VictorJuiz/thesis huggingface dataset:
Water-soluble fullerenes and molecular machines: Supramolecular approaches to nanomedicine

The incursion of the physical sciences into the medical sphere has led to myriad investigations in the use of nanomaterials for diagnostic and therapeutic purposes. In particular, the fullerenes show great promise in a number of areas because of their unique molecular properties. The chemistry of these carbon building blocks can be harnessed through covalent functionalisation and incorporation into supramolecular architectures such as extended self-assembled structures and molecular machines based on mechanically interlocked molecules. This thesis describes the synthesis and characterisation of such supramolecular structures incorporating fullerenes, whose potential utility in nanomedicine is demonstrated.
Water-solubilisation of fullerene C60 is achieved in the first part of this thesis by covalent functionalisation with triethylene glycol monoethyl ether. The resulting complex molecular structure is elucidated and a new method developed for interpreting elemental and thermal gravimetric analyses. It is highly soluble in water (37 mg/mL) and exhibits concentration-dependent photoluminescent behaviour suitable for biomedical applications. Ultraviolet-Visible absorption data points to the formation of self-assembled structures. Over time, these self-assembled structures grow considerably into hydrogels. Optical and scanning electron microscopies show the hydrogels have a tricontinuous hierarchical structure of great promise for use in drug delivery. The same functionalisation protocol is applied to higher fullerenes C70, C84 and C90–92, and extensive hierarchical structures are formed for the latter two. It is proposed that the presence of corannulene-like hydrophobic regions in the functionalised fullerenes affects the formation of hierarchical structures. Atomic force microscopy nanoindentation shows that the strongest of the formed hydrogels (C90–92 derivative, E = 432 ± 286 kPa) fares remarkably well against other supramolecular hydrogel competitors.
In the second part of this thesis, fullerene C60 is functionalised for incorporation into a rotaxane-based molecular machine. Two new iodo-alkyne functionalised fullerene derivatives are isolated in this process. C60 is incorporated into a four-station [3]rotaxane with two peripheral naphthalene diimide stations and two ferrocene-functionalised macrocycles via a copper-catalysed click reaction. The anion-induced motion of the macrocycles leads to a tuneable photoluminescent response due to photoinduced electron transfer. C60 plays a crucial electron-accepting role in this setup. In this way, this fullerene-containing mechanically interlocked architecture demonstrates a unique platform for the sensing of chloride ions. The utility of this [3]rotaxane is expanded into a theranostic tool by the demonstration of tuneable singlet oxygen generation by the central fullerene moiety concomitant with the tuneable photoluminescence.

Keywords: hydrogels
fullerenes
supramolecular chemistry
self-assembly
nanomedicine
Advisor: Porfyrakis, K
An experimental medicine investigation of the effects of potential novel antidepressant interventions on emotion and reward related information processing

Recent attempts to reconcile neuropharmacological and cognitive accounts of depression have led to the development of a cognitive neuropsychological model of antidepressant treatment action. This model suggests that antidepressant drugs exert their clinical effects by acutely inducing positive biases in “hot” (i.e. emotionrelated) cognitive processes which can counteract the negative biases in affective information processing that are inherent to depression. The validity of this model is well supported by a multitude of empirical studies investigating the effects of different established antidepressant drugs which, taken together, suggest that the induction of positive biases is a common and crucial causal mechanism of antidepressant action.
The aim of this thesis is to investigate whether potential novel antidepressant treatments could have similar effects. Taking an experimental medicine approach, three different interventions were studied in healthy volunteers: bright light treatment, practising positive psychology, and administration of the dopamine D2/D3 receptor-preferring agonist pramipexole. In addition to their effects on hot cognitive processes, for each of these interventions, potential effects on subjective state and, where of interest, also effects on other relevant measures (e.g. HPA axis activity for practising positive psychology, gustatory processing for pramipexole treatment) were tested.
Contrary to our predictions, we did not find conclusive evidence for an antidepressant-like effect on emotional information processing for any of the three treatments we studied. However, several interesting patterns in other measures were observed: First, an early memory practice that has previously been used as a supposedly inert control intervention in positive psychology studies showed a blunting effect on cortisol awakening responses and potentially also a general improvement of hot cognitive processes. Second, subacute pramipexole treatment showed a potential effect on exploration-exploitation strategies in an information bias learning task, maintaining random exploration after repeated-testing as compared to placebo. Furthermore, pramipexole also showed a potential effect on gustatory processing, enhancing taste recognition but blunting subjective evaluation of appetitive and aversive taste samples.
In conclusion, previously reported antidepressant effects of the putative novel treatments that were studied in this thesis seem not to be explainable by the induction of positive biases in emotion-related information processing. Further studies on the mechanisms behind their efficacy are warranted. The observed effects of the mental practice and of subacute pramipexole treatment deserve further attention and should be interrogated in closer detail in future research.

