VictorJuiz/thesis huggingface dataset:
Scriptura Scripturam Interpretatur [scripture interprets scripture]: an analysis of the Arabic Bible as used in the Tafsīrs of  Ibn Barrajān (d. 536/1141) and al-Biqāʿī (d. 885/1480)

The Bible remains an indispensable part of the Muslim tradition as a scripture with which the Qurʾān is in close dialogue. From the earliest period of qurʾānic interpretation, questions concerning the exact nature of the Bible and its relationship to the Qurʾān provoked classical Muslim scholars to either defend the text or condemn it for the sake of their own sacred book and prophet. Recent scholarship on Ibn Barrajān (d. 536/1141) and al-Biqāʿī (d. 885/1480) has provided fertile ground for cultivating new perspectives on the relationship between qurʾānic and biblical hermeneutics within tafsīr studies. This dissertation further tills this ground by exploring Ibn Barrajān’s method of qurʾānic interpretation, known as naẓm al-qurʾān, and that of al-Biqāʿī, called ʿilm al-munāsabāt, and by examining how the Arabic Bible is used in their reading of the Qurʾān.
Moreover, this exploration is facilitated through an original comparative analysis between the two authors’ biblical quotations and several Arabic Bible manuscripts believed to have circulated in the milieux of Ibn Barrajān and al-Biqāʿī. How each author transmits and integrates biblical material into their tafsīr will shed light on the reception history of the Bible in the Islamic tradition. Therefore, whether their citations remain true to the biblical source text or, rather, become an islamicised version of the Bible is of primary importance to discover.

Advisor: Whittingham, M
al-Akiti, A
The assembly of CTP synthase into the cytoophidium in Schizosaccharomyces pombe

It is widely known that two factors can affect the activity of enzymes, the total molecular number in the cell or a subcellular compartment, or the activity of the molecule itself. Thus, spatial compartmentalization, such as sequestering enzymes in subcellular organelles, becomes an important method of regulating enzymes. Recently, several metabolic enzymes have been identified being able to form filamentous structures in vivo, indicating a new mode of enzymatic regulation. One of the representatives among these self-assembly enzymes is cytidine-5’triphosohate synthase (CTPS), a critical metabolic enzyme involved in de novo CTP synthesis. Although the catalytic function of CTPS has been well studied over decades, it is only recently observed that CTPS is able to self-assembly into filamentous structure, so called the cytoophidium (plural version as cytoophidia). The cytoophidium is evolutionarily conserved from bacteria (Caulobactor crescentus and Escherichia coli), yeast (Saccharomyces cerevisiae), fruit fly (Drosophila melanogaster) to rat (Genus Rattus) and human (Homo sapiens) cells.
In this thesis I describe using Schizosaccharomyces pombe (shortened as S. pombe) as a model to study the cytoophidium. Taking advantages of the S. pombe easily manipulated genome, I developed a set of basic protocols of manipulating fission yeast in our lab and established several libraries including hundreds of primers, plasmids and S. pombe strains, and therefore starts the yeast research system in our lab. Primary observation was taken in S. pombe, including morphology observation, drug tests and live imaging, to have a general description for cytoophidia. The critical metabolic pathway, MAPK pathway and TOR pathway, were identified as the potential candidates involved in cytoophidia regulation. Several heat shock proteins were proved related with cytoophidia management. In addition, a novel phenomenon was observed that, unlike most other proteins, CTPS remain in filamentous form and are distributed asymmetrically during cytokinesis in S. pombe. All these experimental data can serve as a good primary exploration and provide a basic platform for future cytoophidia research in S. pombe.

Advisor: Liu, J
Bassett, A
Christian Garve's quarrels, rhetoric, and humanism

The philosopher Christian Garve (1742-1798) is now largely forgotten. Some scholars apparently think that this was deserved. However, most will admit that Garve was also a victim of historical developments. He embraced a particular set of intellectual values; he regarded it as the philosopher’s duty to communicate with the public and do work of value to them. During and after his lifetime, this view came to be excluded from German intellectual culture. A very different set of values prevailed: on this view, a dichotomy exists between serious intellectual work and the wider public.
The conflict between these two sets of values is dramatized in several episodes from Garve’s experience. The present thesis analyses four exchanges involving Garve and a range of prominent contemporaries: Kant, Schiller, Goethe, Schlegel, and Schleiermacher. In these exchanges, the contrasting positions of Garve and his opponents take on concrete expression. The thesis draws out the underlying assumptions which inform their arguments. The individual episodes therefore become microcosms for more fundamental developments. This gives them unique significance: the outcome of this conflict still shapes German intellectual culture today.
The thesis interprets Garve’s quarrels as local expressions of a conflict between two views of the intellectual’s vocation. Both go back to ancient models. Plato argued that the philosopher should preserve independence from society; Cicero argued that he must serve his fellow men. Cicero sought to bring philosophy down from heaven; Plato was concerned to send it back. The present thesis identifies Garve with the Ciceronian position, labelled here as ‘humanism’, and his opponents with Plato. It also notes that his arguments frequently draw on rhetorical principles; rhetoric and humanist philosophy were closely linked. Accordingly, the thesis locates each individual exchange against the background of key texts from those two traditions.

