VictorJuiz/thesis huggingface dataset:
Understanding past abrupt climatic change through the reduction of chronological uncertainty

Across Europe, palaeoclimatic records dated to the Last Glacial-Interglacial Transition (LGIT; 16-8 cal. ka BP) provide evidence for several abrupt climatic oscillations on millennial and centennial-timescales. Understanding the spatial and temporal environmental response to these climatic events on a continental scale is important for providing insight into future climate scenarios. This relies on providing precise chronologies for palaeoenvironmental records, but issues with large dating uncertainties, and the practice of tuning/wiggle-matching different records together, has limited our ability to test for (a)synchroneity for abrupt climate transitions.
In this study, the temporal and spatial complexity of LGIT climatic events, specifically, the Younger Dryas (YD) and earliest Holocene (EH) were investigated. Several of the most precisely dated pollen records were selected, spanning from northern to southern Europe. These sites were chosen using selection criteria that required independent chronologies based on radiocarbon dating and tephrochronology. To broaden the geographic range, a cryptotephra investigation was also undertaken on two palaeoenvironmental records from Romania (Lake Lia and Lake Brazi).
Using Bayesian chronological modelling, each site’s ages and the widespread tephra layers were remodelled. Pollen records were also re-investigated using the statistical methods of Principal Curve analysis to assist in identifying abrupt climatic transitions. The INTIMATE Integration tool was utilised to enable quantified comparisons between these terrestrial sites and the high-resolution Greenland ice core records.
The results from the Romanian cryptotephra investigation highlight the importance of this region to expand tephrostratigraphic frameworks across Europe, the Mediterranean and Anatolia. The identification of ultra-distal tephra layers allowed for a broader investigation into the timing of LGIT events.
This study showed that even with the most precisely dated sites and, despite the methodological approaches employed here, identifying a clear time-transgression for the YD and centennial-scale events within the EH remains difficult due to chronological uncertainties. Issues with proxy and dating resolutions currently limit the chronological approach undertaken. Nonetheless, using widespread tephra layers and statistical methods on proxy records can help to evaluate the potential asynchrony of abrupt climate transitions and the possible climatic drivers.
Overall, this study highlights the need to provide robust chronologies by undertaking high-resolution radiocarbon dating and proxy reconstruction, supplemented by tephrochronology. By employing these approaches with Bayesian age modelling, the temporal and spatial response to abrupt climatic shifts can be further explored.

Keywords: Tephrochronology
Time transgression
Romania
Pollen
Radiocarbon
Preboreal Oscillation
Bayesian age-depth models
Palaeoenvironmental records
Abrupt climatic change
Younger Dryas
Tephrostratigraphy
Cryptotephra
Europe
Advisor: Albert, P
Staff, R
Ramsey, CB
LEXICAL innovation and Latin philosophical vocabulary: from Cicero to Boethius

