VictorJuiz/thesis huggingface dataset:
In search of citizens in Citizennagar: The politics of contingent citizenship among the survivors of 2002 Gujarat riots in India
Keywords: Indian Muslims
IDPs in India
biopolitics
citizenship theory
gendered citizenship
Muslim youths
communal riots

This thesis attempts to look at the question of Muslim citizenship in the aftermath of Hindu-Muslim violence in India. With the advance march of Hindu nationalism in India, when media and academic studies increasingly identify Muslims as second-class citizens, very little work has been done to show what this second-class citizenship actually looks on the ground. In my work, I go beyond the legal understanding of formal citizenship, or membership of a nation and look at the quality of substantial citizenship, understood through lived experiences of Muslims in India. Though we have considerable literature on the causal effects of these riots, or the role of Hindu nationalism in such violence and scholarly work on the questions of justice and reconciliation for the Muslim survivors, we know very little about how these riots influence their experience and expectations of citizenship. There is also lack of work on the lives of women survivors of these riots, in my thesis whose path to recovery and quest for citizenship is different than Muslim men.
Drawing on sixteen months of fieldwork among the survivors of the 2002 Gujarat riots who live in the outskirts of the Ahmedabad city, I ask how the politics of contingent citizenship can be situated in the aftermath of Hindu-Muslim conflict in India. I explore the notion of contingent citizenship in my work through the situated analysis of the lives of Muslim survivors in the aftermath of 2002 violence. In this process, I find that the political subjectivity as a citizen is contingent upon negotiations with multiple actors, local specificities and position within fuzzy social dynamics. As working with conflict survivors require attention to complex ethical issues, I used novel methodological approaches such as activist anthropology. In this process, my thesis provides rooted analysis that challenges both the present and the past on the question of Muslim citizenship in India.
The Roman public baths of Central Italy during the Imperial period: an architectural study
Keywords: Euergetism
Construction materials
Architectural design
Italy
Water management
Baths
Heating systems

This thesis considers the architecture and technology of the public, urban baths of Central Italy during the Imperial period (27 BC – AD 250), but excluding the well-preserved and better-known examples of Rome, Ostia and Pompeii, which have dominated the discourse on Italian baths for far too long. Using data from ca. 70 bath buildings, gathered together for the first time, the thesis tackles the design of baths and of bathing rooms, the selection and use of construction materials, the management of water within the baths, and the selection of technological devices for their heating. The question of the funding of baths is considered through the physical aspect of the epigraphy, and comparison with the bathing landscape of Rome, Ostia and Pompeii, the rest of Italy, and selected Roman provinces, is drawn. Finally, the thesis considers the role of the different actors in the building process—the builders, the baths specialists, the architects, the commissioners—and their respective influence in the architectural outcome.
The thesis reveals how economic considerations and local conditions underlaid almost every step of the construction, from the selection of construction materials for the structure and the heating systems, to the strategies of water management and use in the baths; at the same time, it shows how the standardisation of heating systems technology and the use of blueprints for individual rooms simplified the planning and construction processes. This streamlining of the construction of baths leads to arguing that a percentage of the municipal baths offered by benefactors were almost ‘run-of-the-mill’ benefactions. This picture does not preclude the existence of profit-driven technological creations, original architectural room shapes, and expression of some benefactor’s personal interest in the architectural outcome of their bath benefaction.
Endogenous fluctuations in game theory and macroeconomics
Keywords: Best reply structure
Learning
Game theory
Macroeconomics
Non-linear dynamics
Synchronization
Endogenous fluctuations
Networks
Business cycles