Advisor: Hilliard, K
The biophysical and structural mechanisms underlying mechanosensitivity of the TREK-2 potassium channel

The mechanosensitive K2P K+ channels play important roles in a wide range of physiological processes, including touch, balance, pain, and hearing. The ability of these channels to sense changes in pressure within the cell membrane is essential to these processes. However, the structural and biophysical mechanisms underlying this remain unclear. In this thesis, multiscale molecular dynamics simulation techniques were used to investigate the biophysical and structural mechanisms underlying mechanosensitivity of K2P channels. First, how TREK-2 responded to membrane stretch was investigated by simulating TREK-2 embedded in a POPC bilayer subjected to negative pressure (i.e. positive tension). The results show that TREK-2 is intrinsically sensitive to changes in bilayer tension and that the channel switches conformation from the 'Down' state to the 'Up' state in response to membrane stretch. However, although the pressure profile changes symmetrically in both outer and inner leaflets, the structural response of TREK- 2 is highly asymmetric. The changes mainly occurred in the lower half of protein. TREK-2 was therefore next examined under asymmetric tension (i.e. tension only applied in one of two leaflets). Interestingly, TREK-2 only responded to positive tension in the inner leaflet indicating it has the ability to distinguish a variety of force directions within the membrane. Since, the mechanisms underlying mechanosensitivity and intracellular pH sensitivity are thought to be similar, I also examined the role of a critical mutation in the proximal C-terminus of TREK-1 (E306A). This revealed that E306A mimics the protonated state and changes the preferred environment of this residue from water to lipid and consequently assists movement up towards the bilayer. In addition, a new force analysis tool was developed to provide more insight into why some K2P channels are mechanosensitive and some are not. Overall, this thesis improves our understanding of the molecular mechanisms underlying the mechanosensitivity of K2P channels and ion channels in general.

Advisor: Tucker, S
Writing against theodicy: evil, secular ethics, and Victorian realism

This thesis contributes to the ongoing work of rethinking the relationship between secularization and literature by exploring the ways in which three mutually influential authors – James Anthony Froude, Arthur Hugh Clough, and George Eliot – struggled with theodicy. The term theodicy describes a response to the problem of evil in which God’s justice is maintained despite the apparent existence of evil. Because theodicy discourse tends to present suffering as reconcilable with divine goodness, it is frequently considered unethical. Avoiding theodicy is therefore desirable, particularly for those invested in secular ethics. That realism fosters secularity has often been claimed – by Martha Nussbaum, George Levine, Bruce Robbins, for example – and this thesis asks whether, as has also been suggested, realist literature urges readers away from theodicy. Previous studies of theodicy in literature have focused on religious authors; this study takes the opposite approach, looking at authors commonly associated with secularization to highlight the difficulties of staying true to a secular project and the pull towards religious patterns of signification which even realist literature exhorts. Before turning to Victorian writers, the thesis sets up a historical and philosophical context of theodicy discourse from Leibniz and Pope to Voltaire, Goethe, and Coleridge, differentiating between three types of evil (moral, metaphysical, physical) and two types of theodicy (Augustinian, Irenaean). The Victorian authors on which the thesis focuses were chosen because of their role in narratives of secularization and because they are each preoccupied with a different kind of evil, thus their writing exemplifies different kinds of struggle with theodicy. The thesis concludes that while literature, particularly where it claims to represent reality, gravitates towards theodicy, authors and critics can yet foster resistance to those patterns. Rather than trusting formal realism to urge readers away from theodicy, those who want literature and its criticism to champion secular ethics would be well advised to pay renewed attention to those aspects of literature which pull towards religious significance, and the strategies used to resist them.

