Contextual Detection of Anomalies in Hyperspectral Images

The majority of anomaly detectors in Hyperspectral Imaging use only the statistical aspects of the spectral readings in the image. These detectors fail to use the spatial context that is contained in the images. The use of this information can yield detectors that out perform their spatially myopic counterparts. To demonstrate this, we will use an independent component analysis based detector, autonomous global anomaly detector (AutoGAD), developed at AFIT augmented to account for the spatial context of the detected anomalies. Through the use of segmentation algorithms, the anomalies identified are formed into regions. The size and shape of these regions are then used to decide if the region is anomalous or not. A Bayesian Belief Network structure is used to update a posterior probability of the region being anomalous

Montana's Crucial Areas and Connectivity Assessment: An Update and Demonstration of the Crucial Areas Mapping Service

Montana Fish, Wildlife and Parks (FWP) completed the Comprehensive Fish and Wildlife Conservation Strategy (CFWCS) in October 2005 as a landscape level plan to identify aquatic and terrestrial focus areas important to species and habitats of "Greatest Conservation Need." As implementation of the CFWCS began, FWP saw a need to refine the conservation scale and include terrestrial game and sport fish, FWP lands, and other recreational values into a Comprehensive Plan for Conservation. The "Crucial Areas and Connectivity Assessment" is an attempt to refine the conservation scale and identify important game and nongame fish and wildlife habitats, critical corridors, and valued recreational areas using a combination of empirical data, modeling based on these data, and expert opinion. The goal of this project is to identify and display critical and important habitats for fish and wildlife. Multiple benefits are perceived through achievement of this goal: increased efficiency in planning and commenting on development proposals, effective targeting and planning for the conservation of valued habitats, and increased opportunity for coordination with other agencies states. FWP spent the past year developing data layers, vetting the layers both internally and within the scientific community. Layers available to date include: game quality, game fish life history, watershed integrity, species of concern, aquatic connectivity, angler use, terrestrial species richness, and core area index. In parallel, FWP has developed an interactive Crucial Areas Mapping Service (CAMS) that depicts these resource values and allows users to relate each resource value to risk factors including energy development, urbanization, and subdivision. As the project develops and nears completion, best management practices and policy related to critical habitats will be produced. In mid-March, we plan to release CAMS to the public as a preplanning tool and comprehensive decision support system

‘Foreshadows and repercussions’: histories of air war and the recasting of cities and citizens

In the preface to the 1941 edition to his 1908 novel, The War in the Air, H. G. Wells wrote: ‘I told you so. You damned fools’. The books discussed here illustrate how, in the few intervening decades, air war moved from a fearful vision into reality, and detail the varied experiences and consequences of the aerial bombardment of cities and civilians. The histories of air power and the aerial bombardment of cities have centred on the Second World War, moving from the humanising endurance of Londoners during the Blitz to the entirely dehumanised horror of the destruction of Hiroshima and Nagasaki. The texts reviewed here extend the histories of air war and highlight the city and the home as a target for bombing while remaining the place where people carried on their daily lives

Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers.

Although promoter-associated CpG islands have been established as targets of DNA methylation changes in cancer, previous studies suggest that epigenetic dysregulation outside the promoter region may be more closely associated with transcriptional changes. Here we examine DNA methylation, chromatin marks, and transcriptional alterations to define the relationship between transcriptional modulation and spatial changes in chromatin structure. Using human papillomavirus-related oropharyngeal carcinoma as a model, we show aberrant enrichment of repressive H3K9me3 at the transcriptional start site (TSS) with methylation-associated, tumor-specific gene silencing. Further analysis identifies a hypermethylated subtype which shows a functional convergence on MYC targets and association with CREBBP/EP300 mutation. The tumor-specific shift to transcriptional repression associated with DNA methylation at TSSs was confirmed in multiple tumor types. Our data may show a common underlying epigenetic dysregulation in cancer associated with broad enrichment of repressive chromatin marks and aberrant DNA hypermethylation at TSSs in combination with MYC network activation

Global Comparison of Core-Collapse Supernova Simulations in Spherical Symmetry

We present a comparison between several simulation codes designed to study the core-collapse supernova mechanism. We pay close attention to controlling the initial conditions and input physics in order to ensure a meaningful and informative comparison. Our goal is three-fold. First, we aim to demonstrate the current level of agreement between various groups studying the core-collapse supernova central engine. Second, we desire to form a strong basis for future simulation codes and methods to compare to. Lastly, we want this work to be a stepping stone for future work exploring more complex simulations of core-collapse supernovae, i.e., simulations in multiple dimensions and simulations with modern neutrino and nuclear physics. We compare the early (first ~500ms after core bounce) spherically-symmetric evolution of a 20 solar mass progenitor star from six different core-collapse supernovae codes: 3DnSNe-IDSA, AGILE-BOLTZTRAN, FLASH, F{\sc{ornax}}, GR1D, and PROMETHEUS-VERTEX. Given the diversity of neutrino transport and hydrodynamic methods employed, we find excellent agreement in many critical quantities, including the shock radius evolution and the amount of neutrino heating. Our results provide an excellent starting point from which to extend this comparison to higher dimensions and compare the development of hydrodynamic instabilities that are crucial to the supernova explosion mechanism, such as turbulence and convection.Comment: 24 pages, 7 figures, J. Phys. G focus issue on core-collapse supernovae. This document was written collaboratively on Authorea, comments welcome at https://www.authorea.com/users/1943/articles/167397-global-comparison-of-core-collapse-supernova-simulations-in-spherical-symmetr

