VictorJuiz/thesis huggingface dataset:
Automated tracking and collective behaviour in locusts and humans
Keywords: automated tracking
animal behaviour
humans
locusts

The understanding of the motion of animal groups, such as birds, fish and insects, has been greatly advanced by applying principles of self-organisation – the emergence of global patterns from simple, local, interactions between individuals. The desert locust, Schistocerca gregaria, provides a useful model system for the experimental study of collective behaviour. During plague years, the desert locust can form aggregations extending over hundreds of km. Before developing wings, juvenile locusts form marching ‘bands’ which can maintain group cohesion as they migrate over large distances. In this thesis I investigate locust aggregation, group motion and individual interactions. I also apply the same principles to a study of human behaviour.
In Chapter 2, I describe the automated tracking methods that I developed and used to collect the data for the rest of the thesis. In the experiments described in Chapter 3, the relative strengths of the attraction to conspecifics and environmental heterogeneities were explored by presenting groups of locusts with two aggregation sites. I found that locusts had a preference to enter the site with the higher population. The locusts formed dynamic aggregations on the sites; no site was consistently more populated than the other, but individuals were significantly more attracted to the site with the higher current population. In Chapter 4, I consider the effect of marching experience on locust behaviour. Groups of locusts that had experience of directed marching, followed by a sudden reduction in density, behaved indistinguishably from those that had only experienced the lower density throughout, indicating a lack of hysteresis effects in collective responses to change in local population density. In Chapter 5, I investigate a locust’s response to its nearest neighbour. I quantified a locust’s propensity to start or stop moving according to the relative position, orientation and movement of its nearest neighbour. In Chapter 6 the techniques developed studying the locusts were applied to human groups. The response of people to different sized groups was quantified, replicating an earlier study in New York. The response was weaker in Oxford but had the same characteristics of the previous study, showing an initially linear response which saturated. The spatial distribution of gaze copying was anisotropic, tending to occur behind the group.
An ageing population in a family and welfare state: the dynamics of family support and public pension systems, and their impact on late-life happiness in contemporary South Korea
Keywords: national pension scheme
South Korea
intergenerational solidarity
Korean longitudinal study of ageing
happiness
basic old-age pension
middle-aged and older people

The purpose of this thesis is to analyze the dynamics of family support and public pension systems, and their impact on late-life happiness in contemporary South Korea. For this, three specific research questions, namely (1) the dynamics of intergenerational solidarity, public pension systems, and happiness; (2) the association between intergenerational solidarity and happiness; and (3) the association between public pension systems and happiness, are analysed by exploiting the Korean Longitudinal Study of Ageing.
The analyses show that (1) the structural solidarity of older people is relatively stronger than of middle-aged people; (2) contacting is the key player in associational solidarity in later life; (3) middle-aged people supply more financial aid to their adult children than they receive from them, but the reverse applies to older people. Both middle-aged and older people actively exchange food, household items, and health-care supplies; (4) more older men receive the National Pension Scheme benefit than older women but the reverse is true for the Basic Old-Age Pension benefit; (5) the level of happiness in later life is very high but decreases as people age; (6) the number of adult children, frequency of contact, and amount of financial support are positively associated with the happiness of older people; and (7) the National Pension Scheme is positively associated with the happiness of older men while the Basic Old-Age Pension is negatively associated with the happiness of older people.
The results suggest some policy implications for late-life happiness in contemporary South Korea. At the individual level, increased frequency of contact, availability of the children, and the amount of financial support can enhance late-life happiness. At the governmental level, the research suggests that the gendered structure of the National Pension Scheme and means-tested structure of the Basic Old-Age Pension should be reformed.
Ports of empire: immigration, communication, and cholera in Newfoundland, Nova Scotia and New Brunswick, 1830-1870
Keywords: cholera; migration; history of disease; colonialism; port towns; Newfoundland; Nova Scotia; New Brunswick; Atlantic Canada

