VictorJuiz/thesis huggingface dataset:
Virtual play in the Victorian novel
Keywords: literary theory
virtuality
fictionality
novels
charlotte bronte
charles dickens
anthony trollope
hartley coleridge
play
virtual
paracosms
thomas de quincey
william makepeace thackeray
victorian

Novelists in the mid-nineteenth century speculated about the specificity and concreteness of their fictions, and reflected on what it meant to engage with imaginary objects and worlds. W. M. Thackeray is troubled by the novelist’s capacity to ‘see visions, hold conversations with, even draw the likeness of, people invisible’. Anthony Trollope has ‘so realized the place, and the people, and the facts,’ of the setting he invented that ‘to me Barset has been a real county, and its city a real city, and the spires and towers have been before my eyes’. Charlotte Brontë’s heroines always live ‘two lives – the life of thought, and that of reality,’ one fed with ‘daily bread’ and the other with ‘the strange necromantic joys of fancy’.
Such contemporary fascinations with the nature of fictional encounters have fared badly under the twentieth century’s disenchantments with subjectivity, especially with the absorptiveness of novels as a form of potential interpolation. More recently, however, literary studies has increasingly called for other modes of critical engagement with literature than those of detachment and suspicion, suggesting instead sympathy and participation as ways to new interpretations. In particular, the work of Brigid Lowe and John Plotz have brought old critical interests back to the fore with a renewed emphasis on the immersive experience of the novel. As Nicholas Dames has argued, this emerging scholarship engages ‘the challenge of exploring the unique specificities of fictional, or virtual, experiences’.
Virtual Play in the Victorian Novel takes up this challenge of recovering a literary criticism of the fictional. Following the work of philosopher J. David Velleman, this project develops a method for exploring the ‘virtual’ experience of the novel through the heuristic of play; in particular, a historical play phenomenon documented by the biographies and juvenilia of Hartley Coleridge, Thomas De Quincey, Anthony Trollope, and the Brontë siblings. What developmental psychologists now term paracosmic play, seemingly emergent in the early nineteenth century, involves the written elaboration of complex imaginary worlds. This research into play’s archives proposes how its make-believe rules, procedures, and assumptions exemplify a virtual practice, and that this practice offers new perspectives on the analogous rules that govern novel fiction.
The project’s chapters on Brontë, Trollope, Thackeray, and Dickens each begins by examining a documented aspect of paracosmic play (omnipotence, improvisation, affective attachment, and sensory imagination) in relation to a literary critical aspect of the novel (authorship, plot, form, and description), and each concludes with a close analysis of this relation at work in an exemplary text.
Understanding the effect of seasonal variability on the structure of ice shelves and meltwater plumes
Keywords: Channelisation
Shallow Shelf Model
Ice Shelves
Pine Island Glacier
Plume Model

Ice shelves are important to the climate system as they control the release of fresh water from ice sheets into the ocean, with consequences for sea level rise and ocean dynamics. Channels modifying basal melt rates and structural integrity have been observed inscribed in the undersides of some ice shelves. Observations indicate that some channels run in a direction transverse to ice flow and it has been suggested that these form due to seasonal variations in ocean properties.
This thesis analyses the effect of seasonal variability on ice shelves and meltwater plumes in the underlying ocean. A linear perturbation analysis on vertically integrated ice and plume models showed that seasonal forcing of subglacial discharge or ice flux can generate small ripples melted into the base of the ice shelf. These ripples did not develop into overdeepened channels, but the ripples caused by ice flux appear similar to basal terraces observed underneath some ice shelves. Code was developed to run 1-D nonlinear simulations with the vertically-integrated equations, producing similar results to the linear case. However, runs neglecting hydrostatic pressure gradients exhibited a feedback causing ice flux-generated ripples to grow into small proto-channels. A horizontally-integrated plume model was derived, incorporating the Coriolis force and transverse plume flow into a 1-D model which agreed well with a 3-D ocean simulation. Coupling this horizontally-integrated plume with a co-evolving ice shelf prevented proto-channels from forming. It appears unlikely that subglacial discharge or ice flux variations can give rise to observed transverse channels.
A new approach was developed to predict the evolution of internal radar reflectors observed within ice shelves, using vertically-integrated models of ice flow. It is hoped this approach might have applications for inverse modelling and data assimilation.
Fine tuning gene expression levels in mammalian cells with engineered microRNA target sites
Keywords: microRNA
Tumour immunology
Genome engineering
Synthetic biology

