VictorJuiz/thesis huggingface dataset:
Delineating the Gawain-poet: myth, desire, and visuality
Keywords: medieval manuscripts
visual art
the Gawain-poet

This thesis adopts an interdisciplinary approach, drawing on literary, art historical and textual sources to examine how the act of looking, images, and artistic and textual creation are both dramatized and problematized in the works of the Gawain-poet: Pearl, Cleanness, Patience, and Sir Gawain and the Green Knight (with some discussion of St Erkenwald, a work often attributed to the same author). Analyzing in detail the texts and illustrations in the Gawain-manuscript (British Library, Cotton MS Nero A.x), the thesis argues that the poet weaves together classical and biblical narratives, along with exegetical and iconographic traditions, in shaping his distinctive reflections on the use and making of images, body and performance, in response to late fourteenth-century religious controversies.
The thesis starts by tracing a network of ideas about gaze, sin, body and text through late-medieval biblical and mythographical texts and images. Working text-by-text through the poet’s oeuvre, it then discusses the use of Ovidian materials and the motif of metamorphosis in his complex meditation on ethical and specifically gendered practices of reading, writing and looking. It concludes by assessing the poet’s idea of poetic creation and his own role as a creative artist. In doing so, it suggests that the poet’s self-conscious artistry works together with a consistent emphasis on humility in human’s relations with the divine. The thesis contributes to a growing scholarly interest in the Gawain-illustrations, and a developing focus on visuality in studies of late-medieval devotional and literary works. By linking the analysis of classical/biblical intertexts, visual traditions and the manuscript’s own illustrated texts, it suggests a fresh area of study for the Gawain-poet and his milieux.
Identification of novel genes involved in brain abnormality syndromes using next generation sequencing
Keywords: genetics
exome sequencing
medical genetics
next generation sequencing
brain abnormalities
brain malformations
NGS

Since the 1980s there has been a steady increase in the number of genes identified which play a role in human disease. The Human Genome Project and arrival of Next Generation Sequencing (NGS) have helped accelerate the rate of discovery such that the recent update of the Human Gene Mutation Database (HGMD) lists over 140 thousand genetic variants linked to human disease. However, causative genes have only been identified in half of the 7000 rare monogenic disorders. It is predicted that within 10 years the majority of disease-causing genes will be identified. In many ways the era of next-generation sequencing has become the “gold rush” of disease gene discovery.
The aim of this thesis was to demonstrate the validity of an NGS approach to identify novel disease genes associated with brain abnormality phenotypes. In a cohort of 23 families with a range of brain abnormality phenotypes, novel disease genes were found in 2 families and there was an overall clinical diagnosis rate of 38%. The results from this thesis have already expanded the spectrum of brain abnormality mechanisms to include the gene PGAP3. The strategy outlined will become part of the clinical framework for the diagnosis and identification of brain abnormality syndromes with NGS.
Control of the unidirectional motor in Rhodobacter sphaeroides
Keywords: clutch
flagellum
flagellar motor
chemotaxis
rhodobacter
brake

The control of the flagellar motor in Rhodobacter sphaeroides was investigated. Unlike most flagellar motors which are controlled by reversing the direction of rotation, the R. sphaeroides motor is controlled via a stop-start mechanism. Advanced optical microscopy was employed alongside genetic, biochemical, and behavioural techniques.
High-resolution measurements of rotating beads on flagellar stubs revealed that the R. sphaeroides motor is similar to its E. coli counterpart, rotating counterclockwise at comparable torques/speeds (1,300 pNnm/rad at stall torque), and exhibiting transient step changes in speed. The mean stop duration, mean stop frequency (number of stops per s), and run bias (fraction of time spent rotating) of wild-type at steady-state were 0.66 ± 1.01 s, 0.31 ± 0.19 s-1, and 0.80 ± 0.20, respectively.
Manipulating signal inputs to the motor genetically, or by exposing cells to chemotactic stimuli revealed that (i) without chemotactic stimulation the motor rotates continuously, (ii) phosphorylated CheYs are required to stop the motor, and (iii) the chemotaxis system cannot control the speed of rotation of the motor (termed chemokinesis) as previously reported. Complementation studies revealed that CheY3, CheY4, and CheY5 are functionally equivalent. The copy numbers per cell of important CheYs were found to vary greatly under the conditions tested (<1,000, ~3,000, ~60,000 for CheY3, CheY4, and CheY6 respectively).
To determine how CheY-P binding causes the motor to stop, external force (viscous flow or optical tweezers) was applied to chemotactically stopped motors. CheY-P binding might either cause the torque-generating units to disengage from the rotor, analogous to a clutch, or trigger the rotor to jam, analogous to a brake. The rotor resisted re-orientation during a chemotactic stop implying that the motor was held in a locked state. The value of torque resisting forward motion (keeping it locked) was estimated to be 2-3 x stall torque (2,500-4,000 pNnm/rad).
Furthermore beads attached to flagellar stubs stop at fixed angles for several seconds, showing no large-scale Brownian motion. Step analysis revealed that these stop events occur at 27-28 discrete angles around the motor, which most likely reflect the periodicity of the rotor (i.e. copies of FliG). This represents the first experimental resolution of steps in the rotation of a wild-type bacterial flagellar motor with a full complement of torque-generating units.
Shōbōdan: an ethnographic history of Japan's community fire brigades
Keywords: Suwa
Japan
firefighters
voluntarism
fire brigades
civil society
volunteering

