VictorJuiz/thesis huggingface dataset:
Ties that bind: the role of family dynamics in the Islamization of the central Islamic lands, 700-900 CE

This study explores Islamization and conversion as a process of socialisation, one best illustrated in sources discussing daily human interaction, and argues for several nuances to the understanding of Islamization and conversion in the Islamic world. It focuses on the familial relationship as one of the most important types of social interactions that would have facilitated conversion in the central Islamic lands – the Levant, the Arabian Peninsula, Mesopotamia, and Fars during the 8th-9th centuries CE.
This thesis is based upon the concept that it is integral to the study of conversion to Islam in the 700s-800s to be aware of a variety of behaviours associated with conversion ranging from Islamization of outward actions with no religious affiliation to Islam, to full religious conversion in the 8th-9th centuries. With this variety in mind, it has found, first, that the expectations of non-Muslim wives by Muslim husbands, in particular, encouraged religious code switching. Second, even when a person fully converted, family ties often kept them within the social and ritual world of their previous tradition. Third, conversion was not always a choice; women were often passively part of a household conversion. Fourth, Christian women in some communities may have sought conversion to Islam as a way to divorce their husband and retain the potential for remarriage. Fifth, a hierarchy based upon religious affiliation and social class formed in the 9th century; a Muslim man could either marry a woman or only keep her as a concubine depending on her religion and/or status. Sixth, in the 8th-9th centuries several Muslim jurists favoured matrilineal religious inheritance over patrilineal. Seventh, baptism may have been practiced by a majority of Muslims in the 8th-late-9th centuries suggesting not only a required change in how we view Islam in the 700s-800s, but also in how we view Islamization.

Keywords: Conversion
Family Networks
Women in Islam
Code Switching
Christian-Muslim Relations
Advisor: Hoyland, R
Taylor, D
Baun, J
Community engagement for targeted malaria elimination in Lao PDR (Laos)

The emergence of artemisinin-resistant malaria in Southeast Asia has prompted malaria control programs to expedite efforts to eliminate malaria. One suggested approach is the mass administration of antimalarials (MDA) to entire target population regardless of malaria infection. MDA is one of the central components of Targeted Malaria Elimination (TME), an approach recently piloted in Laos. For MDA to be successful (leading to interruption of local malaria transmission), a high population coverage is critical. Among myriad factors, community engagement has been recognized as critical to promoting high coverage. The main aim of this study was to design, execute and assess a locally suitable community engagement strategy that can promote the uptake of and adherence to MDA. This study utilized a longitudinal mixed method approach. In addition to the local social and cultural factors, five main elements of community engagement that contributed to high population coverage were identified: 1. Stakeholder and authority engagement: a stepwise approach from central to the local level; 2. Local human resources: recruitment and training of local community members to execute TME; 3. Formative research: an exploration of the local social and cultural context to guide the community engagement; 4. Responsiveness: flexible and adaptable approach based on the demands and needs of the community and 5. Sharing control/leadership with the community: joint decision making with the community members. Various factors contributed to the high population coverage recorded in the Lao TME study (above 85%): community engagement to promote the concept of asymptomatic malaria and the rationale for MDA, baseline understanding of malaria as a health concern, perceptions that TME was worthwhile, provision of free primary health care, partnering of the research with local volunteers and authorities, building social relationship with community members and the cohesive nature of the communities that boosted the trust and participation in MDA.

Keywords: Community Engagement
Malaria, Elimination
Elements of Community Engagement
Advisor: Cheah, P
Pell, C
Mayxay, M
Day, N
Harnessing the innate immune system for improved VLP-based immunotherapy

Vaccination is deemed as the most successful intervention in public health1. As the overall life span of the human population increases and exposure to pathogens strongly decreased due to efficient vaccine programs, the accepted risks associated with prophylactic measures, such as attenuated vaccines, is substantially reduced and efforts need to be focused on the development of safer and better tolerated vaccines. Recombinant, non-replicating vaccines may therefore represent an attractive alternative. Virus-like particles (VLPs) have emerged as a promising alternative due to their excellent safety profile and remarkable immunogenicity.
Recently, the successful concept of educating the immune system to fight infectious diseases has been expanded not only to prevent but also to treat existing chronic and autoimmune diseases. VLPs are increasingly being explored as a platform for vaccines, delivery of drugs and adjuvants, and as a tool to investigate the immune system in the context of infectious and non-infectious diseases.
Here, applications of VLPs as prophylactic and therapeutic vaccines are explored. The immune response raised in response to immunisation is investigated and the findings directly translated and applied to the development of vaccines against tumours and Influenza. First, the impact on the immune response of the size of vaccine components and mode of presentation of heterologous antigens is evaluated in the context of humoral and cellular responses in a HPV tumour model. Second, the initial events in the immune response mediated by dendritic cells that lead to protective T cell responses induced by VLP-based T cell vaccines is investigated. Thirdly, the ability of VLPs to modulate humoral responses is explored and we show that appropriate TLR7 engagement is crucial for the induction of protective antibody responses against influenza.
Finally, this thesis provides insights into the immune response following immunisation with VLP-based vaccines and considerations for vaccine development.

