Data-driven numerical modelling of the solar coronal magnetic field

The aim of this thesis is the development of numerical models for determining the coronal magnetic field from observations of the magnetic field at the photosphere (coronal magnetic field extrapolation), with an emphasis on numerical methods, computation and code development. Presently, observational methods cannot determine the coronal magnetic field accurately and routinely, motivating numerical modelling. In this thesis we develop improvements to the widely used force-free model of the coronal magnetic field. In Chapter 1 we present motivation for the modelling and its limitations. In Chapter 2 we present free energy estimates for the solar active region AR 11029 derived from a force-free model applied to data from the Hinode Spectropolarimeter and the Synoptic Optical Long-term Investigations of the Sun Vector-Spectromagnetograph. The work illustrates many of the difficulties with modelling discussed in Chapter 1. In Chapter 3 we present a numerical code for solving a magneto-hydrostatic model of the corona which includes pressure forces in the corona. The code is applied to a simple test case to demonstrate its correctness. In Chapter 4 we present a numerical code for solving the nonlinear force-free model in spherical polar coordinates which overcomes the limitations of the Cartesian models. The code is an implementation of the Grad-Rubin method, and is based on a spectral representation of the magnetic field in terms of vector-spherical harmonics. The method is applied to a simple test case to demonstrate the self-consistency of the implementation. In Chapter 5 we derive the vector-spherical harmonic solution to Ampere's law which is presented in Chapter 4 without derivation. This solution forms an important part of the spherical code presented in Chapter 4

Apathy and Impulsivity in Frontotemporal Lobar Degeneration

Apathy and Impulsivity in Frontotemporal Lobar Degeneration Ian Coyle-Gilchrist Frontotemporal Lobar Degeneration (FTLD) is pathologically heterogeneous group of degenerative diseases of the brain. While there are distinct and highly recognisable clinical syndromes associated with FTLD there is also a wider and more diverse spectrum of progressive changes in movement, coordination, language and behaviour. Correlation between clinical syndrome and pathology is variable. Furthermore, over the course of an individual’s illness their syndrome may change, or they may present with features of more than one syndrome at a given time. Apathy and Impulsivity are common, distressing and disabling across the entire spectrum of FTLD and may be particularly prominent compared to other neurodegenerative diseases. In this thesis I outline the current classification of syndromes associated with FTLD and how this has undergone expansion, refinement and fragmentation over time. Despite changes in nosology and advances in understanding of pathological heterogeneity, I argue that the clinical syndrome of FTLD is highly recognisable and has been described for centuries. I suggest that a more unifying transdiagnostic approach to FTLD may provide useful insights into an increasingly fragmented spectrum of disease. Using this approach I conducted a large epidemiological study of FTLD and report prevalence, incidence and lifetime risk estimates. From this cohort of recruits I then surveyed patients and their carers and used a range of assessments of cognition and behaviour. I showed that while reports of apathy and impulsivity are common in FTLD, patient and carer based reports do not correlate well with each other or predict performance on a range of behavioural measures of decision making or goal directed cognition. I conclude that in FTLD, apathy and impulsivity are overlapping and multidimensional constructs and that no single testing modality used in isolation represents them completely, hence a multimodal approach to their assessment is required

The Apparent Critical Decay Index at the Onset of Solar Prominence Eruptions

International audienceA magnetic flux rope (MFR) embedded in a line-tied external magnetic field that decreases with height as-z n is unstable to perturbations if the decay index of the field n is larger than a critical value. The onset of this instability, called torus instability, is one of the main mechanisms that can initiate coronal mass ejections. Since flux ropes often possess magnetic dips that can support prominence plasma, this is also a valuable mechanism to trigger prominence eruptions. Magnetohydrodynamic (MHD) simulations of the formation and/or emergence of MFRs suggest a critical value for the onset of the instability in the range [1.4−2]. However, detailed observations of prominences suggest a value in the range [0.9−1.1]. In this Letter, by using a set of MHD simulations, we show why the large discrepancy between models and observations is only apparent. Our simulations indeed show that the critical decay index at the onset of the eruption is = n 1.4 0.1 when computed at the apex of the flux rope axis, while it is = n 1.1 0.1 when it is computed at the altitude of the topmost part of the distribution of magnetic dips. The discrepancy only arises because weakly twisted curved flux ropes do not have dips up to the altitude of their axis

