WorldWideScience

Sample records for density maps obtained

  1. Biometric recognition via fixation density maps

    Science.gov (United States)

    Rigas, Ioannis; Komogortsev, Oleg V.

    2014-05-01

    This work introduces and evaluates a novel eye movement-driven biometric approach that employs eye fixation density maps for person identification. The proposed feature offers a dynamic representation of the biometric identity, storing rich information regarding the behavioral and physical eye movement characteristics of the individuals. The innate ability of fixation density maps to capture the spatial layout of the eye movements in conjunction with their probabilistic nature makes them a particularly suitable option as an eye movement biometrical trait in cases when free-viewing stimuli is presented. In order to demonstrate the effectiveness of the proposed approach, the method is evaluated on three different datasets containing a wide gamut of stimuli types, such as static images, video and text segments. The obtained results indicate a minimum EER (Equal Error Rate) of 18.3 %, revealing the perspectives on the utilization of fixation density maps as an enhancing biometrical cue during identification scenarios in dynamic visual environments.

  2. Interactive density maps for moving objects

    NARCIS (Netherlands)

    Scheepens, R.J.; Willems, C.M.E.; Wetering, van de H.M.M.; Wijk, van J.J.

    2012-01-01

    Trajectories capture the movements of objects with multiple attributes. A visualization method called density maps shows trends in these trajectories. Density map creation involves aggregating smoothed trajectories in a density field and then visualizing the field. Users can explore attributes along

  3. Synthesizing chaotic maps with prescribed invariant densities

    International Nuclear Information System (INIS)

    Rogers, Alan; Shorten, Robert; Heffernan, Daniel M.

    2004-01-01

    The Inverse Frobenius-Perron Problem (IFPP) concerns the creation of discrete chaotic mappings with arbitrary invariant densities. In this Letter, we present a new and elegant solution to the IFPP, based on positive matrix theory. Our method allows chaotic maps with arbitrary piecewise-constant invariant densities, and with arbitrary mixing properties, to be synthesized

  4. Momentum density maps for molecules

    International Nuclear Information System (INIS)

    Cook, J.P.D.; Brion, C.E.

    1982-01-01

    Momentum-space and position-space molecular orbital density functions computed from LCAO-MO-SCF wavefunctions are used to rationalize the shapes of some momentum distributions measured by binary (e,2e) spectroscopy. A set of simple rules is presented which enable one to sketch the momentum density function and the momentum distribution from a knowledge of the position-space wavefunction and the properties and effects of the Fourier Transform and the spherical average. Selected molecular orbitals of H 2 , N 2 and CO 2 are used to illustrate this work

  5. Covariance and correlation estimation in electron-density maps.

    Science.gov (United States)

    Altomare, Angela; Cuocci, Corrado; Giacovazzo, Carmelo; Moliterni, Anna; Rizzi, Rosanna

    2012-03-01

    Quite recently two papers have been published [Giacovazzo & Mazzone (2011). Acta Cryst. A67, 210-218; Giacovazzo et al. (2011). Acta Cryst. A67, 368-382] which calculate the variance in any point of an electron-density map at any stage of the phasing process. The main aim of the papers was to associate a standard deviation to each pixel of the map, in order to obtain a better estimate of the map reliability. This paper deals with the covariance estimate between points of an electron-density map in any space group, centrosymmetric or non-centrosymmetric, no matter the correlation between the model and target structures. The aim is as follows: to verify if the electron density in one point of the map is amplified or depressed as an effect of the electron density in one or more other points of the map. High values of the covariances are usually connected with undesired features of the map. The phases are the primitive random variables of our probabilistic model; the covariance changes with the quality of the model and therefore with the quality of the phases. The conclusive formulas show that the covariance is also influenced by the Patterson map. Uncertainty on measurements may influence the covariance, particularly in the final stages of the structure refinement; a general formula is obtained taking into account both phase and measurement uncertainty, valid at any stage of the crystal structure solution.

  6. Spatial mapping of humeral head bone density.

    Science.gov (United States)

    Alidousti, Hamidreza; Giles, Joshua W; Emery, Roger J H; Jeffers, Jonathan

    2017-09-01

    Short-stem humeral replacements achieve fixation by anchoring to the metaphyseal trabecular bone. Fixing the implant in high-density bone can provide strong fixation and reduce the risk of loosening. However, there is a lack of data mapping the bone density distribution in the proximal humerus. The aim of the study was to investigate the bone density in proximal humerus. Eight computed tomography scans of healthy cadaveric humeri were used to map bone density distribution in the humeral head. The proximal humeral head was divided into 12 slices parallel to the humeral anatomic neck. Each slice was then divided into 4 concentric circles. The slices below the anatomic neck, where short-stem implants have their fixation features, were further divided into radial sectors. The average bone density for each of these regions was calculated, and regions of interest were compared using a repeated-measures analysis of variance with significance set at P density was found to decrease from proximal to distal regions, with the majority of higher bone density proximal to the anatomic neck of the humerus (P density increases from central to peripheral regions, where cortical bone eventually occupies the space (P density distribution in the medial calcar region was also observed. This study indicates that it is advantageous with respect to implant fixation to preserve some bone above the anatomic neck and epiphyseal plate and to use the denser bone at the periphery. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  7. Molecular surface mesh generation by filtering electron density map.

    Science.gov (United States)

    Giard, Joachim; Macq, Benoît

    2010-01-01

    Bioinformatics applied to macromolecules are now widely spread and in continuous expansion. In this context, representing external molecular surface such as the Van der Waals Surface or the Solvent Excluded Surface can be useful for several applications. We propose a fast and parameterizable algorithm giving good visual quality meshes representing molecular surfaces. It is obtained by isosurfacing a filtered electron density map. The density map is the result of the maximum of Gaussian functions placed around atom centers. This map is filtered by an ideal low-pass filter applied on the Fourier Transform of the density map. Applying the marching cubes algorithm on the inverse transform provides a mesh representation of the molecular surface.

  8. Molecular Surface Mesh Generation by Filtering Electron Density Map

    Directory of Open Access Journals (Sweden)

    Joachim Giard

    2010-01-01

    Full Text Available Bioinformatics applied to macromolecules are now widely spread and in continuous expansion. In this context, representing external molecular surface such as the Van der Waals Surface or the Solvent Excluded Surface can be useful for several applications. We propose a fast and parameterizable algorithm giving good visual quality meshes representing molecular surfaces. It is obtained by isosurfacing a filtered electron density map. The density map is the result of the maximum of Gaussian functions placed around atom centers. This map is filtered by an ideal low-pass filter applied on the Fourier Transform of the density map. Applying the marching cubes algorithm on the inverse transform provides a mesh representation of the molecular surface.

  9. Comparative study of fixation density maps

    NARCIS (Netherlands)

    Engelke, U.; Liu, H.; Wang, Junle; Callet, Le P.; Heynderickx, I.E.J.; Zepernick, H.-J.; Maeder, A.

    2013-01-01

    Fixation density maps (FDM) created from eye tracking experiments are widely used in image processing applications. The FDM are assumed to be reliable ground truths of human visual attention and as such, one expects a high similarity between FDM created in different laboratories. So far, no studies

  10. Analysis of multiplex gene expression maps obtained by voxelation.

    Science.gov (United States)

    An, Li; Xie, Hongbo; Chin, Mark H; Obradovic, Zoran; Smith, Desmond J; Megalooikonomou, Vasileios

    2009-04-29

    Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological disease. Researchers have previously used voxelation in combination with microarrays for acquisition of genome-wide atlases of expression patterns in the mouse brain. On the other hand, some work has been performed on studying gene functions, without taking into account the location information of a gene's expression in a mouse brain. In this paper, we present an approach for identifying the relation between gene expression maps obtained by voxelation and gene functions. To analyze the dataset, we chose typical genes as queries and aimed at discovering similar gene groups. Gene similarity was determined by using the wavelet features extracted from the left and right hemispheres averaged gene expression maps, and by the Euclidean distance between each pair of feature vectors. We also performed a multiple clustering approach on the gene expression maps, combined with hierarchical clustering. Among each group of similar genes and clusters, the gene function similarity was measured by calculating the average gene function distances in the gene ontology structure. By applying our methodology to find similar genes to certain target genes we were able to improve our understanding of gene expression patterns and gene functions. By applying the clustering analysis method, we obtained significant clusters, which have both very similar gene expression maps and very similar gene functions respectively to their corresponding gene ontologies. The cellular component ontology resulted in prominent clusters expressed in cortex and corpus callosum. The molecular function ontology gave prominent clusters in cortex, corpus callosum and hypothalamus. The biological process ontology resulted in clusters in cortex, hypothalamus and choroid plexus. Clusters from all three ontologies combined were most prominently expressed in cortex and corpus callosum. The experimental

  11. Analysis of multiplex gene expression maps obtained by voxelation

    Directory of Open Access Journals (Sweden)

    Smith Desmond J

    2009-04-01

    Full Text Available Abstract Background Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological disease. Researchers have previously used voxelation in combination with microarrays for acquisition of genome-wide atlases of expression patterns in the mouse brain. On the other hand, some work has been performed on studying gene functions, without taking into account the location information of a gene's expression in a mouse brain. In this paper, we present an approach for identifying the relation between gene expression maps obtained by voxelation and gene functions. Results To analyze the dataset, we chose typical genes as queries and aimed at discovering similar gene groups. Gene similarity was determined by using the wavelet features extracted from the left and right hemispheres averaged gene expression maps, and by the Euclidean distance between each pair of feature vectors. We also performed a multiple clustering approach on the gene expression maps, combined with hierarchical clustering. Among each group of similar genes and clusters, the gene function similarity was measured by calculating the average gene function distances in the gene ontology structure. By applying our methodology to find similar genes to certain target genes we were able to improve our understanding of gene expression patterns and gene functions. By applying the clustering analysis method, we obtained significant clusters, which have both very similar gene expression maps and very similar gene functions respectively to their corresponding gene ontologies. The cellular component ontology resulted in prominent clusters expressed in cortex and corpus callosum. The molecular function ontology gave prominent clusters in cortex, corpus callosum and hypothalamus. The biological process ontology resulted in clusters in cortex, hypothalamus and choroid plexus. Clusters from all three ontologies combined were most prominently expressed in

  12. Canopy Density Mapping on Ultracam-D Aerial Imagery in Zagros Woodlands, Iran

    Science.gov (United States)

    Erfanifard, Y.; Khodaee, Z.

    2013-09-01

    Canopy density maps express different characteristics of forest stands, especially in woodlands. Obtaining such maps by field measurements is so expensive and time-consuming. It seems necessary to find suitable techniques to produce these maps to be used in sustainable management of woodland ecosystems. In this research, a robust procedure was suggested to obtain these maps by very high spatial resolution aerial imagery. It was aimed to produce canopy density maps by UltraCam-D aerial imagery, newly taken in Zagros woodlands by Iran National Geographic Organization (NGO), in this study. A 30 ha plot of Persian oak (Quercus persica) coppice trees was selected in Zagros woodlands, Iran. The very high spatial resolution aerial imagery of the plot purchased from NGO, was classified by kNN technique and the tree crowns were extracted precisely. The canopy density was determined in each cell of different meshes with different sizes overlaid on the study area map. The accuracy of the final maps was investigated by the ground truth obtained by complete field measurements. The results showed that the proposed method of obtaining canopy density maps was efficient enough in the study area. The final canopy density map obtained by a mesh with 30 Ar (3000 m2) cell size had 80% overall accuracy and 0.61 KHAT coefficient of agreement which shows a great agreement with the observed samples. This method can also be tested in other case studies to reveal its capability in canopy density map production in woodlands.

  13. Functional magnetic resonance maps obtained by personal computer

    International Nuclear Information System (INIS)

    Gomez, F. j.; Manjon, J. V.; Robles, M.; Marti-Bonmati, L.; Dosda, R.; Molla, E.

    2001-01-01

    Functional magnetic resonance (fMR) is of special relevance in the analysis of certain types of brain activation. The present report describes the development of a simple software program for use with personal computers (PCs) that analyzes these images and provides functional activation maps. Activation maps are based on the temporal differences in oxyhemoglobin in tomographic images. To detect these differences, intensities registered repeatedly during brain control and activation are compared. The experiments were performed with a 1.5-Tesla MR unit. To verify the reliability of the program fMR studies were carried out in 4 healthy individuals (12 contiguous slices, 80 images per slice every 3.1 seconds for a total of 960 images). All the images were transferred to a PC and were processed pixel by pixel within each sequence to obtain an intensity/time curve. The statistical study of the results (Student's test and cross correlation analysis) made it possible to establish the activation of each pixel. The images were prepared using spatial filtering, temporal filtering, baseline correction, normalization and segmentation of the parenchyma. The postprocessing of the results involved the elimination of single pixels, superposition of an anatomical image of greater spatial resolution and anti-aliasing. The application (Xfun 1.0, Valencia, Spain) was developed in Microsoft Visual C++5.0 Developer Studio for Windows NT Workstation. As a representative example, the program took 8.2 seconds to calculate and present the results of the entire study (12 functional maps). In the motor and visual activation experiments, the activation corresponding to regions proximal to the central sulcus of the hemisphere contralateral to the hand that moved and in the occipital cortex were observed. While programs that calculate activation maps are available, the development of software for PCs running Microsoft Windows ensures several key features for its use on a daily basis: it is easy

  14. Soil map density and a nation's wealth and income

    NARCIS (Netherlands)

    Hartemink, A.E.

    2008-01-01

    Little effort has been made to link soil mapping and soil data density to a nation’s welfare. Soil map density in 31 European countries and 44 low and middle income countries is linked to Gross Domestic Product (GDP) per capita and the number of soil scientists per country.

  15. Globally optimal superconducting magnets part I: minimum stored energy (MSE) current density map.

    Science.gov (United States)

    Tieng, Quang M; Vegh, Viktor; Brereton, Ian M

    2009-01-01

    An optimal current density map is crucial in magnet design to provide the initial values within search spaces in an optimization process for determining the final coil arrangement of the magnet. A strategy for obtaining globally optimal current density maps for the purpose of designing magnets with coaxial cylindrical coils in which the stored energy is minimized within a constrained domain is outlined. The current density maps obtained utilising the proposed method suggests that peak current densities occur around the perimeter of the magnet domain, where the adjacent peaks have alternating current directions for the most compact designs. As the dimensions of the domain are increased, the current density maps yield traditional magnet designs of positive current alone. These unique current density maps are obtained by minimizing the stored magnetic energy cost function and therefore suggest magnet coil designs of minimal system energy. Current density maps are provided for a number of different domain arrangements to illustrate the flexibility of the method and the quality of the achievable designs.

  16. The frequency-domain approach for apparent density mapping

    Science.gov (United States)

    Tong, T.; Guo, L.

    2017-12-01

    Apparent density mapping is a technique to estimate density distribution in the subsurface layer from the observed gravity data. It has been widely applied for geologic mapping, tectonic study and mineral exploration for decades. Apparent density mapping usually models the density layer as a collection of vertical, juxtaposed prisms in both horizontal directions, whose top and bottom surfaces are assumed to be horizontal or variable-depth, and then inverts or deconvolves the gravity anomalies to determine the density of each prism. Conventionally, the frequency-domain approach, which assumes that both top and bottom surfaces of the layer are horizontal, is usually utilized for fast density mapping. However, such assumption is not always valid in the real world, since either the top surface or the bottom surface may be variable-depth. Here, we presented a frequency-domain approach for apparent density mapping, which permits both the top and bottom surfaces of the layer to be variable-depth. We first derived the formula for forward calculation of gravity anomalies caused by the density layer, whose top and bottom surfaces are variable-depth, and the formula for inversion of gravity anomalies for the density distribution. Then we proposed the procedure for density mapping based on both the formulas of inversion and forward calculation. We tested the approach on the synthetic data, which verified its effectiveness. We also tested the approach on the real Bouguer gravity anomalies data from the central South China. The top surface was assumed to be flat and was on the sea level, and the bottom surface was considered as the Moho surface. The result presented the crustal density distribution, which was coinciding well with the basic tectonic features in the study area.

  17. Project on comparison of structural parameters and electron density maps of oxalic acid dihydrate

    NARCIS (Netherlands)

    Coppens, Philip; Dam, J.; Harkema, Sybolt; Feil, D.

    1984-01-01

    Results obtained from four X-ray and five neutron data sets collected under a project sponsored by the Commission on Charge, Spin and Momentum Densities are analyzed by comparison of thermal parameters, positional parameters and X - N electron density maps. Three sets of theoretical calculations are

  18. Obtaining parton distribution functions from self-organizing maps

    International Nuclear Information System (INIS)

    Honkanen, H.; Liuti, S.; Loitiere, Y.C.; Brogan, D.; Reynolds, P.

    2007-01-01

    We present an alternative algorithm to global fitting procedures to construct Parton Distribution Functions parametrizations. The proposed algorithm uses Self-Organizing Maps which at variance with the standard Neural Networks, are based on competitive-learning. Self-Organizing Maps generate a non-uniform projection from a high dimensional data space onto a low dimensional one (usually 1 or 2 dimensions) by clustering similar PDF representations together. The SOMs are trained on progressively narrower selections of data samples. The selection criterion is that of convergence towards a neighborhood of the experimental data. All available data sets on deep inelastic scattering in the kinematical region of 0.001 ≤ x ≤ 0.75, and 1 ≤ Q 2 ≤ 100 GeV 2 , with a cut on the final state invariant mass, W 2 ≥ 10 GeV 2 were implemented. The proposed fitting procedure, at variance with standard neural network approaches, allows for an increased control of the systematic bias by enabling the user to directly control the data selection procedure at various stages of the process. (author)

  19. Wild boar mapping using population-density statistics: From polygons to high resolution raster maps.

    Science.gov (United States)

    Pittiglio, Claudia; Khomenko, Sergei; Beltran-Alcrudo, Daniel

    2018-01-01

    The wild boar is an important crop raider as well as a reservoir and agent of spread of swine diseases. Due to increasing densities and expanding ranges worldwide, the related economic losses in livestock and agricultural sectors are significant and on the rise. Its management and control would strongly benefit from accurate and detailed spatial information on species distribution and abundance, which are often available only for small areas. Data are commonly available at aggregated administrative units with little or no information about the distribution of the species within the unit. In this paper, a four-step geostatistical downscaling approach is presented and used to disaggregate wild boar population density statistics from administrative units of different shape and size (polygons) to 5 km resolution raster maps by incorporating auxiliary fine scale environmental variables. 1) First a stratification method was used to define homogeneous bioclimatic regions for the analysis; 2) Under a geostatistical framework, the wild boar densities at administrative units, i.e. subnational areas, were decomposed into trend and residual components for each bioclimatic region. Quantitative relationships between wild boar data and environmental variables were estimated through multiple regression and used to derive trend components at 5 km spatial resolution. Next, the residual components (i.e., the differences between the trend components and the original wild boar data at administrative units) were downscaled at 5 km resolution using area-to-point kriging. The trend and residual components obtained at 5 km resolution were finally added to generate fine scale wild boar estimates for each bioclimatic region. 3) These maps were then mosaicked to produce a final output map of predicted wild boar densities across most of Eurasia. 4) Model accuracy was assessed at each different step using input as well as independent data. We discuss advantages and limits of the method and its

  20. Landslides density map of S. Miguel Island, Azores archipelago

    Science.gov (United States)

    Valadão, P.; Gaspar, J. L.; Queiroz, G.; Ferreira, T.

    The Azores archipelago is located in the Atlantic Ocean and is composed of nine volcanic islands. S. Miguel, the largest one, is formed by three active, E-W trending, trachytic central volcanoes with caldera (Sete Cidades, Fogo and Furnas). Chains of basaltic cinder cones link those major volcanic structures. An inactive trachytic central volcano (Povoação) and an old basaltic volcanic complex (Nordeste) comprise the easternmost part of the island. Since the settlement of the island early in the 15th century, several destructive landslides triggered by catastrophic rainfall episodes, earthquakes and volcanic eruptions occurred in different areas of S. Miguel. One unique event killed thousands of people in 1522. Houses and bridges were destroyed, roads were cut, communications, water and energy supply systems became frequently disrupted and areas of fertile land were often buried by mud. Based on (1) historical documents, (2) aerial photographs and (3) field observations, landslide sites were plotted on a topographic map, in order to establish a landslide density map for the island. Data obtained showed that landslide hazard is higher on (1) the main central volcanoes where the thickness of unconsolidated pyroclastic deposits is considerable high and (2) the old basaltic volcanic complex, marked by deep gullies developed on thick sequences of lava flows. In these areas, caldera walls, fault scarps, steep valley margins and sea cliffs are potentially hazardous.

  1. Land use, forest density, soil mapping, erosion, drainage, salinity limitations

    Science.gov (United States)

    Yassoglou, N. J. (Principal Investigator)

    1973-01-01

    The author has identified the following significant results. The results of analyses show that it is possible to obtain information of practical significance as follows: (1) A quick and accurate estimate of the proper use of the valuable land can be made on the basis of temporal and spectral characteristics of the land features. (2) A rather accurate delineation of the major forest formations in the test areas was achieved on the basis of spatial and spectral characteristics of the studied areas. The forest stands were separated into two density classes; dense forest, and broken forest. On the basis of ERTS-1 data and the existing ground truth information a rather accurate mapping of the major vegetational forms of the mountain ranges can be made. (3) Major soil formations are mapable from ERTS-1 data: recent alluvial soils; soil on quarternary deposits; severely eroded soil and lithosol; and wet soils. (4) An estimation of cost benefits cannot be made accurately at this stage of the investigation. However, a rough estimate of the ratio of the cost for obtaining the same amount information from ERTS-1 data and from conventional operations would be approximately 1:6 to 1:10, in favor of the ERTS-1.

  2. Quantitative X-ray mapping, scatter diagrams and the generation of correction maps to obtain more information about your material

    Science.gov (United States)

    Wuhrer, R.; Moran, K.

    2014-03-01

    Quantitative X-ray mapping with silicon drift detectors and multi-EDS detector systems have become an invaluable analysis technique and one of the most useful methods of X-ray microanalysis today. The time to perform an X-ray map has reduced considerably with the ability to map minor and trace elements very accurately due to the larger detector area and higher count rate detectors. Live X-ray imaging can now be performed with a significant amount of data collected in a matter of minutes. A great deal of information can be obtained from X-ray maps. This includes; elemental relationship or scatter diagram creation, elemental ratio mapping, chemical phase mapping (CPM) and quantitative X-ray maps. In obtaining quantitative x-ray maps, we are able to easily generate atomic number (Z), absorption (A), fluorescence (F), theoretical back scatter coefficient (η), and quantitative total maps from each pixel in the image. This allows us to generate an image corresponding to each factor (for each element present). These images allow the user to predict and verify where they are likely to have problems in our images, and are especially helpful to look at possible interface artefacts. The post-processing techniques to improve the quantitation of X-ray map data and the development of post processing techniques for improved characterisation are covered in this paper.

  3. Quantitative X-ray mapping, scatter diagrams and the generation of correction maps to obtain more information about your material

    International Nuclear Information System (INIS)

    Wuhrer, R; Moran, K

    2014-01-01

    Quantitative X-ray mapping with silicon drift detectors and multi-EDS detector systems have become an invaluable analysis technique and one of the most useful methods of X-ray microanalysis today. The time to perform an X-ray map has reduced considerably with the ability to map minor and trace elements very accurately due to the larger detector area and higher count rate detectors. Live X-ray imaging can now be performed with a significant amount of data collected in a matter of minutes. A great deal of information can be obtained from X-ray maps. This includes; elemental relationship or scatter diagram creation, elemental ratio mapping, chemical phase mapping (CPM) and quantitative X-ray maps. In obtaining quantitative x-ray maps, we are able to easily generate atomic number (Z), absorption (A), fluorescence (F), theoretical back scatter coefficient (η), and quantitative total maps from each pixel in the image. This allows us to generate an image corresponding to each factor (for each element present). These images allow the user to predict and verify where they are likely to have problems in our images, and are especially helpful to look at possible interface artefacts. The post-processing techniques to improve the quantitation of X-ray map data and the development of post processing techniques for improved characterisation are covered in this paper

  4. Ligand identification using electron-density map correlations

    International Nuclear Information System (INIS)

    Terwilliger, Thomas C.; Adams, Paul D.; Moriarty, Nigel W.; Cohn, Judith D.

    2007-01-01

    An automated ligand-fitting procedure is applied to (F o − F c )exp(iϕ c ) difference density for 200 commonly found ligands from macromolecular structures in the Protein Data Bank to identify ligands from density maps. A procedure for the identification of ligands bound in crystal structures of macromolecules is described. Two characteristics of the density corresponding to a ligand are used in the identification procedure. One is the correlation of the ligand density with each of a set of test ligands after optimization of the fit of that ligand to the density. The other is the correlation of a fingerprint of the density with the fingerprint of model density for each possible ligand. The fingerprints consist of an ordered list of correlations of each the test ligands with the density. The two characteristics are scored using a Z-score approach in which the correlations are normalized to the mean and standard deviation of correlations found for a variety of mismatched ligand-density pairs, so that the Z scores are related to the probability of observing a particular value of the correlation by chance. The procedure was tested with a set of 200 of the most commonly found ligands in the Protein Data Bank, collectively representing 57% of all ligands in the Protein Data Bank. Using a combination of these two characteristics of ligand density, ranked lists of ligand identifications were made for representative (F o − F c )exp(iϕ c ) difference density from entries in the Protein Data Bank. In 48% of the 200 cases, the correct ligand was at the top of the ranked list of ligands. This approach may be useful in identification of unknown ligands in new macromolecular structures as well as in the identification of which ligands in a mixture have bound to a macromolecule

  5. Local thermodynamic mapping for effective liquid density-functional theory

    Science.gov (United States)

    Kyrlidis, Agathagelos; Brown, Robert A.

    1992-01-01

    The structural-mapping approximation introduced by Lutsko and Baus (1990) in the generalized effective-liquid approximation is extended to include a local thermodynamic mapping based on a spatially dependent effective density for approximating the solid phase in terms of the uniform liquid. This latter approximation, called the local generalized effective-liquid approximation (LGELA) yields excellent predictions for the free energy of hard-sphere solids and for the conditions of coexistence of a hard-sphere fcc solid with a liquid. Moreover, the predicted free energy remains single valued for calculations with more loosely packed crystalline structures, such as the diamond lattice. The spatial dependence of the weighted density makes the LGELA useful in the study of inhomogeneous solids.

  6. Density equalizing map projections (cartograms) in public health applications

    Energy Technology Data Exchange (ETDEWEB)

    Merrill, D.W.

    1998-05-01

    In studying geographic disease distributions, one normally compares rates among arbitrarily defined geographic subareas (e.g. census tracts), thereby sacrificing some of the geographic detail of the original data. The sparser the data, the larger the subareas must be in order to calculate stable rates. This dilemma is avoided with the technique of Density Equalizing Map Projections (DEMP){copyright}. Boundaries of geographic subregions are adjusted to equalize population density over the entire study area. Case locations plotted on the transformed map should have a uniform distribution if the underlying disease risk is constant. On the transformed map, the statistical analysis of the observed distribution is greatly simplified. Even for sparse distributions, the statistical significance of a supposed disease cluster can be calculated with validity. The DEMP algorithm was applied to a data set previously analyzed with conventional techniques; namely, 401 childhood cancer cases in four counties of California. The distribution of cases on the transformed map was analyzed visually and statistically. To check the validity of the method, the identical analysis was performed on 401 artificial cases randomly generated under the assumption of uniform risk. No statistically significant evidence for geographic non-uniformity of rates was found, in agreement with the original analysis performed by the California Department of Health Services.

  7. Geometrically necessary dislocation densities in olivine obtained using high-angular resolution electron backscatter diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Wallis, David, E-mail: davidwa@earth.ox.ac.uk [Department of Earth Sciences, University of Oxford, South Parks Road, Oxford, Oxfordshire, OX1 3AN (United Kingdom); Hansen, Lars N. [Department of Earth Sciences, University of Oxford, South Parks Road, Oxford, Oxfordshire, OX1 3AN (United Kingdom); Ben Britton, T. [Department of Materials, Imperial College London, Royal School of Mines, Exhibition Road, London SW7 2AZ (United Kingdom); Wilkinson, Angus J. [Department of Materials, University of Oxford, Parks Road, Oxford, Oxfordshire, OX1 3PH (United Kingdom)

    2016-09-15

    Dislocations in geological minerals are fundamental to the creep processes that control large-scale geodynamic phenomena. However, techniques to quantify their densities, distributions, and types over critical subgrain to polycrystal length scales are limited. The recent advent of high-angular resolution electron backscatter diffraction (HR-EBSD), based on diffraction pattern cross-correlation, offers a powerful new approach that has been utilised to analyse dislocation densities in the materials sciences. In particular, HR-EBSD yields significantly better angular resolution (<0.01°) than conventional EBSD (~0.5°), allowing very low dislocation densities to be analysed. We develop the application of HR-EBSD to olivine, the dominant mineral in Earth's upper mantle by testing (1) different inversion methods for estimating geometrically necessary dislocation (GND) densities, (2) the sensitivity of the method under a range of data acquisition settings, and (3) the ability of the technique to resolve a variety of olivine dislocation structures. The relatively low crystal symmetry (orthorhombic) and few slip systems in olivine result in well constrained GND density estimates. The GND density noise floor is inversely proportional to map step size, such that datasets can be optimised for analysing either short wavelength, high density structures (e.g. subgrain boundaries) or long wavelength, low amplitude orientation gradients. Comparison to conventional images of decorated dislocations demonstrates that HR-EBSD can characterise the dislocation distribution and reveal additional structure not captured by the decoration technique. HR-EBSD therefore provides a highly effective method for analysing dislocations in olivine and determining their role in accommodating macroscopic deformation. - Highlights: • Lattice orientation gradients in olivine were measured using HR-EBSD. • The limited number of olivine slip systems enable simple least squares inversion for GND

  8. Density equalizing mapping of the global tuberculosis research architecture.

    Science.gov (United States)

    Groneberg, David A; Weber, Esther; Gerber, Alexander; Fischer, Axel; Klingelhoefer, Doris; Brueggmann, Doerthe

    2015-07-01

    Tuberculosis belongs to the lung infectious diseases with the highest impact on global burden of disease. Yet there is no concise scientometric study about tuberculosis research. Therefore, the NewQiS project elected this subject as focus of an in depth analysis to perform density equalizing mapping in combination with scientometrics. In this retrospective study all publications related to tuberculosis research listed in the Web of Science database between 1900 and 2012 were identified, analyzed and submitted to density equalizing mapping procedures. In total 58,319 entries on TBC were identified with the USA being the most productive country with 11,788 publications, followed by the United Kingdom (4202), India (3456), France (2541), South Africa (1840), Germany (1747) and China (1427). Concerning the citations rate Denmark leads with 43.7 citations per article, followed by Latvia (39.1), Gambia (38.3), Senegal (34.9), and the Netherlands (31.4). Chart techniques demonstrates a widely ramified international network with a focus the joint work of USA, the UK and South Africa. This is the first density equalizing and scientometric study that addresses tuberculosis research over a period of 112 years. It illustrates global tuberculosis research architecture and stresses the need for strengthening global research efforts and funding program. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  9. A facile method to compare EFTEM maps obtained from materials changing composition over time

    KAUST Repository

    Casu, Alberto

    2015-10-31

    Energy Filtered Transmission Electron Microscopy (EFTEM) is an analytical tool that has been successfully and widely employed in the last two decades for obtaining fast elemental maps in TEM mode. Several studies and efforts have been addressed to investigate limitations and advantages of such technique, as well as to improve the spatial resolution of compositional maps. Usually, EFTEM maps undergo post-acquisition treatments by changing brightness and contrast levels, either via dedicated software or via human elaboration, in order to maximize their signal-to-noise ratio and render them as visible as possible. However, elemental maps forming a single set of EFTEM images are usually subjected to independent map-by-map image treatment. This post-acquisition step becomes crucial when analyzing materials that change composition over time as a consequence of an external stimulus, because the map-by-map approach doesn\\'t take into account how the chemical features of the imaged materials actually progress, in particular when the investigated elements exhibit very low signals. In this article, we present a facile procedure applicable to whole sets of EFTEM maps acquired on a sample that is evolving over time. The main aim is to find a common method to treat the images features, in order to make them as comparable as possible without affecting the information there contained. Microsc. Res. Tech. 78:1090–1097, 2015. © 2015 Wiley Periodicals, Inc.

  10. A facile method to compare EFTEM maps obtained from materials changing composition over time

    KAUST Repository

    Casu, Alberto; Genovese, Alessandro; Di Benedetto, Cristiano; Lentijo Mozo, Sergio; Sogne, Elisa; Zuddas, Efisio; Falqui, Andrea

    2015-01-01

    Energy Filtered Transmission Electron Microscopy (EFTEM) is an analytical tool that has been successfully and widely employed in the last two decades for obtaining fast elemental maps in TEM mode. Several studies and efforts have been addressed to investigate limitations and advantages of such technique, as well as to improve the spatial resolution of compositional maps. Usually, EFTEM maps undergo post-acquisition treatments by changing brightness and contrast levels, either via dedicated software or via human elaboration, in order to maximize their signal-to-noise ratio and render them as visible as possible. However, elemental maps forming a single set of EFTEM images are usually subjected to independent map-by-map image treatment. This post-acquisition step becomes crucial when analyzing materials that change composition over time as a consequence of an external stimulus, because the map-by-map approach doesn't take into account how the chemical features of the imaged materials actually progress, in particular when the investigated elements exhibit very low signals. In this article, we present a facile procedure applicable to whole sets of EFTEM maps acquired on a sample that is evolving over time. The main aim is to find a common method to treat the images features, in order to make them as comparable as possible without affecting the information there contained. Microsc. Res. Tech. 78:1090–1097, 2015. © 2015 Wiley Periodicals, Inc.

  11. Field mapping measurements to determine spatial and field dependence of critical current density in YBCO tapes

    International Nuclear Information System (INIS)

    Leclerc, J.; Berger, K.; Douine, B.; Lévêque, J.

    2013-01-01

    Highlights: • A method for characterizing superconducting tapes from field mapping is presented. • A new and efficient field mapping apparatus has been setup. • This method allows the spatial characterization of superconducting tapes. • The critical current density is obtained as a function of the flux density. • This method has been experimentally tested on an YBCO tape. -- Abstract: In this paper a measurement method that allows the determination of the critical current density of superconducting tape from field mapping measurements is presented. This contact-free method allows obtaining characteristics of the superconductor as a function of the position and of the applied flux density. With some modifications, this technique can be used for reel-to-reel measurements. The determination of the critical current density is based on an inverse calculation. This involves calculating the current distribution in the tape from magnetic measurements. An YBaCuO tape has been characterized at 77 K. A defect in this superconductor has been identified. Various tests were carried out to check the efficiency of the method. The inverse calculation was tested theoretically and experimentally. Comparison with a transport current measurement was also performed

  12. Topology in Synthetic Column Density Maps for Interstellar Turbulence

    Science.gov (United States)

    Putko, Joseph; Burkhart, B. K.; Lazarian, A.

    2013-01-01

    We show how the topology tool known as the genus statistic can be utilized to characterize magnetohydrodyanmic (MHD) turbulence in the ISM. The genus is measured with respect to a given density threshold and varying the threshold produces a genus curve, which can suggest an overall ‘‘meatball,’’ neutral, or ‘‘Swiss cheese’’ topology through its integral. We use synthetic column density maps made from three-dimensional 5123 compressible MHD isothermal simulations performed for different sonic and Alfvénic Mach numbers (Ms and MA respectively). We study eight different Ms values each with one sub- and one super-Alfvénic counterpart. We consider sight-lines both parallel (x) and perpendicular (y and z) to the mean magnetic field. We find that the genus integral shows a dependence on both Mach numbers, and this is still the case even after adding beam smoothing and Gaussian noise to the maps to mimic observational data. The genus integral increases with higher Ms values (but saturates after about Ms = 4) for all lines of sight. This is consistent with greater values of Ms resulting in stronger shocks, which results in a clumpier topology. We observe a larger genus integral for the sub-Alfvénic cases along the perpendicular lines of sight due to increased compression from the field lines and enhanced anisotropy. Application of the genus integral to column density maps should allow astronomers to infer the Mach numbers and thus learn about the environments of interstellar turbulence. This work was supported by the National Science Foundation’s REU program through NSF Award AST-1004881.

  13. A Bone Sample Containing a Bone Graft Substitute Analyzed by Correlating Density Information Obtained by X-ray Micro Tomography with Compositional Information Obtained by Raman Microscopy

    Directory of Open Access Journals (Sweden)

    Johann Charwat-Pessler

    2015-06-01

    Full Text Available The ability of bone graft substitutes to promote new bone formation has been increasingly used in the medical field to repair skeletal defects or to replace missing bone in a broad range of applications in dentistry and orthopedics. A common way to assess such materials is via micro computed tomography (µ-CT, through the density information content provided by the absorption of X-rays. Information on the chemical composition of a material can be obtained via Raman spectroscopy. By investigating a bone sample from miniature pigs containing the bone graft substitute Bio Oss®, we pursued the target of assessing to what extent the density information gained by µ-CT imaging matches the chemical information content provided by Raman spectroscopic imaging. Raman images and Raman correlation maps of the investigated sample were used in order to generate a Raman based segmented image by means of an agglomerative, hierarchical cluster analysis. The resulting segments, showing chemically related areas, were subsequently compared with the µ-CT image by means of a one-way ANOVA. We found out that to a certain extent typical gray-level values (and the related histograms in the µ-CT image can be reliably related to specific segments within the image resulting from the cluster analysis.

  14. Densities mixture unfolding for data obtained from detectors with finite resolution and limited acceptance

    Energy Technology Data Exchange (ETDEWEB)

    Gagunashvili, N.D., E-mail: nikolai@unak.is

    2015-04-01

    A procedure based on a Mixture Density Model for correcting experimental data for distortions due to finite resolution and limited detector acceptance is presented. Addressing the case that the solution is known to be non-negative, in the approach presented here, the true distribution is estimated by a weighted sum of probability density functions with positive weights and with the width of the densities acting as a regularization parameter responsible for the smoothness of the result. To obtain better smoothing in less populated regions, the width parameter is chosen inversely proportional to the square root of the estimated density. Furthermore, the non-negative garrote method is used to find the most economic representation of the solution. Cross-validation is employed to determine the optimal values of the resolution and garrote parameters. The proposed approach is directly applicable to multidimensional problems. Numerical examples in one and two dimensions are presented to illustrate the procedure.

  15. Process for obtaining sintered conglomerates with a high density of rare earth oxides and actinides

    International Nuclear Information System (INIS)

    Pasto, A.E.

    1974-01-01

    The invention concerns a method to produce agglomerates of actinide and rare earth oxides possessing a cubic-monoclinic transformation in order to obtain high densities close to the theoretical density, and the articles produced by the method. The process is based on the use of a rare earth or actinide oxide, in particular Eu 2 O 3 , with a cubic-monoclinic phase transformation, the oxide being sintered by hot compression at a temperature 50 deg C to 100 deg C above the transformation temperature. The sintered agglomerates obtained can have a purity of at least 99.9% and a density of practically 100%. These agglomerates are suitable in particular for the formation of nuclear reactor control rods [fr

  16. Effect of electrolysis parameters on the morphologies of copper powder obtained at high current densities

    Directory of Open Access Journals (Sweden)

    Orhan Gökhan

    2012-01-01

    Full Text Available The effects of copper ion concentrations and electrolyte temperature on the morphologies and on the apparent densities of electrolytic copper powders at high current densities under galvanostatic regime were examined. These parameters were evaluated by the current efficiency of hydrogen evolution. In addition, scanning electron microscopy was used for analyzing the morphology of the copper powders. It was found that the morphology was dependent over the copper ion concentration and electrolyte temperature under same current density (CD conditions. At 150 mA cm-2 and the potential of 1000±20 mV (vs. SCE, porous and disperse copper powders were obtained at low concentrations of Cu ions (0.120 M Cu2+ in 0.50 M H2SO4. Under this condition, high rate of hydrogen evolution reaction took place parallel to copper electrodeposition. The morphology was changed from porous, disperse and cauliflower-like to coral-like, shrub-like and stalk-stock like morphology with the increasing of Cu ion concentrations towards 0.120 M, 0.155 M, 0.315 M, 0.475 M and 0.630 M Cu2+ in 0.5 M H2SO4 respectively at the same CD. Similarly, as the temperature was increased, powder morphology and apparent density were observed to be changed. The apparent density values of copper powders were found to be suitable for many of the powder metallurgy applications.

  17. Mapping wood density globally using remote sensing and climatological data

    Science.gov (United States)

    Moreno, A.; Camps-Valls, G.; Carvalhais, N.; Kattge, J.; Robinson, N.; Reichstein, M.; Allred, B. W.; Running, S. W.

    2017-12-01

    Wood density (WD) is defined as the oven-dry mass divided by fresh volume, varies between individuals, and describes the carbon investment per unit volume of stem. WD has been proven to be a key functional trait in carbon cycle research and correlates with numerous morphological, mechanical, physiological, and ecological properties. In spite of the utility and importance of this trait, there is a lack of an operational framework to spatialize plant WD measurements at a global scale. In this work, we present a consistent modular processing chain to derive global maps (500 m) of WD using modern machine learning techniques along with optical remote sensing data (MODIS/Landsat) and climate data using the Google Earth Engine platform. The developed approach uses a hierarchical Bayesian approach to fill in gaps in the plant measured WD data set to maximize its global representativeness. WD plant species are then aggregated to Plant Functional Types (PFT). The spatial abundance of PFT at 500 m spatial resolution (MODIS) is calculated using a high resolution (30 m) PFT map developed using Landsat data. Based on these PFT abundances, representative WD values are estimated for each MODIS pixel with nearby measured data. Finally, random forests are used to globally estimate WD from these MODIS pixels using remote sensing and climate. The validation and assessment of the applied methods indicate that the model explains more than 72% of the spatial variance of the calculated community aggregated WD estimates with virtually unbiased estimates and low RMSE (<15%). The maps thus offer new opportunities to study and analyze the global patterns of variation of WD at an unprecedented spatial coverage and spatial resolution.

