Advancement and applications of the template matching approach to indexing electron backscatter patterns

Electron backscatter diffraction is a well-established characterisation technique used to determine the orientation and crystal phase of a crystalline material. A pattern is formed by dynamical interaction of elections with the crystal lattice, which can be understood and simulated by using Bloch wave theory. The conventional method of indexing a diffraction pattern is to use a Hough transform to convert the lines of the pattern to points that are easily accessible to a computer. As the bands of the pattern are direct projections of the crystal planes, the interplanar angles can then be computed and compared to a look up table to determine phase and orientation. This method works well for most examples, however, is not well suited to more complex unit cells, due to the fact it ignores more subtle features of the patterns. This thesis proposes a refined template matching approach which uses efficient pattern matching algorithms, such as those used in the field of computer vision, for phase determination and orientation analysis. This thesis introduces the method and demonstrates its efficacy, as well as introducing advanced methods for pseudosymmetry analysis and phase mapping. A new metric for phase confidence is also proposed and the refined method is shown to be able to correctly determine phases and pseudosymmetric orientations. Finally, preliminary work on a direct electron detector stage is presented. Work on the development, testing the pattern centre reliability, modulation transfer and an example map is shown.Open Acces

Emergent realities for social wellbeing : environmental, spatial and social pathways

The subject of Space is often perceived as abstract. Yet, our communications infrastructure, navigation on land, sea and air, surveillance, border control and security, agriculture, meteorological observation, monitoring of natural disasters and early warning systems all rely on Space. Furthermore, the understanding of our planet, the solar system and beyond through space science, all rely on investment in the space sector. Space is not a luxury, but it is indeed essential for our daily lives.peer-reviewe

A national-scale assessment of climate change impacts on species: assessing the balance of risks and opportunities for multiple taxa

It is important for conservationists to be able to assess the risks that climate change poses to species, in order to inform decision making. Using standardised and repeatable methods, we present a national-scale assessment of the risks of range loss and opportunities for range expansion, that climate change could pose for over 3,000 plants and animals that occur in England. A basic risk assessment that compared projected future changes in potential range with recently observed changes classified 21% of species as being at high risk and 6% at medium risk of range loss under a B1 climate change scenario. A greater number of species were classified as having a medium (16%) or high (38%) opportunity to potentially expand their distribution. A more comprehensive assessment, incorporating additional ecological information, including potentially confounding and exacerbating factors, was applied to 402 species, of which 35 % were at risk of range loss and 42 % may expand their range extent. This study covers a temperate region with a significant proportion of species at their poleward range limit. The balance of risks and opportunities from climate change may be different elsewhere. The outcome of both risk assessments varied between taxonomic groups, with bryophytes and vascular plants containing the greatest proportion of species at risk from climate change. Upland habitats contained more species at risk than other habitats. Whilst the overall pattern was clear, confidence was generally low for individual assessments, with the exception of well-studied taxa such as birds. In response to climate change, nature conservation needs to plan for changing species distributions and increasing uncertainty of the future

Toxic marine microalgae and shellfish poisoning in the British isles: history, review of epidemiology, and future implications

The relationship between toxic marine microalgae species and climate change has become a high profile and well discussed topic in recent years, with research focusing on the possible future impacts of changing hydrological conditions on Harmful Algal Bloom (HAB) species around the world. However, there is very little literature concerning the epidemiology of these species on marine organisms and human health. Here, we examine the current state of toxic microalgae species around the UK, in two ways: first we describe the key toxic syndromes and gather together the disparate reported data on their epidemiology from UK records and monitoring procedures. Secondly, using NHS hospital admissions and GP records from Wales, we attempt to quantify the incidence of shellfish poisoning from an independent source. We show that within the UK, outbreaks of shellfish poisoning are rare but occurring on a yearly basis in different regions and affecting a diverse range of molluscan shellfish and other marine organisms. We also show that the abundance of a species does not necessarily correlate to the rate of toxic events. Based on routine hospital records, the numbers of shellfish poisonings in the UK are very low, but the identification of the toxin involved, or even a confirmation of a poisoning event is extremely difficult to diagnose. An effective shellfish monitoring system, which shuts down aquaculture sites when toxins exceed regularity limits, has clearly prevented serious impact to human health, and remains the only viable means of monitoring the potential threat to human health. However, the closure of these sites has an adverse economic impact, and the monitoring system does not include all toxic plankton. The possible geographic spreading of toxic microalgae species is therefore a concern, as warmer waters in the Atlantic could suit several species with southern biogeographical affinities enabling them to occupy the coastal regions of the UK, but which are not yet monitored or considered to be detrimental