At all scales, economies undergo substantial fluctuations instead of changing smoothly over time. There exist two alternative views about these fluctuations. According to the first view, fluctuations are caused by exogenous noise. Absent noise, economies would return to stable stationary states. The second view argues instead that such stationary states are unstable, and economies endogenously fluctuate following limit cycles or chaotic attractors. Endogenous fluctuations would occur even without noise. It is not yet clear which of these two interpretations most closely describes economic reality, but it has fundamental intellectual and policy implications. This thesis presents theoretical arguments in favor of the second view, in both micro- and macro-economic systems.
In the first part, we study the smallest scale at which these two alternative views can be compared. This is a normal form game repeatedly played by two players who learn from their mistakes and form beliefs about their opponents' future play. Under the exogenous view, players would converge to a Nash equilibrium, and strategic fluctuations would only be caused by behavioral noise. The endogenous view argues instead that strategic dynamics may fail to converge to equilibrium. Here, we completely characterize convergence in games with two players and two actions per player under a learning rule known as Experience-Weighted Attraction. We also introduce a theory that we call "best-reply structure" to approximately characterize convergence in games with two players and an arbitrary number of actions. Our results show that non-convergence and so endogenous fluctuations are more common in games than what might be thought.
The second part of this thesis studies the largest scale of economic fluctuations, namely business cycles in macroeconomic systems. The two views propose different mechanisms to explain correlation, or comovement, of business cycles across economic sectors and across countries. The first view argues that comovement is caused by the propagation of shocks exogenous to the economy, such as political decisions and natural catastrophes. According to the second view, comovement is instead at least partially caused by the synchronization of non-linear dynamics that describe the business cycle. Here, we introduce a demand-driven model of endogenous business cycles in which synchronization occurs through input-output linkages. We develop a theory that mathematically illustrates the interplay between synchronizing non-linear dynamics, shock propagation and network structure. While exogenous business cycle models have difficulty to generate a level of comovement that is as high as in the data, synchronization of endogenous business cycles generates much stronger comovement, potentially solving long-standing puzzles in macroeconomics.
Forming medieval dominicans: the reappropriation of Augustine’s rule in Humbert of Romans’ Expositio regulae beati Augustini
Keywords: Humbert of Romans
middle ages
Dominican order
Dominican friars
mendicant orders
rule commentaries
Augustine of Hippo
medieval history

This thesis closely examines an understudied but widely-circulated medieval work known as the Expositio regulae beati Augustini (Commentary on the Rule of Augustine) composed by Humbert of Romans (c. 1200–77), the fifth Master of the Order of Friars Preachers (Dominicans). More specifically, it considers the historical context and controversy that prompted Humbert to write the Expositio, its relationship to the internal and external challenges facing the friars, and the extent to which Humbert consciously reinterpreted Augustine’s Rule in order to shape the behaviour and institutional culture of the friars during a crucial stage in the consolidation of the Order’s self-understanding and collective identity.
While the Expositio has typically been interpreted as an apologia in defence of the Rule’s merits, its role as a tool of socialisation aimed at creating a corporate culture and inculcating a sense of distinctiveness has not yet been thoroughly explored. Building upon the work of other scholars, this thesis provides an extended examination of the Expositio, scrutinising the Expositio not only in light of its immediate context but also as part of the long reception history of Augustine’s Rule in the Middle Ages. Along with seeking to better understand Humbert’s goals in authoring the text, the contents of the Expositio are also examined with different questions than have typically been asked, probing their role in shaping the social behaviour, discipline, and self-policing of the friars. Finally, consideration is given to its historical impact, which appears to have been greatest long after Humbert’s death, during the ‘observant movement’ of the late-fourteenth and fifteenth centuries. Evidence also suggests that the Expositio was widely read outside the Dominican Order during this period, shedding further light on the reception history of Augustine’s Rule.
Functional characterisation of a novel heterozygous mutation in the transcriptional activation domain of the human FOXN1 gene
Keywords: thymus
T lymphocytes
Immunodeficiency
forkhead
FOXN1

The competence of the human body to fight infections relies on lymphocytes, which differentiate in the thymus, a primary organ of the immune system. There, thymic epithelial cells (TECs) have a unique role to instruct developing T lymphocytes to discriminate self-proteins from foreign pathogens and react only against the latter. The development, function and maintenance of TECs are primarily dependent on the transcription factor FOXN1, which acts as a master regulator of the thymus organogenesis and maintenance. Its loss of function results in athymia followed by severe immunodeficiency and is the molecular cause of the “nude” phenotype in humans and mice. Despite its crucial role in thymic development, very little is known about the molecular mechanism of its function.
We have recently identified 3 individuals that presented, from as early as a few months of life, with significant lymphopenia, reduced frequency of naïve T cells, absent T cell receptor excision circles (TRECs) and a lack of radiographic signs of thymus tissue. Surprisingly, these individuals were otherwise clinically healthy. Each was heterozygous for a deletion in the genomic sequence encoding the C-terminus of FOXN1 thus causing a frameshift and consequently a premature stop at amino acid 550, leading to a significantly shortened protein (designated Δ550).
Using both in-vitro and in-vivo models that mimicked the heterozygous patients we explored how a co-expression of the wild-type and mutant FOXN1 proteins compromise thymus development and function. Using RNA-seq coupled with ChIPSeq we explored differences in gene expression regulated by the two proteins. We also employed mass-spectrometry proteomics analysis followed by CRISPR arrayed screening, to reveal, to our best of knowledge for the first time, the molecular interactome of FOXN1 and how the Δ550 mutation may interfere with the binding of these interaction partners. With advanced microscopy we showed that FOXN1 participates in the formation of nuclear bodies, essential for its activity as a transcriptional regulator. Finally, we studied the impact of the Δ550 mutation on TEC differentiation and function in a mouse model heterozygous for a mutation equivalent to that of human Δ550. Taken together our studies elucidate aspects of the molecular mechanism by which FOXN1 operates and provide a molecular understanding on how heterozygous FOXN1 mutations can lead to pathologies.
Prime ideals of Iwasawa algebras over solvable groups
Keywords: Rigid geometry
Valuation theory
Two-sided ideals
Iwasawa algebras
Compact p-adic Lie groups

