VictorJuiz/thesis huggingface dataset:
Experimental and theoretical techniques for quantum-enhanced metrology and optical quantum information processing
Keywords: Quantum metrology
Quantum optics
Quantum information processing

Over the last few decades, quantised excitations of the electromagnetic field have proven to be an ideal system with which to investigate and harness quantum optical phenomena. The techniques developed have enabled fundamental tests of quantum mechanics as well as practical applications in quantum metrology and quantum information processing. Advancing to larger-scale entangled quantum systems will open up new regimes of quantum many-body physics, allowing us to probe the limits of quantum mechanics and enabling truly quantum-enhanced technologies. However, moving towards this goal will require further experimental and theoretical innovations. The work described in this thesis focuses on several different aspects of optical quantum information, but are ultimately all linked by this long-term aim. The first part of this thesis describes a novel method for strain-based active control of quantum optical circuits and a new method for the characterisation of high efficiency detectors. Building on this, I discuss in detail two different fields of quantum optics that stand to benefit from these techniques. I initially consider quantum-enhanced metrology, including work aimed towards demonstrating a truly better-than-classical phase measurement, and a theoretical exploration of multiple-phase estimation. Finally, I focus on linear-optical quantum information processing, exploring in detail the use of time-frequency encodings for quantum computing.
Ediacaran discoidal impressions and related structures from Newfoundland, Canada and the Long Mynd, Shropshire, UK: their nature and biogenicity
Keywords: Ediacaran biota
Discoidal Ediacaran fossils
Hiemalora
Aspidella

The nature of the Ediacaran macrobiota (c. 580-541 Ma) remains puzzling. These first assemblages of large, complex fossils may have included early animals; giant microbial forms; and organisms representing radically different body plans that went extinct. Discoidal impressions – some forming the base of Ediacaran fronds but most found as isolated discs – dominate the Ediacaran macrobiota. However round markings may also be formed in a variety of abiogenic ways. This study investigates the nature and biogenicity of discoidal impressions from two Ediacaran successions: the c. 560-Ma upper Burway Formation, Longmyndian Supergroup, Shropshire, UK; and several sites on the Bonavista and Avalon Peninsulas, Newfoundland, Canada, ranging in age from 565–c. 560 Ma.
The investigation involved fieldwork, photography, serial grinding through cross-sections, and optical and scanning electron microscopy. It concludes that several Longmyndian discoidal forms are pseudofossils formed by sediment injection resulting from small-scale fluid escape inferred to be driven by microbial mat sealing. Turning to clearly biogenic impressions, comparison of the varied morphologies of holdfast discs associated with fronds preserved under ash and sand from several Newfoundland sites leads to a generic model of their architecture as consisting of enclosed chambers, a complex construction perhaps for strength or possibly symbiosis. Detailed observations of the rayed disc Hiemalora suggest that it may have had an amoeboid lifestyle. Finally, the key Ediacaran taxon Aspidella is separated from the discs Ediacaria and Spriggia, with which it has been synonymized, and interpreted as a possible polyp-like animal capable of limited movement. This thesis thus demonstrates that the earliest reported Ediacaran discoidal impressions are abiogenic, produced by mat-influenced processes particularly relevant to the Precambrian, and proposes models and interpretations for several key Ediacaran forms that have important implications for both the nature and diversity of the Ediacaran macrobiota, and early animal evolution.
Synthetic phosphorylation of kinases for functional studies in vitro
Keywords: Cysteine
Protein chemical modification
Site-selective protein modification
Phosphocysteine
Phosphorylation
Protein mass spectrometry
Enzyme inhibition
Enzyme kinetics
Biomolecular recognition
p38α
MEK1
Protein kinases
Enzymatic activity

The activity of protein kinases is heavily dependent on the phosphorylation state of the protein. Kinase phosphorylation states have been prepared through biological or enzymatic means for biochemical evaluation, but the use of protein chemical modification as an investigative tool has not been addressed. By chemically reacting a genetically encoded cysteine, phosphocysteine was installed via dehydroalanine as a reactive intermediate. The installed phosphocysteine was intended as a surrogate to the naturally occurring phosphothreonine or phosphoserine of a phosphorylated protein kinase. Two model protein kinases were investigated on: MEK1 and p38α. The development of suitable protein variants and suitable reaction conditions on these two proteins is discussed in turn and in detail, resulting in p38α-pCys180 and MEK1-pCys222. Designed to be mimics of the naturally occurring p38α-pThr180 and MEK1-pSer222, these two chemically modified proteins were studied for their biological function.
The core biological studies entailed the determination of enzymatic activity of both modified proteins, and included the necessary controls against their active counterparts. In addition, the studies on p38α-pCys180 also included a more detailed quantification of enzymatic activity, and the behaviour of this modified protein against known inhibitors of p38α was also investigated. Both modified proteins were shown to be enzymatically active and behave similarly to corresponding active species.
The adaptation of mass spectrometry methods to handle the majority of project's analytical requirements, from monitoring chemical transformations to following enzyme kinetics was instrumental in making these studies feasible. The details of these technical developments are interwoven into the scientific discussion. Also included in this thesis is an introduction to the mechanism and function of protein kinases, and on the protein chemistry methods employed. The work is concluded with a projection of implications that this protein chemical modification technique has on kinase biomedical research.
The use of maps and models to evaluate surveillance policies for dengue
Keywords: map
dengue
global health
mosquito
modelling

