VictorJuiz/thesis huggingface dataset:
Aspects of lithic assemblage variability in the late paleolithic of south-east Italy

This thesis concerns late Palaeolithic settlement in the region of Puglia, south-east Italy, at the close of the Pleistocene. Puglia comprises three sub-regions which contain sites of this period: the Salento peninsula, the Murge, and the Gargano promontory. The late Palaeolithic occupation must be considered in relation to the former existence of an extensive coastal plain, and to the sea-level rise which submerged it. The late Palaeolithic assemblages of the region have been studied previously by Italian archaeologists from a rigid typological stance, with various schemes put forward suggesting evolution of the assemblages through different stages of an Epigravettian tradition. In this thesis, attribute analysis is used to re-examine the principal assemblages, using published data where adequate and supplemented by samples studied by the author in Italy. The results are analyzed to seek the social and economic factors which shaped the various industries, as well as diachronic change wherever it can be demonstrated. Factors such as difficulty in obtaining raw material were clearly crucial to assemblage composition. The existing typological schemes are shown to lack real bases and to mask rather than reveal sociocultural information. Chapter 1 states the aims of the thesis and critically discusses previous theoretical approaches to the late Palaeolithic of the region. Chapters 2 and 3 describe relevant aspects of the regional palaeoenvironment. The author's own methodological approach is explained in Chapter 4, and then used for a detailed study of the assemblages from Grotta delle Cipolliane in Chapter 5. This is followed in Chapter 6 by a broader study of the late Palaeolithic assemblages in Puglia, with discussions of their possible diachronic and synchronic relationships. Chapter 7 develops this latter theme into an attempt to understand the social and economic features of the late Palaeolithic settlement of Puglia, and suggestions are made concerning future work that might improve the quality of the archaeological evidence. Chapter 8 summarizes the main conclusions of the thesis.
Collective dynamics of solid-state spin chains and ensembles in quantum information processing

This thesis is concerned with the collective dynamics in different spin chains and spin ensembles in solid-state materials. The focus is on the manipulation of electron spins, through spin-spin and spin-photon couplings controlled by voltage potentials or electromagnetic fields. A brief review of various systems is provided to describe the possible physical implementation of the ideas, and also outlines the basis of the adopted effective interaction models.
The first two ideas presented explore the collective behaviour of non-interacting spin chains with external couplings. One focuses on mapping the identical state of spin-singlet pairs in two currents onto two distant, static spins downstream, creating distributed entanglement that may be accessed. The other studies a quantum memory consisting of an array of non-interacting, static spins, which may encode and decode multiple flying spins. Both chains could effectively 'enhance' weak couplings in a cumulative fashion, and neither scheme requires active quantum control. Moreover, the distributed entanglement generated can offer larger separation between the qubits than more conventional protocols that only exploit the tunnelling effects between quantum dots. The quantum memory can also 'smooth' the statistical fluctuations in the effects of local errors when the stored information is spread.
Next, an interacting chain of static spins with nearest-neighbour interactions is introduced to connect distant end spins. Previously, it has been shown that this approach provides a cubic speed-up when compared with the direct coupling between the target spins. The practicality of this scheme is investigated by analysing realistic error effects via numerical simulations, and from that perspective relaxation of the nearest-neighbour assumption is proposed.
Finally, a non-interacting electron spin ensemble is reviewed as a quantum memory to store single photons from an on-chip stripline cavity. It is then promoted to a full quantum processor, with major error effects analysed.

Keywords: quantum entanglement
quantum state transfer
spin chain
quantum memory
spin ensemble
Advisor: Lovett, B
Benjamin, S
Category−Theoretic Quantitative Compositional Distributional Models of Natural Language Semantics

This thesis is about the problem of compositionality in distributional semantics. Distributional semantics presupposes that the meanings of words are a function of their occurrences in textual contexts. It models words as distributions over these contexts and represents them as vectors in high dimensional spaces. The problem of compositionality for such models concerns itself with how to produce distributional representations for larger units of text (such as a verb and its arguments) by composing the distributional representations of smaller units of text (such as individual words). This thesis focuses on a particular approach to this compositionality problem, namely using the categorical framework developed by Coecke, Sadrzadeh, and Clark, which combines syntactic analysis formalisms with distributional semantic representations of meaning to produce syntactically motivated composition operations. This thesis shows how this approach can be theoretically extended and practically implemented to produce concrete compositional distributional models of natural language semantics. It furthermore demonstrates that such models can perform on par with, or better than, other competing approaches in the field of natural language processing. There are three principal contributions to computational linguistics in this thesis. The first is to extend the DisCoCat framework on the syntactic front and semantic front, incorporating a number of syntactic analysis formalisms and providing learning procedures allowing for the generation of concrete compositional distributional models. The second contribution is to evaluate the models developed from the procedures presented here, showing that they outperform other compositional distributional models present in the literature. The third contribution is to show how using category theory to solve linguistic problems forms a sound basis for research, illustrated by examples of work on this topic, that also suggest directions for future research.
Structural studies on determinants of receptor/ligand binding in the tumour necrosis factor and T cell receptor protein families