Hooked flare ribbons and flux-rope related QSL footprints

We studied the magnetic topology of active region 12158 on 2014 September 10 and compared it with the observations before and early in the flare which begins at 17:21 UT (SOL2014-09-10T17:45:00). Our results show that the sigmoidal structure and flare ribbons of this active region observed by SDO/AIA can be well reproduced from a Grad-Rubin non linear force free field extrapolation method. Various inverse-S and -J shaped magnetic field lines, that surround a coronal flux rope, coincide with the sigmoid as observed in different extreme ultraviolet wavelengths, including its multi-threaded curved ends. Also, the observed distribution of surface currents in the magnetic polarity where it was not prescribed is well reproduced. This validates our numerical implementation and set-up of the Grad-Rubin method. The modeled double inverse-J shaped Quasi-Separatrix Layer (QSL) footprints match the observed flare ribbons during the rising phase of the flare, including their hooked parts. The spiral-like shape of the latter may be related to a complex pre-eruptive flux rope with more than one turn of twist, as obtained in the model. These ribbon-associated flux-rope QSL-footprints are consistent with the new standard flare model in 3D, with the presence of a hyperbolic flux tube located below an inverse tear drop shaped coronal QSL. This is a new step forward forecasting the locations of reconnection and ribbons in solar flares, and the geometrical properties of eruptive flux ropes.Comment: Accepted for publication in Ap

A Check on the Validity of Magnetic Field Reconstructions

We investigate a method to test whether a numerically computed model coronal magnetic field B departs from the divergence-free condition (also known as the solenoidality condition). The test requires a potential field B0 to be calculated, subject to Neumann boundary conditions, given by the normal components of the model field B at the boundaries. The free energy of the model field may be calculated using the volume integral of (B-B0)^2, where the integral is over the computational volume of the model field. A second estimate of the free energy is provided by calculating the difference between the volume integral of B^2 and the volume integral of B0^2. If B is divergence-free, the two estimates of the free energy should be the same. A difference between the two estimates indicates a departure from div B = 0 in the volume. The test is an implementation of a procedure proposed by Moraitis et al. (Sol. Phys. 289, 4453, 2014) and is a simpler version of the Helmholtz decomposition procedure presented by Valori et al. (Astron. Astrophys. 553, A38, 2013). We demonstrate the test in application to previously published nonlinear force-free model fields, and also investigate the influence on the results of the test of a departure from flux balance over the boundaries of the model field. Our results underline the fact that, to make meaningful statements about magnetic free energy in the corona, it is necessary to have model magnetic fields which satisfy the divergence-free condition to a good approximation.Australian Research Counci

Effects of flood hazard visualization format on house purchasing decisions

We investigated how decision-making is affected by the visual presentation of flood hazard information. We exposed participants to different formats of flood hazard information while they simulated selecting a property to purchase. We compared three flood hazard formats: (i) maps currently used by the UK Environment Agency, (ii) tables that present flood level and frequency information and (iii) graphical representations depicting the level-frequency combination using a cartoon house image as a physical referent. In the experiment participants were presented, via computer screen, side-by-side information about two houses in a series of trials. Participants made a forced choice preference judgement between 108 different pairs of houses to indicate which they would purchase. Our findings indicate that when hazard information is presented in map format, individuals are less accurate in selecting lower-hazard houses, compared to when the same information is presented as a graphic representation of a house or as a table. © 2018, © 2018 Informa UK Limited, trading as Taylor & Francis Group

