VictorJuiz/thesis huggingface dataset:
The symbiosis of people and plants
Keywords: Ontology
Cassava
Agroecology
Makushi
Amazonia
Shamanism
People-Plant Relations
Fermentation
Multispecies
Environmental Anthropology
Guyana
Traditional Ecological Knowledge
Anthropology
Amazon
Cosmology
Charm plants
Guianas
Ethnobotany
Indigenous
Social Anthropology
Farming

This ethnoecological study of the Makushi Amerindians of Amazonian Guyana explores the place of plants in the indigenous culture and cosmology. The North Rupununi, the homeland of the Makushi people, is a bioculturally diverse mosaic of neotropical savannahs, forests, and wetlands. As subsistence hunters, fishers, and horticulturalists, the Makushi live in a constant and dynamic interaction with their ecologically rich surroundings. Against the human-faunal bias latent in much Amazonian anthropology, I place plants firmly at the centre of analysis, a positioning that mirrors their centrality in the ethnographic context. Human-plant encounters explored herein include swidden agriculture, the cultivation of bitter cassava, the fermentation of cassava drinks using a domesticated fungus, the use of a category of charm plants, and the consumption of plant substances in shamanic ritual. With the Makushi, I emphasise the status of plants as living selves and agents of semiosis, occupying perspectives on the world in and outside of their interactions with human beings. In order to investigate ethno-theories of life, I attempt to understand the constitution of the person – and associated notions of body and soul – in the indigenous cosmology. Makushi ontology can be characterised as animic – though as I argue, it also incorporates naturalistic and analogic elements. Thus, it is poly-ontological.
This study pursues a dual goal: first, to pay heed to the trans-specific domain of living entities revealed in the Makushi ethnoecology, and second, to rethink conventional symbolic frameworks characteristic of anthropological approaches to culture. I explore the application of a more robust approach to sign-flows in nature – Peircian ecosemiotics – that allows for the analysis of plant communication, birdcalls, insect stings, and leaf patterns, as well as human language. In tracing these interspecific webs of signification, conclusions are drawn about the varied ways in which Makushi people engage with and think about their living environment. At the same time, many Makushi multispecies engagements are based on the physical transfer of substances between bodies of different kinds. In order to better account for this pervasive ‘substance logic’, greater attention must be paid to indigenous notions of corporeality and personhood. In doing so, I propose a dual analytical model that takes both the flows of signs and the flows of substances as its combined objective. This approach enables new conclusions to be drawn about multispecies relationality in indigenous Amazonian cosmologies.
A new technique for microbubble characterisation and the implications to contrast enhanced ultrasound
Keywords: Ultrasound
Microbubbles
Ultrasound Contrast Agents
Characterisation
Contrast Enhanced Ultrasound

The utility of microbubble agents in a variety of diagnostic and therapeutic ultrasound techniques has been widely demonstrated, most notably in Contrast Enhanced Ultrasound (CEUS) imaging. Unfortunately, the underlying mechanisms of their response to ultrasound excitation are poorly understood, restricting the development of promising techniques, such as quantitative perfusion imaging. A significant reason for this is that current microbubble characterisation techniques suffer from one or more of the following limitations: i) large experimental uncertainties, ii) physical restrictions on microbubble response and iii) failure to provide large data sets suitable for statistical analysis. This thesis presents a new technique to overcome these limitations. A co-axial microfluidic device is used to hydrodynamically confine microbubbles through the focal region of a laser and ultrasound field. The magnitude of light scattered by isolated microbubbles during ultrasound excitation is converted to radius using Mie Scattering theory. This technique is capable of obtaining large samples (>103/min) of microbubbles to be efficiently characterised.
The response of a commercial contrast agent, SonoVue®, is first investigated for a range of ultrasound exposure parameters; frequency (2 MHz – 4.5 MHz), peak negative pressure (6 kPa - 400 kPa) and pulse length (3 cycles – 8 cycles). Second the device is used to investigate the effect of composition and fabrication on microbubble response to similar ultrasound conditions. The results demonstrate a very large variability in microbubble response independent of initial size, indicating a significant lack of uniformity of coating properties. This is further supported by quantitative fluorescence imaging and quasi-static pressure chamber measurements.
The implications of the findings for CEUS imaging and the development of microbubble contrast agents are discussed, as well as the limitations and suggested improvements of the characterisation technique.
Pinchbeck regulars? The role and organisation of the Territorial Army, 1919-1940.
Keywords: Territorial Army
Reserve Forces
Defence Policy
1919-1940
Interwar