In this thesis, we will explore the non-commutative Iwasawa algebra OG of a uniform pro-p group G over the ring of integers O of a finite extension K of Qp. Our aim is to explore the prime ideal structure of OG, and our ultimate goal is to prove that all prime ideals have a standard form for which we have a complete classification. We will focus on the case where G is solvable, and we will divide the problem into two cases, prime ideals containing p and prime ideals not containing p.
In the former case, we may quotient out by p and study the mod-p Iwasawa algebra kG, where k is the residue field of K. For G nilpotent, the classification in this case was completed by Ardakov, using the theory of Mahler expansions of continuous automorphisms of G. In the first half of this thesis, we will recap this theory, and show how it can be generalised to complete the classification for prime ideals in kG for G an abelian-by-procyclic group.
In the latter case, we may tensor with K and study the rational Iwasawa algebra KG. The theory of Mahler expansions ultimately fails in this case, so we will instead explore methods involving p-adic representation theory. We focus on the case where G is nilpotent abelian-by-procyclic, and we will complete the classification for faithful primitive ideals of KG in this case for p > 2. Our main technique will be to study the representation theory of the completed enveloping algebra of the associated Lie algebra L of G, and to describe all primitive ideals of this algebra using a class of canonical representations.
Facial detection of genetic disorders
Keywords: face interpolation
transfer learning
average faces
bias removal
face embeddings
rare genetic disorders

An estimated 400,000 children are born every year with rare genetic disorders that significantly affect their quality of life. Early detection and intervention can significantly improve the quality of life of these children. Craniofacial characteristics contain highly useful information for clinical geneticists for diagnosis. This thesis investigates the use of computer vision to aid in the automatic detection of genetic disorders from ordinary facial photographs. This is a non-trivial task, in part due to patient privacy concerns and the scarcity of training data. In the following, we present several approaches to overcome these challenges.
First, we present a method for creating realistic-looking average faces for individuals sharing a syndrome. These averages remove identifiable features, but retain clinically relevant phenotype information and preserve facial asymmetry. This procedure is completely automated, removing the need to expose patient identities at any point during the process, and could be used to help facilitate facial diagnosis in clinical settings. We also investigate creating transitions between averages and exaggerated caricature faces to highlight phenotype differences between patient groups.
Second, we investigate the classification of eight genetic disorders with shallow and deep representations. We compare shape and appearance descriptors based on local and dense descriptors and report significant improvements upon previous work. Furthermore, we made use of transfer learning and part-based models to train convolutional networks for syndrome classification. Our results show that deep learning can be used in the context of classifying genetic disorders, and is superior to shallow descriptors, despite small training datasets.
Neural networks are prone to learning biases present in training datasets and basing their decisions on them. This is particularly relevant for training on small datasets, as is the case in the domain of genetic disorders. We introduce a bias removal algorithm that aims to overcome this challenge. We report three distinct contributions. First, to ensure that a network is blind to a known bias in the dataset, second, to improve classification performance when faced with an extreme bias, and third, to remove multiple spurious variations from the feature representation of a primary classification task.
Lastly, we introduce a novel image augmentation method for learning a deep face embedding, the “Interpolated Clinical Face Phenotype Space”, that aims to describe clinically relevant face variation. Our contributions are two-fold: 1) Interpolations between faces that share a class improve deep representation training from small datasets. 2) Between-class interpolations that model the space between classes improve the generalisation performance of the deep representation to unseen syndromes.
Tracking chromatin dynamics and bimodal foxd3 mechanism on neural crest gene regulation in vivo
Keywords: gene regulation
-omics
Neural crest
embryogenesis
zebrafish

