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Persistent tuberculosis (TB) in cattle populations in England has been associated with an exchange of infection with badgers ( Meles meles ). A badger control policy (BCP) commenced in 2013. Its aim was to decrease TB incidence in cattle by reducing the badger population available to provide a wildlife reservoir for bovine TB. Monitoring data from 52 BCP intervention areas 200–1600 km 2 in size, starting over several years, were used to estimate the change in TB incidence rate in cattle herds, which was associated with time since the start of the BCP in each area. A difference in differences analysis addressed the non-random selection and starting sequence of the areas. The herd incidence rate of TB reduced by 56% (95% Confidence Interval 41–69%) up to the fourth year of BCP interventions, with the largest drops in the second and third years. There was insufficient evidence to judge whether the incidence rate reduced further beyond 4 years. These estimates are the most precise for the timing of declines in cattle TB associated with interventions primarily targeting badgers. They are within the range of previous estimates from England and Ireland. This analysis indicates the importance of reducing transmission from badgers to reduce the incidence of TB in cattle, noting that vaccination of badgers, fertility control and on farm biosecurity may also achieve this effect.

This thesis contains the analysis of 10 years of ESA Cluster observations using machine learning techniques. In the first study, we investigate solar wind electron populations at 1 au. In the second study, we apply a novel machine learning technique to magnetotail data in order to better characterise particle distribution function. In the third study, we make the first in-situ observations of the tearing instability leading to magnetic reconnection in the magnetotail. Solar wind electron velocity distributions at 1 au consist of three main populations: the thermal `core' population and two suprathermal populations called halo and strahl. We apply unsupervised algorithms to phase space density distributions, to perform a statistical study of how the core/halo and core/strahl breakpoint energies vary. The results of our statistical study show a significant decrease in both breakpoint energies against solar wind speed. By fitting Maxwellians to the core, based on our study, we can discuss the relative importance of the core temperature on halo and strahl electrons. Collisionless space plasma environments are characterised by distinct particle populations that typically do not mix. Although moments of their velocity distributions help in distinguishing different plasma regimes, the distribution functions themselves provide more comprehensive information about the plasma state. By applying dimensionality reduction and clustering methods to electron distributions in pitch angle and energy space, we distinguish between the different plasma regions. We identify several new distinct groups of distributions, that are dependent upon significantly more complex plasma and field dynamics. Magnetic reconnection is a fundamental mechanism responsible for explosive energy release in space and laboratory plasmas. The onset of reconnection is via the tearing instability. Due to its elusive nature, there is an absence of in-situ observations of the tearing instability. We present the first direct observations of the tearing instability and the subsequent evolution of plasma electrons and reconnection, using neural network outlier detection methods. Our analysis of the tearing instability and subsequent reconnection provides new insights into the fundamental understanding of the mechanism responsible for reconnection.

Collisionless space plasma environments are typically characterised by distinct particle populations. Although moments of their velocity distribution functions help in distinguishing different plasma regimes, the distribution functions themselves provide more comprehensive information about the plasma state, especially at times when the distribution function includes non-thermal effects. Unlike moments, however, distribution functions are not easily characterised by a small number of parameters, making their classification more difficult to achieve. In order to perform this classification, we propose to distinguish between the different plasma regions by applying dimensionality reduction and clustering methods to electron distributions in pitch angle and energy space. We utilise four separate algorithms to achieve our plasma classifications: autoencoders, principal component analysis, mean shift, and agglomerative clustering. We test our classification algorithms by applying our scheme to data from the Cluster-PEACE instrument measured in the Earth's magnetotail. Traditionally, it is thought that the Earth's magnetotail is split into three different regions (the plasma sheet, the plasma sheet boundary layer, and the lobes), that are primarily defined by their plasma characteristics. Starting with the ECLAT database with associated classifications based on the plasma parameters, we identify 8 distinct groups of distributions, that are dependent upon significantly more complex plasma and field dynamics. By comparing the average distributions as well as the plasma and magnetic field parameters for each region, we relate several of the groups to different plasma sheet populations, and the rest we attribute to the plasma sheet boundary layer and the lobes. We find clear distinctions between each of our classified regions and the ECLAT results.

We develop and apply a bespoke fitting routine to a large volume of solar wind electron distribution data measured by Parker Solar Probe (PSP) over its first five orbits, covering radial distances from 0.13 to 0.5 au. We characterise the radial evolution of the electron core, halo and strahl populations in the slow solar wind during these orbits. The fractional densities of these three electron populations provide evidence for the growth of the combined suprathermal halo and strahl populations from 0.13 to 0.17 au. Moreover, the growth in the halo population is not matched by a decrease of the strahl population at these distances, as has been reported for previous observations at distances greater than 0.3 au. We also find that the halo is negligible at small heliocentric distances. The fractional strahl density remains relatively constant ~1 % below 0.2 au, suggesting that the rise in the relative halo density is not solely due to the transfer of strahl electrons into the halo.