This thesis examines how Britain’s government and military establishment conceptualised the role of the voluntary Territorial Army (TA) between the World Wars, and explores the relationship with British defence policy during the period. It also evaluates whether or not the TA was capable of carrying out its ascribed role, through a balanced assessment of its organisation, training and military efficiency. It posits that the TA was integral to British defence planning and played a key part in the Army’s mobilisation plans, although the priority given to its role shifted throughout the period in accordance with the direction of Britain’s strategic focus. Additionally, this thesis will emphasise that the Territorial Army had not one purpose but several. Alongside its central function as the framework for a conscript National Army it held key responsibilities for both home and imperial defence.
This thesis examines the TA’s role and organisation in a thematic and broadly chronological manner. Part I deals with the TA’s expeditionary role and its function as the framework for all future military expansion, as well as its role as a voluntary imperial reserve for any medium scale wars conducted without resorting to conscription. Part II focuses on the Territorial Army’s home defence responsibilities, in particular its domestic role in aiding the civil power and its contribution to Britain’s increasingly important air defence capabilities.
Genetic and molecular technologies to optimise novel vaccines for Hepatitis C virus infection
Keywords: Immunology
T-cells
Vaccines
Hepatitis C
Adenovirus
Antigen presentation
modified vaccinia Ankara

Analysis of the immune response during spontaneous clearance and protection upon reinfection with hepatitis C (HCV) has highlighted the importance of T-cells in the control of HCV infection. An effective T-cell vaccine for HCV would have a significant effective on the global burden of disease associated with HCV. No clear immune correlates of protection exists for HCV and we lack immunological competent animal models in which to assess candidate HCV vaccines. I have performed in-depth characterisation of the T-cell response to candidate virally vectored HCV vaccines with regard to the T-cell parameters most likely to impact on their efficacy in a prophylactic and therapeutic setting.
I describe here a heterologous prime/boost vaccine regimen of a simian adenoviral vector (ChAd3), boosted with a modified vaccinia Ankara (MVA) encoding the non-structural (NS) proteins of HCV. This regimen elicits an unprecedented magnitude of HCV-specific CD8+ and CD4+ T-cells; which are broadly targeted, durable, and highly functional. ChAd3-NS/MVA-NS vaccination induces a population of persistent effector memory CD8+ T-cells (Tem) similar in phenotype to those induced by infection with CMV. I show that in these diverse settings the functional and phenotypic characteristics of the CD8+ T-cells are highly conserved and are controlled at the level of gene expression. Vaccination of HCV+ patients induced T-cell response that were significantly lower in magnitude, and viral sequencing at key epitopes demonstrates that the T-cells induced by vaccination show weak cross-recognition of the patients circulating virus.
While working with an industrial collaborator, I have developed our understanding of the mechanism of action of the enhancer element, MHC class II invariant chain. I show that tethering antigen to Ii within virally vectored vaccines targets it for rapid degradation by the proteasome, enhancing its presentation on MHC class I molecules and the concomitant CD8+ T-cell response to vaccination.
The work described here is relevant to T-cell vaccine development, in particular for Ad and MVA constructs, and to our understanding of antigen processing and heterogeneity within the CD8+ T-cell compartment.
Epigenetic regulation of chronological and replicative longevity in Saccharomyces cerevisiae
Keywords: non-coding RNA
Replicative longevity
Saccharomyces cerevisiae
rDNA
Chronological longevity