Dengue is a mosquito-borne disease that has gone from isolated sylvatic spill-overs to a pathogen of global public health importance in less than a century. Surveillance and control efforts have continually lagged behind contemporary needs and this thesis investigates the pressing need to reassess the current geographic limits and case burden of dengue including how these are measured.
First, the global distribution of reported dengue infections was mapped. In many areas dengue reporting is sparse as it can be asymptomatic or clinically similar to other diseases. The maps identified surveillance gaps, particularly in Africa and the Middle East, where targeted efforts are needed to reliably measure the contemporary global extent of dengue transmission.
Second, the global case burden of dengue was estimated by pairing risk maps with longitudinal cohort study data. This gave the first cartographic estimate of dengue cases and at 390 million per year (95% CI: 284-528) was over three times the World Health Organization official estimate. Reconciling these estimates with reported case data allowed an assessment of existing national surveillance strategies.
Third, existing methods for outbreak identification were compared. High burden dengue outbreaks are preventable if timely and appropriate measures are applied. This analysis suggested, however, that commonly used outbreak definitions are not consistent, which could have an adverse effect on outbreak response. An alternative framework for outbreak identification based on healthcare capacities is thus outlined.
Fourth, an analysis was undertaken that quantified how mosquito vectors place geographic and seasonal limits on dengue transmission. This involved updating estimates of mosquito longevity which were integrated with temperature-dependent dynamic transmission models to produce global maps. These suggested that while temperature places strong limits on the distribution of dengue in some settings, mosquito ecology may be more important in others.
Finally, these findings are discussed in the context of global dengue surveillance gaps, with recommendations of how these can be addressed at a time when providing an evidence base for deployment of new control strategies will be critical.
The Ovidian love elegy in England
Keywords: Ovid
Classical Literature
Elegy

This thesis begins by outlining the origins of the elegy as a literary form, passing from the fragmentary remains of the Greek elegy, and of Roman love—poets before Catullus, to a brief discussion of the poetry of Catullus, Propertius and the elegists of the Corpus Tibullianum, indicating in each case the main differences between the literary attitudes of these posts and those of Ovid. A detailed analysis is made of the Ovidian erotic code, as contained in the Amores, the Ars and the Remedia, and other of the Amatoria such as the Heroides and the pseudo-Ovidiun Pulex, demonstrating inter-relationships between these works, and also any correspondences to particular components of Ovid's code in the works of earlier Greek and Roman love-poets.
Some attempt is next made to show to what sitent Ovid's themes and mannerisms were adopted by continental poets of the sixteenth century. Neo-Latin poetry is first dealt with, as represented by Joannes Secundus, Beza, Bonnefonius and the writers included in the Carmina Illustrium Poetarum Italorum, 1576, the Delitiae CC. Italorum Poetarum, 1608, the Delitiae c. Poetarum Gallorum, 1609, and the Delitiae Poeterum Bel icorum, 1614. Vernacular writers discussed in this context include Alamanni, Ariosto, Bembo, Berni, Boiardo, della Casa, Chiabrera, Guarini, Marino, Mauro, Poliziano, Serafino, Tasso and Varchi in Italy and de Balf, du Bellsy, Belleau, Marat, Ronsard and Théophile in France.
[See thesis for complete Abstract]
Searching for new particles at the Large Hadron Collider: theory and methods for extradimensional supersymmetry
Keywords: collider search
supersymmetry
Large Hadron Collider
extradimensional supersymmetry
LHC

