VictorJuiz/thesis huggingface dataset:
On the reproducibility and interpretability of group-level task-fMRI results
Keywords: fMRI
Statistical Inference
Reproducibility
Task-fMRI

In this thesis, we aim to address two topical issues at the forefront of task-based functional magnetic resonance imaging (fMRI). The first of these is a growing apprehension within the field about the reproducibility of findings that make up the neuroimaging literature. To confront this, we assess how the choice of software package for analyzing fMRI data can impact the final group-level results of a neuroimaging study. We reanalyze data from three published task-fMRI studies within the three most widely-used neuroimaging software packages - AFNI, FSL, and SPM - and then apply a range of comparison methods to gauge the scale of variability across the results. While qualitatively we find similarities, our quantitative assessment methods discover considerable differences between the final statistical images obtained with each package. Ultimately, we conclude that exceedingly weak effects may not generalize across fMRI analysis software.
In the second part of this work we shift our attention to the analytical methods applied for fMRI inference. Here, we seek to overcome limitations with the traditional statistical approach, where for sufficiently large data sizes current methods determine universal activation across the brain, rendering the results as uninterpretable. We extend on a method proposed by Sommerfeld, Sain, and Schwartzman (2018) (SSS) to develop spatial Confidence Sets (CSs) on clusters found in thresholded raw blood-oxygen-level-dependent (BOLD) effect size maps. The CSs give statements on the locations where raw effect sizes exceed, and fall short of, a purposeful non-zero threshold. We propose several theoretical and practical implementation advancements to the original method formulated in SSS, delivering a procedure with superior performance in sample sizes as low as N = 60. We validate the method with 3D Monte Carlo simulations that resemble fMRI data. We then compute CSs for the Human Connectome Project (HCP) working memory task contrast images, illustrating the brain regions that show a reliable %BOLD for a given %BOLD threshold.
In the final part of this thesis, we develop the CSs to operate on standardized Cohen's d effect size images. We derive the statistical properties of the Cohen's d estimator to motivate three algorithms for computing Cohen's d CSs, including a novel method based on normalizing the distribution of Cohen's d. With intensive 3D Monte Carlo simulations, we find that two of these methods can be effectively applied to fMRI data. We compute Cohen's d CSs on the HCP data, and by comparing the CSs with results obtained from a standard testing procedure, exemplify the improved localization of effects that can be gained by using the Confidence Sets.
The role of microRNA-31 in cardiac fibrosis associated with atrial fibrillation
Keywords: Micro-RNA-31 in cardiac fibrosis and atrial fibrillation

Cardiac fibrosis is a histological hallmark of atrial arrhythmogenic structural remodelling characterised by increased deposition and accumulation of fibrillar collagen. Despite recent advances in understanding cardiac fibrogenesis, there is a paucity of effective anti-fibrotic therapies. Given the robust effect that single microRNAs can have on gene transcript abundance, these small oligonucleotides have been recognised as potential targets for therapeutic manipulation in a wide range of disease states. Our group has recently shown that increased miR31 expression in cardiomyocytes contributes to electrical remodelling begetting atrial fibrillation and our more recent unpublished data show that miR31 is also upregulated in human atrial fibroblasts derived from patients with chronic AF compared to sinus rhythm controls. Given that miR31 has been shown to drive pro-fibrotic phenotype changes in fibroblasts in other disease models, including ischaemic heart disease, we hypothesised that the observed increase in atrial fibroblast miR31 expression in chronic AF was contributing to fibrotic changes seen in this disease state. Consequently, I conducted experiments whereby miR31 abundance was either enriched or depleted in primary human atrial fibroblasts obtained from healthy patient donors to observe whether manipulation of miR31 in vitro would cause pro-fibrotic gene expression- and phenotype-changes. Results did show significant changes in mRNA of key pro-fibrotic signalling genes however inter-donor variability made it difficult to draw robust conclusions on the role of miR31 in fibroblast phenotype. Additional in vitro experiments in human atrial fibroblasts were conducted to investigate whether the transcription factor ETS1 is involved in regulating miR31 expression and results did show increased miR31abundance following ETS1 depletion. Further, the consequence of miR31 up-regulation on fibrogenesis in vivo was explored in a novel, tamoxifen inducible, global fibroblast-specific miR31 transgenic mouse strain. Results of these mouse experiments demonstrated that increased fibroblast production of miR31 in vivo leads to similar pro-fibrotic gene expression and protein changes observed in human atrial fibroblasts thereby corroborating the separate experimental systems used. Overall, the results of this project are the preliminary evidence that miR31 is involved in the pro-fibrotic response in human atrial fibroblasts, as well as in the intact mouse, and provide the foundation upon which further experiments can be performed and justified.
Remnants of a Roman past: the reuse of Roman objects in early Anglo-Saxon graves, c. AD 5th—7th centuries 
Keywords: Anglo-Saxon
object reuse
Roman
furnished burial
late antique Britain

