VictorJuiz/thesis huggingface dataset:
Neo-traditionalism in the West: navigating modernity, tradition, and politics

The present thesis studies the emergence of neo-traditionalism, its public pedagogues and their students (seekers of sacred knowledge), in the West. These pedagogues, many of whom Western-born converts, emerged in the 1990’s after having culminated their studies in the ‘traditional centres’ of knowledge in the Muslim world. They came back with the intent of transmitting the ‘traditional’ knowledge they attained to the wider Muslim community. Of these, this research focuses primarily on Hamza Yusuf, Abdal Hakim Murad, and Umar Faruq Abd-Allah. To their community of followers and students – known as ‘seekers of sacred knowledge’, they represented a connection to an authentic religious tradition marginalised by modernist voices. Their religious discourse was both highly intellectual and deeply spiritual; at a time when there was a seeming decline in both intellect and spirituality. The shuyūkh disseminate their traditional knowledge in religious retreats. These retreats – often– are isolated from the modern world and imbued with traditional symbolism. In these spaces, the shuyūkh provide the desirable orientations to the sacred world in Islam, and a rejection of the modern world around them. That is, the retreat provides both 'ways of seeing' as well as 'what is to be seen' as part of Islam within modernity. The central thrust of the sites of the transaction of sacred knowledge is to 'school' the learners into different narratives of the spiritual decline under modern condition. In the Muslim specific context, this led to the rise of different modernist post-colonial movements and activist tendencies. Such trends obscured Muslim metaphysical outlook. The shuyūkh’s critiques of modernity and discourses on the side lining of metaphysics interpret these in terms of the wider political and social principles. This research shows, on the one hand, how the neo-traditionalist shuyūkh conceive of modernity, tradition, and how that impacts their political discourse on issues such as dissent, race, belonging, and gender. The research highlights how the critique of ‘modernity’ is interlinked and reaffirms notions of authority and stability. On the other hand, it shows, through field interviews with seekers who attended their religious retreats, how young Muslims negotiate and navigate these discourses on modernity, tradition, and politics.

Keywords: Modernity
Islam in the West
Hamza Yusuf
Neo-traditionalism
Umar Faruq Abd-Allah
Abdal Hakim Murad
Advisor: Talib, M
Armbrust, W
Cell-based assays in flowing and sessile drops

Cell-based assays have been performed in aqueous drops within a bulk immiscible fluid phase, as an alternative to multi-titer plates. Many microfluidic functions have been developed to manipulate these drops, for example, to merge pairs of drops, and sort drops based on size or fluorescence they emit. Whilst these functions have been successfully demonstrated in the proof-of-principle stage, challenges remain in combining them into one working platform for real-life applications. As many microfluidic devices are designed for only one specific application, adjustments are required to perform different tasks. For applications involving cell culture, one must be mindful that cells are subjected to a very different environment in microfluidic devices compared to conventional culture. Small culture volume results in large surface-to-volume ratio which would affect transport of molecules within the drops and with the interfaces. Furthermore, materials used in many microfluidic devices are usually different from those used in conventional culture. Motivated by these challenges, here a passive drop merging method in a single Teflon tube and a liquid handling method using sessile drops on a Petri dish are developed. Biocompatibility of these methods for cell-based assays are assessed using mammalian cells. The first method uses fluid mechanics of three or more immiscible fluids to control the relative speed of individual drops, rather than complex channel geometries. Fluids and surfactants were screened to find a biocompatible combination for this method. The second method concerns performing cell-based assays in sessile drops, overlaid with FC-40, on tissue-culture-treated polystyrene dishes. The impact of this arrangement on cells, and the alternation of the pinning line/interface by Fetal Bovine Serum (FBS) is examined in some details. It is found that constituents of FBS accumulate at the interface which results in an alternation on the pinning line properties that is beneficial to such assays.