Precise, analogue regulation of gene expression is critical for development, homeostasis and regeneration in mammals. In contrast, widely employed experimental and therapeutic approaches such as knock-in/out strategies are more suitable for binary control of gene activity, while RNA interference (RNAi) can lead to pervasive off-target effects and unpredictable levels of repression. In this thesis, I report on a method for precise control of gene expression levels in mammalian cells based on engineered, synthetic microRNA response elements (MREs). To develop this system, we first tested a small panel of rationally designed MREs with various mismatches to miR-17 or miR-21. These MRE variants exerted predictable, stepwise control over reporter gene expression in a human cell line. Next, to improve the precision of MRE-based gene tuning, we established a high-throughput sequencing approach for measuring the efficacy of thousands of miR-17 MRE variants in parallel. This allowed us to create a library of microRNA silencing-mediated fine-tuners (miSFITs) of varying strength that can be employed to control the expression of user specified genes. A selection of miSFITs enabled precise, predictable tuning of PD-1, a co-inhibitory receptor expressed on T-cells and an important target for anti-tumour immunotherapy. In addition to tuning a PD-1 transgene in Jurkat T-cells, we successfully introduced miSFITs into the endogenous PD-1 3’UTR in embryonic stem cells using the CRISPR/Cas9 system. To further demonstrate the value of this technology, we also used a panel of miSFITs to tune the expression of a tumour-associated antigen in a mouse melanoma model. This analysis revealed that antigen expression level is a key determinant of the anti-tumour immune response in vitro and in vivo. miSFITs are a powerful tool for modulating gene expression levels with applications in research and cellular engineering.
Investigation of magnetic field effects on protein photochemistry using cavity enhanced spectroscopy
Keywords: Maquette
Cryptochrome
Radical Pair Mechanism
Cavity Ring Down Spectroscopy
Magnetoreception

Some animals, such as migratory birds, are known to have the ability to sense and use magnetic fields for orientation. At the heart of this remarkable ability is believed to be a photoinduced chemical reaction taking place within a blue-light receptor protein called cryptochrome (Cry). It is hypothesised that magnetic fields can play a decisive role in determining reaction rates (and, hence, yields) by acting on the spin states of spin correlated radical pairs (RPs) formed between a flavin chromophore and a tryptophan (Trp) electron-transfer (ET) chain within Crys.
In this work, cavity ring-down spectroscopy (CRDS) has been used for the detection of magnetic field effects (MFEs) via small changes in the differential absorbance (ΔΔA~10−6) of aqueous protein samples, with sub-microsecond time resolution. The photochemistry and effects of magnetic fields on European robin (Er) Cry, fruit fly Cry, and a plant Cry are characterised. In a key result for this field of research, an MFE in the photochemistry of ErCry is revealed for the first time, lending considerable support to its proposed involvement in bird magnetoreception. Using Cry mutants with modified Trp ET chains, the role of individual Trps in the manifestation of MFEs was explored. Replacing the terminal (i.e. fourth) Trp of the ET chain in ErCry with a redox inert amino acid is shown to significantly increase the optically-detected MFE, indicating that the RP formed between the flavin and the third Trp might be the primarily magnetically sensitive species.
To better understand the relevant biochemical processes in Cry, de novo designed artificial flavoproteins (maquettes) have been used to model the photochemistry of Cry (Chapter 4). The comparatively simple and adaptable design of these model proteins facilitates detailed MFE studies by reducing the complexity of natural Cry. In these maquettes, photoinduced ET leads to the formation of a RP which exhibits MFEs analogous to those in Crys. The profound effect of the donor-acceptor distance on the MFE is demonstrated using flavomaquettes with varying flavin-Trp distances.
The application of cavity enhanced spectroscopy to both natural cryptochromes and artificial flavoproteins, opens up new pathways for the detection and characterisation of MFEs in biologically relevant environments. The enhanced sensitivity of these approaches constitutes a significant step forward in understanding the underlying biochemical processes of animal magnetoreception.
Towards the total synthesis of pectenotoxin-4: synthesis of the CDE and F rings
Keywords: 1,4-addition
asymmetric dihydroxylation
pectenotoxin
rhodium

