VictorJuiz/thesis huggingface dataset:
Developing proxies in secondary carbonates with application to ENSO variability and basin-wide paleo-hydrology

This thesis develops new, and expands existing, methods of reconstructing paleoclimate from geochemical proxies hosted in secondary carbonate precipitates. This is done by: i) Developing a new multi-proxy approach for using lacustrine cave carbonates (LCCs) to reconstruct past shifts in precipitation-evaporation (P-E) over lake drainage basins, and ii) Investigating the suitability of speleothems as paleo-ENSO archives. Chapters 2 and 3 use modelled and measured values from LCC samples to generate a framework for understanding how Mg/Ca, U/Ca and δ44/42Ca in LCCs can be used as a combined multi-proxy approach to reconstruct past shifts in P-E. This multi-proxy approach is subsequently used to generate a novel reconstruction of P-E over the Bonneville Basin (a terminal basin in the Great Basin region of the southwestern United States), during Heinrich Stadial 1. Results suggest that moisture supply to the Great Basin region was impacted by a southwards shift of the ITCZ and variations in the elevation of North American ice sheets during Heinrich Stadial 1. Chapter 4 investigates the suitability of applying speleothem BA03 as a paleo-ENSO archive. Firstly, the impacts of age model and δ18O uncertainties on speleothem ENSO variability reconstructions are quantified. A total of eight high resolution (> 2 samples per year) δ18O time-series are then used to reconstruct shifts in ENSO variability over the Holocene. This new ENSO variability reconstruction suggests a reduction in ENSO variability during the mid-Holocene (5.68 kyr BP – 3.78 kyr BP), the termination of which coincides with the end of the so called “4.2 Kyr Event”. This thesis advances the paleoclimate application of numerous geochemical proxies, expanding the use of precisely dated, high-resolution secondary carbonate archives.

Keywords: ENSO
speleothem
North America
LGM
stable Isotopes
oxygen isotopes
Indo-Pacifc Warm Pool
4.2 Kyr Event
calcium isotopes
uranium thorium chronology
paleoclimate reconstruction
Lake Bonneville
trace elements
Holocene climate
Borneo
Advisor: Carolin, S
Day, C
Khatiwala, S
Gender and nationalism in the Hellenic world, 1836-1897

This thesis is not the history of Greek feminism as such, but rather a history of gender in the Greek context, of which feminist consciousness was just one component. Its chapters discuss the way in which gender, the cultural roles and behaviour prescribed for male and female members of the Hellenic nation by Hellenic society from 1836 and 1897, helped this population and particularly Hellenic women (Hellenides), to acquire a certain sense of national identity. The central question and organising principle of this thesis is the way in which women developed a certain sense of political and national identity by exploiting the overriding conceptions of the national idea in Greece.
The Greek constitution of 1844 conferred voting rights on all male citizens, giving legal sanction to a transformation that had occurred gradually: that from Christian soldier to obedient citizen. Excluded from those spheres traditionally defined as public - military service, public education, and legislation - women deconstructed this patriarchal frame of reference by composing new symbols and language, seeking legitimacy from sources of power which they had previously denied to themselves. This thesis charts these developments, making careful distinctions between the state that provided the government and administered the territory that was Greece, and the nation, namely the ethnic group that identified itself as Hellene regardless of its state of domicile. Concerned above all with the national identity which women created for themselves, this thesis does not offer a detailed explosion of the Megale Idea (Great Idea), a doctrine advocating the liberation and unification of the entire Hellenic genos (the ecumenical community of Balkan Orthodoxy as it existed under the Ottoman Empire) and the establishment of a great Greek state in the lands that had once belonged to the Byzantine Empire. Instead, it examines the cultural significance of the Megale Idea, and its influence on how women began to think about themselves, gender, politics and daily life.

