VictorJuiz/thesis huggingface dataset:
Multi-mode absorption spectroscopy for multi-species and multi-parameter sensing

The extension of Multi-mode Absorption Spectroscopy (MUMAS) to the infra-red spectral region for multi-species gas sensing is reported. A computationally efficient, theoretical model for analysis of MUMAS spectra is presented that avoids approximations used in previous work and treats arbitrary and time-dependent spectral intensity envelopes, thus facilitating the use of commercially available Interband Cascade Lasers (ICLs) and Quantum Cascade Lasers (QCLs).
The first use of an ICL for MUMAS is reported using a multi-mode device operating at 3.7 μm to detect CH4 transitions over a range of 30 nm. Mode-linewidths are measured using the pressure-dependent widths of an isolated absorption feature in HCl. Multi- species sensing is demonstrated by measurement of partial pressures of CH4, C2H2 and H2CO in a low-pressure mixture with uncertainties of around 10%. Detection of CH4 in N2 at 1 bar is demonstrated using a shorter-cavity ICL to resolve spectral features in pressure-broadened and congested spectra.
The first use of a QCL for MUMAS is reported using a commercially available device operating at 5.3 μm to detect multiple absorption transitions of NO at a partial pressure of 2.79 μbar in N2 buffer gas. The revised model is shown to enable good fits to MUMAS data by accounting for the time-variation of the spectral intensity profile during frequency scanning. Individual mode-linewidths are derived from fits to pressure- dependent MUMAS spectra and features from background interferences due to H2O in laboratory air are distinguished from those of the target species, NO. Data obtained at scan rates up to 10 kHz demonstrate the potential for achieving short measurement times.
The development of a balanced ratiometric detection scheme for MUMAS with commercially available multi-mode lasers operating at 1.5 μm is reported for simultaneous detection of CO and CO2 showing improved SNR performance over previous direct transmission methods and suitability for a compact field-employable instrument. In addition, MUMAS spectra of CO2 are used to derive gas temperatures with an uncertainty of 3.2% in the range 300 - 700 K.

Keywords: Interband cascade lasers
Quantum cascade lasers
Laser noise canceller
MUMAS
Advisor: Ewart, P
Inimica amicitia: friendship and the notion of exclusion in early Christian Latin literature

This thesis discusses the notion of amicitia in early Christian literature. By examining letters and normative texts ranging from the third to the early fifth century, the study illuminates not only how contemporary authors shaped friendship conceptually but also how these concepts relate to the actual social practice. Typically, scholars confine their reading of Christian friendship to the late antique period. In so doing, they approach amicitia either as a particular kind of relationship performing crucial social functions or as a subject for theorization that followed the example of a longstanding ancient philosophical tradition. Particularly influential has been the view that links amicitia with affection and love. Hence, scholars tend to stress the inclusiveness of friendship. By contrast, my own study focuses on the aspect of exclusion as the necessary by-product of social inclusion processes. Along these lines, amicita is described as existing in a dialectical opposition with its antonym, inimicitia.
This approach yielded a number of insights. First, as the study moves into uncharted territory, the examination of third century texts highlights a tradition of amicitia-related thought that reached further back than has previously been assumed. From this, a more nuanced picture of friendship emerges that is not constrained by scholarly established boundaries between different fields of study. Second, the principle of inclusion and exclusion, dividing the world into amici and inimici, has been revealed as a powerful tool in church politics and religious controversy that established sharp boundaries between competing Christian factions. This view, which posits the truth of faith as the necessary prerequisite for friendship, is set off against other contemporary voices that did not make amicitia dependent on a particular religious group affiliation. Third, while disentangling friendship from the question of love, the character of Christian amicitia is viewed against the backdrop of the divine household. Though the conceptual overlap between friendship and kinship is not unique to the Christian tradition, such thinking ties in with an idea of community that builds on the paternity of God.
These findings have implications for both the study of ancient friendship and the history of the early church. They improve our understanding of the relation between the conceptualization of amicitia and the actual social practice and moreover offer a deep insight into the social dynamics of contemporary religious controversies.

