VictorJuiz/thesis huggingface dataset:
The origin and development of Maghribī round scripts. Arabic palaeography in the Islamic West (4th/10th-6th/12th centuries)
Keywords: Arabic palaeography

This thesis aims to study the origin and development of Maghrib&imacr; round scripts, i.e. the highly distinctive writing styles employed in the Arabic manuscripts and documents produced from the 4th/10th century onwards in the western Islamic world, and more specifically in the Iberian Peninsula, North-West Africa, and the Balearic Islands. In order to reconstruct the activity of Maghrib&imacr; calligraphers, copyists, and secretaries, and to follow the development of their practices, the present work lists and discusses the earliest dated material written in Maghrib&imacr; scripts, in chronological order: 123 non-Quranic manuscripts, 25 Quranic codices and fragments, nine chancery documents, and two private contracts, all of which produced between 270/883 and 600/1204. The palaeographic analysis of the scripts has made it possible to distinguish between different Maghrib&imacr; sub-styles and 'schools' of calligraphy, some of which have been given a new definition. A particular attention has been devoted to the geographical and historical context in which these scripts developed – i.e. Umayyad al-Andalus – and to the cultural, and even ideological implications of their use and diffusion throughout North-West Africa. Codicological aspects have also been taken into consideration, such as the quality of scribal supports, the composition of quires and gatherings, the methods of ruling the pages, the choice of inks and pigments of different types, the style and techniques of illumination. Where possible, the autoptic study of the material has been combined with the information offered by primary sources of various kinds (historical treatises, biographical dictionaries, handbooks for notaries...) so as to present a comprehensive picture of the Maghrib&imacr; scribal tradition until the Almohad period. The resulting image is that of a calligraphic culture as rich and sophisticated as the eastern one, which constituted a key element in the creation and promulgation of the Andalus&imacr; identity throughout the Mediterranean, but whose formative process and full aesthetic range were still poorly understood.
Ultracold atoms in dressed potentials
Keywords: Magnetic trapping
Ultracold atoms
Multiple-radiofrequency adiabatic potentials
Radiofrequency dressed potentials
Bose-Einstein condensate
Adiabatic potentials

Time-varying fields are widely used to extend the accessible range of trapping potentials for ultracold atoms. This work explores two very different examples of such fields, in the radiofrequency and optical regimes, whose interactions with trapped atoms can both be described in terms of the dressed atom picture.
Forming the basis of this work are radiofrequency dressed adiabatic potentials based on macroscopic trapping coils. Atoms are confined at the south pole of the resultant oblate spheroidal trapping surfaces. This work describes the extension of these potentials by two different methods: the application of multiple dressing radiofrequencies, and addition of a rapidly-scanned optical dipole trap.
This is the first experimental demonstration of a multiple-radiofrequency dressed adiabatic potential, explored using ultracold 87Rb atoms confined in a highly configurable double well. Due to the independent generation of each constituent dressing frequency, the depth of each trapping well and the height of the barrier are easily manipulated, enabling precise and reliable transfer of atoms between the available trapping geometries. Experimental work includes an exploration of the potential-shaping capabilities of the three-radiofrequency system, and characterisation of the potential landscape using radiofrequency spectroscopy with good agreement to the eigenvalues numerically calculated using Floquet theory. This initial exploration of multiple-radiofrequency techniques lays the groundwork for applications in studying double well physics in a two-dimensional system, and independent state or species selective manipulation of trapped atoms. The potential shaping capabilities of this method can also be extended by applying additional trapping frequencies.
In a supplementary line of experimental work, an optical dipole trapping system has been constructed, and the trapping beam aligned to the lower surface of the radiofrequency dressed trapping shell in order to sculpt the radial confinement. Beam shaping is achieved using an acousto-optic deflector, which can be used to produce either a composite array of static deflected beams, a rapidly-scanned painted potential, or some combination of the two approaches.
The development and extension of the experimental apparatus required to implement these enhanced dressed state potentials is explored, and the challenges of their experimental implementation considered.
Child guidance centres in Japan: regional variation in policy implementation and the family-bond
Keywords: Adoption
Child Abuse
Family
Japan
Social Policy
Alternative Care
Foster Care
Social Work
Child Welfare