  18. Automatically Generated Vegetation Density Maps with LiDAR Survey for Orienteering Purpose

    Science.gov (United States)

    Petrovič, Dušan

    2018-05-01

    The focus of our research was to automatically generate the most adequate vegetation density maps for orienteering purpose. Application Karttapullatuin was used for automated generation of vegetation density maps, which requires LiDAR data to process an automatically generated map. A part of the orienteering map in the area of Kazlje-Tomaj was used to compare the graphical display of vegetation density. With different settings of parameters in the Karttapullautin application we changed the way how vegetation density of automatically generated map was presented, and tried to match it as much as possible with the orienteering map of Kazlje-Tomaj. Comparing more created maps of vegetation density the most suitable parameter settings to automatically generate maps on other areas were proposed, too.

  19. Aerial photos for obtaining information on vegetation in areas of high population densities

    Energy Technology Data Exchange (ETDEWEB)

    Kenneweg, H

    1975-01-01

    An air pollution survey was conducted which includes a description of an inventory of Freiburg's roadside trees with the aid of infrared aerial photos, supported by a register of trees by species. Results were mapped by street averages of injury and analyses by species susceptibility and stress factors. Building and traffic density were used as stress indicators presumed to be correlated with others such as road salting or other disturbances. In a ranking based on these factors Tilia sp. was the most and Robinia pseudoacacia the least susceptible, with Aesculus, Acer, Platanus and Crataegus spp. intermediate in descending order of susceptibility. A second survey a year later showed deterioration in most parts of the town, but some improvement was observed in the central Rathausplatz, where traffic had been excluded, salting had been stopped, and certain tree amelioration measures were being tried. Other topics discussed include surveys of total green vegetation in cities and the mapping of air pollution risks near heavily industrialized areas. In a study of 1600 spruce stands near the Ruhr region, no simple correlations with topographic factors were found, though the worst damage was frequently noticed in narrow valleys and near reservoirs.

  20. Patterned growth of carbon nanotubes obtained by high density plasma chemical vapor deposition

    Science.gov (United States)

    Mousinho, A. P.; Mansano, R. D.

    2015-03-01

    Patterned growth of carbon nanotubes by chemical vapor deposition represents an assembly approach to place and orient nanotubes at a stage as early as when they are synthesized. In this work, the carbon nanotubes were obtained at room temperature by High Density Plasmas Chemical Vapor Deposition (HDPCVD) system. This CVD system uses a new concept of plasma generation, where a planar coil coupled to an RF system for plasma generation was used with an electrostatic shield for plasma densification. In this mode, high density plasmas are obtained. We also report the patterned growth of carbon nanotubes on full 4-in Si wafers, using pure methane plasmas and iron as precursor material (seed). Photolithography processes were used to pattern the regions on the silicon wafers. The carbon nanotubes were characterized by micro-Raman spectroscopy, the spectra showed very single-walled carbon nanotubes axial vibration modes around 1590 cm-1 and radial breathing modes (RBM) around 120-400 cm-1, confirming that high quality of the carbon nanotubes obtained in this work. The carbon nanotubes were analyzed by atomic force microscopy and scanning electron microscopy too. The results showed that is possible obtain high-aligned carbon nanotubes with patterned growth on a silicon wafer with high reproducibility and control.

  1. Study of Chromium Multilayers Properties Obtained by Pulsed Current Density: Residual Stress and Microhardness

    Directory of Open Access Journals (Sweden)

    Julieta TORRES-GONZÁLEZ

    2010-12-01

    Full Text Available Chromium multilayers deposits were obtained from three different bath solutions, they were prepared by switching current density between 10 and 70 Adm-2. Two temperatures were studied, 35°C and 55°C. At 35°C two different microstructures are alternated: columnar obtained at 10 Adm-2 and equiaxial obtained at 70 Adm-2. At 55°C only the columnar type microstructure is present, at 10 and 70 Adm-2, the only difference among the layers is a slight disorientation of grains. The properties of these chromium multilayers were characterized by scanning electron microscopy (SEM and X-ray diffraction (XRD. In general the deposits are microcracked with a high microhardness, high residual stress and a small grain size.

  2. Rapid model building of beta-sheets in electron-density maps.

    Science.gov (United States)

    Terwilliger, Thomas C

    2010-03-01

    A method for rapidly building beta-sheets into electron-density maps is presented. beta-Strands are identified as tubes of high density adjacent to and nearly parallel to other tubes of density. The alignment and direction of each strand are identified from the pattern of high density corresponding to carbonyl and C(beta) atoms along the strand averaged over all repeats present in the strand. The beta-strands obtained are then assembled into a single atomic model of the beta-sheet regions. The method was tested on a set of 42 experimental electron-density maps at resolutions ranging from 1.5 to 3.8 A. The beta-sheet regions were nearly completely built in all but two cases, the exceptions being one structure at 2.5 A resolution in which a third of the residues in beta-sheets were built and a structure at 3.8 A in which under 10% were built. The overall average r.m.s.d. of main-chain atoms in the residues built using this method compared with refined models of the structures was 1.5 A.

  3. Reliability of different sampling densities for estimating and mapping lichen diversity in biomonitoring studies

    International Nuclear Information System (INIS)

    Ferretti, M.; Brambilla, E.; Brunialti, G.; Fornasier, F.; Mazzali, C.; Giordani, P.; Nimis, P.L.

    2004-01-01

    Sampling requirements related to lichen biomonitoring include optimal sampling density for obtaining precise and unbiased estimates of population parameters and maps of known reliability. Two available datasets on a sub-national scale in Italy were used to determine a cost-effective sampling density to be adopted in medium-to-large-scale biomonitoring studies. As expected, the relative error in the mean Lichen Biodiversity (Italian acronym: BL) values and the error associated with the interpolation of BL values for (unmeasured) grid cells increased as the sampling density decreased. However, the increase in size of the error was not linear and even a considerable reduction (up to 50%) in the original sampling effort led to a far smaller increase in errors in the mean estimates (<6%) and in mapping (<18%) as compared with the original sampling densities. A reduction in the sampling effort can result in considerable savings of resources, which can then be used for a more detailed investigation of potentially problematic areas. It is, however, necessary to decide the acceptable level of precision at the design stage of the investigation, so as to select the proper sampling density. - An acceptable level of precision must be decided before determining a sampling design

  4. Portable cosmic particle detectors for subsurface density mapping

    Science.gov (United States)

    Oláh, László; Gábor Barnaföldi, Gergely; Hamar, Gergö; Surányi, Gergely; Varga, Dezsö

    2016-04-01

    Muography deduces the density length in the interior of the investigated geological object, such as a mountain or volcano by the measurement of the cosmic muon absorption along different paths through the object. If path lengths (average densities) are measured, the average density (path length) can be deduced along the muon paths. A portable, low power consumption cosmic particle tracking detector based on Close Cathode multi-wire proportional chambers [1,2] has been developed for muography based on our earlier developments and experiences at the Wigner RCP of the HAS in Budapest [3,4,5]. The newly developed tracking system consists of six layers with the sensitive area of 0.25 m2 [6]. The spatial resolution of 2 mm provides an angular resolution of 15 mrad. This instrument has been optimized for underground and outdoor measurements: it has a Raspberry pi controlled data acquisition system which includes a custom designed board with a coincidence unit and allows high level remote control, data management and analysis. The individual trigger signals, number of missed triggers, analogue signals from chambers and the temperature are recorded. The duration of data readout (dead time) is 100 microsec. The DAQ software runs on the Raspberry Pi. For standard operation, a graphical user interface has been developed, running on any remote computer with Internet connection (both of wired and wireless) to the Raspberry Pi. A temperature-controlled high-voltage power supply provides a stable and reasonable (> 95 %) tracking performance for the measurements. With total power consumption of 5W, a portable tracking detector can operate for 5 days with a standard 50 Ah battery and with gas (non flammable Ar-CO2 mixture) consumption of 0.5 liter per hour, a 10 l bottle at pressure of 150 bar is enough for four month. The portability (total weight of less than 30 kg) allowed that our tracking detectors have been applied in underground caverns for subsurface density mapping. The

  5. Obtaining macroscopic quantities for the contact line problem from Density Functional Theory using asymptotic methods

    Science.gov (United States)

    Sibley, David; Nold, Andreas; Kalliadasis, Serafim

    2015-11-01

    Density Functional Theory (DFT), a statistical mechanics of fluids approach, captures microscopic details of the fluid density structure in the vicinity of contact lines, as seen in computations in our recent study. Contact lines describe the location where interfaces between two fluids meet solid substrates, and have stimulated a wealth of research due to both their ubiquity in nature and technological applications and also due to their rich multiscale behaviour. Whilst progress can be made computationally to capture the microscopic to mesoscopic structure from DFT, complete analytical results to fully bridge to the macroscale are lacking. In this work, we describe our efforts to bring asymptotic methods to DFT to obtain results for contact angles and other macroscopic quantities in various parameter regimes. We acknowledge financial support from European Research Council via Advanced Grant No. 247031.

  6. Obtaining raised density connections by thermosonic microwelding in 3D integrated microcircuits

    Directory of Open Access Journals (Sweden)

    Lanin V. L.

    2014-06-01

    Full Text Available The authors consider the processes of obtaining raised density microwelded connections in 3D-integrated microcircuits by the thermosonic microwelding. The processes include the use of the raised frequencies of ultrasound, application of the microinstrument with a thinning of the working end and precision devices for ball formation, which provide reproducibility of connections quality. At a small step of contact pads, the use of a wire of small diameter (not more than 25 µm is necessary for devices with a multilevel arrangement of leads and chess arrangement of contact pads on the chip, providing the maximum length of the formed crosspieces does not exceed 4—5 mm.

  7. Mapping Mangrove Density from Rapideye Data in Central America

    Science.gov (United States)

    Son, Nguyen-Thanh; Chen, Chi-Farn; Chen, Cheng-Ru

    2017-06-01

    Mangrove forests provide a wide range of socioeconomic and ecological services for coastal communities. Extensive aquaculture development of mangrove waters in many developing countries has constantly ignored services of mangrove ecosystems, leading to unintended environmental consequences. Monitoring the current status and distribution of mangrove forests is deemed important for evaluating forest management strategies. This study aims to delineate the density distribution of mangrove forests in the Gulf of Fonseca, Central America with Rapideye data using the support vector machines (SVM). The data collected in 2012 for density classification of mangrove forests were processed based on four different band combination schemes: scheme-1 (bands 1-3, 5 excluding the red-edge band 4), scheme-2 (bands 1-5), scheme-3 (bands 1-3, 5 incorporating with the normalized difference vegetation index, NDVI), and scheme-4 (bands 1-3, 5 incorporating with the normalized difference red-edge index, NDRI). We also hypothesized if the obvious contribution of Rapideye red-edge band could improve the classification results. Three main steps of data processing were employed: (1), data pre-processing, (2) image classification, and (3) accuracy assessment to evaluate the contribution of red-edge band in terms of the accuracy of classification results across these four schemes. The classification maps compared with the ground reference data indicated the slightly higher accuracy level observed for schemes 2 and 4. The overall accuracies and Kappa coefficients were 97% and 0.95 for scheme-2 and 96.9% and 0.95 for scheme-4, respectively.

  8. High-density surface EMG maps from upper-arm and forearm muscles

    Directory of Open Access Journals (Sweden)

    Rojas-Martínez Monica

    2012-12-01

    Full Text Available Abstract Background sEMG signal has been widely used in different applications in kinesiology and rehabilitation as well as in the control of human-machine interfaces. In general, the signals are recorded with bipolar electrodes located in different muscles. However, such configuration may disregard some aspects of the spatial distribution of the potentials like location of innervation zones and the manifestation of inhomogineties in the control of the muscular fibers. On the other hand, the spatial distribution of motor unit action potentials has recently been assessed with activation maps obtained from High Density EMG signals (HD-EMG, these lasts recorded with arrays of closely spaced electrodes. The main objective of this work is to analyze patterns in the activation maps, associating them with four movement directions at the elbow joint and with different strengths of those tasks. Although the activation pattern can be assessed with bipolar electrodes, HD-EMG maps could enable the extraction of features that depend on the spatial distribution of the potentials and on the load-sharing between muscles, in order to have a better differentiation between tasks and effort levels. Methods An experimental protocol consisting of isometric contractions at three levels of effort during flexion, extension, supination and pronation at the elbow joint was designed and HD-EMG signals were recorded with 2D electrode arrays on different upper-limb muscles. Techniques for the identification and interpolation of artifacts are explained, as well as a method for the segmentation of the activation areas. In addition, variables related to the intensity and spatial distribution of the maps were obtained, as well as variables associated to signal power of traditional single bipolar recordings. Finally, statistical tests were applied in order to assess differences between information extracted from single bipolar signals or from HD-EMG maps and to analyze

  9. Surface density mapping of natural tissue by a scanning haptic microscope (SHM).

    Science.gov (United States)

    Moriwaki, Takeshi; Oie, Tomonori; Takamizawa, Keiichi; Murayama, Yoshinobu; Fukuda, Toru; Omata, Sadao; Nakayama, Yasuhide

    2013-02-01

    To expand the performance capacity of the scanning haptic microscope (SHM) beyond surface mapping microscopy of elastic modulus or topography, surface density mapping of a natural tissue was performed by applying a measurement theory of SHM, in which a frequency change occurs upon contact of the sample surface with the SHM sensor - a microtactile sensor (MTS) that vibrates at a pre-determined constant oscillation frequency. This change was mainly stiffness-dependent at a low oscillation frequency and density-dependent at a high oscillation frequency. Two paragon examples with extremely different densities but similar macroscopic elastic moduli in the range of natural soft tissues were selected: one was agar hydrogels and the other silicon organogels with extremely low (less than 25 mg/cm(3)) and high densities (ca. 1300 mg/cm(3)), respectively. Measurements were performed in saline solution near the second-order resonance frequency, which led to the elastic modulus, and near the third-order resonance frequency. There was little difference in the frequency changes between the two resonance frequencies in agar gels. In contrast, in silicone gels, a large frequency change by MTS contact was observed near the third-order resonance frequency, indicating that the frequency change near the third-order resonance frequency reflected changes in both density and elastic modulus. Therefore, a density image of the canine aortic wall was subsequently obtained by subtracting the image observed near the second-order resonance frequency from that near the third-order resonance frequency. The elastin-rich region had a higher density than the collagen-rich region.

  10. Rotavirus - Global research density equalizing mapping and gender analysis.

    Science.gov (United States)

    Köster, Corinna; Klingelhöfer, Doris; Groneberg, David A; Schwarzer, Mario

    2016-01-02

    Rotaviruses are the leading reason for dehydration and severe diarrheal disease and in infants and young children worldwide. An increasing number of related publications cause a crucial challenge to determine the relevant scientific output. Therefore, scientometric analyses are helpful to evaluate quantity as well as quality of the worldwide research activities on Rotavirus. Up to now, no in-depth global scientometric analysis relating to Rotavirus publications has been carried out. This study used scientometric tools and the method of density equalizing mapping to visualize the differences of the worldwide research effort referring to Rotavirus. The aim of the study was to compare scientific output geographically and over time by using an in-depth data analysis and New quality and quantity indices in science (NewQIS) tools. Furthermore, a gender analysis was part of the data interpretation. We retrieved all Rotavirus-related articles, which were published on "Rotavirus" during the time period from 1900 to 2013, from the Web of Science by a defined search term. These items were analyzed regarding quantitative and qualitative aspects, and visualized with the help of bibliometric methods and the technique of density equalizing mapping to show the differences of the worldwide research efforts. This work aimed to extend the current NewQIS platform. The 5906 Rotavirus associated articles were published in 138 countries from 1900 to 2013. The USA authored 2037 articles that equaled 34.5% of all published items followed by Japan with 576 articles and the United Kingdom - as the most productive representative of the European countries - with 495 articles. Furthermore, the USA established the most cooperations with other countries and was found to be in the center of an international collaborative network. We performed a gender analysis of authors per country (threshold was set at a publishing output of more than 100 articles by more than 50 authors whose names could be

  11. A NEW RECIPE FOR OBTAINING CENTRAL VOLUME DENSITIES OF PRESTELLAR CORES FROM SIZE MEASUREMENTS

    International Nuclear Information System (INIS)

    Tassis, Konstantinos; Yorke, Harold W.

    2011-01-01

    We propose a simple analytical method for estimating the central volume density of prestellar molecular cloud cores from their column density profiles. Prestellar cores feature a flat central part of the column density and volume density profiles of the same size indicating the existence of a uniform-density inner region. The size of this region is set by the thermal pressure force which depends only on the central volume density and temperature of the core, and can provide a direct measurement of the central volume density. Thus, a simple length measurement can immediately yield a central density estimate independent of any dynamical model for the core and without the need for fitting. Using the radius at which the column density is 90% of the central value as an estimate of the size of the flat inner part of the column density profile yields an estimate of the central volume density within a factor of two for well-resolved cores.

  12. Density and diversity of OpenStreetMap road networks in China

    Directory of Open Access Journals (Sweden)

    Yingjia Zhang

    2015-12-01

    Full Text Available OpenStreetMap is a geographic information platform designed to provide real-time updates and user-generated content related to its freely available global map, and it is one of the most widely used examples of volunteered geographic information, a technique associated with so-called neogeography. This paper, based on the data from China’s OpenStreetMap road network in May 2014, taking 340 prefecture-level cities in China as its study area, presents the geometric-related (road density and attribute-related (type diversity spatial patterns of the OpenStreetMap road network, and explores their relationship. The results are as follows. (1 The distribution of OpenStreetMap road density in Shenzhen, Shanghai, Hong Kong, and Macao predominantly obeys a “positive skewness distribution”. OpenStreetMap data for eastern China shows a higher overall and circular structure. In central China, there are noticeable discrepancies in the road density, whereas in western China, the road density is low. (2 The OpenStreetMap road diversity shows a normal distribution. The spatial pattern for the so-called “Hu Huanyong line” was broken by the effect of diplomatic and strategic factors, showing a high diversity along the peripheral border, coastal cities, and core inland cites. (3 China’s OpenStreetMap is partitioned into four parts according to road density and diversity: high density and high diversity; low density and low diversity; high density and low diversity; and low density high diversity. (4 The OpenStreetMap geographical information-collection process and mechanism were analyzed, demonstrating that the road density reflects the preponderance of traffic in the real world. OpenStreetMap road diversity reflects the road-related geographic information demand and value, and it also reflects the interests of users toward to OpenStreetMap geographical information.

  13. Towards molecular design using 2D-molecular contour maps obtained from PLS regression coefficients

    Science.gov (United States)

    Borges, Cleber N.; Barigye, Stephen J.; Freitas, Matheus P.

    2017-12-01

    The multivariate image analysis descriptors used in quantitative structure-activity relationships are direct representations of chemical structures as they are simply numerical decodifications of pixels forming the 2D chemical images. These MDs have found great utility in the modeling of diverse properties of organic molecules. Given the multicollinearity and high dimensionality of the data matrices generated with the MIA-QSAR approach, modeling techniques that involve the projection of the data space onto orthogonal components e.g. Partial Least Squares (PLS) have been generally used. However, the chemical interpretation of the PLS-based MIA-QSAR models, in terms of the structural moieties affecting the modeled bioactivity has not been straightforward. This work describes the 2D-contour maps based on the PLS regression coefficients, as a means of assessing the relevance of single MIA predictors to the response variable, and thus allowing for the structural, electronic and physicochemical interpretation of the MIA-QSAR models. A sample study to demonstrate the utility of the 2D-contour maps to design novel drug-like molecules is performed using a dataset of some anti-HIV-1 2-amino-6-arylsulfonylbenzonitriles and derivatives, and the inferences obtained are consistent with other reports in the literature. In addition, the different schemes for encoding atomic properties in molecules are discussed and evaluated.

  14. Mapping low- and high-density clouds in astrophysical nebulae by imaging forbidden line emission

    Science.gov (United States)

    Steiner, J. E.; Menezes, R. B.; Ricci, T. V.; Oliveira, A. S.

    2009-06-01

    Emission line ratios have been essential for determining physical parameters such as gas temperature and density in astrophysical gaseous nebulae. With the advent of panoramic spectroscopic devices, images of regions with emission lines related to these physical parameters can, in principle, also be produced. We show that, with observations from modern instruments, it is possible to transform images taken from density-sensitive forbidden lines into images of emission from high- and low-density clouds by applying a transformation matrix. In order to achieve this, images of the pairs of density-sensitive lines as well as the adjacent continuum have to be observed and combined. We have computed the critical densities for a series of pairs of lines in the infrared, optical, ultraviolet and X-rays bands, and calculated the pair line intensity ratios in the high- and low-density limit using a four- and five-level atom approximation. In order to illustrate the method, we applied it to Gemini Multi-Object Spectrograph (GMOS) Integral Field Unit (GMOS-IFU) data of two galactic nuclei. We conclude that this method provides new information of astrophysical interest, especially for mapping low- and high-density clouds; for this reason, we call it `the ld/hd imaging method'. Based on observations obtained at the Gemini Observatory, which is operated by the Association of Universities for Research in Astronomy, Inc., under a cooperative agreement with the National Science Foundation on behalf of the Gemini partnership: the National Science Foundation (United States); the Science and Technology Facilities Council (United Kingdom); the National Research Council (Canada), CONICYT (Chile); the Australian Research Council (Australia); Ministério da Ciência e Tecnologia (Brazil) and Secretaria de Ciencia y Tecnologia (Argentina). E-mail: steiner@astro.iag.usp.br

  15. Functional magnetic resonance maps obtained by personal computer; Mapas de resonancia magnetica funcional obtenidos con PC

    Energy Technology Data Exchange (ETDEWEB)

    Gomez, F. j.; Manjon, J. V.; Robles, M. [Universidad Politecnica de Valencia (Spain); Marti-Bonmati, L.; Dosda, R. [Cinica Quiron. Valencia (Spain); Molla, E. [Universidad de Valencia (Spain)

    2001-07-01

    Functional magnetic resonance (fMR) is of special relevance in the analysis of certain types of brain activation. The present report describes the development of a simple software program for use with personal computers (PCs) that analyzes these images and provides functional activation maps. Activation maps are based on the temporal differences in oxyhemoglobin in tomographic images. To detect these differences, intensities registered repeatedly during brain control and activation are compared. The experiments were performed with a 1.5-Tesla MR unit. To verify the reliability of the program fMR studies were carried out in 4 healthy individuals (12 contiguous slices, 80 images per slice every 3.1 seconds for a total of 960 images). All the images were transferred to a PC and were processed pixel by pixel within each sequence to obtain an intensity/time curve. The statistical study of the results (Student's test and cross correlation analysis) made it possible to establish the activation of each pixel. The images were prepared using spatial filtering, temporal filtering, baseline correction, normalization and segmentation of the parenchyma. The postprocessing of the results involved the elimination of single pixels, superposition of an anatomical image of greater spatial resolution and anti-aliasing. The application (Xfun 1.0, Valencia, Spain) was developed in Microsoft Visual C++5.0 Developer Studio for Windows NT Workstation. As a representative example, the program took 8.2 seconds to calculate and present the results of the entire study (12 functional maps). In the motor and visual activation experiments, the activation corresponding to regions proximal to the central sulcus of the hemisphere contralateral to the hand that moved and in the occipital cortex were observed. While programs that calculate activation maps are available, the development of software for PCs running Microsoft Windows ensures several key features for its use on a daily basis: it is

  16. Evaluation of macromolecular electron-density map quality using the correlation of local r.m.s. density

    International Nuclear Information System (INIS)

    Terwilliger, Thomas C.; Berendzen, Joel

    1999-01-01

    The correlation of local r.m.s. density is shown to be a good measure of the presence of distinct solvent and macromolecule regions in macromolecular electron-density maps. It has recently been shown that the standard deviation of local r.m.s. electron density is a good indicator of the presence of distinct regions of solvent and protein in macromolecular electron-density maps [Terwilliger & Berendzen (1999 ▶). Acta Cryst. D55, 501–505]. Here, it is demonstrated that a complementary measure, the correlation of local r.m.s. density in adjacent regions on the unit cell, is also a good measure of the presence of distinct solvent and protein regions. The correlation of local r.m.s. density is essentially a measure of how contiguous the solvent (and protein) regions are in the electron-density map. This statistic can be calculated in real space or in reciprocal space and has potential uses in evaluation of heavy-atom solutions in the MIR and MAD methods as well as for evaluation of trial phase sets in ab initio phasing procedures

  17. Obtaining Hartree-Fock and density functional theory doubly excited states with Car-Parrinello density matrix search

    Science.gov (United States)

    Liang, Wenkel; Isborn, Christine M.; Li, Xiaosong

    2009-11-01

    The calculation of doubly excited states is one of the major problems plaguing the modern day excited state workhorse methodology of linear response time dependent Hartree-Fock (TDHF) and density function theory (TDDFT). We have previously shown that the use of a resonantly tuned field within real-time TDHF and TDDFT is able to simultaneously excite both the α and β electrons to achieve the two-electron excited states of minimal basis H2 and HeH+ [C. M. Isborn and X. Li, J. Chem. Phys. 129, 204107 (2008)]. We now extend this method to many electron systems with the use of our Car-Parrinello density matrix search (CP-DMS) with a first-principles fictitious mass method for wave function optimization [X. Li, C. L. Moss, W. Liang, and Y. Feng, J. Chem. Phys. 130, 234115 (2009)]. Real-time TDHF/TDDFT is used during the application of the laser field perturbation, driving the electron density toward the doubly excited state. The CP-DMS method then converges the density to the nearest stationary state. We present these stationary state doubly excited state energies and properties at the HF and DFT levels for H2, HeH+, lithium hydride, ethylene, and butadiene.

  18. Anharmonic thermal vibrations of be metal found in the MEM nuclear density map

    International Nuclear Information System (INIS)

    Takata, Masaki; Sakata, Makoto; Larsen, F.K.; Kumazawa, Shintaro; Iversen, B.B.

    1993-01-01

    A direct observation of the thermal vibrations of Be metal was performed by the Maximum Entropy Method (MEM) using neutron single crystal data. In the previous study, the existence of the small but significant cubic anharmonicity of Be has been found by the conventional least squares refinement of the observed structure factors [Larsen, Lehmann and Merisalo (1980) Acta Cryst. A36, 159-163]. In the present study, the same data were used for the MEM analysis which are comprised of 48 reflections up to sinθ/λ = 1.41A -1 in order to obtain the high resolution nuclear density of Be without using any thermal vibrational model. It was directly visible in the MEM map that not only the cubic terms but also quartic anharmonicities exist in the thermal vibrations of Be nuclei. In order to evaluate thermal parameters of Be including anharmonic terms quantitatively, the least squares refinement of the effective one-particle potential (OPP) parameters up to quartic term was carried out by using the MEM nuclear densities around atomic sites as the data set to be fitted. It was found that the present treatment has a great advantage to decide the most appropriate model of OPP by visually comparing the model with MEM density map. As a result of the least squares refinement, the anharmonic thermal parameters are obtained as α 33 = -0.340(5)[eV/A 3 ], α 40 = 0, β 20 = 9.89(1)[eV/A 4 ] and γ 00 = 0. No other anharmonic term was significant. (author)

  19. SU-E-J-233: Effect of Brachytherapy Seed Artifacts in T2 and Proton Density Maps in MR Images

    Energy Technology Data Exchange (ETDEWEB)

    Mashouf, S [Sunnybrook Odette Cancer Centre, Toronto, Ontario (Canada); University of Toronto, Dept of Radiation Oncology, Toronto, Ontario (Canada); Fatemi-Ardekani, A [Sunnybrook Odette Cancer Centre, Toronto, Ontario (Canada); Sunnybrook Research Institute, Toronto, Ontario (Canada); Song, W [Sunnybrook Odette Cancer Centre, Toronto, Ontario (Canada); University of Toronto, Dept of Radiation Oncology, Toronto, Ontario (Canada); Sunnybrook Research Institute, Toronto, Ontario (Canada)

    2015-06-15

    Purpose: This study aims at investigating the influence of brachytherapy seeds on T2 and proton density (PD) maps generated from MR images. Proton density maps can be used to extract water content. Since dose absorbed in tissue surrounding low energy brachytherapy seeds are highly influenced by tissue composition, knowing the water content is a first step towards implementing a heterogeneity correction algorithm using MR images. Methods: An LDR brachytherapy (IsoAid Advantage Pd-103) seed was placed in the middle of an agar-based gel phantom and imaged using a 3T Philips MR scanner with a 168-channel head coil. A multiple echo sequence with TE=20, 40, 60, 80, 100 (ms) with large repetition time (TR=6259ms) was used to extract T2 and PD maps. Results: Seed artifacts were considerably reduced on T2 maps compared to PD maps. The variation of PD around the mean was obtained as −97% to 125% (±1%) while for T2 it was recorded as −71% to 24% (±1%). Conclusion: PD maps which are required for heterogeneity corrections are susceptible to artifacts from seeds. Seed artifacts on T2 maps, however, are significantly reduced due to not being sensitive to B0 field variation.

  20. Terrestrial gamma radiation baseline mapping using ultra low density sampling methods

    International Nuclear Information System (INIS)

    Kleinschmidt, R.; Watson, D.

    2016-01-01

    Baseline terrestrial gamma radiation maps are indispensable for providing basic reference information that may be used in assessing the impact of a radiation related incident, performing epidemiological studies, remediating land contaminated with radioactive materials, assessment of land use applications and resource prospectivity. For a large land mass, such as Queensland, Australia (over 1.7 million km 2 ), it is prohibitively expensive and practically difficult to undertake detailed in-situ radiometric surveys of this scale. It is proposed that an existing, ultra-low density sampling program already undertaken for the purpose of a nationwide soil survey project be utilised to develop a baseline terrestrial gamma radiation map. Geoelement data derived from the National Geochemistry Survey of Australia (NGSA) was used to construct a baseline terrestrial gamma air kerma rate map, delineated by major drainage catchments, for Queensland. Three drainage catchments (sampled at the catchment outlet) spanning low, medium and high radioelement concentrations were selected for validation of the methodology using radiometric techniques including in-situ measurements and soil sampling for high resolution gamma spectrometry, and comparative non-radiometric analysis. A Queensland mean terrestrial air kerma rate, as calculated from the NGSA outlet sediment uranium, thorium and potassium concentrations, of 49 ± 69 nGy h −1 (n = 311, 3σ 99% confidence level) is proposed as being suitable for use as a generic terrestrial air kerma rate background range. Validation results indicate that catchment outlet measurements are representative of the range of results obtained across the catchment and that the NGSA geoelement data is suitable for calculation and mapping of terrestrial air kerma rate. - Highlights: • A baseline terrestrial air kerma map of Queensland, Australia was developed using geochemical data from a major drainage catchment ultra-low density sampling program

  1. Existence and density theorems for stochastic maps on commutative C*-algebras

    International Nuclear Information System (INIS)

    Alberti, P.M.; Uhlmann, A.

    1979-06-01

    Theorems are presented on the structure of stochastic and normalized positive linear maps over commutative C*-algebras. It is shown how strongly the solution of the n-tupel problem for stochastic maps relates to the fact that stochastic maps of finite rank are weakly dense within stochastic maps in case of a commutative C*-algebra. A new proof of the density theorem is given and (besides the solution of the n-tupel problem) results are derived concerning the extremal maps of certain convex subsets which are weakly dense. All stated facts suggest application in statistical physics (algebraic approach), especially concerning questions around evolution of classical systems. (author)

  2. Obtaining sub-daily new snow density from automated measurements in high mountain regions

    Science.gov (United States)

    Helfricht, Kay; Hartl, Lea; Koch, Roland; Marty, Christoph; Olefs, Marc

    2018-05-01

    The density of new snow is operationally monitored by meteorological or hydrological services at daily time intervals, or occasionally measured in local field studies. However, meteorological conditions and thus settling of the freshly deposited snow rapidly alter the new snow density until measurement. Physically based snow models and nowcasting applications make use of hourly weather data to determine the water equivalent of the snowfall and snow depth. In previous studies, a number of empirical parameterizations were developed to approximate the new snow density by meteorological parameters. These parameterizations are largely based on new snow measurements derived from local in situ measurements. In this study a data set of automated snow measurements at four stations located in the European Alps is analysed for several winter seasons. Hourly new snow densities are calculated from the height of new snow and the water equivalent of snowfall. Considering the settling of the new snow and the old snowpack, the average hourly new snow density is 68 kg m-3, with a standard deviation of 9 kg m-3. Seven existing parameterizations for estimating new snow densities were tested against these data, and most calculations overestimate the hourly automated measurements. Two of the tested parameterizations were capable of simulating low new snow densities observed at sheltered inner-alpine stations. The observed variability in new snow density from the automated measurements could not be described with satisfactory statistical significance by any of the investigated parameterizations. Applying simple linear regressions between new snow density and wet bulb temperature based on the measurements' data resulted in significant relationships (r2 > 0.5 and p ≤ 0.05) for single periods at individual stations only. Higher new snow density was calculated for the highest elevated and most wind-exposed station location. Whereas snow measurements using ultrasonic devices and snow

  3. A high-density linkage map and QTL mapping of fruit-related traits in pumpkin (Cucurbita moschata Duch.).

    Science.gov (United States)

    Zhong, Yu-Juan; Zhou, Yang-Yang; Li, Jun-Xing; Yu, Ting; Wu, Ting-Quan; Luo, Jian-Ning; Luo, Shao-Bo; Huang, He-Xun

    2017-10-06

    Pumpkin (Cucurbita moschata) is an economically worldwide crop. Few quantitative trait loci (QTLs) were reported previously due to the lack of genomic and genetic resources. In this study, a high-density linkage map of C. moschata was structured by double-digest restriction site-associated DNA sequencing, using 200 F2 individuals of CMO-1 × CMO-97. By filtering 74,899 SNPs, a total of 3,470 high quality SNP markers were assigned to the map spanning a total genetic distance of 3087.03 cM on 20 linkage groups (LGs) with an average genetic distance of 0.89 cM. Based on this map, both pericarp color and strip were fined mapped to a novel single locus on LG8 in the same region of 0.31 cM with phenotypic variance explained (PVE) of 93.6% and 90.2%, respectively. QTL analysis was also performed on carotenoids, sugars, tuberculate fruit, fruit diameter, thickness and chamber width with a total of 12 traits. 29 QTLs distributed in 9 LGs were detected with PVE from 9.6% to 28.6%. It was the first high-density linkage SNP map for C. moschata which was proved to be a valuable tool for gene or QTL mapping. This information will serve as significant basis for map-based gene cloning, draft genome assembling and molecular breeding.

  4. Terrestrial gamma radiation baseline mapping using ultra low density sampling methods.

    Science.gov (United States)

    Kleinschmidt, R; Watson, D

    2016-01-01

    Baseline terrestrial gamma radiation maps are indispensable for providing basic reference information that may be used in assessing the impact of a radiation related incident, performing epidemiological studies, remediating land contaminated with radioactive materials, assessment of land use applications and resource prospectivity. For a large land mass, such as Queensland, Australia (over 1.7 million km(2)), it is prohibitively expensive and practically difficult to undertake detailed in-situ radiometric surveys of this scale. It is proposed that an existing, ultra-low density sampling program already undertaken for the purpose of a nationwide soil survey project be utilised to develop a baseline terrestrial gamma radiation map. Geoelement data derived from the National Geochemistry Survey of Australia (NGSA) was used to construct a baseline terrestrial gamma air kerma rate map, delineated by major drainage catchments, for Queensland. Three drainage catchments (sampled at the catchment outlet) spanning low, medium and high radioelement concentrations were selected for validation of the methodology using radiometric techniques including in-situ measurements and soil sampling for high resolution gamma spectrometry, and comparative non-radiometric analysis. A Queensland mean terrestrial air kerma rate, as calculated from the NGSA outlet sediment uranium, thorium and potassium concentrations, of 49 ± 69 nGy h(-1) (n = 311, 3σ 99% confidence level) is proposed as being suitable for use as a generic terrestrial air kerma rate background range. Validation results indicate that catchment outlet measurements are representative of the range of results obtained across the catchment and that the NGSA geoelement data is suitable for calculation and mapping of terrestrial air kerma rate. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

  5. A procedure to obtain a refined European land use/cover map

    NARCIS (Netherlands)

    Batista e Silva, F.; Lavalle, C.; Koomen, E.

    2013-01-01

    Available land use/cover maps differ in their spatial extent and in their thematic, spatial, and temporal resolutions. Due to the costs of producing such maps, there is usually a trade-off between spatial extent and resolution. The only European-wide, consistent, and multi-temporal land use/cover

  6. Construction of the High-Density Genetic Linkage Map and Chromosome Map of Large Yellow Croaker (Larimichthys crocea

    Directory of Open Access Journals (Sweden)

    Jingqun Ao

    2015-11-01

    Full Text Available High-density genetic maps are essential for genome assembly, comparative genomic analysis and fine mapping of complex traits. In this study, 31,191 single nucleotide polymorphisms (SNPs evenly distributed across the large yellow croaker (Larimichthys crocea genome were identified using restriction-site associated DNA sequencing (RAD-seq. Among them, 10,150 high-confidence SNPs were assigned to 24 consensus linkage groups (LGs. The total length of the genetic linkage map was 5451.3 cM with an average distance of 0.54 cM between loci. This represents the densest genetic map currently reported for large yellow croaker. Using 2889 SNPs to target specific scaffolds, we assigned 533 scaffolds, comprising 421.44 Mb (62.04% of the large yellow croaker assembled sequence, to the 24 linkage groups. The mapped assembly scaffolds in large yellow croaker were used for genome synteny analyses against the stickleback (Gasterosteus aculeatus and medaka (Oryzias latipes. Greater synteny was observed between large yellow croaker and stickleback. This supports the hypothesis that large yellow croaker is more closely related to stickleback than to medaka. Moreover, 1274 immunity-related genes and 195 hypoxia-related genes were mapped to the 24 chromosomes of large yellow croaker. The integration of the high-resolution genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits in large yellow croaker.

  7. Comparison of the Volume Charge Density of Nanofiltration Membranes Obtained from Retention and Conductivity Experiments

    DEFF Research Database (Denmark)

    Benavente, J.; Silva, V.; Pradanos, P.

    2010-01-01

    A version of the Donnan steric-partitioning pore model with dielectrical exclusion (DSPM-DE) has been used to get information on the pore size and charge density of a commercial membrane, NF45 from FilmTec, from its retention of KCl solutions. The conductivity inside the pores has been measured b...

  8. A high-density SNP map for accurate mapping of seed fibre QTL in Brassica napus L.

    Directory of Open Access Journals (Sweden)

    Liezhao Liu

    Full Text Available A high density genetic linkage map for the complex allotetraploid crop species Brassica napus (oilseed rape was constructed in a late-generation recombinant inbred line (RIL population, using genome-wide single nucleotide polymorphism (SNP markers assayed by the Brassica 60 K Infinium BeadChip Array. The linkage map contains 9164 SNP markers covering 1832.9 cM. 1232 bins account for 7648 of the markers. A subset of 2795 SNP markers, with an average distance of 0.66 cM between adjacent markers, was applied for QTL mapping of seed colour and the cell wall fiber components acid detergent lignin (ADL, cellulose and hemicellulose. After phenotypic analyses across four different environments a total of 11 QTL were detected for seed colour and fiber traits. The high-density map considerably improved QTL resolution compared to the previous low-density maps. A previously identified major QTL with very high effects on seed colour and ADL was pinpointed to a narrow genome interval on chromosome A09, while a minor QTL explaining 8.1% to 14.1% of variation for ADL was detected on chromosome C05. Five and three QTL accounting for 4.7% to 21.9% and 7.3% to 16.9% of the phenotypic variation for cellulose and hemicellulose, respectively, were also detected. To our knowledge this is the first description of QTL for seed cellulose and hemicellulose in B. napus, representing interesting new targets for improving oil content. The high density SNP genetic map enables navigation from interesting B. napus QTL to Brassica genome sequences, giving useful new information for understanding the genetics of key seed quality traits in rapeseed.

  9. A SNP based high-density linkage map of Apis cerana reveals a high recombination rate similar to Apis mellifera.

    Directory of Open Access Journals (Sweden)

    Yuan Yuan Shi

    Full Text Available BACKGROUND: The Eastern honey bee, Apis cerana Fabricius, is distributed in southern and eastern Asia, from India and China to Korea and Japan and southeast to the Moluccas. This species is also widely kept for honey production besides Apis mellifera. Apis cerana is also a model organism for studying social behavior, caste determination, mating biology, sexual selection, and host-parasite interactions. Few resources are available for molecular research in this species, and a linkage map was never constructed. A linkage map is a prerequisite for quantitative trait loci mapping and for analyzing genome structure. We used the Chinese honey bee, Apis cerana cerana to construct the first linkage map in the Eastern honey bee. RESULTS: F2 workers (N = 103 were genotyped for 126,990 single nucleotide polymorphisms (SNPs. After filtering low quality and those not passing the Mendel test, we obtained 3,000 SNPs, 1,535 of these were informative and used to construct a linkage map. The preliminary map contains 19 linkage groups, we then mapped the 19 linkage groups to 16 chromosomes by comparing the markers to the genome of A. mellfiera. The final map contains 16 linkage groups with a total of 1,535 markers. The total genetic distance is 3,942.7 centimorgans (cM with the largest linkage group (180 loci measuring 574.5 cM. Average marker interval for all markers across the 16 linkage groups is 2.6 cM. CONCLUSION: We constructed a high density linkage map for A. c. cerana with 1,535 markers. Because the map is based on SNP markers, it will enable easier and faster genotyping assays than randomly amplified polymorphic DNA or microsatellite based maps used in A. mellifera.