Keywords: Problem of Evil
Narrative
Secularity
Ethical criticsim
Realism
Theodicy
Victorian literature
Ethics
Advisor: Perry, S
Searches for new physics involving massive invisible particles

One of the most obvious problems with the Standard Model is the lack of any explanation for dark matter: a form of matter predicted from astrophysical observations but not compatible with any known subatomic particle. Many theories of new physics predict dark matter candidates which could be produced in 13 TeV collisions at the LHC. The primary experimental signature expected to accompany the production of a dark matter candidate is an imbalance in measurements of transverse momenta, referred to as ETmiss. This thesis first covers the ETmiss trigger, a system responsible for selecting events with large ETmiss for later use in analyses and a vital component in many analyses. This signature suffers from very large backgrounds from QCD events with little true ETmiss and the high thresholds that would be required to control pass rates pose a risk to the efficiencies of analyses. A technique is presented that is shown to be able to reduce the rate by a factor of almost 4 while retaining high efficiencies in analysis signal regions. This thesis then documents a search for new physics using 36.1 fb−1 of data collected by the ATLAS detector. The search targets final states with no leptons and very high jet multiplicities, ranging from ≥ 7 to ≥ 11 in the tightest signal regions, which are characteristic of long decay chains which can be predicted by certain new physics models, especially supersymmetry. By using this signature the analysis is able to use a looser selection on ETmiss, gaining sensitivity to areas of model spaces which may not be accessible to analyses reliant on the ETmiss trigger. No significant deviation from the Standard Model is observed and the analysis sets strong limits on the masses of supersymmetric particles, excluding gluino masses up to 1.8 TeV at the 95% confidence level.

Keywords: The ATLAS experiment
Particle physics
High energy physics
Advisor: Barr, A
Quantification of cerebral vascular hemodynamics using MRI

Cerebral perfusion is a promising biomarker for the early diagnosis of dementia. Additionally, the change in perfusion in response to vasoactive stimuli, cerebrovascular reactivity (CVR), may also prone to be a valuable dementia biomarker. Arterial spin labeling (ASL) MRI is a non-invasive technique to quantify perfusion and in turn CVR. However, the precise estimation of perfusion using ASL MRI is not only limited by partial volume effects, due to the relatively low resolution of the ASL data, but also affected by confounding factors including arterial transit time (ATT) and blood flow velocity. This thesis investigates the sensitivity of partial volume correction (PVEc) methods for gray matter (GM) perfusion estimation and the impact of confounding factors on CVR measurements.
Linear regression (LR) and spatially regularized PVEc methods were examined using simulated ASL data by comparing the estimation accuracy and the ability to preserve spatial variations in perfusion images. Results indicated that the LR approach was less sensitive to uncertainties in data while the spatially regularized method was superior in preserving spatial details.
The impact of PVEc on the repeatability of GM perfusion was investigated using data from a healthy cohort. The repeatability improved after PVEc using both LR and spatially regularized methods, implying that PVEc is beneficial to increase the reliability of GM perfusion measurements.
CVR quantification was investigated using the standard implementation of ASL (single-PLD PCASL) and a novel ASL technique (Turbo QUASAR ASL). CVR, ATT, and blood flow velocity were estimated before and after acetazolamide administration in healthy volunteers. Regional differences of CVR were found between the two ASL methods. Both PCASL and Turbo QUASAR ASL are limited by the change in blood flow velocity for the use in CVR estimation, while PCASL is also hindered by ATT. Accounting for flow velocity enhanced the CVR estimation for both techniques.

Keywords: MRI
Perfusion
Cerebral blood flow
Arterial spin labeling
Advisor: Chappell, M
Study of CMOS prototypes for the ATLAS detector upgrade and searches for invisible decays of the Higgs boson

The ATLAS experiment at CERN is a large multi-purpose detector operating with outstand- ing performances. For its upgrade phase during the High Luminosity LHC, the tracking system will be replaced with a new system completely made of silicon detectors called ITk. Novel detectors, based on the CMOS process, have been considered for the outer layer of the ITk pixel subsystem. This thesis presents measurements obtained with prototype devices produced in the CMOS technology, and discusses the possibility of including these sensors in the ITk.
One of the biggest achievements of the ATLAS experiment is the discovery of the Higgs boson in 2012. While being a keystone for the validation of the Standard Model, the Higgs boson can also be a probe for new physics, especially by investigating its coupling to invisible particles. In this context, the llνν final state can play a major role. This thesis introduces a data-driven method for estimating the yield of the Z + jets background, one of the most important background processes affecting this analysis. The results obtained with Monte Carlo events prove that the method can accurately reproduce the background yield. This is an important step to improve the evaluation of this difficult background.