Keywords: Inclusion
Friendship
Exclusion
Advisor: McLynn, N
The influence of nicotinic acid adenine dinucleotide phosphate (NAADP) signalling and the significance of the organization of lysosomes in cardiac myocytes

The central role of calcium ions in the generation of contractile force in the heart has been understood for many decades. In many mammals, a large proportion of the calcium responsible for activation of the contractile apparatus is released from the sarcoplasmic reticulum (SR), and this release is regulated via many mechanisms.
One regulatory factor that has earned much attention in recent years is Nicotinic Acid Adenine Dinucleotide Phosphate (NAADP) and its probable receptor, Two-Pore Channel-2 (TPC2), which is found on the surface of lysosomes. NAADP has been found to function in a wide range of tissues from both animals and plants. In the heart, it is thought that NAADP may be generated in response to stimulation of cardiomyocytes with β-adrenergic agonists and that it acts at the lysosome to cause release of calcium. This calcium may then regulate the release and reuptake of calcium by the SR.
Due to the importance of calcium in the heart, substances that modulate calcium release in cardiac cells may be expected to have a broad array of effects. Under some circumstances, the dysregulation of calcium signalling caused by these substances may also be expected to have pathological consequences, both acutely and over the long term.
The exposure of ex-vivo hearts perfused via Langendorff apparatus to the -adrenergic agonist isoprenaline resulted in ventricular arrhythmias following electrical burst pacing in wildtypes, but not in hearts from TPC2 knockout (Tpcn2-/-) animals. This data supports the hypothesis that NAADP is important in the acute cardiac response to -agonists, and more specifically that it has an influence on the calcium handling events that lead to arrhythmogenesis in these cells.
Similarly, chronic treatment of cultured neonatal rat cardiomyocytes with the adrenergic agonists isoprenaline and noradrenaline is known to induce a hypertrophic response associated with re-activation of the foetal gene program. This response was found to be strongly attenuated by the NAADP antagonist Ned-19, which prevented both the increase in cell size and the increase in expression of foetal genes associated with hypertrophy. These results suggest that in addition to the role of NAADP in acute responses to β-adrenergic agonists, it may also be important in chronic responses.
Calcium released from the lysosome in response to NAADP action at TPC2 is thought to modulate calcium release from the SR. This process is likely to require a close spatial relationship between these organelles. Data from confocal microscopy experiments demonstrate an association between lysosomes and the SR, while membrane contact sites (MCS) between these structures are shown to exist using electron microscopy. These observations support the hypothesis that functional calcium signalling microdomains exist between lysosomes and the SR in the heart.

Advisor: Terrar, D
Theoretical study of the binding of metal thiocyanate complexes to gold surfaces

This thesis presents a density functional theory investigation into the nature of NCS based linear and octahedral complexes in the gas-phase, as well as the surface effect of those on an Au(111) substrate. In chapter 3, we start to explore very simple linear complexes of a proton and transition metal centers (M = Cu+, Ag+, Au+). In addition, a trans ligand (L = NH3, CN–) is attached in a linear geometry in terms of the stability of N- and S- coordinated isomers and the shift of resonance structure of NCS ligand. After the geometry optimization, we move to the surface effect caused by Au(111) surface when those complexes chemisorb on the substrate in chapter 4. Three possible chemisorption sites (on-top, side- on, hollow) are examined to measure structural and electrical changes on those linear complexes. The calculation of single molecules is done by ADF software and those with Au surface are done by periodic system in VASP software. In chapter 5, we explore octahedral complexes of Fe(II), mainly Fe(II)(phen)2(NCS)2 with two spin crossover states (singlet and quintet) using an array of different functionals (PBE, OPBE, B3LYP, B3LYP*, PBE0, s12H). It is known that the exchange energy of the functional hugely effects the stability of a particular spin state and we explore those in comparison with structural properties from experimental and theoretical work. In the next section, we focus on the chemisorption of those optimised structures on Au(111) surface. As examined with linear complexes, structural and electrical properties (energy, bond length, spin density) are thoroughly analyzed, and finally we explore U values (U = 0.0, 1.5, 2.5, 3.5) which effects the exchange energy of the periodic calculation.