Advisor: Walsh, E
Hegel, Marx and the state as a prerequisite for freedom

In my thesis, I discuss the dispute between Hegel and Marx over whether or not the state is necessary for human freedom. According to Hegel, the state is necessary for such freedom because he believed that humans require a family life for love and support, but as family life is characterized by natural necessity, it cannot be truly free. Therefore, beyond family life, there must be a civil society where individuals approach one another as self-sufficient beings fully conscious of their independence from one another. But this atomistic relation of individuals to one another within civil society then requires that the state exist beyond it as an institution in which the interests of these different individuals are unified into one will in order to return unity to society. However, Marx believed that the state is incompatible with social freedom because it is an institution for the rule of one class over another rather than a general will for society.
My thesis will discuss the opposition between Marx and Hegel with special reference to Hegel’s 'Elements of the Philosophy of Right' and Marx’s 'Critique of Hegel’s Philosophy of Right,' 'Civil War in France' and 'Critique of the Gotha Programme.' First I will present Hegel’s theory of why the state is necessary for human freedom and then I will present a critique of Hegel’s theory of the rational society. I will then explain Marx’s theory of the state and why Marx believed the state is incompatible with social freedom. Then I will defend Marx’s position against Hegel by arguing that social freedom does not require the state because it is possible for a mediated substantial unity (a unity between individuals in which they still also recognise themselves as particulars) to exist even without the state.

Keywords: political philosophy
Marx
Hegel
Estimating parameter distributions and developing epidemiological methods and tools to support gastrointestinal outbreak investigation

Incubation periods of common gastrointestinal pathogens are cited inconsistently without a solid evidence base for these distributions or factors affecting incubation time. In some high-profile outbreaks, such as the STEC O104 outbreak in Germany or the large 2009 STEC O157 outbreak in South East England, incubation periods were longer than expected complicating the collection of exposure data and the outbreak investigation process. This research aimed to use observational and experimental data to understand the incubation period distribution of some common gastrointestinal pathogens and identify factors that influence these distributions.
I conducted systematic reviews on the incubation period of Campylobacter, STEC and Salmonella Typhi. In addition to using traditional methods for testing and describing the pattern of heterogeneity, I developed methods for analysing data from observational studies which involved using Kolmogorov-Smirnov test and hierarchical cluster analysis. I also extracted and analysed individual patient data of cases associated with outbreaks of STEC reported in England and Wales. Finally, I developed a within-host mathematical model that simulated the process of Salmonella Typhi infection and conducted a sensitivity analysis to identify influencing parameters.
The systematic reviews and meta-analysis of individual patient data indicated the presence of heterogeneity across outbreaks which could not be explained by chance alone. Some factors associated with the distribution of incubation period were age, food vehicle, mode of transmission, attack rate and vaccine history. The mathematical model estimated an incubation period of 9.6 days for Salmonella Typhi, and parameters strongly correlated with incubation period included the net population of bacteria in the colon and bacterial growth during systemic infection.
Outputs of this research will inform the development of policies and public health interventions that contribute towards reducing the burden of disease due to gastrointestinal infections. Further research, developing a stochastic model of the incubation period of Salmonella Typhi, is recommended.

Advisor: McCarthy, N
Hall, I
Ancient Mesopotamian divination: anxiety and methods of decision-making

This study concerns the role of ancient Mesopotamian divination in decision-making. I argue that ancient Mesopotamian divination is a praxis, reflecting the historicity of decisions taken by people in different historical periods of ancient Mesopotamia. From this standpoint, I argue that divination is a response to anxiety stemming from freedom of choice. Freedom of choice (i.e. choosing between different options) leads to the state of anxiety because the outcome of any possible choice is a matter of question, that is, decision-making becomes much complicated under uncertainty. To address this objective, I utilise existential, psychological and sociological theories, with a view to integrate them in a synthetic approach. I also look at the theory of heuristics in judgment and decision-making to underline the biases inherent in predictions and the process of decision-making, that helps to discuss the nature of communication between diviners and their clients. I discuss how divination gives consensus and legitimation to decisions taken by people in difficult and uncertain situations. Although every decision-making process, even though pre-reflective, involves a degree of anxiety, I focus on decisions taken consciously and reflectively for high risk situations, justifying the practice of expensive sessions of divinatory consultations. Previous studies of ancient Mesopotamian divination have not addressed the emotional and anxiety-reassurance function of divination for decisions that cannot be taken easily. To fill this gap, my research is a historical and social analysis of divination in the second millennium BC, which seeks to historicize divination.

