Temperature Sensing Above 1000 C Using Cr-Doped GdAlO3 Spin-Allowed Broadband Luminescence

Cr-doped GdAlO3 (Cr:GdAlO3) is shown to produce remarkably high-intensity spin-allowed broadband luminescence with sufficiently long decay times to make effective luminescence-decay-time based temperature measurements above 1000 C. This phosphor is therefore an attractive alternative to the much lower luminescence intensity rare-earth-doped thermographic phosphors that are typically utilized at these elevated temperatures. In particular, Cr:GdAlO3 will be preferred over rare-earth-doped phosphors, such as Dy:YAG, at temperatures up to 1200 C for intensity-starved situations when the much lower emission intensity from rare-earth-doped phosphors is insufficient for accurate temperature measurements in the presence of significant radiation background. While transition-metal-doped phosphors such as Cr:Al2O3 (ruby) are known to exhibit high luminescence intensity at low dopant concentrations, quenching due to nonradiative decay pathways competing with the (sup 2)E to (sup 4)A(sub 2) radiative transition (R line) has typically restricted their use for temperature sensing to below 600 C. Thermal quenching of the broadband (sup 4)T(sub 2) to (sup 4)A(sub 2) radiative transition from Cr:GdAlO3, however, is delayed until much higher temperatures (above 1000 C). This spin-allowed broadband emission persists to high temperatures because the lower-lying (sup 2)E energy level acts as a reservoir to thermally populate the higher shorter-lived (sup 4)T(sub 2) energy level and because the activation energy for nonradiative crossover relaxation from the (sup 4)T(sub 2) level to the (sup 4)A(sub 2) ground state is high. The strong crystal field associated with the tight bonding of the AlO6 octahedra in the GdAlO3 perovskite structure is responsible for this behavior

Temperature and Pressure Sensors Based on Spin-Allowed Broadband Luminescence of Doped Orthorhombic Perovskite Structures

Systems and methods that are capable of measuring pressure or temperature based on luminescence are discussed herein. These systems and methods are based on spin-allowed broadband luminescence of sensors with orthorhombic perovskite structures of rare earth aluminates doped with chromium or similar transition metals, such as chromium-doped gadolinium aluminate. Luminescence from these sensors can be measured to determine at least one of temperature or pressure, based on either the intense luminescence of these sensors, even at high temperatures, or low temperature techniques discussed herein

Soil Disturbance by Invertebrates in a Semi-arid Eucalypt Woodland: Effects of Grazing Exclusion, Faunal Reintroductions, Landscape and Patch Characteristics

. Soil disturbance by invertebrates in a semiarid eucalypt woodland: effects of grazing exclusion, faunal reintroductions, landscape and patch characteristics. Proceedings of the Linnean Society of New South Wales 134, A11-A18. Soil disturbing invertebrates are common elements of arid and semi-arid landscapes. Disturbances such as burrows, nest entrances, emergence holes and mounds of ejecta soil have large, but often poorly understood, effects on ecosystem properties and processes as broad as pedogenesis, soil movement and water infi ltration. We examined disturbances created by a range of invertebrates in a semi-arid eucalypt woodland in eastern Australia in relation to three levels of disturbance varying from areas currently grazed by domestic herbivores to those where domestic herbivores have been removed, with and without the reintroduction of locally-extinct omnivorous native mammals. Overall, the tunnels and ejecta soil from ant nests comprised 80% of all invertebrate disturbances across all sites and treatments. There were signifi cantly more invertebrate disturbances at sites where domestic herbivores had been excluded, more disturbances on dunes and in the swales than on plains, and more under shrubs than under trees. The cover of disturbances by invertebrates tended to increase with increasing cover of disturbance by native vertebrates, but only under exclosure where no locally-extinct native mammals had been reintroduced. Our results indicate that invertebrate-created disturbances are a common feature of semi-arid woodland soils, and that management activities, such as grazing and the reintroduction of locally-extinct vertebrates, will affect their density, potentially infl uencing a range of ecosystem processes

Mobile element insertions are frequent in oesophageal adenocarcinomas and can mislead paired-end sequencing analysis.

