VictorJuiz/thesis huggingface dataset:
Imperial health: centralisation of medical institutions in the British South Pacific
Keywords: British Empire
health service
medical institutions
imperial health
indigenous healthcare
Pacific Islands
South Pacific
regionalism

This thesis aims to explain the centralisation of medical institutions in the South Pacific, with a focus on the British Empire. It traces the origins of international health in the Pacific to colonial policies by examining the discussions, establishments, and operations of centralised medical institutions. With the British and New Zealand territories as core members, thirteen colonial administrations across five imperial powers were involved in the development and operation of the following institutions: the Central Leper Hospital, the Central Medical School, the Central Nursing School, the Western Pacific Health Service, the South Pacific Health Service, the Fiji Military Forces, and the Second New Zealand Expeditionary Forces. By analysing the discourses surrounding the centralisation process and the operation of centralised institutions, this thesis teases out the intercolonial and sub-imperial relations in the South Pacific. In doing so, this thesis reveals that healthcare in the South Pacific was uniquely shaped by cooperation between colonial administrations to find the most efficient medical services for the Pacific Islands. This thesis is a pioneering study to identify an organised agenda to establish a single healthcare system across colonies.
Modelling the folding pathway of DNA nanostructures
Keywords: oxDNA
Monte Carlo simulation
self assembly
DNA nanotechnology
kinetic Monte Carlo
Gillespie algorithm
domain-level model of DNA
umbrella sampling
coarse-grained modelling
DNA origami

DNA origami is a robust technique for bottom-up nano-fabrication. It encodes a target shape into uniquely addressable interactions between a set of short 'staple' strands and a long 'scaffold' strand. The mechanisms of self-assembly, particularly regarding kinetics, need to be better understood. Origami design usually relies on optimising the thermodynamic stability of the target structure, and thermal annealing remains the most fool-proof assembly protocol. This work focuses on studying the folding pathway of three types of origami through simulations: a reconfigurable T-junction origami, several traditional origami, and origami with coated scaffolds.
The T-junction origami is intended as an economically feasible method of changing the uniqueness of interactions. My contribution to this work is to characterise the basic structural motif through oxDNA, a nucleotide-resolution model of DNA. The thesis then focuses on extending a domain-level model of DNA origami to study several experimental origami designs. We reveal design-dependent free energy barriers using biased simulations and relate this to the observed hysteresis in experiments. We also highlight the role of specific design elements in determining the folding pathway. A novel method of lowering the temperature of error-free assembly using coated scaffolds is then presented, with simulations indicating the existence of an activation barrier. By exposing particular regions of the scaffold, we can lower assembly time and temperature.
New applications of rhodium-catalysed hydroacylation
Keywords: cyclisation
rhodium catalysis
hydroacylation

This thesis describes the development of two new rhodium-catalysed hydroacylation methods. The first involves a one-pot hydroacylation/thio-conjugate addition cascade towards the synthesis of fully saturated sulfur heterocycles. The second exploits novel β-sulfonyl aldehydes to access β-keto-sulfones and sulfonamides.
Chapter 1 delineates a literature review of the evolution of rhodium-catalysed hydroacylation, with focus on catalyst design and chelating groups that hinder decarbonylation. The use of hydroacylation in heterocycle synthesis is also briefly reviewed.
Chapter 2 documents the use of alkynes with pendant sulfur nucleophiles in a highly regioselective rhodium-catalysed hydroacylation reaction, delivering linear α,β-unsaturated enone intermediates. These adducts are further harnessed in intramolecular cyclisation reactions to access diversely substituted, saturated S-heterocycles, in a one-pot fashion.
Chapter 3 outlines initial attempts to develop a rhodium-catalysed hydroacylation methodology for the synthesis of β-keto-sulfones and sulfonamides. The work explores the construction of new β-sulfonyl aldehydes and their use in intermolecular hydroacylation.
Chapter 4 presents the conclusions from the research conducted and future work.
Chapter 5 details the experimental data and procedures.
Modular network comparison with application to labour flow networks
Keywords: labour flow networks
economic geography
knowledge flows
network comparison