This thesis studies the related linguistic phenomena of ‘lexical innovation’ and ‘lexical augmentation’ in selected Latin authors who translated Greek philosophical terminology between the Late Republican era to the sixth century A.D. It is the first kind of comparative study of philosophical lexicalisation in Latin, collating and evaluating lexical data from the corpora of influential Latin authors, using a blend of synchronic and diachronic analyses. One of the arguments of the thesis is the bifurcated tradition of Greco-Roman intellectual thought: one, a continuous transmission of philosophical expression in Ancient Greek from Plato to Byzantium in the East; another, a process of renovation and synthesis, principally from the first century B.C. with authors such as Titus Lucretius Carus and Marcus Tullius Cicero. The findings suggest that the philosophical vocabulary of the Greeks was redefined through the creative literary projects of Latin intellectuals, forging their own terms within the linguistic, stylistic, and conceptual parameters of their language’s grammar. This ‘refraction’ of thought carried far-reaching consequences for early Christian authors and the Scholastic movement of the Middle Ages. To understand the emergence of ‘philosophical Latin’, it is important to note that the development of this technical vocabulary comprised an ensemble of semantic and morpho-syntactic strategies: linguistic practices that engendered the expansion of philosophical expression, (neologism, calques, semantic extensions, and loan-words, among others). The analysis begins with an overview of past scholarship, contextualising this work in the light of modern linguistic and translation theories on the topic, which provide the rationale for the arguments advanced throughout the thesis. The structure is divided over five chapters based around qualitative and quantitative analyses of Latin philosophical terms introduced as the result of translations from Greek terms. This relies on specified criteria applied to new terms and meanings first attested in a given author; that is, there must be some textual ‘signalling’ (such as glossing or direct translation) to indicate certain Latin terms or meanings correspond with Greek ones. These analyses are applied using a case-study approach, beginning with Lucretius and Cicero, then Seneca the Younger, Apuleius, Tertullian, Calcidius, and concluding with Boethius. Within the analyses of Cicero’s and Apuleius’ philosophical works, there are additional selective linguistic commentaries, first on Cicero’s translation of Plato’s Timaeus dialogue in Chapter One followed by Apuleius’ De Platone et Eius Dogmate and his translation of the Pseudo-Aristotelian De Mundo in Chapter Three. The study is accompanied by four sets of appendices for reference, collating and summarising the findings of this thesis.

Keywords: neology
lexical innovation
Latin philosophy
Greek philosophy
Boethius
Cicero
vocabulary
translation
Advisor: Reinhardt, T
Isopeptide bond-locked enzymes to engineer thermal resilience

Despite their high utility, enzymes often require thermal stabilisation prior to use in industrial catalysis. Current stabilisation approaches are time-consuming and require the individual engineering of each enzyme requiring stabilisation. Head-to-tail enzyme cyclisation is an alternative strategy that has the potential to serve as a generic yet effective method for the thermal stabilisation of enzymes. Spontaneous isopeptide bond-forming protein partners SpyTag and SpyCatcher have been used to cyclise enzymes to confer thermal resilience.
In this thesis, I established the application of the novel tripartite SnoopLigase conjugation system for enzyme cyclisation. SnoopLigase catalyses the covalent locking of peptide tags SnoopTagJr and DogTag. N-terminal fusion of SnoopTagJr and C-terminal fusion of DogTag enabled the efficient cyclisation of mesophilic enzymes upon addition of SnoopLigase through the formation of an isopeptide bond between the peptide tags. SnoopLigase cyclisation conferred major improvements in thermal resilience to mesophilic enzymes, enabling them to withstand heat-induced aggregation and inactivation even following incubation at 100 °C.
Until now, cyclisation has only been demonstrated for enzymes whose termini are found in relative proximity. To broaden the scope of isopeptide bond-mediated cyclisation, I applied SnoopLigase cyclisation in conjunction with structured linkers to cyclise industrially important enzymes with larger distances between termini. Linker-appended SnoopLigase cyclisation improved the thermal resilience of already thermostable enzymes, demonstrating the potential for one-step enhancement of thermal resilience for a wider range of enzymes.

Advisor: Howarth, M
Redfield, C
Measuring and forecasting public opinion with non-representative samples

In this doctoral thesis, I reflect on methods to leverage non-representative samples to measure and forecast public opinion in the run-up to an election. The thesis is made up of three separate papers, dealing with a number of issues around the topic of convenience samples; these issues include a) how and where to collect non-representative data, and how to enhance them with external, auxiliary sources; b) how to construct reliable and deep stratification weights, when these are not immediately available from the census, and when no single dataset contains an exhaustive set of the desired post-stratification information; c) how to optimise learning models to automate variable selection, produce accurate out-of-sample predictions, and improve fitting speed. Findings from this thesis suggest unrepresentative samples can be used to obtain real-time readings of public opinion, at a fraction of the cost of traditional survey methods, provided a number of non-trivial and computationally demanding model adjustments are implemented to smooth and re-weight the samples.

