VictorJuiz/thesis huggingface dataset:
Tree biomechanics: a study of the mechanical stability of broadleaf trees
Keywords: FEM
TLS
Wind damage
Forest carbon cycle
Terrestrial laser scanning
Disturbance ecology
Finite element analysis

Wind is a key disturbance agent in forests worldwide, but the interaction between wind and trees is poorly understood in natural forests. Wind damage leads to the formation of canopy gaps, which drive structural and compositional changes in the forest. Trees also adapt to their local wind regime in the absence of any damage, a process known as thigmomorphogenesis. This process alters local height-diameter allometries and so influences forest carbon stocks. Previous work on the wind-tree interaction has focussed on conifer plantations due to their economic importance and the relative simplicity of these systems. In this thesis I use terrestrial laser scanning to map the 3D architecture of broadleaf trees and so simulates their response to wind loading using finite element analysis. I also use field techniques developed in the forestry industry to directly measure the response of broadleaf trees to the wind.
I found that the simulations performed well against field data for trees in Wytham Woods, UK, but that they failed to predict the field data from Danum Valley, Malaysia. This is likely due to the more complex topography and canopy structure in the tropical site. In Wytham Woods, I found that the critical wind speed, a measure of wind damage risk, was related to tree species, growth rate and architecture. I also found an interesting link between critical wind speed and the timing of autumn leaf phenology, although this requires further investigation. In Danum Valley I found that understory trees approach their gravitational limits to height in their struggle to reach the canopy but that gravitational risk factors decrease with tree height. In contrast, I found that wind risk factors increased with tree height meaning that tall trees are likely to be mechanically limited by wind. I also found that the natural frequencies of broadleaf trees do not follow the same simple pattern as those of conifers, a difference which is accounted for by tree architecture. Overall, this thesis emphasises the role of wind damage risk in forest ecology and the importance of tree architecture in determining the response to wind loading for broadleaf trees.
Calibration and analysis of the GCT camera for the Cherenkov Telescope Array
Keywords: SiPM
SST
Cherenkov Telescope Array
GCT
CTA
Calibration
Optical Crosstalk
CHEC

The interaction of very-high-energy astrophysical gamma rays with the Earth’s atmosphere produces extensive electromagnetic particle cascades. These showers of particles travel faster than the speed of light in air, and consequently emit photons of blue wavelength, known as Cherenkov radiation. The Imaging Atmospheric Cherenkov Telescope (IACT) technique enables the probing of the universe at TeV energies through the detection of these Cherenkov showers. The Cherenkov Telescope Array (CTA) will represent the next leap forward in gamma-ray astronomy, improving on the sensitivity of current IACTs by a factor of 10, encompassing energies from 20 GeV to 300TeV, and operating as the first open observatory in this field. A major component of CTA is the Small-Sized Telescopes (SSTs), a necessary ingredient in exploring beyond the present energy frontier in gamma-ray astronomy.
One of three proposed designs for the SST is the Gamma-ray Cherenkov Telescope (GCT). Utilising a dual-mirror Schwarzschild-Couder optical design, GCT enables a 9° Field of View (FoV) with a compact camera design. The camera developed for GCT is the Compact High Energy Camera (CHEC). Two prototypes for CHEC have been built, each utilising different compact photosensor technology. CHEC-M features Multi-Anode Photomultiplier Tubes (MAPMTs), a pixelised extension of the Photomultiplier Tube (PMT) technology extensively used by IACTs. CHEC-S features Silicon Photomultipliers (SiPMs), novel photosensors which utilise semiconductor technology for high-resolution photon counting over a large dynamic range. To fully utilise the signal output from these photosensors, and allow the opportunity for future data analysis procedures to be exploited, the signal received from these photosensors are digitised into waveforms following a trigger. These waveforms have a length of 96 samples with nanosecond precision.
In this thesis, the full calibration and signal-extraction pipeline currently adopted by CHEC to reliably extract the Cherenkov signal from the waveforms is presented. The resulting performance of these procedures, and of the camera designs, is explored with respect to the requirements specified by the CTA Observatory. Potential improvements to the camera and calibration implementations are identified, and simulations of CHEC are utilised to demonstrate the performance increase these proposals provide. Consequently, an improvement to the photosensor that would allow the CHEC-S prototype design to comfortably meet the CTA requirements is specified. Testing of these improvements is anticipated to commence in early 2019. Finally, the results of the second on-telescope campaign for the CHEC-M prototype are presented, during which observations of Cherenkov showers and optical measurements of Jupiter were conducted.
Theory and simulation of twisted DNA duplexes
Keywords: L-DNA
coarse-grained modelling
thymine dimers
DNA modelling
Supercoiling
P-DNA
DNA damage