Ageing and senescence remain among the most intriguing questions in biology. Saccharomyces cerevisiae has become well established as a fertile model system for the investigation of ageing. Remarkable conservation has been found to exist between interventions extending lifespan in higher animals and yeast – genetic, chemical, and nutritional – suggesting a network of common regulatory pathways controlling large-scale shifts in gene expression involved in senescence. While it has been proposed that epigenetic regulation controls these shifts, evidence remains incomplete. To address this question, novel longevity mutants were isolated in S. cerevisiae using a purpose-designed high-precision screen based on ageing culture outgrowth. A novel long-lived mutant in uncharacterised gene YDR026C was discovered and found to participate in a pathway distinct from TOR signalling, but share epistasis with the histone deacetylase SIR2Δ, a well established regulator of replicative longevity and rDNA maintenance. Through equilibrium density centrifugal separation of culture subpopulations, SIR2Δ and Ydr026cΔ cultures were found to demonstrate reduced and improved maintenance of post-diauxic quiescence respectively, previously shown to underlie chronological survival in strains including snf1Δ. Development of a quantified TUNEL-based assay for genome fragmentation indicated early apoptotic-like behaviour in the SIR2Δ strain. Microdissection experiments and sectored-colony assays of strains containing an rDNA-embedded ADE2 reporter determined that Ydr026cΔ cells also exhibit extended replicative lifespan, and reduced recombination at the rDNA spacer region hotspot, abrogated in SIR2Δ strains. SIR2Δ is well established to repress RNA polymerase II-derived transcripts in the rDNA spacer region, including IGS1-R. Northern analysis determined Ydr026c also silences transcription in the spacer, possibly through preventing termination of the main rRNA transcript, interfering with IGS1-R expression. By transformation with a vector overexpressing IGS1-R, partial reconstitution of the SIR2Δ phenotype was observed, including rDNA hyperrecombination, shortened replicative longevity, and higher-order chromatin structure restoration. These data suggests a model whereby non-coding rDNA spacer transcripts epigenetically determine rDNA maintenance through recombination, leading to physiological phenotypes of replicative and chronological ageing.
Investigating the in vivo functions of non-coding RNAs in Drosophila melanogaster
Keywords: long non-coding RNA
Drosophila

The number of annotated non-protein coding genes has increased dramatically in recent years, but the functions of very few are well understood. In this thesis, I study the functions of two classes of non-coding RNA in Drosophila melanogaster. Firstly, through characterisation of six putative long non-coding RNA loci containing transposon insertions, I identified a long non-coding RNA, lnc703, suitable for in depth characterisation. Using a GAL4/UAS fluorescent reporter I found lnc703 to be expressed in the larval fat body and confirmed this using qRT-PCR. Transcriptome profiling identified ribosomal genes as upregulated in two independent lnc703 mutant strains. Additionally, I have identified decreased lifespan in some lnc703gal4 strains and it will be interesting to determine whether there is a relationship between increased ribosomal protein gene expression and reduced lifespan. I also used transcriptome profiling of the musculature and CNS of miR-8 null larvae to determine tissue specific targets of miR-8. Many indirect effects of miR-8 were detected but using MRE prediction algorithms a number of potentially direct targets of miR-8 were identified. One of these, ilp5, which is upregulated in the CNS, was identified as a non-cell autonomous effect of loss of miR-8 in the fat body. Together this work highlights the importance of using multiple, complementary techniques to study the function of non-coding RNAs in vivo.
Rural change in north Wales during the period of the industrial revolution: Livelihoods, poverty and welfare in Nantconwy, 1750-1860.
Keywords: livelihoods
Caernarfonshire
common land
charity
women farmers
Wales
farming
poor relief
poverty
proto-industry
demography
by-employment