In contemporary Japan, approximately 85 per cent of children in alternative care are placed in large institutions. This contrasts with global discourse, encapsulated in the UN Guidelines for the Alternative Care of Children, and with practice in most OECD countries, which use foster care more extensively. Explanations for Japan’s outlier status often focus on a homogenous national culture, yet there is significant regional variation between local authorities in how policy is implemented, most readily visible in the percentage of children in foster care.
The title of this dissertation points to the three original contributions to knowledge of this work. The first is the rich ethnographic description of the child guidance centres and the decision-making process by which a child is removed from the family and placed into care. The second contribution is the explanation of regional variation in policy implementation. This is explained with reference to regional variation in resources, in norms, on the goals of care, the functions of different types of care, and the threshold until which a child is seen as being suitable for foster care, and in the organisational cultures of the child guidance centres.
The final contribution to knowledge is the construction of the family-bond, between child and 'parent'. This is understood as singular and discrete, that is, that a child can only have one family-bond at any moment in time. Where foster care is constructed as anything other than professional or semi-professional care in a family setting it is seen as a threat to the child’s family-bond with their natal parent. This dissertation argues that current attempts to increase the use of foster care by national and local authorities are likely to have limited impact unless they take this construction of the family-bond into account and focus on redefining the function of foster care.
Towards an absolute chronology of early Mesopotamia: a radiocarbon perspective
Keywords: archaeology
Bayesian
Jezirah
Mesopotamia
radiocarbon
Iran

The region of Southern Mesopotamia, modern-day southern Iraq, saw a number of important socio-cultural transformations during the 4th - 3rd millennia BC, which led to the emergence of the world’s first urban, literate civilisation. These crucial developments reverberated across the neighbouring regions and greatly contributed to the later Classical and Judaeo-Christian traditions. Despite the importance of this period, our understanding of its chronology is limited. The main aim of this thesis is to build a reliable absolute chronology for the Uruk, Early Dynastic, and Akkadian periods in Mesopotamia using radiocarbon (14C) dating. Radiocarbon dates published in the archaeological literature underwent a thorough evaluation in order to ensure that only reliable measurements were included in the analysis. New dates were produced for the periods and contexts most lacking in radiocarbon data. Archaeological and textual sources were used to create Bayesian models in order to produce even more precise time estimates. The resulting periodisation of Mesopotamia was compared to the contemporary cultural sequences of ancient Iran and the Syrian Jezirah. While corroborating the standard Middle Chronology model, the results highlighted a number of intricacies relevant to our understanding of the early history of the Mesopotamian civilisation. Most importantly, this thesis argues that the developmental process was one of long periods of cultural continuity punctuated by sudden changes and shorter phases of innovation and creativity.
Intervention methods against mosquito-borne diseases
Keywords: Dengue
Malaria
Wolbachia

Mosquito-borne diseases account for hundreds of thousands of deaths each year, highlighting the need for successful intervention methods, which can be targeted at either the pathogen, mosquito vector, or human host. This thesis aims to contribute to better intervention methods focused against malaria and dengue by either (i) improving available research tools, (ii) enhancing the understanding of a promising intervention method or (iii) designing new intervention candidates. Firstly, a superior method for studying in vitro malaria infection of the liver is shown, with implications for vaccine and drug interventions. Secondly, the biology of Wolbachia infection in Anopheles gambiae mosquitoes in the context of the target of rapamycin signalling cascade is investigated in an attempt to improve our understanding of its malaria inhibitory phenotype and inability to stably infect An. gambiae mosquitoes. Finally, an algorithm is developed for the design of a hypothesis driven conservation-based vaccine against viral mosquito diseases with a particular focus on dengue.
Proteases and inhibitors in the interaction between Nicotiana benthamiana and Agrobacterium tumefaciens – systematic analysis and emerging solutions for molecular farming
Keywords: SlCYS8
proteomics
RNAseq
recombinant protein

Nicotiana benthamiana is now an established platform for molecular farming, the production of biopharmaceuticals in plants. Infiltration with Agrobacterium tumefaciens (agroinfiltration) is commonly used to transiently express one or multiple transgenes in N. benthamiana leaves. Agroinfiltrated N. benthamiana is a flexible and scalable recombinant protein (RP) production platform, but is impeded by low RP yields. Plant proteases can degrade RPs and thus limit RP accumulation.
To inform, design and implement strategies for enhancing RP accumulation, I present four papers about proteases and protease inhibitors in agroinfiltrated N. benthamiana. First, I investigated the transcriptome, extracellular proteome and active secretome to understand the plant response to agroinfiltration and investigate the expressed proteases. I show that an extracellular immune response is mounted at the expense of photosynthesis. Comprehensive annotation and monitoring uncover a large, diverse repertoire of proteases in agroinfiltrated leaves, indicating that broad-range depletion of protease activity may be required to enhance RP accumulation. Second, I reviewed the literature on multifunctional plant protease inhibitors (PIs) and grouped them into three types of multifunctional PIs that evolved independently. Third, I screened candidate PIs and discovered that three new, unrelated PIs enhance RP accumulation. I present universal elements of the RP degradation machinery, uncovering new questions on our understanding of the protease network that degrades RPs. Fourth, I identified targets of SlCYS8, a PI that enhances RP accumulation. The target proteases of SlCYS8 are implicated in RP degradation and the high specificity of SlCYS8 can be used to study their role in other processes.
By elucidating the immune response to agroinfiltration, by uncovering the N. benthamiana protease repertoire and by providing new tools to deplete the activity of specific proteases, this thesis makes a relevant contribution to both basic plant research and molecular farming.
Student Engagement and Empowerment in Higher Education
Keywords: Thematic analysis
Student voice
Citizen participation
Power
Engagement
Capability approach
Focus group
Education
Empowerment
Consumer
Higher education
Amartya Sen
Marketisation
Students
Agency
Qualitative
Student repesentation

