VictorJuiz/thesis huggingface dataset:
Engineering molecular RNA sensors for controlling CRISPR activity in vivo

Cellular RNAs encode important information regarding cell identity, disease status or exposure to environmental factors. The development of CRISPR-based RNA sensors that are conditionally activated upon detection of endogenous RNA biomarkers would enable restricting CRISPR activity to target cells that were not previously targetable using tissue-specific promoters or targeted delivery approaches. My doctoral work is aiming to develop CRISPR-based RNA sensors by engineering Streptococcus pyogenes Cas9 single-guide RNAs (sgRNAs). sgRNAs are engineered to fold into complex secondary structures that, in the ground state, inhibit their activity. Upon recognising complementary RNA biomarkers, these sgRNAs should become activated, enabling Cas9 to perform its function.
In the first part of this project, I implemented a standard Synthetic Biology design-build-test cycle in mammalian HEK293T cells to optimise engineered sgRNA designs. Iterative design optimisations enabled development of a computational pipeline for designing engineered sgRNAs starting from the desired sgRNA and RNA biomarker sequences. Furthermore, insights into the molecular mechanism of RNA detection are also provided. After initial proof-of-concept studies in HEK293T cells, transgenic zebrafish lines were generated to enable rapid screening of different engineered sgRNA designs in vivo. Preliminary results suggest that engineered sgRNAs could be repurposed towards RNA detection in zebrafish embryos.
Proposed CRISPR-based sensors design could open up novel avenues towards development of new therapeutic, research and diagnostic applications. However, in order to reach its full potential, further work is still required for optimising this technology in vivo. We still need to explore chemical modifications that stabilise sgRNA designs in vivo, as well as different endogenous RNA classes that can be efficiently detected. Eukaryotic cells express many classes of transcripts of different sizes, expression levels and subcellular localisations, and these factors are expected to significantly impact dynamic ranges of sgRNA activation.

Keywords: conditional CRISPR
CRISPR-Cas9
RNA detection
Advisor: Sauka Spengler, T
Fulga, T
The UX of things: exploring UX principles to inform security and privacy design in the smart home

Smart homes are under attack. Threats can harm both the security of these homes and the privacy of their inhabitants. As a result, in addition to delivering pleasant and aesthetic experiences, smart devices need to protect households from vulnerabilities and attacks. Further, the need for user-centered security and privacy design is particularly important for such an environment, given that inhabitants are demographically-diverse (e.g., age, gender, educational level) and have different skills and (dis)abilities.
Prior work has explored different usable security and privacy solutions for smart homes; however, the applicability of user eXperience (UX) principles to security and privacy design is under-explored. This research project aims to address the on-going challenge of security and privacy in the smart home through the lens of UX design. The objective of this thesis is two-fold. First, to investigate how UX factors and principles affect the security and privacy of smart home users. Secondly, to inform product design through the development of an empirically-tested framework for UX design of security and privacy in smart home products.
In the first step, we explored the relationship between UX, security, and privacy in smart homes from user and designer perspectives: through (i) conducting a qualitative interview study with smart home users (n=13) and (ii) analyzing an ethnomethodologically informed study of six UK households living in smart homes (n=6); and, we then explored the role of UX in the design of security, privacy and data protection in smart homes through qualitative semi-structured interviews with smart home users, designers and business leaders through two rounds of interviews (n=20, n=20).
In the second step, using conceptual framework analysis, we systematically analyzed our previously collected data and the literature to construct a framework of design heuristics for consent and permission in smart homes. We applied these heuristics in four participatory co-design workshops and reported on their use. We further analyzed the use of the heuristics through thematic analysis highlighting how the heuristics were used, their purpose, and their effectiveness.
By bringing UX design to the smart home security and privacy table, we believe that this research project will have a significant impact on academia, industry, and government organizations. Our thesis will improve design practices for security and privacy in domestic smart devices while addressing wider challenges, opportunities, and future work.