This thesis describes Japan's modern system of community fire brigades, a federated civilian paramilitary organization dedicated to localized fire prevention and response with a current active membership of over 800,000 men and women. Auxiliary firefighting institutions in Japan have had comparatively high rates of participation vis-à-vis those of other nations, but are now facing acute recruitment difficulties in the face of increased competition from alternative venues for civic engagement since the mid-1990s. This suggests both the tractability of civil society as an extra-statal sphere of institutionalized social organization as well as the inherent pluralism of its vernacular expression.
I demonstrate that the nationalization of the fire brigade system in 1894 was predicated on the existence of an autonomous and normative sphere of age-graded practices of inter-household mutual aid in the villages of Tokugawa Japan. The gradual absorption and redirection of these practices into the nation-building projects of the Meiji state and its successors realized the creation of a functional emergency service organ with universal penetration at minimal expense. Nevertheless, drawing on Maurice Bloch's theory of rebounding violence, I argue that the secular rituals and state symbolism used to achieve this encompassment have conferred a legacy of structural ambivalence between civility and uncivility that continues to inform perceptions and representations of the brigade in public discourse. It follows that the phenomenon of organizational aging and questions of recruitment and succession should be seen as ideological in nature, rather than as simple indices of wider demographics or social transformation.
This thesis is based on data collected during twenty months of research in Japan between 2008 and 2010, including eleven months of continuous participant observation with a brigade in Suwa District, Nagano Prefecture. Extensive ethnographic interviews with local firefighters, community members, and town officials are supplemented with data from primary and secondary historical sources, including online discussion forums. This thesis contributes to the literature on local voluntarism in Japan, as well as to the wider anthropological project of documenting non-western models of civil society.
The modulation of information processing by reward expectation and spatial attention
Keywords: reward expectation
perception
cognition
spatial attention
event-related potential

Reward expectation and spatial attention both exert powerful control over behaviour and modulate neural activity. The experiments in this thesis aimed to chart the dynamics of reward expectation effects across the time course of information processing and examine the relationship between reward and attention. Experiments 3.1 and 3.2 parametrically manipulated reward magnitude in the presence or absence of attention and demonstrated reward could influence reaction time (RT) under conditions of time pressure. Experiments 4.1 and 4.2 independently varied reward and spatial probabilities and illustrated independent and interactive effects of reward and attention at late stages of cognitive processing (the P300 potential), as well as modulation of detection sensitivity (d') by reward under conditions of uncertainty when reward was able to work through feature-based attention. The experiment of Chapter 5 cued reward and attention trial by trial and showed under these conditions, not only could reward influence late stages of information processing, but expectation of reward reduced peak latency of the visual N1 potential. Reward and attention also modulated motor preparation with both independent and interactive effects. The experiment of Chapter 6 examined the dynamics of reward association with task-relevant targets and irrelevant distracters during visual search and demonstrated that task-irrelevant but motivationally-salient distracter items could capture attentional resources away from the target, guided by endogenous reward association alone. The experiments of this thesis demonstrated the ability of reward expectation to modulate both behaviour and multiple stages of information processing, with effects predominantly independent from those of attention. Reward could influence processing from early visual analysis and target detection stages. Interaction between the two systems occurred at late processing stages, whereby reward and attentional information may have been integrated to provide a cohesive representation of the stimulus given the current environmental conditions.
Minds of the madrasa: Islamic seminaries, the state, and contests for social control in West Bengal and Bangladesh
Keywords: Religious Education
Madrasas
Madrasa Reform
West Bengal
South Asia
Bangladesh
Madrasa Education
India