This study explores the relationship between emigration and cholera in British North American port towns, between 1832 and 1866. It focuses specifically on three established and growing port towns located directly off of the Atlantic Ocean – St. John's, Newfoundland, Halifax, Nova Scotia and Saint John, New Brunswick. The pressures of mass immigration from the British Isles, the transmission of highly-feared diseases from emigrant and cargo ships to port towns in British North America, and the dependence, vulnerability and constraints felt by colonial governments and their citizens are three important themes that emerge and are continually challenged throughout this dissertation. This thesis presents the way in which colonial port towns managed the recurrent and unpredictable threats to their health, wellbeing and prosperity during this period, and highlights the increasing strain and growing dislocation felt by British North Americans under colonial rule.
The history of cholera in Canada has focused overwhelmingly on Upper and Lower Canada, with little exploration or comparative analysis of the outbreaks in the Atlantic region. The following research examines the interconnected, complex and at times distant relationship between Britain and its North American colonies, under the influence of emigration and transmission of disease from coloniser to colonised. High points of calamity and upheaval clarified the extent to which the colonies were responsible for themselves, forcing many towns to re-evaluate their ability to control emergencies on their soil, with or without the help of the mother country. This study contributes not only to the historical understanding how cholera was managed in British North American ports, but it also provides a unique perspective on understanding the greater struggles of nineteenth-century colonial life.
Understanding the Book of Job: 11Q10, the Peshitta and the Rabbinic Targum. Illustrations from a synoptic analysis of Job 37-39
Keywords: translation techniques
intertestamental
development of targum
early targum
Targum to Job
Job targum
rabbinic targum
scriptural interpretation
Qumran targumim
Peshitta
origins of targum
biblical interpretation
scriptural translation
Peshitta Job.
Dead Sea Scrolls
targum
Qumran
Targum of Job
Qumran targum
11Q10
Book of Job
Onqelos
targumim
Job

This synoptic analysis of verses from Job chapters 37-39 in 11Q10, the Peshitta version (PJob) and the rabbinic targum (RJob) aims to identify the translators’ methods for handling the Hebrew text (HT) and to assess the apparent skills and knowledge brought by them to their task. Additionally, the study engages with recent discussion which challenges the nature of 11Q10 as targum. To this end, PJob and RJob provide accepted models of ‘translation’ and ‘targum’ alongside which to assess 11Q10. The following translation methods are identified, described, compared and contrasted in the three versions: selection,extension, alternative translation, expansion, substitution, adjustment of the consonantal HT, adjustment of the Hebrew word order or division, omission, and conjecture. PJob is confirmed as an attempt to transpose the difficult Hebrew of Job into Syriac. RJob is confirmed as a conservative translation with clear underpinnings in allusion to scripture and to rabbinic traditions attested elsewhere. Significant observations are made regarding an interpretative quality in 11Q10, and new light is cast on its richness and subtlety as an allusive translation. It is proposed that the translation displays deep knowledge of scripture and skill in applying this knowledge. It is further proposed that careful comparison with methods which have been identified in Onqelos is warranted. 11Q10 is identified as an important early witness to scripturally-based motifs which are also found in other intertestamental and rabbinic sources. It is argued that 11Q10’s nature suggests that its purpose was not simply to translate but to understand and subtly explicate the HT, and that it was intended for use alongside it, not as a replacement. The study refutes the categorization of 11Q10 as ‘translation’ rather than ‘targum’, and agrees with its orginal editors that its value lies in its unique witness to the early nature of targum.
Genetic studies in ulcerative colitis
Keywords: inflammatory bowel disease
ulcerative colitis
NOX1
genetics

Inflammatory bowel diseases (IBD), encompassing ulcerative colitis (UC) and Crohn’s disease (CD), are lifelong inflammatory disorders of complex and multifactorial aetiology. Genetic studies have played an important role in the identification of immunological pathways involved in the pathogenesis of IBD. Genome wide association studies have revealed more than 160 genetic polymorphisms associated with IBD, although the expected heritability in UC is smaller than for CD, and the relationship between genotype and phenotype in UC is unclear. The source of the missing heritability in UC, may be at least accounted for by rare variants which carry a larger effect size. In this thesis, the influence of polygenic burden on disease phenotype in UC is investigated. In addition, functional characterisation of a rare genetic variant is performed, in order to investigate for a pathogenic association with a very early onset colitis phenotype.
Polygenic risk burden, as measured using genetic risk scores (GRS), is assessed amongst a well-phenotyped cohort of patients with UC. GRS are shown to be greater amongst patients diagnosed with UC before the age of 10 years, as compared to those diagnosed in adulthood. GRS are also shown to be greater amongst patients with a history of acute severe UC (ASUC), as compared to those with a mild UC disease course. Although lacking in power, variance analysis suggests enrichment of genetic polymorphisms within the IL-10 cytokine signalling pathway amongst patients with a history of ASUC.
Exploration of a possible causal relationship between a novel and rare mutation in the NOX1 gene, encoding NADPH oxidase 1, and a clinical phenotype of very early onset colitis in a single patient is undertaken in this thesis. It is shown that NOX1 mRNA is highly expressed in colonic epithelial cells and that the NOX1 p.N122H variant impairs function of the gene product. The findings implicate that the NOX1 p.N122H variant contributes to development of severe and early onset colitis by attenuating colonic epithelial superoxide production.
Nitric oxide: a chemical effector of pathogenesis in magnaporthe oryzae
Keywords: Nitric Oxide
Magnaporthe oryzae

