VictorJuiz/thesis huggingface dataset:
Metal-insulator-metal plasmonic colour filters for CMOS image sensor applications
Keywords: Cavity resonators
Multispectral Imaging Sensor
Nanofabrication
Extraordinary Optical Transmission
Magnetic and Electric dipoles
CMOS image sensor
Surface Plasmon Polaritons
Hexagonal nanohole arrays
Metal-Insulator-Metal
Plasmonic Colour Filters
Narrow-band Optical Filters

Significant improvement in using plasmonic nanostructures for practical colour filtering and multispectral imaging applications is achieved by exploiting the coupling of surface plasmon polaritons with dielectric optical cavity resonances within a hexagonal array of subwavelength holes in a thin CMOS-compatible metal-insulator-metal (MIM) stack. This architecture overcomes the limitations of all previously reported plasmonic colour filters, namely poor transmission and broad band-pass characteristic, effectively providing a compact approach to selectively filter light. The physical insights established from the electromagnetic near-field patterns and parametric simulation studies are used to accurately tailor the optical properties of the filters.
Measured transmission efficiencies up to 60% and full-width at half-maximum between 45 nm and 55 nm along the entire visible spectrum are achieved - an impressive and unique combination of features that has never been reported before. The non-ideality of the fabrication at the nanoscale is addressed, the issues encountered highlighted and alternative solutions proposed and verified, demonstrating that the working principle of the MIM structure can be successfully extended to other materials and structural parameters.
Quantifying the adaptive power of the mobile integron
Keywords: experimental evolution
integron
antibiotic resistance

Mobile integrons are widespread and clinically relevant drivers of antibiotic resistance. Acting as genetic platforms, they allow bacteria to capture, express and re-order mobile antibiotic resistance gene cassettes, whose expression levels depend on their distance from the promoter, located at the integration site. Cassettes can be integrated and excised by the integrase enzyme, produced by the bacteria in time of stress. It has been hypothesized that integrons allow bacteria to adapt quickly to changing antibiotic pressures by reshuffling the cassette order, and therefore their resistance levels, such that integrons provide ‘adaptation on demand’.
To test this ‘adaptation on demand’ hypothesis, I used a custom three-cassette integron system transformed in both E. coli and P. aeruginosa. I first investigated the effect of cassette position on cassette expression at the phenotypic, transcriptional and translational level and confirmed a transcriptional origin of the cassette expression gradient, which was either strengthened or reduced by additional translational effects. I then combined experimental evolution and whole genome sequencing to quantify the evolvability benefits of cassette shuffling against increasing concentrations of antibiotics. By comparing strains with and without a functional integrase and focusing on two different cassettes and antibiotics, I observed striking differences in population survival rates and evolutionary pathways depending on the cassette and on the antibiotic. On one hand, with the antibiotic gentamicin and the aadB cassette, I saw an increase in evolvability and identified extensive cassettes rearrangements as well as cassette duplications in the populations with a functional integrase. On the other hand, with piperacillin and blaVEB-1, integrase activity was linked with decreased evolvability and a much lower rearrangement frequency, but I observed unexpected integron-mediated recombinations in the plasmid conjugation machinery.
These results highlight the key impact of antibiotics and cassette characteristics on the potential integrase shuffling benefits and provide novel insights on the dynamics controlling cassettes and integrase prevalence in the environment. In my experiments, high cassette mobility was necessary to compensate for the high fitness cost of integrase expression, or the integrase was a burden for bacteria survival. Moreover, I showed integrase activity was not limited to cassette shuffling or cassette acquisition but may also promote cassette duplication and beneficial off-target recombination, with far-reaching consequences on plasmid and antibiotic resistance evolution.
Structural determinants of Bunyavirus entry and neutralisation
Keywords: cryo-EM
virology
virus
hantavirus
structural biology
electron microscopy