A multicentre, randomised controlled trial to compare the clinical and cost-effectiveness of Lee Silverman Voice Treatment versus standard NHS Speech and Language Therapy versus control in Parkinson’s disease: a study protocol for a randomised controlled trial

Abstract: Background: Parkinson’s disease (PD) affects approximately 145,519 people in the UK. Speech impairments are common with a reported prevalence of 68%, which increase physical and mental demands during conversation, reliance on family and/or carers, and the likelihood of social withdrawal reducing quality of life. In the UK, two approaches to Speech and Language Therapy (SLT) intervention are commonly available: National Health Service (NHS) SLT or Lee Silverman Voice Treatment (LSVT LOUD®). NHS SLT is tailored to the individuals’ needs per local practice typically consisting of six to eight weekly sessions; LSVT LOUD® comprises 16 sessions of individual treatment with home-based practice over 4 weeks. The evidence-base for their effectiveness is inconclusive. Methods/design: PD COMM is a phase III, multicentre, three-arm, unblinded, randomised controlled trial. Five hundred and forty-six people with idiopathic PD, reporting speech or voice problems will be enrolled. We will exclude those with a diagnosis of dementia, laryngeal pathology or those who have received SLT for speech problems in the previous 2 years. Following informed consent and completion of baseline assessments, participants will be randomised in a 1:1:1 ratio to no-intervention control, NHS SLT or LSVT LOUD® via a central computer-generated programme, using a minimisation procedure with a random element, to ensure allocation concealment. Participants randomised to the intervention groups will start treatment within 4 (NHS SLT) or 7 (LSVT LOUD®) weeks of randomisation. Primary outcome: Voice Handicap Index (VHI) total score at 3 months. Secondary outcomes include: VHI subscales, Parkinson’s Disease Questionnaire-39; Questionnaire on Acquired Speech Disorders; EuroQol-5D-5 L; ICECAP-O; resource utilisation; adverse events and carer quality of life. Mixed-methods process and health economic evaluations will take place alongside the trial. Assessments will be completed before randomisation and at 3, 6 and 12 months after randomisation. The trial started in December 2015 and will run for 77 months. Recruitment will take place in approximately 42 sites around the UK. Discussion: The trial will test the hypothesis that SLT is effective for the treatment of speech or voice problems in people with PD compared to no SLT. It will further test whether NHS SLT or LSVT LOUD® provide greater benefit and determine the cost-effectiveness of both interventions. Trial registration: International Standard Randomised Controlled Trials Number (ISRCTN) Registry, ID: 12421382. Registered on 18 April 2016

A multicentre, randomised controlled trial to compare the clinical and cost-effectiveness of Lee Silverman Voice Treatment versus standard NHS Speech and Language Therapy versus control in Parkinson’s disease: a study protocol for a randomised controlled trial