Advisor: McGrady, J
Royalism, religion, and revolution: the gentry of North-East Wales, 1640-1688

This thesis focuses specifically on the gentry of North-East Wales. It addresses the question of the uniqueness of the region’s gentry in relation to societal organisation, authority, identity, religion, and political culture. The thesis examines the impact of the events of 1640 to 1688 on the conservative culture of the region. It assesses the extent to which the seventeenth-century crises changed that culture. Additionally, it discusses the distinctiveness of the Welsh response to those events.
This thesis offers new arguments, or breaks new ground, in relation to three principal areas of historiography: the questions of Welsh identity, religion, and political culture. Within Welsh historiography this thesis argues for a continuation of Welsh identity and ideals. It uncovers a royalist, loyalist, and Anglican culture that operated using ancient ideals of territorial power and patronage to achieve its ends. In doing so it overturns a lingering idea that the Welsh gentry were anglicised and alienated from the populace. The thesis also interacts with English debates on the same themes. In exploring the unique aspects of the culture of North-East Wales, the assertion of an anglicised monoculture across England and Wales can be disproven. This allows for a more complex picture of British identity, religion, and politics to emerge.
This thesis musters correspondence, material objects, diaries, notebooks, accounts, official documents, and architectural features to aid in its analysis. This breadth of evidence allows for a broad analysis of regional patterns while allowing for depth when required. The first three chapters of the thesis examine the North-East Welsh gentry in relation to the themes of Welsh society and identity; religion; and finally political culture. The final chapter comprises three case studies that explore aspects of the aforementioned themes in further depth.

Keywords: Royalism
Language
Early modern Wales
Anglicanism
Loyalism
Historical identity
Advisor: Tapsell, G
Adverse events of common psychiatric medications: an umbrella review

BACKGROUND: Psychiatric medications were the second most prescribed therapeutic class in the United States in 2015 with 547 million prescriptions. Adverse events of medications are very common, can be distressing to patients and are often underreported in the primary studies. The purpose of this thesis is to systematically review the scientific literature to estimate the prevalence and burden of adverse events among the most common psychiatric medications.
METHODS: The 23 most commonly prescribed psychiatric medications in the United States as well as eight psychiatric medications from the World Health Organization's Essential Medicine List were included. A systematic and comprehensive search was conducted to retrieve all published and unpublished systematic reviews with meta-analyses to assess adverse events of individual psychiatric medications (this process of collecting secondary publications and not primary studies is called "umbrella review"). Seven databases (Cochrane Database of Systematic Reviews, Database of Abstracts of Reviews of Effects, Embase, Medline, PreMedline, PsycINFO and PubMed) were searched between 1946 and 2016. Prevalence rates and effect estimates were extracted by two independent reviewers and summarised. A quality analysis was performed on included reviews using the AMSTAR (assessing the methodological quality of systematic reviews) tool and all were rated as medium or high quality reviews.
RESULTS: 69 systematic reviews and meta-analyses published were eligible for data extraction, quality appraisal and quantitative synthesis. Antipsychotic medications (60%) accounted for the majority of the findings, followed by antidepressants (16%), stimulants (13%), mood stabilisers (8%) and anxiolytics (3%). The strongest associations were between amitriptyline and sexual dysfunction (N=442, odds ratio [OR] 16.6; 95% Confidence Intervals [CI] 4.6 to 60.6), aripiprazole and somnolence (N=569, OR 25.8; 95% CI 1.3 to 112.3) and olanzapine and weight gain (N=249, OR 32.0; 95% CI 1.7 to 98.4). Overall, neurological adverse events were reported most frequently for antidepressant, antipsychotic and anxiolytic medication classes. Patient characteristics, particularly age and diagnosis, explained differences in adverse events across and within medication classes.
DISCUSSION & CONCLUSION:
To my knowledge, this is the first umbrella review on the tolerability profiles of 31 common psychiatric medications worldwide. Many medications were linked to adverse events through a weak or moderate strength of association and additional factors contributed to the variability in adverse outcome reporting aside from patient characteristics. Findings from this review need to be examined with the efficacy profiles of the medications and the clinical circumstances of the individual patients. 