Advisor: Bachmann, M
Agency in contemporary German cinema: Tykwer, Akın and Petzold

This thesis demonstrates that an interest in human agency is a significant trend in contemporary German cinema. It includes analyses of Tom Tykwer’s Heaven (2002) and The International (2009), Fatih Akın’s Gegen die Wand (2004) and Auf der anderen Seite (2007) and Christian Petzold’s Barbara (2012) and Phoenix (2014), which illustrate that these three directors, who belong to different traditions in German cinema, have a focus on agency in common. A theoretical framework primarily made up of scholarship by Michel Foucault, Michel de Certeau, John Fiske and Laura Mulvey illuminates the portrayals of human control in the films. Tykwer, Akın and Petzold share a sense, also articulated in post-structuralist theory and theory which followed it, of the considerable limitations on human agency, which the three filmmakers work into their films for their characters to grapple with. I show that these filmmakers are investigating how individuals can be agents within this context.
The agency which is available to the characters in the films is personal rather than political, but the narratives are situated in political milieus, which complicates the idea of contemporary cinema simply turning towards the personal. Five of the films portray a mixture of scope for action and constraint, whereas The International paints a more pessimistic picture of agency, but illustrates the problems with such a negative portrayal, and problems that filmmakers must deal with when representing human control. This thesis addresses the question of how agency is portrayed in the filmic medium, illustrating how space and place, the gaze, the human body and characters’ appearances more widely are used to convey the phenomenon visually.

Keywords: contemporary
petzold
Akın
tykwer
twenty-first century
agency
german
film
cinema
Advisor: Morgan, B
Investigating the effect of H3K4 and H3K79 methylation on gene expression noise in Saccharomyces cerevisiae

Gene expression noise, the stochastic variation in a gene’s protein level in a population of genetically identical cells, has been shown to play an important role in several biological processes. However, it is not yet understood how gene expression noise is controlled. Following Newman et al. (2006)’s work, where a library of GFP-tagged genes at COOH termini and FACS was used to analyse noise levels in S. cerevisiae for 2,204 genes, we discovered at the genome-wide level a strong correlation between H3K4 methylation, H3K79 methylation, H3K123 ubiquitylation and high levels of noise, out of 1,180 gene features. Histone methyltransferases, Set1 and Dot1 which are responsible for H3K4 and H3K79 methylation, respectively, both depend on ubiquitination of H2B on lysine 123. H3K4 and H3K79 methylation are found on the majority of genes, therefore, the aim of this work was to examine whether the correlation between H3K4 and H3K79 methylation, and noise was causal or not. The hypothesis that removing H3K4 tri-methylation would affect noise was first tested by deleting SPP1, which is encoding a subunit of the Set1 complex (Set1C). Deletion of SPP1, which primarily affected H3K4me3, developed noise and reduced gene expression in certain genes. However, deletion of SET1 had the opposite effect on noise and gene expression, at genes that were sensitive to changes in H3K4 methylation. Both of these results were consistent with the observed bioinformatic correlation. Despite the strong correlation between noise and H3K4 methylation, only ~20% of the 18 genes tested showed changes in gene expression noise with a change in levels of H3K4 methylation, suggesting that the effect is limited to certain genes. Since H3K79 methylation also shows a strong correlation with noise, further work was conducted to investigate the possibility that H3K79 methylation functions redundantly with H3K4 methylation. Interestingly, Dot1 redundantly functions with Spp1 and only at genes where the loss of H3K4me3 increases noise. The increase in noise that was observed on the loss of H3K4me3 was reduced to the wild-type level in the double knock-out of DOT1 and SPP1. In conclusion, this study provides evidence that gene expression noise may be regulated by histone methylation, particularly H3K4 and H3K79, and that Dot1 (H3K79me3) could redundantly function with Spp1 (H3K4me3).