Student engagement, which emphasises students’ role in shaping their higher education experiences, has become embedded as a core aim of national policy and the everyday management of universities. It has provoked a reconceptualisation of traditional hierarchies within higher education and offers the potential to be empowering for students. However, it has also been criticised for diminishing student agency by reinforcing ideas of student-as-consumer. Drawing on focus groups with students across three universities in England, this study aims to explore students’ experiences and perspectives of empowerment in the context of student engagement policy. The research finds that students who do not have a representative role face significant barriers to shaping their academic experiences; they are excluded from decision-making processes and rarely get to experience any changes that result from their feedback. Although students’ consumer identities give them confidence to demand more of their institutions, consumer rationales for student engagement may limit students’ sphere of influence. A sense of community, enhanced by the quality and quantity of student-staff contact, can be truly empowering but the effects of massification and marketisation present significant challenges to promoting this. These findings lead to a number of policy recommendations, which can be used by those who wish to create empowering opportunities for students to influence their life at university.
Fast and accurate hot-spot estimation in electrical machines
Keywords: hot-spot
Thermal analysis
homogenisation
Electrical machines
Multiple scales

Temperature is one of the parameters that limits the output torque and reduces the lifespan of electrical machines. Models that can provide accurate estimation of the temperature field in the most critical components (e.g. windings) at lower computational effort can be useful to improve the design process and reduce the time to market. Depending on the application, engineers usually rely on hi-fidelity models, e.g. based on the finite elements method (FEM), or lower order models, e.g. thermal equivalent circuits (TECs). The aim of the present work is to provide new tools and methodologies to obtain the temperature distribution within the windings using reduced order hi-fidelity models or improved TEC that could account for any working condition, including AC effects.
A new methodology, based on the multiple scales method (MSM), is introduced which homogenises the complex windings domain and allows for the estimation of its effective thermal properties. The homogenisation through the MSM is performed solving a single elementary cell. The MSM also allows for the reconstruction of the actual thermal field. Extensive numerical and experimental validation is provided, in particular for the case of electrical windings encapsulated with epoxy.
The thermal homogenisation is then combined with an electromagnetic homogenisation technique to estimate winding losses including AC effects, such as proximity and skin effects. The coupled analysis is validated numerically on reference test problems, and experimentally, on a suitably built "motorette". The method is proven to correctly predict losses including thermal effects and to estimate magnitude and location of the temperature hotspot within the winding domain.
This work also introduces a new approach for building thermal equivalent circuits that represents the most commonly employed modelling technique for electrical machine thermal analysis. Here the TEC approaches are thoroughly analysed, highlighting limitations. The proposed new technique extends the range of numerical accuracy, accounting for high Biot numbers (up to Bi = 2) and internal heat generation. The result of this approach is higher spatial resolution about the temperature field within the winding domain and thus enables improved information on hotspot location and magnitude. The method is experimentally validated and also applied to model an electrical machine for full-electric in-wheel vehicle propulsion.
Rigid origami of thick panels and deployable membranes
Keywords: deployable membrane
offset crease

Rigid origami is about folding flat inextensional facets which are connected by creases. It is gaining popularity and being used in an increasing number of engineering applications. Since this is a relatively new field, a number of challenges exist, e.g., folding facets with a finite thickness and achieving folding compactness. This dissertation summarises two attempts to address these two issues. Specific attention has been drawn to the offset crease technique and the wrapping membrane patterns.
In the first part of this dissertation, I have established a kinematic model describing the offset crease models, which leads to a proof that the motion of the thick panel folding is kinematically equivalent to that of its parent pattern with zero thickness. A detailed design approach for adapting this technique has been proposed and proven to be effective by various physical implementations. In order to achieve a higher compactness, an anisotropic tessellation has been derived from the traditional Miura-ori pattern. Its compatibility with pre-existing thickness accommodation approaches has been demonstrated via thick-panel models.
The second part of the dissertation examines a number of deployable membrane patterns. Firstly, the hexagonal winding membrane has been validated with a strict mathematical proof that a rigid transition is non-existent. Therefore, a number of newly proposed wrapping patterns have been designed and their motions have been studied via numerical simulation to discover the adequate rigid-foldable patterns. The algorithm of the simulation has been synthesised to create visualisation software for simulating general origami patterns. Furthermore, we have proposed a comprehensive scheme to allow arbitrary material thickness to be accommodated for the wrapping patterns. Finally, a sequential square twist pattern with a high deployed-to-stowed ratio has been created.
Unravelling the links between psychotic-like experiences, sleep and circadian rhythms
Keywords: heart rate variability
cortisol
acitgraphy
insomnia
melatonin
circadian rhythms
polysomnography
sleep
psychotic experiences