BACKGROUND: Mobile elements are active in the human genome, both in the germline and cancers, where they can mutate driver genes. RESULTS: While analysing whole genome paired-end sequencing of oesophageal adenocarcinomas to find genomic rearrangements, we identified three ways in which new mobile element insertions appear in the data, resembling translocation or insertion junctions: inserts where unique sequence has been transduced by an L1 (Long interspersed element 1) mobile element; novel inserts that are confidently, but often incorrectly, mapped by alignment software to L1s or polyA tracts in the reference sequence; and a combination of these two ways, where different sequences within one insert are mapped to different loci. We identified nine unique sequences that were transduced by neighbouring L1s, both L1s in the reference genome and L1s not present in the reference. Many of the resulting inserts were small fragments that include little or no recognisable mobile element sequence. We found 6 loci in the reference genome to which sequence reads from inserts were frequently mapped, probably erroneously, by alignment software: these were either L1 sequence or particularly long polyA runs. Inserts identified from such apparent rearrangement junctions averaged 16 inserts/tumour, range 0-153 insertions in 43 tumours. However, many inserts would not be detected by mapping the sequences to the reference genome, because they do not include sufficient mappable sequence. To estimate total somatic inserts we searched for polyA sequences that were not present in the matched normal or other normals from the same tumour batch, and were not associated with known polymorphisms. Samples of these candidate inserts were verified by sequencing across them or manual inspection of surrounding reads: at least 85 % were somatic and resembled L1-mediated events, most including L1Hs sequence. Approximately 100 such inserts were detected per tumour on average (range zero to approximately 700). CONCLUSIONS: Somatic mobile elements insertions are abundant in these tumours, with over 75 % of cases having a number of novel inserts detected. The inserts create a variety of problems for the interpretation of paired-end sequencing data.Funding was primarily from Cancer Research UK program grants to RCF and ST (C14478/A15874 and C14303/A17197), with additional support awarded to RCF from UK Medical Research Council, NHS National Institute for Health Research (NIHR), the Experimental Cancer Medicine Centre Network and the NIHR Cambridge Biomedical Research Centre, and Cancer Research UK Project grant C1023/A14545 to PAWE. JMJW was funded by a Wellcome Trust Translational Medicine and Therapeutics grant

Dwarf koa (Desmanthus virgatus)

This is the final version. It was first published by BioMed Central at http://www.biomedcentral.com/1471-2164/16/473.Background: Mobile elements are active in the human genome, both in the germline and cancers, where they can\ud mutate driver genes.\ud Results: While analysing whole genome paired-end sequencing of oesophageal adenocarcinomas to find genomic\ud rearrangements, we identified three ways in which new mobile element insertions appear in the data, resembling\ud translocation or insertion junctions: inserts where unique sequence has been transduced by an L1 (Long interspersed\ud element 1) mobile element; novel inserts that are confidently, but often incorrectly, mapped by alignment software to\ud L1s or polyA tracts in the reference sequence; and a combination of these two ways, where different sequences within\ud one insert are mapped to different loci. We identified nine unique sequences that were transduced by neighbouring\ud L1s, both L1s in the reference genome and L1s not present in the reference. Many of the resulting inserts were small\ud fragments that include little or no recognisable mobile element sequence. We found 6 loci in the reference genome to\ud which sequence reads from inserts were frequently mapped, probably erroneously, by alignment software: these were\ud either L1 sequence or particularly long polyA runs. Inserts identified from such apparent rearrangement junctions\ud averaged 16 inserts/tumour, range 0?153 insertions in 43 tumours. However, many inserts would not be detected by\ud mapping the sequences to the reference genome, because they do not include sufficient mappable sequence. To\ud estimate total somatic inserts we searched for polyA sequences that were not present in the matched normal or other\ud normals from the same tumour batch, and were not associated with known polymorphisms. Samples of these candidate\ud inserts were verified by sequencing across them or manual inspection of surrounding reads: at least 85 % were somatic\ud and resembled L1-mediated events, most including L1Hs sequence. Approximately 100 such inserts were detected per\ud tumour on average (range zero to approximately 700).\ud Conclusions: Somatic mobile elements insertions are abundant in these tumours, with over 75 % of cases having a\ud number of novel inserts detected. The inserts create a variety of problems for the interpretation of paired-end\ud sequencing data.Funding\ud was primarily from Cancer Research UK program grants to RCF and ST\ud (C14478/A15874 and C14303/A17197), with additional support awarded to\ud RCF from UK Medical Research Council, NHS National Institute for Health\ud Research (NIHR), the Experimental Cancer Medicine Centre Network and\ud the NIHR Cambridge Biomedical Research Centre, and Cancer Research UK\ud Project grant C1023/A14545 to PAWE. JMJW was funded by a Wellcome\ud Trust Translational Medicine and Therapeutics grant

A national survey of services for the prevention and management of falls in the UK

Background: The National Health Service (NHS) was tasked in 2001 with developing service provision to prevent falls in older people. We carried out a national survey to provide a description of health and social care funded UK fallers services, and to benchmark progress against current practice guidelines. Methods: Cascade approach to sampling, followed by telephone survey with senior member of the fall service. Characteristics of the service were assessed using an internationally agreed taxonomy. Reported service provision was compared against benchmarks set by the National Institute for Health and Clinical Excellence (NICE). Results: We identified 303 clinics across the UK. 231 (76%) were willing to participate. The majority of services were based in acute or community hospitals, with only a few in primary care or emergency departments. Access to services was, in the majority of cases, by health professional referral. Most services undertook a multi-factorial assessment. The content and quality of these assessments varied substantially. Services varied extensively in the way that interventions were delivered, and particular concern is raised about interventions for vision, home hazard modification, medication review and bone health. Conclusion: The most common type of service provision was a multi-factorial assessment and intervention. There were a wide range of service models, but for a substantial number of services, delivery appears to fall below recommended NICE guidance

Whole-genome sequencing of nine esophageal adenocarcinoma cell lines.

