VictorJuiz/thesis huggingface dataset:
Tree biomechanics: a study of the mechanical stability of broadleaf trees

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.

Keywords: FEM
TLS
Wind damage
Forest carbon cycle
Terrestrial laser scanning
Disturbance ecology
Finite element analysis
Advisor: Shenkin, A
Malhi, Y
Calibration and analysis of the GCT camera for the Cherenkov Telescope Array

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.

Keywords: SiPM
SST
Cherenkov Telescope Array
GCT
CTA
Calibration
Optical Crosstalk
CHEC
Advisor: Cotter, G
Theory and simulation of twisted DNA duplexes

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.

Keywords: L-DNA
coarse-grained modelling
thymine dimers
DNA modelling
Supercoiling
P-DNA
DNA damage
Advisor: Louis, A
Doye, J
Thessaly: from the late Bronze Age to the early Iron Age (c. 1600-700 BC)

Thessaly during the Late Bronze (LBA) and Early Iron Age (EIA) is a relatively little-known region that only recently has started to be studied more thoroughly. The present thesis seeks to examine Thessaly during those two periods and understand its social, cultural and political character and the way it changes from the one period to the other.
The focus of this thesis is the transformation of Thessaly from the LBA to the EIA. This research will offer a new approach to the changing network of interactions among sites within Thessaly and their connections with the rest of the Greek mainland and the Aegean. This thesis will explore the similarities and differences among the Mycenaean centres of power in the Pagasetic Gulf, namely Kastro, Dimini and Pefkakia and attempt to define their relationship and in what ways they related to each other and with other places in Thessaly and the Aegean and ultimately, try to understand the extent and organisation of the local Mycenaean administrative system. Another issue that is explored is how Thessaly overcame the crisis after the collapse of the Mycenaean palaces during the transition from the LBA to the EIA. Through the study of changes in the settlement and cemetery patterns throughout these periods in Thessaly, this thesis explores population movements to and from Thessaly and re-evaluates theories about the societal structure, outside influences, invasions and population decline. It is concluded that Thessaly emerges as part of the Mycenaean world and not as a peripheral entity, certain ‘big’ sites show a remarkable degree of continuity from the LBA to the EIA, which is also reflected in the burial practices, and finally the emergence of new centres of power in the inner route that connects the Almiros plain with the region of Elasson.
Chapter 1 provides a brief history of research and sets the aims of the thesis: to examine Thessalian settlements, sanctuaries and burials from the LBA to the EIA to understand how Thessaly changed socio-politicaly and culturally from the one period to the other. Chapter 2 examines closely the site of Kastro Volou which I employ as a case study for those two periods since it is one among few in Thessaly occupied continuously and one of the rare sites for which we have evidence from both the settlement and the cemeteries. Chapter 3 explores in detail the LBA and EIA Thessalian settlements. The chapter focuses on 12 sites throughout Thessaly which offer more substantial evidence, while other smaller sites that could offer valuable information are also mentioned. The settlements are examined in a geographical order and the evidence of the remains of architecture and other small movable finds are assessed in a chronological order. Chapter 4 presents the evidence for Thessalian sanctuaries in a chronological order. Chapter 5 offers a study of the burial practices in Thessaly during the LBA and EIA. The chapter explores the similarities and differences in burial practices and is organised by grave types. Chapter 6 presents a summary of the evidence and a final discussion.

Advisor: Lemos, IS
Development of targeted exosomes for delivery of biotherapeutics

Cells release nanosized membrane-enclosed vesicles termed extracellular vesicles. These naturally occurring vesicles have been established as important players in communication between cells, mainly through transfer of their content. This inherent ability makes extracellular vesicles outstanding candidates for development into drug delivery vehicles.
Cells are considered to release a number of extracellular vesicle types with unique size, biogenesis, and cargo: exosomes, microvesicles, and apoptotic bodies. Exosomes are the most well studied vesicle type and are considered to have homogenous characteristics. However, fractionation of isolated exosomes with sucrose density gradient flotation allowed for identification of two distinct exosome subpopulations with unique size and composition. Subpopulations derived from melanoma cells were found to have differential effects on gene expression of recipient cells. Secondly, development of a size exclusion chromatography based approach allowed for more in-depth study on exosome heterogeneity. Four exosome subpopulations with different size and composition were derived from ovarian cancer cells. Preliminary findings point to a potential pathophysiological role of ovarian-cancer derived exosomes, with unique roles of subpopulations in ovarian cancer metastasis.
In addition, differential properties of exosome subpopulations were explored in development of B cell targeted exosomes. Single chain variable fragments targeting B cell surface antigens CD19 and CD22 were successfully expressed on exosomes. Targeting of CD22 resulted in increased and rapid uptake as compared to targeting of CD19. Moreover, data suggested that specific exosome subpopulations are responsible for the latter observation. Findings demonstrate a promising approach for the delivery of biotherapeutics into malignant B cells.
In conclusion, this works shows the heterogeneous nature of exosomes and the release of subpopulations with potential unique biological roles. Addressing heterogeneity is one of the key topics of research on extracellular vesicles and will allow for in depth study on their underlying biogenesis and in turn benefit development of extracellular vesicle based therapeutics.

