VictorJuiz/thesis huggingface dataset:
Characterisation of the genomic region around the TNF locus within the human major histocompatibility complex in the chromosome band 6p21.3

It is becoming increasingly apparent that many of the genes in the class III region of the human Major Histocompatibility Complex encode proteins involved in the immune and inflammatory responses. Furthermore, genetic studies have indicated that genes within the class III region, particularly the telomeric segment containing the TNF gene, could contribute to susceptibility to diseases of immune-related aetiology. To further characterise this region and to identify candidate disease susceptibility genes, two overlapping cosmids, TN62 and TN82, covering an ~82kb segment of DNA around the TNF gene were selected for sequence analysis.
The eight known genes in this region have been precisely positioned with the order: Gl/AIF-1, 1C7, LST1 (B144), LTB, TNF, LTA, IKBL, BAT1 (centromere to telomere) and their genomic structures have been defined. Comparison of the Gl genomic region with previously described cDNA and genomic sequences, together with the results of RT-PCR, indicates that three alternative transcripts, Gl, Allograft Inflammatory Factor-1 and Interferon-γ Responsive Transcript-1, are all derived from this gene. The completion of the sequence of 1C7 (D6S2570) has revealed that this gene encodes a putative novel member of the immunoglobulin superfamily. A number of alternatively spliced transcripts of 1C7 were identified by RT-PCR, all of which are expressed in immune-related cell lines. Alternative splicing within the immunoglobulin domain- encoding region was seen to result in possible set switching between an IgV domain and an IgC2 domain. In addition to this, a previously unidentified gene, homologous to a number of V- ATPase G-subunits, has been located 1kb telomeric of IKBL. Lastly, the pseudogene UCRH-L and an AIF-1 gene fragment have been identified in the intergenic region between AIF-1 and 1C7.
In order to assess the contribution of loci in this region to disease susceptibility, the genes AIF-1, 1C7, ATP6G and the BAT1 promoter region were subjected to mutation analysis. A total of 28 polymorphisms have been identified, 8 in AIF-1, 10 in 1C7, 7 in ATP6G and 3 in the BAT1 promoter region. Work is at present underway to genotype a number of the identified polymorphisms in control DNAs and in DNA samples from patients with combined variable immunodeficiency (CVID). The information generated from this analysis will bring us closer to explaining the reported linkage of CVID with the telomeric end of the human MHC class III region.
Inter-theory relations in physics: case studies from quantum mechanics and quantum field theory

I defend three general claims concerning inter-theoretic reduction in physics. First, the popular notion that a superseded theory in physics is generally a simple limit of the theory that supersedes it paints an oversimplified picture of reductive relations in physics. Second, where reduction specifically between two dynamical systems models of a single system is concerned, reduction requires the existence of a particular sort of function from the state space of the low-level (purportedly more accurate and encompassing) model to that of the high-level (purportedly less accurate and encompassing) model that approximately commutes, in a specific sense, with the rules of dynamical evolution prescribed by the models. The third point addresses a tension between, on the one hand, the frequent need to take into account system-specific details in providing a full derivation of the high-level theory’s success in a particular context, and, on the other hand, a desire to understand the general mechanisms and results that under- write reduction between two theories across a wide and disparate range of different systems; I suggest a reconciliation based on the use of partial proofs of reduction, designed to reveal these general mechanisms of reduction at work across a range of systems, while leaving certain gaps to be filled in on the basis of system-specific details.
After discussing these points of general methodology, I go on to demonstrate their application to a number of particular inter-theory reductions in physics involving quantum theory. I consider three reductions: first, connecting classical mechanics and non-relativistic quantum mechanics; second,connecting classical electrodynamics and quantum electrodynamics; and third, connecting non-relativistic quantum mechanics and quantum electrodynamics. I approach these reductions from a realist perspective, and for this reason consider two realist interpretations of quantum theory - the Everett and Bohm theories - as potential bases for these reductions. Nevertheless, many of the technical results concerning these reductions pertain also more generally to the bare, uninterpreted formalism of quantum theory. Throughout my analysis, I make the application of the general methodological claims of the thesis explicit, so as to provide concrete illustration of their validity.