Keywords: Hellenic world
19th century
nineteenth century
nationalism
gender and nationalism
Greece
Sex role
Developing kinetically facile routes to robust B-F containing compounds for bioconjugation and imaging applications

This thesis reports on investigations into fluoroborate compounds with a view to their application in 18F-PET tracer design. The principle aim was to understand how advances could be made to the functionalisation of fluoroborate compounds for bioconjugation, in addition to improving their hydrolytic stability and optimising synthesis via efficient fluoride uptake routes.
Chapter 3 reports on investigations into the synthesis and fluoride binding capabilities of 1,8-bis(boryl)-naphthalene scaffolds featuring boronic acid and ester functional groups. These bidentate “ligands” were investigated for potential thermodynamic enhancement that may be attained by chelating fluoride in such a structure, and the opportunity this offered for hydrolytically robust fluoride complexes. The diboronic acid system is established to be incompatible for this application due to the formation of an exceptionally robust intramolecular anhydride that effectively blocks the binding pocket. An unsymmetrical framework featuring a single boronic ester group is demonstrated to be suitable for chelation, although fluoride binding was subsequently compromised by a thermodynamically driven, functional group rearrangement that positions fluoride in a more labile terminal position, with a B–O–B bridge again being generated.
Chapter 4 explores how highly robust N-heterocyclic carbene boron trifluoride adducts may be diversified to facilitate a range of methods for bioconjugation. The modular design of N-heterocyclic carbenes is exploited in this endeavour. Thus, a series of adducts has been synthesised featuring systematic variation of the carbene backbone, and the impact on their hydrolytic stability assessed. The preparation of a N-alkyne appended NHC-BF3 derivatives is also described, and their bioconjugation to a folic acid derivative detailed.
Chapter 5 describes the investigation of carbene stabilised boron complexes and their fluoride binding reactions. Three-coordinate carbene-stabilised catecholato-boreniums have been investigated together with related series of four-coordinate complexes featuring either an additional anionic or neutral donor group. Systematic variation of the carbene donor and the leaving group substituent have been used to tune the rate of fluoride binding by these complexes, in addition to their hydrolytic stability. Neutral and cationic boron complexes are thus explored, with the four-coordinate boronium cations being determined to offer the greatest scope for optimising reactivity and stability. Careful choice of the secondary donor (based on pKa) offers a workable compromise between the kinetics of fluoride uptake at 60 °C and the stability of the boronium precursor to hydrolysis. Thus, systematic optimisation allows rapid, promoter-free fluoride binding to be achieved with a bench-stable boronium complex.

Keywords: bioconjugation
hydrolytic stability
boron
fluoride
18F-PET tracer design
Advisor: Aldridge, S
Faulkner, S
Cornelissen, B
Investigating loading programmes for tendon tissue engineering

Rotator cuff injuries are the most common cause of shoulder pain in adults and are growing in prevalence due to an aging demographic. These injuries present a substantial socio-economic burden. Despite a high prevalence of rotator cuff damage and symptoms, treatment outcomes are not promising; it is estimated that upwards of 40 % of rotator cuff repairs fail within the first few months post-operatively due to poor tissue healing. Development of engineered tendon grafts for clinical use is a promising strategy to address this growing challenge. To produce clinically relevant grafts, advanced bioreactor systems are needed.
This thesis presents a novel approach to develop physiologically relevant tendon grafts for eventual clinical application, using an advanced humanoid bioreactor platform to provide mechanical stimulation. The main objectives of this work were to investigate whether the humanoid robot could replicate the kinematic and kinetic profiles experienced by the supraspinatus tendon in vivo and whether loading from the humanoid robot could be effectively transmitted to scaffold material for growing tendon tissue.
To achieve the first objective, a motion study was conducted which involved the humanoid arm replicating abduction/adduction tasks that a group of 40 healthy human participants completed. Results from the motion study indicated that the humanoid arm was capable of replicating the kinematic profile or the kinetic profile of human participants during task completion, but not both simultaneously. The motion study helped identify future areas of development for the humanoid arm and further potential applications for musculoskeletal humanoid robots, such as implant testing.
Digital image correlation was used to accomplish the second objective. This investigation indicated that the humanoid robot is capable of providing strain ranges to the scaffold that have been shown to result in optimal tissue growth. The average strain values reported in this study were also within the range reported in studies examining supraspinatus deformation during abduction/adduction movements in vivo. Limitations associated with digital image correlation for characterisation of biological samples were discussed in this section.
This study represents a first step in exploring musculoskeletal humanoid robots as a platform for tendon tissue engineering. Although more work is necessary to enhance the humanoid model and further assess the viability of this strategy for development of clinically useful tendon grafts, the humanoid robot presented in this study has demonstrated the potential to overcome limitations associated with current bioreactor systems. This research has the potential to benefit individuals, healthcare systems, and society, by improving patient outcomes and quality of life following shoulder injury, thereby reducing the overall burden of tendon disease.