Protein-protein recognition plays a central role in the surveillance of self and non-self in the mammalian immune system and ultimately in cellular survival within the organism. Two systems of fundamental importance to the immune system are the Tumour Necrosis Factor (TNF) and the T cell receptor (TCR) families.
High-throughput methods developed within the Oxford Protein Production Facility have been successfully applied to the production of members of the TNF receptor and ligand superfamilies for structural characterisation. The TNF receptor DR6 was successfully refolded from E.coli inclusion bodies using a rapid-dilution technique and yielded diffraction quality crystals. Data collected from these crystals will be used to obtain an x-ray crystallographic model of DR6. Vascular Endothelial Growth Inhibitor (VEGI) was produced as a soluble recombinant protein in E.coli, and formed a number of poorly diffracting crystals, it is hoped that further trials and optimization of conditions will lead to improved data quality. Lymphotoxin β receptor was produced in a Eukaryotic system. This has shed light on the complications posed by signal peptide cleavage and glycosylation on the production of protein for crystallization trials.
TNF superfamily proteins are ideal targets for the design of novel therapeutic agents due to their involvement in a number of disease pathologies. Various methods of molecular docking and small molecule design were applied to the search for potential inhibitors of receptor binding for the TNF ligand proteins TRAIL and BAFF. A number of potential drug leads were identified from the National Cancer Institute drug database.
The Natural Killer (NK) T cell restricted TCRs recognise CD1d-presented glycolipid. Determination of the crystal structures of the invariant NK TCR and the NK restricted TCRs 5E and 5B shows that these proteins adopt the canonical structures of class I MHC restricted TCRs. This suggests that the binding of CD1d-glycolipid by these receptors will conform to the same model of binding seen for the class I MHC restricted TCRs.

Keywords: T-Cell Receptor
TNF
X-ray crystallography
Advisor: Jones, E
Modelling affinity maturation in the immune system

The affinity of antibody for antigen increases during an immune response. This is achieved by mutation of the genes encoding for the antibody and subsequent selection of the best binder. The process takes place in a special microenvironment, the germinal centre. In this dissertation, a mathematical model is presented, which reproduces experimental data on the kinetics of this process and on the affinity maturation observed during the reaction. It further allows predictions to be made about parameters such as the selection rate of centrocytes and the recycling probability of selected centrocytes. Additionally it is shown that termination of somatic hypermutation several days before the end of the germinal centre reaction is beneficial for affinity maturation as is a start of memory cell formation well after the onset of somatic hypermutation. Selection of B cells during the germinal centre reaction is based on antigen recognition and is believed to involve interaction of B cells with membrane bound antigen. It has been shown that such encounter of membrane bound antigen leads to a re-organisation of proteins and lipids such that raft lipids are accumulating in the contact zone. In a second project possible driving forces for such a lipid re-organisation are investigated and the analysis shows that the accumulation of a special lipid sort in the contact zone can be understood by their high affinity for proteins engaged in the contact zone. Interaction between lipids themselves has no positive impact on the accumulation of lipids in the contact zone and strong interactions between lipids may even prohibit the domain formation in the contact zone by the trapping of lipids in patches elsewhere on the cell surface.
Cell signalling in response to heat shock in Arabidopsis thaliana