The neural crest (NC) is a transient embryonic stem cell-like population characterised by its multipotency and broad developmental potential. The core NC transcription factor foxd3, known to mediate late NC lineage decisions via transcriptional repression, is also pervasively expressed in the pre-migratory NC progenitors, where its putative role remains elusive.
To elucidate the mechanistic and temporal mode of foxd3 action, we analysed its genomewide binding profiles across multiple stages of zebrafish development. To this end, we have developed and used our novel biotin ChIP-seq approach allowing to specifically biotinylate factors of interest, such as foxd3 protein, in vivo. Foxd3 binding maps interpreted within the context of NC-specific transcriptional and epigenomic profiles of foxd3-mutant and control cells reveal that foxd3 acts bimodally throughout the NC ontogeny. We showed that first foxd3 functions globally as a pioneer factor to prime the onset of NC specification and migration genes by re-arranging their chromatin landscape. Strikingly, foxd3 then gradually switches from an activator to its well-described role as a transcriptional repressor and potentially uses different partners for each role.
By employing two enhancer reporter zebrafish lines, imaging and -omics tools, we have also shown that auto-regulation of foxd3 gene locus is involved during early cell-fate decisions and embryo patterning. In the cranial embryo regions, positive auto-regulatory foxd3 feedback is driving foxd3 expression that is needed for the NC and nervous system development. This auto-regulatory loop is ensured by a set of foxd3 cis-regulatory elements that exhibit NC-like regulatory signatures. Contrarily, foxd3 is auto-regulated by a different set of enhancers and, as a result, is expressed to lower levels during the apparent neuromesodermal progenitor specification in the caudal embryo regions.
Taken together, this thesis demonstrates that foxd3 needs to be tightly auto-regulated during early cell lineage decisions. Also, later in the NC development, foxd3 switches from a chromatin activator to a repressor in order to maintain NC multipotency and define its cell fates.
The nature of the atonement in Athanasius
Keywords: Athanasius
patristics
history of theology
atonement

This research investigated Athanasius’ understanding of the atonement. It first orientated the reader by defending the category of ‘atonement’, briefly outlined Athanasius’ context, the goals of the study, and defended the use of a theological and textual approach rather than a historical and narrative methodology. It then proceeded by means of a sustained reading of substantial extracts from Athanasius to establish his understanding of the atonement. These explorations were organized topically, beginning with his views on creation and humanity, and then turning to his account of the fall and its progress and effects, before then examining his atonement views with regards to creation, the image, the law, and the demonic. The final chapter then summarized the main findings and explored the most important of these at some length.
There are three major findings from this research. The most evident, because it has informed the structure of the dissertation, is that Athanasius’ atonement thinking can only be understood against the backdrop of his exposition of creation, humanity, and the fall, rather than another theological topic such as the Trinity. The second is that Athanasius’ thinking on the atonement reflects fundamental principles and assumptions evident in some of his most significant topics, suggesting that this topic is also close to the heart of his theological vision. Finally, that his concept of the atonement is multivalent rather than monistic, with more than one mechanism, or ‘model’, on display. Three of these, creation, image, and law, can be compared to each other and their atoning mechanisms can be shown to operate by principles that vary along differing axis. The fourth, the demonic, is more radically different still, acting as an intensification and personification of the problem and solution matrix of the previous three categories. Athanasius’ atonement thought is irreducibly pluralistic.
Deformation and strain concentrations in coarse-grained alpha-uranium
Keywords: neutron diffraction
mechanical testing
digital image correlation
uranium
strain concentration

This thesis presents an experimental characterisation of the deformation of coarse-grained cast alpha-uranium to assist the development of crystal plasticity finite element (CPFE) models.
Uranium exhibits elastic and plastic anisotropy and deforms heterogeneously via multiple slip and twinning modes. Strain concentrations that develop in the deforming grains may initiate fracture. There is an industrially-motivated drive to perform CPFE simulations that incorporate the unique properties of uranium to allow a better understanding of the conditions leading to fracture. Experiments have been performed by the author to provide data for calibration and validation of a CPFE model for cast α-uranium.
Time-of flight neutron diffraction was used to measure internal lattice strain development and texture changes during in-situ tension and compression. The coarse microstructure raises experimental challenges these are solved in a subsequent experiment. Deformation twinning causes a lattice reorientation that is detectable as a macroscopic texture change. A novel analysis was performed allowing active twinning modes to be identified from the texture changes. Twinning accounts for the observed tension-compression asymmetry in the material.
Digital image correlation (DIC) was used to measure the full-field surface strains during tensile deformation of cast uranium. The measured strains were highly heterogeneous the locations of strain concentrations were related to the crystallographic orientations measured with electron backscatter diffraction (EBSD).
The data generated in this thesis are found to be suitable to calibrate and validate a crystal plasticity model of cast α-uranium.