Psychotic-like experiences (PLEs) are prevalent occurrences deemed comparable with the symptoms of psychosis, but not sufficiently severe to warrant a diagnosis upon clinical presentation. Their presence is associated with several adverse clinical outcomes: the onset of various common mental health disorders (e.g. anxiety, mood, substance abuse), poorer functioning, non-remission and relapse.
Sleep and circadian rhythm disruption (SCRD) is observed in 30-80% of patients with psychosis. The omnipotence of SCRD across all phases of the disorder (including the prodromal, acute, chronic and residual phases) raises the question as to whether SCRD may directly contribute to the development of psychosis. Assuming that PLEs are along the same continuum to developing psychosis, a logical next step to further disentangle the sleep-psychosis relationship is to examine whether SCRD relates to the experience of PLEs and whether this relationship is bi-directional.
This thesis begins by examining the core predictions made by a continuum model of understanding psychosis and how specific parameters of sleep may influence PLEs. A smaller high-definition cross-sectional study follows, examining biological underpinnings (electroencephalography (EEG), electrocardiography (ECG), endogenous melatonin rhythms and actigraphy) of a complaint of poor sleep and their relation to the occurrence of PLEs. We then refocus on which parameters of sleep are most integral to the sleep-PLE relationship and close with an investigation of how Hypothalamic Pituitary Adrenal (HPA) axis activity may further our knowledge of this relationship.
The findings of this thesis demonstrate specificity in the parameters of sleep shown to impact certain PLEs. The importance of objective sleep and biologically driven measures in this line of research are underscored, with group differences in EEG, ECG and melatonin. This thesis also highlights dissociative symptomatology as a candidate mediator for the sleep-psychosis relationship, and emphasises the ties between paranoia and negative affect. Finally, this thesis also illuminates the challenges of examining the relationship between sleep and PLEs in isolation, and suggests that they must be considered within the broader framework of co-existing mental health problems.
Bacterial protein import mediated by an iron transporter
Keywords: Transporter
Antibiotic
Outer membrane receptor
Pseudomonas aeruginosa
Pyocin

Multidrug resistant bacteria (MDR) have the potential to push back society to the pre-antibiotic era. Although discovered before penicillin, the inexorable rise in antibiotic resistance has revitalised interest in bacteriocins as treatments for bacterial infections. Bacteriocins are protein antibiotics principal to competition amongst pathogens and commensals, but the mechanisms by which they translocate across the Gram-negative cell envelope are poorly understood. The work presented in this thesis demonstrates how the endonuclease bacteriocin pyocin S2 (pyoS2) exploits the iron transporter FpvAI to translocate across the outer membrane (OM) of Pseudomonas aeruginosa. FpvAI is a 22-strand β-barrel and virulence factor in P. aeruginosa that transports iron into the cell in the form of a small siderophore, ferripyoverdine (Fe-Pvd). Uptake of Fe-Pvd requires the proton motive force (PMF), which is transduced to the ligand-bound receptor by TonB1 and its partner proteins ExbB-ExbD in the inner membrane (IM). The crystal structure of the high affinity complex (Kd = 240 pM) formed between the N-terminal domain of pyoS2 (pyoS2NTD) and FpvAI is presented, which shows pyoS2NTD mimics Fe-Pvd, and induces the same conformational changes in the receptor. Fluorescently-labelled pyoS2NTD was actively imported into P. aeruginosa PAO1 cells and this import was dependent on the PMF, TonB1 and a TonB1-box motif at the N-terminus of pyoS2NTD. Finally, photo-activated crosslinking of stalled translocation intermediates demonstrated pyoS2NTD translocates through the FpvAI β-barrel lumen by a process analogous to that of Fe-Pvd. Following binding to FpvAI, translocation begins by the unfolding of a force-labile portion of the plug domain, opening a narrow channel through FpvAI. This enables pyoS2 to deliver its own TonB1-box to the periplasm where contact with TonB1 activates its import through the same channel, most likely as an unfolded polypeptide. Hence, this study demonstrates that bacteria possess a rudimentary protein import system that exploits energised nutrient transporters in the OM.