Increases in temperature damage plant cells, and plants react to heat stress by inducing of a number of protective mechanisms. In this study, it has been shown that heat damages cells both directly while the plants are being heated, and indirectly through heat induced oxidative stress during recovery from heating. Different stress response pathways are induced in each case. Evidence implicates salicylic acid, abscisic acid, ACC (a precursor of ethylene), calcium ions and active oxygen species in pathways resulting in thermotolerance (i.e. increased survival at high temperature). Addition of these potential second messengers results in increased survival and decreased oxidative damage after heating (as measured using the TBARS assay), while silencing the pathways through use of mutants, inhibitors or transgenes results in decreased thermotolerance. In vivo calcium measurements show cytosolic calcium transients only at initiation of cooling after heat stress. Calcium chloride also induces thermotolerance when added after heating, as does ACC. These substances can induce early increases in ascorbate peroxidase activity after heating, and induce expression of antioxidant genes. Thus they may play a role in heat induced oxidative stress response pathways in recovery. Two different pathways induced during heating appear to result in the expression of genes for heat shock proteins. The predominant pathway induced at 30oC involves ABA, while that at 35-40oC involves an oxidative burst generated through the NADPH oxidase, atrbohB. Addition of SA can induce HSP (heat shock protein) expression, but there is little evidence that this occurs endogenously in plant cells, although nahG plants unable to signal via SA are thermosensitive. Results in this study indicate that there are several signalling pathways associated with heat shock. The pathway induced during recovery from heating involves calcium ions and ethylene, and results in increased antioxidant capacity. During heating two pathways induce expression of HSPs: one involving abscisic acid and possibly salicylic acid and one involving an oxidative burst. At least one further pathway is believed to exist, which involves protein kinases and phosphatases as heat shock causes up-regulation of expression of certain genes for these signalling components.

Keywords: cell signalling
abiotic stress
arabidopsis
heat shock
Advisor: Knight, M
From the un-mixing to the re-mixing of peoples: Understanding the quest to “reverse ethnic cleansing” in Bosnia

This dissertation focuses on international actors' response to the ethnic cleansing perpetrated during the 1992 – 1995 Bosnian War. The work illuminates the multilateral attempt to reverse one of the outcomes of ethnic cleansing following the war, through the return of displaced people. The policy emphasis on "re-mixing" people, interpreted through a strategy of minority returns, and supported and coordinated on an international scale, was unprecedented.
This dissertation asks: why did powerful states and international organizations pursue a re-mixing policy as a response to ethnic cleansing in Bosnia? At first glance, the choice seems counterintuitive. The policy was expensive. Post-1989, the West no longer needed "to keep Yugoslavia afloat." Furthermore, reversal required a degree and duration of international involvement that, at the time, was thought to be politically, militarily, and financially impossible.
There are two existing explanations for this surprising phenomenon: international moralism and norm evolutionism. International moralists posit that international actors were moved to re-mix Bosnians out of a sense of guilt. Norm evolutionists argue that international norms governing appropriate responses to ethnic cleansing have shifted during the twentieth century towards support for re-mixing.
In contrast to these two dominant views, this dissertation argues that the re-mixing policy initially emerged as a practical fix to a series of pressing, context-specific political challenges. State policymakers justified the re-mixing policy, however, on normative grounds. Though not the original incentive for action, international organizations on the ground then adopted the policy, empowered by states' normative justifications and thereby transformed the political rhetoric into concrete action.
This dissertation corrects a common assumption that the origins and motivations behind the re-mixing policy were normative in nature, it contributes to a better understanding of how normative discourses emerge, mature, and transform into policy and it offers policy recommendations based on lessons learnt from this important and seemingly contradictory case.

Keywords: Bosnia
Refugees
Post-conflict Peace Building
Ethnic Conflict
Advisor: MacFarlane, N
Betts, A
Single-molecule DNA sensors and cages for transcription factors in vitro and in vivo