The order Bunyavirales is comprised of numerous emerging zoonotic pathogens which present a global threat to human health. Many bunyaviruses are arboviruses including members of the family Nairovirdae such as the tick-borne Crimean-Congo haemorrhagic fever virus that is responsible for deadly outbreaks in Africa, East Asia and Southern Europe. Also among them are members of the family Hantaviridae which include Andes and Sin Nombre virus in the American continent and Hantaan and Puumala virus in Asia and Europe respectively. These are a hosted predominantly by rodents and frequently spill over into humans populations leading to hantavirus pulmonary syndrome and haemorrhagic fever with renal syndrome.
Bunyaviruses are often pleomorphic and are enveloped in a membrane harbouring just two surface glycoproteins, Gn and Gc. These glycoproteins are responsible for budding of the virus from the host cell, attachment to new target cells and release of viral RNA by membrane fusion. Furthermore, these glycoproteins are the target of the antibody-mediated host immune response and could form the basis for the development of future vaccines and immunotherapeutic medical interventions. The precise arrangement of these glycoproteins, and how these processes are mediated, are only partially understood for members of Hantaviridae and Nairoviridae. The goal of this thesis is to contribute to our understanding by addressing these topics using cryogenic electron microscopy (cryo-EM).
An initial description of the nairovirus surface is presented which displays a novel lattice of glycoproteins across its surface. An improvement to our understanding of the hantavirus glycoprotein array is made which enables, in combination with available crystallographic models, a near-complete pseudo-atomic model of the hantavirus surface to be proposed. In addition, the metastable nature of this lattice is demonstrated after exposure to low pH conditions equivalent of the endocytic pathway. A hantaviral virus-like particle (VLP) system is developed to provide a safe platform for structural studies of otherwise dangerous pathogenic species. This is then used to gain insights into hantavirus receptor interactions including Andes virus and the cell surface protein protocadherin-1. The VLP system is also used to study the structural mechanism of antibody-mediated host immune responses to Puumala virus and Hantaan virus. Finally, a number of tools and optimisations to assist and improve the cryo-ET and subtomogram averaging workflows that enable these structural studies are presented.
Tailoring nanomaterials for energy applications
Keywords: silicon
MWCNTs
carbon nanotube
Li-ion battery
anode

Silicon-based materials present high theoretical capacities (4200 mAh/g), making them among the most promising materials for Li-ion battery anodes. However, the major problem with them is massive volume change (∼ 300%) that occurs during cycling, resulting in pulverisation and significant capacity drop of these anode materials. Besides, the use of additives and metallic current collectors to make the anodes reduces the overall battery energy density as these components could not contribute any capacities to the battery. In this work, free-standing silicon-coated multi-wall carbon nanotube (MWCNT) anodes were developed without any polymeric binders and carbonaceous additives being added. These materials were achieved through exploiting atmospheric pressure chemical vapour deposition as well as advanced nanomaterials fabrication and processing methods. Electrodes were prepared utilising MWCNT papers (so-called buckypapers) as robust, electrically conductive flexible (22.2 S/cm) and free-standing scaffolds since the capacity of these buckypapers is too low to use as a new active material for the battery (0.3 mAh/cm2 in the 300th cycle). Hence, these buckypapers were functionalised with silicon nanoparticles attached through a strong silicon carbide interface and coated with a protective amorphous carbon layer. The SiC interface was partially developed between Si NPs and MWCNTs as excessive SiC could reduce electrochemical capability on the material due to its low electroactivity. The coin cell battery test demonstrated a high areal capacity of up to 2.01 mAh/cm2. These free-standing Si-CNT-SiC-C materials showed good rate capability and stability performance (0.55 mAh/cm2 after 300 cycles with coulombic efficiency of 99.7%). As a result, the material interface design, which is the key of this work, enhances the connection of Si NPs to the MWCNT walls and addresses the issue of Si detachment. A post-mortem result also revealed the structural stabilisation of the electrode after the repeated cycling test. In addition, the pouch-cell battery was fabricated to confirm the use of this free-standing Si-CNT-SiC-C electrode without the influence of the battery component. This new anode architecture performs better than the buckypaper, thereby increasing the areal capacity by 83.3%, allowing better functionality for this material to be implemented in a full-cell battery system.
Pursuing the universal: formalism, pragmatism and the project of modernity in contemporary critical democratic theory
Keywords: Frankfurt School
democratic theory
Habermas
pragmatism
Arendt
modernity