Keywords: emergence
reduction
quantum field theory
measurement problem
classical mechanics
inter-theory relations
Everett
de Broglie-Bohm
correspondence principle
Bohm
quantum mechanics
decoherence
Advisor: Wallace, D
Saunders, S
The acoustic properties of gassy soil

Compression wave sound speed and attenuation measurements are made in the laboratory over frequencies in the range from 10 kHz to 1 MHz on samples of estuarine silty clay that have been provided with varying amounts of uniformly distributed gas bubbles. The soil can be idealised as a two phase material of spherical gas pockets within a matrix of saturated soil, where the pocket sizes are in the range from 100 to 2000 μm diameter. It is shown that the acoustic response of this soil is dominated by the gas fraction and bubble size of the gas phase, and by the elastic moduli of the matrix phase, within the frequency range that causes bubbles to pulsate radially (resonate). Below this range, it is shown that the sound speed response is not significantly affected by bubble size, except close to the saturated soil condition. The gas fraction and bubble size distribution of each sample is measured and used, with values of the appropriate elastic moduli from the literature, to provide curves from current theory. The theory is evaluated in comparison to the experiment results, and proposals are made, which may provide the basis for the prediction of the gas fraction and bubble sizes of sea-bed sediments that are suspected of containing gas. Such a process would involve the use of an acoustic probe to obtain in situ sound speed and attenuation measurements using the signal analysis techniques developed in this study.

Keywords: clay
gas
Advisor: Sills, G
The effect of individual agricultural insurance on transfers by smallholder farmers in informal  risk-sharing networks: empirical evidence from Tigray, Ethiopia

We investigate the effect of formal individual agricultural insurance on transfers by farmers in informal risk sharing networks using an experiment conducted in rural Tigray in Ethiopia. Both index and indemnity insurance are investigated for a holistic picture. However, we focus on index insurance, particularly when there is basis risk.We employ a multi-stage sampling design in a framed field experiment, simulating three possibilities, namely, insurance availability, insurance take-up and insurance rejection.
Based on empirical considerations, we treat transfers as categorical and use multilevel analysis to fit a Cumulative Link Mixed-effects Model (CLMM). Thus we compare the odds of transfers under the three possibilities; insurance availability, insurance take-up and insurance rejection to transfers in a control in which formal insurance is unavailable. Having explored how transfers change in response to the three possibilities, we tentatively explore the underlying motives.
We find that farmers do not offer compensation for basis risk. When there is basis risk, farmers are 48% less likely to make transfers. This non-compensation for basis risk is worst for farmers in prescribed groups. Assuming socio-economic-dependent factors to be the underlying motives, we posit that the resultant economic incentives motivate farmers to punish their partners for their insurance decisions.
Providers of micro insurance in low-income farming markets will find the empirical findings useful in that they show the need for careful evaluation when designing agricultural insurance interventions aimed at realising a mutually beneficial relationship between index insurance and informal risk sharing. The findings also highlight the need for caution in prescribing farmers into groups as a condition for offering insurance.

Keywords: agricultural insurance
indemnity insurance
basis risk
index insurance
risk-sharing
informal risk-sharing
group insurance
Advisor: Steinsaltz, D
Morsink, K
Theoretical nuclear physics