The widespread curation and deposition of Roman material culture in the graves of the Anglo-Saxon dead has long been acknowledged in archaeological study. These reused artefacts have been interpreted in myriad ways: as found curiosities, scrap materials, protective amulets, replacements for contemporary objects, heirlooms, and biographical objects. The first large-scale examination of the typology and use of Roman material was conducted by Roger White in 1988. This thesis builds off the platform set by White to create a wholly new assessment and understanding of the available data.
This methodology is the first to investigate the occurrence of Roman objects in the Anglo-Saxon furnished burial rite throughout space and time by means of a systematic analysis of 5th—7th century burial data. A dataset of 671 objects from 117 cemetery sites is assessed. In four primary veins of multivariate analysis, reused Roman materials are investigated for typological factors and uses, regional distributions, demographic associations, and chronological patterning. Though a wide array of object types is recorded, coins and items which could be used in display are the most numerous. Regionally, the funerary use of Roman artefacts is established to have been most prevalent in the culturally Saxon territories of the Upper Thames Valley and modern-day Wiltshire and Hampshire. Statistical analysis further reveals a disproportionate association between these items and the graves of women and juveniles.
The results of this analysis demonstrate that Roman objects were deposited in different ways and imbued with different social meanings over time, ultimately challenging the ways in which we think about the interactions of 5th—7th century communities and cultures in Britain. These artefacts are interpreted to have played a role in the formation and maintenance of a new cultural identity in late antique Britain through the construction of a shared ‘memory’ of the Roman past.
Aspects of Q-ball theory
Keywords: Beyond-the-Standard Model
Field Theory
Q-balls

Q-balls are an example of non-topological soliton that can appear in the spectrum of scalar field theories. They are semi-classical states that minimise the energy for a given Noether charge. If isolated from other sectors, these spherically symmetric objects are kept absolutely stable by energy and Noether charge conservation. Though the properties of Q-balls cannot be determined analytically in general, progress can be made in two opposite limits: the thin-wall (large charge) limit; and the thick-wall (small charge) limit. Q-balls are both interesting phenomenologically and as formal objects in their own right, as evidenced by the large body of work on this subject.
This thesis represents a study on the formal properties of field theories, with the aim to determine the subclass of models that admit Q-ball solutions. To that end, its goals are two-fold. Firstly, to constrain the theories that possess stable Q-ball states by: (i) determining the differential equations that govern the VEV of the constituent scalar in the thin-wall limit, together with the physical properties of the resulting Q- ball; (ii) constraining the small-field expansions that lead to stable thick-wall Q-balls by demanding that the minimum of energy be classically stable against decay to the underlying quanta of the scalar field. Secondly, to determine whether stable Q-balls, in both the thick- and thin-wall limit, can form from scalar mesons, arising from the breaking of an approximate chiral symmetry, in the SM and in a specific BSM theory. We will not discuss the phenomenology of these theories in this thesis.
The content of this thesis is laid out in three parts. Part I is concerned with Q-balls in theories possessing only one scalar field, and comprises Chapters 2 and 3, whereas Part II is concerned with theories with multiple scalar fields, and comprises Chapters 4-6. In these parts, we perform an analysis to determine the existence of Q-ball states, and any constraints required by the theories that possess them. In particular, in Part I, the thick-wall analysis presents us with necessary conditions, whereas in Part II, the thick-wall analysis presents us with sufficient conditions. Fi- nally, Part III analyses theories when the underlying scalars of the theory are pseudo- Nambu-Goldstone bosons arising from the breaking of an approximate chiral sym- metry, as in the Standard Model – this final part comprises Chapters 7 and 8. We show that stable Q-balls are not part of the spectrum of the leading-order Chiral lagrangian, but that they can arise in the class of BSM models we study.
The bulk of the original work of this thesis can be found in Refs. [18,19,100–102], with the remaining work unpublished.
States of the union: federalism and the origins of American intergovernmental relations, c. 1789-1820
Keywords: history
Native Americans
constitutional law
American founding
Slavery
federalism
early American republic
politics
constitutional studies
eighteenth century
United States Constitution
nineteenth century