Advisor: Mellor, J
Legal culture, legality and the determination of the grounds of judicial review of administrative action in England and Australia

This thesis studies the principle of legality in English and Australian administrative law relating to their legal systems’ legal culture and the determination of the scope of judicial review of administrative action. It demonstrates that the distinctive constitutional orders that are embedded in legal culture of England and Australia, influence the courts’ deep understanding of what legality means and covers. These different understandings result in the English and Australian courts applying different doctrinal approaches when determining the grounds of judicial review, namely, error of law, jurisdictional error, jurisdictional fact, rationality, proportionality and substantive legitimate expectations.
On the one hand, the English courts have flexibility to apply various justifications, doctrines and applications in their determination of the mentioned grounds of judicial review. These are products of the English legal culture based on the absence of a written constitution, the balancing process between parliamentary sovereignty and the rule of law, and the fluid separation of powers between court and executive. On the other hand, the Australian courts apply relatively fixed doctrinal approaches to determine these grounds under a central approach of jurisdictional error. This is because, whether empowered or limited, they rigidly follow the framework of separation of powers prescribed in the written constitution, discussed as distinctive elements of Australian legal culture.
Rather than supporting the way of one legal system over the other, this thesis upholds a comprehensive understanding of the English and Australian determination of the grounds of judicial review in the light of their deep understanding of legality and legal cultures. The implications of these methodological approaches constitute an in-depth explanation of the way common law judicial reviews are embedded in different legal systems.

Keywords: Judicial Review of Administrative Action
Legal Culture
The Principle of Legality
Advisor: Fisher, L
Search for dark matter with the LUX–ZEPLIN detector – acoustic sensor performance and detector response

The LUX-ZEPLIN experiment needs acoustic sensors to monitor the liquid xenon contained in its time projection chamber (TPC) for irregularities that could spoil a stable liquid xenon environment that is required for a dark matter search. I have developed and implemented algorithms that distinguish the occurrence of bubbling and other sounds, and I have carried out tests using a PVDF sensor and a readout system developed at Oxford; demonstrating that the hardware and analysis meet the requirements for their purpose in LUX-ZEPLIN. Acoustic sensors can be used as a veto to strengthen the fidelity of detector data.
The primary event data in LUX-ZEPLIN will come from arrays of photomultiplier tubes, which detect light emitted from recoil events in the TPC. Waveform data from TPC events will be collected through a bespoke data acquisition system. A simulation of the detector response is needed in order to ensure that reliable event analysis will be possible when the experiment starts taking data. I have constructed an analytical model of the full signal chain from the photomultiplier tubes to the digitisers, including all analogue front-end electronics and interconnecting cabling, and I created a Monte Carlo simulation software package in which I have embedded this model. I have used the model and the software to carry out simulations to evaluate the design of the LUXZEPLIN electronics readout system. The model and the simulation I have created play a central role in performing event analysis on simulated data in preparation for real data taking with the LUX-ZEPLIN experiment.

Advisor: Kraus, H
The biomechanics of the dipteran wing hinge

Dipteran insects include some of the most aerobatic animals on the planet, including species such as drone flies (Eristalis tenax) which are able to hold a steady hover in the face of environmental perturbations before executing rapid and precise manoeuvres. A deep understanding of the mechanisms of wing kinematic control that afford such abilities is vital if we are to emulate these capabilities in our own bio-inspired machines. This thesis makes use of cutting-edge techniques to visualise these mechanisms in unparalleled detail and determine how they function to control the way in which the wings move. My work here begins by documenting the mechanical interaction of two exoskeletal components around the wing hinge that forms the gear change mechanism of dipteran wing kinematic control. I show its effects on the movement of the wings and explain how the mechanism acts to bring about these changes in Calliphora vicina and E. tenax. I then move on to study another enigmatic structure near the wing hinge, the Pterale C, and argue against a role of this component in mechanically altering wing movement. Instead, I conclude that the Pterale C may be a sensory structure which informs the insect's central nervous system of the position and speed of the wing during the latter half of the downstroke. Finally, I utilise time-resolved synchrotron X-ray computed microtomography to visualise the internal musculature of C. vicina during flight, where I assert that several muscles influence wing movements by restricting the motion of wing hinge components. Throughout this thesis, the inhibition of wing motion and energy absorption pervades each mechanism. Through the application of our understanding of dipteran flight, it may be possible to design bio-inspired machines which begin to approach the aerial capabilities of these insects.