The states in the mass 18 and 19 nuclei which are strongly excited in three- and four-nucleon transfer reactions are considered. A cluster model employing a local effective interaction with the core and approximating the requirements of the Pauli principle with an orthogonality condition is used. We present a microscopic derivation of the effective cluster-core potentials for alpha cluster states in 18F and 19F based on the shell model approximations to the ground states of 14N and 15N respectively and an alpha-nucleon scattering potential. In 19F phenomenological and microscopic calculations yield essentially identical results. The predicted splitting of doublets is very small and mixing with non- cluster states is apparent in the experimental spectrum. In 18F a tensor force between cluster and core is predominantly responsible for the splitting of the observed triplets. Close agreement between phenomenological and microscopic treatments occurs again. However, the latter shows that mixing of states with differing orbital angular momenta by the tensor force is important. This leads to a re-examination of the experimental candidates for cluster states, which indicates that mixing with two-particle shell model states may be important. A similar microscopic treatment is developed for trinucleon cluster states in 18F and 18O but is hindered by the lack of information concerning the spin-dependent terms in the nucleon-trinucleon potential. Some of the forces between cluster and core are closely related, and the results are linked with phenomenology to see what sort of nucleon-trinucleon forces are needed to reproduce the observed spectrum. Finally, the effect of core polarization on the alpha spectrum in 18F is considered by mixing bands based on the ground state and excited 1+ states of 14N via the tensor force.

Advisor: Buck, B
Rowley, N
Constructing Minnesang musically

While troubadour and trouvère repertoires have recently received fresh attention from music scholars, the study of medieval German vernacular song—Minnesang—continues to be located firmly outside the canon(s) of musicology. The present thesis seeks to re-insert Minnesang into musicological discourse by demonstrating the ways in which the repertoire has been constructed as musical, both by the creators of medieval manuscript sources and by modern scholars.
The modern ontology of music as defined by notation and performance has prevented scholars from understanding manuscripts such as the Codex Manesse (C) as intrinsically musical. While the texts alone may have sufficed to enable their intended audiences to view them as musical entities, C’s 137 author miniatures further contribute to the manuscript’s musicality: the Minnesänger are depicted as authors and experiencing personae, revealing a strong concern for oral communication—which, in the Middle Ages, was inherently musical. The Jenaer Liederhandschrift (J) and other manuscripts equally reveal their musicality when scrutinised beyond the search for musical notation: through ordering and folio design.
The thesis establishes the influence exerted by previous scholarship on today’s lack of interest in the music of Minnesang, and outlines the importance of scholarly discourse and its study in a historiographical context. Before the 1970s, an existing musical discourse on Minnesang encouraged musicologists and philologists to continue to engage in it—despite the fact that the dominant interest in contrafacture and rhythm found few answers in the surviving source material. A concluding case study of Walther von der Vogelweide’s Palästinalied exemplifies the musicality of medieval manuscripts and its complex (mis)construction by modern scholarship. The thesis provides the basis for a fresh assessment of the music of Minnesang: beyond the confines of modern ontologies of music, and as part of the study of medieval song.

Keywords: manuscripts
Minnesang
musicology
medieval song
historiography
Advisor: Leach, E
Ultrafast spectroscopy of charge separation, transport and recombination processes in functional materials for thin-film photovoltaics

Dye-sensitized solar cells (DSSCs) and perovskite solar cells are emerging as promising potential low-cost alternatives to established crystalline silicon photovoltaics. Of the employed functional materials, however, many fundamental optoelectronic properties governing photovoltaic device operation are not sufficiently well understood. This thesis reports on a series of studies using ultrafast THz and photoluminescence spectroscopy on two classes of such materials, providing insight into the dynamics of charge-transport and recombination processes following photoexcitation.
For TiO2-nanotubes, which have been proposed as easy-to-fabricate electron transporters for DSSCs, fast, shallow electron trapping is identified as a limiting factor for efficient charge collection. Trapping lifetimes are found to be about an order of magnitude shorter than in the prevalently employed sintered nanoparticles under similar excitation conditions and trap saturation effects are not observed, even at very high excitation densities.
In organo-lead halide perovskites - specifically CH3NH3PbI3 and CH3NH3PbI3-xClx, which have only recently emerged as highly efficient absorbers and charge transporters for thin-film solar cells, carrier mobilities and fundamental recombination dynamics are revealed. Extremely low bi-molecular recombination rates at least four orders of magnitude below the prediction of Langevin's model are found as well as relatively high charge-carrier mobilities in comparison to other solution-processable materials. Furthermore a very low influence of trap-mediated recombination channels was observed. Due to a combination of these factors, diffusion lengths reach hundreds of nanometres for CH3NH3PbI3 and several microns for CH3NH3PbI3-xClx. These results are shown to hold for both, solution processed and vapour-deposited CH3NH3PbI3-xClx and underline the superb suitability of the materials as absorbers in solar cells, even in planar heterojunction architectures.
The THz-frequency spectrum of the conductivity of the investigated perovskites is consistent with Drude-like charge transport additionally exhibiting weak signatures of phonon coupling. These coupling effects are also reflected in the luminescence of CH3NH3PbI3-xClx, where they are believed to be the cause of the observed homogeneous spectral broadening. Further photoluminescence measurements were performed at temperatures between 4 K and room temperature to study the nature of recombination pathways in the material.