This thesis critically evaluates the role of form and formalism in contemporary Frankfurt School critical democratic theory’s treatment of ethical pluralism. It examines how three contemporary theorists, Jurgen Habermas, Rainer Forst and Alessandro Ferrara, deploy methodological formalism, and a certain ideal of aesthetic or theoretical ‘form’, in support of the Kantian ‘project of modernity’. The thesis has two related aims: the first is to diagnose and critically evaluate the role of form and formalism as an instrument of mediation between ethical identity, value pluralism and the ‘project of modernity.’ In the course of identifying and assessing the intellectual resources that underpin the role of form and formalism in the relevant critical theories of democracy, this thesis argues that the strategies for normative and constitutional integration pursued by Habermas, Forst and Ferrara suffer from a hermeneutical deficit. Consequently, while they set out to develop an ethically non-impositional framework for negotiating between normative universality and ethical particularity, these three theorists also continue several of the weaknesses of Kantianism, including its dichotomous separation of normative ‘form’ from the texture of ethical life and its resident meanings. While Habermas, Forst and Ferrara all seek creatively to integrate the insights of philosophical pragmatism by developing immanently grounded ‘inter-subjective’ theories of normativity, their deployment of form as an ethically diminutive binding agent displays a limited reflexivity regarding the ideological specificity of aesthetic and methodological formalism.
The second aim, in light of these criticisms, is to suggest an alternative method by which to theorise a deliberatively developed normative commonality amidst ethical pluralism - one that draws upon the philosophical pragmatism of John Dewey, Hans Joas, James Bohman and others. I argue, in conversation with these thinkers of a pragmatist bent, and with reference to recent contributions to the sociology of religion, for an account of value generalisation as a form of ‘world-building’ deliberative action oriented towards what Hannah Arendt calls ‘a common world.’ In so doing, I question the role of the ‘comprehensive social theory’ of normative integration amidst value pluralism, and instead look to theoretically enunciate and develop deliberative practices that plausibly effect ‘practical transformations’ of existing social challenges.
Study of electrode kinetics
Keywords: Surface quinone
Thermal convection
Mass transport corrected Tafel analysis
Electrode kinetics
Mass transport
Band electrode
Microelectrode
Electrocatalysis
Tafel analysis

This thesis reports the use of Tafel analysis in the study of electrode kinetics from both theoretical and experimental perspectives.
During electrochemical measurements, any changes in temperature cause changes in diffusion coefficient of the species, the electrochemical rate constant and the equilibrium potential. Concequently, the improtance of temperature control in electrochemical systems is first investigated. When and how thermally induced convective flows in bulk solution influence the votlammetric behaviour are presented in Chapter 3.
Chapters 4 and 5 theoretically discuss what fraction of a voltammetric wave is appropriate to use as the Tafel region for accurate analysis under linear, quasi-steady-state and steady-state mass-transport regimes for an irreversible one-electron transfer process. The measured transfer coefficient is found to deviate significantly from its true value as a function of potential due to the mass-transport limitation at high overpotentials. If and how a simple analytical mass-transport correction using a plot of ln |1I-1Ilim| against potential can be used to improve the measurement of transfer coefficient is investigated. The methodology of measuring transfer coefficient is further employed in the electrochemical characterisation of a single microband electrode with unknown dimensions (Chapter 6). Such Tafel analysis is applied to an experimental study where the intrinsic surface quinones on carbon substrates can catalyse Fe2+/3+ redox reaction evidenced by a potential dependent transfer coefficient (Chapter 7).
Last but not least, a new simulation techinique is developed in Chapter 8 to extract the kinetic information from experimental voltammograms for electrodes under both radial and liner regimes on the basis of the prior knowledge of the physical parameters defining the system, most importantly the diffusion coefficient, analyte concentration and electrode radius.
Investigation of type 2 cytokine pathways as modulators of haematopoiesis during chronic inflammation
Keywords: Anaemia
Haematopoiesis
Spondyloarthritis
Erythropoiesis
Immunology
Inflammation
Haematology