Keywords: non-representative surveys
MrP
public opinion
boosting
social-media
random forests
machine learning
Advisor: Fisher, S
The United Kingdom and the European Community’s Common Fisheries Policy, 1971–1983

This thesis examines how the United Kingdom negotiated the Common Fisheries Policy with the European Community in two rounds: firstly, between 1971 and 1972, before Britain’s joining of the Community in 1973; secondly, between 1976 and 1983, when negotiations on the comprehensive Common Fisheries Policy package concluded. It is based upon primary archival research, as well as elite interviews and secondary sources.
This case-study traces Britain’s bargaining objectives, and assesses the United Kingdom’s performance in these intensely contested negotiations. Drawing on new institutionalism and Putnam’s two-level game theory, this thesis demonstrates how European Community membership affected Britain’s bargaining capacity at the European level. It reveals, counterintuitively, that membership of the European Community did not in itself bring bargaining success to the United Kingdom. Nevertheless, in fisheries bargaining, the United Kingdom consistently pursued its interests in a rational, utility-oriented manner, and it acted cooperatively in order to secure agreement with its partners at the European level.
By demonstrating how the United Kingdom negotiated on fisheries, the thesis also explores the broader paradigm of, and assumptions about, ‘British exceptionalism’ in the European Community. It makes clear that even powerful states have to navigate carefully through the Community’s dense institutional network in order to negotiate successfully.

Keywords: Negotiation Analysis
EU Politics
Common Fisheries Policy
European Community
British Politics
European Economic Community
Advisor: Zielonka, J
Structure-aware tools for the development of therapeutic antibodies from natural immunoglobulins

In this thesis, we establish the foundations for structure-based antibody drug discovery from natural immunoglobulin sequences. This is achieved through two novel software packages: ‘Repertoire Structural Profiling’ (RSP), as a means of generating structurally-diverse virtual screening libraries, and the ‘Therapeutic Antibody Profiler’ (TAP), for rapid structure-aware developability assessment of candidates in early-stage antibody drug discovery. Our approaches are orthogonal to existing work in these fields and yield new insights into the diversity of the adaptive immune system and the physicochemical characteristics of therapeutic antibodies. We also describe a new database (Thera-SAbDab), which provides the increased therapeutic antibody sequence and structural data necessary to benchmark RSP and TAP, and to facilitate future investigations in the area. Finally, we report our work in the COVID-19 response effort, which, through a novel database of thousands of coronavirus antibody-binders (CoV-AbDab), has already contributed functional annotations to SARS-CoV-2 immune response repertoires.

Keywords: therapeutic antibodies
screening library
antibody database
developability
antibody repertoire
coronavirus
B-cell receptors
structural profiling
Advisor: Deane, C
Solvodynamic printed silver nanowire composite films for pressure sensing applications

This thesis examines some of the current issues with the use of non-contact printing techniques for fabricating conductive structures for applications in flexible pressure sensors.
Firstly, the concept of solvodynamic printing was introduced as a method to improve printing resolution using solvent-solvent interactions. By including an additional carrier solvent into the ink delivery system, both the footprint of the ejected ink and the degree of ink spreading on the substrate could be reduced. The proof-of-concept of this technique was demonstrated by printing lines of silver nanoparticles on polyethylene naphthalate substrates. Silver nanoparticle tracks with widths of 35.2 ± 7.0 m were achieved using a 300 μm nozzle. This is equivalent to 11.7 ± 2.3 % of the nozzle diameter. The result shows great potential in solvodynamic printing as not many modern printing techniques can achieve such nozzle to feature size ratios.
Next, the use of ligand exchange on silver nanowires to formulate a post-treatment free ink which can produce highly conductive printed silver nanowire structures was explored. The use of rigid bidentate linking ligands was studied. Among the ligands used, fumaric acid was shown to be the most effective in improving the film conductivity, reducing the sheet resistance by 70 % of a control sample from 26.5 Ω/□ to 7.66 Ω/□. The decrease in sheet resistance was attributed to the decrease in junction resistance of the nanowire film.
Lastly, a simple fabrication method was used to make piezoresistive composite films consisting of silver nanowires embedded in an ethylene-co-vinyl acetate matrix. The performances of the pressure sensor using compressive and tensile strains were compared. The properties of the pressure sensor were highly tunable based on the composition and design of the film. Overall, the films showed a low detection limit (1.47 ± 0.13 Pa), fast response time (11-22 ± 2.9 ms) and high sensitivity (67.3 ± 5.9 kPa-1). We further showed the successful application of the film as a pulse monitoring device.