Esophageal adenocarcinoma (EAC) is highly mutated and molecularly heterogeneous. The number of cell lines available for study is limited and their genome has been only partially characterized. The availability of an accurate annotation of their mutational landscape is crucial for accurate experimental design and correct interpretation of genotype-phenotype findings. We performed high coverage, paired end whole genome sequencing on eight EAC cell lines-ESO26, ESO51, FLO-1, JH-EsoAd1, OACM5.1 C, OACP4 C, OE33, SK-GT-4-all verified against original patient material, and one esophageal high grade dysplasia cell line, CP-D. We have made available the aligned sequence data and report single nucleotide variants (SNVs), small insertions and deletions (indels), and copy number alterations, identified by comparison with the human reference genome and known single nucleotide polymorphisms (SNPs). We compare these putative mutations to mutations found in primary tissue EAC samples, to inform the use of these cell lines as a model of EAC.This work was funded by an MRC Programme Grant to R.C.F. and a Cancer Research UK grant to PAWE. The pipeline for mutation calling is funded by Cancer Research UK as part of the International Cancer Genome Consortium. G.C. is a National Institute for Health Research Lecturer as part of a NIHR professorship grant to R.C.F. AGL is supported by a Cancer Research UK programme grant (C14303/A20406) to Simon Tavaré and the European Commission through the Horizon 2020 project SOUND (Grant Agreement no. 633974)

Modeling the Effects of Star Formation Histories on Halpha and Ultra-Violet Fluxes in Nearby Dwarf Galaxies

We consider the effects of non-constant star formation histories (SFHs) on Halpha and GALEX far ultra-violet (FUV) star formation rate (SFR) indicators. Under the assumption of a fully populated Chabrier IMF, we compare the distribution of Halpha-to-FUV flux ratios from ~ 1500 simple, periodic model SFHs with observations of 185 galaxies from the Spitzer Local Volume Legacy survey. We find a set of SFH models that are well matched to the data, such that more massive galaxies are best characterized by nearly constant SFHs, while low mass systems experience bursts amplitudes of ~ 30 (i.e., an increase in the SFR by a factor of 30 over the SFR during the inter-burst period), burst durations of tens of Myr, and periods of ~ 250 Myr; these SFHs are broadly consistent with the increased stochastic star formation expected in systems with lower SFRs. We analyze the predicted temporal evolution of galaxy stellar mass, R-band surface brightness, Halpha-derived SFR, and blue luminosity, and find that they provide a reasonable match to observed flux distributions. We find that our model SFHs are generally able to reproduce both the observed systematic decline and increased scatter in Halpha-to-FUV ratios toward low mass systems, without invoking other physical mechanisms. We also compare our predictions with those from the Integrated Galactic IMF theory with a constant SFR. We find that while both predict a systematic decline in the observed ratios, only the time variable SFH models are capable of producing the observed population of low mass galaxies ($M_{*}$ < 10$^{7}$ Msun) with normal Halpha-to-FUV ratios. These results demonstrate that a variable IMF alone has difficulty explaining the observed scatter in the Halpha-to-FUV ratios. We conclude by considering the limitations of the model SFHs, and discuss the use of additional empirical constraints to improve future SFH modeling efforts.Comment: 15 pages, 11 Figures. Accepted for publication in Ap

Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas

Oesophageal adenocarcinoma (OAC) provides an ideal case study to characterize large-scale rearrangements. Using whole genome short-read sequencing of 383 cases, for which 214 had matched whole transcriptomes, we observed structural variations (SV) with a predominance of deletions, tandem duplications and inter-chromosome junctions that could be identified as LINE-1 mobile element (ME) insertions. Complex clusters of rearrangements resembling breakage-fusion-bridge cycles or extrachromosomal circular DNA accounted for 22% of complex SVs affecting known oncogenes. Counting SV events affecting known driver genes substantially increased the recurrence rates of these drivers. After excluding fragile sites, we identified 51 candidate new drivers in genomic regions disrupted by SVs, including ETV5, KAT6B and CLTC. RUNX1 was the most recurrently altered gene (24%), with many deletions inactivating the RUNT domain but preserved the reading frame, suggesting an altered protein product. These findings underscore the importance of identification of SV events in OAC with implications for targeted therapies.</p