We use basic statistical mechanics and computer simulations with coarse-grained models to investigate the response of (inhomogeneous) DNA duplexes to linear and torsional mechanical stress. While the response of homogeneous DNA to more modest external stresses has been studied in detail, much less is know about DNA response to very strong over or under twisting, or about the biologically relevant case of inhomogeneous DNA under external torsion. By simulating geometries that resemble single-molecule molecular tweezers experiments previously reported in the literature, we validate our basic models, and measure the end-to-end duplex extension, torque, and the denaturation states of individual base-pairs, as well as the position of plectonemes when present in the post-buckling state. We generalise previous observations that plectonemes are preferentially localised (i.e. pinned) on sequence mismatches to predict that any sequence that is either significantly more bent or more flexible than the rest of the duplex should present a similar effect. We develop a simple theory to quantify this preference and test it in simulations, observing a semi-quantitative agreement. We also propose a general protocol to extend the popular oxDNA coarse-grained model of DNA to treat such bent/flexible sequences, and apply it to model thymine dimers, the most common DNA photoproducts. The theory provides almost quantitative agreement with simulations; in particular, the prediction that the pinning is dependent only on the bending angle and flexibility of the sequence, but not on the detail of how these are generated, is confirmed. Some consequences of the presence of a thymine dimer in biological DNA are also proposed. Finally, we use oxDNA to investigate the boundaries between the pre-buckling, post-buckling, and torsionally melted states, as well as the features of torsionally-melted underwound and overwound DNA, respectively called L-DNA and P-DNA. Unexpectedly, we observe that both torsionally-melted forms preferentially relax writhe by forming solenoids, rather than plectonemes. We compare our results with previous experimental and theoretical work and propose some experiments to confirm or deny this peculiar feature.
The aftermath of wrongful convictions: addressing the needs of the wrongfully convicted in England and Wales
Keywords: miscarriage of justice
wrongful conviction

Past research has demonstrated that a wrongful conviction imposes on its victims significant unjust harms, rendering it a traumatic experience. However, far less is known about what can be done to help the wrongfully convicted try to recover from this trauma and repair their lives once a conviction is overturned. This is particularly so in England and Wales, where there has been little empirical work on the lives of the wrongfully convicted to date.
Adopting a narrative criminological approach, this thesis fills the empirical and theoretical gap in the literature on wrongful convictions in England and Wales. It explores the lived experiences of those who have had a conviction quashed by the Court of Appeal at the final possible opportunity: after a referral from the Criminal Cases Review Commission (or, prior to that, the Home Secretary) or an appeal out-of-time. The thesis draws on interview data, as well as data gathered from client files of the only State sanctioned support organisation for the wrongfully convicted in England and Wales: the Miscarriages of Justice Support Service.
Using a framework of trauma and its impact on a persons’ identity, the thesis seeks to further explore the impacts of wrongful convictions on various aspects of people’s identities, including the emotional, social, reintegrative and financial impacts, following their journeys after their conviction is quashed. In doing so, it considers why wrongful convictions are so traumatic: it demonstrates how wrongful convictions can dislocate identities, which imposes almost impossible difficulties for those faced with rebuilding their lives after a conviction is quashed by the Court of Appeal. Conclusions are drawn from the narratives as to efficacy of post-exoneration support currently provided in England and Wales, and suggestions are made for how that might be improved to better repair the harms caused by wrongful convictions.
In silico molecular understanding of opioid receptor activation
Keywords: Enhanced Sampling
Molecular Dynamics
Opioid

This thesis explores the behaviour the homo sapiens δ opioid receptor (δ OR) in complex with a variety of morphinan (morphine derivatives) opioids, aiming to answer whether molecular dynamics (MD) tools can be used to determine the molecular underpinning of opioid structure-activity relationship.
To do so, the results of conventional MD simulations are reported and analysed to shed light on the local changes to the binding pocket, and a novel method, N-Body Information Theory, is adapted to study concerted motions within the receptor as a result of morphinan binding. The reported simulations reveal an interesting connection between Tyr130 3.30 and Trp173 4.50 (superscripts correspond to the Ballesteros-Weinstein numbering scheme), the latter of which is critical in stabilising inactive states of the receptor.
Due to sampling limitations of medium timescale (100 ns) conventional MD is not capable of exploring large conformational changes (necessary for receptor activation, e.g. outer movement of TM6), a novel collective variable (CV) based on unique contacts between two receptor states was developed. Using the μ OR, this new CV (termed FNC) was designed to explore the transition path from inactive to active states (and vice-versa) of the receptor. Umbrella sampling simulations showed that, despite the high free energy values, the presence of the agonist DIPP-NH2 lowered the energetic barrier for activation, agreeing with previously reported experimental results.
Encouraged by this, FNC were generated for the δ OR. Enhanced sampling simulations of the δ OR bound to four ligands (the antagonists naltrindole and naltrexone, and the agonists morphine and oxycodone), however, failed to elucidate the differences between agonists and antagonists, likely due to poor phase space sampling borne from umbrella sampling. Improvements to the work performed are suggested, particularly with respect to the sampling of the FNC CV and orthogonal states.
Recognizing epiphany: exploring the theme of epiphany in the epics of Homer, Apollonius, and Vergil
Keywords: Epiphany