Chapter 1: Introduction
This chapter outlines the isolation and structural identification of the pectenotoxin (PTX) family of natural products, as well as their reported biological activity. Finally, the chapter will be concluded with the completed total syntheses of members of the pectentoxin family by Evans and Fujiwara.
Chapter 2: Development of a Conjugate Addition-Cyclisation Approach towards the D ring
This chapter outlines previous approaches to forming the bicyclic D ring, our proposed approach using a rhodium-catalysed 1,4-addition as the key C–C bond-forming reaction to synthesis PTX-4, and model studies to test the feasibility of this disconnection.
Chapter 3: Synthesis of the desired E ring fragment
This chapter outlines our current synthesis of the E ring of PTX-4 and the elaborations on the E ring side chain to utilise the rhodium-catalysed 1,4-addition and dihydroxylation/cyclisation sequence as developed in Chapter 2.
Chapter 4: Synthesis of the desired F ring fragment
This chapter outlines the reoptimisation and scale-up of the F ring synthesis previously published, with modifications to the protecting group strategy employed in preparation for the Julia coupling with the ABCDE fragment in our total synthesis of PTX-4.
Chapter 5: Experimental
This chapter outlines all the experimental procedures for the reactions described in this thesis, as well as the characterisation data for the compounds synthesised.
Chapter 6: Appendices
This chapter contains the Mosher’s ester analyses of compounds 282, 331, 463 and 539; as well as nOe analysis of compounds 351, 399, 400, 403, 447, 451 and 469 along with their 1H and 13C NMR spectra.
Chapter 7: References
This chapter contains the references cited within.
Science, scientism, and pseudoscience in die Reihe
Keywords: Epistemology
Eimert
Music
Darmstadt
die Reihe
Scientism
Complexity
Tuba
Stockhausen
Performance
Algorithmic
Piano
Composition
Oboe

This thesis examines the association of science and musical thought that surrounded the Anglophone reception of the West German publication die Reihe (German publication: 1955 – 1962; English edition: 1957 – 1968). While die Reihe presented the early writings of what would become some of the central figures in European compositional circles, the journal’s initial reception was damned through the association of writings of die Reihe with pseudoscience, therefore suggesting that the work was false and to be dismissed. In order to examine the various roles of scientific thought and processes in die Reihe three central areas are explored: to what extent can the epistemological stance of scientism account for the science-like content of the journal? Can a musical journal be considered as a work of pseudoscience? And how did the journal’s portrayal of the composer Anton Webern assist in codifying the musical practices of the authors with the processes and structures of scientific work? It can be seen that scientism can permeate thought and society in multiple and discreet ways, and that scientism can be seen to have influenced policy-makers in post-Second World War West Germany by encouraging a wider application of scientific ideas than had been seen previously. In the same way, the rhetoric of die Reihe’s chief editor, Herbert Eimert, indicates an epistemological stance that is consistent with scientistic values. The initial reception that accused die Reihe of being a work of pseudoscience is critically examined, and it is found that there is insufficient justification for the journal to be considered a work of pseudoscience, because that while it bears a superficial similarity with scientific writing, die Reihe is not itself engaged with scientific work. Finally, it is seen that the way in which Webern’s work and legacy is depicted in the journal is quite unlike how Webern’s work was actually conceived, and as such the framing of Webern as a proto-scientistic composer is another indication of scientism in the thought of die Reihe’s contributors.
Their allotted place: social conditions, survival strategies and comparative respectability among naval wives in mid-nineteenth century Portsea island
Keywords: Nineteenth century
Royal Navy
Sailors' women
Naval wives
Portsmouth