Keywords: humanoid robot
tissue engineering
tendon
musculoskeletal robot
regenerative medicine
Advisor: Mouthuy, P
Stebbins, J
Carr, A
Optoelectronic devices using 2D layered materials

The new diverse family of two-dimensional (2D) materials has aroused researchers’ enormous interest as key components in next-generation optoelectronic devices. In this thesis, ultrathin all-2D devices based on graphene, molybdenum disulphide (MoS2) and tungsten disulphide (WS2), synthesized using the scalable bottom-up approach, are investigated in both single- and multi-stacked configurations.
The first chapter of results demonstrates a novel stacking method for assembling uniform-patterned periodic 2D arrays into vertical-layered heterostructures. The fabricated heterostructure, showing the photovoltaic effect, can serve as photodetectors, with graphene as electrodes and MoS2 as the photo-absorber. All 2D materials used are grown into continuous films with only mono- or bilayer thickness. Each layer is prepatterned into a specific shape on a substrate and then transferred to the device substrate with aligned precision in the microrange by using interlocking marker pairs. Hundreds of identical devices are produced with 2D periodic spacing on a 1 cm × 1 cm SiO2/Si substrate, which is a fundamental prerequisite for future pixelated detectors.
The second chapter of results explores the graphene-WS2 van der Waals Schottky heterojunction. The device of WS2 with laterally spaced graphene electrodes behaves as a diode with a rectification ratio up to 90 under a laser power of 1.37 μW at a bias voltage of ±3 V. This is attributed by the different dielectric environments of two graphene electrodes, leading to asymmetric Schottky barriers of graphenebottom-WS2 and graphenetop-WS2. Both the laser illumination and back-gate voltage can tune the rectification behaviour of the device. Furthermore, a constant bias voltage applied to the device causes a strong electroluminescence in the junction area, with an average current of 2.16 ×10-5 A. This work contributes to the current understanding of the 2D metal−semiconductor heterojunction and offers an idea to obtain all-2D Schottky diodes by retaining the ultrathin device concept.
The third chapter of results shows a new type of photodetectors with an enhanced photodetecting efficiency by creating the multi-stacked heterostructure. The optoelectronic performances under different illumination intensities are studied. The average net photocurrent of the multi-stacked (graphene/WS2/MoS2/graphene/MoS2/WS2/graphene) device is around 2.3 times than that of the single-stacked (graphene/WS2/MoS2/graphene) one due to the improved light absorbed. This study brings forward a novel concept of multi-stacked architectures which extends the current research range and paves up ways for the high efficiency yet ultrathin photodetectors.