Keywords: CH3NH3PbI(3-x)Clx
solar cells
photoluminescence
perovskites
TiO2
CH3NH3PbI3
dye-sensitized
terahertz
charge carrier dynamics
THz
nanotubes
Advisor: Herz, L
High magnetic field effects in low-dimensional carbon nanostructures

This thesis describes studies of graphene, single walled carbon nanotubes (SWNTs) and InSb. Optical and electronic measurements probe the effects of high magnetic fields on these low-dimensional systems.
Chapter 1 introduces a theoretical description and background behind the materials and physical phenomena studied in this work. The structure and unique properties of carbon nano-materials are described. The experimental methods used in this thesis are described in Chapter 2.
Chapter 3 describes magnetotransport measurements on InSb/AlInSb heterostructures revealing that the large energy gaps, and extremely high mobility, associated with this system leads to exceptionally well defined quantum Hall plateaux for both even (Landau level) and odd (spin-split) filling factors. Even higher cyclotron energy gaps are expected in graphene. Chapter 4 reveals that due to a combination of large cyclotron energy gaps and fast electron-phonon energy loss rates, the quantum Hall effect (QHE) in graphene can be observed to unprecedented current densities (43 A/m) and temperatures (> 45 K). The behaviour of epitaxial graphene grown on silicon carbide in the quantum Hall regime is shown to be characterised by a strongly magnetic field dependent carrier density due to charge transfer from surface donor states in the substrate.
Chapter 5 shows that polymer wrapping of SWNTs can achieve high quality purified samples. Individual SWNTs were probed using micro-photoluminescence measurements in magnetic fields up to 30 T. The combination of high magnetic fields and high spectral and spatial resolution allowed a detailed study of exciton fine structure. High intensity laser irradiation is shown to induce bound excitons in pristine tubes. The optical properties of a number of tubes are dominated by defect sites which may be imaged along the tube using the magnetic brightening of dark excitons associated with such defects.

Keywords: Physics
Nanotechnology
Carbon nanotubes
Graphene
Advisor: Nicholas, R
Generalized compactification in heterotic string theory

In this thesis, we consider heterotic string vacua based on a warped product of a four-dimensional domain wall and a six-dimensional internal manifold preserving only two supercharges. Thus, they correspond to half-BPS states of heterotic supergravity. The constraints on the internal manifolds with SU(3) structure are derived. They are found to be a generalization of half-flat manifolds with a particular pattern of torsion classes and they include half-flat manifolds and Strominger's complex non-Kahler manifolds as special cases. We also verify that heterotic compactifications on half-flat mirror manifolds are based on this class of solutions.
Furthermore, within this context, we construct specific examples based on six-dimensional nearly-Kahler homogeneous manifolds and non-trivial vector bundles thereon. Our solutions are based on three specific group coset spaces satisfying the half-flat torsion class conditions. It is shown how to construct line bundles over these manifolds, compute their properties and build up vector bundles consistent with supersymmetry and the heterotic anomaly cancellation. It turns out that the most interesting solutions are obtained from SU(3)/U(1)². This space supports a large number of vector bundles leading to consistent heterotic vacua with GUT group and, for some of them, with three chiral families.