Keywords: smart home
internet of things
user sxperience
privacy
security
design
Advisor: Flechais, I
Light-induced pulsed dipolar spectroscopy and other electron spin resonance studies of photogenerated paramagnetic species

This thesis is concerned with the development of new methodologies in the field of Light-induced Pulsed Electron Spin Resonance Dipolar Spectroscopy (LiPDS), with the aim of applying them to the structural investigation of complex biological macromolecular systems with endogenous or artificially-added chromophores that can be photoexcited to form triplet states.
The orientational effects in previously reported LiPDS techniques and how to exploit them to extract additional molecular conformational information are explored in Chapter 2. The ReLaserIMD and LiDEER techniques are combined to fully characterise the relative orientation of the two spin centres in porphyrin-nitroxide model peptides, and a new two-dimensional LiPDS technique (frequency-correlated ReLaserIMD) is introduced to capture the complete orientational dependence of the dipolar interaction with a single experiment. These novel methodologies are extended to non-porphyrin chromophores.
Chapter 3 goes a step further to tackle the challenge of measuring the dipolar interaction between two photogenerated triplets, removing the need for having any permanent spin centre in LiPDS. The new Light-Induced Triplet-Triplet Electron Resonance spectroscopy (LITTER) technique is developed using bis-porphyrin model peptides and an in-depth conformational study of a spectroscopic molecular ruler is performed exploiting the orientational effects. LITTER is also compared to conventional DEER spectroscopy, showing superior results, and is applied to the structural study of a dimeric heme protein and a supramolecular porphyrin tetramer.
Chapter 4 addresses some of the limitation of the LITTER technique by using non-identical chromophores and two-colour photoexcitation in bis-labelled model peptides, improved performance and direct combination with F¨orster Resonance Energy Transfer.
This thesis constitutes an important step forward in the knowledge and development of the novel field of LiPDS, by introducing new triplet spin labels, improving existing techniques, developing new experiments and analysis methods, and combining them with other experimental tools for integrative structural biology.

Keywords: molecular conformation
pulsed dipolar spectroscopy
distance measurement
spin labels
electron spin resonance
photoexcited triplet state
electron paramagnetic resonance
porphyrin
Advisor: Timmel, C
Bowen, A
From a better use of instrumentation to new detection methods in NMR and EPR spectroscopy

NMR and EPR spectroscopy are two of the most important techniques to get quantitative, structural or dynamical information on molecular systems. After covering the fundamentals of these magnetic resonance techniques, this thesis explores ways to improve the usage of current spectrometers and to create new instruments altogether using different detection methods with quantum sensing.
First, to deal with bandwidth and oscillating magnetic field limitations typically present for 19F nuclei in NMR or unpaired electrons in EPR, improved methods based on frequency-swept pulses are presented. The implementation of the CHORUS sequence in EPR spectroscopy is detailed. New pulse sequences, namely CHORUSCPMG, PROCHORUS and superposed frequency-swept pulses, are presented in the context of solution-state NMR spectroscopy.
Then, on-the-fly optimisation is proposed as a tool to automate EPR experiments and even develop new ones. A software package, ESR-POISE, was released to allow EPR users with commercial spectrometers to access such methods.
Finally, the construction of a spectrometer which can conduct magnetic resonance at unconventionally small scales thanks to quantum sensors (NV centres) is detailed. After describing design choices for the different elements of the instrument, a focus is made on the static magnetic field with Finite Element Analysis.

Keywords: EDNMR
pulse superposition
broadband pulses
NV centre
arbitrary waveform generator (AWG)
quantum sensing
nitrogen vacancy (NV)
automation
permanent magnet simulation
CHORUS-CPMG
J-modulation
PROCHORUS
chirped pulse
FT-EPR
finite elements method (FEM)
19F NMR
electron paramagnetic resonance (EPR)
DEER
HS pulse
spectrometer design
software
CHORUS
spectroscopy
derivate-free optimisation
optimisation
perfect-echo
frequency-swept pulse
shaped pulses
ultra-broadband NMR
B1-tolerant pulses
electron spin resonance (ESR)
adiabatic pulses
nuclear magnetic resonance (NMR)
CPMG
finite element analysis (FEA)
hardware compensation
Advisor: Foroozandeh, M
Claridge, T
Structured low-rank methods for robust 3D multi-shot EPI

Magnetic resonance imaging (MRI) has inherently slow acquisition speed, and Echo-Planar Imaging (EPI), as an efficient acquisition scheme, has been widely used in functional magnetic resonance imaging (fMRI) where an image series with high temporal resolution is needed to measure neuronal activity. Recently, 3D multi-shot EPI which samples data from an entire 3D volume with repeated shots has been drawing growing interest for fMRI with its high isotropic spatial resolution, particularly at ultra-high fields. However, compared to single-shot EPI, multi-shot EPI is sensitive to any inter-shot instabilities, e.g., subject movement and even physiologically induced field fluctuations. These inter-shot inconsistencies can greatly negate the theoretical benefits of 3D multi-shot EPI over conventional 2D multi-slice acquisitions.
Structured low-rank image reconstruction which regularises under-sampled image reconstruction by exploiting the linear dependencies in MRI data has been successfully demonstrated in a variety of applications. In this thesis, a structured low-rank reconstruction method is optimised for 3D multi-shot EPI imaging together with a dedicated sampling pattern termed seg-CAIPI, in order to enhance the robustness to physiological fluctuations and improve the temporal stability of 3D multi-shot EPI for fMRI at 7T. Moreover, a motion compensated structured low-rank reconstruction framework is also presented for robust 3D multi-shot EPI which further takes into account inter-shot instabilities due to bulk motion. Lastly, this thesis also investigates into the improvement of structured low-rank reconstruction from an algorithmic perspective and presents the locally structured low-rank reconstruction scheme.