Keywords: tansition-metal dichalcogenide
graphene
optoelectronics
all-2D device
Advisor: Warner, J
Optimisation of ultrasound-mediated delivery of mRNA to mammalian cells

Gene delivery will cure all. That was the hope of many since the discovery and therapeutic implementation of genetic research. Although some of that hope has been realised, the delivery of nucleotides to cells in the body remains a major barrier in wider application. Ultrasound-mediated delivery of drugs has been investigated in various forms for decades and continues to be an area of engineering and science that is much explored. The body of work presented in this thesis strides to bring the two areas of research endeavour together.
Ultrasound-mediated delivery of drugs and antibody particles, normally in conjunction with cavitation nucleation agents, has been shown to be effective both in vitro and in vivo. In this work, we focus on nucleotide delivery, in particular mRNA, which has yet to be fully explored, especially in the context of achieving delivery of non-encapsulated, ‘free’ mRNA. Data presented here explores the relationship between cavitation and the transfer of, and protein expression from, free mRNA. The protein expression exhibited in various cell lines in vitro was further tested in vivo, using either sub-micron or micron-sized cavitation nuclei and the effects on transfection efficiency and expression time were examined. A luciferase reporter gene assay was used to characterise events in vitro across different cell lines including cancer and non-cancerous types. The impact and varying acoustic exposure parameters and cavitation on expression were assessed, and differences in expression time and transfection rate were observed. These data were used to determine appropriate acoustic parameters for in vivo delivery. Cavitation-mediated delivery was examined in vivo in two types of cancer tumours, and mRNA expression was quantified using in vivo fluorescence imaging and using excised homogenised tumour tissue. The results presented here lay the foundations for cavitation-mediated delivery and transfection of free mRNA both in vitro and in vivo by identifying appropriate acoustic parameters and cavitation nucleation agents, which result in enhanced delivery and by identifying the appropriate time windows for measurements to quantify expression.

Keywords: ultrasound
gene delivery
tumour
in vivo ultrasound delivery
mRNA delivery
high intensity focused ultrasound
ultrasound-mediated delivery
in vitro ultrasound delivery
tumour model
cavitation
cancer
Advisor: Cleveland, R
Carlisle, R
Defence and response during bacterial warfare

At the heart of most microbial communities lie competitive interactions. These interactions are often mediated by a wide array of dedicated weapons that bacteria use to kill and inhibit competitors. In response, bacteria have therefore had to evolve ways to cope with these attacks. However, our understanding of how bacteria deal with such stresses is largely confined to the effects of clinical antibiotics. Here we argue that there is need for a dedicated focus on how bacteria respond and defend themselves against other bacterial competitors. In this thesis, we use lab-based experiments and agent-based modelling to investigate two different ways bacteria respond to assaults from competitors, filamentation and biofilm formation.
Under stress, many bacterial cells will elongate without dividing to generate long filaments. We found that DNase colicins, narrow-spectrum toxins of E. coli, trigger dramatic filamentation in susceptible conspecifics, which is associated with cells actively pushing themselves out from microcolonies. We explored whether this behaviour could be a strategy for escaping from toxins by deleting the gene reported to control filamentation. However, this locus and several others tested, failed to prevent inhibition meaning that tests of a dispersal benefit were inconclusive. However, with a second toxin that induces filamentation --- the drug mitomycin C --- I found evidence that filamentation does indeed provide a strong benefit by allowing cells to disperse better from growing colonies.
A second widespread response to toxins is for bacteria to increase biofilm formation. We explored the potential benefit of this response in competition with other bacteria using agent-based modelling. We found that making a thicker biofilm is a good way to compete even without the effects of toxins, because of the well-known benefits of reaching nutrients first. Moreover, when toxin competition occurs, we found that thick biofilms can serve to mop up toxins and help defend a strain against incoming attacks. Overall, the biofilm response can be clearly rationalised in the context of interbacterial warfare.
Finally, we present a review of the ecology and evolution of bacterial warfare, which includes an extensive survey of currently known bacterial weapons, and how and when they are used.
My thesis stresses the importance of toxin-mediated warfare for shaping the ecology and evolution of bacteria. But there is still much to learn about bacterial defences, and we argue that greater understanding will be needed if we are to effectively control bacterial communities for our own ends.