  10. Extensive cochleotopic mapping of human auditory cortical fields obtained with phase-encoding FMRI.

    Directory of Open Access Journals (Sweden)

    Ella Striem-Amit

    Full Text Available The primary sensory cortices are characterized by a topographical mapping of basic sensory features which is considered to deteriorate in higher-order areas in favor of complex sensory features. Recently, however, retinotopic maps were also discovered in the higher-order visual, parietal and prefrontal cortices. The discovery of these maps enabled the distinction between visual regions, clarified their function and hierarchical processing. Could such extension of topographical mapping to high-order processing regions apply to the auditory modality as well? This question has been studied previously in animal models but only sporadically in humans, whose anatomical and functional organization may differ from that of animals (e.g. unique verbal functions and Heschl's gyrus curvature. Here we applied fMRI spectral analysis to investigate the cochleotopic organization of the human cerebral cortex. We found multiple mirror-symmetric novel cochleotopic maps covering most of the core and high-order human auditory cortex, including regions considered non-cochleotopic, stretching all the way to the superior temporal sulcus. These maps suggest that topographical mapping persists well beyond the auditory core and belt, and that the mirror-symmetry of topographical preferences may be a fundamental principle across sensory modalities.

  11. Constraining Saturn's interior density profile from precision gravity field measurement obtained during Grand Finale

    Science.gov (United States)

    Movshovitz, N.; Fortney, J. J.; Helled, R.; Hubbard, W. B.; Mankovich, C.; Thorngren, D.; Wahl, S. M.; Militzer, B.; Durante, D.

    2017-12-01

    The external gravity field of a planetary body is determined by the distribution of mass in its interior. Therefore, a measurement of the external field, properlyinterpreted, tells us about the interior density profile, ρ(r), which in turn can be used to constrain the composition in the interior and thereby learn about theformation mechanism of the planet. Recently, very high precision measurements of the gravity coefficients for Saturn have been made by the radio science instrument on the Cassini spacecraft during its Grand Finale orbits. The resulting coefficients come with an associated uncertainty. The task of matching a given density profile to a given set of gravity coefficients is relatively straightforward, but the question of how to best account for the uncertainty is not. In essentially all prior work on matching models to gravity field data inferences about planetary structure have rested on assumptions regarding the imperfectly known H/He equation of state and the assumption of an adiabatic interior. Here we wish to vastly expand the phase space of such calculations. We present a framework for describing all the possible interior density structures of a Jovian planet constrained by a given set of gravity coefficients and their associated uncertainties. Our approach is statistical. We produce a random sample of ρ(a) curves drawn from the underlying (and unknown) probability distribution of all curves, where ρ is the density on an interior level surface with equatorial radius a. Since the resulting set of density curves is a random sample, that is, curves appear with frequency proportional to the likelihood of their being consistent with the measured gravity, we can compute probability distributions for any quantity that is a function of ρ, such as central pressure, oblateness, core mass and radius, etc. Our approach is also Bayesian, in that it can utilize any prior assumptions about the planet's interior, as necessary, without being overly

  12. Models of asthma: density-equalizing mapping and output benchmarking

    Directory of Open Access Journals (Sweden)

    Fischer Tanja C

    2008-02-01

    Full Text Available Abstract Despite the large amount of experimental studies already conducted on bronchial asthma, further insights into the molecular basics of the disease are required to establish new therapeutic approaches. As a basis for this research different animal models of asthma have been developed in the past years. However, precise bibliometric data on the use of different models do not exist so far. Therefore the present study was conducted to establish a data base of the existing experimental approaches. Density-equalizing algorithms were used and data was retrieved from a Thomson Institute for Scientific Information database. During the period from 1900 to 2006 a number of 3489 filed items were connected to animal models of asthma, the first being published in the year 1968. The studies were published by 52 countries with the US, Japan and the UK being the most productive suppliers, participating in 55.8% of all published items. Analyzing the average citation per item as an indicator for research quality Switzerland ranked first (30.54/item and New Zealand ranked second for countries with more than 10 published studies. The 10 most productive journals included 4 with a main focus allergy and immunology and 4 with a main focus on the respiratory system. Two journals focussed on pharmacology or pharmacy. In all assigned subject categories examined for a relation to animal models of asthma, immunology ranked first. Assessing numbers of published items in relation to animal species it was found that mice were the preferred species followed by guinea pigs. In summary it can be concluded from density-equalizing calculations that the use of animal models of asthma is restricted to a relatively small number of countries. There are also differences in the use of species. These differences are based on variations in the research focus as assessed by subject category analysis.

  13. Local activation time sampling density for atrial tachycardia contact mapping: how much is enough?

    Science.gov (United States)

    Williams, Steven E; Harrison, James L; Chubb, Henry; Whitaker, John; Kiedrowicz, Radek; Rinaldi, Christopher A; Cooklin, Michael; Wright, Matthew; Niederer, Steven; O'Neill, Mark D

    2018-02-01

    Local activation time (LAT) mapping forms the cornerstone of atrial tachycardia diagnosis. Although anatomic and positional accuracy of electroanatomic mapping (EAM) systems have been validated, the effect of electrode sampling density on LAT map reconstruction is not known. Here, we study the effect of chamber geometry and activation complexity on optimal LAT sampling density using a combined in silico and in vivo approach. In vivo 21 atrial tachycardia maps were studied in three groups: (1) focal activation, (2) macro-re-entry, and (3) localized re-entry. In silico activation was simulated on a 4×4cm atrial monolayer, sampled randomly at 0.25-10 points/cm2 and used to re-interpolate LAT maps. Activation patterns were studied in the geometrically simple porcine right atrium (RA) and complex human left atrium (LA). Activation complexity was introduced into the porcine RA by incomplete inter-caval linear ablation. In all cases, optimal sampling density was defined as the highest density resulting in minimal further error reduction in the re-interpolated maps. Optimal sampling densities for LA tachycardias were 0.67 ± 0.17 points/cm2 (focal activation), 1.05 ± 0.32 points/cm2 (macro-re-entry) and 1.23 ± 0.26 points/cm2 (localized re-entry), P = 0.0031. Increasing activation complexity was associated with increased optimal sampling density both in silico (focal activation 1.09 ± 0.14 points/cm2; re-entry 1.44 ± 0.49 points/cm2; spiral-wave 1.50 ± 0.34 points/cm2, P density (0.61 ± 0.22 points/cm2 vs. 1.0 ± 0.34 points/cm2, P = 0.0015). Optimal sampling densities can be identified to maximize diagnostic yield of LAT maps. Greater sampling density is required to correctly reveal complex activation and represent activation across complex geometries. Overall, the optimal sampling density for LAT map interpolation defined in this study was ∼1.0-1.5 points/cm2. Published on behalf of the European Society of

  14. Cowichan Valley energy mapping and modelling. Report 5 - Energy density mapping projections. Final report. [Vancouver Island, Canada

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2012-06-15

    The driving force behind the Integrated Energy Mapping and Analysis project was the identification and analysis of a suite of pathways that the Cowichan Valley Regional District (CVRD) can utilise to increase its energy resilience, as well as reduce energy consumption and GHG emissions, with a primary focus on the residential sector. Mapping and analysis undertaken will support provincial energy and GHG reduction targets, and the suite of pathways outlined will address a CVRD internal target that calls for 75% of the region's energy within the residential sector to come from locally sourced renewables by 2050. The target has been developed as a mechanism to meet resilience and climate action target. The maps and findings produced are to be integrated as part of a regional policy framework currently under development. Task 5 focused on energy projection mapping to estimate and visualise the energy consumption density and GHG emissions under different scenarios. The scenarios from task 4 were built around the energy consumption density of the residential sector under future land use patterns and rely on different energy source combinations (the suite of pathways). In task 5 the energy usage under the different scenarios were fed back into GIS, thereby giving a visual representation of forecasted residential energy consumption per unit area. The methodology is identical to that used in task 2 where current usage was mapped, whereas the mapping in this task is for future forecasts. These results are documented in this report. In addition, GHG mapping under the various scenarios was also undertaken. (LN)

  15. Hydrogen concentration and mass density of diamondlike carbon films obtained by x-ray and neutron reflectivity

    DEFF Research Database (Denmark)

    Findeisen, E.; Feidenhans'l, R.; Vigild, Martin Etchells

    1994-01-01

    Specular reflectivity of neutrons and x rays can be used to determine the scattering length density profile of a material perpendicular to its surface. We have applied these techniques to study amorphous, diamondlike, hydrocarbon films. By the combination of these two techniques we obtain not onl...

  16. A comparison of spatial analysis methods for the construction of topographic maps of retinal cell density.

    Directory of Open Access Journals (Sweden)

    Eduardo Garza-Gisholt

    Full Text Available Topographic maps that illustrate variations in the density of different neuronal sub-types across the retina are valuable tools for understanding the adaptive significance of retinal specialisations in different species of vertebrates. To date, such maps have been created from raw count data that have been subjected to only limited analysis (linear interpolation and, in many cases, have been presented as iso-density contour maps with contour lines that have been smoothed 'by eye'. With the use of stereological approach to count neuronal distribution, a more rigorous approach to analysing the count data is warranted and potentially provides a more accurate representation of the neuron distribution pattern. Moreover, a formal spatial analysis of retinal topography permits a more robust comparison of topographic maps within and between species. In this paper, we present a new R-script for analysing the topography of retinal neurons and compare methods of interpolating and smoothing count data for the construction of topographic maps. We compare four methods for spatial analysis of cell count data: Akima interpolation, thin plate spline interpolation, thin plate spline smoothing and Gaussian kernel smoothing. The use of interpolation 'respects' the observed data and simply calculates the intermediate values required to create iso-density contour maps. Interpolation preserves more of the data but, consequently includes outliers, sampling errors and/or other experimental artefacts. In contrast, smoothing the data reduces the 'noise' caused by artefacts and permits a clearer representation of the dominant, 'real' distribution. This is particularly useful where cell density gradients are shallow and small variations in local density may dramatically influence the perceived spatial pattern of neuronal topography. The thin plate spline and the Gaussian kernel methods both produce similar retinal topography maps but the smoothing parameters used may affect

  17. A comparison of spatial analysis methods for the construction of topographic maps of retinal cell density.

    Science.gov (United States)

    Garza-Gisholt, Eduardo; Hemmi, Jan M; Hart, Nathan S; Collin, Shaun P

    2014-01-01

    Topographic maps that illustrate variations in the density of different neuronal sub-types across the retina are valuable tools for understanding the adaptive significance of retinal specialisations in different species of vertebrates. To date, such maps have been created from raw count data that have been subjected to only limited analysis (linear interpolation) and, in many cases, have been presented as iso-density contour maps with contour lines that have been smoothed 'by eye'. With the use of stereological approach to count neuronal distribution, a more rigorous approach to analysing the count data is warranted and potentially provides a more accurate representation of the neuron distribution pattern. Moreover, a formal spatial analysis of retinal topography permits a more robust comparison of topographic maps within and between species. In this paper, we present a new R-script for analysing the topography of retinal neurons and compare methods of interpolating and smoothing count data for the construction of topographic maps. We compare four methods for spatial analysis of cell count data: Akima interpolation, thin plate spline interpolation, thin plate spline smoothing and Gaussian kernel smoothing. The use of interpolation 'respects' the observed data and simply calculates the intermediate values required to create iso-density contour maps. Interpolation preserves more of the data but, consequently includes outliers, sampling errors and/or other experimental artefacts. In contrast, smoothing the data reduces the 'noise' caused by artefacts and permits a clearer representation of the dominant, 'real' distribution. This is particularly useful where cell density gradients are shallow and small variations in local density may dramatically influence the perceived spatial pattern of neuronal topography. The thin plate spline and the Gaussian kernel methods both produce similar retinal topography maps but the smoothing parameters used may affect the outcome.

  18. Cowichan Valley energy mapping and modelling. Report 2 - Energy consumption and density mapping. Final report. [Vancouver Island, Canada

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2012-06-15

    The driving force behind the Integrated Energy Mapping and Analysis project was the identification and analysis of a suite of pathways that the Cowichan Valley Regional District (CVRD) can utilise to increase its energy resilience, as well as reduce energy consumption and GHG emissions, with a primary focus on the residential sector. Mapping and analysis undertaken will support provincial energy and GHG reduction targets, and the suite of pathways outlined will address a CVRD internal target that calls for 75% of the region's energy within the residential sector to come from locally sourced renewables by 2050. The target has been developed as a mechanism to meet resilience and climate action target. The maps and findings produced are to be integrated as part of a regional policy framework currently under development. The second task in the overall project was the mapping of regional energy consumption density. Combined with the findings from task one, this enables comparison of energy consumption density per area unit with the renewable energy resource availability. In addition, it provides an energy baseline against which future energy planning activities can be evaluated. The mapping of the energy consumption density was divided into categories to correspond with local British Columbia Assessment Authority (BCAA) reporting. The residential sub-categories were comprised of single family detached dwellings, single family attached dwellings, apartments, and moveable dwellings. For commercial and industrial end-users the 14 sub-categories are also in line with BCAA as well as the on-going provincial TaNDM project of which the CVRD is a partner. The results of task two are documented in this report. (LN)

  19. Collinear and transverse momentum dependent parton densities obtained with a parton branching method

    Energy Technology Data Exchange (ETDEWEB)

    Lelek, Aleksandra

    2017-10-15

    We present a solution of the DGLAP evolution equations, written in terms of Sudakov form factors to describe the branching and no-branching probabilities, using a parton branching Monte Carlo method. We demonstrate numerically that this method reproduces the semi-analytical solutions. We show how this method can be used to determine Transverse Momentum Dependent (TMD) parton distribution functions, in addition to the usual integrated parton distributions functions. We discuss numerical effects of the boundary of soft gluon resolution scale parameter on the resulting parton distribution functions. We show that a very good fit of the integrated TMDs to high precision HERA data can be obtained over a large range in x and Q{sup 2}.

  20. Investigations on the conditions for obtaining high density boron carbide by sintering

    International Nuclear Information System (INIS)

    Kislyj, P.S.; Grabtschuk, B.L.

    1975-01-01

    The results of investigations on kinetics of condensation and mechanisms of mass transfer in the process of sintering of technical, chemically pure and synthesized boron carbide are generalized. Laws on boron carbide densification depending upon temperature, time of isothermic endurance, thermal speed, size of powder particles and variable composition in homogeneity are determined. From the results obtained on condensation kinetics and special experiments on studying the changes in properties after heating under different conditions, the role of dislocation and diffusion processes in mass transfer during boron carbide sintering is exposed. The properties of sintered boron carbide are 15-20% lower than the properties of high-pressed one, that is conditioned by intercrystallite distortion of the first one and transcrystallite of the second one

  1. Collinear and transverse momentum dependent parton densities obtained with a parton branching method

    International Nuclear Information System (INIS)

    Lelek, Aleksandra

    2017-10-01

    We present a solution of the DGLAP evolution equations, written in terms of Sudakov form factors to describe the branching and no-branching probabilities, using a parton branching Monte Carlo method. We demonstrate numerically that this method reproduces the semi-analytical solutions. We show how this method can be used to determine Transverse Momentum Dependent (TMD) parton distribution functions, in addition to the usual integrated parton distributions functions. We discuss numerical effects of the boundary of soft gluon resolution scale parameter on the resulting parton distribution functions. We show that a very good fit of the integrated TMDs to high precision HERA data can be obtained over a large range in x and Q 2 .

  2. The multifractal structure of satellite sea surface temperature maps can be used to obtain global maps of streamlines

    Directory of Open Access Journals (Sweden)

    A. Turiel

    2009-10-01

    Full Text Available Nowadays Earth observation satellites provide information about many relevant variables of the ocean-climate system, such as temperature, moisture, aerosols, etc. However, to retrieve the velocity field, which is the most relevant dynamical variable, is still a technological challenge, specially in the case of oceans. New processing techniques, emerged from the theory of turbulent flows, have come to assist us in this task. In this paper, we show that multifractal techniques applied to new Sea Surface Temperature satellite products opens the way to build maps of ocean currents with unprecedented accuracy. With the application of singularity analysis, we show that global ocean circulation patterns can be retrieved in a daily basis. We compare these results with high-quality altimetry-derived geostrophic velocities, finding a quite good correspondence of the observed patterns both qualitatively and quantitatively; and this is done for the first time on a global basis, even for less active areas. The implications of this findings from the perspective both of theory and of operational applications are discussed.

  3. StreamMap: Smooth Dynamic Visualization of High-Density Streaming Points.

    Science.gov (United States)

    Li, Chenhui; Baciu, George; Han, Yu

    2018-03-01

    Interactive visualization of streaming points for real-time scatterplots and linear blending of correlation patterns is increasingly becoming the dominant mode of visual analytics for both big data and streaming data from active sensors and broadcasting media. To better visualize and interact with inter-stream patterns, it is generally necessary to smooth out gaps or distortions in the streaming data. Previous approaches either animate the points directly or present a sampled static heat-map. We propose a new approach, called StreamMap, to smoothly blend high-density streaming points and create a visual flow that emphasizes the density pattern distributions. In essence, we present three new contributions for the visualization of high-density streaming points. The first contribution is a density-based method called super kernel density estimation that aggregates streaming points using an adaptive kernel to solve the overlapping problem. The second contribution is a robust density morphing algorithm that generates several smooth intermediate frames for a given pair of frames. The third contribution is a trend representation design that can help convey the flow directions of the streaming points. The experimental results on three datasets demonstrate the effectiveness of StreamMap when dynamic visualization and visual analysis of trend patterns on streaming points are required.

  4. Increasing the Accuracy of Mapping Urban Forest Carbon Density by Combining Spatial Modeling and Spectral Unmixing Analysis

    Directory of Open Access Journals (Sweden)

    Hua Sun

    2015-11-01

    Full Text Available Accurately mapping urban vegetation carbon density is challenging because of complex landscapes and mixed pixels. In this study, a novel methodology was proposed that combines a linear spectral unmixing analysis (LSUA with a linear stepwise regression (LSR, a logistic model-based stepwise regression (LMSR and k-Nearest Neighbors (kNN, to map the forest carbon density of Shenzhen City of China, using Landsat 8 imagery and sample plot data collected in 2014. The independent variables that contributed to statistically significantly improving the fit of a model to data and reducing the sum of squared errors were first selected from a total of 284 spectral variables derived from the image bands. The vegetation fraction from LSUA was then added as an independent variable. The results obtained using cross-validation showed that: (1 Compared to the methods without the vegetation information, adding the vegetation fraction increased the accuracy of mapping carbon density by 1%–9.3%; (2 As the observed values increased, the LSR and kNN residuals showed overestimates and underestimates for the smaller and larger observations, respectively, while LMSR improved the systematical over and underestimations; (3 LSR resulted in illogically negative and unreasonably large estimates, while KNN produced the greatest values of root mean square error (RMSE. The results indicate that combining the spatial modeling method LMSR and the spectral unmixing analysis LUSA, coupled with Landsat imagery, is most promising for increasing the accuracy of urban forest carbon density maps. In addition, this method has considerable potential for accurate, rapid and nondestructive prediction of urban and peri-urban forest carbon stocks with an acceptable level of error and low cost.

  5. A novel matrix approach for controlling the invariant densities of chaotic maps

    International Nuclear Information System (INIS)

    Rogers, Alan; Shorten, Robert; Heffernan, Daniel M.

    2008-01-01

    Recent work on positive matrices has resulted in a new matrix method for generating chaotic maps with arbitrary piecewise constant invariant densities, sometimes known as the inverse Frobenius-Perron problem (IFPP). In this paper, we give an extensive introduction to the IFPP, describing existing methods for solving it, and we describe our new matrix approach for solving the IFPP

  6. Partition coefficients of methylated DNA bases obtained from free energy calculations with molecular electron density derived atomic charges.

    Science.gov (United States)

    Lara, A; Riquelme, M; Vöhringer-Martinez, E

    2018-05-11

    Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have also been used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study, atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in a vacuum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases, the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account, and when the energy needed to polarize the electron density of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogs. Comparison of the two partitioning methods, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS), revealed some deficiencies in the Hirshfeld-I method related to the unstable isolated anionic nitrogen pro-atom used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model

  7. An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce

    Science.gov (United States)

    Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W.

    2013-01-01

    We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa. The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. PMID:23550116

  8. An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce.

    Science.gov (United States)

    Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W

    2013-04-09

    We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F 7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. Copyright © 2013 Truco et al.

  9. On the fluctuations of density and temperature in outer space atmosphere obtained from orbital shift of TAIYO

    International Nuclear Information System (INIS)

    Kato, Yoshio; Onishi, Nobuto; Shimizu, Osamu; Enmi, Sachiko; Hirao, Kunio.

    1976-01-01

    The temperature and density in outer space atmosphere were obtained from the change of the orbital period of the artificial satellite TAIYO which was launched on February 24, 1975, from Kagoshima. An equation to calculate atmospheric density with the characteristic values of the satellite is presented in the first part together with the observed variation of the orbital elements of TAIYO. The weekly changes of temperature and density in outer space atmosphere at the altitude of 250 km, which is the perigee of the satellite, from April 1975 to May 1976 were obtained. The relations between outer space temperature and sigma KP, F10.7, and the position of the perigee were also obtained. The outer space temperature as a function of local time is presented, and it is observed that the temperature change in relation to the local time agrees with the atmospheric model, and that the ratio of maximum or minimum temperature within a day becomes nearly 1.3. It is commented that more data will be available for the further detailed analysis because TAIYO is still orbiting normally. (Aoki, K.)

  10. Repeat Mapping in the Lower Monterey Submarine Canyon Sheds Light on Morphological Change During Discrete Sediment Density Flow Events

    Science.gov (United States)

    Anderson, K.; Lundsten, E. M.; Caress, D. W.; Thomas, H. J.; Paull, C. K.; Maier, K. L.; Gales, J. A.; Gwiazda, R.; Talling, P.; Xu, J.; Parsons, D. R.

    2017-12-01

    The Coordinated Canyon Experiment (CCE), a multi-institutional collaboration effort, was designed to monitor the passage of sediment density flows along the axis of Monterey Canyon, offshore California, between 200 and 1850 m water depth. An array of moorings and sensors were deployed for three 6-month periods from October 2015 to April 2017. Aligned with the CCE deployments, repeat high-resolution multibeam bathymetric surveys of the Monterey Canyon floor were conducted with a mapping AUV (Autonomous Underwater Vehicle). The AUV carried a Reson 7125 multibeam echosounder (vertical precision of 0.15 m and horizontal resolution of 1.0 m). An inertial navigation system combined with a Doppler velocity logger allowed the AUV to fly pre-programmed grids at 3 knots, while maintaining an altitude of 50 m above the seafloor, to obtain a nominal line spacing of 130 m. The floor and lower flanks of the canyon between 200 to 540 m and 1350 to 1880 m water depths were mapped six times during the CCE. These repeat maps are subtracted to create bathymetry difference grids to show morphological change. Coupling the sensor observations with the bathymetric surveys, the CCE successfully documented sediment density flow events as well as the associated changes in seafloor morphology. Between repeat surveys, three sediment density flow events reached the lower canyon, extending to at least 1850 m water depth. On January 15, 2016, a particularly large density flow traveled more than 50 km down Monterey Canyon. Unlike in the upper canyon where this event caused wholesale reorganization of geomorphological features, changes to the lower canyon morphology involved a more moderate re-sculpting of the features. The effect of a sediment density flow of known magnitude and duration on the seafloor morphology has never been documented in a deep-sea setting before.

  11. Kernel density estimation and transition maps of Moldavian Neolithic and Eneolithic settlement

    Directory of Open Access Journals (Sweden)

    Robin Brigand

    2018-04-01

    Full Text Available The data presented in this article are related to the research article entitled “Neo-Eneolithic settlement pattern and salt exploitation in Romanian Moldavia” (Brigand and Weller, 2018 [1]. Kernel density estimation (KDE is used in order to move beyond the discrete distribution of sites and to enable us to work on a continuous surface that reflects the intensity of the occupation in the space. Maps of density per period – Neolithic I (Cris, Neolithic II (LBK, Eneolithic I (Precucuteni, Eneolithic II (Cucuteni A, Eneolithic III-IV (Cucuteni A-B and B – are used to create maps of density difference (Figs. 1–4 in order to analyse the dynamic (either non-existent, negative or positive between two chronological sequences.

  12. Mapping QTL for Seed Germinability under Low Temperature Using a New High-Density Genetic Map of Rice

    Directory of Open Access Journals (Sweden)

    Ningfei Jiang

    2017-07-01

    Full Text Available Mapping major quantitative trait loci (QTL responsible for rice seed germinability under low temperature (GULT can provide valuable genetic source for improving cold tolerance in rice breeding. In this study, 124 rice backcross recombinant inbred lines (BRILs derived from a cross indica cv. Changhui 891 and japonica cv. 02428 were genotyped through re-sequencing technology. A bin map was generated which includes 3057 bins covering distance of 1266.5 cM with an average of 0.41 cM between markers. On the basis of newly constructed high-density genetic map, six QTL were detected ranging from 40 to 140 kb on Nipponbare genome. Among these, two QTL qCGR8 and qGRR11 alleles shared by 02428 could increase GULT and seed germination recovery rate after cold stress, respectively. However, qNGR1 and qNGR4 may be two major QTL affecting indica Changhui 891germination under normal condition. QTL qGRR1 and qGRR8 affected the seed germination recovery rate after cold stress and the alleles with increasing effects were shared by the Changhui 891 could improve seed germination rate after cold stress dramatically. These QTL could be a highly valuable genetic factors for cold tolerance improvement in rice lines. Moreover, the BRILs developed in this study will serve as an appropriate choice for mapping and studying genetic basis of rice complex traits.

  13. Muographic mapping of the subsurface density structures in Miura, Boso and Izu peninsulas, Japan.

    Science.gov (United States)

    Tanaka, Hiroyuki K M

    2015-02-09

    While the benefits of determining the bulk density distribution of a landmass are evident, established experimental techniques reliant on gravity measurements cannot uniquely determine the underground density distribution. We address this problem by taking advantage of traffic tunnels densely distributed throughout the country. Cosmic ray muon flux is measured in the tunnels to determine the average density of each rock overburden. After analyzing the data collected from 146 observation points in Miura, South-Boso and South-Izu Peninsula, Japan as an example, we mapped out the shallow density distribution of an area of 1340 km(2). We find a good agreement between muographically determined density distribution and geologic features as described in existing geological studies. The average shallow density distribution below each peninsula was determined with a great accuracy (less than ±0.8%). We also observed a significant reduction in density along fault lines and interpreted that as due to the presence of multiple cracks caused by mechanical stress during recurrent seismic events. We show that this new type of muography technique can be applied to estimate the terrain density and porosity distribution, thus determining more precise Bouguer reduction densities.

  14. Modelling risk of tick exposure in southern Scandinavia using machine learning techniques, satellite imagery, and human population density maps

    DEFF Research Database (Denmark)

    Kjær, Lene Jung; Korslund, L.; Kjelland, V.

    30 sites (forests and meadows) in each of Denmark, southern Norway and south-eastern Sweden. At each site we measured presence/absence of ticks, and used the data obtained along with environmental satellite images to run Boosted Regression Tree machine learning algorithms to predict overall spatial...... and Sweden), areas with high population densities tend to overlap with these zones.Machine learning techniques allow us to predict for larger areas without having to perform extensive sampling all over the region in question, and we were able to produce models and maps with high predictive value. The results...

  15. Derivation of elastic stiffness from site-matched mineral density and acoustic impedance maps

    International Nuclear Information System (INIS)

    Raum, Kay; Cleveland, Robin O; Peyrin, Francoise; Laugier, Pascal

    2006-01-01

    200 MHz acoustic impedance maps and site-matched synchrotron radiation micro computed tomography (SR-μCT) maps of tissue degree of mineralization of bone (DMB) were used to derive the elastic coefficient c 33 in cross sections of human cortical bone. To accomplish this goal, a model was developed to relate the DMB accessible with SR-μCT to mass density. The formulation incorporates the volume fractions and densities of the major bone tissue components (collagen, mineral and water), and accounts for tissue porosity. We found that the mass density can be well modelled by a second-order polynomial fit to DMB (R 2 = 0.999) and appears to be consistent with measurements of many different types of mineralized tissues. The derived elastic coefficient c 33 correlated more strongly with the acoustic impedance (R 2 = 0.996) than with mass density (R 2 = 0.310). This finding suggests that estimates of c 33 made from measurements of the acoustic impedance are more reliable than those made from density measurements. Mass density and elastic coefficient were in the range between 1.66 and 2.00 g cm -3 and 14.8 and 75.4 GPa, respectively. Although SAM inspection is limited to the evaluation of carefully prepared sample surfaces, it provides a two-dimensional quantitative estimate of elastic tissue properties at the tissue level

  16. Obtaining source current density related to irregularly structured electromagnetic target field inside human body using hybrid inverse/FDTD method.

    Science.gov (United States)

    Han, Jijun; Yang, Deqiang; Sun, Houjun; Xin, Sherman Xuegang

    2017-01-01

    Inverse method is inherently suitable for calculating the distribution of source current density related with an irregularly structured electromagnetic target field. However, the present form of inverse method cannot calculate complex field-tissue interactions. A novel hybrid inverse/finite-difference time domain (FDTD) method that can calculate the complex field-tissue interactions for the inverse design of source current density related with an irregularly structured electromagnetic target field is proposed. A Huygens' equivalent surface is established as a bridge to combine the inverse and FDTD method. Distribution of the radiofrequency (RF) magnetic field on the Huygens' equivalent surface is obtained using the FDTD method by considering the complex field-tissue interactions within the human body model. The obtained magnetic field distributed on the Huygens' equivalent surface is regarded as the next target. The current density on the designated source surface is derived using the inverse method. The homogeneity of target magnetic field and specific energy absorption rate are calculated to verify the proposed method.

  17. MRSA: a density-equalizing mapping analysis of the global research architecture.

    Science.gov (United States)

    Addicks, Johann P; Uibel, Stefanie; Jensen, Anna-Maria; Bundschuh, Matthias; Klingelhoefer, Doris; Groneberg, David A

    2014-09-30

    Methicillin-resistant Staphylococcus aureus (MRSA) has evolved as an alarming public health thread due to its global spread as hospital and community pathogen. Despite this role, a scientometric analysis has not been performed yet. Therefore, the NewQIS platform was used to conduct a combined density-equalizing mapping and scientometric study. As database, the Web of Science was used, and all entries between 1961 and 2007 were analyzed. In total, 7671 entries were identified. Density equalizing mapping demonstrated a distortion of the world map for the benefit of the USA as leading country with a total output of 2374 publications, followed by the UK (1030) and Japan (862). Citation rate analysis revealed Portugal as leading country with a rate of 35.47 citations per article, followed by New Zealand and Denmark. Country cooperation network analyses showed 743 collaborations with US-UK being most frequent. Network citation analyses indicated the publications that arose from the cooperation of USA and France as well as USA and Japan as the most cited (75.36 and 74.55 citations per collaboration article, respectively). The present study provides the first combined density-equalizing mapping and scientometric analysis of MRSA research. It illustrates the global MRSA research architecture. It can be assumed that this highly relevant topic for public health will achieve even greater dimensions in the future.

  18. Boson mapping of the shell model algebra obtained from a seniority-dictated similarity transformation

    International Nuclear Information System (INIS)

    Geyer, H.B.

    1986-01-01

    The qualitative ideas put forward by Geyer and Lee are given quantitative content by constructing a similarity transformation which reexpresses the Dyson boson images of the single-j shell fermion operators in terms of seniority bosons. It is shown that the results of Otsuka, Arima, and Iachello, or generalizations thereof which include g bosons or even bosons with J>4, can be obtained in an economic and transparent way without resorting to any comparison of matrix elements

  19. Construction of an SNP-based high-density linkage map for flax (Linum usitatissimum L.) using specific length amplified fragment sequencing (SLAF-seq) technology.

    Science.gov (United States)

    Yi, Liuxi; Gao, Fengyun; Siqin, Bateer; Zhou, Yu; Li, Qiang; Zhao, Xiaoqing; Jia, Xiaoyun; Zhang, Hui

    2017-01-01

    Flax is an important crop for oil and fiber, however, no high-density genetic maps have been reported for this species. Specific length amplified fragment sequencing (SLAF-seq) is a high-resolution strategy for large scale de novo discovery and genotyping of single nucleotide polymorphisms. In this study, SLAF-seq was employed to develop SNP markers in an F2 population to construct a high-density genetic map for flax. In total, 196.29 million paired-end reads were obtained. The average sequencing depth was 25.08 in male parent, 32.17 in the female parent, and 9.64 in each F2 progeny. In total, 389,288 polymorphic SLAFs were detected, from which 260,380 polymorphic SNPs were developed. After filtering, 4,638 SNPs were found suitable for genetic map construction. The final genetic map included 4,145 SNP markers on 15 linkage groups and was 2,632.94 cM in length, with an average distance of 0.64 cM between adjacent markers. To our knowledge, this map is the densest SNP-based genetic map for flax. The SNP markers and genetic map reported in here will serve as a foundation for the fine mapping of quantitative trait loci (QTLs), map-based gene cloning and marker assisted selection (MAS) for flax.

  20. A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut

    Directory of Open Access Journals (Sweden)

    Nagy Ervin D

    2012-09-01

    Full Text Available Abstract Background Cultivated peanut (Arachis hypogaea is an allotetraploid species whose ancestral genomes are most likely derived from the A-genome species, A. duranensis, and the B-genome species, A. ipaensis. The very recent (several millennia evolutionary origin of A. hypogaea has imposed a bottleneck for allelic and phenotypic diversity within the cultigen. However, wild diploid relatives are a rich source of alleles that could be used for crop improvement and their simpler genomes can be more easily analyzed while providing insight into the structure of the allotetraploid peanut genome. The objective of this research was to establish a high-density genetic map of the diploid species A. duranensis based on de novo generated EST databases. Arachis duranensis was chosen for mapping because it is the A-genome progenitor of cultivated peanut and also in order to circumvent the confounding effects of gene duplication associated with allopolyploidy in A. hypogaea. Results More than one million expressed sequence tag (EST sequences generated from normalized cDNA libraries of A. duranensis were assembled into 81,116 unique transcripts. Mining this dataset, 1236 EST-SNP markers were developed between two A. duranensis accessions, PI 475887 and Grif 15036. An additional 300 SNP markers also were developed from genomic sequences representing conserved legume orthologs. Of the 1536 SNP markers, 1054 were placed on a genetic map. In addition, 598 EST-SSR markers identified in A. hypogaea assemblies were included in the map along with 37 disease resistance gene candidate (RGC and 35 other previously published markers. In total, 1724 markers spanning 1081.3 cM over 10 linkage groups were mapped. Gene sequences that provided mapped markers were annotated using similarity searches in three different databases, and gene ontology descriptions were determined using the Medicago Gene Atlas and TAIR databases. Synteny analysis between A. duranensis, Medicago

  1. Construction of High Density Sweet Cherry (Prunus avium L. Linkage Maps Using Microsatellite Markers and SNPs Detected by Genotyping-by-Sequencing (GBS.

    Directory of Open Access Journals (Sweden)

    Verónica Guajardo

    Full Text Available Linkage maps are valuable tools in genetic and genomic studies. For sweet cherry, linkage maps have been constructed using mainly microsatellite markers (SSRs and, recently, using single nucleotide polymorphism markers (SNPs from a cherry 6K SNP array. Genotyping-by-sequencing (GBS, a new methodology based on high-throughput sequencing, holds great promise for identification of high number of SNPs and construction of high density linkage maps. In this study, GBS was used to identify SNPs from an intra-specific sweet cherry cross. A total of 8,476 high quality SNPs were selected for mapping. The physical position for each SNP was determined using the peach genome, Peach v1.0, as reference, and a homogeneous distribution of markers along the eight peach scaffolds was obtained. On average, 65.6% of the SNPs were present in genic regions and 49.8% were located in exonic regions. In addition to the SNPs, a group of SSRs was also used for construction of linkage maps. Parental and consensus high density maps were constructed by genotyping 166 siblings from a 'Rainier' x 'Rivedel' (Ra x Ri cross. Using Ra x Ri population, 462, 489 and 985 markers were mapped into eight linkage groups in 'Rainier', 'Rivedel' and the Ra x Ri map, respectively, with 80% of mapped SNPs located in genic regions. Obtained maps spanned 549.5, 582.6 and 731.3 cM for 'Rainier', 'Rivedel' and consensus maps, respectively, with an average distance of 1.2 cM between adjacent markers for both 'Rainier' and 'Rivedel' maps and of 0.7 cM for Ra x Ri map. High synteny and co-linearity was observed between obtained maps and with Peach v1.0. These new high density linkage maps provide valuable information on the sweet cherry genome, and serve as the basis for identification of QTLs and genes relevant for the breeding of the species.

  2. FOLD-EM: automated fold recognition in medium- and low-resolution (4-15 Å) electron density maps.

    Science.gov (United States)

    Saha, Mitul; Morais, Marc C

    2012-12-15

    Owing to the size and complexity of large multi-component biological assemblies, the most tractable approach to determining their atomic structure is often to fit high-resolution radiographic or nuclear magnetic resonance structures of isolated components into lower resolution electron density maps of the larger assembly obtained using cryo-electron microscopy (cryo-EM). This hybrid approach to structure determination requires that an atomic resolution structure of each component, or a suitable homolog, is available. If neither is available, then the amount of structural information regarding that component is limited by the resolution of the cryo-EM map. However, even if a suitable homolog cannot be identified using sequence analysis, a search for structural homologs should still be performed because structural homology often persists throughout evolution even when sequence homology is undetectable, As macromolecules can often be described as a collection of independently folded domains, one way of searching for structural homologs would be to systematically fit representative domain structures from a protein domain database into the medium/low resolution cryo-EM map and return the best fits. Taken together, the best fitting non-overlapping structures would constitute a 'mosaic' backbone model of the assembly that could aid map interpretation and illuminate biological function. Using the computational principles of the Scale-Invariant Feature Transform (SIFT), we have developed FOLD-EM-a computational tool that can identify folded macromolecular domains in medium to low resolution (4-15 Å) electron density maps and return a model of the constituent polypeptides in a fully automated fashion. As a by-product, FOLD-EM can also do flexible multi-domain fitting that may provide insight into conformational changes that occur in macromolecular assemblies.

  3. A hybrid genetic linkage map of two ecologically and morphologically divergent Midas cichlid fishes (Amphilophus spp.) obtained by massively parallel DNA sequencing (ddRADSeq).

    Science.gov (United States)

    Recknagel, Hans; Elmer, Kathryn R; Meyer, Axel

    2013-01-01

    Cichlid fishes are an excellent model system for studying speciation and the formation of adaptive radiations because of their tremendous species richness and astonishing phenotypic diversity. Most research has focused on African rift lake fishes, although Neotropical cichlid species display much variability as well. Almost one dozen species of the Midas cichlid species complex (Amphilophus spp.) have been described so far and have formed repeated adaptive radiations in several Nicaraguan crater lakes. Here we apply double-digest restriction-site associated DNA sequencing to obtain a high-density linkage map of an interspecific cross between the benthic Amphilophus astorquii and the limnetic Amphilophus zaliosus, which are sympatric species endemic to Crater Lake Apoyo, Nicaragua. A total of 755 RAD markers were genotyped in 343 F(2) hybrids. The map resolved 25 linkage groups and spans a total distance of 1427 cM with an average marker spacing distance of 1.95 cM, almost matching the total number of chromosomes (n = 24) in these species. Regions of segregation distortion were identified in five linkage groups. Based on the pedigree of parents to F(2) offspring, we calculated a genome-wide mutation rate of 6.6 × 10(-8) mutations per nucleotide per generation. This genetic map will facilitate the mapping of ecomorphologically relevant adaptive traits in the repeated phenotypes that evolved within the Midas cichlid lineage and, as the first linkage map of a Neotropical cichlid, facilitate comparative genomic analyses between African cichlids, Neotropical cichlids and other teleost fishes.

  4. Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers.

    Directory of Open Access Journals (Sweden)

    Huihui Yu

    Full Text Available Huge efforts have been invested in the last two decades to dissect the genetic bases of complex traits including yields of many crop plants, through quantitative trait locus (QTL analyses. However, almost all the studies were based on linkage maps constructed using low-throughput molecular markers, e.g. restriction fragment length polymorphisms (RFLPs and simple sequence repeats (SSRs, thus are mostly of low density and not able to provide precise and complete information about the numbers and locations of the genes or QTLs controlling the traits. In this study, we constructed an ultra-high density genetic map based on high quality single nucleotide polymorphisms (SNPs from low-coverage sequences of a recombinant inbred line (RIL population of rice, generated using new sequencing technology. The quality of the map was assessed by validating the positions of several cloned genes including GS3 and GW5/qSW5, two major QTLs for grain length and grain width respectively, and OsC1, a qualitative trait locus for pigmentation. In all the cases the loci could be precisely resolved to the bins where the genes are located, indicating high quality and accuracy of the map. The SNP map was used to perform QTL analysis for yield and three yield-component traits, number of tillers per plant, number of grains per panicle and grain weight, using data from field trials conducted over years, in comparison to QTL mapping based on RFLPs/SSRs. The SNP map detected more QTLs especially for grain weight, with precise map locations, demonstrating advantages in detecting power and resolution relative to the RFLP/SSR map. Thus this study provided an example for ultra-high density map construction using sequencing technology. Moreover, the results obtained are helpful for understanding the genetic bases of the yield traits and for fine mapping and cloning of QTLs.

  5. Mapping the Local Density of Optical States of a Photonic Crystal with Single Quantum Dots

    DEFF Research Database (Denmark)

    Wang, Qin; Stobbe, Søren; Lodahl, Peter

    2011-01-01

    We use single self-assembled InGaAs quantum dots as internal probes to map the local density of optical states of photonic crystal membranes. The employed technique separates contributions from nonradiative recombination and spin-flip processes by properly accounting for the role of the exciton...... fine structure. We observe inhibition factors as high as 70 and compare our results to local density of optical states calculations available from the literature, thereby establishing a quantitative understanding of photon emission in photonic crystal membranes. © 2011 American Physical Society....