This thesis explores the versatile theme of epiphany in the Iliad, Odyssey, Argonautica, and Aeneid. Chapter 1 sets forth the major scene patterns to be adopted, arguing that an understanding of the traditional narrative elements of epiphany helps to enhance, rather than limit, the reader’s appreciation of these scenes. Part I then considers how these motifs intersect with the themes of agency and recognition in the Homeric poems. Chapter 2 examines three scenes in which a mortal’s usurpation of a divine motif challenges the epiphanic hierarchy. The Iliad represents such attempts as transgressive, whereas the Odyssey shows Athena willingly transferring a motif to Odysseus before casting him as a divine agent in her plot against the suitors. Chapter 3 explores the extent to which the Ithacan recognition scenes evoke the theme of epiphany as a result of Odysseus’s “theoxenic” role. In Chapter 4, Nausicaa is discussed as a parallel example of a mortal who is authorised, as a divine agent, to appear temporarily as an epiphanic figure.
Part II turns to Apollonius and Vergil. As with other “typical” elements, Apollonius demonstrates his ability to reproduce Homeric narrative conventions of epiphany, but his interest in problematizing recognition leads him to reject any semblance of structural unity in his epiphanies. Chapter 6 examines how Vergil, by contrast, signals his intent to follow Homeric models through an excessive adherence to traditional motifs in his first epiphany. Chapter 7 explores questions of agency tied to Vergil’s extension of epiphanic roles to figures on the margins between humanity and divinity, focusing on the epiphanies of Tiberinus, Juturna, and Anchises. Finally, Chapter 8 considers how Vergil evokes both Odyssean and Iliadic models of “mortal epiphany” in his treatment of Aeneas’s future divinity, only to reject them in favour of a distinctly Roman model of apotheosis.
Exploring the impact of neurocriminological ideas on public sentencing preferences and moral behaviour
Keywords: Social psychology
Neuroscience
Public sentencing preferences
Neurocriminology
Moral behaviour
Public opinion

While the focus of criminology has traditionally been the sociological correlates of criminal behaviour, there is growing interest in the neurobiological correlates of offending. Theorists predict that this emerging area of research, known as neurocriminology, will change how people view crime, punishment and their own behaviour. The veracity of this prediction will rest on the question of whether neurocriminology can challenge the belief that offenders make a morally relevant choice to offend (or not). By suggesting that offenders are less able to make such choices, neurocriminology could lead offenders to appear more dangerous yet less blameworthy. Indeed, learning about neurocriminology may actually promote deviant behaviour, if people internalise the idea that they are not really responsible for their actions, because their brain ‘made them do it’. This thesis tested such hypotheses through two online survey experiments and three field experiments, with a total of 8153 participants. In every study, participants learned about some neurocriminological idea that could explain why a person, without any mental disorder, committed an impulsive offence – a common combination of factors in many individual acts of crime. The communication of neurocriminology significantly reduced attributions of blame, albeit to a small extent, and had no (or even an ameliorating) effect on perceived dangerousness. In the largest study, after exposure to neurocriminology, participants punished the offender significantly less, a response to ascribing him a significantly more moral character and significantly less self-control; though these effects remained small. Neurocriminological evidence also led participants to recall significantly more acts of prior deviance, but not to act less morally in the study. The fear that neurocriminology could promote deviance might explain the final finding: participants in the richest and poorest boroughs of London – but not those in between – were significantly more inclined to disrupt a scientific campaign aimed at communicating neurocriminology to offenders (rather than non-offenders). In sum, the implications of communicating neurocriminology were in the direction of promoting lenience for offenders, yet the effects were small. Hence this thesis concludes that lay people will not relinquish the notion that offenders deserve to be punished in the face of neurocriminology. Given its function in communicating censure, the human tendency to attribute blame may be too ingrained to be overthrown by science, at least at the present point in time.
Melody and meaning: the semiotics of ancient Greek music in the late classical and early Hellenistic eras
Keywords: Mimesis
Philosophy
Music
Ethos Theory
Semiotics