Keywords: structured low-rank
3D multi-shot EPI
MRI
Advisor: Chiew, M
Wu, W
Humor out of place: laughing counterpublics and transnational satire in nineteenth century Japan

In the historiography of Japan, the bakumatsu years have been positioned as a period of particular turmoil and unrest that witnessed an explosion in humorous and satirical cultural production. What has been described as an Edo popular culture of play arising from the expansion of urban centers, developed social imaginations and forms of knowledge, which subverted the official Tokugawa order. Japan’s mid-nineteenth century opening to the West and the establishment of the new Meiji government, which embarked on a serious mission of modern nation-state building, are said to have extinguished these popular critical energies and closed this cultural space of play. The Meiji state and influential intellectuals rendered humorous cultural production as an evil custom of the past as it elicited a laughter that was out of place with official ideologies of civilization and enlightenment.
Shifting the locus of attention to foreground popular sources such as the work of writers of playful literature, artists and cartoonists, satirical newspapers, and an active audience for these cultural productions, this dissertation discloses the surprising abundance of laughter and networks of people who adaptively laughed out of place in the second half of nineteenth century Japan. In particular, I illuminate the emergence of a distinct intellectual and cultural space of a ‘laughing counterpublic,’ which became a world-articulating project that was in tension with and undermined the Meiji state’s national public building and imperial subject formation. Delineating how transnational encounters of satirical cultures on the non-state level reconfigured the laughing counterpublic and forged a practice of laughing at imperializing and hierarchizing discourses of Western civilizational progress across an imagined East-West divide, this thesis contributes to understandings of the meanings of Japan’s opening beyond narratives of Western modernity or binary oppositional notions of anti-modernity and nativist reactionism.

Keywords: Meiji newspapers
Gesaku
counterpublic
Bakumatsu
Japan
Punch
satire
Advisor: Konishi, S
The decline (and fall) of English: why aren't readers taking English Literature A Level?

This study investigates why students who enjoy reading are not taking English literature at A level. It is undertaken during a time when there are concerns amongst English educators about the decline in the numbers of students taking an English A level, by focusing on the most popular of the three English A levels – English literature. The research asked a small sample of students in their first year of sixth form who did not take any English A levels about their choice of A levels, specifically their decision not to take English literature A level. It focused on students who enjoy reading, as it was predicted that readers might be more interested than other students in taking the A level. The research aims to contribute to an understanding of how students experience and view English literature by hearing from the students. The study used opportunistic sampling to attract participants, advertising across a variety of sixth form educational establishments. Despite the only criteria being those who were studying A levels, not taking English literature, and enjoy reading, the students who responded were all taking mathematics A level and had achieved high grades at GCSE. Through the use of individual semi-structured interviews, it was found that students had a number of reasons for not choosing to continue with the study of English literature post-GCSE. The interviews were coded and thematically analysed. One of the key findings related to their future ambitions. Participants reported they had based their decisions regarding their A level subjects in consideration of their university subject choice which, in most cases, related to their anticipated career. Additionally, it was found that participants recalled a less than positive experience of English literature at GCSE, identifying their difficulties with essay writing and the subjective nature of English. However, they did recall the texts they had studied with enthusiasm. The students’ reading tastes were discussed and it was found that most participants enjoyed reading science fiction and fantasy novels for ‘escapism’. They reported a confidence that they could continue to enjoy reading without receiving further formal literary instruction through studying A level English literature. These findings suggest that while students are required to limit their A level choice to a maximum of three or four subjects, facing a difficult choice about which A levels will best serve them, English literature will continue to see a decline in numbers. It is acknowledged that this small and highly skewed sample, consisting of ambitious young people, may not be representative of sixth form students as a whole and generalisations cannot be drawn from the data. The impact of the Coronavirus pandemic on this group of students is also discussed. While recognising the limitations of the research, the study concludes with suggestions for further research in this area.