  6. High current density ion beam obtained by a transition to a highly focused state in extremely low-energy region

    Energy Technology Data Exchange (ETDEWEB)

    Hirano, Y., E-mail: y.hirano@aist.go.jp, E-mail: hirano.yoichi@phys.cst.nihon-u.ac.jp [Innovative Plasma Processing Group, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568 (Japan); College of Science and Technologies, Nihon University, Chiyodaku, Tokyo 101-0897 (Japan); Kiyama, S.; Koguchi, H. [Innovative Plasma Processing Group, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568 (Japan); Fujiwara, Y.; Sakakita, H. [Innovative Plasma Processing Group, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568 (Japan); Department of Engineering Mechanics and Energy, University of Tsukuba, Ibaraki 305-8577 (Japan)

    2015-11-15

    A high current density (≈3 mA/cm{sup 2}) hydrogen ion beam source operating in an extremely low-energy region (E{sub ib} ≈ 150–200 eV) has been realized by using a transition to a highly focused state, where the beam is extracted from the ion source chamber through three concave electrodes with nominal focal lengths of ≈350 mm. The transition occurs when the beam energy exceeds a threshold value between 145 and 170 eV. Low-level hysteresis is observed in the transition when E{sub ib} is being reduced. The radial profiles of the ion beam current density and the low temperature ion current density can be obtained separately using a Faraday cup with a grid in front. The measured profiles confirm that more than a half of the extracted beam ions reaches the target plate with a good focusing profile with a full width at half maximum of ≈3 cm. Estimation of the particle balances in beam ions, the slow ions, and the electrons indicates the possibility that the secondary electron emission from the target plate and electron impact ionization of hydrogen may play roles as particle sources in this extremely low-energy beam after the compensation of beam ion space charge.

  7. High-density Integrated Linkage Map Based on SSR Markers in Soybean

    Science.gov (United States)

    Hwang, Tae-Young; Sayama, Takashi; Takahashi, Masakazu; Takada, Yoshitake; Nakamoto, Yumi; Funatsuki, Hideyuki; Hisano, Hiroshi; Sasamoto, Shigemi; Sato, Shusei; Tabata, Satoshi; Kono, Izumi; Hoshi, Masako; Hanawa, Masayoshi; Yano, Chizuru; Xia, Zhengjun; Harada, Kyuya; Kitamura, Keisuke; Ishimoto, Masao

    2009-01-01

    A well-saturated molecular linkage map is a prerequisite for modern plant breeding. Several genetic maps have been developed for soybean with various types of molecular markers. Simple sequence repeats (SSRs) are single-locus markers with high allelic variation and are widely applicable to different genotypes. We have now mapped 1810 SSR or sequence-tagged site markers in one or more of three recombinant inbred populations of soybean (the US cultivar ‘Jack’ × the Japanese cultivar ‘Fukuyutaka’, the Chinese cultivar ‘Peking’ × the Japanese cultivar ‘Akita’, and the Japanese cultivar ‘Misuzudaizu’ × the Chinese breeding line ‘Moshidou Gong 503’) and have aligned these markers with the 20 consensus linkage groups (LGs). The total length of the integrated linkage map was 2442.9 cM, and the average number of molecular markers was 90.5 (range of 70–114) for the 20 LGs. We examined allelic diversity for 1238 of the SSR markers among 23 soybean cultivars or lines and a wild accession. The number of alleles per locus ranged from 2 to 7, with an average of 2.8. Our high-density linkage map should facilitate ongoing and future genomic research such as analysis of quantitative trait loci and positional cloning in addition to marker-assisted selection in soybean breeding. PMID:19531560

  8. Phenotypic transition maps of 3D breast acini obtained by imaging-guided agent-based modeling

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Jonathan; Enderling, Heiko; Becker-Weimann, Sabine; Pham, Christopher; Polyzos, Aris; Chen, Chen-Yi; Costes, Sylvain V

    2011-02-18

    We introduce an agent-based model of epithelial cell morphogenesis to explore the complex interplay between apoptosis, proliferation, and polarization. By varying the activity levels of these mechanisms we derived phenotypic transition maps of normal and aberrant morphogenesis. These maps identify homeostatic ranges and morphologic stability conditions. The agent-based model was parameterized and validated using novel high-content image analysis of mammary acini morphogenesis in vitro with focus on time-dependent cell densities, proliferation and death rates, as well as acini morphologies. Model simulations reveal apoptosis being necessary and sufficient for initiating lumen formation, but cell polarization being the pivotal mechanism for maintaining physiological epithelium morphology and acini sphericity. Furthermore, simulations highlight that acinus growth arrest in normal acini can be achieved by controlling the fraction of proliferating cells. Interestingly, our simulations reveal a synergism between polarization and apoptosis in enhancing growth arrest. After validating the model with experimental data from a normal human breast line (MCF10A), the system was challenged to predict the growth of MCF10A where AKT-1 was overexpressed, leading to reduced apoptosis. As previously reported, this led to non growth-arrested acini, with very large sizes and partially filled lumen. However, surprisingly, image analysis revealed a much lower nuclear density than observed for normal acini. The growth kinetics indicates that these acini grew faster than the cells comprising it. The in silico model could not replicate this behavior, contradicting the classic paradigm that ductal carcinoma in situ is only the result of high proliferation and low apoptosis. Our simulations suggest that overexpression of AKT-1 must also perturb cell-cell and cell-ECM communication, reminding us that extracellular context can dictate cellular behavior.

  9. High-density genetic map using whole-genome re-sequencing for fine mapping and candidate gene discovery for disease resistance in peanut

    Science.gov (United States)

    High-density genetic linkage maps are essential for fine mapping QTLs controlling disease resistance traits, such as early leaf spot (ELS), late leaf spot (LLS), and Tomato spotted wilt virus (TSWV). With completion of the genome sequences of two diploid ancestors of cultivated peanut, we could use ...

  10. Genotyping-by-Sequencing derived High-Density Linkage Map and its Application to QTL Mapping of Flag Leaf Traits in Bread Wheat

    Science.gov (United States)

    Hard red winter wheat parents ‘Harry’ (drought tolerant) and ‘Wesley’ (drought susceptible) was used to develop a recombinant inbred population to identify genomic regions associated with drought and adaptation. To precisely map genomic regions high-density linkage maps are a prerequisite. In this s...

  11. Galaxy bias from the Dark Energy Survey Science Verification data: combining galaxy density maps and weak lensing maps

    Energy Technology Data Exchange (ETDEWEB)

    Chang, C.; Pujol, A.; Gaztañaga, E.; Amara, A.; Réfrégier, A.; Bacon, D.; Becker, M. R.; Bonnett, C.; Carretero, J.; Castander, F. J.; Crocce, M.; Fosalba, P.; Giannantonio, T.; Hartley, W.; Jarvis, M.; Kacprzak, T.; Ross, A. J.; Sheldon, E.; Troxel, M. A.; Vikram, V.; Zuntz, J.; Abbott, T. M. C.; Abdalla, F. B.; Allam, S.; Annis, J.; Benoit-Lévy, A.; Bertin, E.; Brooks, D.; Buckley-Geer, E.; Burke, D. L.; Capozzi, D.; Rosell, A. Carnero; Kind, M. Carrasco; Cunha, C. E.; D' Andrea, C. B.; da Costa, L. N.; Desai, S.; Diehl, H. T.; Dietrich, J. P.; Doel, P.; Eifler, T. F.; Estrada, J.; Evrard, A. E.; Flaugher, B.; Frieman, J.; Goldstein, D. A.; Gruen, D.; Gruendl, R. A.; Gutierrez, G.; Honscheid, K.; Jain, B.; James, D. J.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Li, T. S.; Lima, M.; Marshall, J. L.; Martini, P.; Melchior, P.; Miller, C. J.; Miquel, R.; Mohr, J. J.; Nichol, R. C.; Nord, B.; Ogando, R.; Plazas, A. A.; Reil, K.; Romer, A. K.; Roodman, A.; Rykoff, E. S.; Sanchez, E.; Scarpine, V.; Schubnell, M.; Sevilla-Noarbe, I.; Smith, R. C.; Soares-Santos, M.; Sobreira, F.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Thomas, D.; Walker, A. R.

    2016-04-15

    We measure the redshift evolution of galaxy bias from a magnitude-limited galaxy sample by combining the galaxy density maps and weak lensing shear maps for a $\\sim$116 deg$^{2}$ area of the Dark Energy Survey (DES) Science Verification data. This method was first developed in Amara et al. (2012) and later re-examined in a companion paper (Pujol et al., in prep) with rigorous simulation tests and analytical treatment of tomographic measurements. In this work we apply this method to the DES SV data and measure the galaxy bias for a magnitude-limited galaxy sample. We find the galaxy bias and 1$\\sigma$ error bars in 4 photometric redshift bins to be 1.33$\\pm$0.18 (z=0.2-0.4), 1.19$\\pm$0.23 (z=0.4-0.6), 0.99$\\pm$0.36 ( z=0.6-0.8), and 1.66$\\pm$0.56 (z=0.8-1.0). These measurements are consistent at the 1-2$\\sigma$ level with mea- surements on the same dataset using galaxy clustering and cross-correlation of galaxies with CMB lensing. In addition, our method provides the only $\\sigma_8$-independent constraint among the three. We forward-model the main observational effects using mock galaxy catalogs by including shape noise, photo-z errors and masking effects. We show that our bias measurement from the data is consistent with that expected from simulations. With the forthcoming full DES data set, we expect this method to provide additional constraints on the galaxy bias measurement from more traditional methods. Furthermore, in the process of our measurement, we build up a 3D mass map that allows further exploration of the dark matter distribution and its relation to galaxy evolution.

  12. MCTP system model based on linear programming optimization of apertures obtained from sequencing patient image data maps

    Energy Technology Data Exchange (ETDEWEB)

    Ureba, A. [Dpto. Fisiología Médica y Biofísica. Facultad de Medicina, Universidad de Sevilla, E-41009 Sevilla (Spain); Salguero, F. J. [Nederlands Kanker Instituut, Antoni van Leeuwenhoek Ziekenhuis, 1066 CX Ámsterdam, The Nederlands (Netherlands); Barbeiro, A. R.; Jimenez-Ortega, E.; Baeza, J. A.; Leal, A., E-mail: alplaza@us.es [Dpto. Fisiología Médica y Biofísica, Facultad de Medicina, Universidad de Sevilla, E-41009 Sevilla (Spain); Miras, H. [Servicio de Radiofísica, Hospital Universitario Virgen Macarena, E-41009 Sevilla (Spain); Linares, R.; Perucha, M. [Servicio de Radiofísica, Hospital Infanta Luisa, E-41010 Sevilla (Spain)

    2014-08-15

    irradiation case (Case II) solved with photon and electron modulated beams (IMRT + MERT); and a prostatic bed case (Case III) with a pronounced concave-shaped PTV by using volumetric modulated arc therapy. In the three cases, the required target prescription doses and constraints on organs at risk were fulfilled in a short enough time to allow routine clinical implementation. The quality assurance protocol followed to check CARMEN system showed a high agreement with the experimental measurements. Conclusions: A Monte Carlo treatment planning model exclusively based on maps performed from patient imaging data has been presented. The sequencing of these maps allows obtaining deliverable apertures which are weighted for modulation under a linear programming formulation. The model is able to solve complex radiotherapy treatments with high accuracy in an efficient computation time.

  13. MCTP system model based on linear programming optimization of apertures obtained from sequencing patient image data maps

    International Nuclear Information System (INIS)

    Ureba, A.; Salguero, F. J.; Barbeiro, A. R.; Jimenez-Ortega, E.; Baeza, J. A.; Leal, A.; Miras, H.; Linares, R.; Perucha, M.

    2014-01-01

    irradiation case (Case II) solved with photon and electron modulated beams (IMRT + MERT); and a prostatic bed case (Case III) with a pronounced concave-shaped PTV by using volumetric modulated arc therapy. In the three cases, the required target prescription doses and constraints on organs at risk were fulfilled in a short enough time to allow routine clinical implementation. The quality assurance protocol followed to check CARMEN system showed a high agreement with the experimental measurements. Conclusions: A Monte Carlo treatment planning model exclusively based on maps performed from patient imaging data has been presented. The sequencing of these maps allows obtaining deliverable apertures which are weighted for modulation under a linear programming formulation. The model is able to solve complex radiotherapy treatments with high accuracy in an efficient computation time

  14. MCTP system model based on linear programming optimization of apertures obtained from sequencing patient image data maps.

    Science.gov (United States)

    Ureba, A; Salguero, F J; Barbeiro, A R; Jimenez-Ortega, E; Baeza, J A; Miras, H; Linares, R; Perucha, M; Leal, A

    2014-08-01

    with photon and electron modulated beams (IMRT + MERT); and a prostatic bed case (Case III) with a pronounced concave-shaped PTV by using volumetric modulated arc therapy. In the three cases, the required target prescription doses and constraints on organs at risk were fulfilled in a short enough time to allow routine clinical implementation. The quality assurance protocol followed to check CARMEN system showed a high agreement with the experimental measurements. A Monte Carlo treatment planning model exclusively based on maps performed from patient imaging data has been presented. The sequencing of these maps allows obtaining deliverable apertures which are weighted for modulation under a linear programming formulation. The model is able to solve complex radiotherapy treatments with high accuracy in an efficient computation time.

  15. Effect of Co-segregating Markers on High-Density Genetic Maps and Prediction of Map Expansion Using Machine Learning Algorithms.

    Science.gov (United States)

    N'Diaye, Amidou; Haile, Jemanesh K; Fowler, D Brian; Ammar, Karim; Pozniak, Curtis J

    2017-01-01

    Advances in sequencing and genotyping methods have enable cost-effective production of high throughput single nucleotide polymorphism (SNP) markers, making them the choice for linkage mapping. As a result, many laboratories have developed high-throughput SNP assays and built high-density genetic maps. However, the number of markers may, by orders of magnitude, exceed the resolution of recombination for a given population size so that only a minority of markers can accurately be ordered. Another issue attached to the so-called 'large p, small n' problem is that high-density genetic maps inevitably result in many markers clustering at the same position (co-segregating markers). While there are a number of related papers, none have addressed the impact of co-segregating markers on genetic maps. In the present study, we investigated the effects of co-segregating markers on high-density genetic map length and marker order using empirical data from two populations of wheat, Mohawk × Cocorit (durum wheat) and Norstar × Cappelle Desprez (bread wheat). The maps of both populations consisted of 85% co-segregating markers. Our study clearly showed that excess of co-segregating markers can lead to map expansion, but has little effect on markers order. To estimate the inflation factor (IF), we generated a total of 24,473 linkage maps (8,203 maps for Mohawk × Cocorit and 16,270 maps for Norstar × Cappelle Desprez). Using seven machine learning algorithms, we were able to predict with an accuracy of 0.7 the map expansion due to the proportion of co-segregating markers. For example in Mohawk × Cocorit, with 10 and 80% co-segregating markers the length of the map inflated by 4.5 and 16.6%, respectively. Similarly, the map of Norstar × Cappelle Desprez expanded by 3.8 and 11.7% with 10 and 80% co-segregating markers. With the increasing number of markers on SNP-chips, the proportion of co-segregating markers in high-density maps will continue to increase making map expansion

  16. Effect of Co-segregating Markers on High-Density Genetic Maps and Prediction of Map Expansion Using Machine Learning Algorithms

    Directory of Open Access Journals (Sweden)

    Amidou N’Diaye

    2017-08-01

    Full Text Available Advances in sequencing and genotyping methods have enable cost-effective production of high throughput single nucleotide polymorphism (SNP markers, making them the choice for linkage mapping. As a result, many laboratories have developed high-throughput SNP assays and built high-density genetic maps. However, the number of markers may, by orders of magnitude, exceed the resolution of recombination for a given population size so that only a minority of markers can accurately be ordered. Another issue attached to the so-called ‘large p, small n’ problem is that high-density genetic maps inevitably result in many markers clustering at the same position (co-segregating markers. While there are a number of related papers, none have addressed the impact of co-segregating markers on genetic maps. In the present study, we investigated the effects of co-segregating markers on high-density genetic map length and marker order using empirical data from two populations of wheat, Mohawk × Cocorit (durum wheat and Norstar × Cappelle Desprez (bread wheat. The maps of both populations consisted of 85% co-segregating markers. Our study clearly showed that excess of co-segregating markers can lead to map expansion, but has little effect on markers order. To estimate the inflation factor (IF, we generated a total of 24,473 linkage maps (8,203 maps for Mohawk × Cocorit and 16,270 maps for Norstar × Cappelle Desprez. Using seven machine learning algorithms, we were able to predict with an accuracy of 0.7 the map expansion due to the proportion of co-segregating markers. For example in Mohawk × Cocorit, with 10 and 80% co-segregating markers the length of the map inflated by 4.5 and 16.6%, respectively. Similarly, the map of Norstar × Cappelle Desprez expanded by 3.8 and 11.7% with 10 and 80% co-segregating markers. With the increasing number of markers on SNP-chips, the proportion of co-segregating markers in high-density maps will continue to increase

  17. Improving snow density estimation for mapping SWE with Lidar snow depth: assessment of uncertainty in modeled density and field sampling strategies in NASA SnowEx

    Science.gov (United States)

    Raleigh, M. S.; Smyth, E.; Small, E. E.

    2017-12-01

    The spatial distribution of snow water equivalent (SWE) is not sufficiently monitored with either remotely sensed or ground-based observations for water resources management. Recent applications of airborne Lidar have yielded basin-wide mapping of SWE when combined with a snow density model. However, in the absence of snow density observations, the uncertainty in these SWE maps is dominated by uncertainty in modeled snow density rather than in Lidar measurement of snow depth. Available observations tend to have a bias in physiographic regime (e.g., flat open areas) and are often insufficient in number to support testing of models across a range of conditions. Thus, there is a need for targeted sampling strategies and controlled model experiments to understand where and why different snow density models diverge. This will enable identification of robust model structures that represent dominant processes controlling snow densification, in support of basin-scale estimation of SWE with remotely-sensed snow depth datasets. The NASA SnowEx mission is a unique opportunity to evaluate sampling strategies of snow density and to quantify and reduce uncertainty in modeled snow density. In this presentation, we present initial field data analyses and modeling results over the Colorado SnowEx domain in the 2016-2017 winter campaign. We detail a framework for spatially mapping the uncertainty in snowpack density, as represented across multiple models. Leveraging the modular SUMMA model, we construct a series of physically-based models to assess systematically the importance of specific process representations to snow density estimates. We will show how models and snow pit observations characterize snow density variations with forest cover in the SnowEx domains. Finally, we will use the spatial maps of density uncertainty to evaluate the selected locations of snow pits, thereby assessing the adequacy of the sampling strategy for targeting uncertainty in modeled snow density.

  18. Effect of ionizing radiation on nanocomposites of high density polyethylene with pseudoboehmite obtained by sol-gel process

    International Nuclear Information System (INIS)

    Miranda, Leila F.; Munhoz Junior, Antonio H.; Terence, Mauro C.; Alves, Alexandre P.

    2009-01-01

    Nanocomposites are polymeric hybrid materials where inorganic substances of nanometric dimensions are dispersed in a polymeric matrix. The fillers present area of raised surface, promoting better dispersion in the polymeric matrix and therefore an improvement of the physical properties of the composite that depends on the homogeneity of the material. The nanocomposites preparation with polymeric matrix allows in many cases to find a relation enters a low cost, due to the use of minor amount of filler, and a raised performance level. Nanocomposites were obtained with pseudoboehmite synthesized by sol-gel process and high density polyethylene with different concentrations of pseudoboehmite. The aim of this work was to study the effects of ionizing radiation on the properties of the nanocomposites obtained. The nanocomposites were prepared by melt intercalation technique and subsequently, the samples were molded by injection, irradiated and submitted to thermal and mechanical tests. The mechanical properties (impact strength and tensile strength), temperature of thermal distortion (HDT) and Vicat softening temperature of the non irradiated and irradiated nanocomposites were determined. The irradiation doses were of 30, 50 and 100kGy in a gamma cell. The results showed an increase in the values of tensile strength; a decrease in the impact strength and an increase in the temperature of thermal distortion (HDT) evidencing the interaction of nanofiller with the polymeric matrix. (author)

  19. Magnetic resonance imaging. Density equalizing mapping analysis of global research architecture; Magnetresonanztomographie. Eine Density-equalizing-mapping-Analyse der globalen Forschungsarchitektur

    Energy Technology Data Exchange (ETDEWEB)

    Ohlendorf, D.; Schwarze, B.; Groneberg, D.A.; Schwarzer, M. [Goethe-Universitaet Frankfurt/M, Institut fuer Arbeitsmedizin, Sozialmedizin und Umweltmedizin, Frankfurt/M (Germany)

    2015-09-15

    Despite the great medical importance, there is still no comprehensive scientometric analysis regarding the results of magnetic resonance imaging (MRI) and the development of the importance for the healthcare system. This paper evaluated and analyzed the entire research publication results on the topic of MRI for the period 1981-2007 based on scientometric methods and parameters. A scientometric analysis (database: ISI Web of Science 1981-2007, search terms MRI and magnetic resonance imaging) was performed. The following parameters were analyzed: number of publications, countries of publication, number of citations, citation rate and collaborations, using various analytical and display techniques, including density equalizing map projections. Most of the 49,122 publications on MRI could be attributed to the USA (32.5 %), which also has the most cooperative collaborations. Within Europe, Germany (10.3 %) is the country with the highest number of publications followed by the UK (9.3 %). The western industrialized nations dominate over the rest of the world in terms of scientific developments of MRI. The thematic focus of the publications lies in the fields of radiology and neuroscience. In addition to the journal Neurology most scientific articles were published in Magnetic Resonance in Medicine and Circulation. The results show that the current trend is continuing and the scientific interest in MRI is continuously increasing. (orig.) [German] Trotz der grossen medizinischen Bedeutung existiert bis heute keine umfassende szientometrische Analyse bzgl. der Forschungsergebnisse zur Magnetresonanztomographie (MRT) und der Entwicklung ihrer Bedeutung fuer das Gesundheitssystem. Im vorliegenden Beitrag soll anhand szientometrischer Methoden und Parameter das gesamte Forschungsaufkommen zum Thema MRT fuer den Zeitraum 1981-2007 evaluiert und analysiert werden. Es wurde eine szientometrische Analyse (Datenbank: ISI-Web of Science, 1981-2007; Suchterm &apos

  20. Comparing 511 keV Attenuation Maps Obtained from Different Energy Mapping Methods for CT Based Attenuation Correction of PET Data

    Directory of Open Access Journals (Sweden)

    Maryam Shirmohammad

    2008-06-01

    Full Text Available Introduction:  The  advent  of  dual-modality  PET/CT  scanners  has  revolutionized  clinical  oncology  by  improving lesion localization and facilitating treatment planning for radiotherapy. In addition, the use of  CT images for CT-based attenuation correction (CTAC decreases the overall scanning time and creates  a noise-free  attenuation  map  (6map.  CTAC  methods  include  scaling,  segmentation,  hybrid  scaling/segmentation, bilinear and dual energy methods. All CTAC methods require the transformation  of CT Hounsfield units (HU to linear attenuation coefficients (LAC at 511 keV. The aim of this study is  to compare the results of implementing different methods of energy mapping in PET/CT scanners.   Materials and Methods: This study was conducted in 2 phases, the first phase in a phantom and the  second  one  on  patient  data.  To  perform  the  first  phase,  a  cylindrical  phantom  with  different  concentrations of K2HPO4 inserts was CT scanned and energy mapping methods were implemented on  it. For performing the second phase, different energy  mapping  methods  were implemented on several  clinical studies and compared to the transmission (TX image derived using Ga-68 radionuclide source  acquired on the GE Discovery LS PET/CT scanner.   Results: An ROI analysis was performed on different positions of the resultant 6maps and the average  6value of each ROI was compared to the reference value. The results of the 6maps obtained for 511 keV  compared to the theoretical  values showed that in the phantom for low  concentrations  of K 2 HPO 4 all  these  methods  produce  511  keV  attenuation  maps  with  small  relative  difference  compared  to  gold  standard. The relative difference for scaling, segmentation, hybrid, bilinear and dual energy methods was  4.92,  3.21,  4.43,  2.24  and  2.29%,  respectively.  Although  for  high  concentration

  1. Mapping the ‘End Austerity Now’ protest day in Central London using a 3D Twitter density grid

    Directory of Open Access Journals (Sweden)

    Seungho Yoo

    2016-01-01

    Full Text Available The mapping and spatial analysis of social media data can show the dynamics of activities in urban space, such as protest events. This work focuses on the spatial relationship between the density of geo-tagged tweets and a large anti-government protest in London on 20 June 2015. The tweets are aggregated to hexagonal grid cells to visualize activity density in different Central London areas. The results of the mapping illustrate very high densities at the beginning and endpoints of the protest (the Bank of England and Parliament Square. Additionally, there are high tweet densities in the West End and Bank than in other neighbouring areas.

  2. REJUVENATING THE MATTER POWER SPECTRUM: RESTORING INFORMATION WITH A LOGARITHMIC DENSITY MAPPING

    International Nuclear Information System (INIS)

    Neyrinck, Mark C.; Szalay, Alexander S.; Szapudi, Istvan

    2009-01-01

    We find that nonlinearities in the dark matter power spectrum are dramatically smaller if the density field first undergoes a logarithmic mapping. In the Millennium simulation, this procedure gives a power spectrum with a shape hardly departing from the linear power spectrum for k ∼ -1 at all redshifts. Also, this procedure unveils pristine Fisher information on a range of scales reaching a factor of 2-3 smaller than in the standard power spectrum, yielding 10 times more cumulative signal to noise at z = 0.

  3. Van der Waals potentials between metal clusters and helium atoms obtained with density functional theory and linear response methods

    International Nuclear Information System (INIS)

    Liebrecht, M.

    2014-01-01

    The importance of van der Waals interactions in many diverse research fields such as, e. g., polymer science, nano--materials, structural biology, surface science and condensed matter physics created a high demand for efficient and accurate methods that can describe van der Waals interactions from first principles. These methods should be able to deal with large and complex systems to predict functions and properties of materials that are technologically and biologically relevant. Van der Waals interactions arise due to quantum mechanical correlation effects and finding appropriate models an numerical techniques to describe this type of interaction is still an ongoing challenge in electronic structure and condensed matter theory. This thesis introduces a new variational approach to obtain intermolecular interaction potentials between clusters and helium atoms by means of density functional theory and linear response methods. It scales almost linearly with the number of electrons and can therefore be applied to much larger systems than standard quantum chemistry techniques. The main focus of this work is the development of an ab-initio method to account for London dispersion forces, which are purely attractive and dominate the interaction of non--polar atoms and molecules at large distances. (author) [de

  4. Construction and analysis of a high-density genetic linkage map in cabbage (Brassica oleracea L. var. capitata

    Directory of Open Access Journals (Sweden)

    Wang Wanxing

    2012-10-01

    Full Text Available Abstract Background Brassica oleracea encompass a family of vegetables and cabbage that are among the most widely cultivated crops. In 2009, the B. oleracea Genome Sequencing Project was launched using next generation sequencing technology. None of the available maps were detailed enough to anchor the sequence scaffolds for the Genome Sequencing Project. This report describes the development of a large number of SSR and SNP markers from the whole genome shotgun sequence data of B. oleracea, and the construction of a high-density genetic linkage map using a double haploid mapping population. Results The B. oleracea high-density genetic linkage map that was constructed includes 1,227 markers in nine linkage groups spanning a total of 1197.9 cM with an average of 0.98 cM between adjacent loci. There were 602 SSR markers and 625 SNP markers on the map. The chromosome with the highest number of markers (186 was C03, and the chromosome with smallest number of markers (99 was C09. Conclusions This first high-density map allowed the assembled scaffolds to be anchored to pseudochromosomes. The map also provides useful information for positional cloning, molecular breeding, and integration of information of genes and traits in B. oleracea. All the markers on the map will be transferable and could be used for the construction of other genetic maps.

  5. Magnetic resonance fiber density mapping of age-related white matter changes

    International Nuclear Information System (INIS)

    Stadlbauer, Andreas; Ganslandt, Oliver; Salomonowitz, Erich; Buchfelder, Michael; Hammen, Thilo; Bachmair, Johanna; Eberhardt, Knut

    2012-01-01

    Objectives: To introduce fiber density mapping (FDM) for investigation of age-related white matter (WM) changes and to compare its capabilities with conventional diffusion tensor imaging (DTI) post-processing. Methods: DTI data with 1.9 mm 3 isotropic voxels were acquired from 44 healthy volunteers (18–88 years) at 3 T. FDM is a 3-step approach which includes diagonalization of the diffusion tensor, fiber reconstruction for the whole brain, and calculation of fiber density (FD) values. Maps of fractional anisotropy (FA) and mean diffusivity (MD) were additionally calculated. Voxel-based analyses were performed to determine volume clusters of significant correlation with age. Bivariate linear regression models and Hotelling–Williams tests were used to detect significant differences between correlations. Results: FDM detected a larger WM volume affected by age-related changes concomitant with fewer significant clusters compared to FA and MD. This indicates that WM alterations due to normal aging occur rather globally than locally. FD values showed a significant stronger correlation with age in frontal lobes (prefrontal and precentral gyrus), limbic lobes (cingulate and parahippocampal gyrus), the corpus callosum (genu) and temporal lobes. Conclusions: FDM shows higher sensitivity for detection of age-related WM changes because it includes all surrounding fiber structures into the evaluation of each DTI data voxel.

  6. Magnetic resonance fiber density mapping of age-related white matter changes

    Energy Technology Data Exchange (ETDEWEB)

    Stadlbauer, Andreas, E-mail: andi@nmr.at [MR Physics Group, Department of Radiology, Landesklinikum St. Poelten, Propst Fuehrer Strasse 4, A-3100 St. Poelten (Austria); Department of Neurosurgery, University of Erlangen-Nuremberg, Schwabachanlage 6, 91054 Erlangen (Germany); Ganslandt, Oliver [Department of Neurosurgery, University of Erlangen-Nuremberg, Schwabachanlage 6, 91054 Erlangen (Germany); Salomonowitz, Erich [MR Physics Group, Department of Radiology, Landesklinikum St. Poelten, Propst Fuehrer Strasse 4, A-3100 St. Poelten (Austria); Buchfelder, Michael [Department of Neurosurgery, University of Erlangen-Nuremberg, Schwabachanlage 6, 91054 Erlangen (Germany); Hammen, Thilo [Department of Neurology, Epilepsy Center, University of Erlangen-Nuremberg, Schwabachanlage 6, D-90429 Erlangen (Germany); Bachmair, Johanna [MR Physics Group, Department of Radiology, Landesklinikum St. Poelten, Propst Fuehrer Strasse 4, A-3100 St. Poelten (Austria); Eberhardt, Knut [Krankenhaus Schloss Werneck, MRT-Kompetenzzentrum, Balthasar-Neumann-Platz 1, D-97440 Werneck (Germany)

    2012-12-15

    Objectives: To introduce fiber density mapping (FDM) for investigation of age-related white matter (WM) changes and to compare its capabilities with conventional diffusion tensor imaging (DTI) post-processing. Methods: DTI data with 1.9 mm{sup 3} isotropic voxels were acquired from 44 healthy volunteers (18–88 years) at 3 T. FDM is a 3-step approach which includes diagonalization of the diffusion tensor, fiber reconstruction for the whole brain, and calculation of fiber density (FD) values. Maps of fractional anisotropy (FA) and mean diffusivity (MD) were additionally calculated. Voxel-based analyses were performed to determine volume clusters of significant correlation with age. Bivariate linear regression models and Hotelling–Williams tests were used to detect significant differences between correlations. Results: FDM detected a larger WM volume affected by age-related changes concomitant with fewer significant clusters compared to FA and MD. This indicates that WM alterations due to normal aging occur rather globally than locally. FD values showed a significant stronger correlation with age in frontal lobes (prefrontal and precentral gyrus), limbic lobes (cingulate and parahippocampal gyrus), the corpus callosum (genu) and temporal lobes. Conclusions: FDM shows higher sensitivity for detection of age-related WM changes because it includes all surrounding fiber structures into the evaluation of each DTI data voxel.

  7. Evaluation of realistic layouts for next generation on-scalp MEG: spatial information density maps.

    Science.gov (United States)

    Riaz, Bushra; Pfeiffer, Christoph; Schneiderman, Justin F

    2017-08-01

    While commercial magnetoencephalography (MEG) systems are the functional neuroimaging state-of-the-art in terms of spatio-temporal resolution, MEG sensors have not changed significantly since the 1990s. Interest in newer sensors that operate at less extreme temperatures, e.g., high critical temperature (high-T c ) SQUIDs, optically-pumped magnetometers, etc., is growing because they enable significant reductions in head-to-sensor standoff (on-scalp MEG). Various metrics quantify the advantages of on-scalp MEG, but a single straightforward one is lacking. Previous works have furthermore been limited to arbitrary and/or unrealistic sensor layouts. We introduce spatial information density (SID) maps for quantitative and qualitative evaluations of sensor arrays. SID-maps present the spatial distribution of information a sensor array extracts from a source space while accounting for relevant source and sensor parameters. We use it in a systematic comparison of three practical on-scalp MEG sensor array layouts (based on high-T c SQUIDs) and the standard Elekta Neuromag TRIUX magnetometer array. Results strengthen the case for on-scalp and specifically high-T c SQUID-based MEG while providing a path for the practical design of future MEG systems. SID-maps are furthermore general to arbitrary magnetic sensor technologies and source spaces and can thus be used for design and evaluation of sensor arrays for magnetocardiography, magnetic particle imaging, etc.

  8. Joint Mapping of Mobility and Trap Density in Colloidal Quantum Dot Solids

    KAUST Repository

    Stadler, Philipp

    2013-07-23

    Field-effect transistors have been widely used to study electronic transport and doping in colloidal quantum dot solids to great effect. However, the full power of these devices to elucidate the electronic structure of materials has yet to be harnessed. Here, we deploy nanodielectric field-effect transistors to map the energy landscape within the band gap of a colloidal quantum dot solid. We exploit the self-limiting nature of the potentiostatic anodization growth mode to produce the thinnest usable gate dielectric, subject to our voltage breakdown requirements defined by the Fermi sweep range of interest. Lead sulfide colloidal quantum dots are applied as the active region and are treated with varying solvents and ligands. In an analysis complementary to the mobility trends commonly extracted from field-effect transistor studies, we focus instead on the subthreshold regime and map out the density of trap states in these nanocrystal films. The findings point to the importance of comprehensively mapping the electronic band- and gap-structure within real quantum solids, and they suggest a new focus in investigating quantum dot solids with an aim toward improving optoelectronic device performance. © 2013 American Chemical Society.

  9. Principal component analysis of the CT density histogram to generate parametric response maps of COPD

    Science.gov (United States)

    Zha, N.; Capaldi, D. P. I.; Pike, D.; McCormack, D. G.; Cunningham, I. A.; Parraga, G.

    2015-03-01

    Pulmonary x-ray computed tomography (CT) may be used to characterize emphysema and airways disease in patients with chronic obstructive pulmonary disease (COPD). One analysis approach - parametric response mapping (PMR) utilizes registered inspiratory and expiratory CT image volumes and CT-density-histogram thresholds, but there is no consensus regarding the threshold values used, or their clinical meaning. Principal-component-analysis (PCA) of the CT density histogram can be exploited to quantify emphysema using data-driven CT-density-histogram thresholds. Thus, the objective of this proof-of-concept demonstration was to develop a PRM approach using PCA-derived thresholds in COPD patients and ex-smokers without airflow limitation. Methods: Fifteen COPD ex-smokers and 5 normal ex-smokers were evaluated. Thoracic CT images were also acquired at full inspiration and full expiration and these images were non-rigidly co-registered. PCA was performed for the CT density histograms, from which the components with the highest eigenvalues greater than one were summed. Since the values of the principal component curve correlate directly with the variability in the sample, the maximum and minimum points on the curve were used as threshold values for the PCA-adjusted PRM technique. Results: A significant correlation was determined between conventional and PCA-adjusted PRM with 3He MRI apparent diffusion coefficient (p<0.001), with CT RA950 (p<0.0001), as well as with 3He MRI ventilation defect percent, a measurement of both small airways disease (p=0.049 and p=0.06, respectively) and emphysema (p=0.02). Conclusions: PRM generated using PCA thresholds of the CT density histogram showed significant correlations with CT and 3He MRI measurements of emphysema, but not airways disease.

  10. Rapid genotyping with DNA micro-arrays for high-density linkage mapping and QTL mapping in common buckwheat (Fagopyrum esculentum Moench)

    Science.gov (United States)

    Yabe, Shiori; Hara, Takashi; Ueno, Mariko; Enoki, Hiroyuki; Kimura, Tatsuro; Nishimura, Satoru; Yasui, Yasuo; Ohsawa, Ryo; Iwata, Hiroyoshi

    2014-01-01

    For genetic studies and genomics-assisted breeding, particularly of minor crops, a genotyping system that does not require a priori genomic information is preferable. Here, we demonstrated the potential of a novel array-based genotyping system for the rapid construction of high-density linkage map and quantitative trait loci (QTL) mapping. By using the system, we successfully constructed an accurate, high-density linkage map for common buckwheat (Fagopyrum esculentum Moench); the map was composed of 756 loci and included 8,884 markers. The number of linkage groups converged to eight, which is the basic number of chromosomes in common buckwheat. The sizes of the linkage groups of the P1 and P2 maps were 773.8 and 800.4 cM, respectively. The average interval between adjacent loci was 2.13 cM. The linkage map constructed here will be useful for the analysis of other common buckwheat populations. We also performed QTL mapping for main stem length and detected four QTL. It took 37 days to process 178 samples from DNA extraction to genotyping, indicating the system enables genotyping of genome-wide markers for a few hundred buckwheat plants before the plants mature. The novel system will be useful for genomics-assisted breeding in minor crops without a priori genomic information. PMID:25914583

  11. High-resolution mapping of linear antibody epitopes using ultrahigh-density peptide microarrays

    DEFF Research Database (Denmark)

    Buus, Søren; Rockberg, Johan; Forsström, Björn

    2012-01-01

    Antibodies empower numerous important scientific, clinical, diagnostic, and industrial applications. Ideally, the epitope(s) targeted by an antibody should be identified and characterized, thereby establishing antibody reactivity, highlighting possible cross-reactivities, and perhaps even warning...... against unwanted (e.g. autoimmune) reactivities. Antibodies target proteins as either conformational or linear epitopes. The latter are typically probed with peptides, but the cost of peptide screening programs tends to prohibit comprehensive specificity analysis. To perform high-throughput, high......-resolution mapping of linear antibody epitopes, we have used ultrahigh-density peptide microarrays generating several hundred thousand different peptides per array. Using exhaustive length and substitution analysis, we have successfully examined the specificity of a panel of polyclonal antibodies raised against...

  12. Pauli potential from Heilmann-Lieb electron density obtained by summing hydrogenic closed-shell densities over the entire bound-state spectrum

    International Nuclear Information System (INIS)

    Bogar, Ferenc; Bartha, Ferenc; Bartha, Ferenc A.; March, Norman H.

    2011-01-01

    Independently, in the mid-1980s, several groups proposed to bosonize the density-functional theory (DFT) for fermions by writing a Schroedinger equation for the density amplitude ρ(r) 1/2 , with ρ(r) as the ground-state electron density, the central tool of DFT. The resulting differential equation has the DFT one-body potential V(r) modified by an additive term V P (r) where P denotes Pauli. To gain insight into the form of the Pauli potential V P (r), here, we invoke the known Coulombic density, ρ ∞ (r) say, calculated analytically by Heilmann and Lieb (HL), by summation over the entire hydrogenic bound-state spectrum. We show that V P∞ (r) has simple limits for both r tends to infinity and r approaching zero. In particular, at large r, V P∞ (r) precisely cancels the attractive Coulomb potential -Ze 2 /r, leaving V(r)+V P∞ (r) of O(r -2 ) as r tends to infinity. The HL density ρ ∞ (r) is finally used numerically to display V P∞ (r) for all r values.

  13. High-Density LiDAR Mapping of the Ancient City of Mayapán

    Directory of Open Access Journals (Sweden)

    Timothy Hare

    2014-09-01

    Full Text Available A 2013 survey of a 40 square kilometer area surrounding Mayapán, Yucatan, Mexico used high-density LiDAR data to map prehispanic architecture and related natural features. Most of the area is covered by low canopy dense forest vegetation over karstic hilly terrain that impedes full coverage archaeological survey. We used LiDAR at 40 laser points per square meter to generate a bare earth digital elevation model (DEM. Results were evaluated with comparisons to previously mapped areas and with traditional archaeological survey methods for 38 settlement clusters outside of the city wall. Ground checking employed full coverage survey of selected 500 m grid squares, as well as documentation of the chronology and detail of new public and domestic settlement features and cenotes. Results identify the full extent of continued, contemporary Postclassic settlement (A.D. 1150–1450 outside of the city wall to at least 500 meters to the east, north, and west. New data also reveal an extensive modified landscape of terraformed residential hills, rejolladas, and dense settlement dating from Preclassic through Classic Periods. The LiDAR data also allow for the identification of rooms, benches, and stone property walls and lanes within the city.

  14. Polycystic ovary syndrome: analysis of the global research architecture using density equalizing mapping.

    Science.gov (United States)

    Brüggmann, Dörthe; Berges, Lea; Klingelhöfer, Doris; Bauer, Jan; Bendels, Michael; Louwen, Frank; Jaque, Jenny; Groneberg, David A

    2017-06-01

    Polycystic ovary syndrome (PCOS) is the most common cause of female infertility worldwide. Although the related research output is constantly growing, no detailed global map of the scientific architecture has so far been created encompassing quantitative, qualitative, socioeconomic and gender aspects. We used the NewQIS platform to assess all PCOS-related publications indexed between 1900 and 2014 in the Web of Science, and applied density equalizing mapping projections, scientometric techniques and economic benchmarking procedures. A total of 6261 PCOS-specific publications and 703 international research collaborations were found. The USA was identified as the most active country in total and collaborative research activity. In the socioeconomic analysis, the USA was also ranked first (25.49 PCOS-related publications per gross domestic product [GDP]/capita), followed by the UK, Italy and Greece. When research activity was related to population size, Scandinavian countries and Greece were leading the field. For many highly productive countries, gender analysis revealed a high ratio of female scientists working on PCOS with the exception of Japan. In this study, we have created the first picture of global PCOS research, which largely differs from other gynaecologic conditions and indicates that most related research and collaborations originate from high-income countries. Copyright © 2017 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

  15. Development and Integration of Genome-Wide Polymorphic Microsatellite Markers onto a Reference Linkage Map for Constructing a High-Density Genetic Map of Chickpea.