Gene regulation is vital to the success of all living organisms. Understanding this complex process is crucial to our knowledge of how cells function and how in some cases they can lead to debilitating or even fatal disease. In this thesis I focus on a set of DNA-binding proteins known as transcription factors (TFs), proteins fundamental to the process of gene regulation at the level of transcription. I develop assays and techniques for the detection and quantitation of TFs in vitro and in vivo as well as a method for TF encapsulation and release.
The advantages of the TF detection assays in this thesis are made possible through the use of single-molecule (sm) fluorescence. This methodology enables detection of individually labeled molecules allowing discrimination of sample heterogeneities inaccessible with ensemble techniques. Here I present two different TF assays based on two sm observables: relative probe stoichiometry and Förster resonance energy transfer (FRET).
The first assay design, based on stoichiometry, detects TFs using TF-dependent coincidence of two distinctly labelled DNA ‘half-sites’. I demonstrate sensitive detection (~ pM) in solution and on surfaces, multiplexed detection of multiple TFs, and detection in cell lysates. A kinetic model of the system is also developed, verified experimentally and used to quantify TF concentrations without the need for a calibration curve.
The second assay design, based on FRET, is a novel approach to TF detection using TFmediated DNA bending. TFs are detected by bending the sensor and monitored with FRET at the single-molecule or ensemble level. I demonstrate TF detection in purifed form and expressed in cell lysates. As this sensor was designed for use in vivo, methods to hinder nuclease degradation are explored.
For TF detection in vivo, I describe a successful strategy to internalise fluorescently labeled molecules into live E.coli. Viability and internalisation efficiency are characterised and ensemble measurements with FRET standards are demonstrated. Importantly, sm FRET measurements in vivo are achieved opening many exciting possibilities. The FRET based TF sensor is then internalised as a step towards real-time in vivo monitoring of TF concentrations.
Finally a system based on DNA nanotechnology is presented for the non-covalent encapsulation and release of TFs. Such a system could be delivered into a cell to alter levels of gene expression using external stimuli as inputs.
We believe these tools will generate valuable information in the study of prokaryotic gene expression as well as providing a potential commercial avenue towards diagnostics.

Keywords: single-molecule
drug-delivery
ALEX
FRET
biosensors
Advisor: Kapanidis, A
The estimation of recombination rates from population genetic data

Genetic recombination is an important process that generates new combinations of genes on which natural selection can operate. As such, an understanding of recombination in the human genome will provide insight into the evolutionary processes that have shaped our genetic history. The aim of this thesis is to use samples of population genetic data to explore the patterns of variation in the rate of recombination in the human genome. To do this I introduce a novel means of estimating recombination rates from population genetic data. The new, computationally efficient method incorporates a model of recombination hotspots that was absent in existing methods.
I use samples from the International HapMap Project to obtain recombination rate estimates for the autosomal portion of the genome. Using these estimates, I demonstrate that recombination has a number of interesting relationships with other genome features such as genes, DNA repeats, and sequence motifs. Furthermore, I show that genes of differing function have significantly different rates of recombination. I explore the relationship between recombination and specific sequence motifs and argue that while sequence motifs are an important factor in determining the location of recombination hotspots, the factor that controls motif activity is unknown.
The observation of many relationships between recombination and other genome features motivates an attempt to quantify the contributions to the recombination rate from specific features. I employ a wavelet analysis to investigate scale-specific patterns of recombination. In doing so, I reveal a number of highly significant correlations between recombination and other features of the genome at both the fine and broad scales, but find that relatively little of the variation in recombination rates can be explained. I conclude with a discussion of the results contained in the body of the thesis, and suggest a number of areas for future research.

Keywords: genetic recombination
Advisor: McVean, G
The auxilia and numeri raised in the Roman province of Syria

In classical times the military value of the Semitic peoples was often called into doubt. A superficial examination does not support the charges of the classical writers. This thesis sets out to examine the military contribution made by the native population of the province of Syria to the non-citizen regiments of the Roman army.
Introduction: the current state of knowledge about the Syrian auxilia is briefly summarised.
Chapter 1 defines the scope and objectives of the thesis: temporally, from the late Republic until the mid-third century; spatially, the area of the province of Syria on the eve of the annexation of Arabia; while, the units treated are those which are described as alae, cohortes and 'numeri'.
Chapter 2 is devoted to a treatment of the literary, epigraphic, papyrological, archaeological and artistic sources. Attention is then given to fundamental criteria relevant to the examination of the individual units.
Chapter 3 treats the background to the employment of Syrian soldiers from the Persian Wars onwards, but especially in the late Republic and very early Principate.
Chapter 4 is the main part of the thesis, being a detailed discussion of all the evidence for some 57 regiments. Each group of units - characterised by its tribal name - is preceded by a brief discussion of the region and its contribution to the legions and equestrian militiae.
Chapter 5 resumes the preceding work and offers some general conclusions concerning the (considerable) contribution of Syria to the auxilia, their recruitment pattern (probably little different to that of the auxilia as a whole), and tabulates the evidence for formation dates and subsequent distribution.
Six appendices look at: 'Tables' presenting the evidence for Syrian legionaries and Syrian auxiliaries on the diplomas; 'Dynastic Titles'; 'The Career of C. Velius Rufus...'; 'Mesopotam,ian Soldiers in the Roman Army'; the date Of the career of Valerius Lollianus; and, a study of Josephus BJ,III,66.
Illustrations consist of maps and photographs.