The molecular phenotype of human cardiac myosin associated with hypertrophic obstructive cardiomyopathy

AIM: The aim of the study was to compare the functional and structural properties of the motor protein, myosin, and isolated myocyte contractility in heart muscle excised from hypertrophic cardiomyopathy patients by surgical myectomy with explanted failing heart and non-failing donor heart muscle. METHODS: Myosin was isolated and studied using an in vitro motility assay. The distribution of myosin light chain-1 isoforms was measured by two-dimensional electrophoresis. Myosin light chain-2 phosphorylation was measured by sodium dodecyl sulphate-polyacrylamide gel electrophoresis using Pro-Q Diamond phosphoprotein stain. RESULTS: The fraction of actin filaments moving when powered by myectomy myosin was 21% less than with donor myosin (P = 0.006), whereas the sliding speed was not different (0.310 +/- 0.034 for myectomy myosin vs. 0.305 +/- 0.019 microm/s for donor myosin in six paired experiments). Failing heart myosin showed 18% reduced motility. One myectomy myosin sample produced a consistently higher sliding speed than donor heart myosin and was identified with a disease-causing heavy chain mutation (V606M). In myectomy myosin, the level of atrial light chain-1 relative to ventricular light chain-1 was 20 +/- 5% compared with 11 +/- 5% in donor heart myosin and the level of myosin light chain-2 phosphorylation was decreased by 30-45%. Isolated cardiomyocytes showed reduced contraction amplitude (1.61 +/- 0.25 vs. 3.58 +/- 0.40%) and reduced relaxation rates compared with donor myocytes (TT(50%) = 0.32 +/- 0.09 vs. 0.17 +/- 0.02 s). CONCLUSION: Contractility in myectomy samples resembles the hypocontractile phenotype found in end-stage failing heart muscle irrespective of the primary stimulus, and this phenotype is not a direct effect of the hypertrophy-inducing mutation. The presence of a myosin heavy chain mutation causing hypertrophic cardiomyopathy can be predicted from a simple functional assay

Publisher Correction: Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers.

The original version of this Article contained an error in the author affiliations. Trey Ideker was incorrectly associated with 'Department of Medicine (Oncology), Stanford University School of Medicine, 875 Blake Wilbur Dr, Palo Alto, CA 94304, USA.' This has now been corrected in both the PDF and HTML versions of the Article

A community-maintained standard library of population genetic models

The explosion in population genomic data demands ever more complex modes of analysis, and increasingly, these analyses depend on sophisticated simulations. Recent advances in population genetic simulation have made it possible to simulate large and complex models, but specifying such models for a particular simulation engine remains a difficult and error-prone task. Computational genetics researchers currently re-implement simulation models independently, leading to inconsistency and duplication of effort. This situation presents a major barrier to empirical researchers seeking to use simulations for power analyses of upcoming studies or sanity checks on existing genomic data. Population genetics, as a field, also lacks standard benchmarks by which new tools for inference might be measured. Here, we describe a new resource, stdpopsim, that attempts to rectify this situation. Stdpopsim is a community-driven open source project, which provides easy access to a growing catalog of published simulation models from a range of organisms and supports multiple simulation engine backends. This resource is available as a well-documented python library with a simple command-line interface. We share some examples demonstrating how stdpopsim can be used to systematically compare demographic inference methods, and we encourage a broader community of developers to contribute to this growing resource.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Nearly neutral evolution across the Drosophila melanogaster genome

Under the nearly neutral theory of molecular evolution, the proportion of effectively neutral mutations is expected to depend upon the effective population size (Ne). Here, we investigate whether this is the case across the genome of Drosophila melanogaster using polymorphism data from North American and African lines. We show that the ratio of the number of nonsynonymous and synonymous polymorphisms is negatively correlated to the number of synonymous polymorphisms, even when the nonindependence is accounted for. The relationship is such that the proportion of effectively neutral nonsynonymous mutations increases by ∼45% as Ne is halved. However, we also show that this relationship is steeper than expected from an independent estimate of the distribution of fitness effects from the site frequency spectrum. We investigate a number of potential explanations for this and show, using simulation, that this is consistent with a model of genetic hitchhiking: Genetic hitchhiking depresses diversity at neutral and weakly selected sites, but has little effect on the diversity of strongly selected sites