Persistent tuberculosis (TB) in cattle populations in England has been associated with an exchange of infection with badgers (Meles meles). A badger control policy (BCP) commenced in 2013. Its aim was to decrease TB in cattle by reducing the badger population available to provide a wildlife reservoir for bovine TB. Monitoring data from 52 BCP intervention areas 200-1600 km2 in size, starting over several years, were used to estimate the change in TB incidence rate in cattle herds, which was associated with time since the start of the BCP in each area. A Difference in Differences analysis addressed the non-random selection and starting sequence of the areas. Herd incidence rate of TB reduced by 56% (95% Confidence Interval 43-67%) up to the fourth year of BCP interventions, with the largest reductions in the second and third years. There was insufficient evidence to judge whether incidence rate reduced further beyond four years. These estimates are the most precise for the timing of decline in cattle TB associated with interventions primarily targeting badgers. They are within the range of previous estimates from England and Ireland. This analysis indicates the importance of reducing transmission from badgers to reduce the incidence of TB in cattle, noting that vaccination of badgers, fertility control and on farm biosecurity may also achieve this effect.

We analyze the micro-kinetic stability of the electron strahl in the solar wind depending on heliocentric distance. The oblique fast-magnetosonic/whistler (FM/W) instability has emerged in the literature as a key candidate mechanism for the effective scattering of the electron strahl into the electron halo population. Using data from Parker Solar Probe (PSP) and Helios, we compare the measured strahl properties with the analytical thresholds for the oblique FM/W instability in the low- and high-\\(_ c\\) regimes, where \\(_ c\\) is the ratio of the core parallel thermal pressure to the magnetic pressure. Our PSP and Helios data show that the electron strahl is on average stable against the oblique FM/W instability in the inner heliosphere. Our analysis suggests that the instability, if at all, can only be excited sporadically and on short timescales. We discuss the caveats of our analysis and potential alternative explanations for the observed scattering of the electron strahl in the solar wind. Furthermore, we recommend the numerical evaluation of the stability of individual distributions in the future to account for any uncertainties in the validity of the analytical expressions for the instability thresholds.

Solar wind electron velocity distributions at 1 au consist of a thermal \"core\" population and two suprathermal populations: \"halo\" and \"strahl\". The core and halo are quasi-isotropic, whereas the strahl typically travels radially outwards along the parallel and/or anti-parallel direction with respect to the interplanetary magnetic field. With Cluster-PEACE data, we analyse energy and pitch angle distributions and use machine learning techniques to provide robust classifications of these solar wind populations. Initially, we use unsupervised algorithms to classify halo and strahl differential energy flux distributions to allow us to calculate relative number densities, which are of the same order as previous results. Subsequently, we apply unsupervised algorithms to phase space density distributions over ten years to study the variation of halo and strahl breakpoint energies with solar wind parameters. In our statistical study, we find both halo and strahl suprathermal breakpoint energies display a significant increase with core temperature, with the halo exhibiting a more positive correlation than the strahl. We conclude low energy strahl electrons are scattering into the core at perpendicular pitch angles. This increases the number of Coulomb collisions and extends the perpendicular core population to higher energies, resulting in a larger difference between halo and strahl breakpoint energies at higher core temperatures. Statistically, the locations of both suprathermal breakpoint energies decrease with increasing solar wind speed. In the case of halo breakpoint energy, we observe two distinct profiles above and below 500 km/s. We relate this to the difference in origin of fast and slow solar wind.

The internationally recognised method for diagnosis of avian influenza (AI) is virus isolation (VI) in specific pathogen-free embryonated fowls’ eggs (EFEs). In Great Britain (GB), AI virus isolation currently involves two passages in EFEs; the first typically of two days duration followed by a second lasting up to four days meaning that premises may remain under restriction for up to six days. Shorter time lengths for AIV isolation were investigated to reduce the time that businesses remain under official restrictions to safely negate AI infection, whilst maintaining test sensitivity. Both experimental inoculations of EFEs and analyses of VI attempts from high pathogenicity (HP) AI disease incursions in GB since 2016 demonstrated that HP viruses were isolated during first passage while for low pathogenicity AI outbreaks, the second passage could be reduced to two days. Power analysis showed that the benefit of reducing the number of days outweighed the risk of missing a positive isolate. This approach will substantially reduce costs to government and industry by releasing restrictions at least two days earlier where samples are negative for viral nucleic acid. Critically, it will reduce welfare implications of housing birds under restriction and improve international standards without loss of test performance.

Magnetic reconnection is a sporadic process responsible for energy release in space and laboratory plasmas. It is believed that the tearing mode instability may be responsible for the onset of reconnection in the magnetotail. However, due to its elusive nature, there is an absence of in-situ observations of the tearing instability prior to magnetic reconnection in our nearest natural plasma laboratory. Using neural network outlier detection methods in conjunction with Cluster spacecraft data, we find unique electron pitch angle distributions that are consistent with simulation predictions of the tearing instability and the subsequent evolution of plasma electrons and reconnection. We confirm that the events identified via our neural network outlier method are well above the tearing stability threshold based on the criterion detailed in this paper. We find signatures of magnetic reconnection minutes after the majority of tearing observations. Our analysis of the tearing instability provides new insights into the fundamental understanding of the mechanism responsible for reconnection, a process that is ubiquitous in different astrophysical plasma regimes across the universe and in laboratory experiments on Earth.