This thesis explores how a typical area of rural Wales participated in and was shaped by social and economic change during the period of the Industrial Revolution. It investigates how increasing numbers of people made a livelihood in the Caernarvonshire hundred of Nantconwy over the period 1750-1860, including the role of women in the local economy. A wide range of record types are used to explore inter-relationships between population growth, agriculture, proto-industry, the organisation of farming households, and the livelihoods of the poor. The thesis covers a key gap in the historical literature, as most studies of agrarian change at this period concentrate on England, and there has been little investigation of the experience in rural Wales.
Unlike many parts of England where economic modernization was accompanied by growing inequality involving a transition from a household economy to a capitalist tripartite society of landowners, tenant farmers and landless wage labourers, Nantconwy experienced a growth of subsistence smallholding, as more people faced with a shortage of waged employment sought to make a livelihood from the land. Family by-employment and proto-industry also played a crucial role in the local economy. Bringing the commons and wastes into private ownership had relatively little impact on the poor, but smallholders’ livelihoods were adversely affected after 1815 by the mechanization of spinning and declining earnings from stocking knitting. Living standards began to improve after 1830 with the expansion of male employment in slate quarrying, while the role of women on family farms was enhanced. Parishes evolved a low-cost system of poor relief which supported mainly older residents who were no longer able to quite make ends meet from the traditional cottager economy, while encouraging the young to leave the land or migrate to local towns or quarrying areas with better employment prospects.
Combining single-molecule fluorescence and single-channel recording in droplet interface bilayers
Keywords: ion channel
droplet interface bilayer
fluorescence spectroscopy
single-molecule

Single-channel recordings (SCR) and single-molecule Fluorescence (SMF) are invaluable tools for studying membrane proteins. Combining these two techniques would allow for structural dynamics to be correlated with function at the single-molecule level. However, the different requirements of SCR and SMF measurements present a long-standing challenge. Droplet interface bilayers (DIBs) are a model membrane system in which parallelisation of such measurements is possible using optical single-channel recording to resolve the conductance of multiple proteins simultaneously. In this project, two approaches were evaluated for obtaining simultaneous measurements in DIBs: the first sought to report on structural changes associated with a gating bacterial mechanosensitive channel, MscS; the second sought to resolve kinetics of the spontaneous β-barrel folding mechanism. For both approaches, functional, labelled protiens were produced and characterised using ensemble measurements to confirm that the state-transition of interest was accompanied by a change in fluorescent signal. Characterisation of MscS in DIBs revealed that control of lateral tension (a requirement to stimulate mechanosensitive channel gating) posed a major experimental challenge, rendering further pursuit of this candidate impossible. However in the case of β-barrel folding, the single-molecule fluorescence alone revealed a rare but fast transition from a membrane-associated unfolded to a folded state. While further work is needed to fully exploit simultaneous measurements, significant progress towards this goal is presented in this work, in particular the development of reagents, experimental procedures and analytical tools.
Imaging nociceptive brain activity in the newborn infant
Keywords: Pain
Neonates
Infants
EEG
fMRI
Brain imaging

In this thesis electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) are used to investigate the temporal and spatial patterns of noxious-evoked brain activity in newborn infants. EEG was used to investigate responses to graded intensities of experimental noxious stimulation, and evoked brain activity was compared with behavioural and spinal cord activity constituting common surrogate measures of pain in infants. Nociceptive-specific brain activity was elicited in response to all forces of experimental noxious stimulation (applied forces: 32 - 128 mN). In addition, the magnitude of the noxious-evoked response was positively correlated with the magnitude of reflex leg withdrawal, and this relationship was observed in the absence of changes in facial expression.
As fMRI had not previously been used to investigate nociceptive processing in infants at 3 Tesla, initial experiments were conducted to optimise the acquisition parameters. The results from optimisation showed that an echo time of approximately 50 ms should be used in future fMRI studies in infants. Experiments conducted alongside this optimisation used fMRI to investigate the cortical and subcortical structures activated by experimental noxious stimulation (applied forces: 32 - 128 mN) in newborn infants (0 - 11 days old). This was compared with noxious-evoked brain activity in adults (applied forces: 32 - 512 mN). Experimental noxious stimulation evoked a widespread pattern of brain activity in newborn infants that overlapped with the network of brain regions activated by nociceptive processing in adults.
Symmetries in physics, metaphysics, and logic
Keywords: Symmetries
Equivalence
Translation