Spirit, mind and body: the archaeology of monastic healing

Archaeology and material culture are used in this chapter to consider how monastic experience responded to illness, ageing and disability. The approach taken is influenced by the material study of religion, which interrogates how bodies and things engage to construct the sensory experience of religion, and by practice-based approaches in archaeology, which examine the active role of space and material culture in shaping religious agency and embodiment. The archaeology of monastic healing focuses on the full spectrum of healing technologies, from managing the body in order to prevent illness, through to the treatment of the sick and preparation of the corpse for burial

High-Throughput Detection of Induced Mutations and Natural Variation Using KeyPoint™ Technology

Reverse genetics approaches rely on the detection of sequence alterations in target genes to identify allelic variants among mutant or natural populations. Current (pre-) screening methods such as TILLING and EcoTILLING are based on the detection of single base mismatches in heteroduplexes using endonucleases such as CEL 1. However, there are drawbacks in the use of endonucleases due to their relatively poor cleavage efficiency and exonuclease activity. Moreover, pre-screening methods do not reveal information about the nature of sequence changes and their possible impact on gene function. We present KeyPoint™ technology, a high-throughput mutation/polymorphism discovery technique based on massive parallel sequencing of target genes amplified from mutant or natural populations. KeyPoint combines multi-dimensional pooling of large numbers of individual DNA samples and the use of sample identification tags (“sample barcoding”) with next-generation sequencing technology. We show the power of KeyPoint by identifying two mutants in the tomato eIF4E gene based on screening more than 3000 M2 families in a single GS FLX sequencing run, and discovery of six haplotypes of tomato eIF4E gene by re-sequencing three amplicons in a subset of 92 tomato lines from the EU-SOL core collection. We propose KeyPoint technology as a broadly applicable amplicon sequencing approach to screen mutant populations or germplasm collections for identification of (novel) allelic variation in a high-throughput fashion

BAT117213:Ileal bile acid transporter (IBAT) inhibition as a treatment for pruritus in primary biliary cirrhosis: study protocol for a randomised controlled trial

BACKGROUND: Pruritus (itch) is a symptom commonly experienced by patients with cholestatic liver diseases such as primary biliary cholangitis (PBC, previously referred to as primary biliary cirrhosis). Bile acids (BAs) have been proposed as potential pruritogens in PBC. The ileal bile acid transporter (IBAT) protein expressed in the distal ileum plays a key role in the enterohepatic circulation of BAs. Pharmacological inhibition of IBAT with GSK2330672 may reduce BA levels in the systemic circulation and improve pruritus. METHODS: This clinical study (BAT117213 study) is sponsored by GlaxoSmithKline (GSK) with associated exploratory studies supported by the National Institute for Health Research (NIHR). It is a phase 2a, multi-centre, randomised, double bind, placebo controlled, cross-over trial for PBC patients with pruritus. The primary objective is to investigate the safety and tolerability of repeat doses of GSK2330672, and explore whether GSK2330672 administration for 14 days improves pruritus compared with placebo. The key outcomes include improvement in pruritus scores evaluated on a numerical rating scale and other PBC symptoms in an electronic diary completed twice daily by the patients. The secondary outcomes include the evaluation of the effect of GSK2330672 on total serum bile acid (BA) concentrations, serum markers of BA synthesis and steady-state pharmacokinetics of ursodeoxycholic acid (UDCA). DISCUSSION: BAT117213 study is the first randomised controlled crossover trial of ileal bile acid transporter inhibitor, a novel class of drug to treat pruritus in PBC. The main strengths of the trial are utility of a novel, study specific, electronic symptom diary as patient reported outcome to measure the treatment response objectively and the crossover design that allows estimating the treatment effect in a smaller number of patients. The outcome of this trial will inform the trial design of future development phase of the IBAT inhibitor drug. The trial will also provide opportunity to conduct metabonomic and gut microbiome studies as explorative and mechanistic research in patients with cholestatic pruritus. TRIAL REGISTRATION: EudraCT number: 2012-005531-84, ClinicalTrials.gov Identifier: NCT01899703, registered on 3(rd) July 201