Keywords: filamentation
simulations
interference competition
biofilms
bacterial warfare
Advisor: Foster, K
Smith, W
The structure of large random graphs

We obtain universality results on the structure of random graphs from two different angles. Naturally, there is a trade-off between the generality of the assumptions on a model and the specificity of the results one may obtain. The strength of the first work is its generality: we obtain non-asymptotic universal tail bounds on the height of random trees that do not require any assumptions on e.g. the tail behaviour of the degrees. In the second work, we need stronger assumptions, but our description of the structure is more specific: we do not study a real-valued statistic of the random graph model, but show convergence in distribution under rescaling of the graph itself, which entails the convergence of a whole panoply of such statistics.
Firstly, we obtain new non-asymptotic universal tail bounds for the height of uniformly random trees with a given degree sequence. We also obtain universal tail bounds for the height of simply generated trees and conditioned Bienaymé trees (the family trees of branching processes) that settle several conjectures from the literature. Moreover, we define a partial ordering on degree sequences and show that it induces a stochastic ordering on the heights of uniformly random trees with given degree sequences. The latter result implies that sub-binary random trees are stochastically the tallest trees with a given number of vertices and leaves.
Secondly, we consider the strongly connected components (SCCs) of a uniform directed graph on n vertices with i.i.d. in- and out-degree pairs distributed as (D−, D+), with E[D^+] = E[D^_−] = μ. We condition on equal total in- and out-degree. A phase transition for the emergence of a giant SCC is known to occur at the critical point where E[D^−D^+] = μ. We study the model at this critical point and show that, under some additional finite moment conditions, the SCCs ranked by decreasing number of edges with distances rescaled by n^{−1/3} converge in distribution to a sequence of finite strongly connected directed multigraphs with edge lengths, and that these are either 3-regular or loops almost surely. This is the first universality result for the scaling limit of a critical directed graph model and the first quantitative result on the directed configuration model at criticality.

Keywords: scaling limit
Galton-Watson trees
directed graphs
Bienayme trees
height of random trees
configuration model
random graphs
random trees
Advisor: Goldschmidt, C
Addario-Berry, L
The fragility and potential of the Rome Statute system: an empirical study of international and domestic trial justice paths in the situation of Uganda

Since 1998 the Rome Statute system and the International Criminal Court have become the most prominent international institutional set-up created to address the question of formal accountability for international crimes. While the ICC has been the subject of in-depth studies and critiques, a holistic analysis of the Rome Statute system’s limitations and potential is still missing. In this thesis I turn this overarching question into a question viable for an empirical analysis of the system of Rome: What factors affect the success or failure of ICC-led and state-led trial justice paths in the context of the Rome Statute system? I address this question by viewing the system of Rome as an operational system designed to produce courtroom-based justice through the actions of the ICC and state actors on the basis of the roadmap of the Rome Statute. From this definitional standpoint, I analyse what factors hinder or determine the ICC and state actors’ ability to bring trials to fruition in practice and thus make them effective vehicles of trial justice. I conduct this analysis ethnograpically, analysing the case study of Uganda, where an international and a domestic trial justice route have been pursued concomitantly by the ICC and state institutions. Through the analysis of this case study, I demonstrate that factors related to the institutional nature of and rapport between the ICC, domestic courts and state actors, to the day-to-day practice of trial justice and to the Rome Statute’s blueprint for action, all impact the potential for success of ICC and state-led prosecutorial paths. By extension I demonstrate that systemic fragility and potential can be found in the system’s architectural institutional framework, in the practice of trial justice and in the Rome Statute’s ability to function as a ‘best practice’ model for the ICC and domestic courts alike. This thesis is based on extensive fieldwork conducted at the ICC and in Uganda.

Keywords: transitional justice
International Criminal Court
Lord's Resistance Army
International Crimes Division
Dominic Ongwen
Uganda
trial justice
Rome Statute system
Thomas Kwoyelo
Rome Statute
Advisor: Kurkchiyan, M