Keywords: heterotic string theory
compactification
torsion classes
fluxes
Advisor: Lukas, A
Unfolding and refolding of monomeric and heptameric α-hemolysin

Alpha-hemolysin (αHL) is a membrane protein derived from Staphylococcus aureus. The structural stability of the monomeric and heptameric protein was investigated under high pH conditions (8.0−13.0) and in various concentrations of urea (0−8.0 M). The dimensions of the αHL heptameric pore are ideal for the translocation of single-stranded polynucleotides such as DNA or RNA. Therefore, it could potentially be used as a DNA sequencing device. Exploring the pore’s ability to withstand harsh conditions would help determine whether it could be used in the translocation of double stranded DNA (dsDNA), which dissociates into single-stranded DNA (ssDNA) at high pH or ssDNA that loses its secondary structure in the presence of urea. Studying the behavior of monomeric αHL under various denaturing and renaturing conditions will aid in improving the conditions used to purify and refold mutated forms of αHL.
The pH and urea studies revealed that the heptamer is more resistant to structural change than the monomer. The heptamer remained stable up to pH 12.0, which is ideal since dsDNA dissociates into ssDNA at pH 11.7. The majority of the heptamer’s structure was lost at pH conditions above 12.5. Structural studies on the heptamer at various urea concentrations revealed that a fraction of the heptamer was still intact even at 8.0 M urea whereas the monomer seems to unfold completely at high urea concentrations. However, upon refolding via dilution, the monomer seems to regain its structure and function. Urea was determined as an ideal denaturant even after incubating the monomer in guanidinium chloride (GdnCl) or organic acids.
The structural stability of the αHL monomer and heptamer was elucidated using techniques such as circular dichroism, intrinsic tryptophan emission spectroscopy, SDS-PAGE, light scattering hemolytic assays and single-channel recording experiments.

Keywords: alpha-hemolysin
protein structure
protein folding
Advisor: Bayley, H
T cell phenotype and function in Spondyloarthritis

Th17 cells are implicated in a variety of inflammatory disorders including Spondyloarthritis (SpA). Ankylosing spondylitis (AS), the most common SpA, is genetically associated with HLA-B27 and IL-23R polymorphisms, although the link remains unexplained. In addition to classically folded heterotrimers, HLA-B27 can form β2m-free homodimers (B272). B272, as well as free heavy chains, are able to interact with KIR3DL2.
I have shown an expansion of KIR3DL2+ CD4+ T cells in peripheral blood of AS patients and HLA-B27+ healthy controls. Although KIR3DL2+ CD4+ T cells comprise a minority of CD4+ T cells in peripheral blood, KIR3DL2+ CD4+ T cells account for the majority of peripheral blood CD4+ T cell IL-23R expression. KIR3DL2+ CD4+ T cells from synovial fluid are also enriched for IL-23R expression compared to matched peripheral blood samples. Moreover, treatment exposure to rIL-1/23 significantly increases IL-17 production by KIR3DL2+ CD4+ T cells in AS patients but not RA patients and healthy controls.
KIR3DL2+ CD4+ T cells from AS patients produce more IL-17 than KIR3DL2+ CD4+ T cells from HLA-B27- healthy controls. KIR3DL2+ CD4+ T cells from AS patients and healthy controls are also enriched for dual production of IL-17 and IFNγ, consistent with the theory that AS is a Th17 or a Th17/1 driven disease.
I have shown that naïve CD4+ T cells express KIR3DL2 de novo after activation. Interaction with B272-expressing cells acts to maintain and/or further increase KIR3DL2 expression. Interaction with B272-expressing cells also increases expression of Bcl-2. I propose that interaction of KIR3DL2+ CD4+ T cells with B272 preferentially promotes the survival of these pro-inflammatory cytokine-producing KIR3DL2+ CD4+ T cells in SpA. HD6, a B272-specific monoclonal antibody, decreases IL-17 production by PBMCs from AS patients, making it an attractive candidate therapeutic reagent in the treatment of AS and other HLA-B27-associated SpA.

Keywords: immunomodulatory receptors
Spondyloarthritis
HLA-B27
Th17
Advisor: Paul, B