Advisor: Bortoletto, D
Total synthesis of rubriflordilactone B and pseudo-rubriflordilactone B

Rubriflordilactones B is a highly oxygenated nortriterpenoid natural product first isolated from Schisandra rubriflora in the year 2006. This natural product is of considerable interest due to its highly oxygenated polycyclic structure and significant anti-HIV activity. However, since the spectral data of the synthetically made natural product doesn’t match the isolated natural product, there is an ambiguity regarding the exact structure of the molecule. This thesis attempts to resolves the uncertainty around the structural motifs by synthesising both rubriflordilactone B and pseudo-rubriflordilactone B; the proposed compound responsible for the spectra in the isolation report.
A highly convergent strategy for the synthesis of the natural product rubriflordilactone B and pseudo-rubriflordilactone B is described hereafter. A common AB ring aldehyde is involved in the late stage coupling with the diynes containing the FG rings of the rubriflordilactone B as well as pseudo-rubriflordilactone B. The coupling is followed by a rhodium-catalysed [2+2+2] cyclotrimerisation reaction to form the ABCDEFG core of the natural product skeleton which is only a step away from the completion.

Keywords: Total Synthesis
Advisor: Anderson, E
Scalable two-phase flow solvers

Two-phase flows arise in many areas of application such as in the study of coastal and hydraulic processes. Often the fluids involved can be modelled by incompressible phases which have disparate physical properties such as density and viscosity.
We utilise a two-phase flow model of immiscible Newtonian fluids. A key part of this model is a set of variable coefficient Navier–Stokes equations. This thesis focuses on the numerical solution of the linear systems which arise after linearisation of these equations. Solving these systems often dominates the computation time when running simulations.
One of the challenges in solving the model is that the density and viscosity coefficients are discontinuous and can have large jumps between the two phases. In this work we consider preconditioned iterative Krylov methods to solve the large and sparse linear systems and pay particular attention to incorporating the highly varying coefficients into the block preconditioners that we propose. We will see that such considerations can be essential in order to obtain good performance.
An important issue is the scalability of the solution methodology. Here, we will study how the convergence of the iterative solver depends on a grid parameter which controls the refinement of the computational mesh. We will see that the novel preconditioners we propose can lead to convergence which is effectively independent of the grid parameter. We also investigate dependence on other model parameters such as the Reynolds number as well as the density and viscosity ratios between the two fluids.
Another topic we examine is the use of a multipreconditioned iterative method allowing more than one preconditioner to be used simultaneously. Our results using this approach show some promising features.
Finally, we consider an implementation within a more realistic model used in practice for simulating complex air–water flows. In particular, we will provide results for a problem modelling the breaking of a dam.

Keywords: Preconditioning
Two-phase flow
Finite elements
Navier-Stokes
Saddle point problems
Iterative methods
Schur complement
Advisor: Wathen, A
Kees, C
Modeling and signal processing for flash memory

This thesis examines the effects of noise and interference on the performance of NAND flash memory.
Chapter 3 studies the probabilistic input/output relation between the data stored and the read threshold voltage of a cell and generalizes it to a group of cells. It is then concluded that adjacent cells are correlated due to common aggressors. This motivates the study of adequate signal processing techniques to optimize the reliability performance.
Chapter 4 proposes two techniques that can reduce the error rate in light of the result of the previous chapter. The first is based on dividing a group of cells into sub-groups and detecting each sub-group independently. The second approximates the flash system model by a hidden Markov model, then uses the sum-product algorithm to detect the inputs. The soft outputs of the proposed detectors are passed on to the ECC soft decoder. It is shown that the second approach provides significant improvements. Then, it is shown that quantization negatively affects the performance of the sum-product algorithm more in comparison with the first approach. To partially mitigate this effect, an iterative detection/decoding strategy is proposed and shown to improve the performance.
Chapter 5 proposes a novel data representation scheme that provides a trade-off between reliability and the amount of data stored per cell, and partially mitigates the effects of device degradation. The scheme divides the stored data into two streams stored in the indices and levels of the non-erased cells, respectively, allowing the first to be detected without any knowledge about the channel. The simulation results show an improvement in the error rate while partially mitigating the need to track the channel parameters and the read references as the device degrade.

Keywords: Flash memory
Index Modulation
Error Correcting Codes
Inter-cell Interference
Signal Processing
Advisor: Coon, J