Keywords: pressure sensor
additive manufacturing
printed electronics
silver nanowires
flexible electronics
nanocomposite
Advisor: Watt, A
Dicer-dependent transfer RNA-derived small RNAs and their role in gene regulation

Endogenous small non-coding RNAs (sncRNAs) are employed in mammalian cells to negatively regulate gene expression in a sequence-specific manner. This phenomenon is known as RNA interference (RNAi). Depending on the molecular mechanism, RNAi can be categorised into post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS). PTGS involves direct cleavage of mature messenger RNA (mRNA) or destabilisation of mRNA and/or translational repression in the cytoplasm. TGS is mediated by the establishment of heterochromatin at target loci in the nucleus. Transfer RNAs (tRNAs), which are essential for protein synthesis, have recently been identified as a source for a novel class of regulatory sncRNAs, termed tRNA-derived small RNAs (tsRNAs). The biogenesis of tsRNAs and their role in gene regulation remain largely elusive. By using a combination of unbiased bioinformatic prediction and classic molecular biology methodologies, I have studied the role of tsRNAs in the regulation of gene expression. Here I propose that Dicer is involved in tsRNA biogenesis and Dicer-dependent tsRNAs can promote gene silencing through a mechanism that is distinct from well-known PTGS and TGS. I show that Dicer-dependent tsRNAs may lead to gene silencing by targeting nascent transcripts, a mechanism termed nascent RNA silencing (NRS). Finally, I explored the therapeutic potential of tsRNAs and demonstrated the silencing of multiple genes by employing tsRNA mimics.

Keywords: tRNA-derived small RNAs
small non-coding RNAs
gene regulation
RNA interference
Advisor: Gullerova, M
Developing Papua New Guinea teachers’ mathematical knowledge for teaching: prospective teachers and algebra concept

Mathematics teachers must have Mathematical Knowledge for Teaching (MKfT) as this is the knowledge required to teach in a school. It is seen that teachers who do not have an adequate knowledge of the MKfT are less well equipped to help students learn. A school curriculum that is meaningful and useful for Papua New Guineans is the driving force behind the recent educational reformations. However, school children still lack the application of the mathematical knowledge (SMK) in their everyday life which makes the learning of mathematics meaningless problematic in Papua New Guinea (PNG) and which could be attributed to mathematics teachers’ lack of MKfT. Hence, this study took an action reaction approach whereby cycle one was a base line survey that was conducted with beginning teachers and other stake holders in Goroka gauging their perceptions of the MKfT required by teachers to teach in secondary schools in PNG and the issues and challenges in developing this knowledge. Findings from cycle 1 showed that, some respondents perceived that trainee teachers’ SMK was good but needed PCK (an aspect of MKfT) development through a workshop. Therefore in cycle two the findings from the base line data were used to develop a workshop designed to enhance student teachers’ MKfT, and overall, the evaluation of the workshop found it successful in beginning this enhancement. It also found that more sustained professional development work with beginning teachers, mentors and teacher educators needed to be conducted in the PNG context.