Keywords: psychotropic medication
meta review
psychiatric medication
adverse events
umbrella review
Advisor: Fazel, S
Atypical attention and autism spectrum disorders (ASD) symptoms: Development and interactions with learning and memory

This thesis investigates the nature of atypical attention in relation to autism spectrum disorders (ASD) symptoms, as well as the mechanisms by which it may relate to social impairment. First, does atypical non-social attention predict social impairment over time in the context of ASD, suggestive of a causal relationship? Second, if atypical attention plays a role in social impairments in ASD, what is the mechanism?
With regards to the first question, longitudinal data with children at familial risk for ASD demonstrated a unidirectional relationship between non-social attention and social functioning at the cognitive level: 2-year-old non-social attention predicted 3- year-old face recognition, but there was no relationship between 2-year-old face popout and 3-year-old visual search. Additionally, we examined the relationships between ASD and ADHD symptoms over three years in children at high risk for both—children with fragile X syndrome. This allowed for investigating atypical non-social attention and social impairment at the symptoms level, again revealing a unidirectional relationship with ADHD symptoms predicting ASD symptoms over time but not the reverse. These findings suggest that atypical non-social attention may contribute to social impairment.
With regards to the second question, a novel eye-tracking and visual search paradigm revealed how task irrelevant social stimuli in natural scenes can lead to poorer subsequent explicit spatial contextual memory and altered memory-guided attention orienting—effects that were moderated by autistic traits and social anxiety within a neurotypical population. Further, this research found cross-sectional development, comparing 6-10-year-old children to young adults, and investigated the neural markers of social stimuli's effect on memory. These studies suggest a possible mechanism whereby a reduced social attention bias could lead autistic individuals to learn and remember less about people and the social world and result in social impairment.

Keywords: ADHD
attention
development
memory
learning
autism
Advisor: Scerif, G
Nobre, AC
Developing surface ionisation charge-transfer dynamics of hydrogen Rydberg atoms into an energy-resolved probe of surfaces

As a Rydberg atom approaches a surface, it will eventually undergo ionisation by charge transfer into the surface at a distance of about 100nm (for principal quantum numbers n > 20). The dynamics of this process are sensitive to the electronic and geometric structure of the surface and can display signature characteristics. As such, Rydberg atoms can be used to probe image-charge effects or to measure small superficial electric stray or patch fields. The charge-transfer process can be in resonance between the Rydberg energies and the energetically discrete surface states (image states) in a bandgap. Surface ionisation of Rydberg atoms is investigated for graphene, which is a zero-bandgap semiconductor and can behave either as a metal or a semiconductor. The charge-transfer dynamics observed here exhibit the characteristics of a metal with enlarged ion detection efficiency compared to a copper sample -- in accordance with other properties of graphene, such as conductivity, that are enlarged compared with a regular metal. For hydrogen Rydberg atoms, surface ionisation is detected for distances up to 10 µm, with a double series of high-lying image states extending far from the graphene film possibly creating a quasi-continuum at large atom-surface separations with a density of states beyond the resolution of the Rydberg states from n=20 to 40. The resonance behaviour for graphene is explored with a range of Rydberg H-atom collisional velocities whose effect on the charge transfer process introduces an additional handle on the probing of electronically discrete features of a surface. A wave-packet propagation study of a hydrogen atom incident at a free-metal surface up to n=20 displays shifts in ionisation towards greater distances and over a narrower range when acceleration of the ion core is not included. The thereby significantly reduced effect of the collisional velocity of Rydberg surface ionisation is also observed in an experimental study with a limited velocity range available from supersonic expansion directed at a gold sample. This either suggests that the range of Rydberg projectile velocities is to narrow to have observable effects or that a pronounced velocity dependency is merely detected for distinct electronic resonances. With the aim to further elucidate the velocity dependence and to prospectively remove ambiguities that arise from the nature of the experiment, a chip-based decelerator is constructed and integrated into the experimental apparatus for the first time. Within the constraints of the design and the existing apparatus, the chip device is not able to produce sufficient densities of decelerated particles to be employed in surface-ionisation experiments. Extensive modelling of the deceleration process indicates that modifications to the existing design and the experimental apparatus could achieve a tunable-velocity source of hydrogen Rydberg atoms with greatly enhanced densities for future investigations.