The hierarchy problem of the electroweak scale is an intriguing puzzle which can conceivably be solved during upcoming runs of the Large Hadron Collider (LHC). Supersymmetry (SUSY) is an attractive potential solution to this problem, though the fact that no supersymmetric particles have been discovered thus far raises fine tuning of most models to &order;(1%). Extradimensional SUSY is especially interesting in light of this fact since certain models are easier to reconcile with LHC data. This thesis discusses two different extradimensional SUSY scenarios: auto-concealment and Maximally Natural SUSY (MNSUSY). The auto-concealment mechanism applies when the lightest ordinary superymmetric particle (LOSP), a brane localized state, promptly decays to the Kaluza-Klein (KK) tower of a bulk lightest supersymmetric particle (LSP). This dynamically realizes the compression mechanism for hiding SUSY as decays into the more numerous heavier KK LSP states are favored. LHC limits on LOSP squarks weaken to ≲ 450 GeV while limits on LOSP right-handed sleptons evaporate. Slepton searches perform poorly in this case because LHC analyses are blind to compressed slepton spectra. To help fill this gap, this thesis presents a monojet-like search sensitive to the very compressed range 3 GeV < m &itilde; − m&Tilde;x01 < 24 GeV. The analysis should allow LHC14 with 100 fb−1 to search for degenerate left-handed selectrons and smuons in the compressed region up to m &itilde;L ≲ 150 GeV. In addition, it should be sensitive to m &itilde;L ≲ 110 GeV for auto-concealed SUSY. To expand the class of extradimensional SUSY models the LHC is able to test this thesis also describes the Lagrangian and mass matrices of MNSUSY, which are needed to implement this model in the Feynman rules generator program FeynRules for use in Monte Carlo programs for collider simulations. It also describes benchmark scenarios useful for the first collider phenomenology studies.
Understanding the psychological health and experiences of dementia care staff
Keywords: psychological health
self-efficacy
dementia
care staff

Care work is emotionally and physically demanding and is coupled with organisational challenges. As such, care work has been associated with emotional exhaustion which not only negatively impacts staff but also the care that they provide. Greater understanding of the psychological health of dementia care staff and their perceptions of their work will provide insights into how this group may be better supported.
The first paper provides a review of the literature relating to psychological outcomes in dementia care staff. The literature identified was viewed in terms of an existing model of psychological health, the BASIC Ph, with the aim of evaluating the evidence and enhancing understanding of psychological health in this group. The utility of this model was also evaluated. The model highlighted areas for potential intervention as well as those for future research. Clinical implications for Clinical Psychologists were also discussed.
The second paper aimed to increase understanding of the experiences of dementia care assistants who perceived themselves to be competent in their role. Eight care assistants who had high levels of self-efficacy were interviewed. Interpretative Phenomenological Analysis (IPA) revealed four superordinate themes. Accounts of experiencing dilemmas provided important contextual information and constituted the first superordinate theme. The second theme 'togetherness and connection' described participants' experience of the need for support, closeness and the value of engaging with older people with dementia. The third theme encompassed the attunement between care assistants and the older people for whom they cared and described empathy, personal perspective-taking and circularity of emotion as guides to care. The final theme 'caring as part of life' described the link between caring and identity as well as a genuine interest in people, an accepting attitude and motivation to care. These themes provide fruitful areas for further research and have implications for care staff training.
The nature of configurationality in LFG
Keywords: Configurational languages
Discontinuous expressions
Lexical-Functional Grammar
Non-configurational languages
Binding
Configurationality
Free word order

The central issue in this thesis is configurationality, which has broadly been defined in terms of a division of the world's languages based on their core syntactic structure. Specifically, languages are traditionally divided into so-called configurational and non-configurational languages. Configurational languages are assumed to be languages with many restrictions on word order, and non-configurational languages are assumed to be languages with very few or no word order restrictions. Many linguists posit a strict division between the two different types of languages. In this thesis I propose a non-derivational approach to configurationality, and I discuss in detail three posited characteristics of non-configurational languages (in comparison to configurational languages): free word order, discontinuous expressions and subject-object asymmetries in binding. I propose a four-way classification of languages instead of a two-way one, based on constraints on annotations on phrase structure nodes, both for argument functions and for information structural roles (such as topic and focus). I propose that this four-way distinction is what underlies configurationality. I show that discontinuous expressions and potentially subject-object symmetries follow from the nature of languages that have traditionally been classified as non-configurational. For my analysis I employ Lexical Functional Grammar (LFG), a non-derivational framework which is particularly well-suited to account for languages in which grammatical functions are not tied to specific phrase structural positions, due to its parallel architecture. This characteristic of LFG enables me to provide a straightforward classification of languages, by the ability to separate the influence of grammatical functions and information structural roles on word order and phrase structural configuration.
The dwelling perspective
Keywords: Heidegger