Advisor: Dahl, J
Design and operation of tidal arrays in channels

Tidal currents are a promising source of clean and renewable power in many locations worldwide. In channels with suitable bathymetric conditions for strong currents, arrays of tidal stream turbines have been proposed as a useful method for generating energy. The modelling of tidal arrays is complicated, involving multiple spatial and temporal scales. The large scale deployment of tidal turbines will greatly alter the surrounding flow field, making resource assessment difficult and also complicating the design and operation (‘tuning’) of tidal turbine arrays. This thesis presents a tidal turbine model that is used to explore the interaction between power extraction devices and tidal flows. The resulting knowledge is used to inform different designs and operational strategies for tidal turbine arrays.
As an introductory work, a model of the Bohai Sea in China is considered. Flow is simulated through the strait using a depth-averaged numerical model and tidal arrays are introduced using an idealised actuator disc model, while turbine arrangement strategies are considered with the goal of maximising the available power to the array. The results of this study have served to direct the focus of the research to the investigation of a more realistic turbine representation and different tuning strategies for array optimisation.
A blockage-corrected blade element momentum theory is implemented to capture more accurately the performance of the tidal turbine. The implementation procedure and key limitations are discussed. A more realistic tidal rotor turbine representation is then used to examine both full-width and partial-width tidal arrays placed within idealised analytical and numerical channel domains. Analysis is undertaken to reexamine and expand on existing theoretical work.
Notable results from this research include the reduced significance of tuning for tidal rotors as compared to actuator discs. This is true for both temporally fixed and varying tuning strategies, thus suggesting simpler operational strategies to be sufficient as well as more costefficient. As well, the maximum amount of power produced by tidal rotors, averaged over the tidal cycle, is typically 60–70% of that produced by actuator discs. This range can potentially serve as a useful correction factor generally applicable to present and future resource assessments of candidate tidal sites.
Finally, through analysis of the optimal arrangement for partial-width arrays under oscillatory flow and the significance of the local blockage effect, it is revealed that the two-scale theory, though appropriate for a majority of realistic turbine deployments, may underestimate the available power in certain flow conditions where the inertia of the flow becomes important. It is hoped that the present results will assist marine energy developers in selecting suitable models with which to determine optimal operation and arrangements for tidal stream turbines and to estimate the amount of tidal energy resource available.

Advisor: Adcock, T
Magnetic-field amplification in turbulent laser-plasmas

Understanding magnetic-field generation in turbulent plasma is essential for explain- ing the presence of dynamically significant magnetic fields in astrophysical environments such as the intracluster medium. Seemingly plausible theoretical frameworks attributing the origin and sustainment of these fields to amplification by the so-called fluctuation dynamo are somewhat hampered by conceptual uncertainties concerning the validity of the models in which these frameworks are formulated. A recent experiment on the OMEGA laser facility attempted to overcome some of these uncertainties by demonstrating the feasibility of magnetic-field amplification by stochastic motions up to dynamical strengths in actual turbulent plasma. In order to realise the scientific goals of this experiment, accurate measurements of stochastic magnetic fields arising in turbulent laser-plasmas were required. This thesis reports on the development of an analysis technique which meets this requirement by recover- ing the magnetic-energy spectrum from proton imaging data, as well as the mean magnetic-energy density and characteristic structure sizes. The general applicability and reliability of the technique is considered in depth. On application to data derived from the OMEGA experiment, the magnetic-energy density is found to increase over five hundred times in the experiment from its initial value; in addition, estimates of the maximum magnetic field strength indicate that the field is likely to be dynamically significant. The experiment therefore constitutes the first demonstration in the laboratory of the fluctuation dynamo. The results of a second experiment on the OMEGA laser facility – in which a remodelled variant of the previously employed experimental platform is used to provide a time-resolved characterisation of a plasma dynamo’s evolution, measuring temperatures, densities, flow velocities and magnetic fields – are also described. It is shown that the initial growth of the dynamo-generated fields occurs exponentially at a rate which significantly exceeds the turnover rate of the driving-scale stochastic motions in the plasma. Both experiments validate the claim that the fluctuation dynamo is indeed capable of amplifying magnetic fields significantly.