In exploring the social condition and survival strategies of wives and families of Royal Navy’s lower-deck seamen, this thesis brings to light a subset of the nineteenth-century population whose welfare and circumstances were capable of affecting naval manning. Located primarily in naval port towns, these women were dependent upon ill-paid men whose seagoing occupation necessitated long absences and placed them in situations of risk. In the eighteenth and nineteenth centuries a combination of low income, irregular pay, heightened chance of disability and breadwinner-absence had reduced many naval families to destitution, prompting family men to abandon naval service for better-paid work on shore. Anxious to stem the loss of experienced sailors, the Navy introduced a system by which families could be supported financially in their men’s absence. Surviving records of this allotment system - known to, but little explored by historians - are used here to reconstruct a previously neglected naval community. Mid-nineteenth century allotment declarations have identified more than 1500 naval dependants living in Portsea Island (modern-day Portsmouth). From cross-referencing of census and parish records, civil registration data and maps, study of this cohort reveals naval women’s geographical origins, family backgrounds, nuptiality, the timing and size of their families, their occupations, household structures and economic security, with context and proportion provided via local and national equivalents and selected comparator-groups. The emerging picture is of a near-tribal community of females whose roles as wife and mother, domestic stability and social standing were deeply affected by their connection to the Royal Navy.
Fate amenable to change: a technical and social history of Virtual Reality in the United States of America, from 1965 to 2005
Keywords: American Cultural Trends
Cyberpunk
Virtual Environments
American Popular Culture
Cyberspace
American Military Research
Virtual Space
Virtual Reality
Cold War
History
VR
Computers
American Social History

Virtual Reality (VR) technology lacks a clear definition, unique application, or history, leading to difficulties in identifying primary source materials. This thesis establishes a workable definition of VR, incorporating it into cross-disciplinary methodologies to reveal and arrange newly-uncovered sources into a narrative, spanning 1965-2005. This narrative will hopefully encourage crystallisation around the proposed definition, providing value to developers and historians of technology.
Combining online database sampling, stacked surveys of diverse materials, and interviews, the author situates VR within a broader context of 20th and 21st century American social history. By integrating methodologies from Contemporary History, Economics, and Sociology, the newly-established definition is tested via the narrative, which is itself supported by new-found primary materials. That historical narrative assesses the impact of missing social and technical ‘standards’ in VR’s tumultuous past, with implications for both historians and designers of VR, as well as other modern technologies. The results suggest that, since the mid-1980s, exaggerated capabilities and science fiction applications, extolled by both developers and media writers, far outstripped technical reality (unbeknownst to consumers), forming reverse salients on the research and innovation crucial to any modern technological system’s viability. The period spanning the mid-1960s to mid-1980s witnessed much more limited research, centred around identifying valuable applications concurrently with system development, and long before the release of products. This earlier, more cautious period was demonstrably more successful because its VR applications, such as medical training and virtual design, persisted through the ‘VR Winter’ of the late 1990s when later ‘VRs’ did not. Thus, the definition provided is useful for reliably identifying new source materials through the database sampling and analytics methodology, developed therein, which is valuable to historians of VR.
Regulation of class II pilin gene expression in Neisseria meningitidis
Keywords: Sigma factors
Gene regulation
pilE