This interdisciplinary thesis is about dwelling, both as a method in archaeology and as a mode of existence. My thesis has two principal aims. Firstly, to explore the 'dwelling perspective' as this has been outlined in recent archaeological theory. This will involve discussion of phenomenological philosophy and the figure of Martin Heidegger. The term 'dwelling' is a technical one originating in Heidegger's philosophy of being. Phenomenology has been making inroads into archaeological theory as a consequence of the interpretive turn of the 1980s. The theoretical commitment of this thesis is that phenomenological inquiry is a useful project in archaeological research. Reflexive archaeological research in the present might articulate and confirm certain phenomenological dimensions of present experience so as to inform and enhance our understanding of the past. Secondly, I discuss the notion of dwelling in the existential sense as a mode of existence in terms that might allow us to deploy this concept in Palaeolithic archaeology, with specific reference to mortuary practice and "art". I propose two case studies in order to explore this. Firstly, mortuary practice and existential awareness of death will be explored with reference to the site of the Sima de los Huesos. Secondly, Heidegger's notion of artistic production as a world-opening event will be explored in relation to Upper Palaeolithic art in caves. The focus on mortuary practice and art is not arbitrary: both are central planks of Heidegger's account of dwelling and both are linked by 'heterotopic' space. Heidegger presented a novel account of human existence as 'Dasein'. Dasein is being-in-the-world and being-in-the-world is unified by what Heidegger called 'care' (Sorge). Heidegger's account of Dasein remains anthropocentric: I argue that we should move away from Heidegger's own anthropocentric view of being-in-the-world, dwelling or care toward a phenomenological archaeology that goes 'beyond the human'. I argue that care or dwelling is evidenced by the archaeological record of human becoming and that our ancestors 'cared for' or 'dwelled with' their dead. Care is evidenced by appropriating the world and by looking after compatriots within the world, and I argue that such an existential state had been reached before the advent of the Upper Palaeolithic. I argue that Upper Palaeolithic "art" opened up a hunter-gatherer world that enabled others, including animal others, and objects, to become meaningful to groups of Daseins, and so to become part of particular "dwelling places". Heidegger remains the key theorist of dwelling but his anthropocentrism should be abandoned. Suitably revised, Heidegger's account of dwelling will provoke us to look at Palaeolithic archaeology from a fresh perspective.
Clustering genes by function to understand disease phenotypes
Keywords: biological networks
protein-protein interactions
copy number variation

Developmental disorders including: autism, intellectual disability, and congenital abnormalities are present in 3-8% of live births and display a huge amount of phenotypic and genetic heterogeneity. Traditionally, geneticists have identified individual monogenic diseases among these patients but a majority of patients fail to receive a clinical diagnosis. However, the genomes of these patients frequently harbour large copynumber variants (CNVs) but their interpretation remains challenging. Using pathway analysis I found significant functional associations for 329 individual phenotypes and show that 39% of these could explain the patients’ multiple co-morbid phenotypes; and multiple associated genes clustered within individual CNVs. I showed there was significantly more such clustering than expected by chance. In addition, the presence of a multiple functionally-related genes is a significant predictor of CNV pathogenicity beyond the presence of known disease genes and size of the CNV. This clustering of functionally-related genes was part of a broader pattern of functional clusters across the human genome. These genome-wide functional clusters showed tissuespecific expression and some evidence of chromatin-domain level regulation. Furthermore, many genome-wide functional clusters were enriched in segmental duplications making them prone to CNV-causing mutations and were frequently seen disrupted in healthy individuals. However, the majority of the time a pathogenic CNV affected the entire functional cluster, where as benign CNVs tended to affect only one or two genes. I also showed that patients with CNVs affecting the same functional cluster are significantly more phenotypically similar to each other than expected even if their CNVs do not affect any of the same genes. Lastly, I considered one of the major limitations in pathway analysis, namely ascertainment biases in functional information due to the prioritization of genes linked to human disease, and show how the modular nature of gene-networks can be used to identify and prioritize understudied genes.
On the standing of states : Latin America in nineteenth-century international society
Keywords: English School
Recognition
Expansion of International Society
Status
Standing
Latin America

The present dissertation offers a critical examination of the place accorded to Latin American states in the English School account of the expansion of international society. It pursues two aims. First, the study contributes to understanding the nature and scope of international order, and its historical transformation over the course of the ‘long nineteenth century’. Because of the profound impact that European colonization had on the region, the English School has conventionally treated the entry of Latin American states into international society as an unproblematic historical fact achieved with diplomatic recognition in the 1820s. The crucial cases of Argentina, Brazil, and Mexico, however, indicate that more attention needs to the paid to the hierarchical nature of the international order. The central argument of this historical-comparative study posits that the three Latin American states were recognized diplomatically, but they were not regarded as fully-fledged members of the community of ‘civilized’ states.
Second, the dissertation examines the implications of hierarchy in international politics. Building on a critique of the legal-formalist conception of ‘standing’ in English School theorizing, three ideal-typical dimensions of international stratification are identified: the distribution of material capabilities (stature), the function states perform in international society (role), and estimations of honour and prestige (status) among states. The interpretative framework sheds light on how agents understand international society, and the way in which they deal with its hierarchical nature. The study analyzes how Latin American elites perceived the standing of their state, and how these perceptions shaped politics through their corresponding ‘logics of social action’. The study finds that nineteenth-century elites in Argentina, Mexico, and Brazil conceived of the standing of their states predominantly in terms of status, and demonstrates how these perceptions informed politics.