Advisor: Harmer, C
Cowen, P
Browning, M
Droplet transport by bendotaxis

In this thesis, we study bendotaxis – a novel, passive droplet transport mech- anism driven by the coupling between capillary pressure within the droplet and bending deformations of the channel confining it. This mechanism is inspired by observations of the legs of Gerris Regimis, which are covered in setae rendering them superhydrophobic; the setae deform by bending in re- sponse to the capillary pressure of vapour droplets as they condense between setae, resulting in their dynamic expulsion, and thus helping to maintain a superhydrophobic leg.
In the first half of this thesis, we focus on two dimensional scenarios to isolate the underlying competition between bending and capillarity. In this setup, the direction of droplet transport is, surprisingly, always the same, regardless of the wettability of the channel. We use a combination of experiments at a macroscopic scale and a simple mathematical model to study this motion, focusing in particular on the time scale associated with the motion. We make observations that may inform the design of superhydrophobic surfaces ex- ploiting bendotaxis for anti-fogging and also investigate two physical effects – contact angle hysteresis and droplet self-trapping – which can impede droplet transport by bendotaxis.
In the second half of this thesis, we focus on the influence of channel geom- etry on droplet transport by bendotaxis. Further motivation is provided by experiments in which a regular, periodic pattern emerges as liquid droplets are condensed into deformable microchannels and move in a manner similar to bendotaxis. We hypothesize that this wavelength selection is the result of a novel instability, reminiscent of the Rayleigh-Plateau instability but mediated by channel elasticity. By developing and analyzing a mathematical model of a system susceptible to this instability, we study its characteristic behaviour and the consider the effect of adding liquid to the channel as the instability develops.
Finally, we consider how collaborative effects of droplet transport by bendo- taxis in neighbouring channels may lead to clustering. We first develop a mathematical model for an array of droplet-channel systems, each of which would undergo bendotaxis in isolation, and, using this, identify two distinct regimes for the cluster sizes in the limits of weak and strong surface tension, which are then derived analytically using asymptotic methods.

Advisor: Vella, D
Hewitt, H
London chronicles and the civic sense of the past, circa 1430-1516

Each society generates a historical culture, which here is understood to encompass the media through which the past is discussed, the institutions that seek to shape and form ideas about the past, and the prevailing ideas, ideologies and approaches that influence thinking about the past. This thesis examines the historical culture that was endemic to citizens of London in the fifteenth and early sixteenth centuries.
The fifteenth century saw rising literacy amongst urban dwellers, an increase in manuscript production, and the onset of print culture. London also saw a localised phenomenon: the development of a civic chronicling tradition, the London chronicles, that had its high point in the period 1430-1516. This thesis situates London chronicles within the broader historical and literary culture of the period. It focuses on urban citizens, namely the merchants, craftsmen and others enfranchised freemen of London. In order to understand the historical writing of this period, education and governance are vital contexts.
Many chronicles were used in households, in the education of young people and apprentices. Prevailing ideas encouraged both authors and audiences of historical literature to view history as a pedagogic genre. Citizen household turned to historical literature as a means to teach morals, manners and political education.
Governance is also vital to understanding London historical culture. Governing institutions such as the Guildhall commissioned historical writing and founded archives and libraries to direct and control access to information. Citizens used origin stories to discuss the purpose and meaning of the institutions and offices of the city. Many officeholders owned or authored histories. Londoners used historical literature to reflect upon the politics of the day, discussing both the ideals and reality of government in London and the wider realm.

Keywords: medieval literature
history
London
medieval history
English literature
chronicles
urban history
historiography
Advisor: Watts, J
Novel approaches towards characterising the HIV reservoir: A combined microfluidic and target enrichment approach