Keywords: Astrophysical plasmas
Proton radiography
Plasma dynamo
Proton imaging
Advisor: Gregori, G
Schekochihin, A
Diets in England: change, continuity and regionality between the Iron Age and Domesday Book (700 B.C -1086 A.D.)

Quantitative MRI has promise to provide precise measures for assessing neurological disorders such as amyotrophic lateral sclerosis (ALS). While MRI is very sensitive to pathological changes in tissue, it lacks the specificity needed for biological interpretability. One way to address this is to compare MRI to more direct measurements, such as histopathology. In this thesis, I present methods that enable direct comparison of quantitative T2 imaging to histopathology in the same post-mortem tissue samples, with the aim of better understanding alterations to T2 in ALS. This requires that we address several challenges to acquiring T2 maps in post-mortem brains, particularly in the context of our study at 7 tesla. First, 7T MRI exhibits considerable spatial inhomogeneity of the B1 field, leading to non-exponential signal evolution. To more accurately model the signal, we utilize the extended phase graph (EPG) model and derive voxel-wise maps of B1, T2 and S0 simultaneously. We show that EPG fitting provides improved T2 mapping under inhomogeneous B1 field. A second issue for quantitative T2 mapping in post-mortem brains is the influence of formalin fixation, which can dramatically reduce the T2 value in proportion with the formalin concentration distribution. We propose a kinetic tensor (KT) model to simulate 4D formalin flux under Fick’s diffusion law. Based on the KT prediction of formalin concentration, we propose a simple linear correction of quantitative T2 maps. Combining EPG fitting with the KT correction, we demonstrate that quantitative T2 map values in motor cortex can distinguish ALS brains from the control group, and that quantitative T2 value is significantly correlated to the tissue ferritin content. This work provides evidence that quantitative T2 mapping may provide a non-invasive marker of cortical iron deposition in ALS.

Keywords: Isotope
Advisor: Gosden, C
Quantitative T2 imaging of whole post-mortem brains in ALS

Quantitative MRI has promise to provide precise measures for assessing neurological disorders such as amyotrophic lateral sclerosis (ALS). While MRI is very sensitive to pathological changes in tissue, it lacks the specificity needed for biological interpretability. One way to address this is to compare MRI to more direct measurements, such as histopathology. In this thesis, I present methods that enable direct comparison of quantitative T2 imaging to histopathology in the same post-mortem tissue samples, with the aim of better understanding alterations to T2 in ALS. This requires that we address several challenges to acquiring T2 maps in post-mortem brains, particularly in the context of our study at 7 tesla. First, 7T MRI exhibits considerable spatial inhomogeneity of the B1 field, leading to non-exponential signal evolution. To more accurately model the signal, we utilize the extended phase graph (EPG) model and derive voxel-wise maps of B1, T2 and S0 simultaneously. We show that EPG fitting provides improved T2 mapping under inhomogeneous B1 field. A second issue for quantitative T2 mapping in post-mortem brains is the influence of formalin fixation, which can dramatically reduce the T2 value in proportion with the formalin concentration distribution. We propose a kinetic tensor (KT) model to simulate 4D formalin flux under Fick’s diffusion law. Based on the KT prediction of formalin concentration, we propose a simple linear correction of quantitative T2 maps. Combining EPG fitting with the KT correction, we demonstrate that quantitative T2 map values in motor cortex can distinguish ALS brains from the control group, and that quantitative T2 value is significantly correlated to the tissue ferritin content. This work provides evidence that quantitative T2 mapping may provide a non-invasive marker of cortical iron deposition in ALS.