This thesis examines the idea that when a physical theory contains symmetries, the theory should be interpreted in such a way that symmetry-related models represent the same physical state of affairs. It argues that we can best do so by drawing on analogies to ideas in philosophy of logic and language: specifically, by thinking of symmetries as a means of translating a theory into itself. It consists of six chapters, together with an introduction and conclusion.
In Chapter 1, I set up the main ideas needed to more precisely frame the question at hand: namely, the notions of symmetry, interpretation, and possibility. I make some remarks about how I take these to be connected.
In Chapter 2, I argue that isomorphic models should be interpreted as equivalent. After giving some motivations for doing so, I consider the main obstruction: how to provide an account of de re modality. I review how counterpart theory may be used to overcome this obstruction, and clarify how counterpart theory relates to other positions in the debate over modality de re.
In Chapter 3, I show that the metaphysical debate over quidditism can be made precise by drawing on notions of translation from model theory, and argue in favour of an anti-quidditist attitude towards interpreting theories. I then consider the special case of translating a theory into itself: how such a theory should be interpreted, and what reformulations of the theory such an interpretation suggests.
In Chapter 4, I turn my attention to physics. I define the notion of an internal symmetry for a theory, and argue that they may be regarded as translations from a theory into itself (in the sense of Chapter 3); and, hence, that symmetry-related models should be interpreted as equivalent. Drawing on the analogy further, I look at how the theory may be reformulated to take this interpretation into account.
In Chapter 5, I look at external symmetries. I argue, drawing on ideas from Chapters 2 and 3, that models related by external symmetries should also be interpreted as equivalent. I discuss how implementing this interpretational lesson bears on finding the spacetime structure appropriate to a theory.
In Chapter 6, I consider a specific external symmetry: the accelerative symmetry of Newtonian gravitation. I show that one can reformulate the theory to take this into account, setting gravitation on a spacetime structure that has absolute rotation but no absolute acceleration.
Graphs of algebraic objects
Keywords: Enumeration
Racks
Commuting Graph

A rack on [𝑛] can be thought of as a set of permutations (𝑓𝑥)𝑥 ∈ [𝑛] such that 𝑓(𝑥)𝑓y = 𝑓y-1𝑓x𝑓y for all 𝑥 and y; additionally, a rack such that (𝑥)𝑓𝑥 = 𝑥 for all 𝑥 is a quandle, and a quandle such that 𝑓x2 = ɩ for all 𝑥 is a kei. These objects can be represented by loopless, edge-coloured directed multigraphs on [𝑛]; we put an edge of colour y between 𝑥 and z if and only if (𝑥)𝑓y = z. This thesis studies racks and kei via these graphical representations.
In 2013, Blackburn showed that for any ε &GT; 0 and 𝑛 sufficiently large, the number of isomorphism classes of kei on [𝑛] is at least 2(1/4 - ε)𝑛2, while the number of isomorphism classes of racks on [𝑛] is at most 2(c+ε)𝑛2 for a constant c. The main result of this thesis is that the lower bound is asymptotically correct; for any ε &GT; 0 the number of isomorphism classes of racks on [𝑛] is at most 2(1/4 + ε)𝑛2, for 𝑛 sufficiently large. We also show that in almost all of these racks almost all components of the corresponding graph have size 2. Additionally, we show several more detailed results regarding kei, including a full classification of all kei in which each component has size equal to an odd prime.
This thesis also contains several partial results on another topic. The commuting graph of a finite group is defined to be the graph on the non-trivial cosets of G/Z(G) where x̄ȳ is an edge if and only if 𝑥 and y commute. In 2012, Hegarty and Zhelezov proposed a family of random groups and published some results on the corresponding family of random graphs; this thesis contains some generalisations and extensions of these results.