    Directory of Open Access Journals (Sweden)

    Yash Paul Khajuria

    Full Text Available The identification of informative in silico polymorphic genomic and genic microsatellite markers by comparing the genome and transcriptome sequences of crop genotypes is a rapid, cost-effective and non-laborious approach for large-scale marker validation and genotyping applications, including construction of high-density genetic maps. We designed 1494 markers, including 1016 genomic and 478 transcript-derived microsatellite markers showing in-silico fragment length polymorphism between two parental genotypes (Cicer arietinum ICC4958 and C. reticulatum PI489777 of an inter-specific reference mapping population. High amplification efficiency (87%, experimental validation success rate (81% and polymorphic potential (55% of these microsatellite markers suggest their effective use in various applications of chickpea genetics and breeding. Intra-specific polymorphic potential (48% detected by microsatellite markers in 22 desi and kabuli chickpea genotypes was lower than inter-specific polymorphic potential (59%. An advanced, high-density, integrated and inter-specific chickpea genetic map (ICC4958 x PI489777 having 1697 map positions spanning 1061.16 cM with an average inter-marker distance of 0.625 cM was constructed by assigning 634 novel informative transcript-derived and genomic microsatellite markers on eight linkage groups (LGs of our prior documented, 1063 marker-based genetic map. The constructed genome map identified 88, including four major (7-23 cM longest high-resolution genomic regions on LGs 3, 5 and 8, where the maximum number of novel genomic and genic microsatellite markers were specifically clustered within 1 cM genetic distance. It was for the first time in chickpea that in silico FLP analysis at genome-wide level was carried out and such a large number of microsatellite markers were identified, experimentally validated and further used in genetic mapping. To best of our knowledge, in the presently constructed genetic map, we mapped

  16. Construction of an ultrahigh-density genetic linkage map for Jatropha curcas L. and identification of QTL for fruit yield.

    Science.gov (United States)

    Xia, Zhiqiang; Zhang, Shengkui; Wen, Mingfu; Lu, Cheng; Sun, Yufang; Zou, Meiling; Wang, Wenquan

    2018-01-01

    As an important biofuel plant, the demand for higher yield Jatropha curcas L. is rapidly increasing. However, genetic analysis of Jatropha and molecular breeding for higher yield have been hampered by the limited number of molecular markers available. An ultrahigh-density linkage map for a Jatropha mapping population of 153 individuals was constructed and covered 1380.58 cM of the Jatropha genome, with average marker density of 0.403 cM. The genetic linkage map consisted of 3422 SNP and indel markers, which clustered into 11 linkage groups. With this map, 13 repeatable QTLs (reQTLs) for fruit yield traits were identified. Ten reQTLs, qNF - 1 , qNF - 2a , qNF - 2b , qNF - 2c , qNF - 3 , qNF - 4 , qNF - 6 , qNF - 7a , qNF - 7b and qNF - 8, that control the number of fruits (NF) mapped to LGs 1, 2, 3, 4, 6, 7 and 8, whereas three reQTLs, qTWF - 1 , qTWF - 2 and qTWF - 3, that control the total weight of fruits (TWF) mapped to LGs 1, 2 and 3, respectively. It is interesting that there are two candidate critical genes, which may regulate Jatropha fruit yield. We also identified three pleiotropic reQTL pairs associated with both the NF and TWF traits. This study is the first to report an ultrahigh-density Jatropha genetic linkage map construction, and the markers used in this study showed great potential for QTL mapping. Thirteen fruit-yield reQTLs and two important candidate genes were identified based on this linkage map. This genetic linkage map will be a useful tool for the localization of other economically important QTLs and candidate genes for Jatropha .

  17. Current density distribution mapping in PEM fuel cells as an instrument for operational measurements

    Energy Technology Data Exchange (ETDEWEB)

    Geske, M.; Heuer, M.; Heideck, G.; Styczynski, Z. A. [Otto-von-Guericke University Magdeburg, Chair Electric Power Networks and Renewable Energy Sources, Magdeburg (Germany)

    2010-07-01

    A newly developed measurement system for current density distribution mapping has enabled a new approach for operational measurements in proton exchange membrane fuel cells (PEMFC). Taking into account previously constructed measurement systems, a method based on a multi layer printed circuit board was chosen for the development of the new system. This type of system consists of a sensor, a special electronic device and the control and visualization PC. For the acquisition of the current density distribution values, a sensor device was designed and installed within a multilayer printed circuit board with integrated shunt resistors. Varying shunt values can be taken into consideration with a newly developed and evaluated calibration method. The sensor device was integrated in a PEM fuel cell stack to prove the functionality of the whole measurement system. A software application was implemented to visualize and save the measurement values. Its functionality was verified by operational measurements within a PEMFC system. Measurement accuracy and possible negative reactions of the sensor device during PEMFC operation are discussed in detail in this paper. The developed system enables operational measurements for different operating phases of PEM fuel cells. Additionally, this can be seen as a basis for new opportunities of optimization for fuel cell design and operation modes. (author)

  18. Current Density Distribution Mapping in PEM Fuel Cells as An Instrument for Operational Measurements

    Directory of Open Access Journals (Sweden)

    Martin Geske

    2010-04-01

    Full Text Available A newly developed measurement system for current density distribution mapping has enabled a new approach for operational measurements in proton exchange membrane fuel cells (PEMFC. Taking into account previously constructed measurement systems, a method based on a multi layer printed circuit board was chosen for the development of the new system. This type of system consists of a sensor, a special electronic device and the control and visualization PC. For the acquisition of the current density distribution values, a sensor device was designed and installed within a multilayer printed circuit board with integrated shunt resistors. Varying shunt values can be taken into consideration with a newly developed and evaluated calibration method. The sensor device was integrated in a PEM fuel cell stack to prove the functionality of the whole measurement system. A software application was implemented to visualize and save the measurement values. Its functionality was verified by operational measurements within a PEMFC system. Measurement accuracy and possible negative reactions of the sensor device during PEMFC operation are discussed in detail in this paper. The developed system enables operational measurements for different operating phases of PEM fuel cells. Additionally, this can be seen as a basis for new opportunities of optimization for fuel cell design and operation modes.

  19. A Larger Chocolate Chip—Development of a 15K Theobroma cacao L. SNP Array to Create High-Density Linkage Maps

    Directory of Open Access Journals (Sweden)

    Donald Livingstone

    2017-12-01

    Full Text Available Cacao (Theobroma cacao L. is an important cash crop in tropical regions around the world and has a rich agronomic history in South America. As a key component in the cosmetic and confectionary industries, millions of people worldwide use products made from cacao, ranging from shampoo to chocolate. An Illumina Infinity II array was created using 13,530 SNPs identified within a small diversity panel of cacao. Of these SNPs, 12,643 derive from variation within annotated cacao genes. The genotypes of 3,072 trees were obtained, including two mapping populations from Ecuador. High-density linkage maps for these two populations were generated and compared to the cacao genome assembly. Phenotypic data from these populations were combined with the linkage maps to identify the QTLs for yield and disease resistance.

  20. A Larger Chocolate Chip-Development of a 15K Theobroma cacao L. SNP Array to Create High-Density Linkage Maps.

    Science.gov (United States)

    Livingstone, Donald; Stack, Conrad; Mustiga, Guiliana M; Rodezno, Dayana C; Suarez, Carmen; Amores, Freddy; Feltus, Frank A; Mockaitis, Keithanne; Cornejo, Omar E; Motamayor, Juan C

    2017-01-01

    Cacao ( Theobroma cacao L.) is an important cash crop in tropical regions around the world and has a rich agronomic history in South America. As a key component in the cosmetic and confectionary industries, millions of people worldwide use products made from cacao, ranging from shampoo to chocolate. An Illumina Infinity II array was created using 13,530 SNPs identified within a small diversity panel of cacao. Of these SNPs, 12,643 derive from variation within annotated cacao genes. The genotypes of 3,072 trees were obtained, including two mapping populations from Ecuador. High-density linkage maps for these two populations were generated and compared to the cacao genome assembly. Phenotypic data from these populations were combined with the linkage maps to identify the QTLs for yield and disease resistance.

  1. Development of spatial density maps based on geoprocessing web services: application to tuberculosis incidence in Barcelona, Spain

    Science.gov (United States)

    2011-01-01

    Background Health professionals and authorities strive to cope with heterogeneous data, services, and statistical models to support decision making on public health. Sophisticated analysis and distributed processing capabilities over geocoded epidemiological data are seen as driving factors to speed up control and decision making in these health risk situations. In this context, recent Web technologies and standards-based web services deployed on geospatial information infrastructures have rapidly become an efficient way to access, share, process, and visualize geocoded health-related information. Methods Data used on this study is based on Tuberculosis (TB) cases registered in Barcelona city during 2009. Residential addresses are geocoded and loaded into a spatial database that acts as a backend database. The web-based application architecture and geoprocessing web services are designed according to the Representational State Transfer (REST) principles. These web processing services produce spatial density maps against the backend database. Results The results are focused on the use of the proposed web-based application to the analysis of TB cases in Barcelona. The application produces spatial density maps to ease the monitoring and decision making process by health professionals. We also include a discussion of how spatial density maps may be useful for health practitioners in such contexts. Conclusions In this paper, we developed web-based client application and a set of geoprocessing web services to support specific health-spatial requirements. Spatial density maps of TB incidence were generated to help health professionals in analysis and decision-making tasks. The combined use of geographic information tools, map viewers, and geoprocessing services leads to interesting possibilities in handling health data in a spatial manner. In particular, the use of spatial density maps has been effective to identify the most affected areas and its spatial impact. This

  2. Development of spatial density maps based on geoprocessing web services: application to tuberculosis incidence in Barcelona, Spain.

    Science.gov (United States)

    Dominkovics, Pau; Granell, Carlos; Pérez-Navarro, Antoni; Casals, Martí; Orcau, Angels; Caylà, Joan A

    2011-11-29

    Health professionals and authorities strive to cope with heterogeneous data, services, and statistical models to support decision making on public health. Sophisticated analysis and distributed processing capabilities over geocoded epidemiological data are seen as driving factors to speed up control and decision making in these health risk situations. In this context, recent Web technologies and standards-based web services deployed on geospatial information infrastructures have rapidly become an efficient way to access, share, process, and visualize geocoded health-related information. Data used on this study is based on Tuberculosis (TB) cases registered in Barcelona city during 2009. Residential addresses are geocoded and loaded into a spatial database that acts as a backend database. The web-based application architecture and geoprocessing web services are designed according to the Representational State Transfer (REST) principles. These web processing services produce spatial density maps against the backend database. The results are focused on the use of the proposed web-based application to the analysis of TB cases in Barcelona. The application produces spatial density maps to ease the monitoring and decision making process by health professionals. We also include a discussion of how spatial density maps may be useful for health practitioners in such contexts. In this paper, we developed web-based client application and a set of geoprocessing web services to support specific health-spatial requirements. Spatial density maps of TB incidence were generated to help health professionals in analysis and decision-making tasks. The combined use of geographic information tools, map viewers, and geoprocessing services leads to interesting possibilities in handling health data in a spatial manner. In particular, the use of spatial density maps has been effective to identify the most affected areas and its spatial impact. This study is an attempt to demonstrate how web

  3. Mapping of trap densities and hotspots in pentacene thin-film transistors by frequency-resolved scanning photoresponse microscopy.

    Science.gov (United States)

    Westermeier, Christian; Fiebig, Matthias; Nickel, Bert

    2013-10-25

    Frequency-resolved scanning photoresponse microscopy of pentacene thin-film transistors is reported. The photoresponse pattern maps the in-plane distribution of trap states which is superimposed by the level of trap filling adjusted by the gate voltage of the transistor. Local hotspots in the photoresponse map thus indicate areas of high trap densities within the pentacene thin film. © 2013 WILEY-VCH Verlag GmbH 8 Co. KGaA, Weinheim.

  4. Genome-Wide Single-Nucleotide Polymorphisms Discovery and High-Density Genetic Map Construction in Cauliflower Using Specific-Locus Amplified Fragment Sequencing

    Science.gov (United States)

    Zhao, Zhenqing; Gu, Honghui; Sheng, Xiaoguang; Yu, Huifang; Wang, Jiansheng; Huang, Long; Wang, Dan

    2016-01-01

    Molecular markers and genetic maps play an important role in plant genomics and breeding studies. Cauliflower is an important and distinctive vegetable; however, very few molecular resources have been reported for this species. In this study, a novel, specific-locus amplified fragment (SLAF) sequencing strategy was employed for large-scale single nucleotide polymorphism (SNP) discovery and high-density genetic map construction in a double-haploid, segregating population of cauliflower. A total of 12.47 Gb raw data containing 77.92 M pair-end reads were obtained after processing and 6815 polymorphic SLAFs between the two parents were detected. The average sequencing depths reached 52.66-fold for the female parent and 49.35-fold for the male parent. Subsequently, these polymorphic SLAFs were used to genotype the population and further filtered based on several criteria to construct a genetic linkage map of cauliflower. Finally, 1776 high-quality SLAF markers, including 2741 SNPs, constituted the linkage map with average data integrity of 95.68%. The final map spanned a total genetic length of 890.01 cM with an average marker interval of 0.50 cM, and covered 364.9 Mb of the reference genome. The markers and genetic map developed in this study could provide an important foundation not only for comparative genomics studies within Brassica oleracea species but also for quantitative trait loci identification and molecular breeding of cauliflower. PMID:27047515

  5. A High-Density Genetic Linkage Map and QTL Fine Mapping for Body Weight in Crucian Carp (Carassius auratus Using 2b-RAD Sequencing

    Directory of Open Access Journals (Sweden)

    Haiyang Liu

    2017-08-01

    Full Text Available A high-resolution genetic linkage map is essential for a wide range of genetics and genomics studies such as comparative genomics analysis and QTL fine mapping. Crucian carp (Carassius auratus is widely distributed in Eurasia, and is an important aquaculture fish worldwide. In this study, a high-density genetic linkage map was constructed for crucian carp using 2b-RAD technology. The consensus map contains 8487 SNP markers, assigning to 50 linkage groups (LGs and spanning 3762.88 cM, with an average marker interval of 0.44 cM and genome coverage of 98.8%. The female map had 4410 SNPs, and spanned 3500.42 cM (0.79 cM/marker, while the male map had 4625 SNPs and spanned 3346.33 cM (0.72 cM/marker. The average recombination ratio of female to male was 2.13:1, and significant male-biased recombination suppressions were observed in LG47 and LG49. Comparative genomics analysis revealed a clear 2:1 syntenic relationship between crucian carp LGs and chromosomes of zebrafish and grass carp, and a 1:1 correspondence, but extensive chromosomal rearrangement, between crucian carp and common carp, providing evidence that crucian carp has experienced a fourth round of whole genome duplication (4R-WGD. Eight chromosome-wide QTL for body weight at 2 months after hatch were detected on five LGs, explaining 10.1–13.2% of the phenotypic variations. Potential candidate growth-related genes, such as an EGF-like domain and TGF-β, were identified within the QTL intervals. This high-density genetic map and QTL analysis supplies a basis for genome evolutionary studies in cyprinid fishes, genome assembly, and QTL fine mapping for complex traits in crucian carp.

  6. Plasma density evolution in plasma opening switch obtained by a time-resolved sensitive He-Ne interferometer

    Science.gov (United States)

    Chen, Lin; Ren, Jing; Guo, Fan; Zhou, LiangJi; Li, Ye; He, An; Jiang, Wei

    2014-03-01

    To understand the formation process of vacuum gap in coaxial microsecond conduction time plasma opening switch (POS), we have made measurements of the line-integrated plasma density during switch operation using a time-resolved sensitive He-Ne interferometer. The conduction current and conduction time in experiments are about 120 kA and 1 μs, respectively. As a result, more than 85% of conduction current has been transferred to an inductive load with rise time of 130 ns. The radial dependence of the density is measured by changing the radial location of the line-of-sight for shots with the same nominal POS parameters. During the conduction phase, the line-integrated plasma density in POS increases at all radial locations over the gun-only case by further ionization of material injected from the guns. The current conduction is observed to cause a radial redistribution of the switch plasma. A vacuum gap forms rapidly in the plasma at 5.5 mm from the center conductor, which is consistent with the location where magnetic pressure is the largest, allowing current to be transferred from the POS to the load.

  7. A new software routine that automates the fitting of protein X-ray crystallographic electron-density maps.

    Science.gov (United States)

    Levitt, D G

    2001-07-01

    The classical approach to building the amino-acid residues into the initial electron-density map requires days to weeks of a skilled investigator's time. Automating this procedure should not only save time, but has the potential to provide a more accurate starting model for input to refinement programs. The new software routine MAID builds the protein structure into the electron-density map in a series of sequential steps. The first step is the fitting of the secondary alpha-helix and beta-sheet structures. These 'fits' are then used to determine the local amino-acid sequence assignment. These assigned fits are then extended through the loop regions and fused with the neighboring sheet or helix. The program was tested on the unaveraged 2.5 A selenomethionine multiple-wavelength anomalous dispersion (SMAD) electron-density map that was originally used to solve the structure of the 291-residue protein human heart short-chain L-3-hydroxyacyl-CoA dehydrogenase (SHAD). Inputting just the map density and the amino-acid sequence, MAID fitted 80% of the residues with an r.m.s.d. error of 0.43 A for the main-chain atoms and 1.0 A for all atoms without any user intervention. When tested on a higher quality 1.9 A SMAD map, MAID correctly fitted 100% (418) of the residues. A major advantage of the MAID fitting procedure is that it maintains ideal bond lengths and angles and constrains phi/psi angles to the appropriate Ramachandran regions. Recycling the output of this new routine through a partial structure-refinement program may have the potential to completely automate the fitting of electron-density maps.

  8. A journey from a SSR-based low density map to a SNP-based high density map for identification of disease resistance quantitative trait loci in peanut

    Science.gov (United States)

    Mapping and identification of quantitative trait loci (QTLs) are important for efficient marker-assisted breeding. Diseases such as leaf spots and Tomato spotted wilt virus (TSWV) cause significant loses to peanut growers. The U.S. Peanut Genome Initiative (PGI) was launched in 2004, and expanded to...

  9. Uncertainty relations and reduced density matrices: Mapping many-body quantum mechanics onto four particles

    Science.gov (United States)

    Mazziotti, David A.; Erdahl, Robert M.

    2001-04-01

    For the description of ground-state correlation phenomena an accurate mapping of many-body quantum mechanics onto four particles is developed. The energy for a quantum system with no more than two-particle interactions may be expressed in terms of a two-particle reduced density matrix (2-RDM), but variational optimization of the 2-RDM requires that it corresponds to an N-particle wave function. We derive N-representability conditions on the 2-RDM that guarantee the validity of the uncertainty relations for all operators with two-particle interactions. One of these conditions is shown to be necessary and sufficient to make the RDM solutions of the dispersion condition equivalent to those from the contracted Schrödinger equation (CSE) [Mazziotti, Phys. Rev. A 57, 4219 (1998)]. In general, the CSE is a stronger N-representability condition than the dispersion condition because the CSE implies the dispersion condition as well as additional N-representability constraints from the Hellmann-Feynman theorem. Energy minimization subject to the representability constraints is performed for a boson model with 10, 30, and 75 particles. Even when traditional wave-function methods fail at large perturbations, the present method yields correlation energies within 2%.

  10. Spatiotemporal norepinephrine mapping using a high-density CMOS microelectrode array.

    Science.gov (United States)

    Wydallis, John B; Feeny, Rachel M; Wilson, William; Kern, Tucker; Chen, Tom; Tobet, Stuart; Reynolds, Melissa M; Henry, Charles S

    2015-10-21

    A high-density amperometric electrode array containing 8192 individually addressable platinum working electrodes with an integrated potentiostat fabricated using Complementary Metal Oxide Semiconductor (CMOS) processes is reported. The array was designed to enable electrochemical imaging of chemical gradients with high spatiotemporal resolution. Electrodes are arranged over a 2 mm × 2 mm surface area into 64 subarrays consisting of 128 individual Pt working electrodes as well as Pt pseudo-reference and auxiliary electrodes. Amperometric measurements of norepinephrine in tissue culture media were used to demonstrate the ability of the array to measure concentration gradients in complex media. Poly(dimethylsiloxane) microfluidics were incorporated to control the chemical concentrations in time and space, and the electrochemical response at each electrode was monitored to generate electrochemical heat maps, demonstrating the array's imaging capabilities. A temporal resolution of 10 ms can be achieved by simultaneously monitoring a single subarray of 128 electrodes. The entire 2 mm × 2 mm area can be electrochemically imaged in 64 seconds by cycling through all subarrays at a rate of 1 Hz per subarray. Monitoring diffusional transport of norepinephrine is used to demonstrate the spatiotemporal resolution capabilities of the system.

  11. Tobacco Control: Visualisation of Research Activity Using Density-Equalizing Mapping and Scientometric Benchmarking Procedures

    Directory of Open Access Journals (Sweden)

    Beatrix Groneberg-Kloft

    2009-06-01

    Full Text Available Background: Tobacco smoking continues to be a major preventable cause of death and disease and therefore tobacco control research is extremely important. However, research in this area is often hampered by a lack in funding and there is a need for scientometric techniques to display research efforts. Methods: The present study combines classical bibliometric tools with novel scientometric and visualizing techniques in order to analyse and categorise research in the field of tobacco control. Results: All studies related to tobacco control and listed in the ISI database since 1900 were identified by the use of defined search terms.Using bibliometric approaches, a continuous increase in qualitative markers such as collaboration numbers or citations were found for tobacco control research. The combination with density equalizing mapping revealed a distinct global pattern of research productivity and citation activity. Radar chart techniques were used to visualize bi- and multilateral research cooperation and institutional cooperation. Conclusions: The present study supplies a first scientometricapproach that visualises research activity in the field of tobacco control. It provides data that can be used for funding policy and the identification of research clusters.

  12. Caesarean Section--A Density-Equalizing Mapping Study to Depict Its Global Research Architecture.

    Science.gov (United States)

    Brüggmann, Dörthe; Löhlein, Lena-Katharina; Louwen, Frank; Quarcoo, David; Jaque, Jenny; Klingelhöfer, Doris; Groneberg, David A

    2015-11-17

    Caesarean section (CS) is a common surgical procedure. Although it has been performed in a modern context for about 100 years, there is no concise analysis of the international architecture of caesarean section research output available so far. Therefore, the present study characterizes the global pattern of the related publications by using the NewQIS (New Quality and Quantity Indices in Science) platform, which combines scientometric methods with density equalizing mapping algorithms. The Web of Science was used as a database. 12,608 publications were identified that originated from 131 countries. The leading nations concerning research activity, overall citations and country-specific h-Index were the USA and the United Kingdom. Relation of the research activity to epidemiologic data indicated that Scandinavian countries including Sweden and Finland were leading the field, whereas, in relation to economic data, countries such as Israel and Ireland led. Semi-qualitative indices such as country-specific citation rates ranked Sweden, Norway and Finland in the top positions. International caesarean section research output continues to grow annually in an era where caesarean section rates increased dramatically over the past decades. With regard to increasing employment of scientometric indicators in performance assessment, these findings should provide useful information for those tasked with the improvement of scientific achievements.

  13. World-wide architecture of osteoporosis research: density-equalizing mapping studies and gender analysis.

    Science.gov (United States)

    Brüggmann, D; Mäule, L-S; Klingelhöfer, D; Schöffel, N; Gerber, A; Jaque, J M; Groneberg, D A

    2016-10-01

    While research activities on osteoporosis grow constantly, no concise description of the global research architecture exists. Hence, we aim to analyze and depict the world-wide scientific output on osteoporosis combining bibliometric tools, density-equalizing mapping projections and gender analysis. Using the NewQIS platform, we analyzed all osteoporosis-related publications authored from 1900 to 2012 and indexed by the Web of Science. Bibliometric details were analyzed related to quantitative and semi-qualitative aspects. The majority of 57 453 identified publications were original research articles. The USA and Western Europe dominated the field regarding cooperation activity, publication and citation performance. Asia, Africa and South America played a minimal role. Gender analysis revealed a dominance of male scientists in almost all countries except Brazil. Although the scientific performance on osteoporosis is increasing world-wide, a significant disparity in terms of research output was visible between developed and low-income countries. This finding is particularly concerning since epidemiologic evaluations of future osteoporosis prevalences predict enormous challenges for the health-care systems in low-resource countries. Hence, our study underscores the need to address these disparities by fostering future research endeavors in these nations with the aim to successfully prevent a growing global burden related to osteoporosis.

  14. Hirschsprung Disease: Critical Evaluation of the Global Research Architecture Employing Scientometrics and Density-Equalizing Mapping.

    Science.gov (United States)

    Schöffel, Norman; Gfroerer, Stefan; Rolle, Udo; Bendels, Michael H K; Klingelhöfer, Doris; Groneberg-Kloft, Beatrix

    2017-04-01

    Introduction  Hirschsprung disease (HD) is a congenital bowel innervation disorder that involves several clinical specialties. There is an increasing interest on the topic reflected by the number of annually published items. It is therefore difficult for a single scientist to survey all published items and to gauge their scientific importance or value. Thus, tremendous efforts were made to establish sustainable parameters to evaluate scientific work within the past decades. It was the birth of scientometrics. Materials and Methods  To quantify the global research activity in this field, a scientometric analysis was conducted. We analyzed the research output of countries, individual institutions, authors, and their collaborative networks by using the Web of Science database. Density-equalizing maps and network diagrams were employed as state of the art visualization techniques. Results  The United States is the leading country in terms of published items ( n  = 685), institutions ( n  = 347), and cooperation ( n  = 112). However, although there is dominance in quantity, the most intensive international networks between authors and institutions are not linked to the United States. By contrast, most of the European countries combine the highest impact of publications. Further analysis reveal the influence of international cooperation and associated phenomena on the research field HD. Conclusion  We conclude that the field of HD is constantly progressing. The importance of international cooperation in the scientific community is continuously growing. Georg Thieme Verlag KG Stuttgart · New York.

  15. [Magnetic resonance imaging. Density equalizing mapping analysis of global research architecture].

    Science.gov (United States)

    Ohlendorf, D; Schwarze, B; Groneberg, D A; Schwarzer, M

    2015-09-01

    Despite the great medical importance, there is still no comprehensive scientometric analysis regarding the results of magnetic resonance imaging (MRI) and the development of the importance for the healthcare system. This paper evaluated and analyzed the entire research publication results on the topic of MRI for the period 1981-2007 based on scientometric methods and parameters. A scientometric analysis (database: ISI Web of Science 1981-2007, search terms MRI and magnetic resonance imaging) was performed. The following parameters were analyzed: number of publications, countries of publication, number of citations, citation rate and collaborations, using various analytical and display techniques, including density equalizing map projections. Most of the 49,122 publications on MRI could be attributed to the USA (32.5 %), which also has the most cooperative collaborations. Within Europe, Germany (10.3 %) is the country with the highest number of publications followed by the UK (9.3 %). The western industrialized nations dominate over the rest of the world in terms of scientific developments of MRI. The thematic focus of the publications lies in the fields of radiology and neuroscience. In addition to the journal Neurology most scientific articles were published in Magnetic Resonance in Medicine and Circulation. The results show that the current trend is continuing and the scientific interest in MRI is continuously increasing.

  16. Fast and sensitive rigid-body fitting into cryo-EM density maps with PowerFit

    NARCIS (Netherlands)

    C.p.van Zundert, Gydo; M.j.j. Bonvin, Alexandre

    2015-01-01

    Cryo-EM is a rapidly developing method to investigate the three dimensional structure of large macromolecular complexes. In spite of all the advances in the field, the resolution of most cryo-EM density maps is too low for de novo model building. Therefore, the data are often complemented by fitting

  17. Regression modeling and mapping of coniferous forest basal area and tree density from discrete-return lidar and multispectral data

    Science.gov (United States)

    Andrew T. Hudak; Nicholas L. Crookston; Jeffrey S. Evans; Michael K. Falkowski; Alistair M. S. Smith; Paul E. Gessler; Penelope Morgan

    2006-01-01

    We compared the utility of discrete-return light detection and ranging (lidar) data and multispectral satellite imagery, and their integration, for modeling and mapping basal area and tree density across two diverse coniferous forest landscapes in north-central Idaho. We applied multiple linear regression models subset from a suite of 26 predictor variables derived...

  18. Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

    Directory of Open Access Journals (Sweden)

    Wang Nian

    2012-08-01

    Full Text Available Abstract Background Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP marker development. Results An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations. Conclusions The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison.

  19. Investigating the Capability of IRS-P6-LISS IV Satellite Image for Pistachio Forests Density Mapping (case Study: Northeast of Iran)

    Science.gov (United States)

    Hoseini, F.; Darvishsefat, A. A.; Zargham, N.

    2012-07-01

    In order to investigate the capability of satellite images for Pistachio forests density mapping, IRS-P6-LISS IV data were analyzed in an area of 500 ha in Iran. After geometric correction, suitable training areas were determined based on fieldwork. Suitable spectral transformations like NDVI, PVI and PCA were performed. A ground truth map included of 34 plots (each plot 1 ha) were prepared. Hard and soft supervised classifications were performed with 5 density classes (0-5%, 5-10%, 10-15%, 15-20% and > 20%). Because of low separability of classes, some classes were merged and classifications were repeated with 3 classes. Finally, the highest overall accuracy and kappa coefficient of 70% and 0.44, respectively, were obtained with three classes (0-5%, 5-20%, and > 20%) by fuzzy classifier. Considering the low kappa value obtained, it could be concluded that the result of the classification was not desirable. Therefore, this approach is not appropriate for operational mapping of these valuable Pistachio forests.

  20. Brugada syndrome is associated with scar and endocardial involvement: Insights from high-density mapping with the Rhythmia™ mapping system.

    Science.gov (United States)

    Providência, Rui; Carmo, Pedro; Moscoso Costa, Francisco; Cavaco, Diogo; Morgado, Francisco; Scanavacca, Mauricio; Adragão, Pedro

    2017-10-01

    The authors report the first catheter ablation of Brugada syndrome in the literature using the Rhythmia™ mapping system. Learning points include: (1) low voltage areas can be documented while mapping in some individuals, suggesting that Brugada syndrome may not be a pure ion channel disorder; (2) typical long fractionated potentials can also be identified in the endocardium, supporting the need to map the endocardium in all Brugada patients requiring ablation; (3) disappearance of the typical coved pattern following ablation does not necessarily predict cure, as the patient we present experienced ventricular fibrillation recurrence a few months later. Copyright © 2017 Sociedade Portuguesa de Cardiologia. Publicado por Elsevier España, S.L.U. All rights reserved.

  1. Genetic dissection of maize plant architecture with an ultra-high density bin map based on recombinant inbred lines.

    Science.gov (United States)

    Zhou, Zhiqiang; Zhang, Chaoshu; Zhou, Yu; Hao, Zhuanfang; Wang, Zhenhua; Zeng, Xing; Di, Hong; Li, Mingshun; Zhang, Degui; Yong, Hongjun; Zhang, Shihuang; Weng, Jianfeng; Li, Xinhai

    2016-03-03

    Plant architecture attributes, such as plant height, ear height, and internode number, have played an important role in the historical increases in grain yield, lodging resistance, and biomass in maize (Zea mays L.). Analyzing the genetic basis of variation in plant architecture using high density QTL mapping will be of benefit for the breeding of maize for many traits. However, the low density of molecular markers in existing genetic maps has limited the efficiency and accuracy of QTL mapping. Genotyping by sequencing (GBS) is an improved strategy for addressing a complex genome via next-generation sequencing technology. GBS has been a powerful tool for SNP discovery and high-density genetic map construction. The creation of ultra-high density genetic maps using large populations of advanced recombinant inbred lines (RILs) is an efficient way to identify QTL for complex agronomic traits. A set of 314 RILs derived from inbreds Ye478 and Qi319 were generated and subjected to GBS. A total of 137,699,000 reads with an average of 357,376 reads per individual RIL were generated, which is equivalent to approximately 0.07-fold coverage of the maize B73 RefGen_V3 genome for each individual RIL. A high-density genetic map was constructed using 4183 bin markers (100-Kb intervals with no recombination events). The total genetic distance covered by the linkage map was 1545.65 cM and the average distance between adjacent markers was 0.37 cM with a physical distance of about 0.51 Mb. Our results demonstrated a relatively high degree of collinearity between the genetic map and the B73 reference genome. The quality and accuracy of the bin map for QTL detection was verified by the mapping of a known gene, pericarp color 1 (P1), which controls the color of the cob, with a high LOD value of 80.78 on chromosome 1. Using this high-density bin map, 35 QTL affecting plant architecture, including 14 for plant height, 14 for ear height, and seven for internode number were detected

  2. Obtaining muonic density estimates via application of matrix formalism to proposed surface detector upgrade at the Pierre Auger Observatory

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, David; Engel, Ralph; Roth, Markus [Karlsruhe Institute of Technology, Karlsruhe (Germany); Collaboration: Pierre Auger-Collaboration

    2015-07-01

    Event-by-event identification of cosmic ray primary composition lends itself to enhanced event selection in the search for anisotropic arrival directions. Principally, the number of muons reaching Earth's surface in an extensive air shower is indicative of composition. The Pierre Auger Observatory seeks to capitalize on this axiom by improving reconstructed muonic density estimates via an upgrade to its surface detector array. This upgrade, consisting of placing a scintillator on top of each existing water Cherenkov detector, exploits the differing response of two detectors to muonic and electromagnetic particles. Exploitation of this difference may be expressed in a matrix formalism whose application to simulated proton and iron showers is presented here.

  3. A high density barley microsatellite consensus map with 775 SSR loci

    NARCIS (Netherlands)

    Varshney, R.K.; Marcel, T.C.; Ramsay, L.; Russell, J.; Roder, M.S.; Stein, N.; Waugh, R.; Langridge, P.; Niks, R.E.; Graner, A.

    2007-01-01

    A microsatellite or simple sequence repeat (SSR) consensus map of barley was constructed by joining six independent genetic maps based on the mapping populations 'Igri x Franka', 'Steptoe x Morex', 'OWBRec x OWBDom', 'Lina x Canada Park', 'L94 x Vada' and 'SusPtrit x Vada'. Segregation data for

  4. Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations

    Energy Technology Data Exchange (ETDEWEB)

    Carr, J. K.; Roy, S.; Skinner, J. L. [Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin 53706 (United States); Zabuga, A. V.; Rizzo, T. R. [Laboratoire de Chimie Physique Moleculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne (Switzerland)

    2014-06-14

    The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed “maps,” which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala){sub 5}-Lys-H{sup +} in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly {sup 13}C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and {sup 13}C{sup 18}O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm{sup −1} for both frequencies and couplings, having larger errors only for the frequencies of terminal amides.

  5. Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations

    International Nuclear Information System (INIS)

    Carr, J. K.; Roy, S.; Skinner, J. L.; Zabuga, A. V.; Rizzo, T. R.

    2014-01-01

    The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed “maps,” which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala) 5 -Lys-H + in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly 13 C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and 13 C 18 O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm −1 for both frequencies and couplings, having larger errors only for the frequencies of terminal amides

  6. Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations

    Science.gov (United States)

    Carr, J. K.; Zabuga, A. V.; Roy, S.; Rizzo, T. R.; Skinner, J. L.

    2014-01-01

    The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed “maps,” which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala)5-Lys-H+ in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly 13C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and 13C18O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm−1 for both frequencies and couplings, having larger errors only for the frequencies of terminal amides. PMID:24929378

  7. Obtaining the conversion curve of CT numbers to electron density from the effective energy of the CT using the dummy SEFM

    International Nuclear Information System (INIS)

    Martin-Viera Cueto, J. A.; Garcia Pareja, S.; Benitez Villegas, E. M.; Moreno Saiz, E. M.; Bodineau Gil, C.; Caudepon Moreno, F.

    2011-01-01

    The objective of this work is to obtain the conversion curve of Hounsfield units (A) versus electron densities using a mannequin with different tissue equivalent materials. This provides for the effective energy beam CT and is used to characterize the linear coefficients of absorption of different materials that comprise the dummy.

  8. Evaluation of the physico-chemical properties of nanocomposites of low density linear polyethylene and organophilic montmorillonite obtained by fusion

    International Nuclear Information System (INIS)

    Arndt, Aline; Sandrin, Bianca M.; Pezzin, A.P.T.; Meier, Marcia M.; Balzer, Palova S.; Tavares, Maria I.B.

    2016-01-01

    In this project they were produced and characterized nanocomposite organoclay applied to linear low density polyethylene in order to improve their physicochemical properties. Samples were produced by means of extrusion and injection process, varying proportions of nanoclay (2; 2.5; 3.0 and 3.5%) in LLDPE. Samples nanocomposites were characterized by TGA, DSC and Flammability test (UL-94). The TGA analysis showed that adding nanoclay increased thermal stability, especially for LLDPE / OMMT2,0 sample increased thermal stability at 4.4%. By DSC it was found that samples with nanoclay incorporation did not affect the Tm of LLDPE, though the increase of nanoclay raised the degree of crystallinity of the samples 52.7% in LLDPE / 2.5 OMMT sample. The flammability results show that the sample LLDPE / OMMT 2.0 showed a decrease of 37.77% in the flame propagation velocity. The NMR showed that the samples up LLDPE / 2.5 OM has an exfoliated nanocomposite formation. (author)

  9. Yellow fever disease: density equalizing mapping and gender analysis of international research output.

    Science.gov (United States)

    Bundschuh, Matthias; Groneberg, David A; Klingelhoefer, Doris; Gerber, Alexander

    2013-11-18

    A number of scientific papers on yellow fever have been published but no broad scientometric analysis on the published research of yellow fever has been reported.The aim of the article based study was to provide an in-depth evaluation of the yellow fever field using large-scale data analysis and employment of bibliometric indicators of production and quantity. Data were retrieved from the Web of Science database (WoS) and analyzed as part of the NewQis platform. Then data were extracted from each file, transferred to databases and visualized as diagrams. Partially by means of density-equalizing mapping makes the findings clear and emphasizes the output of the analysis. In the study period from 1900 to 2012 a total of 5,053 yellow fever-associated items were published by 79 countries. The United States (USA) having the highest publication rate at 42% (n = 751) followed by far from Brazil (n = 203), France (n = 149) and the United Kingdom (n = 113). The most productive journals are the "Public Health Reports", the "American Journal of Tropical Medicine and Hygiene" and the "Journal of Virology". The gender analysis showed an overall steady increase of female authorship from 1950 to 2011. Brazil is the only country of the five most productive countries with a higher proportion of female scientists. The present data shows an increase in research productivity over the entire study period, in particular an increase of female scientists. Brazil shows a majority of female authors, a fact that is confirmed by other studies.

  10. Functional connectivity density mapping of depressive symptoms and loneliness in non-demented elderly male

    Directory of Open Access Journals (Sweden)

    Chen-Chia eLan

    2016-01-01

    Full Text Available Background: Depression and loneliness are prevalent and highly correlated phenomena among the elderly and influence both physical and mental health. Brain functional connectivity changes associated with depressive symptoms and loneliness are not fully understood.Methods: A cross-sectional functional MRI study was conducted among 85 non-demented male elders. Geriatric depression scale-short form and loneliness scale were used to evaluate the severity of depressive symptoms and loneliness, respectively. Whole brain voxel-wise resting-state functional connectivity density (FCD mapping was performed to delineate short-range FCD (SFCD and long-range FCD (LFCD. Regional correlations between depressive symptoms or loneliness and SFCD or LFCD were examined using general linear model, with age incorporated as a covariate and depressive symptoms and loneliness as predictors.Results: Positive correlations between depressive symptoms and LFCD were observed in left rectal gyrus, left superior frontal gyrus, right supraorbital gyrus, and left inferior temporal gyrus. Positive correlations between depressive symptoms and SFCD were observed in left middle frontal gyrus, left superior frontal gyrus, bilateral superior medial frontal gyrus, left inferior temporal gyrus, and left middle occipital region. Positive correlations between SFCD and loneliness were centered over bilateral lingual gyrus.Conclusion: Depressive symptoms are associated with FCD changes over frontal and temporal regions, which may involve the cognitive control, affective regulation, and default mode networks. Loneliness is associated with FCD changes in bilateral lingual gyri that are known to be important in social cognition. Depressive symptoms and loneliness may be associated with different brain regions in non-demented elderly male.

  11. A high density genetic map and QTL for agronomic and yield traits in Foxtail millet [Setaria italica (L.) P. Beauv].

    Science.gov (United States)

    Fang, Xiaomei; Dong, Kongjun; Wang, Xiaoqin; Liu, Tianpeng; He, Jihong; Ren, Ruiyu; Zhang, Lei; Liu, Rui; Liu, Xueying; Li, Man; Huang, Mengzhu; Zhang, Zhengsheng; Yang, Tianyu

    2016-05-04

    Foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China, has been adopted as a model crop for studying C-4 photosynthesis, stress biology and biofuel traits. Construction of a high density genetic map and identification of stable quantitative trait loci (QTL) lay the foundation for marker-assisted selection for agronomic traits and yield improvement. A total of 10598 SSR markers were developed according to the reference genome sequence of foxtail millet cultivar 'Yugu1'. A total of 1013 SSR markers showing polymorphism between Yugu1 and Longgu7 were used to genotype 167 individuals from a Yugu1 × Longgu7 F2 population, and a high density genetic map was constructed. The genetic map contained 1035 loci and spanned 1318.8 cM with an average distance of 1.27 cM between adjacent markers. Based on agronomic and yield traits identified in 2 years, 29 QTL were identified for 11 traits with combined analysis and single environment analysis. These QTL explained from 7.0 to 14.3 % of phenotypic variation. Favorable QTL alleles for peduncle length originated from Longgu7 whereas favorable alleles for the other traits originated from Yugu1 except for qLMS6.1. New SSR markers, a high density genetic map and QTL identified for agronomic and yield traits lay the ground work for functional gene mapping, map-based cloning and marker-assisted selection in foxtail millet.