Keywords: Flight
Biomechanics
Diptera
CT
Insect
Advisor: Walker, S
Taylor, G
On the role of receptor downregulation and costimulation in shaping the T cell response

T cells are critical decision-makers in the immune system and their activation determines whether a cell or molecule constitutes a threat to the body and needs to be eliminated or whether it should be ignored and tolerated by the immune system. Many molecules that play a role in T cell activation and their interactions with each other have been identified, but an overall understanding of the decision-making processes that lead to changes in T cell behaviour remain enigmatic. We are studying human T cell activation through a combination of in vitro experimental stimulation experiments and mathematical modelling. Our minimal experimental platform allows us to systematically vary the input signals the T cell receives by modulating antigen dose, antigen affinity, stimulation time and costimulatory ligands, and by stimulating through either a TCR or a CAR. We show here that T cell activation (measured as cytokine production) shows an adaptation phenotype in response to all antigen doses and affinities. A detailed study of TCR downregulation and the incorporation into a mathematical model revealed that TCR downregulation is sufficient to explain this adaptation. The intrinsic inactivation of the T cells is contextdependent and the cells can be re-activated with a higher affinity ligand. Furthermore, we show that the inactivated cells can be re-activated when a non-stimulating pMHC is presented together with a costimulatory ligand. We generated a similar dataset for CAR T cells and showed that they can equally get desensitised by antigen and that the CAR is also downregulated depending on antigen dose and affinity, suggesting that a similar model may apply. We used the resulting mathematical model of T cell activation to predict the potential effects of costimulatory molecules on the dose response profiles, including, for example, adhesion effects or signal amplification. We then systematically stimulated T cells with ligands to CD2 and CD28 and compared the responses to the model predictions. We found that CD28 primarily lowers the threshold for T cell activation downstream of the TCR whereas CD2 showed a more complex phenotype with a strong adhesion effect combined with amplifying effects on downstream signalling.

Keywords: T Cell
TCR
Costimulation
CAR
Modelling
Advisor: Dushek, O
Transannular cascade approaches to diterpene analogues

Abstract The aim of this project is to apply the chemistry developed in our group and to extend it to asymmetric transannular methodology for the generation of different fused, diterpene like, polycyclic ring systems. Construction of these ring systems is predicated on an intramolecular Michael reaction cascade or an ionic Diels Alder reaction catalysed by chiral quaternary ammonium salts under basic phase transfer conditions. We demonstrate a rapid synthesis of the transannular cascade precursor that undergoes cyclisation producing three new stereocenters in high enantioselectivity (Scheme I & II). Furthermore we demonstrate an isomerisation of the precursor under UV irradiation obtaining all the enone Z,E isomers of the cascade precursor scaffold. We were able to obtain either a single Michael addition or a cyclisation, via transannular Diels Alder or Michael Michael cascade reaction depending on the configuration of the enones. These cascades undergo cyclisation in moderate to high enantioselectivity (Scheme II).

Advisor: Smith, M
Constant rank operators: lower semi-continuity and L1-estimates

In the first part of this work we investigate lower semi-continuity of integral functionals defined on vector fields that satisfy linear pde constraints that satisfy the so-called constant rank condition. In particular, we simplify the definition of A-quasiconvexity and characterize a class of A-free generalized Young measures by duality with A-quasiconvex functions.
In the second part we investigate linear L1-estimates, i.e., study linear (overdetermined) elliptic systems with L1-data. We extend Van Schaftingen's inequalities to constant rank operators, give a new embedding into bounded functions at the endpoint of the theory, study pointwise properties and integrability of restrictions of solutions, and give a generalization of the Gagliardo-Nirenberg inequality on domains.

Advisor: Kristensen, J
Seregin, G
Molecular imaging probes for 31P contrast

31P magnetic resonance has yet to realise its clinical potential principally due to the relatively low sensitivity of the 31P nucleus. While 31P-MRS can uniquely provide vital information regarding in vivo phosphorus metabolism, the long acquisition times required are incompatible with observing dynamic changes in phosphorus speciation (e.g. monitoring ATP/phosphocreatine ratios in real time).
This thesis reports how heptadentate Gd.DO3A derivatives can be used to enhance 31P relaxivity reducing T1 values by more than an order of magnitude per millimolar Gd. This enables shorter repetition times markedly improving the signal to noise ratio (SNR) per unit time. These complexes bind in fast exchange with phosphate species, while linear commercial Gd complexes were found to demonstrate competitive binding of ATP to Gd.
Structural modifications of the DO3A complex were found to alter the affinity for specific phosphate species, as monitored by luminescence spectroscopy of the europium complexes, and also influenced the relaxivity of the Gd complex.
In vivo, the phosphate species of interest reside intracellularly and therefore cellular uptake of these complexes was investigated, using fluorescence microscopy on luminescent complexes and NMR diffusion methods for the gadolinium complexes themselves. The complexes were found to remain extracellular or display endosomal uptake. These results indicate that these systems have clear potential as extracellular 31P contrast agents. Alternative approaches will be required to achieve intracellular 31P contrast.

Keywords: 31P contrast media
Advisor: Faulkner, S
Schneider, J
Farrer, N