Keywords: qualitative
RDM
RDM2022
KS4
KS3
books
reading
Mathematics
texts
A Level
English Literature
interviews
Advisor: Elliott, V
A qualitative investigation of parental aspirations to international education in China

The 2020s witnessed a scene in terms of health, international relations, and policies. This article inquires into the shifting landscape of decision to international education in the People’s Republic of China (PRC). Shuangjian and other recently enacted educational policies point to a trend in decentralization of English language and discouragement of mass liberal education in the Chinese context. While covid does not bring about a decrease in number of Chinese students studying in western countries in these two years, there is pervasive concerns surrounding health, safety, and discrimination that cloud student and parents’ decision-making. China’s world class university movement witnesses a rise in Chinese universities on global university rankings (GURs) schemes and China’s emergence as a regional education hub attracting international students. With the increasing uncertainty in pursuing an international degree and growing quality in domestic education, this article explores shifting parental aspirations for international education in Shanghai.

Keywords: interviews
parental aspirations
HE2022
HE
international student mobility
Chinese policy
Advisor: Robson, J
'Low value courses': understanding how arts and humanities students perceive their choice of degree subject

In the wake of recent policy decisions and governmental rhetoric that directly targets Arts and Humanities degrees in the UK, this thesis investigates how Arts and Humanities students perceive their choice of degree subject. Using a conceptual framework that combines the Foucauldian concept of discourse, and the work of Foucault, Bernstein and other authors who explore how power is structured in society, a thematic and critical discourse analysis of the data reveals to what extent certain discourses were present in student’s perceptions. The effect of neoliberalism in Higher Education constructs students as consumers and Arts and Humanities degrees as ‘low value’, intrinsic value directly related to monetary worth. These form the neoliberal discourses addressed in the study. Reflecting upon the marketisation of Higher Education, the study argues that students are unwilling participants in neoliberal imaginings, their perceptions a site of resistance and struggle between interpretations inside and outside the dominant discourse. Overall, the ‘student as consumer’ and ‘low value’ discourses had not, by any means fully embedded themselves within student perceptions. Rather, corresponding with an important and raging academic debate surrounding the purpose of university and the value of degrees, given the realms of their reality, students were able to confidently and imaginatively envision alternative discourses that challenged neoliberal ideals. Such a challenge poses significant questions around how universities are conceptualised and managed going forward, and to what organising principles governments should prioritise for a healthy and happy society.

Keywords: critical discourse analysis
HE2022
qualitative data
thematic analysis
university
interviews
arts and humanities
discourse
students
degree choice
HE
policy
perceptions
Advisor: Robson, J
Humanism, English Literature, and the Translation of Greek, c.1480–1560

This study reveals the underappreciated extent to which early Tudor literature was influenced by the Quattrocento rebirth of Greek scholarship. Combining close reading with source study, it shows how English translations from Greek change our perception of the diffuse character of Tudor humanism. Rehabilitating many understudied translations – some of which exist only in manuscript, lack modern editions, and have received scant attention – this thesis also calls for a radically more diverse view of the classical tradition and its evolution in early Tudor England. Developing previous scholarship that has focused on secular pagan literature, it focuses on translations of both ‘classical’ and early Christian Greek. There are six chapters. Chapter 1 sketches the background of Greek translation c.1400–80 through a case study of Lydgate’s works. Chapter 2 focuses on Skelton’s translation of Diodorus Siculus’ Bibliotheke, placing this work in new intellectual and political contexts in late fifteenth-century England. Chapter 3, picking up a theme that emerges from Skelton’s work, demonstrates how attentiveness to Greek translation in More’s Utopia highlights the mediation of Greek literature through Roman intermediaries. Chapter 4 surveys verse translations from Homer by Elyot, Ascham, and Udall and establishes the significance of these translations to the development of vernacular poetics. Chapter 5 argues that Berthelet’s marketing strategies for translations from Greek shed new light on the shape of the classical tradition in Henrician England. Chapter 6 examines translations of early Christian Greek works in Edwardian and Marian England, scrutinizing the relationship between humanism and confessionalization. The Conclusion summarizes how attention to Greek calls for new ways of thinking about early Tudor translation and humanism: it underscores the value of a model for classical reception that unifies the study of Christian and pagan sources, and which more readily considers more diffuse and less ostensibly classical vectors of reception.

Keywords: Roger Ascham
Humanism
Early Tudor literature
Thomas More
Greek
William Barker
Thomas Berthelet
Mildred Cecil
Thomas Elyot
Nicholas Udall
Mary Roper Clarke Bassett
John Skelton
Classical reception