Evolutionary economic geography emphasises the role of locally embedded skills and knowledge in regional economic development processes. A region grows into new economic activities by combining locally available skills. This is typically modelled as a branching process on an inter-industry labour flow network, where a region’s probability of entering an industry is a function of the related industries available. In this thesis, we develop new methodologies that support the analysis of these labour flow network models.
In the first part of this thesis, we develop new metrics to compare the modular structure of different networks. The motivating application is the comparison of different countries’ inter-industry labour flow networks. More specifically, we present a novel approach for the global modular comparison of two node-aligned networks. The measure quantifies the difference in the quality of the partition of two graphs by projecting the community structure of each graph onto the other. The technique is advantageous as it captures the influence of the underlying network structure and applies to a broad range of networks as it is agnostic to the quality function adopted.
Building on this framework, we also present a fine-grained modular comparison technique, which compares the modular structure of a single community across two networks. The measure compares the expected escape probability of a random walker, initially starting in the community, across the two networks. The measure is advantageous as it captures the impact of edge density and connectivity on the modular structure of the community.
In the second part of the thesis, we investigate two economic questions. First, we investigate whether the presence of related multinational enterprises (MNE) results in knowledge spillovers that foster new related domestic industries in Irish regions. We propose a new dynamic-based cohesion measure for an inter-industry labour flow network that captures the impact of higher-order linkages between an industry and the industrial portfolio of a region. We find that industries containing both domestic and MNE firms enhance the entry and survival of related domestic industries within a region, while industries dominated by MNEs have the opposite effect.
Finally, we consider the indirect impact of an affirmative action policy on inter-industry gendered labour mobility patterns in South Africa. By harnessing a regression discontinuity design with an entropy-based centrality measure, we investigate how the policy has impacted the sectoral diversity of new employees in firms. We find that the policy widened the sectoral diversity of female workers, particularly the related variety of skilled female workers. However, unlike results in the literature, this did not translate into any significant impact on firms’ performance.
Radio wave activated chemotherapy
Keywords: nanotechnology
smart materials
nanomedicine
remote activation
targeted drug delivery

As one of the most common cancer treatments used in treating patients, chemotherapy has saved countless lives. However, due to the lack of specificity provided by conventional chemotherapy, healthy tissue as well as tumour tissue is destroyed as a result of collateral damage. The side-affects reduce the quality of life of patients so much so, that in some cases, they refuse the potentially lifesaving treatment altogether. The underlying problem with conventional chemotherapy lies in the fact it is not discriminant enough in targeting cancerous cells.
This thesis presents a nanoparticle copolymer complex that is capable of actively targeting cancer cells and limiting drug release until an external stimulus “activates” the complex. The targeting manifests itself through the enhanced permeation and retention effect between nanoparticles and cancer cells, and magnetic localisation at the target location in vivo. Activation is triggered by radio wave induced inductive heating of an iron oxide nanoparticle core that causes a structure change in the grafted copolymer, releasing drug bearing proteins. The novel grafted copolymer has been meticulously designed to reversibly immobilise drug bearing proteins and undergo a structure change at a temperature of 42.5 ˚C, above that of human body temperature, but below that of hyperthermic temperatures.
Ultimately, this nanoparticle copolymer complex would be administered to patients via injection or consumption, magnetically localised in tumour locations within the body using external magnets, and selectively taken up by cancer cells due to the EPR effect. When particles have accumulated in the desired site, a harmless alternating magnetic field would be induced in target areas around the body and the drugs released. If successful, this complex treatment could provide an effective delivery system for many types of chemotherapy molecules while eliminating side effects of treatment completely.
Understanding mechanisms of pathogenesis and resistance in Neisseria gonorrhoeae
Keywords: Neisseria gonorrhoeae
conjugation
serum resistance
plasmid
CFHR

Neisseria gonorrhoeae is a leading cause of sexually transmitted disease worldwide. Recently, N. gonorrhoeae has become a significant public health concern due to increasing antimicrobial resistance (AMR). Therefore, novel ways to tackle N. gonorrhoeae infection are required. My work aimed to address this by further understanding gonococcal interactions with complement and by providing insights into plasmid-mediated AMR.
Previous research demonstrated that N. gonorrhoeae binds Complement Factor H (CFH), a negative regulator of the human complement system, to avoid complement killing. Here, I showed that N. gonorrhoeae also binds to Complement Factor H Related protein 5 (CFHR5) which does not negatively regulate the complement system. I demonstrated that CFHR5 binds to PorB, a gonococcal surface porin, and that CFHR5 and CFH bind to several of the same external loops of PorB.
The spread of plasmid-mediated AMR in N. gonorrhoeae is due to the conjugative plasmid, pConj. Therefore, I investigated the spread and maintenance of pConj. I showed that pConj is largely restricted to N. gonorrhoeae, is extremely stable once acquired, and is highly conserved. I investigated the basis of why pConj is mostly found in particular gonococcal lineages, and showed a correlation between prevalence of the plasmid in a lineage, and the ability of strains from that lineage to acquire pConj. A subsequent unbiased genetic screen failed to identify chromosomal genes involved in pConj acquisition.
Finally, I defined the mechanisms of pConj maintenance and showed that both partitioning and toxin-antitoxin (TA) systems are involved in plasmid maintenance; TA systems on the gonococcal cryptic plasmid could contribute to pConj maintenance through a split TA system. Lastly, I showed that pConj can be cured by interfering with plasmid partitioning.
Overall, my findings provide insights into novel ways of that could be exploited for tackling gonococcal disease through immunotherapy or plasmid destabilisation.
Musical warriors: British military music and musicians during the French Revolutionary and Napoleonic Wars
Keywords: music
popular politics
army
war and society
military
musicians