This dissertation explores how American state governments adapted to governing in a new kind of federal union in the three decades following the ratification of the U.S. Constitution. Although existing political histories generally pay only anecdotal attention to the activities of state governments in the early national period, this thesis demonstrates that the creation and implementation of national policy was significantly shaped by interactions between state and federal officials. Minimal manpower and vast distances limited the capacity of the federal government to enforce its own laws across the nation, leaving the federal executive and Congress reliant on the support of state officials and institutions in the implementation of federal policies within the states. The line between state and federal areas of responsibility under the Constitution was often unclear, and the question of which government had the right to legislate in which policy area arose frequently. While state and federal officials regularly disagreed with one another about the interpretation of federal laws and of the Constitution, they learned to resolve these conflicts through negotiation, in most cases avoiding formal litigation. I denominate this pattern of interactions ‘co-ordinated federalism.’
On the basis of archival research in five states, this dissertation builds an administrative history of early American federalism, investigating the impact of intergovernmental interactions on the making and execution of national policies concerning trade and finance, national defence, Indian affairs, and slavery. An introductory chapter summarizes the principal mechanisms by which the state and federal governments conducted their ongoing negotiations, and explores the roles of state governors and legislators in producing regulations, resolutions, and remonstrances designed to influence federal policy. While state governments generally co-operated in the enforcement of federal law, even where it was highly controversial, their considerable capacity for independent action could also pose a threat to the success of federal policies.
Impact of land-use change on bird communities of a Rwandan biodiversity hotspot
Keywords: Agrobiodiversity
Tropical montane forest
Birds
land-use change
Taxonomic, functional and phylogenetic diversity
Forest restoration
Avian ecology
Nyungwe National Park, Rwanda

Although land-use change is increasingly flagged as the top driver of biodiversity loss in the tropics, there are important information gaps on its effects on particular facets of biodiversity, particularly in the Afrotropics. To contribute to this research agenda, and with a focus on birds, this study explores how the varying degrees of anthropogenic habitat transformations have affected the patterns of species composition, species diversity, functional and phylogenetic diversity. The study employed a range of methods, however, the core results are based on avian point-count sampling and habitat assessment conducted within major land-use types in the Nyungwe landscape, a tropical montane rainforest and adjacent croplands in Rwanda. Further data on avian functional traits were obtained from museum specimens. The study shows the following in relation to relatively undisturbed forest habitats of the Nyungwe landscape. 1) Species composition was altered and species diversity levels declined in all alternative land-uses. 2) Restored and cultivated areas experienced loss of functional diversity, with steeper falls for the trophic-related traits in the former land-use. 3) Phylogenetic diversity was stable across land-uses, except for cultivated areas, which registered marked declines, particularly in monoculture farms of tea. 4) At the landscape scale, avian diversity was influenced by elevation, soil moisture and the lower vegetation height, however, within cultivated areas and regenerating forests, vegetation composition, and tree cover extent were of high importance. 5) There was no evident superiority of the assisted natural regeneration approach over the passive restoration approach with respect to supported avian diversity, reflecting the long time needed for a full recovery. This study provides evidence of the irreplaceability of primary forests in the tropics, and the crucial roles habitat heterogeneity plays in maintaining avian diversity. The thesis also considers how these findings may inform the conservation planning of multiple-use landscapes in Rwanda, and similar landscapes in the tropics, with attention also to the use of birds as flagships for conservation.
Characteristics of Saharan dust emission mechanisms in boreal summer: a satellite and modelling approach
Keywords: Sahara
climate
Fennec
cold pool outflow
meteorology
mineral dust
aerosols
met office unified model
low-level jet
dust emission
winds
SEVIRI

Mineral dust is one of the most abundant atmospheric aerosols and has a wide range of impacts on climate, meteorology, health and biogeochemistry. North African sources are responsible for about half of the total atmospheric burden, peaking as an emission source in the boreal summer months of June, July and August. In-situ data from the Fennec observation campaign of 2011 and 2012 indicates that cold pool outflows (CPOs) from convective downdrafts are the primary meteorological driver of these summertime emissions, followed by nocturnal low-level jet (LLJ) breakdown, both mesoscale phenomena which numerical models struggle to represent faithfully. Very few surface observations are available to characterise these emission mechanisms, however, and the extent to which Fennec observations are representative remains unclear. Satellite data from the Spinning Enhanced Visible and Infrared Imager (SEVIRI) offers both the volume of data and resolution to observe emission mechanisms on the long term.
In this thesis, two sets of automated algorithms are applied to 14 years of summertime SEVIRI data, the first of which categorises automatically identified and tracked dust by emission mechanism and the second of which tracks and characterises dust-laden cold pool outflows. CPOs account for 82% of the total observed dust and 88% at the point of emission in the central and western Sahara during boreal summer, which is the highest estimate yet of their contribution. Whereas CPO dust is widespread and the majority of dust source regions are primarily CPO-driven, LLJs dominate a small number of hotspots such as the Tidihelt Depression. CPOs are far-reaching, with 22.5% travelling over 300 km. They also follow a clear diurnal cycle which favours emissions in the late afternoon and evening. Unlike dust emission, CPO frequency peaks in August in southern Algeria.
In the final component of the thesis, satellite observations are used to support a Met Office Unified Model experiment diagnosing the role of orography in driving dust-emitting LLJs over central Algeria. Fluvial drainage from mountains is thought to contribute erodible sediment to western Saharan dust sources, but their effect upon emission mechanisms there is untested. Removing the Hoggar mountains reduces LLJ emission frequency by approximately 30% as an elevated heating anomaly helps sustain the strong pressure gradient driving low-level winds across the region in summer.
This thesis offers a meteorological perspective on satellite dust source maps, showing the contribution of erosivity to known summertime emission hotspots on climatic timescales. The fact that most central and western Saharan dust sources are predominantly activated by CPOs poses a challenge for numerical modelling of the dust cycle given the inadequate representation of downdrafts in models with convective parameterization.
Memory, implication and moral injury in the work of Vasilii Grossman and Heinrich Böll
Keywords: Jewish studies
Trauma studies
Comparative literature
German literature
Complicity &amp; implication
Memory politics
Holocaust studies
Perpetrator studies
Böll, Heinrich
Moral injury
Soviet literature
Grossman, Vasilii
Russia
Germany
Twentieth century history