Advisor: Miller, K
Tendler, B
Hurley, S
ETS2 regulation of tissue size in early mouse embryogenesis

ETS2 is a transcription factor with both oncogenic and tumour suppressive roles, yet the mechanisms underlying these opposing effects remain unclear. I have analysed an Ets2- loss-of-function mouse mutant that displays a diminished extra-embryonic ectoderm (ExE) on one hand and a thickened anterior visceral endoderm (AVE) on the other. The opposing effects of ETS2 on tissue size, relevant to its tumour suppressive and oncogenic properties, appear to manifest in this mutant. Here I showed that the ExE defect is due to increased peri-implantation apoptosis, verified by phenotypic rescue via apoptosis inhibition. I demonstrated that the AVE transforms from a simple to stratified epithelium due to increased proliferation and perpendicular cell divisions, reminiscent of neoplastic transformation. Inhibition of MEK, which acts upstream of ETS2, phenocopied the AVE defect in wild type (WT) embryos. To identify ETS2 transcriptional targets that cause these AVE defects, I conducted single-cell RNA-sequencing (scRNA-seq), which showed that all cell types in the Ets2-mutant retain normal character; and revealed upregulation of several WNT/β-CATENIN pathway agonists in the mutant AVE. Pharmacological activation of the WNT/β-CATENIN pathway in WT recapitulated the mutant AVE phenotype, supporting scRNA-seq results. 2C-HR-CRIPSR mediated misexpression of candidate WNT agonists in the VE of WT embryos was attempted to verify whether the novel ETS2-WNT axis of AVE tissue size regulation is relevant in vivo. Overall, I have demonstrated the opposing effects of ETS2 on tissue size in early mouse embryogenesis: ETS2 protects the peri-implantation ExE from apoptosis, while dampens WNT/β-CATENIN signalling in the AVE to prevent overproliferation and maintain simple epithelial integrity.

Advisor: Srinivas, S
Freedom and ethics in Madhyamaka Buddhism

This research project articulates the relationship between freedom and ethics in Indian Madhyamaka. Chapter 1 provides a defence of anti-realist interpretations of Madhyamaka, the ramifications of which are felt throughout the remainder of the investigation. Chapter 2 introduces the reconstructive, cross-cultural and, at times, a-historical methodology used to explicate Madhyamaka’s implied stance on issues such as free will and the naturalistic fallacy. Chapter 3 examines the suitability of ‘paleo-compatibilism’ as a potential solution to the Buddhist free will problem, arguing that, with some modifications, it could be viable in a Madhyamaka context. Chapter 4 investigates the similarities and differences between the Western theory of causal determinism and the Madhyamaka doctrine of dependent origination: dependency relations encompass but are not coterminous with causal relations. Chapter 5 examines ‘perspectivalism,’ another proposed solution to the Buddhist free will problem, but contends that it is better conceived of as a meta-theory about free will rather than as simply another theory. From chapter 6 onwards, the focus moves from ‘free will’ to ‘freedom’ of a spiritual kind. Chapter 6 seeks to negotiate the tension in Madhyamaka’s conception of karma as both that which binds beings to saṃsāra and, through the accumulation of merit, as a facilitator of liberation. Chapter 7 introduces the ethical ideal of the bodhisattva figure and considers the coherence of Madhyamaka’s conception of a Buddha’s non-karmic moral action. Chapters 8 and 9 articulate the implied Madhyamaka view on a range of meta-ethical questions, such as whether moral sentences can be truth-apt and whether Madhyamaka can respond to accusations that it commits the naturalistic fallacy. Chapter 10 offers some concluding remarks on the value of cross-cultural philosophical engagement and summarizes this project’s key findings.

Keywords: Moral Responsibility
Madhyamaka
Paleo-compatibilism
Free Will
Advisor: Westerhoff, J