Keywords: MTED
MTED 2020
No hands up: An investigation into the impact of cold-calling on primary school teacher expectations

Teacher expectations have a significant impact on pupil outcomes. Expectations are the beliefs teachers hold about pupils’ potential academic achievements. Previous studies have investigated the impact of incorporating the strategies of high-expectation teacher on pupils’ attainment. Teacher expectations appear to be related to teachers’ self-efficacy beliefs and beliefs about intelligence. This study aimed to investigate the impact of cold-calling on teachers’ expectations. Cold-calling is a questioning strategy where teachers choose children from the whole class to answer their questions rather than rely on volunteers raising their hands. It is referred to frequently in professional documentation relating to high expectations. There is a lack of existing research into the decision-making process of teachers when choosing children to answer questions. The intervention was to incorporate cold-calling into the classroom practice of four participants in an English primary school setting. The Coronavirus school closures meant that the study had to be adapted due to no data being able to be collected. Had data collection been possible, a mixed-methods approach would have been used.
Quantitative data including potential changes to predictions of attainment and teacher self-efficacy using the established Teacher Self Efficacy Scale would have been collected. Focus groups would have provided qualitative data which would have been analysed using grounded theory. The potential findings have been considered based on existing findings in the literature and a critical analysis of the proposed research methods. Including cold-calling in a teacher’s practice may increase their expectations but there are additional factors which might affect this; however, it may also communicate increased expectations to pupils, which is strongly proven to raise outcomes due to initiating or encouraging a change to their behaviour to meet increased expectations.

Keywords: MLT
MLT2020
How can I help?  A case study of parental engagement and its impact on student reading

This practitioner research investigated the links between Year 7 students’ achievement in and engagement with reading and the amount of parental engagement they received at home with their reading. This work draws strongly on previous research that highlights the importance of parental engagement, whilst also providing a clear outline of what has been undertaken in the intervention.
Parents were invited to attend a Reading Information Evening which highlighted why reading was important to academic achievement and future careers. The evening also explained how the school was encouraging their child’s reading and what they could do at home to support their child’s reading engagement. Attendance at the intervention was optional which potentially meant that those who took part were already engaged, as opposed to the intervention creating engagement itself. This was a mixed-methods research project with qualitative data being collected from group interviews with Year 7 students and questionnaires completed by Year 7 students and quantitative data being collected through the Accelerated Reader Standardised Test for Assessment of Reading (STAR) and New Group Reading Tests (NGRT). All of these methods were used to determine whether students’ reading had been influenced by their parents, however, some data is missing due to the Covid-19 pandemic and subsequent school closure.
Despite the limitations of school closure, the findings indicate that increased parental engagement has positive repercussions on student reading achievement. Teachers also noted increased engagement from those students who indicated that they received parental support at home with their reading or that their parents displayed an interest in the Accelerated Reader (AR) programme. From looking at the relationship between students’ reading and the parental engagement they receive, the school can now consider how they harness the power of parents to maximise student outcomes.

Keywords: MLT
MLT2020
Modular Calabi-Yau threefolds in string compactifications

All elliptic curves defined over Q are modular. This is the statement of the modularity theorem that relates arithmetic properties of an elliptic curve to a modular form for a subgroup of SL(2,Z). This modularity has been (and still is) the subject of much research in number theory. At first, one might suspect that this kind of modularity is irrelevant for physics. Nevertheless, we will show in this thesis that modular Calabi-Yau threefolds are distinguished by certain physical processes. Most notably, by the attractor mechanism of IIB supergravity.
We will see that the zeta-function associated to an attractor variety of rank two will factor in a specified manner and that a search for such factorisations leads to an effective strategy for identifying examples of rank two attractor varieties with small h2,1 . We will also find and study a number of attractor varieties of rank two by taking the Hadamard product of two Picard-Fuchs equations of families of elliptic curves. As we will see, in many cases, the Hadamard product admits an involution with fixed points that are attractor points of rank two. We are able to identify the associated modular forms in both types of examples.
In the remainder of this thesis, we will explore the physical implication of mod- ularity. We will show that certain arithmetically interesting quantities such as critical values of the associated L-functions determine the area of the horizon of certain dyonic N = 2 black holes. Similarly, we find that topological string free energies, when evaluated at the mirror of a rank two attractor point, may also be expressed in terms of arithmetically interesting quantities.

Keywords: String Theory
Modularity Modular Form Zeta Function
Dyonic Black Hole Attractor Mechanism IIB
Calabi Yau
Advisor: Candelas, P