Military music was pervasive in Britain and Ireland during the French Wars but has received limited attention from historians. This thesis interprets martial music-making as a core military activity and an integral part of wider musical culture. A critical tool of communication and discipline, music sounded the alarm, aided recruitment, and governed soldiers’ routines and bodily movements. Officers invested heavily in military bands, regarding them as social amenities, sources of prestige, and essential for maintaining soldiers’ morale. Regiments competed and cooperated in a seller’s market for musical labour, engaging knowledgeable civilian performers and training a mass of novice instrumentalists through a cogent instructional programme.
Attention to music reveals the depth and reciprocity of interactions between the military and society. Regimental bands provided sought-after entertainment at myriad public events, staged free open-air concerts for socially diverse audiences, and amplified wartime expressions of patriotism. Military performers also promoted cultural dissemination and exchange, rehearsing eclectic repertoires and adopting melodies from other regiments, armies, and peoples.
Military mobilisation palpably shaped nineteenth-century musical culture. Volunteer and militia bands established in wartime continued playing together for decades after Waterloo while discharged regimental instrumentalists actively contributed to provincial and colonial musical life as teachers, performers, and retailers. The expansion of military music-making also encouraged the post-war spread of amateur wind and brass bands, which were often led by old soldiers and modelled on regimental lines. Ingrained in popular culture after two decades of conflict, martial music was widely emulated by political reformers with the involvement of musically trained ex-servicemen.
Military music, in sum, was an everyday and intrusive part of wartime life, a source of entertainment and opportunity, and a politically charged exponent of both patriotism and protest. The legacies of martial music-making, as this thesis argues, echoed far beyond the barrack gates.
Variational autoencoders for supervision, calibration and multimodal learning
Keywords: VAEs
semi-supervised learning
calibration
multi-model Learning

Learning representations of data has long been a desirable goal in machine learning. Constructing such representations enables downstream tasks such as classification or object detection to be preformed efficiently. Furthermore, it is desirable to have these representations be constructed in such a way so they are interpretable, which allows for fine grained intervention and reasoning on characteristics of the input. Other tasks may include, cross-generation between modalities, or calibrating predictions such that their confidence matches their accuracy. An effective way to learn representations is through a Variational Autoencoder (VAE), which performs variational inference on the latent variables of the observable input. In this thesiswe show how the VAE, can be utilised to: incorporate label information into the learning process; learn shared-representations of multimodal data; and calibrate predictions of existing neural classifiers.
Data sources are often accompanied by additional label information, which may indicate the presence of a characteristic in the input. A question naturally arises as to whether the additional label information can be used to structure the representation such that it provides a notion of interoperability about the characteristic; such as “to what extent is the person smiling?”. The first contribution of this thesis is to address the aforementioned problem and propose a method which successfully uses label information to structure the latent space. Furthermore, this allows us to perform additional tasks such as fine grained interventions; classification; and conditional generations. Moreover, we are also successfully able to handle the case when label information is missing, drastically reducing the data burden when training these models.
Rather than being presented with labels, we sometimes instead observe another unstructured observation of the same object, e.g. a caption of an image. In this scenario, the objective changes slightly to one where the model is able to learn shared-representations of data, allowing it to perform cross-generations between modalities. The second contribution of this theses addresses this problem. Here, learning is performed by employing mutual supervision between the modalities and introducing a bi-directional objective, which faithfully ensures symmetry in the model. Furthermore, by virtue of this approach, we are able to learn these representations in situations where some of the modalities may be missing during training.
Uncertainty quantification is an important task in machine learning, with it now being well known that current deep learning models severely overestimate their confidence. The final contribution of this thesis is to address how the representations of VAEs can be used to extract reliable confidence estimates for neural-classifiers. This investigation leads to a novel approach to calibrate neural-classifiers, which is applied post-hoc to off the shelf classifiers and is very fast to train and test.
Signatures of quantum gravity
Keywords: quantum gravity
quantum information
events
spacetime