The latent reservoir in human immunodeficiency virus (HIV) infection is a small population of long-lived infected cells that remain quiescent during suppressive antiretroviral therapy (ART). This reservoir is widely considered to be the major barrier to HIV cure, as in the absence of effective therapy the cells can become reactivated and cause recrudescent viraemia. A number of assays have been developed in an attempt to both quantify and improve our understanding of the reservoir. However, despite early promise the key factors that contribute to its establishment and persistence remain elusive.
The work undertaken in this thesis was directed primarily at improving the suite of tools available to clinicians and researchers targeting the latent reservoir in HIV infection. To date, the assays that have been designed to quantify and characterise the reservoir have limitations leading to either imprecise measurements or potentially biased analysis of viral sequences. By developing a modified target enrichment protocol, it was shown that diverse full-length proviral sequences can be captured whilst avoiding the bias commonly introduced by PCR-based sequencing methods. In addition, this pipeline allows for the identification of integration sites from the same sample.
The major hurdle facing reservoir assays is the inability to distinguish a latently infected cell from an uninfected cell by cell surface markers. To bypass this requirement, this thesis presents a microfluidics pipeline aimed at using the resident provirus as a means of identifying a latently infected cell. By encapsulating single cells in water-in-oil droplets, it is possible to lyse the cells and perform a PCR reaction targeting the HIV genome. In the presence of HIV, droplets fluoresce and are labelled for dielectrophoretic sorting. Post sorting, nucleic acids can be reclaimed from the droplets for downstream analysis on a purified subset of latently infected cells.
The two assays proposed within this thesis have the potential to profoundly change our understanding of HIV latency. In addition to this, as clinicians enter a new era of treatment interruption studies, changes in reservoir size and composition are becoming a desirable metric.
Overall, the foundation laid down in this thesis provides a solid base from which to begin applying both assays to clinical cohorts.

Keywords: next-gen sequencing
single-cell
latent reservoir
HIV
droplet microfluidics
Advisor: Frater, J
Ansari, A
Thomas Kling: a poet in the late Bonn Republic

This dissertation looks at Thomas Kling’s poetry in the context of the late Bonn Republic. While several studies have already investigated how Kling created history in his poetry, they rarely discussed how he himself was exposed to it. Thus, one of the main objectives of the following dissertation is to scrutinise Kling’s own historicisations and to expose the underlying assumptions of his version of the past and their rootedness in the current cultural climate. While many studies have echoed the opposition that Kling himself created between his poetry and that of the 1970s, this dissertation focusses on continuities instead. For this purpose, it looks at the history of the late Bonn Republic and West German poetry after 1945 in terms of changing emotional styles. The dissertation shows how Kling’s early poetry in the late 1970s was rooted in the emotional practices of the alternative Left (part I) and how their political and ecological concerns continued to resonate with his poetry in the following decade (part II). The question is how Kling went beyond the narrow concept of authenticity imposed by the alternative scene’s emotional style and which role models were available for his new self-stylisation (part III). While Kling’s poetry in the 1980s revealed authenticity and history as fundamentally unstable concepts that resulted from a set of culturally and historically determined practices (part IV), his poetry in the 1990s returned to more conservative and hierarchical models of history and authenticity characterised by modernist nostalgia (part V). Kling’s investment in an idealised version of the avant-garde and European modernity thus led to a limited version of the past that erased memories of German colonialism and its continuities with the First World War and the Holocaust.

Keywords: history of emotion
Thomas Kling (1957-2005)
colonialism
World War I
German identity
German Poetry after 1945
Holocaust
environmentalism
1980s
avantgarde poetry
World War II
gender
exoticism
masculinity
primitivism
German poetry
1970s
collective memory
Advisor: Morgan, B
Icelandic insular romance: replication, reflection, and networks of narrative and meaning

Critical study of Icelandic insular romances has been limited due to assumptions of poor literary quality and a lack of editions. This thesis constructs a corpus of Icelandic insular riddarasögur from thirty-four texts and explores the ways in which meaning is interwoven into their seemingly simple narratives through widespread repetitions and connections. The study introduces the concepts of “replication” (overt linking of two distinct elements) and “reflection” (the implications of such a comparison). Examples include lexical repetitions, recognisable narrative structures such as tripartite episodes, and broader semiotic features such as names and intertextual references. The aim of this thesis is threefold: to accumulate evidence in support of these conceptual networks; to explain and explore the effects these techniques have across the selected texts; and to interact with existing discussions about medieval Icelandic literature.
The first chapter focuses on a subgenre of romances, maiden-king narratives, to establish the basic principles of replication and reflection, while also considering the influence of exemplary literature. The second chapter uses the models of Continental romance to assess the presentation of knightly characters and demonstrates how replication and reflection can convey the value judgements of a particular composer or redactor. The third chapter contrasts this knightly world with a pool of broadly “Germanic” or “legendary” inherited material, showing how the composers engage in textual debates regarding the significance of Icelandic and Scandinavian heritage. The final chapter considers religious influences upon the romances, and how the narrative structures explored in the previous chapters can be augmented or subverted for spiritual purposes.
This thesis provides groundwork for further work on the genre. The study provides readings of specific texts, carefully situated within detailed analysis of their language and structures, and also introduces methodology and terminology for broader use.