  12. Field, temperature, and angle dependent critical current density Jc(H,T,θ) in coated conductors obtained via contact-free methods

    International Nuclear Information System (INIS)

    Thompson, J R; Christen, D K; Zhang Yifei; Zuev, Y L; Cantoni, C; Sinclair, J W; Chen Yimin; Selvamanickam, V

    2010-01-01

    Applications of coated conductors based on high- T c superconductors often require detailed knowledge of their critical current density J c as a function of magnetic field orientation as well as field strength and temperature. This work demonstrates experimental methods for obtaining the angularly dependent J c using contact-free magnetic measurements, and qualifies those methods using several well defined conditions. The studies complement traditional transport techniques and are readily extended to conditions of field and temperature where the current density is very large and transport methods become difficult. Results on representative materials are presented.

  13. Field, temperature, and angle dependent critical current density Jc(H,T, ) in coated conductors obtained via contact-free methods

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, James R [ORNL; Sinclair IV, John W [ORNL; Christen, David K [ORNL; Zhang, Yifei [ORNL; Zuev, Yuri L [ORNL; Cantoni, Claudia [ORNL; Chen, Y [SuperPower Incorporated, Schenectady, New York; Selvamanickam, V. [SuperPower Incorporated, Schenectady, New York

    2010-01-01

    Applications of coated conductors based on high-Tc superconductors often require detailed knowledge of their critical current density Jc as a function of magnetic field orientation as well as field strength and temperature. This work demonstrates experimental methods to obtain the angularly dependent Jc using contact-free magnetic measurements, and qualifies those methods using several well defined conditions. The studies complement traditional transport techniques and are readily extended to conditions of field and temperature where the current density is very large and transport methods become difficult. Results on representative materials are presented.

  14. Field, temperature, and angle dependent critical current density J{sub c}(H,T,{theta}) in coated conductors obtained via contact-free methods

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, J R; Christen, D K; Zhang Yifei; Zuev, Y L; Cantoni, C [Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6092 (United States); Sinclair, J W [Department of Physics, University of Tennessee, Knoxville, TN 37996-1200 (United States); Chen Yimin; Selvamanickam, V [SuperPower, Incorporated, 450 Duane Avenue, Schenectady, NY 12304 (United States)

    2010-01-15

    Applications of coated conductors based on high- T{sub c} superconductors often require detailed knowledge of their critical current density J{sub c} as a function of magnetic field orientation as well as field strength and temperature. This work demonstrates experimental methods for obtaining the angularly dependent J{sub c} using contact-free magnetic measurements, and qualifies those methods using several well defined conditions. The studies complement traditional transport techniques and are readily extended to conditions of field and temperature where the current density is very large and transport methods become difficult. Results on representative materials are presented.

  15. Snakebite Envenoming - A Combined Density Equalizing Mapping and Scientometric Analysis of the Publication History.

    Directory of Open Access Journals (Sweden)

    David A Groneberg

    2016-11-01

    Full Text Available Estimates suggest that more than 25,000 to 125,000 people die annually from snakebite envenomation worldwide. In contrast to this major disease burden, thorough bibliometric studies do not exist so far that illustrate the overall research activity over a long time span. Therefore, the NewQIS-platform conducted an analysis on snakebite envenoming using the Thomson Reuters database Web of Science. To determine and assess changes regarding the scientific activities and to specifically address the more recent situation we analyzed two time intervals (t. During the first time interval from 1900 to 2007 (t1 13,015 publications (p were identified. In the following period (2008-2016 = t2 4,982 publications were identified by the same search strategy. They originate from 114 (t1 respectively 121 countries (t2, with the USA (p = 3518, Brazil (p = 1100 and Japan (p = 961 being most productive in the first period, and the USA (p = 1087, Brazil (p = 991 and China (p = 378 in the second period, respectively. Setting the publication numbers in relation to GDP/capita, Brazil leads with 92 publications per 10,000 Int$GDP/capita, followed by India with 79 publications per 10000 Int$GDP/capita (t1. Comparing the country's publication activity with the Human Development Index level indicates that the majority of the publications is published by highly developed countries. When calculating the average citation rates (citations per published item = CR mainly European countries show the highest ranks: From 1900-2007 Sweden ranks first with a CR = 27, followed by the Netherlands (CR = 24.8, Switzerland (CR = 23, Spain, Austria and the USA (CR = 22. From 2008 to 2016 the highest rate achieves Switzerland with a value of 24.6, followed by Belgium (CR = 18.1, Spain (CR = 16.7, Costa Rica (CR = 14.9 and Netherlands (CR = 14. Compared with this, the USA was placed at rank 13 (CR = 9,5. In summary, the present study represents the first density-equalizing map projection and

  16. Global architecture of gestational diabetes research: density-equalizing mapping studies and gender analysis.

    Science.gov (United States)

    Brüggmann, Dörthe; Richter, Theresa; Klingelhöfer, Doris; Gerber, Alexander; Bundschuh, Matthias; Jaque, Jenny; Groneberg, David A

    2016-04-04

    Gestational diabetes mellitus (GDM) is associated with substantial morbidity for mothers and their offspring. While clinical and basic research activities on this important disease grow constantly, there is no concise analysis of global architecture of GDM research. Hence, it was the objective of this study to assess the global scientific performance chronologically, geographically and in relation to existing research networks and gender distribution of publishing authors. On the basis of the New Quality and Quantity Indices in Science (NewQIS) platform, scientometric methods were combined with modern visualizing techniques such as density equalizing mapping, and the Web of Science database was used to assess GDM-related entries from 1900 to 2012. Twelve thousand five hundred four GDM-related publications were identified and analyzed. The USA (4295 publications) and the UK (1354 publications) dominated the field concerning research activity, overall citations and country-specific Hirsch-Index, which quantified the impact of a country's published research on the scientific community. Semi-qualitative indices such as country-specific citation rates ranked New Zealand and the UK at top positions. Annual collaborative publications increased steeply between the years 1990 and 2012 (71 to 1157 respectively). Subject category analysis pointed to a minor interest of public health issues in GDM research. Gender analysis in terms of publication authorship revealed a clear dominance of the male gender until 2005; then a trend towards gender equity started and the activity of female scientists grew visibly in many countries. The country-specific gender analysis revealed large differences, i.e. female scientists dominated the scientific output in the USA, whereas the majority of research was published by male authors in countries such as Japan. This study provides the first global sketch of GDM research architecture. While North-American and Western-European countries were

  17. An autoradiographic method of mapping the distribution and density of monoamine neurons in mouse brain

    International Nuclear Information System (INIS)

    Masuoka, D.T.; Alcaraz, A.F.

    1975-01-01

    A combined in vitro uptake and autoradiographic procedure as an important complement to the histochemical fluorescence method is described. Slabs of fresh mouse brain were incubated with 14 C-NE, 14 C-DA or 14 C-5-HT, freeze-dried, and placed against X-ray film for autoradiography. Catecholamine nerve terminals were labeled by in vitro incubation with 14 C-NE or 14 C-DA. Dopaminergic terminals were labeled by 14 C-NE incubation preceded by desipramine (to block uptake into NE terminals). With 14 C-5-HT incubation, the uptake pattern indicated the possibility that 5-HT nerve terminals were being labeled. Advantages of this method are that it allows the visualization of overall density and distribution of selected monoamine nerve terminals or uptake sites of other putative neurotransmitters in whole coronal or sagittal sections, so that data are obtained from many areas of brain or spinal cord rather than in only those areas preselected for microscopic viewing

  18. Modeling Poroelastic Wave Propagation in a Real 2-D Complex Geological Structure Obtained via Self-Organizing Maps

    Science.gov (United States)

    Itzá Balam, Reymundo; Iturrarán-Viveros, Ursula; Parra, Jorge O.

    2018-03-01

    Two main stages of seismic modeling are geological model building and numerical computation of seismic response for the model. The quality of the computed seismic response is partly related to the type of model that is built. Therefore, the model building approaches become as important as seismic forward numerical methods. For this purpose, three petrophysical facies (sands, shales and limestones) are extracted from reflection seismic data and some seismic attributes via the clustering method called Self-Organizing Maps (SOM), which, in this context, serves as a geological model building tool. This model with all its properties is the input to the Optimal Implicit Staggered Finite Difference (OISFD) algorithm to create synthetic seismograms for poroelastic, poroacoustic and elastic media. The results show a good agreement between observed and 2-D synthetic seismograms. This demonstrates that the SOM classification method enables us to extract facies from seismic data and allows us to integrate the lithology at the borehole scale with the 2-D seismic data.

  19. Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information

    Science.gov (United States)

    2012-01-01

    Background Cotton is the world’s most important natural textile fiber and a significant oilseed crop. Decoding cotton genomes will provide the ultimate reference and resource for research and utilization of the species. Integration of high-density genetic maps with genomic sequence information will largely accelerate the process of whole-genome assembly in cotton. Results In this paper, we update a high-density interspecific genetic linkage map of allotetraploid cultivated cotton. An additional 1,167 marker loci have been added to our previously published map of 2,247 loci. Three new marker types, InDel (insertion-deletion) and SNP (single nucleotide polymorphism) developed from gene information, and REMAP (retrotransposon-microsatellite amplified polymorphism), were used to increase map density. The updated map consists of 3,414 loci in 26 linkage groups covering 3,667.62 cM with an average inter-locus distance of 1.08 cM. Furthermore, genome-wide sequence analysis was finished using 3,324 informative sequence-based markers and publicly-available Gossypium DNA sequence information. A total of 413,113 EST and 195 BAC sequences were physically anchored and clustered by 3,324 sequence-based markers. Of these, 14,243 ESTs and 188 BACs from different species of Gossypium were clustered and specifically anchored to the high-density genetic map. A total of 2,748 candidate unigenes from 2,111 ESTs clusters and 63 BACs were mined for functional annotation and classification. The 337 ESTs/genes related to fiber quality traits were integrated with 132 previously reported cotton fiber quality quantitative trait loci, which demonstrated the important roles in fiber quality of these genes. Higher-level sequence conservation between different cotton species and between the A- and D-subgenomes in tetraploid cotton was found, indicating a common evolutionary origin for orthologous and paralogous loci in Gossypium. Conclusion This study will serve as a valuable genomic resource

  20. High Density Nodes in the Chaotic Region of 1D Discrete Maps

    Directory of Open Access Journals (Sweden)

    George Livadiotis

    2018-01-01

    Full Text Available We report on the definition and characteristics of nodes in the chaotic region of bifurcation diagrams in the case of 1D mono-parametrical and S-unimodal maps, using as guiding example the logistic map. We examine the arrangement of critical curves, the identification and arrangement of nodes, and the connection between the periodic windows and nodes in the chaotic zone. We finally present several characteristic features of nodes, which involve their convergence and entropy.

  1. Genome wide SSR high density genetic map construction from an interspecific cross of Gossypium hirsutum × Gossypium tomentosum

    Directory of Open Access Journals (Sweden)

    Muhammad Kashif Riaz eKhan

    2016-04-01

    Full Text Available A high density genetic map was constructed using F2 population derived from an interspecific cross of G. hirsutum x G. tomentosum. The map consisted of 3,093 marker loci distributed across all the 26 chromosomes and covered 4,365.3 cM of cotton genome with an average inter-marker distance of 1.48 cM. The maximum length of chromosome was 218.38 cM and the minimum was 122.09 cM with an average length of 167.90 cM. A sub-genome covers more genetic distance (2,189.01 cM with an average inter loci distance of 1.53 cM than D sub-genome which covers a length of 2,176.29 cM with an average distance of 1.43 cM. There were 716 distorted loci in the map accounting for 23.14% and most distorted loci were distributed on D sub-genome (25.06%, which were more than on A sub-genome (21.23%. In our map 49 segregation hotspots (SDR were distributed across the genome with more on D sub-genome as compared to A genome. Two post-polyploidization reciprocal translocations of A2/A3 and A4/A5 were suggested by 7 pairs of duplicate loci. The map constructed through these studies is one of the three densest genetic maps in cotton however; this is the first dense genome wide SSR interspecific genetic map between G. hirsutum and G. tomentosum.

  2. Construction of a high-density genetic map using specific length amplified fragment markers and identification of a quantitative trait locus for anthracnose resistance in walnut (Juglans regia L.).

    Science.gov (United States)

    Zhu, Yufeng; Yin, Yanfei; Yang, Keqiang; Li, Jihong; Sang, Yalin; Huang, Long; Fan, Shu

    2015-08-18

    Walnut (Juglans regia, 2n = 32, approximately 606 Mb per 1C genome) is an economically important tree crop. Resistance to anthracnose, caused by Colletotrichum gloeosporioides, is a major objective of walnut genetic improvement in China. The recently developed specific length amplified fragment sequencing (SLAF-seq) is an efficient strategy that can obtain large numbers of markers with sufficient sequence information to construct high-density genetic maps and permits detection of quantitative trait loci (QTLs) for molecular breeding. SLAF-seq generated 161.64 M paired-end reads. 153,820 SLAF markers were obtained, of which 49,174 were polymorphic. 13,635 polymorphic markers were sorted into five segregation types and 2,577 markers of them were used to construct genetic linkage maps: 2,395 of these fell into 16 linkage groups (LGs) for the female map, 448 markers for the male map, and 2,577 markers for the integrated map. Taking into account the size of all LGs, the marker coverage was 2,664.36 cM for the female map, 1,305.58 cM for the male map, and 2,457.82 cM for the integrated map. The average intervals between two adjacent mapped markers were 1.11 cM, 2.91 cM and 0.95 cM for three maps, respectively. 'SNP_only' markers accounted for 89.25% of the markers on the integrated map. Mapping markers contained 5,043 single nucleotide polymorphisms (SNPs) loci, which corresponded to two SNP loci per SLAF marker. According to the integrated map, we used interval mapping (Logarithm of odds, LOD > 3.0) to detect our quantitative trait. One QTL was detected for anthracnose resistance. The interval of this QTL ranged from 165.51 cM to 176.33 cM on LG14, and ten markers in this interval that were above the threshold value were considered to be linked markers to the anthracnose resistance trait. The phenotypic variance explained by each marker ranged from 16.2 to 19.9%, and their LOD scores varied from 3.22 to 4.04. High-density genetic maps for walnut containing 16

  3. MODELING THE ANOMALY OF SURFACE NUMBER DENSITIES OF GALAXIES ON THE GALACTIC EXTINCTION MAP DUE TO THEIR FIR EMISSION CONTAMINATION

    Energy Technology Data Exchange (ETDEWEB)

    Kashiwagi, Toshiya; Suto, Yasushi; Taruya, Atsushi; Yahata, Kazuhiro [Department of Physics, The University of Tokyo, Tokyo 113-0033 (Japan); Kayo, Issha [Department of Physics, Toho University, Funabashi, Chiba 274-8510 (Japan); Nishimichi, Takahiro, E-mail: kashiwagi@utap.phys.s.u-tokyo.ac.jp [Institute for the Physics and Mathematics of the Universe, University of Tokyo, Kashiwa, Chiba 277-8568 (Japan)

    2015-02-01

    The most widely used Galactic extinction map is constructed assuming that the observed far-infrared (FIR) fluxes come entirely from Galactic dust. According to the earlier suggestion by Yahata et al., we consider how FIR emission of galaxies affects the SFD map. We first compute the surface number density of Sloan Digital Sky Survey (SDSS) DR7 galaxies as a function of the r-band extinction, A {sub r,} {sub SFD}. We confirm that the surface densities of those galaxies positively correlate with A {sub r,} {sub SFD} for A {sub r,} {sub SFD} < 0.1, as first discovered by Yahata et al. for SDSS DR4 galaxies. Next we construct an analytical model to compute the surface density of galaxies, taking into account the contamination of their FIR emission. We adopt a log-normal probability distribution for the ratio of 100 μm and r-band luminosities of each galaxy, y ≡ (νL){sub 100} {sub μm}/(νL) {sub r}. Then we search for the mean and rms values of y that fit the observed anomaly, using the analytical model. The required values to reproduce the anomaly are roughly consistent with those measured from the stacking analysis of SDSS galaxies. Due to the limitation of our statistical modeling, we are not yet able to remove the FIR contamination of galaxies from the extinction map. Nevertheless, the agreement with the model prediction suggests that the FIR emission of galaxies is mainly responsible for the observed anomaly. Whereas the corresponding systematic error in the Galactic extinction map is 0.1-1 mmag, it is directly correlated with galaxy clustering and thus needs to be carefully examined in precision cosmology.

  4. New 3D gas density maps of NaI and CaII interstellar absorption within 300 pc

    Science.gov (United States)

    Welsh, B. Y.; Lallement, R.; Vergely, J.-L.; Raimond, S.

    2010-02-01

    Aims: We present new high resolution (R > 50 000) absorption measurements of the NaI doublet (5889-5895 Å) along 482 nearby sight-lines, in addition to 807 new measurements of the CaII K (3933 Å) absorption line. We have combined these new data with previously reported measurements to produce a catalog of absorptions towards a total of 1857 early-type stars located within 800 pc of the Sun. Using these data we have determined the approximate 3-dimensional spatial distribution of neutral and partly ionized interstellar gas density within a distance-cube of 300 pc from the Sun. Methods: All newly recorded spectra were analyzed by means of a multi-component line profile-fitting program, in most cases using simultaneous fits to the line doublets. Normalized absorption profiles were fitted by varying the velocity, doppler width and column density for all intervening interstellar clouds. The resulting total column densities were then used in conjunction with the Hipparcos distances of the target stars to construct inversion maps of the 3D spatial density distribution of the NaI and CaII bearing gas. Results: A plot of the equivalent width of NaI versus distance reveals a wall of neutral gas at ~80 pc that can be associated with the boundary wall to the central rarefied Local Cavity region. In contrast, a similar plot for the equivalent width of CaII shows no sharply increasing absorption at 80 pc, but instead we observe a slowly increasing value of CaII equivalent width with increasing sight-line distance sampled. Low values for the volume density of NaI (nNaI values in the range 10-8 >nNaI > 10-10 cm-3 are found for sight-lines with distance >300 pc. Both high and low values of the volume density of CaII (nCaII) are found for sight-lines 100 pc a value of nCaII ~ 10-9 cm-3 is typical for most sight-lines, indicating that the distribution of CaII bearing gas is fairly uniform throughout the general ISM. Our three maps of the 3D spatial distribution of local neutral Na

  5. Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley

    Directory of Open Access Journals (Sweden)

    Bartoš Jan

    2008-06-01

    Full Text Available Abstract Background Flow cytometry facilitates sorting of single chromosomes and chromosome arms which can be used for targeted genome analysis. However, the recovery of microgram amounts of DNA needed for some assays requires sorting of millions of chromosomes which is laborious and time consuming. Yet, many genomic applications such as development of genetic maps or physical mapping do not require large DNA fragments. In such cases time-consuming de novo sorting can be minimized by utilizing whole-genome amplification. Results Here we report a protocol optimized in barley including amplification of DNA from only ten thousand chromosomes, which can be isolated in less than one hour. Flow-sorted chromosomes were treated with proteinase K and amplified using Phi29 multiple displacement amplification (MDA. Overnight amplification in a 20-microlitre reaction produced 3.7 – 5.7 micrograms DNA with a majority of products between 5 and 30 kb. To determine the purity of sorted fractions and potential amplification bias we used quantitative PCR for specific genes on each chromosome. To extend the analysis to a whole genome level we performed an oligonucleotide pool assay (OPA for interrogation of 1524 loci, of which 1153 loci had known genetic map positions. Analysis of unamplified genomic DNA of barley cv. Akcent using this OPA resulted in 1426 markers with present calls. Comparison with three replicates of amplified genomic DNA revealed >99% concordance. DNA samples from amplified chromosome 1H and a fraction containing chromosomes 2H – 7H were examined. In addition to loci with known map positions, 349 loci with unknown map positions were included. Based on this analysis 40 new loci were mapped to 1H. Conclusion The results indicate a significant potential of using this approach for physical mapping. Moreover, the study showed that multiple displacement amplification of flow-sorted chromosomes is highly efficient and representative which

  6. Development of admixture mapping panels for African Americans from commercial high-density SNP arrays

    Directory of Open Access Journals (Sweden)

    Dunston Georgia M

    2010-07-01

    Full Text Available Abstract Background Admixture mapping is a powerful approach for identifying genetic variants involved in human disease that exploits the unique genomic structure in recently admixed populations. To use existing published panels of ancestry-informative markers (AIMs for admixture mapping, markers have to be genotyped de novo for each admixed study sample and samples representing the ancestral parental populations. The increased availability of dense marker data on commercial chips has made it feasible to develop panels wherein the markers need not be predetermined. Results We developed two panels of AIMs (~2,000 markers each based on the Affymetrix Genome-Wide Human SNP Array 6.0 for admixture mapping with African American samples. These two AIM panels had good map power that was higher than that of a denser panel of ~20,000 random markers as well as other published panels of AIMs. As a test case, we applied the panels in an admixture mapping study of hypertension in African Americans in the Washington, D.C. metropolitan area. Conclusions Developing marker panels for admixture mapping from existing genome-wide genotype data offers two major advantages: (1 no de novo genotyping needs to be done, thereby saving costs, and (2 markers can be filtered for various quality measures and replacement markers (to minimize gaps can be selected at no additional cost. Panels of carefully selected AIMs have two major advantages over panels of random markers: (1 the map power from sparser panels of AIMs is higher than that of ~10-fold denser panels of random markers, and (2 clusters can be labeled based on information from the parental populations. With current technology, chip-based genome-wide genotyping is less expensive than genotyping ~20,000 random markers. The major advantage of using random markers is the absence of ascertainment effects resulting from the process of selecting markers. The ability to develop marker panels informative for ancestry from

  7. Joint Mapping of Mobility and Trap Density in Colloidal Quantum Dot Solids

    KAUST Repository

    Stadler, Philipp; Sutherland, Brandon R.; Ren, Yuan; Ning, Zhijun; Simchi, Arash; Thon, Susanna M.; Hoogland, Sjoerd; Sargent, Edward H.

    2013-01-01

    to be harnessed. Here, we deploy nanodielectric field-effect transistors to map the energy landscape within the band gap of a colloidal quantum dot solid. We exploit the self-limiting nature of the potentiostatic anodization growth mode to produce the thinnest

  8. High-Density Genetic Map Construction and Stem Total Polysaccharide Content-Related QTL Exploration for Chinese Endemic Dendrobium (Orchidaceae)

    Science.gov (United States)

    Lu, Jiangjie; Liu, Yuyang; Xu, Jing; Mei, Ziwei; Shi, Yujun; Liu, Pengli; He, Jianbo; Wang, Xiaotong; Meng, Yijun; Feng, Shangguo; Shen, Chenjia; Wang, Huizhong

    2018-01-01

    Plants of the Dendrobium genus are orchids with not only ornamental value but also high medicinal value. To understand the genetic basis of variations in active ingredients of the stem total polysaccharide contents (STPCs) among different Dendrobium species, it is of paramount importance to understand the mechanism of STPC formation and identify genes affecting its process at the whole genome level. Here, we report the first high-density single-nucleotide polymorphism (SNP) integrated genetic map with a good genome coverage of Dendrobium. The specific-locus amplified fragment sequencing (SLAF-seq) technology led to identification of 7,013,400 SNPs from 1,503,626 high-quality SLAF markers from two parents (Dendrobium moniliforme ♀ × Dendrobium officinale ♂) and their interspecific F1 hybrid population. The final genetic map contained 8, 573 SLAF markers, covering 19 linkage groups (LGs). This genetic map spanned a length of 2,737.49 cM, where the average distance between markers is 0.32 cM. In total, 5 quantitative trait loci (QTL) related to STPC were identified, 3 of which have candidate genes within the confidence intervals of these stable QTLs based on the D. officinale genome sequence. This study will build a foundation up for the mapping of other medicinal-related traits and provide an important reference for the molecular breeding of these Chinese herb. PMID:29636767

  9. MO-F-CAMPUS-J-04: Tissue Segmentation-Based MR Electron Density Mapping Method for MR-Only Radiation Treatment Planning of Brain

    Energy Technology Data Exchange (ETDEWEB)

    Yu, H [Sunnybrook Health Sciences Centre, Toronto, Ontario (Canada); Lee, Y [Sunnybrook Odette Cancer Centre, Toronto, Ontario (Canada); Ruschin, M [Odette Cancer Centre, Toronto, ON (Canada); Karam, I [Sunnybrook Odette Cancer Center, Toronto, Ontario (Canada); Sahgal, A [University of Toronto, Toronto, ON (Canada)

    2015-06-15

    Purpose: Automatically derive electron density of tissues using MR images and generate a pseudo-CT for MR-only treatment planning of brain tumours. Methods: 20 stereotactic radiosurgery (SRS) patients’ T1-weighted MR images and CT images were retrospectively acquired. First, a semi-automated tissue segmentation algorithm was developed to differentiate tissues with similar MR intensities and large differences in electron densities. The method started with approximately 12 slices of manually contoured spatial regions containing sinuses and airways, then air, bone, brain, cerebrospinal fluid (CSF) and eyes were automatically segmented using edge detection and anatomical information including location, shape, tissue uniformity and relative intensity distribution. Next, soft tissues - muscle and fat were segmented based on their relative intensity histogram. Finally, intensities of voxels in each segmented tissue were mapped into their electron density range to generate pseudo-CT by linearly fitting their relative intensity histograms. Co-registered CT was used as a ground truth. The bone segmentations of pseudo-CT were compared with those of co-registered CT obtained by using a 300HU threshold. The average distances between voxels on external edges of the skull of pseudo-CT and CT in three axial, coronal and sagittal slices with the largest width of skull were calculated. The mean absolute electron density (in Hounsfield unit) difference of voxels in each segmented tissues was calculated. Results: The average of distances between voxels on external skull from pseudo-CT and CT were 0.6±1.1mm (mean±1SD). The mean absolute electron density differences for bone, brain, CSF, muscle and fat are 78±114 HU, and 21±8 HU, 14±29 HU, 57±37 HU, and 31±63 HU, respectively. Conclusion: The semi-automated MR electron density mapping technique was developed using T1-weighted MR images. The generated pseudo-CT is comparable to that of CT in terms of anatomical position of

  10. The Fate of High-Density Lesions on the Non-contrast CT Obtained Immediately After Intra-arterial Thrombolysis in Ischemic Stroke Patients

    International Nuclear Information System (INIS)

    Jang, Yu Mi; Lee, Deok Hee; Kim, Ho Sung; Ryu, Chang Woo; Lee, Jeong Hyun; Choi, Choong Gon; Kim, Sang Joon; Suh, Dae Chul

    2006-01-01

    Hyperdense lesions can frequently be observed on the CT obtained immediately after intra-arterial (IA) thrombolysis, and it is sometimes difficult to differentiate contrast extravasation from the hemorrhagic lesions. The purposes of this study are to classify the hyperdense lesions according to their morphologic features and to track the outcome of those lesions. Among the 94 patients who suffered with anterior circulation ischemic stroke and who were treated with IA thrombolysis, 31 patients revealed hyperdense lesions on the CT obtained immediately after the procedure. The lesions were categorized into four types according to their volume, shape, location and density: cortical high density (HD), soft HD, metallic HD and diffuse HD. The follow-up images were obtained 3 5 days later in order to visualize the morphologic changes and hemorrhagic transformation of the lesions. Among the 31 patients with HD lesions, 18 (58%) showed hemorrhagic transformation of their lesion, and six of them were significant. All the cortical HD lesions (n = 4) revealed spontaneous resolution. Seven of the soft HD lesions (n = 13) showed spontaneous resolution, while the rest of the group showed hemorrhagic transformation. Among them the hemorrhage was significant in only two patients (2/6) who did not achieve successful recanalization. All the metallic HD lesions (n = 10) resulted in hemorrhagic transformation; among them, three cases (30%) with a maximum CT value more than 150 HU (Hounsfield unit) subsequently showed significant hemorrhagic transformation on the follow-up CT. There were four diffuse HD lesions, and two of them showed hemorrhagic transformation. The parenchymal hyperdense lesions observed on the CT obtained immediately after IA thrombolysis in ischemic stroke patients exhibited varying features and they were not always hemorrhagic. Most of the soft HD lesions were benign, and although all of the metallic HD lesions were hemorrhagic, some of them were ultimately found

  11. Mapping surface charge density of lipid bilayers by quantitative surface conductivity microscopy

    DEFF Research Database (Denmark)

    Klausen, Lasse Hyldgaard; Fuhs, Thomas; Dong, Mingdong

    2016-01-01

    Local surface charge density of lipid membranes influences membrane-protein interactions leading to distinct functions in all living cells, and it is a vital parameter in understanding membrane-binding mechanisms, liposome design and drug delivery. Despite the significance, no method has so far...

  12. Mapping brucellosis increases relative to elk density using hierarchical Bayesian models

    Science.gov (United States)

    Cross, Paul C.; Heisey, Dennis M.; Scurlock, Brandon M.; Edwards, William H.; Brennan, Angela; Ebinger, Michael R.

    2010-01-01

    The relationship between host density and parasite transmission is central to the effectiveness of many disease management strategies. Few studies, however, have empirically estimated this relationship particularly in large mammals. We applied hierarchical Bayesian methods to a 19-year dataset of over 6400 brucellosis tests of adult female elk (Cervus elaphus) in northwestern Wyoming. Management captures that occurred from January to March were over two times more likely to be seropositive than hunted elk that were killed in September to December, while accounting for site and year effects. Areas with supplemental feeding grounds for elk had higher seroprevalence in 1991 than other regions, but by 2009 many areas distant from the feeding grounds were of comparable seroprevalence. The increases in brucellosis seroprevalence were correlated with elk densities at the elk management unit, or hunt area, scale (mean 2070 km2; range = [95–10237]). The data, however, could not differentiate among linear and non-linear effects of host density. Therefore, control efforts that focus on reducing elk densities at a broad spatial scale were only weakly supported. Additional research on how a few, large groups within a region may be driving disease dynamics is needed for more targeted and effective management interventions. Brucellosis appears to be expanding its range into new regions and elk populations, which is likely to further complicate the United States brucellosis eradication program. This study is an example of how the dynamics of host populations can affect their ability to serve as disease reservoirs.

  13. Mapping brucellosis increases relative to elk density using hierarchical Bayesian models.

    Directory of Open Access Journals (Sweden)

    Paul C Cross

    Full Text Available The relationship between host density and parasite transmission is central to the effectiveness of many disease management strategies. Few studies, however, have empirically estimated this relationship particularly in large mammals. We applied hierarchical Bayesian methods to a 19-year dataset of over 6400 brucellosis tests of adult female elk (Cervus elaphus in northwestern Wyoming. Management captures that occurred from January to March were over two times more likely to be seropositive than hunted elk that were killed in September to December, while accounting for site and year effects. Areas with supplemental feeding grounds for elk had higher seroprevalence in 1991 than other regions, but by 2009 many areas distant from the feeding grounds were of comparable seroprevalence. The increases in brucellosis seroprevalence were correlated with elk densities at the elk management unit, or hunt area, scale (mean 2070 km(2; range = [95-10237]. The data, however, could not differentiate among linear and non-linear effects of host density. Therefore, control efforts that focus on reducing elk densities at a broad spatial scale were only weakly supported. Additional research on how a few, large groups within a region may be driving disease dynamics is needed for more targeted and effective management interventions. Brucellosis appears to be expanding its range into new regions and elk populations, which is likely to further complicate the United States brucellosis eradication program. This study is an example of how the dynamics of host populations can affect their ability to serve as disease reservoirs.

  14. Whole brain analysis of postmortem density changes of grey and white matter on computed tomography by statistical parametric mapping

    Energy Technology Data Exchange (ETDEWEB)

    Nishiyama, Yuichi; Mori, Hiroshi; Katsube, Takashi; Kitagaki, Hajime [Shimane University Faculty of Medicine, Department of Radiology, Izumo-shi, Shimane (Japan); Kanayama, Hidekazu; Tada, Keiji; Yamamoto, Yasushi [Shimane University Hospital, Department of Radiology, Izumo-shi, Shimane (Japan); Takeshita, Haruo [Shimane University Faculty of Medicine, Department of Legal Medicine, Izumo-shi, Shimane (Japan); Kawakami, Kazunori [Fujifilm RI Pharma, Co., Ltd., Tokyo (Japan)

    2017-06-15

    This study examined the usefulness of statistical parametric mapping (SPM) for investigating postmortem changes on brain computed tomography (CT). This retrospective study included 128 patients (23 - 100 years old) without cerebral abnormalities who underwent unenhanced brain CT before and after death. The antemortem CT (AMCT) scans and postmortem CT (PMCT) scans were spatially normalized using our original brain CT template, and postmortem changes of CT values (in Hounsfield units; HU) were analysed by the SPM technique. Compared with AMCT scans, 58.6 % and 98.4 % of PMCT scans showed loss of the cerebral sulci and an unclear grey matter (GM)-white matter (WM) interface, respectively. SPM analysis revealed a significant decrease in cortical GM density within 70 min after death on PMCT scans, suggesting cytotoxic brain oedema. Furthermore, there was a significant increase in the density of the WM, lenticular nucleus and thalamus more than 120 min after death. The SPM technique demonstrated typical postmortem changes on brain CT scans, and revealed that the unclear GM-WM interface on early PMCT scans is caused by a rapid decrease in cortical GM density combined with a delayed increase in WM density. SPM may be useful for assessment of whole brain postmortem changes. (orig.)

  15. Whole brain analysis of postmortem density changes of grey and white matter on computed tomography by statistical parametric mapping

    International Nuclear Information System (INIS)

    Nishiyama, Yuichi; Mori, Hiroshi; Katsube, Takashi; Kitagaki, Hajime; Kanayama, Hidekazu; Tada, Keiji; Yamamoto, Yasushi; Takeshita, Haruo; Kawakami, Kazunori

    2017-01-01

    This study examined the usefulness of statistical parametric mapping (SPM) for investigating postmortem changes on brain computed tomography (CT). This retrospective study included 128 patients (23 - 100 years old) without cerebral abnormalities who underwent unenhanced brain CT before and after death. The antemortem CT (AMCT) scans and postmortem CT (PMCT) scans were spatially normalized using our original brain CT template, and postmortem changes of CT values (in Hounsfield units; HU) were analysed by the SPM technique. Compared with AMCT scans, 58.6 % and 98.4 % of PMCT scans showed loss of the cerebral sulci and an unclear grey matter (GM)-white matter (WM) interface, respectively. SPM analysis revealed a significant decrease in cortical GM density within 70 min after death on PMCT scans, suggesting cytotoxic brain oedema. Furthermore, there was a significant increase in the density of the WM, lenticular nucleus and thalamus more than 120 min after death. The SPM technique demonstrated typical postmortem changes on brain CT scans, and revealed that the unclear GM-WM interface on early PMCT scans is caused by a rapid decrease in cortical GM density combined with a delayed increase in WM density. SPM may be useful for assessment of whole brain postmortem changes. (orig.)

  16. A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus

    Science.gov (United States)

    2011-01-01

    Background Technological advances are progressively increasing the application of genomics to a wider array of economically and ecologically important species. High-density maps enriched for transcribed genes facilitate the discovery of connections between genes and phenotypes. We report the construction of a high-density linkage map of expressed genes for the heterozygous genome of Eucalyptus using Single Feature Polymorphism (SFP) markers. Results SFP discovery and mapping was achieved using pseudo-testcross screening and selective mapping to simultaneously optimize linkage mapping and microarray costs. SFP genotyping was carried out by hybridizing complementary RNA prepared from 4.5 year-old trees xylem to an SFP array containing 103,000 25-mer oligonucleotide probes representing 20,726 unigenes derived from a modest size expressed sequence tags collection. An SFP-mapping microarray with 43,777 selected candidate SFP probes representing 15,698 genes was subsequently designed and used to genotype SFPs in a larger subset of the segregating population drawn by selective mapping. A total of 1,845 genes were mapped, with 884 of them ordered with high likelihood support on a framework map anchored to 180 microsatellites with average density of 1.2 cM. Using more probes per unigene increased by two-fold the likelihood of detecting segregating SFPs eventually resulting in more genes mapped. In silico validation showed that 87% of the SFPs map to the expected location on the 4.5X draft sequence of the Eucalyptus grandis genome. Conclusions The Eucalyptus 1,845 gene map is the most highly enriched map for transcriptional information for any forest tree species to date. It represents a major improvement on the number of genes previously positioned on Eucalyptus maps and provides an initial glimpse at the gene space for this global tree genome. A general protocol is proposed to build high-density transcript linkage maps in less characterized plant species by SFP genotyping

  17. Mapping Tree Density in Forests of the Southwestern USA Using Landsat 8 Data

    Directory of Open Access Journals (Sweden)

    Kamal Humagain

    2017-08-01

    Full Text Available The increase of tree density in forests of the American Southwest promotes extreme fire events, understory biodiversity losses, and degraded habitat conditions for many wildlife species. To ameliorate these changes, managers and scientists have begun planning treatments aimed at reducing fuels and increasing understory biodiversity. However, spatial variability in tree density across the landscape is not well-characterized, and if better known, could greatly influence planning efforts. We used reflectance values from individual Landsat 8 bands (bands 2, 3, 4, 5, 6, and 7 and calculated vegetation indices (difference vegetation index, simple ratios, and normalized vegetation indices to estimate tree density in an area planned for treatment in the Jemez Mountains, New Mexico, characterized by multiple vegetation types and a complex topography. Because different vegetation types have different spectral signatures, we derived models with multiple predictor variables for each vegetation type, rather than using a single model for the entire project area, and compared the model-derived values to values collected from on-the-ground transects. Among conifer-dominated areas (73% of the project area, the best models (as determined by corrected Akaike Information Criteria (AICc included Landsat bands 2, 3, 4, and 7 along with simple ratios, normalized vegetation indices, and the difference vegetation index (R2 values for ponderosa: 0.47, piñon-juniper: 0.52, and spruce-fir: 0.66. On the other hand, in aspen-dominated areas (9% of the project area, the best model included individual bands 4 and 2, simple ratio, and normalized vegetation index (R2 value: 0.97. Most areas dominated by ponderosa, pinyon-juniper, or spruce-fir had more than 100 trees per hectare. About 54% of the study area has medium to high density of trees (100–1000 trees/hectare, and a small fraction (4.5% of the area has very high density (>1000 trees/hectare. Our results provide a

  18. Drowning - a scientometric analysis and data acquisition of a constant global problem employing density equalizing mapping and scientometric benchmarking procedures

    Directory of Open Access Journals (Sweden)

    Groneberg David A

    2011-10-01

    Full Text Available Abstract Background Drowning is a constant global problem which claims approximately half a million victims worldwide each year, whereas the number of near-drowning victims is considerably higher. Public health strategies to reduce the burden of death are still limited. While research activities in the subject drowning grow constantly, yet there is no scientometric evaluation of the existing literature at the present time. Methods The current study uses classical bibliometric tools and visualizing techniques such as density equalizing mapping to analyse and evaluate the scientific research in the field of drowning. The interpretation of the achieved results is also implemented in the context of the data collection of the WHO. Results All studies related to drowning and listed in the ISI-Web of Science database since 1900 were identified using the search term "drowning". Implementing bibliometric methods, a constant increase in quantitative markers such as number of publications per state, publication language or collaborations as well as qualitative markers such as citations were observed for research in the field of drowning. The combination with density equalizing mapping exposed different global patterns for research productivity and the total number of drowning deaths and drowning rates respectively. Chart techniques were used to illustrate bi- and multilateral research cooperation. Conclusions The present study provides the first scientometric approach that visualizes research activity on the subject of drowning. It can be assumed that the scientific approach to this topic will achieve even greater dimensions because of its continuing actuality.

  19. Drowning - a scientometric analysis and data acquisition of a constant global problem employing density equalizing mapping and scientometric benchmarking procedures

    Science.gov (United States)

    2011-01-01

    Background Drowning is a constant global problem which claims approximately half a million victims worldwide each year, whereas the number of near-drowning victims is considerably higher. Public health strategies to reduce the burden of death are still limited. While research activities in the subject drowning grow constantly, yet there is no scientometric evaluation of the existing literature at the present time. Methods The current study uses classical bibliometric tools and visualizing techniques such as density equalizing mapping to analyse and evaluate the scientific research in the field of drowning. The interpretation of the achieved results is also implemented in the context of the data collection of the WHO. Results All studies related to drowning and listed in the ISI-Web of Science database since 1900 were identified using the search term "drowning". Implementing bibliometric methods, a constant increase in quantitative markers such as number of publications per state, publication language or collaborations as well as qualitative markers such as citations were observed for research in the field of drowning. The combination with density equalizing mapping exposed different global patterns for research productivity and the total number of drowning deaths and drowning rates respectively. Chart techniques were used to illustrate bi- and multilateral research cooperation. Conclusions The present study provides the first scientometric approach that visualizes research activity on the subject of drowning. It can be assumed that the scientific approach to this topic will achieve even greater dimensions because of its continuing actuality. PMID:21999813

  20. First Volcanological-Probabilistic Pyroclastic Density Current and Fallout Hazard Map for Campi Flegrei and Somma Vesuvius Volcanoes.

    Science.gov (United States)

    Mastrolorenzo, G.; Pappalardo, L.; Troise, C.; Panizza, A.; de Natale, G.

    2005-05-01

    Integrated volcanological-probabilistic approaches has been used in order to simulate pyroclastic density currents and fallout and produce hazard maps for Campi Flegrei and Somma Vesuvius areas. On the basis of the analyses of all types of pyroclastic flows, surges, secondary pyroclastic density currents and fallout events occurred in the volcanological history of the two volcanic areas and the evaluation of probability for each type of events, matrixs of input parameters for a numerical simulation have been performed. The multi-dimensional input matrixs include the main controlling parameters of the pyroclasts transport and deposition dispersion, as well as the set of possible eruptive vents used in the simulation program. Probabilistic hazard maps provide of each points of campanian area, the yearly probability to be interested by a given event with a given intensity and resulting demage. Probability of a few events in one thousand years are typical of most areas around the volcanoes whitin a range of ca 10 km, including Neaples. Results provide constrains for the emergency plans in Neapolitan area.