Advisor: Softley, T
Cation-directed atropselective synthesis of BINOL derivatives

The use of chiral counterions to facilitate enantioselective mono-C-alkylation of enolates has been explored extensively over the past century. We have demonstrated that an alternative mode of reactivity – O-alkylation – predominates if the C-alkylation is impeded. We have applied this concept to the atropselective dynamic kinetic resolution of 1-aryl-2-tetralones, leading to an organocatalytic synthesis of enantio-enriched BINOL derivatives.
In this reaction, the chiral counterion plays a key role as both a phase-transfer catalyst and also as the agent to facilitate atropselective alkylation of rapidly interconverting axially chiral enolates. Treatment of 2-tetralones with base in the presence of an ammonium salt leads to intermediate atropisomeric dihydro-BINOL; oxidation with DDQ leads to BINOLs without loss of e.r. This transformation leads to high enantioselectivity and the scope of this reaction is significant: we can insert substituents into any position around the BINOL core, and we can also generate heavily functionalized derivatives without compromising stereochemical integrity.
By employing a substoichiometric amount of alkylating agent, we have applied our reaction protocol to the kinetic resolution of MeBINOL with good selectivity.

Advisor: Smith, M
Buying the story: transaction and narrative value in Balzac, Dostoevsky and Zola

This thesis explores narrative as a self-reflexive commentary on the conditions of its own production. It argues that the need for narratives to perform economic functions, such as to provide an income for the author or to promote subscription to a host publication, affects how texts are written. It suggests that this approach is particularly suited to nineteenth-century prose fiction. It proposes a methodology for approaching this analysis based on treating the text as an exchange commodity in a transaction between author and reader whose economic function can be investigated and analysed.
The thesis illustrates the application of this approach to major works of three nineteenth-century authors, following the evolution of the book format in France from its subordination to the roman-feuilleton in the late 1830s to its revival as an economically independent format in the 1880s, and contrasting this to the situation in contemporary Russia.
A chapter on Balzac, which focusses on Splendeurs et misères des courtisanes, shows how this work can be seen as both a mirror of the rapidly evolving world of publishing during the 1830s and 1840s and as an extended discussion on the constituents of narrative value. It demonstrates how Balzac first adopts, then rejects and parodies, literary devices developed for the rapidly commercialising world of the roman-feuilleton.
A chapter on Dostoevsky's The Brothers Karamazov, serialised in 1879-80, examines how an author could develop strategies to create literary and economic value within a contemporary readership which was far less developed than that in France. It demonstrates how important literary devices which Dostoevsky uses can be shown to have economic as well as aesthetic effect.
The thesis concludes by an analysis of Zola's role in the industrialisation of narrative, which mirrors the rise of the story itself as a key tool of commercialisation. It illustrates this by a discussion of L'Argent (1891) as an allegory of the rise of the story as big business.
The thesis promotes the relevance of economic criticism as an underrecognised critical discipline.

Advisor: Farrant, T
Curtis, J