Abstract: Background: Parkinson’s disease (PD) affects approximately 145,519 people in the UK. Speech impairments are common with a reported prevalence of 68%, which increase physical and mental demands during conversation, reliance on family and/or carers, and the likelihood of social withdrawal reducing quality of life. In the UK, two approaches to Speech and Language Therapy (SLT) intervention are commonly available: National Health Service (NHS) SLT or Lee Silverman Voice Treatment (LSVT LOUD®). NHS SLT is tailored to the individuals’ needs per local practice typically consisting of six to eight weekly sessions; LSVT LOUD® comprises 16 sessions of individual treatment with home-based practice over 4 weeks. The evidence-base for their effectiveness is inconclusive. Methods/design: PD COMM is a phase III, multicentre, three-arm, unblinded, randomised controlled trial. Five hundred and forty-six people with idiopathic PD, reporting speech or voice problems will be enrolled. We will exclude those with a diagnosis of dementia, laryngeal pathology or those who have received SLT for speech problems in the previous 2 years. Following informed consent and completion of baseline assessments, participants will be randomised in a 1:1:1 ratio to no-intervention control, NHS SLT or LSVT LOUD® via a central computer-generated programme, using a minimisation procedure with a random element, to ensure allocation concealment. Participants randomised to the intervention groups will start treatment within 4 (NHS SLT) or 7 (LSVT LOUD®) weeks of randomisation. Primary outcome: Voice Handicap Index (VHI) total score at 3 months. Secondary outcomes include: VHI subscales, Parkinson’s Disease Questionnaire-39; Questionnaire on Acquired Speech Disorders; EuroQol-5D-5 L; ICECAP-O; resource utilisation; adverse events and carer quality of life. Mixed-methods process and health economic evaluations will take place alongside the trial. Assessments will be completed before randomisation and at 3, 6 and 12 months after randomisation. The trial started in December 2015 and will run for 77 months. Recruitment will take place in approximately 42 sites around the UK. Discussion: The trial will test the hypothesis that SLT is effective for the treatment of speech or voice problems in people with PD compared to no SLT. It will further test whether NHS SLT or LSVT LOUD® provide greater benefit and determine the cost-effectiveness of both interventions. Trial registration: International Standard Randomised Controlled Trials Number (ISRCTN) Registry, ID: 12421382. Registered on 18 April 2016

Structural control and genesis of barite veins in the Adelaide Fold Belt, South Australia

Barite veins hosted by Neoproterozoic sedimentary rocks have widespread distribution in the Adelaide Fold Belt, South Australia. The largest deposit is the vein system of the Oraparinna Mine in the Central Flinders Ranges, where the major structures, including fractures occupied by the barite veins, can be explained by a N-S dextral shear couple. Vein formation apparently took place during a basin-wide hydrothermal event approximately 590Ma ago, and barite deposition resulted from mixing of a basinal fluid with formation water and/or seawater

Isotopic and geochemical characterisation of the Cambrian Kanmantoo Group, South Australia: implications for stratigraphy and provenance

The Early Cambrian Kanmantoo Group of southeastern South Australia is a thick marine succession of immature and predominantly turbiditic sandstone and mudstone, and metamorphic equivalents, that was deposited within a continental-margin delta and submarine-fan complex. Deposition was very rapid and occurred just prior to the onset of deformation and metamorphism by the Delamerian Orogeny. The Kanmantoo Group contrasts with older units of the Adelaide Rift Complex (Adelaide Geosyncline) in terms of sedimentary facies, rapidity of deposition, composition and provenance. Importantly, the Kanmantoo Group represents the earliest appearance in Australia of a sedimentary sequence characterised by the 'Pan-Gondwanaland' detrital-zircon signature. Here we present geochemical and Nd-Sr isotope data for sandstone-mudstone pairs collected throughout the Kanmantoo Group. Interestingly, sandstone-mudstone pairs do not have a consistent polarity in terms of their Nd values. This argues against simple mixing/unmixing between two distinct sediment components and suggests a more complex and incompletely mixed multicomponent provenance. There appears to be an abrupt change in isotopic character within the Backstairs Passage Formation in the mid-Kanmantoo Group. Although the origin of this change remains problematic, an overall shift to more negative Nd(†) numbers up-section may reflect progressive exhumation of the provenance region(s) and accessing of increasingly ancient materials. Based on detrital-zircon signature the Kanmantoo Group must be sourced from an area containing abundant 0.7-0.5 Ga magmatism, with other components supplying 'Grenvillian' (1.2-0.9 Ga) and older zircons back to about 3.5 Ga. Large latest Neoproterozoic to Early Paleozoic orogenic and magmatic belts include the Ross Orogen in Antarctica and the Prydz-Leeuwin Belt on the inferred former suture between East Antarctica, India and Western Australia. The former is closer, but lacks known magmatism older than 0.55 Ga. The latter appears to be a more suitable provenance based on the zircon signature, and our Nd data show significant overlap with some existing datasets from along this belt. Recent suggestions that equivalent rocks may extend beneath the central East Antarctic ice sheet (including the Gamburtsev Subglacial Mountains) may provide a more geographically suitable location, particularly from the perspective of paleocurrent data, but are not testable with our present dataset.16 page(s