This qualitative study analytically compares State-madrasa and inter-madrasa relations in Hindu-majority West Bengal and Muslim-majority Bangladesh. It uses Migdal’s State-in-Society approach to explain the nature and bases of these interactions as expressed in three interrelated arenas: educational, organisational, and political. The central question addressed in the educational arena is why some madrasas (recognised madrasas) respond positively to State-initiated incentives for reform while others (unrecognised madrasas) reject the same. In resolving this puzzle, the study seeks also: 1) to classify madrasas in each setting according to their relative thresholds for engagement with the State; and, 2) to identify how, and to what extent, the State can extend the appeal of its reform scheme to unrecognised madrasas.
In the organisational arena, the study focuses exclusively on those madrasas that reject State-initiated reform, asking how they organise independently of the State. A key objective here is to determine how inter-madrasa relations vary between Muslim-minority and –majority contexts, and which specific aspects of the State’s policies most encourage such variation.
The study’s third empirical section examines State-madrasa relations as expressed through two phenomena in the political arena. The first phenomenon involves the politicisation of recognised madrasas by the State (represented by political parties and their student wings). The study explicates the mechanisms through which this politicisation occurs, identifies the factors facilitating/impeding such politicisation, and assesses the impact of this politicisation on the political allegiances of individual students. The second phenomenon sees representatives of unrecognised madrasas (attempting to) reach into the State complex by launching madrasa-based political parties. The study focuses on this phenomenon to gauge the relationship between a madrasa man’s careers in the educational, organisational, and political arenas: To what extent can madrasa-based political entrepreneurs leverage influence wielded in the educational and organisational arenas towards success in the political arena? And do those who succeed in entering the State complex use this opportunity to promote the societal interests they represent in the educational arena, or in pursuit of increased authority in the organisational realm?
International assistance and cooperation in access to essential medicines: a study of the issues in governance and implementation
Keywords: International law

International assistance and cooperation for access to essential medicines can be established as an obligation of developed countries based on international human rights law and an array of authoritative guidance. The research aim of this thesis was to understand how developed countries can be influenced to meet this obligation under the current international order with a view to the improvement of international governance over this issue.
To address this aim, this thesis conducted an analysis based on three sub-questions: (1) what is the current international order governing access to essential medicines, (2) what are the processes and mechanisms that the international order has used to influence developed countries and how have the countries responded, and (3) is there an alternative model to the current governance structure that could lead to improved implementation of international assistance and cooperation by developed countries.
The analysis of the international order involved a study of the World Health Organization and its interactions with the World Trade Organization and the development-related institutions involved in access to medicines (i.e. the World Bank, UNAIDS, and the Global Fund). The lack of leadership by the WHO in governing access to essential medicines has led to significant tensions between the institutions in the form of conflicts, overlaps, and other issues.
The thesis proceeds with a country case study to understand how states interact with the international order and how they can be influenced towards norm implementation. It was determined that the international order possesses an influential array of ‘socialization’ methods that have been successful in inducing states toward norm compliance (when backed by the support of international NGO networks and domestic pressure). However, the level of disarray that remains in the international order continues to have a negative effect on international assistance and cooperation.
The thesis concludes with an analysis of emerging changes to the current system of governance over access to essential medicines and considers whether these changes might bring an improvement to developed country support of access to essential medicines.
Towards ultrafast photoassociation of ultracold atoms
Keywords: ultracold
photoassociation
ultrafast
quantum

In the ultracold regime, where the interactions between atoms become quantum mechanical in nature, we can investigate the fundamental properties of matter. A natural progression from the catalogue of pioneering experiments using ultracold atoms is to extend the size of our quantum system by producing ultracold molecules in prescribed low-energy internal states. Techniques for cold molecule production are split into two methods: direct and indirect cooling. While direct cooling methods have yet to realize ultracold temperatures, collisional relaxation in the molecules leads to low internal energy states. By contrast, indirect cooling — the association of molecules from pre-cooled atoms—has produced a range of molecules at ultracold temperatures; the challenge with this technique is to control the internal state.
This thesis concentrates on a technique that is complementary to those already in existence: ultrafast photoassociation. Key to this technique is the formation of time non-stationary wavepackets in the excited-state in order to improve FranckCondon overlap of the excited state with deeply bound ground-state vibrational levels. A pump-probe experiment was designed and built to demonstrate the formation of bound excited-state dimers. In this work we show that the initial state from which the wavepacket originates is of critical importance to the evolution of excited-state population. We find that the internuclear separation of the wavepacket produced in a rubidium magneto-optical trap is too large to observe coherent oscillations in the excited state. The implications of this are discussed along with recommendations for future ultrafast photoassociation experiments. Consequently, a new ultracold atom apparatus was built utilizing magnetic and dipole-force trapping to increase the density of the atomic sample; this apparatus will enable future experiments combining the exciting fields of ultracold matter and ultrafast light.
A genomic approach to investigate the evolution of exophagy in Anopheles mosquitoes
Keywords: Genomics
Population Genetics
Anopheles