Chronic inflammatory diseases often promote bone marrow (BM) myelopoiesis at the expense of erythropoiesis and lymphopoiesis, facilitating production of mature myeloid cells to sustain the inflammatory response. In previous studies, type 2 cytokines, including IL-4, IL-5, and IL-33, have been suggested as possible regulators of haematopoiesis, but their role in modulation of haematopoiesis during inflammation was unknown. Spondyloarthritis (SpA) is a chronic inflammatory disease of people that has systemic sequelae, including anaemia. Although associated with type 17 immune responses, there is evidence of a concurrent type 2 response in the intestine of people with SpA. In this thesis, I sought to bring these areas of investigation together by asking if a possible type 2 immune module in murine SpA might be implicated in changes in haematopoiesis, and whether this would be important for progression of disease.
I find inflammation perturbs haematopoiesis in murine SpA, causing a marked bias towards myelopoiesis in the BM, as well as accumulation of myeloid progenitors in spleen and inflamed joints. Conversely, BM erythropoiesis is suppressed, resulting in anaemia. I find that mice also have evidence of a type 2 immune module in the intestine, with increased numbers of cells producing IL-4 and IL-5, and increased production of IL-33. Of these cytokines, IL-4 has pro-myelopoietic effects in vivo and ex vivo, but my results suggest this pathway is not important for development of clinical disease or expansion of myelopoiesis in SpA. Conversely, I find that IL-33 specifically suppresses differentiation of erythroid progenitors. This effect is implicated in development of anaemia in SpA, with IL-33 also causing resistance to the effects of erythropoietin (EPO). Interleukin-33 also promotes myelopoiesis through a combination of direct and indirect effects on progenitor stages, indicating that IL-33 has co-ordinated effects in different parts of the haematopoietic system that may be consistent with its role as an alarmin.
Collectively, my work reveals IL-4 and IL-33 as regulators of myelopoiesis, which may be important in disease settings associated with increased production of these cytokines. I further identify IL-33 as a mediator of anaemia of inflammatory disease and EPO resistance in murine SpA, suggesting that IL-33 could be a therapeutic target for this prevalent and debilitating comorbidity in people with chronic inflammation.
Understanding why quality circles work in primary health care: a realist approach about how, why and under what circumstances they work
Keywords: Quality in Health Care
Quality Circle
Primary Health Care
Continuous Professional Development
Quality Improvement
Continuous Medical Education
Knowledge Translation
Peer Review Group

Quality circles and similarly structured small groups are commonly used in primary health care in Europe to reflect on and improve standard practice over time. They are a complex social intervention in the fast-changing system of primary health care. Many controlled trials and reviews have documented their positive effects on behaviour change. As effect sizes vary, I sought to understand how and why quality circles achieved their results by using a realist approach.
I conducted a co-inquiry with stakeholders to determine their interests and preferences concerning the direction of my research, and their mental model of quality circles, which I used as a framework for my realist review. After identifying relevant papers and selecting and extracting appropriate data, I labelled and analysed configurations of context and mechanism that shaped the outcomes of quality circle work. From these, I built propositions to develop a programme theory underlying quality circles, then refined and consolidated this in sequential interviews with participants, facilitators and managers of quality circles.
The programme theory suggests that government trust in GPs’ ability to achieve quality improvement, with appropriate professional and administrative support, will motivate them to participate in quality circle work. Professional support includes training in relevant techniques, access to educational materials and personal performance data. Administrative support includes protected time, an appropriate venue and financial resources for meetings. Group dynamics are at the core of the process. Facilitators help participants to build social bonds and mutual trust so that the group becomes a safe environment where participants link insights to everyday practice to develop their professional role. They reflect on their personal experiences, add information from evidence-based or personal performance data and thus create new concepts for improving their practice. With repetition, they gain confidence in their quality improvement skills and can put their innovations into practice.
Time-lapse super-resolution imaging reveals key principles for cis-limited Xist RNA localisation
Keywords: SPEN
3D-SIM
X chromosome inactivation
Xist
Super-resolution microscopy
Ciz-1

