problems are resolved through the careful material procurement and development of a successful calibration procedure.
The ionisation signal plays an important role in the reconstruction of event energies and in interaction type discrimination. However, detector-specific phenomena cause an inherent position dependence. The origins of this position dependence are examined, along with the development of a method to correct signals using dispersed calibration sources. A consideration of the detector contraction is made along with a calibration of the level sensors. Together the position dependence in the ionisation signal, along with these level sensors enables the detector to be precisely levelled.
This work concludes by examining techniques to improve the sensitivity of the experiment below nominal capabilities. Specifically, this includes an examination of realistic pulse shape characteristics to improve the energy threshold of the experiment. Crucially, this provides a series of techniques which can be utilised within LZ analyses.
The design of Montaigne's Essais
Keywords: design
Montaigne
disegno
dessein

Dessein is, in the sixteenth century, a polysemic term whose meanings cover the entire spectrum of the creative process: from an originating idea, project or intention, to a material plan or visual design. This thesis reads Montaigne’s Essais through the lens of this spectrum of meanings, showing that attending to the uses of, and approaches to, design in the Essais reveals the ways in which Montaigne conceived of his writing project as the product of a mode of experimentation and mediation between thought and world. One of the contentions of this thesis is that much like the practice of drawing that was central to the Renaissance artistic process, Montaigne’s writing retains a marked indeterminacy, possessing an unresolved, ‘sketch-like’ quality. Like Renaissance artists, who in the century preceding the publication of the Essais had become increasingly interested in the process of artistic creation (a change reflected in the growing importance and value of drawing), Montaigne is also fascinated by the process of translating an internal notion or idea into its public manifestation. This fascination animates the Essais, and influences Montaigne’s position on questions of authorial intention, posthumous reputation, and his relationship to both real and imagined readers, including Montaigne himself. Making use of a hybrid methodology that brings together word history, art theory, image analysis, close reading and design theory, this thesis uncovers what Montaigne has to say about design; how the notion of design functions in the Essais; and how Montaigne’s relationship to designed objects sheds light on what we might call a ‘Montaignian aesthetics’. Understanding Montaigne’s uses of, and attitudes to, design ultimately allows us to reimagine the kind of project constituted by the Essais.
Chemogenetic silencing of sensory neuron populations to uncover their role in touch and pain 
Keywords: Chemogenetics
Touch
Pain
Neuroscience
Nav1.7

The ability of humans to experience touch and pain sensation is critical for our survival. The experience of pain is typically a protective mechanism, and ensures we avoid dangerous environmental cues. However, following incidences of genetic mutations, injury or disease of the somatosensory nervous system, protective pain can become pathological. Indeed, neuropathic pain affects seven to ten percent of the general population, and our current treatment strategies show poor efficacy and tolerability.
Currently, mechanisms surrounding neuropathic pain involve both peripheral and central sensitisation. However, there is an incomplete understanding of the functional roles of different sensory neuron populations, the sensory modalities they encode, and how they change under neuropathic conditions. Therefore, it is unclear which primary afferent subpopulations contribute to the induction and maintenance of neuropathic pain and which should be therapeutically targeted. This is largely due to the fact that peripheral sensory neurons within dorsal root ganglia (DRG) are highly heterogeneous and are thought to contain up to 17 different subpopulations.
A key aim of this work is to ascribe roles to primary afferent subpopulations in naïve rodents and those that have undergone traumatic nerve injury. Therefore, I have developed a novel chemogenetic toolbox to facilitate selective, reversible and repeatable neuronal silencing of defined sensory neuron populations. I have employed AAV9-GluClv2.0 to broadly silence all DRG neurons and observed functional recovery from neuropathic pain in vivo. Subsequently, I used AAV9-GluCl.CreON to target two populations of sensory neurons: the Nav1.8 positive (largely nociceptive) population, and the tyrosine hydroxylase positive C-low threshold mechanoreceptor (C-LTMR) population. Silencing each of these populations resulted in population-specific sensory phenotypes, with subtle or no changes in neuropathic mechanical hypersensitivity. Finally, using a molecule to man approach, the role of the voltage-gated sodium channel Nav1.7 was investigated in C-LTMRs and pleasant touch sensation. In humans and mice either genetic or pharmacological disruption of Nav1.7 resulted in deficits in C-LTMR function. This work challenges the current dogma that therapeutically targeting Nav1.7 will only effect the nociceptive system. Together, this work illustrates the need to better understand the roles of different primary afferent subpopulations and provides chemogenetic tools to achieve this. Ultimately, this work will facilitate the development of therapeutics which are better targeted towards the appropriate sensory neuron populations.
The active brain: relationships between physical activity, fitness, cognitive performance and brain structure in young adolescents
Keywords: Cognition
Adolescence
Brain
Physical activity

Governmental, scientific and public health communities have become increasingly interested in the potential of physical activity to promote neurocognitive health across the lifespan. While research in adults has advanced rapidly in the past 20 years, much less is known about the effects of a physically active lifestyle on cognitive and brain health in young people, especially adolescents. Using magnetic resonance imaging (MRI) and cognitive data from the Fit to Study cluster randomised controlled trial, this thesis therefore examined relationships between neurocognitive health and markers of physical activity and cardiorespiratory fitness in this age group.
A cross-sectional study involving baseline Fit to Study data showed that higher levels of physical activity and fitness are associated with superior performance on domain-specific cognitive assessments (working memory, cognitive flexibility, inhibitory control, visual memory and processing speed) in a large sample of young British adolescents (n = 16,017), but that relationships are small and explain less than 10% of the variance in cognitive outcomes. It also showed that relationships may be stronger in females compared to males and that a physically active lifestyle is linked with more favourable cognitive outcomes. In a sub-sample of adolescents (n = 61), however, no significant relationships between markers of a physically active lifestyle and volumes or multi-modal MRI markers of tissue (micro)structure in the anterior hippocampus were observed.
An intervention study explored whether increasing the amount of vigorous intensity physical activity during school physical education (PE) lessons for one academic year could improve cardiorespiratory fitness and induce neurocognitive changes in the Fit to Study sample (n = 93 schools). The intervention, designed with PE teachers to be scalable and feasible, did not significantly improve fitness or cognitive performance. In addition, no robust intervention-related changes in anterior hippocampal MRI metrics were observed. These findings should, however, be interpreted with caution given low implementation fidelity and high drop-out.
This thesis supports the hypothesis that higher levels of physical activity and cardiorespiratory fitness are associated with superior cognitive performance in young adolescents. However, no physical-activity induced effects on neurocognitive health were observed. Further investigation of whether and how physical activity may promote positive brain and cognitive changes in adolescents is needed.