This thesis compares the work of the Soviet-Jewish author Vasilii Grossman and the West German Nobel Laureate Heinrich Böll in the context of memory studies. It particularly analyses these authors’ fictional representations of the Stalinist and National Socialist regimes, predominantly in texts written after 1945. In contrast to traditional approaches to the study of post-atrocity fiction that focus on depictions of victimhood and psychoanalytic notions of trauma, this project highlights the need to consider the ways that literature thematizes morally ambiguous experiences of historical violence that do not sit comfortably into categories of ‘victim’ and ‘perpetrator’. To do so, the thesis critically draws on and develops two theoretical prisms through which to compare Grossman’s and Böll’s works. First, the concept of ‘implication’, which denotes ambiguous and indirect forms of involvement in structural violence (Rothberg 2019). Second, the notion of ‘moral injury’, which highlights the psychological consequences of committing, witnessing or failing to prevent an act that transgresses the individual’s personal moral code (Litz et al. 2009; Pederson 2021). These lenses provide a transformational means of studying Grossman’s and Böll’s literary approaches by elucidating their underappreciated focus on reckoning with ambiguous types of association with historical violence. On the one hand, they highlight the authors’ shared preference for multi-vocal narratives that emphasize the complexity of individual perspectives on the past. On the other hand, they show the writers’ similar broader conceptualizations of memory, which cast remembrance of as an ever-evolving, critical task that begins with the individual. Overall, the analysis reveals not only fresh insights into Grossman’s and Böll’s works, but also new avenues for broader comparison between post-National Socialist German and post-Stalinist Russian literatures and for the study of memory literature across contexts.
Clinical decision making in uncertainty; an ethnography of a complex intervention in the ambulatory emergency care setting
Keywords: Ethnography
Clinical Decision-Making
Emergency Care
Ambulatory
Complex Intervention
Clinical Uncertainty

Clinical Decision Making in Uncertainty; An Ethnography of a Complex Intervention in the Ambulatory Emergency Care setting
Objectives:
AEC (Ambulatory Emergency Care) provides acute assessment and treatment in the community for acutely unwell complex older patients, with patients staying in their own homes overnight. The investigation aimed to understand the Clinical Decision-Making of the senior clinicians in the AEC environment as an example of working in Clinical Uncertainty.
Methods:
Three AEC sites were purposively sampled to recruit twelve clinicians with backgrounds in Geriatrics, General Practice, Emergency and Acute Medicine. This qualitative investigation used focused ethnography within a case study approach to understand the decision-making processes in the context of the AEC environment. Observation during an AEC shift was complemented by informant interviews. A framework approach to thematic analysis used “a priori” and data derived codes to develop explanatory themes. Ethnographic principles of constant comparison and Cognitive Task Analysis were used to evaluate the clinicians’ decision-making processes for index patient cases.
Findings:
The work of AEC is complex negotiated distributed team-based decision-making to deliver an individually tailored care plan for patients with urgent healthcare needs suitable for out-of-hospital management. Key decision-making stages included triage, diagnostic, management and prognostic decisions. Variation in the delivery of these components was achieved through negotiation and individual tailoring. The participating AEC clinicians had a diverse background training and were boundary spanning individuals with cognitive flexibility and contextual adroitness. Clinicians mitigated the cognitive load of working in urgent care settings by altering their tasks, referral thresholds and clinical behaviours. Effective team working was enhanced by team reflexivity. Team based decision-making was required to manage the complexity and uncertainty of working in the AEC environment.
Conclusions:
This critical example of AEC decision-making demonstrates how complexity, negotiation and teamwork affect clinicians working in urgent care environments with high clinical uncertainty and cognitive load. These findings could inform the development of medical training curricula, interdisciplinary working and health service design.