Research detailed in this thesis investigated the generation of Nitric Oxide (NO) and its role in the pathogenesis of the rice blast fungus Magnaporthe oryzae. Two putative nitric oxide synthase genes and single copy nitrate and nitrite reductase genes were cloned as potential sources of NO in M. oryzae. Single and double gene disrupted mutants were generated and their phenotypes assessed.
Detection of NO is problematic. Herein, a fluorescent plate reader assay was developed, exploiting the NO sensitive dye DAR-4M AM and the NO scavenger PTIO, to compare wildtype NO generation with the mutant strains. All strains were assessed for infection-related development on an artificial surface inductive to appressorium formation and maturation in the wildtype strain. Appressorium formation in the presence of PTIO and the NO donor DETANONOate was recorded for all strains on this surface. The pathogenicity of the wildtype and mutant strains were assessed, in terms of their ability to infect rice and barley plants. Finally, the capacity of each strain to metabolise nitrogen was evaluated to confirm the disruption of the nitrate and nitrite reductase genes.
Collectively, the data demonstrate that the plate reader assay provides robust evidence for the generation of NO in M. oryzae. However, none of the various mutant strains showed a reduction in NO emission during germling morphogenesis. However, they exhibited significantly different infection-related development on an inductive artificial surface as compared with the wildtype strain. Moreover, exogenous application of PTIO to the wildtype strain provided evidence for NO and its involvement in germination and appressorium development. No significant differences in the infection of rice and barley leaves were observed between the wildtype and mutant strains, indicating their disrupted genes are dispensable for pathogenesis. The nitrate and nitrite reductase genes were found to be essential for nitrate assimilation.
In summary, this work provides the most robust evidence for the generation of NO in fungi to-date, but the molecular mechanism underpinning the generation of NO in M. oryzae remains elusive.
Modelling optimal strategies for novel genetics-based pest management
Keywords: mathematical modelling

Genetic transformation techniques for pest insects have enabled the development of novel methods to mitigate the enormous harm done by insects to human health (through transmission of diseases) and to agriculture (through damage to crops or livestock). I use mathematical modelling to analyse strategies using autocidal genetic constructs (dominant lethal genes that are repressible during mass-rearing); in parallel several research groups are developing the strains and the laboratory and field experimental work. Engineered insects would be released in large numbers and compete for mates, and their progeny would inherit one copy of a dominant lethal gene and die. The lethal mechanism can be made stage- or sex-specific. The aim is to reduce the number of pest insects in a population, suppressing numbers to a less harmful level or local elimination. I examine the evolutionary, ecological, and economic cost and benefit aspects of these novel interventions. I consider application of this genetic technology against agricultural pest insects, combined with genetically modified crop plants engineered to produce insecticidal toxins, to which field-evolved resistance is emerging. Using a theoretical framework, I analyse the gene frequency evolution of resistant alleles and show that strategies using genetic constructs that are selectively lethal only to females could help to manage both pests and resistance. I investigate potential resistance to the lethal mechanism of the genetic construct itself. I use population genetics and population dynamics models to explore the impact of heritable biochemically-based resistance on the effectiveness of genetic strategies for reducing populations of important pests in agriculture or public health. Released insects are homozygous for susceptibility to the lethal construct; this has an inherent element of resistance dilution. Finally, I analyse genetic vector control methods to reduce the transmission of human disease. I combine vector population dynamics and epidemiological models with techniques for assessing cost-effectiveness of a genetic strategy for controlling a vector mosquito, and show that disease elimination is feasible on a practical timescale and economically beneficial.
Substrate recognition by the proteasome 
Keywords: SPR
ITC
fluorescence anisotropy
proteasome
NMR
x-ray crystallography
ubiquitin

The ubiquitin proteasome system targets proteins to the proteasome where they are degraded. Substrate recognition and processing prior to degradation take place at the 19S regulatory particle of the proteasome. A polyubiquitin chain, linked through isopeptide bonds formed between the C-terminal G76 and K48, is the signal responsible for delivery to the proteasome. Because chains linked via any of the seven lysine residues of ubiquitin exist in vivo and encode signals unrelated to protein degradation it is crucial for cells to avoid crosstalk between these different pathways. Several ubiquitin receptors related to proteasomal degradation have been identified but the selectivity between the different ubiquitin chains has not been assessed quantitatively while avoiding artefacts attributed to GST-dimerisation. By employing isothermal titration calorimetry, analytical ultracentrifugation and nuclear magnetic resonance, discrimination between K48- and K63-linked diubiquitin was established for the S. pombe proteasomal receptor Rpn10 and the shuttle protein Rhp23. The same methods allowed us to propose a discriminatory model for Rpn10. The crystal structures of the 19S regulatory particle subunits Rpn101-193 and Rpn121-224 have been determined and possible protein-protein interaction sites were identified by surface conservation and electrostatics analysis. Rpn12 surface residues were identified that had a negative effect on Rpn10-binding. This interaction was studied by surface plasmon resonance, fluorescence anisotropy and nuclear magnetic resonance. These experiments revealed a binding site on Rpn10 that is exclusively occupied by either ubiquitin or Rpn12 and for the first time demonstrated the interaction of a ubiquitin interacting motif with a protein other than ubiquitin.
Structure–function studies of the oxidoreductase bilirubin oxidase from Myrothecium verrucaria using an electrochemical quartz crystal microbalance with dissipation
Keywords: adsorption
voltammetry
reduction
laccase
Electrochemical quartz-crystal microbalance
QCM
enzyme catalysis
surface chemistry
fuel cell
bilirubin oxidase
E-QCM
redox enzyme
oxygen reduction
gold electrodes
Quartz-crystal microbalance
electrochemistry