  1. Collinearity Analysis and High-Density Genetic Mapping of the Wheat Powdery Mildew Resistance Gene Pm40 in PI 672538

    Science.gov (United States)

    Fatima, Syeda Akash; Yang, Jiezhi; Chen, Wanquan; Liu, Taiguo; Hu, Yuting; Li, Qing; Guo, Jingwei; Zhang, Min; Lei, Li; Li, Xin; Tang, Shengwen; Luo, Peigao

    2016-01-01

    The wheat powdery mildew resistance gene Pm40, which is located on chromosomal arm 7BS, is effective against nearly all prevalent races of Blumeria graminis f. sp tritici (Bgt) in China and is carried by the common wheat germplasm PI 672538. A set of the F1, F2 and F2:3 populations from the cross of the resistant PI 672538 with the susceptible line L1034 were used to conduct genetic analysis of powdery mildew resistance and construct a high-density linkage map of the Pm40 gene. We constructed a high-density linkage genetic map with a total length of 6.18 cM and average spacing between markers of 0.48 cM.Pm40 is flanked by Xwmc335 and BF291338 at genetic distances of 0.58 cM and 0.26 cM, respectively, in deletion bin C-7BS-1-0.27. Comparative genomic analysis based on EST-STS markers established a high level of collinearity of the Pm40 genomic region with a 1.09-Mbp genomic region on Brachypodium chromosome 3, a 1.16-Mbp genomic region on rice chromosome 8, and a 1.62-Mbp genomic region on sorghum chromosome 7. We further anchored the Pm40 target intervals to the wheat genome sequence. A putative linear index of 85 wheat contigs containing 97 genes on 7BS was constructed. In total, 9 genes could be considered as candidates for the resistances to powdery mildew in the target genomic regions, which encoded proteins that were involved in the plant defense and response to pathogen attack. These results will facilitate the development of new markers for map-based cloning and marker-assisted selection of Pm40 in wheat breeding programs. PMID:27755575

  2. Bacterial meningitis: a density-equalizing mapping analysis of the global research architecture.

    Science.gov (United States)

    Pleger, Niklas; Kloft, Beatrix; Quarcoo, David; Zitnik, Simona; Mache, Stefanie; Klingelhoefer, Doris; Groneberg, David A

    2014-09-30

    Bacterial meningitis is caused by a variety of pathogens and displays an important public health threat all over the world. Despite the necessity to develop customized public health-related research projects, a thorough study of global meningitis research is not present, so far. Therefore, the aim of this study was a combined density-equalizing and scientometric study. To evaluate the scientific efforts of bibliometric methods, density-equalizing algorithms and large-scale data analysis of the Web of Science were applied in the period between 1900 and 2007. From this, 7998 publications on bacterial meningitis have been found. With a number of 2698, most publications have been written by U.S. authors, followed by the UK (912), Germany (749) and France (620). This dominance can also be shown in the international cooperation. The specific citation analyses reveal that the nation with the highest average citation rate (citations per publications) was Norway (26.36), followed by Finland (24.16) and the U.S. (24.06). This study illustrates the architecture of global research on bacterial meningitis and points to the need for customized research programs with a focus on local public health issues in countries with a low development index, but high incidences, to target this global public health problem.

  3. A Comparison of Spectral Angle Mapper and Artificial Neural Network Classifiers Combined with Landsat TM Imagery Analysis for Obtaining Burnt Area Mapping

    Directory of Open Access Journals (Sweden)

    Marko Scholze

    2010-03-01

    Full Text Available Satellite remote sensing, with its unique synoptic coverage capabilities, can provide accurate and immediately valuable information on fire analysis and post-fire assessment, including estimation of burnt areas. In this study the potential for burnt area mapping of the combined use of Artificial Neural Network (ANN and Spectral Angle Mapper (SAM classifiers with Landsat TM satellite imagery was evaluated in a Mediterranean setting. As a case study one of the most catastrophic forest fires, which occurred near the capital of Greece during the summer of 2007, was used. The accuracy of the two algorithms in delineating the burnt area from the Landsat TM imagery, acquired shortly after the fire suppression, was determined by the classification accuracy results of the produced thematic maps. In addition, the derived burnt area estimates from the two classifiers were compared with independent estimates available for the study region, obtained from the analysis of higher spatial resolution satellite data. In terms of the overall classification accuracy, ANN outperformed (overall accuracy 90.29%, Kappa coefficient 0.878 the SAM classifier (overall accuracy 83.82%, Kappa coefficient 0.795. Total burnt area estimates from the two classifiers were found also to be in close agreement with the other available estimates for the study region, with a mean absolute percentage difference of ~1% for ANN and ~6.5% for SAM. The study demonstrates the potential of the examined here algorithms in detecting burnt areas in a typical Mediterranean setting.

  4. High density genetic mapping identifies new susceptibility loci for rheumatoid arthritis

    Science.gov (United States)

    Eyre, Steve; Bowes, John; Diogo, Dorothée; Lee, Annette; Barton, Anne; Martin, Paul; Zhernakova, Alexandra; Stahl, Eli; Viatte, Sebastien; McAllister, Kate; Amos, Christopher I.; Padyukov, Leonid; Toes, Rene E.M.; Huizinga, Tom W.J.; Wijmenga, Cisca; Trynka, Gosia; Franke, Lude; Westra, Harm-Jan; Alfredsson, Lars; Hu, Xinli; Sandor, Cynthia; de Bakker, Paul I.W.; Davila, Sonia; Khor, Chiea Chuen; Heng, Khai Koon; Andrews, Robert; Edkins, Sarah; Hunt, Sarah E; Langford, Cordelia; Symmons, Deborah; Concannon, Pat; Onengut-Gumuscu, Suna; Rich, Stephen S; Deloukas, Panos; Gonzalez-Gay, Miguel A.; Rodriguez-Rodriguez, Luis; Ärlsetig, Lisbeth; Martin, Javier; Rantapää-Dahlqvist, Solbritt; Plenge, Robert; Raychaudhuri, Soumya; Klareskog, Lars; Gregersen, Peter K; Worthington, Jane

    2012-01-01

    Summary Using the Immunochip custom single nucleotide polymorphism (SNP) array, designed for dense genotyping of 186 genome wide association study (GWAS) confirmed loci we analysed 11,475 rheumatoid arthritis cases of European ancestry and 15,870 controls for 129,464 markers. The data were combined in meta-analysis with GWAS data from additional independent cases (n=2,363) and controls (n=17,872). We identified fourteen novel loci; nine were associated with rheumatoid arthritis overall and 5 specifically in anti-citrillunated peptide antibody positive disease, bringing the number of confirmed European ancestry rheumatoid arthritis loci to 46. We refined the peak of association to a single gene for 19 loci, identified secondary independent effects at six loci and association to low frequency variants (minor allele frequency <0.05) at 4 loci. Bioinformatic analysis of the data generated strong hypotheses for the causal SNP at seven loci. This study illustrates the advantages of dense SNP mapping analysis to inform subsequent functional investigations. PMID:23143596

  5. Linear-scaling time-dependent density-functional theory beyond the Tamm-Dancoff approximation: Obtaining efficiency and accuracy with in situ optimised local orbitals

    Energy Technology Data Exchange (ETDEWEB)

    Zuehlsdorff, T. J., E-mail: tjz21@cam.ac.uk; Payne, M. C. [Cavendish Laboratory, J. J. Thomson Avenue, Cambridge CB3 0HE (United Kingdom); Hine, N. D. M. [Department of Physics, University of Warwick, Coventry CV4 7AL (United Kingdom); Haynes, P. D. [Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ (United Kingdom); Department of Physics, Imperial College London, Exhibition Road, London SW7 2AZ (United Kingdom); Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, Exhibition Road, London SW7 2AZ (United Kingdom)

    2015-11-28

    We present a solution of the full time-dependent density-functional theory (TDDFT) eigenvalue equation in the linear response formalism exhibiting a linear-scaling computational complexity with system size, without relying on the simplifying Tamm-Dancoff approximation (TDA). The implementation relies on representing the occupied and unoccupied subspaces with two different sets of in situ optimised localised functions, yielding a very compact and efficient representation of the transition density matrix of the excitation with the accuracy associated with a systematic basis set. The TDDFT eigenvalue equation is solved using a preconditioned conjugate gradient algorithm that is very memory-efficient. The algorithm is validated on a small test molecule and a good agreement with results obtained from standard quantum chemistry packages is found, with the preconditioner yielding a significant improvement in convergence rates. The method developed in this work is then used to reproduce experimental results of the absorption spectrum of bacteriochlorophyll in an organic solvent, where it is demonstrated that the TDA fails to reproduce the main features of the low energy spectrum, while the full TDDFT equation yields results in good qualitative agreement with experimental data. Furthermore, the need for explicitly including parts of the solvent into the TDDFT calculations is highlighted, making the treatment of large system sizes necessary that are well within reach of the capabilities of the algorithm introduced here. Finally, the linear-scaling properties of the algorithm are demonstrated by computing the lowest excitation energy of bacteriochlorophyll in solution. The largest systems considered in this work are of the same order of magnitude as a variety of widely studied pigment-protein complexes, opening up the possibility of studying their properties without having to resort to any semiclassical approximations to parts of the protein environment.

  6. Processing of A New Digital Orthoimage Map of The Martian Western Hemisphere Using Data Obtained From The Mars Orbiter Camera At A Resolution of 256 Pixel/deg

    Science.gov (United States)

    Wählisch, M.; Niedermaier, G.; van Gasselt, S.; Scholten, F.; Wewel, F.; Roatsch, T.; Matz, K.-D.; Jaumann, R.

    We present a new digital orthoimage map of Mars using data obtained from the CCD line scanner Mars Orbiter Camera (MOC) of the Mars Global Surveyor Mis- sion (MGS) [1,2]. The map covers the Mars surface from 0 to 180 West and from 60 South to 60 North with the MDIM2 resolution of 256 pixel/degree and size. Image data processing has been performed using multiple programs, developed by DLR, Technical University of Berlin [3], JPL, and the USGS. 4,339 Context and 183 Geodesy images [2] were included. After radiometric corrections, the images were Mars referenced [4], geometrically corrected [5] and orthoprojected using a global Martian Digital Terrain Model (DTM) with a resolution of 64 pixel/degree, developed at DLR and based on MGS Mars Orbiter Laser Altimeter (MOLA) data [6]. To elim- inate major differences in brightness between the individual images of the mosaics, high- and low-pass filter processing techniques were applied for each image. After filtering, the images were mosaicked without registering or using block adjustment techniques in order to improve the geometric quality. It turns out that the accuracy of the navigation data has such a good quality that the orthoimages fit very well to each other. When merging the MOC mosaic with the MOLA data using IHS- trans- formation, we recognized very good correspondence between these two datasets. We create a topographic image map of the Coprates region (MC­18) adding contour lines derived from the global DTM to the mosaic. These maps are used for geological and morphological interpretations in order to review and improve our current Viking-based knowledge about the Martian surface. References: [1] www.mssss.com, [2] Caplinger, M. and M. Malin, "The Mars Or- biter Camera Geodesy Campaign, JGR, in press, [3] Scholten, F., Vol XXXI, Part B2, Wien 1996, p.351-356, [4] naïf.jpl.nasa.gov, [5] R.L.Kirk. et al. (2001), "Geometric Calibration of the Mars Orbiter Cameras and Coalignment with Mars Orbiter Laser Altimeter

  7. Abnormal pain processing in chronic tension-type headache: a high-density EEG brain mapping study

    DEFF Research Database (Denmark)

    Buchgreitz, L.; Egsgaard, L.L.; Jensen, R.

    2008-01-01

    Central sensitization caused by prolonged nociceptive input from muscles is considered to play an important role for chronification of tension-type headache. In the present study we used a new high-density EEG brain mapping technique to investigate spatiotemporal aspects of brain activity...... in response to muscle pain in 19 patients with chronic tension-type headache (CTTH) and 19 healthy, age- and sex-matched controls. Intramuscular electrical stimuli (single and train of five pulses delivered at 2 Hz) were applied to the trapezius muscle and somatosensory evoked potentials were recorded...... with 128-channel EEG both in- and outside a condition with induced tonic neck/shoulder muscle pain (glutamate injection into the trapezius muscle). Significant reduction in magnitude during and after induced tonic muscle pain was found in controls at the P200 dipole in response to both the first (baseline...

  8. Multivariate quantile mapping bias correction: an N-dimensional probability density function transform for climate model simulations of multiple variables

    Science.gov (United States)

    Cannon, Alex J.

    2018-01-01

    Most bias correction algorithms used in climatology, for example quantile mapping, are applied to univariate time series. They neglect the dependence between different variables. Those that are multivariate often correct only limited measures of joint dependence, such as Pearson or Spearman rank correlation. Here, an image processing technique designed to transfer colour information from one image to another—the N-dimensional probability density function transform—is adapted for use as a multivariate bias correction algorithm (MBCn) for climate model projections/predictions of multiple climate variables. MBCn is a multivariate generalization of quantile mapping that transfers all aspects of an observed continuous multivariate distribution to the corresponding multivariate distribution of variables from a climate model. When applied to climate model projections, changes in quantiles of each variable between the historical and projection period are also preserved. The MBCn algorithm is demonstrated on three case studies. First, the method is applied to an image processing example with characteristics that mimic a climate projection problem. Second, MBCn is used to correct a suite of 3-hourly surface meteorological variables from the Canadian Centre for Climate Modelling and Analysis Regional Climate Model (CanRCM4) across a North American domain. Components of the Canadian Forest Fire Weather Index (FWI) System, a complicated set of multivariate indices that characterizes the risk of wildfire, are then calculated and verified against observed values. Third, MBCn is used to correct biases in the spatial dependence structure of CanRCM4 precipitation fields. Results are compared against a univariate quantile mapping algorithm, which neglects the dependence between variables, and two multivariate bias correction algorithms, each of which corrects a different form of inter-variable correlation structure. MBCn outperforms these alternatives, often by a large margin

  9. The Effects of Vent Location, Event Scale, and Time Forecasts on Pyroclastic Density Current Hazard Maps at Campi Flegrei Caldera (Italy

    Directory of Open Access Journals (Sweden)

    Andrea Bevilacqua

    2017-09-01

    Full Text Available This study presents a new method for producing long-term hazard maps for pyroclastic density currents (PDC originating at Campi Flegrei caldera. Such method is based on a doubly stochastic approach and is able to combine the uncertainty assessments on the spatial location of the volcanic vent, the size of the flow and the expected time of such an event. The results are obtained by using a Monte Carlo approach and adopting a simplified invasion model based on the box model integral approximation. Temporal assessments are modeled through a Cox-type process including self-excitement effects, based on the eruptive record of the last 15 kyr. Mean and percentile maps of PDC invasion probability are produced, exploring their sensitivity to some sources of uncertainty and to the effects of the dependence between PDC scales and the caldera sector where they originated. Conditional maps representative of PDC originating inside limited zones of the caldera, or of PDC with a limited range of scales are also produced. Finally, the effect of assuming different time windows for the hazard estimates is explored, also including the potential occurrence of a sequence of multiple events. Assuming that the last eruption of Monte Nuovo (A.D. 1538 marked the beginning of a new epoch of activity similar to the previous ones, results of the statistical analysis indicate a mean probability of PDC invasion above 5% in the next 50 years on almost the entire caldera (with a probability peak of ~25% in the central part of the caldera. In contrast, probability values reduce by a factor of about 3 if the entire eruptive record is considered over the last 15 kyr, i.e., including both eruptive epochs and quiescent periods.

  10. Depression and Suicide Publication Analysis, Using Density Equalizing Mapping and Output Benchmarking

    Science.gov (United States)

    Vogelzang, B. H.; Scutaru, C.; Mache, S.; Vitzthum, K.; Quarcoo, David; Groneberg, D. A.

    2011-01-01

    Background: Depression is a major cause of suicide worldwide. This association has been reflected by numerous scientific publications reporting about studies to this theme. There is currently no overall evaluation of the global research activities in this field. Aim: The aim of the current study was to analyze long-term developments and recent research trends in this area. Material and Methods: We searched the Web of Science databases developed by the Thompson Institute of Scientific Information for items concerning depression and suicide published between 1900 and 2007 and analyzed the results using scientometric methods and density-equalizing calculations. Results: We found that publications on this topic increased dramatically in the time period 1990 to 2007. The comparison of the different Journals showed that the Archives of General Psychiatry had the highest average citation rate (more than twice that of any other Journal). When comparing authors, we found that not all the authors who had high h-indexes cooperated much with other authors. The analysis of countries who published papers on this topic showed that they published papers in relation to their Gross Domestic Product and Purchasing Power Parity. Among the G8 countries, Russia had the highest male suicide rate in 1999 (more than twice that of any of the other G8 countries), despite having published least papers and cooperating least with other countries among the G8. Conclusion: We conclude that, although there has been an increase in publications on this topic from 1990 to 2006, this increase is of a lower gradient than that of psoriasis and rheumatoid arthritis. PMID:22021955

  11. Visual sensory processing deficits in patients with bipolar disorder revealed through high-density electrical mapping.

    LENUS (Irish Health Repository)

    Yeap, Sherlyn

    2009-11-01

    BACKGROUND: Etiological commonalities are apparent between bipolar disorder and schizophrenia. For example, it is becoming clear that both populations show similar electrophysiological deficits in the auditory domain. Recent studies have also shown robust visual sensory processing deficits in patients with schizophrenia using the event-related potential technique, but this has not been formally tested in those with bipolar disorder. Our goal here was to assess whether early visual sensory processing in patients with bipolar disorder, as indexed by decreased amplitude of the P1 component of the visual evoked potential (VEP), would show a similar deficit to that seen in those with schizophrenia. Since the P1 deficit has already been established as an endophenotype in schizophrenia, a finding of commonality between disorders would raise the possibility that it represents a measure of common genetic liability. METHODS: We visually presented isolated-check stimuli to euthymic patients with a diagnosis of bipolar disorder and age-matched healthy controls within a simple go\\/no-go task and recorded VEPs using high-density (72-channel) electroencephalography. RESULTS: The P1 VEP amplitude was substantially reduced in patients with bipolar disorder, with an effect size of f = 0.56 (large according to Cohen\\'s criteria). LIMITATIONS: Our sample size was relatively small and as such, did not allow for an examination of potential relations between the physiologic measures and clinical measures. CONCLUSION: This reduction in P1 amplitude among patients with bipolar disorder represents a dysfunction in early visual processing that is highly similar to that found repeatedly in patients with schizophrenia and their healthy first-degree relatives. Since the P1 deficit has been related to susceptibility genes for schizophrenia, our results raise the possibility that the deficit may in fact be more broadly related to the development of psychosis and that it merits further

  12. Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

    Energy Technology Data Exchange (ETDEWEB)

    Chojnowski, Grzegorz, E-mail: gchojnowski@genesilico.pl [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); Waleń, Tomasz [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); University of Warsaw, Banacha 2, 02-097 Warsaw (Poland); Piątkowski, Paweł; Potrzebowski, Wojciech [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); Bujnicki, Janusz M. [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); Adam Mickiewicz University, Umultowska 89, 61-614 Poznan (Poland)

    2015-03-01

    A computer program that builds crystal structure models of nucleic acid molecules is presented. Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx.

  13. Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

    International Nuclear Information System (INIS)

    Chojnowski, Grzegorz; Waleń, Tomasz; Piątkowski, Paweł; Potrzebowski, Wojciech; Bujnicki, Janusz M.

    2015-01-01

    A computer program that builds crystal structure models of nucleic acid molecules is presented. Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx

  14. Merging field mapping and modeling to interpret the lithofacies variations from unsteady ash-rich pyroclastic density currents on uneven topography

    Science.gov (United States)

    Doronzo, Domenico; Dellino, Pierfrancesco; Sulpizio, Roberto; Lucchi, Federico

    2017-04-01

    In order to obtain significant volcanological results from computer simulations of explosive eruptions, one either needs a systematic statistical approach to test a wide range of initial and boundary conditions, or needs using a well-constrained field case study. Here we followed the second approach, using data obtained from field mapping of the Grotta dei Palizzi 2 pyroclastic deposits (Vulcano Island, Italy) as input for numerical modeling. This case study deals with impulsive phreatomagmatic explosions that generated ash-rich pyroclastic density currents, interacting with the high topographic obstacle of the La Fossa Caldera rim. We demonstrate that by merging field data with 3D numerical simulation it is possible to highlight the details of the dynamical current-terrain interaction, and to interpret the lithofacies variations of the associated deposits as a function of topography-induced sedimentation rate. Results suggest that a value of the sedimentation rate lower than 5 kg/m2s at the bed load can still be sheared by the overlying current, producing tractional structures in the deposit. Instead, a sedimentation rate in excess of that threshold can preclude the formation of tractional structures, producing thick massive deposits. We think that the approach used in this study could be applied to other case studies to confirm or refine such threshold value of the sedimentation rate, which is to be considered as an upper value as for the limitations of the numerical model.

  15. Park Facilities, Boundaries were determined from parcel mapping lines & site specific items, such as shelter locations, were obtained by field GPS observation, Published in 2010, Not Applicable scale, Chippewa County Government.

    Data.gov (United States)

    NSGIC Local Govt | GIS Inventory — Park Facilities dataset current as of 2010. Boundaries were determined from parcel mapping lines & site specific items, such as shelter locations, were obtained...

  16. Spatiotemporal Built-up Land Density Mapping Using Various Spectral Indices in Landsat-7 ETM+ and Landsat-8 OLI/TIRS (Case Study: Surakarta City)

    Science.gov (United States)

    Risky, Yanuar S.; Aulia, Yogi H.; Widayani, Prima

    2017-12-01

    Spectral indices variations support for rapid and accurate extracting information such as built-up density. However, the exact determination of spectral waves for built-up density extraction is lacking. This study explains and compares the capabilities of 5 variations of spectral indices in spatiotemporal built-up density mapping using Landsat-7 ETM+ and Landsat-8 OLI/TIRS in Surakarta City on 2002 and 2015. The spectral indices variations used are 3 mid-infrared (MIR) based indices such as the Normalized Difference Built-up Index (NDBI), Urban Index (UI) and Built-up and 2 visible based indices such as VrNIR-BI (visible red) and VgNIR-BI (visible green). Linear regression statistics between ground value samples from Google Earth image in 2002 and 2015 and spectral indices for determining built-up land density. Ground value used amounted to 27 samples for model and 7 samples for accuracy test. The classification of built-up density mapping is divided into 9 classes: unclassified, 0-12.5%, 12.5-25%, 25-37.5%, 37.5-50%, 50-62.5%, 62.5-75%, 75-87.5% and 87.5-100 %. Accuracy of built-up land density mapping in 2002 and 2015 using VrNIR-BI (81,823% and 73.235%), VgNIR-BI (78.934% and 69.028%), NDBI (34.870% and 74.365%), UI (43.273% and 64.398%) and Built-up (59.755% and 72.664%). Based all spectral indices, Surakarta City on 2000-2015 has increased of built-up land density. VgNIR-BI has better capabilities for built-up land density mapping on Landsat-7 ETM + and Landsat-8 OLI/TIRS.

  17. SU-G-JeP2-02: A Unifying Multi-Atlas Approach to Electron Density Mapping Using Multi-Parametric MRI for Radiation Treatment Planning

    Energy Technology Data Exchange (ETDEWEB)

    Ren, S [Stanford University, Stanford, CA (United States); Tianjin University, Tianjin (China); Hara, W; Le, Q; Wang, L; Xing, L; Li, R [Stanford University, Stanford, CA (United States)

    2016-06-15

    Purpose: MRI has a number of advantages over CT as a primary modality for radiation treatment planning (RTP). However, one key bottleneck problem still remains, which is the lack of electron density information in MRI. In the work, a reliable method to map electron density is developed by leveraging the differential contrast of multi-parametric MRI. Methods: We propose a probabilistic Bayesian approach for electron density mapping based on T1 and T2-weighted MRI, using multiple patients as atlases. For each voxel, we compute two conditional probabilities: (1) electron density given its image intensity on T1 and T2-weighted MR images, and (2) electron density given its geometric location in a reference anatomy. The two sources of information (image intensity and spatial location) are combined into a unifying posterior probability density function using the Bayesian formalism. The mean value of the posterior probability density function provides the estimated electron density. Results: We evaluated the method on 10 head and neck patients and performed leave-one-out cross validation (9 patients as atlases and remaining 1 as test). The proposed method significantly reduced the errors in electron density estimation, with a mean absolute HU error of 138, compared with 193 for the T1-weighted intensity approach and 261 without density correction. For bone detection (HU>200), the proposed method had an accuracy of 84% and a sensitivity of 73% at specificity of 90% (AUC = 87%). In comparison, the AUC for bone detection is 73% and 50% using the intensity approach and without density correction, respectively. Conclusion: The proposed unifying method provides accurate electron density estimation and bone detection based on multi-parametric MRI of the head with highly heterogeneous anatomy. This could allow for accurate dose calculation and reference image generation for patient setup in MRI-based radiation treatment planning.

  18. SU-G-JeP2-02: A Unifying Multi-Atlas Approach to Electron Density Mapping Using Multi-Parametric MRI for Radiation Treatment Planning

    International Nuclear Information System (INIS)

    Ren, S; Hara, W; Le, Q; Wang, L; Xing, L; Li, R

    2016-01-01

    Purpose: MRI has a number of advantages over CT as a primary modality for radiation treatment planning (RTP). However, one key bottleneck problem still remains, which is the lack of electron density information in MRI. In the work, a reliable method to map electron density is developed by leveraging the differential contrast of multi-parametric MRI. Methods: We propose a probabilistic Bayesian approach for electron density mapping based on T1 and T2-weighted MRI, using multiple patients as atlases. For each voxel, we compute two conditional probabilities: (1) electron density given its image intensity on T1 and T2-weighted MR images, and (2) electron density given its geometric location in a reference anatomy. The two sources of information (image intensity and spatial location) are combined into a unifying posterior probability density function using the Bayesian formalism. The mean value of the posterior probability density function provides the estimated electron density. Results: We evaluated the method on 10 head and neck patients and performed leave-one-out cross validation (9 patients as atlases and remaining 1 as test). The proposed method significantly reduced the errors in electron density estimation, with a mean absolute HU error of 138, compared with 193 for the T1-weighted intensity approach and 261 without density correction. For bone detection (HU>200), the proposed method had an accuracy of 84% and a sensitivity of 73% at specificity of 90% (AUC = 87%). In comparison, the AUC for bone detection is 73% and 50% using the intensity approach and without density correction, respectively. Conclusion: The proposed unifying method provides accurate electron density estimation and bone detection based on multi-parametric MRI of the head with highly heterogeneous anatomy. This could allow for accurate dose calculation and reference image generation for patient setup in MRI-based radiation treatment planning.

  19. Thermal conductivity of partially graphitized biocarbon obtained by carbonization of medium-density fiberboard in the presence of a Ni-based catalyst

    Science.gov (United States)

    Orlova, T. S.; Parfen'eva, L. S.; Smirnov, B. I.; Gutierrez-Pardo, A.; Ramirez-Rico, J.

    2016-01-01

    The thermal conductivity k and resistivity ρ of biocarbon matrices, prepared by carbonizing medium-density fiberboard at T carb = 850 and 1500°C in the presence of a Ni-based catalyst (samples MDF-C( Ni)) and without a catalyst (samples MDF-C), have been measured for the first time in the temperature range of 5-300 K. X-ray diffraction analysis has revealed that the bulk graphite phase arises only at T carb = 1500°C. It has been shown that the temperature dependences of the thermal conductivity of samples MDFC- 850 and MDF-C-850(Ni) in the range of 80-300 K are to each other and follow the law of k( T) ˜ T 1.65, but the use of the Ni-catalyst leads to an increase in the thermal conductivity by a factor of approximately 1.5, due to the formation of a greater fraction of the nanocrystalline phase in the presence of the Ni-catalyst at T carb = 850°C. In biocarbon MDF-C-1500 prepared without a catalyst, the dependence is k( T) ˜ T 1.65, and it is controlled by the nanocrystalline phase. In MDF-C-1500(Ni), the bulk graphite phase formed increases the thermal conductivity by a factor of 1.5-2 compared to the thermal conductivity of MDF-C-1500 in the entire temperature range of 5-300 K; k( T = 300 K) reaches the values of ˜10 W m-1 K-1, characteristic of biocarbon obtained without a catalyst only at high temperatures of T carb = 2400°C. It has been shown that MDF-C-1500(Ni) in the temperature range of 40‒300 K is characterized by the dependence, k( T) ˜ T 1.3, which can be described in terms of the model of partially graphitized biocarbon as a composite of an amorphous matrix with spherical inclusions of the graphite phase.

  20. The development of audiovisual multisensory integration across childhood and early adolescence: a high-density electrical mapping study.

    Science.gov (United States)

    Brandwein, Alice B; Foxe, John J; Russo, Natalie N; Altschuler, Ted S; Gomes, Hilary; Molholm, Sophie

    2011-05-01

    The integration of multisensory information is essential to forming meaningful representations of the environment. Adults benefit from related multisensory stimuli but the extent to which the ability to optimally integrate multisensory inputs for functional purposes is present in children has not been extensively examined. Using a cross-sectional approach, high-density electrical mapping of event-related potentials (ERPs) was combined with behavioral measures to characterize neurodevelopmental changes in basic audiovisual (AV) integration from middle childhood through early adulthood. The data indicated a gradual fine-tuning of multisensory facilitation of performance on an AV simple reaction time task (as indexed by race model violation), which reaches mature levels by about 14 years of age. They also revealed a systematic relationship between age and the brain processes underlying multisensory integration (MSI) in the time frame of the auditory N1 ERP component (∼ 120 ms). A significant positive correlation between behavioral and neurophysiological measures of MSI suggested that the underlying brain processes contributed to the fine-tuning of multisensory facilitation of behavior that was observed over middle childhood. These findings are consistent with protracted plasticity in a dynamic system and provide a starting point from which future studies can begin to examine the developmental course of multisensory processing in clinical populations.

  1. A High-Density Integrated DArTseq SNP-Based Genetic Map of Pisum fulvum and Identification of QTLs Controlling Rust Resistance

    Directory of Open Access Journals (Sweden)

    Eleonora Barilli

    2018-02-01

    Full Text Available Pisum fulvum, a wild relative of pea is an important source of allelic diversity to improve the genetic resistance of cultivated species against fungal diseases of economic importance like the pea rust caused by Uromyces pisi. To unravel the genetic control underlying resistance to this fungal disease, a recombinant inbred line (RIL population was generated from a cross between two P. fulvum accessions, IFPI3260 and IFPI3251, and genotyped using Diversity Arrays Technology. A total of 9,569 high-quality DArT-Seq and 8,514 SNPs markers were generated. Finally, a total of 12,058 markers were assembled into seven linkage groups, equivalent to the number of haploid chromosomes of P. fulvum and P. sativum. The newly constructed integrated genetic linkage map of P. fulvum covered an accumulated distance of 1,877.45 cM, an average density of 1.19 markers cM−1 and an average distance between adjacent markers of 1.85 cM. The composite interval mapping revealed three QTLs distributed over two linkage groups that were associated with the percentage of rust disease severity (DS%. QTLs UpDSII and UpDSIV were located in the LGs II and IV respectively and were consistently identified both in adult plants over 3 years at the field (Córdoba, Spain and in seedling plants under controlled conditions. Whenever they were detected, their contribution to the total phenotypic variance varied between 19.8 and 29.2. A third QTL (UpDSIV.2 was also located in the LGIVand was environmentally specific as was only detected for DS % in seedlings under controlled conditions. It accounted more than 14% of the phenotypic variation studied. Taking together the data obtained in the study, it could be concluded that the expression of resistance to fungal diseases in P. fulvum originates from the resistant parent IFPI3260.

  2. Entrainment and high-density three-dimensional mapping in right atrial macroreentry provide critical complementary information: Entrainment may unmask "visual reentry" as passive.

    Science.gov (United States)

    Pathik, Bhupesh; Lee, Geoffrey; Nalliah, Chrishan; Joseph, Stephen; Morton, Joseph B; Sparks, Paul B; Sanders, Prashanthan; Kistler, Peter M; Kalman, Jonathan M

    2017-10-01

    With the recent advent of high-density (HD) 3-dimensional (3D) mapping, the utility of entrainment is uncertain. However, the limitations of visual representation and interpretation of these high-resolution 3D maps are unclear. The purpose of this study was to determine the strengths and limitations of both HD 3D mapping and entrainment mapping during mapping of right atrial macroreentry. Fifteen patients were studied. The number and type of circuits accounting for ≥90% of the tachycardia cycle length using HD 3D mapping were verified using systematic entrainment mapping. Entrainment sites with an unexpectedly long postpacing interval despite proximity to the active circuit were evaluated. Based on HD 3D mapping, 27 circuits were observed: 12 peritricuspid, 2 upper loop reentry, 10 lower loop reentry, and 3 lateral wall circuits. With entrainment, 17 of the 27 circuits were active: all 12 peritricuspid and 2 upper loop reentry. However, lower loop reentry was confirmed in only 3 of 10, and none of the 3 lateral wall circuits were present. Mean percentage of tachycardia cycle length covered by active circuits was 98% ± 1% vs 97% ± 2% for passive circuits (P = .09). None of the 345 entrainment runs terminated tachycardia or changed tachycardia mechanism. In 8 of 15 patients, 13 examples of unexpectedly long postpacing interval were observed at entrainment sites located distal to localized zones of slow conduction seen on HD 3D mapping. Using HD 3D mapping, "visual reentry" may be due to passive circuitous propagation rather than a critical reentrant circuit. HD 3D mapping provides new insights into regional conduction and helps explain unusual entrainment phenomena. Copyright © 2017 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

  3. Characterization of methane-hydrate formation inferred from insitu Vp-density relationship for hydrate-bearing sediment cores obtained off the eastern coast of India

    Science.gov (United States)

    Kinoshita, M.; Hamada, Y.; Hirose, T.; Yamada, Y.

    2017-12-01

    In 2015, the Indian National Gas Hydrate Program (NGHP) Drilling Expedition 02 was carried out off the eastern margin of the Indian Peninsula in order to investigate distribution and occurrence of gas hydrates. From 25 drill sites, downhole logging data, cored samples, and drilling performance data were collected. One of the target areas (area B) is located on the axial and flank of an anticline, where the BSR is identified 100 m beneath the summit of anticline. 3 sites were drilled in the crest. The lower potential hydrate zone II was suggested by downhole logging (LWD) at 270-290 m below seafloor across the top of anticline. Core samples from this interval is characterized by a higher natural gamma radiation, gamma-ray-based higher bulk density and lower porosity, and higher electrical resistivity. All these features are in good agreement with LWD results. During this expedition, numerous special core sampling operations (PCAT) were carried out, keeping its insitu pressure in a pressure-tight vessel. They enabled acquiring insitu P-wave velocity and gamma-ray attenuation density measurements. In-situ X-CT images exhibit very clear hydrate distribution as lower density patches. Hydrate-bearing sediments exhibit a Vp-density trend that is clearly different from the ordinary formation. Vp values are significantly higher than 2 km/s whereas the density remains constant at 2-2.2 g/cm3 in hydrate zones. At some hydrate-bearing sediments, we noticed that Vp is negatively correlated to the density in the deeper portion (235-285 mbsf). On the other hand, in the shallower portion they are positively correlated. From lithostratigraphy the shallower portion consists of sand, whereas deeper portion are silty-clay dominant. We infer that the sand-dominant, shallower hydrate is a pore-filling type, and Vp is correlated positively to density. On the other hand, the clay-dominant, deeper hydrate is filled in vertical veins, and Vp is negatively correlated to density. Negative

  4. A high-density genetic map for anchoring genome sequences and identifying QTLs associated with dwarf vine in pumpkin (Cucurbita maxima Duch.).

    Science.gov (United States)

    Zhang, Guoyu; Ren, Yi; Sun, Honghe; Guo, Shaogui; Zhang, Fan; Zhang, Jie; Zhang, Haiying; Jia, Zhangcai; Fei, Zhangjun; Xu, Yong; Li, Haizhen

    2015-12-24

    Pumpkin (Cucurbita maxima Duch.) is an economically important crop belonging to the Cucurbitaceae family. However, very few genomic and genetic resources are available for this species. As part of our ongoing efforts to sequence the pumpkin genome, high-density genetic map is essential for anchoring and orienting the assembled scaffolds. In addition, a saturated genetic map can facilitate quantitative trait locus (QTL) mapping. A set of 186 F2 plants derived from the cross of pumpkin inbred lines Rimu and SQ026 were genotyped using the genotyping-by-sequencing approach. Using the SNPs we identified, a high-density genetic map containing 458 bin-markers was constructed, spanning a total genetic distance of 2,566.8 cM across the 20 linkage groups of C. maxima with a mean marker density of 5.60 cM. Using this map we were able to anchor 58 assembled scaffolds that covered about 194.5 Mb (71.7%) of the 271.4 Mb assembled pumpkin genome, of which 44 (183.0 Mb; 67.4%) were oriented. Furthermore, the high-density genetic map was used to identify genomic regions highly associated with an important agronomic trait, dwarf vine. Three QTLs on linkage groups (LGs) 1, 3 and 4, respectively, were recovered. One QTL, qCmB2, which was located in an interval of 0.42 Mb on LG 3, explained 21.4% phenotypic variations. Within qCmB2, one gene, Cma_004516, encoding the gibberellin (GA) 20-oxidase in the GA biosynthesis pathway, had a 1249-bp deletion in its promoter in bush type lines, and its expression level was significantly increased during the vine growth and higher in vine type lines than bush type lines, supporting Cma_004516 as a possible candidate gene controlling vine growth in pumpkin. A high-density pumpkin genetic map was constructed, which was used to successfully anchor and orient the assembled genome scaffolds, and to identify QTLs highly associated with pumpkin vine length. The map provided a valuable resource for gene cloning and marker assisted breeding in pumpkin and

  5. An Evaluation of Population Density Mapping and Built up Area Estimates in Sri Lanka Using Multiple Methodologies

    Science.gov (United States)

    Engstrom, R.; Soundararajan, V.; Newhouse, D.

    2017-12-01

    In this study we examine how well multiple population density and built up estimates that utilize satellite data compare in Sri Lanka. The population relationship is examined at the Gram Niladhari (GN) level, the lowest administrative unit in Sri Lanka from the 2011 census. For this study we have two spatial domains, the whole country and a 3,500km2 sub-sample, for which we have complete high spatial resolution imagery coverage. For both the entire country and the sub-sample we examine how consistent are the existing publicly available measures of population constructed from satellite imagery at predicting population density? For just the sub-sample we examine how well do a suite of values derived from high spatial resolution satellite imagery predict population density and how does our built up area estimate compare to other publicly available estimates. Population measures were obtained from the Sri Lankan census, and were downloaded from Facebook, WorldPoP, GPW, and Landscan. Percentage built-up area at the GN level was calculated from three sources: Facebook, Global Urban Footprint (GUF), and the Global Human Settlement Layer (GHSL). For the sub-sample we have derived a variety of indicators from the high spatial resolution imagery. Using deep learning convolutional neural networks, an object oriented, and a non-overlapping block, spatial feature approach. Variables calculated include: cars, shadows (a proxy for building height), built up area, and buildings, roof types, roads, type of agriculture, NDVI, Pantex, and Histogram of Oriented Gradients (HOG) and others. Results indicate that population estimates are accurate at the higher, DS Division level but not necessarily at the GN level. Estimates from Facebook correlated well with census population (GN correlation of 0.91) but measures from GPW and WorldPop are more weakly correlated (0.64 and 0.34). Estimates of built-up area appear to be reliable. In the 32 DSD-subsample, Facebook's built- up area measure

  6. Dynamical Mapping of Anopheles darlingi Densities in a Residual Malaria Transmission Area of French Guiana by Using Remote Sensing and Meteorological Data.

    Directory of Open Access Journals (Sweden)

    Antoine Adde

    Full Text Available Local variation in the density of Anopheles mosquitoes and the risk of exposure to bites are essential to explain the spatial and temporal heterogeneities in the transmission of malaria. Vector distribution is driven by environmental factors. Based on variables derived from satellite imagery and meteorological observations, this study aimed to dynamically model and map the densities of Anopheles darlingi in the municipality of Saint-Georges de l'Oyapock (French Guiana. Longitudinal sampling sessions of An. darlingi densities were conducted between September 2012 and October 2014. Landscape and meteorological data were collected and processed to extract a panel of variables that were potentially related to An. darlingi ecology. Based on these data, a robust methodology was formed to estimate a statistical predictive model of the spatial-temporal variations in the densities of An. darlingi in Saint-Georges de l'Oyapock. The final cross-validated model integrated two landscape variables-dense forest surface and built surface-together with four meteorological variables related to rainfall, evapotranspiration, and the minimal and maximal temperatures. Extrapolation of the model allowed the generation of predictive weekly maps of An. darlingi densities at a resolution of 10-m. Our results supported the use of satellite imagery and meteorological data to predict malaria vector densities. Such fine-scale modeling approach might be a useful tool for health authorities to plan control strategies and social communication in a cost-effective, targeted, and timely manner.

  7. Dynamical Mapping of Anopheles darlingi Densities in a Residual Malaria Transmission Area of French Guiana by Using Remote Sensing and Meteorological Data.

    Science.gov (United States)

    Adde, Antoine; Roux, Emmanuel; Mangeas, Morgan; Dessay, Nadine; Nacher, Mathieu; Dusfour, Isabelle; Girod, Romain; Briolant, Sébastien

    2016-01-01

    Local variation in the density of Anopheles mosquitoes and the risk of exposure to bites are essential to explain the spatial and temporal heterogeneities in the transmission of malaria. Vector distribution is driven by environmental factors. Based on variables derived from satellite imagery and meteorological observations, this study aimed to dynamically model and map the densities of Anopheles darlingi in the municipality of Saint-Georges de l'Oyapock (French Guiana). Longitudinal sampling sessions of An. darlingi densities were conducted between September 2012 and October 2014. Landscape and meteorological data were collected and processed to extract a panel of variables that were potentially related to An. darlingi ecology. Based on these data, a robust methodology was formed to estimate a statistical predictive model of the spatial-temporal variations in the densities of An. darlingi in Saint-Georges de l'Oyapock. The final cross-validated model integrated two landscape variables-dense forest surface and built surface-together with four meteorological variables related to rainfall, evapotranspiration, and the minimal and maximal temperatures. Extrapolation of the model allowed the generation of predictive weekly maps of An. darlingi densities at a resolution of 10-m. Our results supported the use of satellite imagery and meteorological data to predict malaria vector densities. Such fine-scale modeling approach might be a useful tool for health authorities to plan control strategies and social communication in a cost-effective, targeted, and timely manner.