Advisor: Wood, M
Andaloussi, SE
A landscape of conflict? Rural fortifications in the Argolid (400 – 146 BC)

This thesis presents the first systematic study of rural fortified structures in the Argolid between 400 and 146 BC. By placing these fortifications in the context of their surrounding landscape, this study aims to cast new light on the sites’ “military-strategic” and “civilian” functions and explores their implications for wider political, social and economic structures in the region and beyond. Methodologically, the study combines traditional approaches (e.g. architectural comparisons and extensive on-site observation) with GIS-based methods of data collection, visualisation and analysis.
The thesis is structured in eight chapters. The introductory chapter 1 discusses the study’s chronological framework, geographical scope, aims and structure, as well as the history of the scholarship on this subject. Chapters 2–4 “set the scene” for the analysis of fortified sites in the Argolid.
Chapter 2 works towards reconstructing the region’s ancient environment, discussing important landscape changes such as erosion, alluviation and coastline developments, as well as the available evidence for ancient vegetation and land use. Chapter 3 lays out the typology of ancient fortifications employed in this study, while chapter 4 aims to create the first systematic framework for dating fortified sites in the Argolid.
In chapters 5–7, the study turns to the analysis of the Late Classical and Hellenistic rural fortifications in the Argolid. Chapter 5 discusses the region’s political structure and settlement patterns, chapter 6 explores the fortifications’ “strategic military” role, and chapter 7 considers the structures’ possible significance beyond a strictly “military-strategic” function, especially as places of refuge, habitation, production and agricultural processing.
Chapter 8 concludes the study with a summary of the main results, before discussing their significance for the wider field of research and exploring the future potential of GIS-based methods of data analysis in the Argolid and beyond.

Advisor: Stamatopoulou, M
External dimensions of in-the-moment teacher decision-making

The dynamic nature of teaching often presents schoolteachers with unforeseen challenges that need to be resolved through in-the-moment decision-making. Faced with the pressures of settling challenging teaching situations, teachers must find ways to respond that fit the specific practical requirements of their classrooms. The research literature on teacher decision-making has, however, maintained a one-sided focus on internal psychological processes, omitting its external dimensions.
This study develops a theoretical perspective that accounts for external dimensions of teacher decision-making, focusing on how enactment of decisions requires the use of external support in the form of physical objects, writing, visual depictions, spoken language, gestures and sounds. The study focuses on two interrelated research questions; the first concerns the function of teachers’ use of external supports during in-the-moment decision-making; and the second relates to the role of physical and cultural circumstances in shaping teachers’ use of external supports. The data includes detailed lesson observations and post-lesson interviews with five teachers from an English secondary school, as well as documents and observations of staffroom meetings. The data is analysed by ‘zooming in’ on instances of in-the-moment teacher decision-making, unpacking the moment-by-moment unfolding of these instances, using analytical procedures which were developed on the basis of the cultural-historical method of double stimulation.
Drawing on cultural-historical research traditions, the study shows how the teachers relied on strings of artefacts, by means of which they redesigned problematic student tasks to resolve emerging challenges. The teachers’ enactments of decisions were constrained and enabled by the artefacts they were able to produce in-the-moment; and the specific physical and cultural arrangements of their teaching situations were instrumental in making some artefacts more useful than others. The thesis develops theoretical concepts for understanding teachers’ use of external supports during in-the-moment decision-making, presenting a conceptual model that helps shed light on what makes the external enactment of in-the-moment teacher decisions practical.

Advisor: Thompson, I
Daniels, H
The aftermath of wrongful convictions: addressing the needs of the wrongfully convicted in England and Wales

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.

Keywords: miscarriage of justice
wrongful conviction
Advisor: Hoyle, C
How did the iron industry from the Iron Age to the Roman Period in Southern Britain?

This thesis explores the transition between the Iron Age and Roman periods in Britain using one of the most survivable and data packed archaeological artefacts, iron smelting slag. By using a series of complimentary analytical methods it is possible to reconstruct the smelting process. Not just on a purely metallurgical level but also revealing some of the actions of the smelters. The transition from the Iron Age to the Roman period has been a longstanding area of discussion in European archaeology, marking the change from prehistory to protohistory. A geographical limitation has been placed on this study to southern Britain, this is to cover the area with the most complete coverage of archaeological sites and also with a distinct archaeological change between the two periods. The analysis of smelting slag at a macromorphological level reveals furnace morphology and operation. The microstructure of the slag examined using reflective light microscopy reveals under what conditions the slag solidified. The chemical composition of slag determined using Scanning Electron Microscopy Energy Dispersive Spectroscopy (SEM-EDS) reveals the inputs to the smelting process and through their interaction the temperature and chemical change within the furnace. Combining these methods adds further information about the smelt, giving the reasons for the identifiable characteristics of the smelt. Traditional metallurgical analysis of iron smelting slag has focussed on the purely technical result of the smelt, effectively how efficient the smelt was and what ore was being used. The results of this study indicate that the production of iron from the earliest period in Britain was part of a complicated wider picture of resource exploitation, interaction between groups geographically and temporarily.

Advisor: Pollard, M
Morrison, W
In silico molecular understanding of opioid receptor activation

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.

Keywords: Enhanced Sampling
Molecular Dynamics
Opioid
Advisor: Biggin, P