The development of behavioural resistance in Anopheles mosquitoes is an important threat to the sustainability of current vector interventions, which selectively target mosquitoes that are found indoors. Changes in the following behaviour have been reported in several Anopheles vectors: biting time, host preference, biting and resting behaviour. However, a critical review of the published literature reveals that behavioural resistance has not been demonstrated clearly in Anopheles, highlighting important limitations in using entomological data to investigate the evolution of behaviour.
The availability of next generation sequencing and low-cost custom genotyping technologies makes it possible to investigate behavioural resistance using genetic information as an alternative approach. Using such technologies, this thesis aims to investigate whether Anopheles vectors are evolving towards outdoor-biting behaviour ('exophagy') by examining the genetic difference between the indoor- and -outdoor population of the main African malaria vectors, An. coluzzii and An. gambiae from The Gambia and Uganda, respectively. We also investigated the role of olfactory-related genes in driving the potential genetic difference between the two populations.
We found limited divergence between the two populations overall, however close inspection identified SNPs potentially associated with outdoor-biting behaviour as well as genomic regions displaying elevated levels of differentiation between the two populations. Most notably, gustatory receptors, Gr11 and Gr12 and the odour receptor, OR1 were identified as well as, genes related to transcription, signal transduction and catalysis. We discuss the potential role of these genes in determining biting behaviour and suggest that further investigation of these genomic regions is required to confirm the early-stage divergence of indoor- and outdoor-biting Anopheles populations.
Crosstalk between histone modifications in Saccharomyces cerevisiae
Keywords: histone methylation
histone acetylation
Saccharomyces cerevisiae
transcription
histone modifications
histone H3
chromatin
crosstalk
gene expression
yeast
proline isomerisation

The N-terminal tails of histone proteins protrude from the nucleosome core and are extensively post-translationally modified. These modifications are proposed to affect many DNA-based processes such as transcription, DNA replication and repair. Post-translational modifications on histone tails do not act independently but are subject to crosstalk. One example of crosstalk is on histone H3 between lysine 14 (H3K14) and trimethylated lysine 4 (H3K4me3), a modification found at the 5’ end of most active or poised genes. In this work, Western blots and chromatin immunoprecipitation (ChIP) experiments show that different amino acid substitutions at histone H3 position 14 cause varying degrees of H3K4me3 loss, indicating that H3K14 is not essential for H3K4me3 but acts as a modulator of H3K4me3 levels. A neighbouring residue, H3P16 is also important for H3K4me3 and may operate in concert with H3K14 to control H3K4me3. These crosstalk pathways have gene-specific effects and the levels of H3K4me3 are influenced to different extents on genes that fall into functionally distinct classes. A model is proposed to explain how H3K14/H3P16 may exert these varying effects on H3K4me3 at individual genes. In addition to its ability to regulate H3K4me3, H3K14 also influences the levels of two modifications on H3K18, acetylation and monomethylation. A ChIP-sequencing experiment has shown that H3K18me1, a previously uncharacterised modification in S. cerevisiae, is widely distributed throughout the genome and correlates strongly with histone H3 levels. The potential for a functional acetyl/methyl switch at H3K18 is explored. Together, these data indicate that, with gene-specific effects, crosstalk between histone modifications may be even more complex than originally thought.
War in chronicles: temple faithfulness and Israel's place in the land
Keywords: land
Chronicles
Old Testament
temple
Hebrew Bible
war

This thesis contends that the Chronicler includes many episodes of war in his retelling of Israel’s monarchic history to demonstrate the benefits and consequences of temple faithfulness. Several scholars have long pointed out the Chronicler’s reworking of texts in Samuel-Kings to show that Yahweh rewards the good and punishes the wicked (i.e. retribution theology). Some recent scholars, however, have put forward several exceptions to this rule. The analysis of passages in this thesis demonstrates that the Chronicler maintains this cause-effect relationship with the dual themes of war and temple. To do this, it divides the various kings into different categories.
First, David belongs in a category all by himself since he (according to the Chronicler) pioneered the two most foundational elements of the temple cult (i.e. gathering all Israel and providing the building materials). For this reason, he also won many battles to secure Israel’s place in the land. The next two groups of kings either show complete faithfulness to (re)establishing the temple cult and its practices (e.g. Solomon, Hezekiah), or neglect it (e.g. Ahaz, Jehoram). Based on their attitude toward the temple, the Chronicler illustrates how they either prosper in the land through military victory, or suffer attack. The Chronicler presents mixed cases with the last two categories. On the one hand, he reports how many faithful kings (in varying degrees) support orthodox temple practices and so prosper on the battlefield. However, none of these kings persevere in their faithfulness so that either their success immediately stops or they suffer attack. On the other hand, the Chronicler also tells how two thoroughly wicked kings committed some of the worse sins in Israel’s history, yet repented after suffering swift punishment. Through all these cases, the Chronicler demonstrates that temple faithfulness always brought Israel peace and security.