This thesis discusses the hurdles that are frequently encountered in attempts to quantize gravity or rather, while gravitizing quantum mechanics. Among the issues we consider here are the lack of observable signatures of the quantum nature of gravity despite the considerable amount of effort directed towards theoretical approaches such as string theory and loop quantum gravity, to name a few. Here, we examine observable consequences of quantum gravity through superpositions of primordial massive particles and quantum witnesses in table top experiments involving Bose Einstein Condensates. We compute the decoherence timescales of a primordial superposition and outline its effects in the form of an interference pattern, characteristic absorption spectra or entanglement effects. While it is difficult to conceive of a way to control measurements that occur in the early universe, such as the measurement of curvature perturbations during inflation, we have a significant degree of control over quantum systems in the laboratory such as Bose Einstein Condensates for which we propose a non-Gaussianity based witness of the quantum nature of gravity. Non-Gaussianities are also discussed in the context of cosmological observations where it becomes important to distinguish primoridal non-Gaussianities from secondary effects. While observing any of these signatures can give credence to the requirement that gravity should be quantum, insight can also be drawn between conflicts that exist between general relativity and quantum mechanics. One such anomaly we discuss is the cosmic censorship conjecture and its reconciliation with quantum information theory. In particular by employing the complexity-volume conjecture from the AdS/CFT correspondence, we show that for Kerr black holes, spacetime must continue across the Cauchy Horizon where solutions to the Einstein field equations break down. Finally, we introduce a formalism that attempts to bridge the gap between quantum theory and relativity by putting spacelike and timelike events on the same footing. The notion of an event, redefined as a correspondence between a system and an apparatus, gives rise to interesting predictive phenomena and allows us to apply the tools of quantum information theory in their characterisation.
Engagement, surprise and exploration in the macaque frontal lobe
Keywords: learning
motivation
fMRI
decision-making
macaque

In this thesis I investigate how macaque monkeys make reward-guided decisions. Specifically, I investigate behavioural, computational, and neural mechanisms for detecting and learning from surprising events, choosing whether to explore or exploit, and staying engaged. Using fMRI data of macaques performing different tasks, I identify neural activity patterns underlying these types of behaviours. I demonstrate that macaques notice reward-based surprises beyond scalar reward prediction errors: I link neural activity on the orbital surface both to obtaining a surprisingly rare amount of reward (Chapter 2), and to counterfactual prediction errors associated with an unchosen option (Chapter 3). I show that the signals related to rare reward surprise only occur when the reward-environment is sufficiently complex and incentivises learning: such surprise signals could only be detected when the underlying reward probabilities changed over the course of a session, while I find no surprise signal for static reward environments. I also demonstrate that macaques strategically modulate their tendency to explore or exploit depending on the reward-environment, and link such behaviours to different signs of reward-value signals in anterior- and mid-cingulate gyrus (Chapter 3). Finally, I identify general neural signals associated with engaging with a task rather than pausing to respond (Chapter 4). To this end, I show that a network of regions spanning perigenual anterior cingulate cortex, orbitofrontal cortex and striatum is more active when animals are engaged with a task, and causally link activity in perigenual anterior cingulate to task engagement using transcranial ultrasound stimulation. By contrast, mid- and posterior cingulate are more active when animal spontaneously disengage from a task. Using data from four distinct decision-making tasks, and controlling for all factors that were manipulated in these tasks, allows me to show that these engagement-patterns are task-independent and capture an intrinsic component of motivation not previously studied.
'You can write whatever you want': exploring the relationship between student self-concept and creative writing practices
Keywords: MLT 2020
MLT

This project sought to investigate whether guided creative writing processes can have an impact on students’ self-concept in domains related to the topics about which they are writing. To investigate this, a creative writing project focused on prose science fiction was designed and delivered to a class group of secondary school students in Dublin, Ireland. A second class group from the same school took part in a poetry writing project and served as the control group for this study. A questionnaire to measure self-concept in two domains (creative and scientific) was delivered to both groups before and after the intervention. Results were to be triangulated using semi-structured interviews with participants in the intervention group and the adult collaborators who worked with them but, as a result of the COVID-19 pandemic, these could not be completed. Due to the disrupted research, conclusions could not be drawn from the data collected. An evaluation of the intervention design, however, indicates that it satisfied most of the criteria suggested by the literature review and that a repeat investigation, when circumstances allow, is warranted.