2,082 research outputs found

    Degree of Cajal-Retzius cell mislocalisation correlates with the severity of structural brain defects in mouse models of dystroglycanopathy

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    The secondary dystroglycanopathies are characterized by the hypoglycosylation of alpha dystroglycan, and are associated with mutations in at least 18 genes that act on the glycosylation of this cell surface receptor rather than the Dag1 gene itself. At the severe end of the disease spectrum, there are substantial structural brain defects, the most striking of which is often cobblestone lissencephaly. The aim of this study was to determine the gene‐specific aspects of the dystroglycanopathy brain phenotype through a detailed investigation of the structural brain defects present at birth in three mouse models of dystroglycanopathy—the FKRPKD, which has an 80% reduction in Fkrp transcript levels; the Pomgnt1null, which carries a deletion of exons 7–16 of the Pomgnt1 gene; and the Largemyd mouse, which carries a deletion of exons 5–7 of the Large gene. We show a rostrocaudal and mediolateral gradient in the severity of brain lesions in FKRPKD, and to a lesser extent Pomgnt1null mice. Furthermore, the mislocalization of Cajal–Retzius cells is correlated with the gradient of these lesions and the severity of the brain phenotype in these models. Overall these observations implicate gene‐specific differences in the pathogenesis of brain lesions in this group of disorders

    Concentration dependent interdiffusion in InGaAs/GaAs as evidenced by high resolution x-ray diffraction and photoluminescence spectroscopy

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    Article copyright 2005 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The article appeared in Journal of Applied Physics 97, 013536 (2005) and may be found at

    Core-level photoemission spectroscopy of nitrogen bonding in GaNxAs1–x alloys

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    The nitrogen bonding configurations in GaNxAs1–x alloys grown by molecular beam epitaxy with 0.07=0.03, the nitrogen is found to exist in a single bonding configuration – the Ga–N bond; no interstitial nitrogen complexes are present. The amount of nitrogen in the alloys is estimated from the XPS using the N 1s photoelectron and Ga LMM Auger lines and is found to be in agreement with the composition determined by x-ray diffraction

    Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks

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    © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hopkinson, B. M., King, A. C., Owen, D. P., Johnson-Roberson, M., Long, M. H., & Bhandarkar, S. M. Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks. PLoS One, 15(3), (2020): e0230671, doi: 10.1371/journal.pone.0230671.Coral reefs are biologically diverse and structurally complex ecosystems, which have been severally affected by human actions. Consequently, there is a need for rapid ecological assessment of coral reefs, but current approaches require time consuming manual analysis, either during a dive survey or on images collected during a survey. Reef structural complexity is essential for ecological function but is challenging to measure and often relegated to simple metrics such as rugosity. Recent advances in computer vision and machine learning offer the potential to alleviate some of these limitations. We developed an approach to automatically classify 3D reconstructions of reef sections and assessed the accuracy of this approach. 3D reconstructions of reef sections were generated using commercial Structure-from-Motion software with images extracted from video surveys. To generate a 3D classified map, locations on the 3D reconstruction were mapped back into the original images to extract multiple views of the location. Several approaches were tested to merge information from multiple views of a point into a single classification, all of which used convolutional neural networks to classify or extract features from the images, but differ in the strategy employed for merging information. Approaches to merging information entailed voting, probability averaging, and a learned neural-network layer. All approaches performed similarly achieving overall classification accuracies of ~96% and >90% accuracy on most classes. With this high classification accuracy, these approaches are suitable for many ecological applications.This study was funded by grants from the Alfred P. Sloan Foundation (BMH, BR2014-049; https://sloan.org), and the National Science Foundation (MHL, OCE-1657727; https://www.nsf.gov). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript

    Vegetation height products between 60° S and 60° N from ICESat GLAS data.

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    We present new coarse resolution (0.5� ×0.5�)vegetation height and vegetation-cover fraction data sets between 60� S and 60� N for use in climate models and ecological models. The data sets are derived from 2003–2009 measurements collected by the Geoscience Laser Altimeter System (GLAS) on the Ice, Cloud and land Elevation Satellite (ICESat), the only LiDAR instrument that provides close to global coverage. Initial vegetation height is calculated from GLAS data using a development of the model of Rosette et al. (2008) with further calibration on desert sites. Filters are developed to identify and eliminate spurious observations in the GLAS data, e.g. data that are affected by clouds, atmosphere and terrain and as such result in erroneous estimates of vegetation height or vegetation cover. Filtered GLAS vegetation height estimates are aggregated in histograms from 0 to 70m in 0.5m intervals for each 0.5�×0.5�. The GLAS vegetation height product is evaluated in four ways. Firstly, the Vegetation height data and data filters are evaluated using aircraft LiDAR measurements of the same for ten sites in the Americas, Europe, and Australia. Application of filters to the GLAS vegetation height estimates increases the correlation with aircraft data from r =0.33 to r =0.78, decreases the root-mean-square error by a factor 3 to about 6m (RMSE) or 4.5m (68% error distribution) and decreases the bias from 5.7m to −1.3 m. Secondly, the global aggregated GLAS vegetation height product is tested for sensitivity towards the choice of data quality filters; areas with frequent cloud cover and areas with steep terrain are the most sensitive to the choice of thresholds for the filters. The changes in height estimates by applying different filters are, for the main part, smaller than the overall uncertainty of 4.5–6m established from the site measurements. Thirdly, the GLAS global vegetation height product is compared with a global vegetation height product typically used in a climate model, a recent global tree height product, and a vegetation greenness product and is shown to produce realistic estimates of vegetation height. Finally, the GLAS bare soil cover fraction is compared globally with the MODIS bare soil fraction (r = 0.65) and with bare soil cover fraction estimates derived from AVHRR NDVI data (r =0.67); the GLAS treecover fraction is compared with the MODIS tree-cover fraction (r =0.79). The evaluation indicates that filters applied to the GLAS data are conservative and eliminate a large proportion of spurious data, while only in a minority of cases at the cost of removing reliable data as well. The new GLAS vegetation height product appears more realistic than previous data sets used in climate models and ecological models and hence should significantly improve simulations that involve the land surface

    Introduction of standardised packaging and availability of illicit cigarettes: a difference-in-difference analysis of European Union survey data 2015-2018.

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    Standardised packaging of tobacco products is intended to reduce the appeal of smoking, but the tobacco industry claims this increases illicit trade. We examined the percentage of people reporting being offered illicit cigarettes before and after full implementation of standardised packaging in the UK, Ireland and France and compared this to other European Union countries. Reported ever illicit cigarette exposure fell from 19.8% to 18.1% between 2015 and 2018 in the three countries fully implementing the policy, and from 19.6% to 17.0% in control countries (p for difference=0.320). Standardised packaging does not appear to increase the availability of illicit cigarettes
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