This thesis presents the development and redesign of a commercial electrochemical quartz crystal microbalance with dissipation (E–QCM–D). This was used to study factors affecting the efficiency of the four electron reduction catalysed by the fuel cell enzyme bilirubin oxidase from Myrothecium verrucaria immobilised on thiol modified gold surfaces.
Within this thesis, the E–QCM–D was used to show that application of a constant potential to bilirubin oxidase adsorbed to thiol-modified gold surfaces causes activity loss that can be attributed to a change in structural arrangement. Varying the load by potential cycling distorts the enzyme by inducing rapid mass loss and denaturation. Attaching the enzyme covalently reduces the mass loss caused by potential cycling but does not mitigate activity loss. Covalent attachment also changes the orientation of the surface bound enzyme as verified by the position of the catalytic wave (related to the overpotential for catalysis) and reactive labelling followed by mass spectrometry analysis.
The E–QCM–D was used to show how electrostatic interactions affect enzyme conformation where high pH causes a reduction in both mass loading at the electrode and a reduction in activity. At pH lower than the enzyme isoelectric point, there is a build up of multilayers in a clustered adsorption. When enzyme adsorbs to hydrophobic surfaces there is a rapid denaturation which completely inactivates the enzyme. Changing the surface chemistry from carboxyl groups to hydroxyl and acetamido groups shows that catalysis is shifted to more negative potentials as a result of an enzyme misorientation. Further to this, increasing the chain length of the thiol modifier indicates that an increased distance between surface and enzyme reduces activity, enzyme loading and results in a conformational rearrangement that permits electron transfer over longer distances.
Characterisation of engineered nanoparticles and their interaction with natural biological and non-biological material
Keywords: Zinc Oxide
ROS
Reactive Oxygen Species
EPS
Suspension
Extra-cellular Polymeric Species
Silver
Algae
Ecotoxicology Nanoparticle Characterisation Nanoparticle Fate Nanoparticle Toxicity Algae and Cyanobacteria
Fate
Cell Viability
Ecotoxicology
Cyanobacteria
Stability
Toxicity
Coatings
Materials

Form, mobility, toxicity and the eventual fate of engineered nanomaterials in environmental ecosystems are currently not well defined and are needed to improve risk assessment and legislation. The present study subjected uncoated zinc oxide (ZnO) nanoparticles (30nm and 200nm) and coated silver (Ag) nanoparticles (Paraffin: 3-8nm and citrate/PVP: 50nm) to different ionic strength media and different types of algal/bacterial extracellular-polymeric species (EPS) at long (6 months) and short (2 weeks) timescales. Changes in particle size distribution and stability were examined using a multi-method approach. Sample concentration and sample polydispersity are important factors when selecting techniques. Uncoated ZnO nanoparticles aggregated heavily in water at high concentrations (1000mg/L). However silver nanoparticles (1-10mg/L) remained stable at all ionic strengths and EPS in this study due to the steric component of their coatings. Nano-toxicological experiments involving cyanobacteria S.leopoliensis and green algae C.reinhardtii showed size-dependent toxicity from coated nanosilver particles. Smaller nanoparticles (3-8nm) showed greater dissolution over 72h and greater toxicity to both species than 50nm particles indicating silver ions are an important toxicity mechanism. Nanoparticle coatings were likely important in controlling dissolution levels. Cell viability and production of reactive oxygen species (ROS) were shown to be important mechanisms of toxicity to phycological species. Species specific effects were noted for both silver nanoparticles. EPS from S.leopoliensis were noted to remove ionic silver from suspension and different types of C.reinhardtii EPS were produced when particles underwent different levels of toxic stress indicating that EPS could both affect particle toxicity and be affected by it. This work has demonstrated that coated nanoparticles could remain stable under various ionic strengths and with exposure to algal organic matter for timescales up to 6 months. This could result in adverse effects to aquatic organisms were they to reach environmental systems and is of concern to nanomaterial risk assessors.