Keywords: Icelandic literature
riddarasögur
medieval romance
narrative studies
Advisor: O'Donoghue, H
Learning to reconstruct and segment 3D objects

To endow machines with the ability to perceive the real-world in a three dimensional representation as we do as humans is a fundamental and long-standing topic in Artificial Intelligence. Given different types of visual inputs such as images or point clouds acquired by 2D/3D sensors, one important goal is to understand the geometric structure and semantics of the 3D environment. Traditional approaches usually leverage hand-crafted features to estimate the shape and semantics of objects or scenes. However, they are difficult to generalize to novel objects and scenarios, and struggle to overcome critical issues caused by visual occlusions. By contrast, we aim to understand scenes and the objects within them by learning general and robust representations using deep neural networks, trained on large-scale real-world 3D data. To achieve these aims, this thesis makes three core contributions from object-level 3D shape estimation from single or multiple views to scene-level semantic understanding.
In Chapter 3, we start by estimating the full 3D shape of an object from a single image. To recover a dense 3D shape with geometric details, a powerful encoder-decoder architecture together with adversarial learning is proposed to learn feasible geometric priors from large-scale 3D object repositories. In Chapter 4, we build a more general framework to estimate accurate 3D shapes of objects from an arbitrary number of images. By introducing a novel attention-based aggregation module together with a two-stage training algorithm, our framework is able to integrate a variable number of input views, predicting robust and consistent 3D shapes for objects. In Chapter 5, we extend our study to 3D scenes which are generally a complex collection of individual objects. Real-world 3D scenes such as point clouds are usually cluttered, unstructured, occluded, and incomplete. By drawing on previous work in point-based networks, we introduce a brand-new end-to-end pipeline to recognize, detect, and segment all objects simultaneously in a 3D point cloud.
Overall, this thesis develops a series of novel data-driven algorithms to allow machines to perceive our real-world 3D environment, arguably pushing the boundaries of Artificial Intelligence and machine understanding.

Keywords: 3D Segmentation
3D Reconstruction
3D Point Clouds
3D Scene Understanding
Advisor: Trigoni, A
Markham, A
Uncovering the role of RNA-binding proteins in plant immunity

RNA-binding proteins (RBPs) are essential regulators of RNA fate, from synthesis to decay. Hence, changes in the RBPome orchestrate the reprograming of RNA metabolism and gene expression that occur during plant responses to a myriad of cues, including pathogen attack. Although RBPs are known to play critical roles in plants, we lack comprehensive information on the identity and function of RBPs in different species. Moreover, it remains unknown how RBPs globally respond to different environmental, physiological and pathological cues.
Here, we have developed ‘plant RNA-interactome capture’ (ptRIC), a variant of RNA-interactome capture (RIC) optimised for plant tissues that allows efficient system-wide identification of RBPs in leaves. We used ptRIC to identify the most extensive Arabidopsis RBPome to date, which includes more than 1100 RBPs, and showed that it displays all the hallmarks expected from a high-quality RBPome. We have used ptRIC to uncover, for the first time, the RBPome of six additional plant species that span across the plant kingdom. This revealed hundreds of unconventional RBPs with no known RNA-binding domains or previously unlinked to RNA biology, including photosynthetic components and metabolic enzymes. By comparing the RBPomes discovered in these different species we have determined the ‘core plant RBPome’, which is composed by RBPs conserved from bryophytes to angiosperms. Using ptRIC we discovered that the Arabidopsis RBPome is extensively reconfigured during plant immune responses. Almost 300 RBPs displayed altered association with RNA in response to the bacterial elicitor flg22. Moreover, these alterations that cannot be explained due to changes in protein abundance, indicating that they are due to changes in RNA-binding activity. Through immunity-based mutant screens, we have discovered that several of these flg22- responsive RBPs play a role in immunity against bacterial pathogens.
Taken together, the results from this thesis provide a significant advance in the knowledge of RBPs in plants and their regulation during immunity. Hence, my results provide a framework for future studies on the role of RBPs in regulating important processes in plants.

Keywords: Nicotiana benthamiana
RBPome
Solanum lycopersicum
plants
RBP
Physcomitrella
Oryza sativa
Arabidopsis
immune system
RNA-binding proteome
ptRIC
PAMP-triggered immunity
Plant pathology
RNA-interactome capture
flg22
RIC
Marchantia
Nicotiana tabacum
RNA-binding proteins
Phaseolus vulgaris
Zea mays
Solanum tuberosum
Pseudomonas syringae
immunity
Advisor: Preston, G
Van Der Hoorn, R
Castello Palomares, A