Melody and Meaning asks what music can communicate, and how, according to critics and philosophers from the late Classical and early Hellenistic periods. What can melody express, if anything, and how does it exert its powerful emotional force on those who listen to it? These are among the most enduring and difficult questions in aesthetics – they have been subjects of lively debate among modern scholars such as (to name just a few) Eduard Hanslick, Susanne Langer, Kofi Agawu, Jenefer Robinson, and Roger Scruton. Much of this modern thought is rooted in theories of musical affect articulated by Plato and by others, such as Aristotle and Diogenes of Babylon, who took Plato’s work forward. The ideas which underlay such theories – ideas such as representation (μίμησις) and ethical disposition (ἦθος) – are issues of longstanding interest in Classical scholarship. But there has not yet been a monograph devoted directly to musical representation in the Hellenic tradition, despite the centrality of the subject to the subsequent philosophy of art. This dissertation fills that gap in the literature by offering an intellectual history of musical representation and expression in Greek thought from its seminal description in Plato until its fulsome rejection in the 1st century BC by Philodemus of Gadara.
Assembly of nucleic acids with site-specific modifications
Keywords: copper(I)-catalysed azide-alkyne cycloaddition (CuAAC)
nucleic acid ligation
rolling circle translation

The ability to synthesise large nucleic acids with site-specific chemical modifications would be invaluable for applications including therapeutics, epigenetics, and nanotechnology. Current approaches mainly rely on polymerase enzymes or solid-phase chemical synthesis, both of which have their limitations. The former is restricted to enzyme-tolerated modifications and cannot achieve site-specificity beyond the level of Watson-Crick base pairing; the latter is constrained to oligonucleotide lengths of around 150 nucleotides for DNA (75 nucleotides for RNA) due to imperfect monomer coupling. To address these issues, ligation of chemically synthesised oligonucleotides is investigated for the assembly of long nucleic acids (beyond 100 nucleotides) with site-specific modifications.
The limits of enzymatic ligation are determined by optimising DNA and RNA assembly using ligases, before chemical ligation is explored as a potentially more scalable and cost-effective alternative. In particular, copper(I)-catalysed azide-alkyne cycloaddition (CuAAC) is investigated for the chemical ligation of RNA oligonucleotides. The reaction produces an unnatural triazole backbone at the ligation site. While the triazole backbone has been shown to be tolerated by DNA and RNA polymerases in replication and transcription, it has been unexplored for translation. An assay that involves rolling circle translation of a circular mRNA template, assembled by CuAAC and enzymatic ligation, is developed using a prokaryotic cell-free protein synthesis system. The effects of the local sequence environment and triazole position relative to the codon reading frame are examined, with special attention placed on the codon wobble position. Prokaryotic ribosomes are able to read triazole-containing mRNA to produce polypeptide translation products. The yields are lower than that of the natural backbone control, possibly due to destabilised hybridisation between the tRNA and mRNA, a feature that requires further optimisation.
The Victorian intergenerational migrant cohort: Socioeconomic outcomes 1851-1901
Keywords: immigration
19th century
record linkage
England

Intergenerational outcome (IO) studies model the transmission of socioeconomic status between familial generations. Given the balancing of time horizons and future expectations implicit in migration decisions, IO studies are particularly salient to an empirical understanding of migration. However, few datasets exist which provide the necessary longitudinal observations for migrant populations, therefore such IO studies remain rare.
This paper presents a novel cohort of 288,000 individuals from fifty years of English census data (1851-1861 and 1881-1901), representing some 36,000 core family groups who originated beyond the national boundary of England prior to 1851. The intercensal linking method employed here (network persistence linkage, or NPL) is also unique. It exploits persistent coresident proximity to enrich individual identifiers and includes an equal number of females as well as males.
Socioeconomic outcomes are defined with the HISCAM scale, a measure of social proximity derived by statistical correspondence analysis of occupations within historic civil and genealogical records. Descriptive analysis of outcomes over three generations shows that immigrants had significant socioeconomic mobility, especially females, although this was not always an upward move. Immigrant families with very advantaged positions may have experienced rapid regression to the mean. An ordinary least squares (OLS) estimate of intergenerational transmission finds that both males and females transmitted a significant effect to their children’s status through their own socioeconomic prestige. This effect is stronger between the immigrant and his/her child than between that child and the third generation. The country of origin had a significant effect on the status of both subsequent generations, although there is also evidence that this dissipated among the grandchildren of British Isles immigrants. This study demonstrates that it is possible to link females as well as males across historical population datasets, and that omitting them from intergenerational outcome models may overestimate inheritance and underestimate mobility.