Dosage compensation in XX female mammals is achieved by X chromosome inactivation (XCI). The key player in this process is the long noncoding RNA Xist (X inactive specific transcript), which associates in cis with the inactive X chromosome elect (Xi) to mediate gene silencing and heterochromatization. Xist spreads across the entire Xi, but little is known about the dynamics of this process, particularly in the context of single cells. This thesis documents the development of a new, time-resolved super-resolution imaging methodology: RNA-SPLIT (Sequential Pulse Localisation Imaging over Time) combining Bgl-stem-loop labelling, HaloTag technology and 3D structured illumination microscopy (3D-SIM) to detect individual Xist RNA molecules in single mouse embryonic stem cells (mESC) with high spatial and temporal resolution.
XY and XX mESCs expressing inducible autosomal transgenic or endogenous Bgl-stem-loop tagged Xist in tandem with BglG-Halo fusion protein were used to visualise distinct, functional Xist foci and analyse their spreading behaviour across the Xi during early XCI. RNA-SPLIT yielded important insights into Xist RNA kinetics, localisation and spreading behaviour during XCI and a feedback mechanism linking Xist RNA synthesis and degradation. RNA-SPLIT also uncovered novel coupling behaviour of Xist RNA molecules which, using perturbation experiments with CIZ-1 and SPEN, was shown to be independent of Xist localisation to the Xi, but dependent upon SPEN. In depth analysis demonstrated SPEN to have separable, SPOC domain independent functions in Xist RNA localisation, stability and coupling behaviour.
Strikes and discontent in the French empire and beyond 1947-48
Keywords: French Empire
Transnational Modern French History
Post-World War II France
Industrial Unrest
French Strikes 1947-1948

This thesis examines French post-war strikes in a new light. The first half exhumes the subterranean sources of discontent which powered these movements. The memory of wartime hardships or torture endured long after hostilities ended. The preservation of concentration-camp like detention centres, and the erection of confining ONCOR barracks, ensured l’univers concentrationnaire remained a permanent fixture in the psychological and architectural landscape of the immediate post-war years. These factors, combined with exhaustion from overwork, the selective heroism of the battle for production, the judicial persecution of respected maquisards, and rose-tinted portrayal of Eastern Europe in the communist and even centrist press, describe the ‘impossibility of demobilization’ which lurked behind demands for more food or higher wages. Post-war strikes signalled the continuation of grudges left over from World War II and the Occupation. Moreover, news of anti-labour legislation and repression abroad, kept CGT unionists on a constant war-footing and bred fears that similar measures could intrude on French soil.
The second part of the thesis contextualises the 47-48 strikes in a global setting and argues an ‘impossibility of demobilization’ infected police, intelligence services, and administrations throughout France and its empire as well. Colonial authorities interpreted benign strikes as attempts to topple French rule, while anti-communism and xenophobia resulted in the mistreatment and deportation of Polish, Spanish, Italian, and Romanian workers or associations in the metropole; actions which had significant repercussions. Democracies in the West and emerging communist regimes in the East exploited the fallout of the 47-48 strikes. They prompted Quebecois authorities to overreact to unrest in Asbestos, while Dutch economic courts punished trade unionists for sending financial aid to French strikers. Meanwhile, Hungarian, Czech, and Polish communist propaganda machines instrumentalized French strikes, both to discredit capitalist nations in the West at home and to market the ‘superiority’ of communism abroad.