Neisseria meningitidis expresses multi-component organelles called Type four pili (Tfp), which are key virulence factors involved in interactions with host cells. Pilin (PilE) is the main component of Tfp and N. meningitidis can express either class I pilins that undergo antigenic variation or class II pilins, which are highly conserved. The region upstream of the pilE gene contains two putative promoters which are recognised by distinct sigma factors: sigma70 family and sigmaN. We aimed to investigate regulation of class II pilE by characterising the role of multiple sigma factors in class II pilE transcription.
We confirmed the presence of conserved sigma70 family- and sigmaN-dependent promoter sequences in a large collection of meningococcal genomes. We show that the promoters are functional in E. coli, however in N. meningitidis PilE expression under steady state is initiated from the sigma70 family-dependent promoter. Furthermore, neither the absence nor overexpression of sigmaN had any effect on pilin levels in N. meningitidis which indicates that sigmaN does not contribute to class II pilin regulation, and also suggests that sigmaN does not function as a -12/-24 sequence-dependent activator. Strikingly, Neisseria elongata sigma N, which is known to function as an activator of pilE in commensal N. elongata, was able to reduce meningococcal pilin expression. The negative effect exerted by N. elongata sigmaN on class II pilin expression raises a possibility that in pathogenic Neisseria the sigma-dependent network responsible for the expression of pilE has been modified to maintain Tfp expression, considering their key role in colonisation and pathogenesis.
Studying transcription patterns of virulence factors offers an interesting possibility to understand features that define pathogenic Neisseria. We analysed sigmaH regulon in N. meningitidis by RNA sequencing and our results suggest that sigmaH might be implicated in the response to diverse stimuli including the canonical heat shock response.
In summary, results presented here provide new insights into class II pilE regulation and the role of sigmaH in N. meningitidis. Future work will focus on identifying signalling networks that govern pilE expression in response to environmental stimuli and will explore the sigma factor cross-talk in pathogenic Neisseria. This will expand our knowledge of meningococcal adaptation to niches within the host.
Bureaucrats and social policy processes in low and middle income countries
Keywords: Public Bureaucrats
World Bank
Policymaking
Millennium Development Goals
Developing Countries
Social Policy Diffusion
Mid-Level Bureaucrats
Turkey
Indonesia
Mergers in Public Administration
International Organisations
Public Policy Processes
Social Policy Processes
Low and Middle Income Countries
Bureaucratic Policy Bargains
Policy Learning
Conditional Cash Transfer Model
Bureaucratic Politics
Bureaucratic Quality

This dissertation examines bureaucrats’ engagement in social policy processes in low- and middle-income countries. Each paper in the dissertation investigates a different set of factors that affect the scope and nature of bureaucrats’ policy engagement.
“The Millennium Effect?: When and Where does Bureaucratic Quality Matter for Human Development” looks at an international factor, the global advocacy for Millennium Development Goals, and examines its effect on the relationship between bureaucratic quality and social policy outcomes across different policy areas and task types. Designed as a cross-country comparative study, it uses country-level quantitative data.
“Trusting Relations, Learning Bureaucrats: International Organisations and Early-Stage Policy Diffusion” focusses on another international factor, the World Bank, and examines its role in the adoption of the conditional cash transfer model in Turkey and Indonesia. The study employs within-case process tracing with a comparative lens and uses data from interviews and document reviews.
“The Bargaining Bureaucrat: Policy Bargains and Effects of Political Context and Organisational Traits on Bureaucrats’ Policy Influence” investigates the influence of individual bureaucrats in policymaking processes with a focus on the effects of political context and organisational traits. The study uses data from interviews and employs a novel analytical model built on bargaining theory.
“After the Dust Settles: Mergers, Policymaking Processes, Mid-Level Bureaucrats” examines the effect of organisational structure on policymaking processes and bureaucrats’ engagement in these processes. It is a case study of the merger of five social policy agencies in Turkey and uses data from interviews and document reviews.
By putting a spotlight on the often-invisible bureaucrats, these four papers contribute to our understanding about the factors shaping the scope of bureaucrats’ policy influence in low- and middle-income countries. More generally, this dissertation draws attention to the need for a more systematic incorporation of bureaucracy into our analyses of social policy change.