  8. Insights Into Upland Cotton (Gossypium hirsutum L.) Genetic Recombination Based on 3 High-Density Single-Nucleotide Polymorphism and a Consensus Map Developed Independently With Common Parents. Genomics Insights

    Science.gov (United States)

    High-density linkage maps are vital to supporting the correct placement of scaffolds and gene sequences on chromosomes and fundamental to contemporary organismal research and scientific approaches to genetic improvement; high-density linkage maps are especially important in paleopolyploids with exce...

  9. Scanning micro-Hall probe mapping of magnetic flux distributions and current densities in YBa{sub 2}Cu{sub 3}O{sub 7}

    Energy Technology Data Exchange (ETDEWEB)

    Xing, W.; Heinrich, B. [Simon Fraser Univ., British Columbia (Canada); Zhou, H. [CTF Systems, Inc., British Columbia (Canada)] [and others

    1994-12-31

    Mapping of the magnetic flux density B{sub z} (perpendicular to the film plane) for a YBa{sub 2}Cu{sub 3}O{sub 7} thin-film sample was carried out using a scanning micro-Hall probe. The sheet magnetization and sheet current densities were calculated from the B{sub z} distributions. From the known sheet magnetization, the tangential (B{sub x,y}) and normal components of the flux density B were calculated in the vicinity of the film. It was found that the sheet current density was mostly determined by 2B{sub x,y}/d, where d is the film thickness. The evolution of flux penetration as a function of applied field will be shown.

  10. Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high-density linkage mapping.

    Science.gov (United States)

    Patil, Gunvant; Vuong, Tri D; Kale, Sandip; Valliyodan, Babu; Deshmukh, Rupesh; Zhu, Chengsong; Wu, Xiaolei; Bai, Yonghe; Yungbluth, Dennis; Lu, Fang; Kumpatla, Siva; Grover Shannon, J; Varshney, Rajeev K; Nguyen, Henry T

    2018-04-04

    The cultivated [Glycine max (L) Merr.] and wild [Glycine soja Siebold & Zucc.] soybean species comprise wide variation in seed composition traits. Compared to wild soybean, cultivated soybean contains low protein, high oil and high sucrose. In this study, an inter-specific population was derived from a cross between G. max (Williams 82) and G. soja (PI 483460B). This recombinant inbred line (RIL) population of 188 lines was sequenced at 0.3x depth. Based on 91,342 single nucleotide polymorphisms (SNPs), recombination events in RILs were defined, and a high-resolution bin map was developed (4,070 bins). In addition to bin mapping, QTL analysis for protein, oil and sucrose was performed using 3,343 polymorphic SNPs (3K-SNP), derived from Illumina Infinium BeadChip sequencing platform. The QTL regions from both platforms were compared and a significant concordance was observed between bin and 3K-SNP markers. Importantly, the bin map derived from next generation sequencing technology enhanced mapping resolution (from 1325 Kb to 50 Kb). A total of 5, 9 and 4 QTLs were identified for protein, oil and sucrose content, respectively and some of the QTLs coincided with soybean domestication related genomic loci. The major QTL for protein and oil was mapped on Chr. 20 (qPro_20) and suggested negative correlation between oil and protein. In terms of sucrose content, a novel and major QTL was identified on Chr. 8 (qSuc_08) and harbors putative genes involved in sugar transport. In addition, genome-wide association (GWAS) using 91,342 SNPs confirmed the genomic loci derived from QTL mapping. A QTL based haplotype using whole genome resequencing of 106 diverse soybean lines identified unique allelic variation in wild soybean that could be utilized to widen the genetic base in cultivated soybean. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  11. Utility of histogram analysis of apparent diffusion coefficient maps obtained using 3.0T MRI for distinguishing uterine carcinosarcoma from endometrial carcinoma.

    Science.gov (United States)

    Takahashi, Masahiro; Kozawa, Eito; Tanisaka, Megumi; Hasegawa, Kousei; Yasuda, Masanori; Sakai, Fumikazu

    2016-06-01

    We explored the role of histogram analysis of apparent diffusion coefficient (ADC) maps for discriminating uterine carcinosarcoma and endometrial carcinoma. We retrospectively evaluated findings in 13 patients with uterine carcinosarcoma and 50 patients with endometrial carcinoma who underwent diffusion-weighted imaging (b = 0, 500, 1000 s/mm(2) ) at 3T with acquisition of corresponding ADC maps. We derived histogram data from regions of interest drawn on all slices of the ADC maps in which tumor was visualized, excluding areas of necrosis and hemorrhage in the tumor. We used the Mann-Whitney test to evaluate the capacity of histogram parameters (mean ADC value, 5th to 95th percentiles, skewness, kurtosis) to discriminate uterine carcinosarcoma and endometrial carcinoma and analyzed the receiver operating characteristic (ROC) curve to determine the optimum threshold value for each parameter and its corresponding sensitivity and specificity. Carcinosarcomas demonstrated significantly higher mean vales of ADC, 95th, 90th, 75th, 50th, 25th percentiles and kurtosis than endometrial carcinomas (P Histogram analysis of ADC maps might be helpful for discriminating uterine carcinosarcomas and endometrial carcinomas. J. Magn. Reson. Imaging 2016;43:1301-1307. © 2015 Wiley Periodicals, Inc.

  12. A high-density SNP genetic linkage map for the silver-lipped pearl oyster, Pinctada maxima: a valuable resource for gene localisation and marker-assisted selection.

    Science.gov (United States)

    Jones, David B; Jerry, Dean R; Khatkar, Mehar S; Raadsma, Herman W; Zenger, Kyall R

    2013-11-20

    The silver-lipped pearl oyster, Pinctada maxima, is an important tropical aquaculture species extensively farmed for the highly sought "South Sea" pearls. Traditional breeding programs have been initiated for this species in order to select for improved pearl quality, but many economic traits under selection are complex, polygenic and confounded with environmental factors, limiting the accuracy of selection. The incorporation of a marker-assisted selection (MAS) breeding approach would greatly benefit pearl breeding programs by allowing the direct selection of genes responsible for pearl quality. However, before MAS can be incorporated, substantial genomic resources such as genetic linkage maps need to be generated. The construction of a high-density genetic linkage map for P. maxima is not only essential for unravelling the genomic architecture of complex pearl quality traits, but also provides indispensable information on the genome structure of pearl oysters. A total of 1,189 informative genome-wide single nucleotide polymorphisms (SNPs) were incorporated into linkage map construction. The final linkage map consisted of 887 SNPs in 14 linkage groups, spans a total genetic distance of 831.7 centimorgans (cM), and covers an estimated 96% of the P. maxima genome. Assessment of sex-specific recombination across all linkage groups revealed limited overall heterochiasmy between the sexes (i.e. 1.15:1 F/M map length ratio). However, there were pronounced localised differences throughout the linkage groups, whereby male recombination was suppressed near the centromeres compared to female recombination, but inflated towards telomeric regions. Mean values of LD for adjacent SNP pairs suggest that a higher density of markers will be required for powerful genome-wide association studies. Finally, numerous nacre biomineralization genes were localised providing novel positional information for these genes. This high-density SNP genetic map is the first comprehensive linkage

  13. A comparison of conventional maximum intensity projection with a new depth-specific topographic mapping technique in the CT analysis of proximal tibial subchondral bone density

    International Nuclear Information System (INIS)

    Johnston, James D.; Kontulainen, Saija A.; Masri, Bassam A.; Wilson, David R.

    2010-01-01

    The objective was to identify subchondral bone density differences between normal and osteoarthritic (OA) proximal tibiae using computed tomography osteoabsorptiometry (CT-OAM) and computed tomography topographic mapping of subchondral density (CT-TOMASD). Sixteen intact cadaver knees from ten donors (8 male:2 female; mean age:77.8, SD:7.4 years) were categorized as normal (n = 10) or OA (n = 6) based upon CT reconstructions. CT-OAM assessed maximum subchondral bone mineral density (BMD). CT-TOMASD assessed average subchondral BMD across three layers (0-2.5, 2.5-5 and 5-10 mm) measured in relation to depth from the subchondral surface. Regional analyses of CT-OAM and CT-TOMASD included: medial BMD, lateral BMD, and average BMD of a 10-mm diameter area that searched each medial and lateral plateau for the highest ''focal'' density present within each knee. Compared with normal knees, both CT-OAM and CT-TOMASD demonstrated an average of 17% greater whole medial compartment density in OA knees (p 0.05). CT-TOMASD focal region analyses revealed an average of 24% greater density in the 0- to 2.5-mm layer (p = 0.003) and 36% greater density in the 2.5- to 5-mm layer (p = 0.034) in OA knees. Both CT-OAM and TOMASD identified higher medial compartment density in OA tibiae compared with normal tibiae. In addition, CT-TOMASD indicated greater focal density differences between normal and OA knees with increased depth from the subchondral surface. Depth-specific density analyses may help identify and quantify small changes in subchondral BMD associated with OA disease onset and progression. (orig.)

  14. High Density Linkage Map Construction and Mapping of Yield Trait QTLs in Maize (Zea mays) Using the Genotyping-by-Sequencing (GBS) Technology

    Science.gov (United States)

    Su, Chengfu; Wang, Wei; Gong, Shunliang; Zuo, Jinghui; Li, Shujiang; Xu, Shizhong

    2017-01-01

    Increasing grain yield is the ultimate goal for maize breeding. High resolution quantitative trait loci (QTL) mapping can help us understand the molecular basis of phenotypic variation of yield and thus facilitate marker assisted breeding. The aim of this study is to use genotyping-by-sequencing (GBS) for large-scale SNP discovery and simultaneous genotyping of all F2 individuals from a cross between two varieties of maize that are in clear contrast in yield and related traits. A set of 199 F2 progeny derived from the cross of varieties SG-5 and SG-7 were generated and genotyped by GBS. A total of 1,046,524,604 reads with an average of 5,258,918 reads per F2 individual were generated. This number of reads represents an approximately 0.36-fold coverage of the maize reference genome Zea_mays.AGPv3.29 for each F2 individual. A total of 68,882 raw SNPs were discovered in the F2 population, which, after stringent filtering, led to a total of 29,927 high quality SNPs. Comparative analysis using these physically mapped marker loci revealed a higher degree of synteny with the reference genome. The SNP genotype data were utilized to construct an intra-specific genetic linkage map of maize consisting of 3,305 bins on 10 linkage groups spanning 2,236.66 cM at an average distance of 0.68 cM between consecutive markers. From this map, we identified 28 QTLs associated with yield traits (100-kernel weight, ear length, ear diameter, cob diameter, kernel row number, corn grains per row, ear weight, and grain weight per plant) using the composite interval mapping (CIM) method and 29 QTLs using the least absolute shrinkage selection operator (LASSO) method. QTLs identified by the CIM method account for 6.4% to 19.7% of the phenotypic variation. Small intervals of three QTLs (qCGR-1, qKW-2, and qGWP-4) contain several genes, including one gene (GRMZM2G139872) encoding the F-box protein, three genes (GRMZM2G180811, GRMZM5G828139, and GRMZM5G873194) encoding the WD40-repeat protein, and

  15. Free-Energy Landscape of Reverse tRNA Translocation through the Ribosome Analyzed by Electron Microscopy Density Maps and Molecular Dynamics Simulations

    Science.gov (United States)

    Ishida, Hisashi; Matsumoto, Atsushi

    2014-01-01

    To understand the mechanism of reverse tRNA translocation in the ribosome, all-atom molecular dynamics simulations of the ribosome-tRNAs-mRNA-EFG complex were performed. The complex at the post-translocational state was directed towards the translocational and pre-translocational states by fitting the complex into cryo-EM density maps. Between a series of the fitting simulations, umbrella sampling simulations were performed to obtain the free-energy landscape. Multistep structural changes, such as a ratchet-like motion and rotation of the head of the small subunit were observed. The free-energy landscape showed that there were two main free-energy barriers: one between the post-translocational and intermediate states, and the other between the pre-translocational and intermediate states. The former corresponded to a clockwise rotation, which was coupled to the movement of P-tRNA over the P/E-gate made of G1338, A1339 and A790 in the small subunit. The latter corresponded to an anticlockwise rotation of the head, which was coupled to the location of the two tRNAs in the hybrid state. This indicates that the coupled motion of the head rotation and tRNA translocation plays an important role in opening and closing of the P/E-gate during the ratchet-like movement in the ribosome. Conformational change of EF-G was interpreted to be the result of the combination of the external motion by L12 around an axis passing near the sarcin-ricin loop, and internal hinge-bending motion. These motions contributed to the movement of domain IV of EF-G to maintain its interaction with A/P-tRNA. PMID:24999999

  16. Free-energy landscape of reverse tRNA translocation through the ribosome analyzed by electron microscopy density maps and molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Hisashi Ishida

    Full Text Available To understand the mechanism of reverse tRNA translocation in the ribosome, all-atom molecular dynamics simulations of the ribosome-tRNAs-mRNA-EFG complex were performed. The complex at the post-translocational state was directed towards the translocational and pre-translocational states by fitting the complex into cryo-EM density maps. Between a series of the fitting simulations, umbrella sampling simulations were performed to obtain the free-energy landscape. Multistep structural changes, such as a ratchet-like motion and rotation of the head of the small subunit were observed. The free-energy landscape showed that there were two main free-energy barriers: one between the post-translocational and intermediate states, and the other between the pre-translocational and intermediate states. The former corresponded to a clockwise rotation, which was coupled to the movement of P-tRNA over the P/E-gate made of G1338, A1339 and A790 in the small subunit. The latter corresponded to an anticlockwise rotation of the head, which was coupled to the location of the two tRNAs in the hybrid state. This indicates that the coupled motion of the head rotation and tRNA translocation plays an important role in opening and closing of the P/E-gate during the ratchet-like movement in the ribosome. Conformational change of EF-G was interpreted to be the result of the combination of the external motion by L12 around an axis passing near the sarcin-ricin loop, and internal hinge-bending motion. These motions contributed to the movement of domain IV of EF-G to maintain its interaction with A/P-tRNA.

  17. First High-Density Linkage Map and Single Nucleotide Polymorphisms Significantly Associated With Traits of Economic Importance in Yellowtail Kingfish Seriola lalandi

    Directory of Open Access Journals (Sweden)

    Nguyen H. Nguyen

    2018-04-01

    Full Text Available The genetic resources available for the commercially important fish species Yellowtail kingfish (YTK (Seriola lalandi are relative sparse. To overcome this, we aimed (1 to develop a linkage map for this species, and (2 to identify markers/variants associated with economically important traits in kingfish (with an emphasis on body weight. Genetic and genomic analyses were conducted using 13,898 single nucleotide polymorphisms (SNPs generated from a new high-throughput genotyping by sequencing platform, Diversity Arrays Technology (DArTseqTM in a pedigreed population comprising 752 animals. The linkage analysis enabled to map about 4,000 markers to 24 linkage groups (LGs, with an average density of 3.4 SNPs per cM. The linkage map was integrated into a genome-wide association study (GWAS and identified six variants/SNPs associated with body weight (P < 5e-8 when a multi-locus mixed model was used. Two out of the six significant markers were mapped to LGs 17 and 23, and collectively they explained 5.8% of the total genetic variance. It is concluded that the newly developed linkage map and the significantly associated markers with body weight provide fundamental information to characterize genetic architecture of growth-related traits in this population of YTK S. lalandi.

  18. First High-Density Linkage Map and Single Nucleotide Polymorphisms Significantly Associated With Traits of Economic Importance in Yellowtail Kingfish Seriola lalandi.

    Science.gov (United States)

    Nguyen, Nguyen H; Rastas, Pasi M A; Premachandra, H K A; Knibb, Wayne

    2018-01-01

    The genetic resources available for the commercially important fish species Yellowtail kingfish (YTK) ( Seriola lalandi) are relative sparse. To overcome this, we aimed (1) to develop a linkage map for this species, and (2) to identify markers/variants associated with economically important traits in kingfish (with an emphasis on body weight). Genetic and genomic analyses were conducted using 13,898 single nucleotide polymorphisms (SNPs) generated from a new high-throughput genotyping by sequencing platform, Diversity Arrays Technology (DArTseq TM ) in a pedigreed population comprising 752 animals. The linkage analysis enabled to map about 4,000 markers to 24 linkage groups (LGs), with an average density of 3.4 SNPs per cM. The linkage map was integrated into a genome-wide association study (GWAS) and identified six variants/SNPs associated with body weight ( P 5e -8 ) when a multi-locus mixed model was used. Two out of the six significant markers were mapped to LGs 17 and 23, and collectively they explained 5.8% of the total genetic variance. It is concluded that the newly developed linkage map and the significantly associated markers with body weight provide fundamental information to characterize genetic architecture of growth-related traits in this population of YTK S. lalandi .

  19. Performance potential of low-defect density silicon thin-film solar cells obtained by electron beam evaporation and laser crystallisation

    Directory of Open Access Journals (Sweden)

    Kim K. H.

    2013-01-01

    Full Text Available A few microns thick silicon films on glass coated with a dielectric intermediate layer can be crystallised by a single pass of a line-focused diode laser beam. Under favorable process conditions relatively large linear grains with low defect density are formed. Most grain boundaries are defect-free low-energy twin-boundaries. Boron-doped laser crystallised films are processed into solar cells by diffusing an emitter from a phosphorous spin-on-dopant source, measuring up to 539 mV open-circuit voltage prior to metallisation. After applying a point-contact metallisation the best cell achieves 7.8% energy conversion efficiency, open-circuit voltage of 526 mV and short-circuit current of 26 mA/cm2. The efficiency is significantly limited by a low fill-factor of 56% due to the simplified metallisation approach. The internal quantum efficiency of laser crystallised cells is consistent with low front surface recombination. By improving cell metallisation and enhancing light-trapping the efficiencies of above 13% can be achieved.

  20. CLUMPING AND THE INTERPRETATION OF kpc-SCALE MAPS OF THE INTERSTELLAR MEDIUM: SMOOTH H I AND CLUMPY, VARIABLE H{sub 2} SURFACE DENSITY

    Energy Technology Data Exchange (ETDEWEB)

    Leroy, Adam K. [National Radio Astronomy Observtory, 520 Edgemont Road, Charlottesville, VA 22903 (United States); Lee, Cheoljong [Department of Astronomy, University of Virginia, 530 McCormick Road, Charlottesville, VA 22904 (United States); Schruba, Andreas [California Institute for Technology, 1200 E California Blvd, Pasadena, CA 91125 (United States); Bolatto, Alberto [Department of Astronomy, University of Maryland, College Park, MD 20742 (United States); Hughes, Annie; Sandstrom, Karin; Schinnerer, Eva; Walter, Fabian [Max Planck Institute fuer Astronomie, Koenigstuhl 17, D-69117 Heidelberg (Germany); Pety, Jerome [Institut de Radioastronomie Millimetrique, 300 Rue de la Piscine, F-38406 Saint Martin d' Heres (France)

    2013-05-20

    Many recent models consider the structure of individual interstellar medium (ISM) clouds as a way to explain observations of large parts of galaxies. To compare such models to observations, one must understand how to translate between surface densities observed averaging over large ({approx}kpc) scales and surface densities on the scale of individual clouds ({approx}pc scale), which are treated by models. We define a ''clumping factor'' that captures this translation as the ratio of the mass-weighted surface density, which is often the quantity of physical interest, to the area-weighted surface density, which is observed. We use high spatial resolution (sub-kpc) maps of CO and H I emission from nearby galaxies to measure the clumping factor of both atomic and molecular gas. The molecular and atomic ISM exhibit dramatically different degrees of clumping. As a result, the ratio H{sub 2}/H I measured at {approx}kpc resolution cannot be trivially interpreted as a cloud-scale ratio of surface densities. H I emission appears very smooth, with a clumping factor of only {approx}1.3. Based on the scarce and heterogeneous high-resolution data available, CO emission is far more clumped with a widely variable clumping factor, median {approx}7 for our heterogeneous data. Our measurements do not provide evidence for a universal mass-weighted surface density of molecular gas, but also cannot conclusively rule out such a scenario. We suggest that a more sophisticated treatment of molecular ISM structure, one informed by high spatial resolution CO maps, is needed to link cloud-scale models to kpc-scale observations of galaxies.

  1. Superior critical current density obtained in MgB_2 bulks via employing carbon-coated boron and minor Cu addition

    International Nuclear Information System (INIS)

    Peng, Junming; Liu, Yongchang; Ma, Zongqing; Shahriar Al Hossain, M.; Xin, Ying; Jin, Jianxun

    2016-01-01

    Highlights: • Usage of carbon-coated boron leads to high level of homogeneous carbon doping. • Cu addition improves MgB_2 grain connectivity, leading to higher J_c at low fields. • Cu addition reduces MgO impurity, also contributing to the improvement of J_c. - Abstract: High performance Cu doped MgB_2 bulks were prepared by an in-situ method with carbon-coated amorphous boron as precursor. It was found that the usage of carbon-coated boron in present work leads to the formation of uniformly refined MgB_2 grains, as well as a high level of homogeneous carbon doping in the MgB_2 samples, which significantly enhance the J_c in both Cu doped and undoped bulks compared to MgB_2 bulks with normal amorphous boron precursor. Moreover, minor Cu can service as activator, and thus facilitates the growth of MgB_2 grains and improves crystallinity and grain connectivity, which can bring about the excellent critical current density (J_c) at self fields and low fields (the best values are 7 × 10"5 A/cm"2 at self fields, and 1 × 10"5 A/cm"2 at 2 T, 20 K, respectively). Simultaneously, minor Cu addition can reduce the amount of MgO impurity significantly, also contributing to the improvement of J_c at low fields. Our work suggests that Cu-activated sintering combined with employment of carbon-coated amorphous boron as precursor could be a promising technique to produce practical MgB_2 bulks or wires with excellent J_c on an industrial scale.

  2. Superior critical current density obtained in MgB{sub 2} bulks via employing carbon-coated boron and minor Cu addition

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Junming; Liu, Yongchang [State Key Laboratory of Hydraulic Engineering Simulation and Safety, School of Materials Science & Engineering, Tianjin University, Tianjin 300072 (China); Ma, Zongqing, E-mail: mzq0320@163.com [State Key Laboratory of Hydraulic Engineering Simulation and Safety, School of Materials Science & Engineering, Tianjin University, Tianjin 300072 (China); Institute for Superconducting and Electronic Materials, AIIM, University of Wollongong, Squires Way, North Wollongong, NSW 2500 (Australia); Shahriar Al Hossain, M. [Institute for Superconducting and Electronic Materials, AIIM, University of Wollongong, Squires Way, North Wollongong, NSW 2500 (Australia); Xin, Ying; Jin, Jianxun [Tianjin University – Futong Group Research Center of Applied Superconductivity, Tianjin University, Tianjin 300072 (China)

    2016-09-15

    Highlights: • Usage of carbon-coated boron leads to high level of homogeneous carbon doping. • Cu addition improves MgB{sub 2} grain connectivity, leading to higher J{sub c} at low fields. • Cu addition reduces MgO impurity, also contributing to the improvement of J{sub c}. - Abstract: High performance Cu doped MgB{sub 2} bulks were prepared by an in-situ method with carbon-coated amorphous boron as precursor. It was found that the usage of carbon-coated boron in present work leads to the formation of uniformly refined MgB{sub 2} grains, as well as a high level of homogeneous carbon doping in the MgB{sub 2} samples, which significantly enhance the J{sub c} in both Cu doped and undoped bulks compared to MgB{sub 2} bulks with normal amorphous boron precursor. Moreover, minor Cu can service as activator, and thus facilitates the growth of MgB{sub 2} grains and improves crystallinity and grain connectivity, which can bring about the excellent critical current density (J{sub c}) at self fields and low fields (the best values are 7 × 10{sup 5} A/cm{sup 2} at self fields, and 1 × 10{sup 5} A/cm{sup 2} at 2 T, 20 K, respectively). Simultaneously, minor Cu addition can reduce the amount of MgO impurity significantly, also contributing to the improvement of J{sub c} at low fields. Our work suggests that Cu-activated sintering combined with employment of carbon-coated amorphous boron as precursor could be a promising technique to produce practical MgB{sub 2} bulks or wires with excellent J{sub c} on an industrial scale.

  3. A high-density genetic map and QTL analysis of agronomic traits in foxtail millet [Setaria italica (L.) P. Beauv.] using RAD-seq.

    Science.gov (United States)

    Wang, Jun; Wang, Zhilan; Du, Xiaofen; Yang, Huiqing; Han, Fang; Han, Yuanhuai; Yuan, Feng; Zhang, Linyi; Peng, Shuzhong; Guo, Erhu

    2017-01-01

    Foxtail millet (Setaria italica), a very important grain crop in China, has become a new model plant for cereal crops and biofuel grasses. Although its reference genome sequence was released recently, quantitative trait loci (QTLs) controlling complex agronomic traits remains limited. The development of massively parallel genotyping methods and next-generation sequencing technologies provides an excellent opportunity for developing single-nucleotide polymorphisms (SNPs) for linkage map construction and QTL analysis of complex quantitative traits. In this study, a high-throughput and cost-effective RAD-seq approach was employed to generate a high-density genetic map for foxtail millet. A total of 2,668,587 SNP loci were detected according to the reference genome sequence; meanwhile, 9,968 SNP markers were used to genotype 124 F2 progenies derived from the cross between Hongmiaozhangu and Changnong35; a high-density genetic map spanning 1648.8 cM, with an average distance of 0.17 cM between adjacent markers was constructed; 11 major QTLs for eight agronomic traits were identified; five co-dominant DNA markers were developed. These findings will be of value for the identification of candidate genes and marker-assisted selection in foxtail millet.

  4. A High Density Genetic Map Derived from RAD Sequencing and Its Application in QTL Analysis of Yield-Related Traits in Vigna unguiculata

    Directory of Open Access Journals (Sweden)

    Lei Pan

    2017-09-01

    Full Text Available Cowpea [Vigna unguiculata (L. Walp.] is an annual legume of economic importance and widely grown in the semi-arid tropics. However, high-density genetic maps of cowpea are still lacking. Here, we identified 34,868 SNPs (single nucleotide polymorphisms that were distributed in the cowpea genome based on the RAD sequencing (restriction-site associated DNA sequencing technique using a population of 170 individuals (two cowpea parents and 168 F2:3 progenies. Of these, 17,996 reliable SNPs were allotted to 11 consensus linkage groups (LGs. The length of the genetic map was 1,194.25 cM in total with a mean distance of 0.066 cM/SNP marker locus. Using this map and the F2:3 population, combined with the CIM (composite interval mapping method, eleven quantitative trait loci (QTL of yield-related trait were detected on seven LGs (LG4, 5, 6, 7, 9, 10, and 11 in cowpea. These QTL explained 0.05–17.32% of the total phenotypic variation. Among these, four QTL were for pod length, four QTL for thousand-grain weight (TGW, two QTL for grain number per pod, and one QTL for carpopodium length. Our results will provide a foundation for understanding genes related to grain yield in the cowpea and genus Vigna.

  5. The development of a high density linkage map for black tiger shrimp (Penaeus monodon based on cSNPs.

    Directory of Open Access Journals (Sweden)

    Matthew Baranski

    Full Text Available Transcriptome sequencing using Illumina RNA-seq was performed on populations of black tiger shrimp from India. Samples were collected from (i four landing centres around the east coastline (EC of India, (ii survivors of a severe WSSV infection during pond culture (SUR and (iii the Andaman Islands (AI in the Bay of Bengal. Equal quantities of purified total RNA from homogenates of hepatopancreas, muscle, nervous tissue, intestinal tract, heart, gonad, gills, pleopod and lymphoid organs were combined to create AI, EC and SUR pools for RNA sequencing. De novo transcriptome assembly resulted in 136,223 contigs (minimum size 100 base pairs, bp with a total length 61 Mb, an average length of 446 bp and an average coverage of 163× across all pools. Approximately 16% of contigs were annotated with BLAST hit information and gene ontology annotations. A total of 473,620 putative SNPs/indels were identified. An Illumina iSelect genotyping array containing 6,000 SNPs was developed and used to genotype 1024 offspring belonging to seven full-sibling families. A total of 3959 SNPs were mapped to 44 linkage groups. The linkage groups consisted of between 16-129 and 13-130 markers, of length between 139-10.8 and 109.1-10.5 cM and with intervals averaging between 1.2 and 0.9 cM for the female and male maps respectively. The female map was 28% longer than the male map (4060 and 2917 cM respectively with a 1.6 higher recombination rate observed for female compared to male meioses. This approach has substantially increased expressed sequence and DNA marker resources for tiger shrimp and is a useful resource for QTL mapping and association studies for evolutionarily and commercially important traits.

  6. A generalized operational formula based on total electronic densities to obtain 3D pictures of the dual descriptor to reveal nucleophilic and electrophilic sites accurately on closed-shell molecules.

    Science.gov (United States)

    Martínez-Araya, Jorge I

    2016-09-30

    By means of the conceptual density functional theory, the so-called dual descriptor (DD) has been adapted to be used in any closed-shell molecule that presents degeneracy in its frontier molecular orbitals. The latter is of paramount importance because a correct description of local reactivity will allow to predict the most favorable sites on a molecule to undergo nucleophilic or electrophilic attacks; on the contrary, an incomplete description of local reactivity might have serio us consequences, particularly for those experimental chemists that have the need of getting an insight about reactivity of chemical reagents before using them in synthesis to obtain a new compound. In the present work, the old approach based only on electronic densities of frontier molecular orbitals is replaced by the most accurate procedure that implies the use of total electronic densities thus keeping consistency with the essential principle of the DFT in which the electronic density is the fundamental variable and not the molecular orbitals. As a result of the present work, the DD will be able to properly describe local reactivities only in terms of total electronic densities. To test the proposed operational formula, 12 very common molecules were selected as the original definition of the DD was not able to describe their local reactivities properly. The ethylene molecule was additionally used to test the capability of the proposed operational formula to reveal a correct local reactivity even in absence of degeneracy in frontier molecular orbitals. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  7. High-density genetic mapping of a major QTL for resistance to multiple races of loose smut in a tetraploid wheat cross

    Science.gov (United States)

    Kumar, Sachin; Knox, Ron E.; Singh, Asheesh K.; DePauw, Ron M.; Campbell, Heather L.; Isidro-Sanchez, Julio; Clarke, Fran R.; Pozniak, Curtis J.; N’Daye, Amidou; Meyer, Brad; Sharpe, Andrew; Ruan, Yuefeng; Cuthbert, Richard D.; Somers, Daryl; Fedak, George

    2018-01-01

    Loose smut, caused by Ustilago tritici (Pers.) Rostr., is a systemic disease of tetraploid durum wheat (Triticum turgidum L.). Loose smut can be economically controlled by growing resistant varieties, making it important to find and deploy new sources of resistance. Blackbird, a variety of T. turgidum L. subsp. carthlicum (Nevski) A. Love & D. Love, carries a high level of resistance to loose smut. Blackbird was crossed with the loose smut susceptible durum cultivar Strongfield to produce a doubled haploid (DH) mapping population. The parents and progenies were inoculated with U. tritici races T26, T32 and T33 individually and as a mixture at Swift Current, Canada in 2011 and 2012 and loose smut incidence (LSI) was assessed. Genotyping of the DH population and parents using an Infinium iSelect 90K single nucleotide polymorphism (SNP) array identified 12,952 polymorphic SNPs. The SNPs and 426 SSRs (previously genotyped in the same population) were mapped to 16 linkage groups spanning 3008.4 cM at an average inter-marker space of 0.2 cM in a high-density genetic map. Composite interval mapping analysis revealed three significant quantitative trait loci (QTL) for loose smut resistance on chromosomes 3A, 6B and 7A. The loose smut resistance QTL on 6B (QUt.spa-6B.2) and 7A (QUt.spa-7A.2) were derived from Blackbird. Strongfield contributed the minor QTL on 3A (QUt.spa-3A.2). The resistance on 6B was a stable major QTL effective against all individual races and the mixture of the three races; it explained up to 74% of the phenotypic variation. This study is the first attempt in durum wheat to identify and map loose smut resistance QTL using a high-density genetic map. The QTL QUt.spa-6B.2 would be an effective source for breeding resistance to multiple races of the loose smut pathogen because it provides near-complete broad resistance to the predominant virulence on the Canadian prairies. PMID:29485999

  8. High-density genetic mapping of a major QTL for resistance to multiple races of loose smut in a tetraploid wheat cross.

    Directory of Open Access Journals (Sweden)

    Sachin Kumar

    Full Text Available Loose smut, caused by Ustilago tritici (Pers. Rostr., is a systemic disease of tetraploid durum wheat (Triticum turgidum L.. Loose smut can be economically controlled by growing resistant varieties, making it important to find and deploy new sources of resistance. Blackbird, a variety of T. turgidum L. subsp. carthlicum (Nevski A. Love & D. Love, carries a high level of resistance to loose smut. Blackbird was crossed with the loose smut susceptible durum cultivar Strongfield to produce a doubled haploid (DH mapping population. The parents and progenies were inoculated with U. tritici races T26, T32 and T33 individually and as a mixture at Swift Current, Canada in 2011 and 2012 and loose smut incidence (LSI was assessed. Genotyping of the DH population and parents using an Infinium iSelect 90K single nucleotide polymorphism (SNP array identified 12,952 polymorphic SNPs. The SNPs and 426 SSRs (previously genotyped in the same population were mapped to 16 linkage groups spanning 3008.4 cM at an average inter-marker space of 0.2 cM in a high-density genetic map. Composite interval mapping analysis revealed three significant quantitative trait loci (QTL for loose smut resistance on chromosomes 3A, 6B and 7A. The loose smut resistance QTL on 6B (QUt.spa-6B.2 and 7A (QUt.spa-7A.2 were derived from Blackbird. Strongfield contributed the minor QTL on 3A (QUt.spa-3A.2. The resistance on 6B was a stable major QTL effective against all individual races and the mixture of the three races; it explained up to 74% of the phenotypic variation. This study is the first attempt in durum wheat to identify and map loose smut resistance QTL using a high-density genetic map. The QTL QUt.spa-6B.2 would be an effective source for breeding resistance to multiple races of the loose smut pathogen because it provides near-complete broad resistance to the predominant virulence on the Canadian prairies.

  9. Discovery and Fine-Mapping of Glycaemic and Obesity-Related Trait Loci Using High-Density Imputation.

    Directory of Open Access Journals (Sweden)

    Momoko Horikoshi

    2015-07-01

    Full Text Available Reference panels from the 1000 Genomes (1000G Project Consortium provide near complete coverage of common and low-frequency genetic variation with minor allele frequency ≥0.5% across European ancestry populations. Within the European Network for Genetic and Genomic Epidemiology (ENGAGE Consortium, we have undertaken the first large-scale meta-analysis of genome-wide association studies (GWAS, supplemented by 1000G imputation, for four quantitative glycaemic and obesity-related traits, in up to 87,048 individuals of European ancestry. We identified two loci for body mass index (BMI at genome-wide significance, and two for fasting glucose (FG, none of which has been previously reported in larger meta-analysis efforts to combine GWAS of European ancestry. Through conditional analysis, we also detected multiple distinct signals of association mapping to established loci for waist-hip ratio adjusted for BMI (RSPO3 and FG (GCK and G6PC2. The index variant for one association signal at the G6PC2 locus is a low-frequency coding allele, H177Y, which has recently been demonstrated to have a functional role in glucose regulation. Fine-mapping analyses revealed that the non-coding variants most likely to drive association signals at established and novel loci were enriched for overlap with enhancer elements, which for FG mapped to promoter and transcription factor binding sites in pancreatic islets, in particular. Our study demonstrates that 1000G imputation and genetic fine-mapping of common and low-frequency variant association signals at GWAS loci, integrated with genomic annotation in relevant tissues, can provide insight into the functional and regulatory mechanisms through which their effects on glycaemic and obesity-related traits are mediated.

  10. Discovery and Fine-Mapping of Glycaemic and Obesity-Related Trait Loci Using High-Density Imputation.

    Science.gov (United States)

    Horikoshi, Momoko; Mӓgi, Reedik; van de Bunt, Martijn; Surakka, Ida; Sarin, Antti-Pekka; Mahajan, Anubha; Marullo, Letizia; Thorleifsson, Gudmar; Hӓgg, Sara; Hottenga, Jouke-Jan; Ladenvall, Claes; Ried, Janina S; Winkler, Thomas W; Willems, Sara M; Pervjakova, Natalia; Esko, Tõnu; Beekman, Marian; Nelson, Christopher P; Willenborg, Christina; Wiltshire, Steven; Ferreira, Teresa; Fernandez, Juan; Gaulton, Kyle J; Steinthorsdottir, Valgerdur; Hamsten, Anders; Magnusson, Patrik K E; Willemsen, Gonneke; Milaneschi, Yuri; Robertson, Neil R; Groves, Christopher J; Bennett, Amanda J; Lehtimӓki, Terho; Viikari, Jorma S; Rung, Johan; Lyssenko, Valeriya; Perola, Markus; Heid, Iris M; Herder, Christian; Grallert, Harald; Müller-Nurasyid, Martina; Roden, Michael; Hypponen, Elina; Isaacs, Aaron; van Leeuwen, Elisabeth M; Karssen, Lennart C; Mihailov, Evelin; Houwing-Duistermaat, Jeanine J; de Craen, Anton J M; Deelen, Joris; Havulinna, Aki S; Blades, Matthew; Hengstenberg, Christian; Erdmann, Jeanette; Schunkert, Heribert; Kaprio, Jaakko; Tobin, Martin D; Samani, Nilesh J; Lind, Lars; Salomaa, Veikko; Lindgren, Cecilia M; Slagboom, P Eline; Metspalu, Andres; van Duijn, Cornelia M; Eriksson, Johan G; Peters, Annette; Gieger, Christian; Jula, Antti; Groop, Leif; Raitakari, Olli T; Power, Chris; Penninx, Brenda W J H; de Geus, Eco; Smit, Johannes H; Boomsma, Dorret I; Pedersen, Nancy L; Ingelsson, Erik; Thorsteinsdottir, Unnur; Stefansson, Kari; Ripatti, Samuli; Prokopenko, Inga; McCarthy, Mark I; Morris, Andrew P

    2015-07-01

    Reference panels from the 1000 Genomes (1000G) Project Consortium provide near complete coverage of common and low-frequency genetic variation with minor allele frequency ≥0.5% across European ancestry populations. Within the European Network for Genetic and Genomic Epidemiology (ENGAGE) Consortium, we have undertaken the first large-scale meta-analysis of genome-wide association studies (GWAS), supplemented by 1000G imputation, for four quantitative glycaemic and obesity-related traits, in up to 87,048 individuals of European ancestry. We identified two loci for body mass index (BMI) at genome-wide significance, and two for fasting glucose (FG), none of which has been previously reported in larger meta-analysis efforts to combine GWAS of European ancestry. Through conditional analysis, we also detected multiple distinct signals of association mapping to established loci for waist-hip ratio adjusted for BMI (RSPO3) and FG (GCK and G6PC2). The index variant for one association signal at the G6PC2 locus is a low-frequency coding allele, H177Y, which has recently been demonstrated to have a functional role in glucose regulation. Fine-mapping analyses revealed that the non-coding variants most likely to drive association signals at established and novel loci were enriched for overlap with enhancer elements, which for FG mapped to promoter and transcription factor binding sites in pancreatic islets, in particular. Our study demonstrates that 1000G imputation and genetic fine-mapping of common and low-frequency variant association signals at GWAS loci, integrated with genomic annotation in relevant tissues, can provide insight into the functional and regulatory mechanisms through which their effects on glycaemic and obesity-related traits are mediated.

  11. Combined effect of pulse density and grid cell size on predicting and mapping aboveground carbon in fast-growing Eucalyptus forest plantation using airborne LiDAR data.

    Science.gov (United States)

    Silva, Carlos Alberto; Hudak, Andrew Thomas; Klauberg, Carine; Vierling, Lee Alexandre; Gonzalez-Benecke, Carlos; de Padua Chaves Carvalho, Samuel; Rodriguez, Luiz Carlos Estraviz; Cardil, Adrián

    2017-12-01

    LiDAR remote sensing is a rapidly evolving technology for quantifying a variety of forest attributes, including aboveground carbon (AGC). Pulse density influences the acquisition cost of LiDAR, and grid cell size influences AGC prediction using plot-based methods; however, little work has evaluated the effects of LiDAR pulse density and cell size for predicting and mapping AGC in fast-growing Eucalyptus forest plantations. The aim of this study was to evaluate the effect of LiDAR pulse density and grid cell size on AGC prediction accuracy at plot and stand-levels using airborne LiDAR and field data. We used the Random Forest (RF) machine learning algorithm to model AGC using LiDAR-derived metrics from LiDAR collections of 5 and 10 pulses m -2 (RF5 and RF10) and grid cell sizes of 5, 10, 15 and 20 m. The results show that LiDAR pulse density of 5 pulses m -2 provides metrics with similar prediction accuracy for AGC as when using a dataset with 10 pulses m -2 in these fast-growing plantations. Relative root mean square errors (RMSEs) for the RF5 and RF10 were 6.14 and 6.01%, respectively. Equivalence tests showed that the predicted AGC from the training and validation models were equivalent to the observed AGC measurements. The grid cell sizes for mapping ranging from 5 to 20 also did not significantly affect the prediction accuracy of AGC at stand level in this system. LiDAR measurements can be used to predict and map AGC across variable-age Eucalyptus plantations with adequate levels of precision and accuracy using 5 pulses m -2 and a grid cell size of 5 m. The promising results for AGC modeling in this study will allow for greater confidence in comparing AGC estimates with varying LiDAR sampling densities for Eucalyptus plantations and assist in decision making towards more cost effective and efficient forest inventory.

  12. High-density single nucleotide polymorphism (SNP) array mapping in Brassica oleracea: identification of QTL associated with carotenoid variation in broccoli florets.

    Science.gov (United States)

    Brown, Allan F; Yousef, Gad G; Chebrolu, Kranthi K; Byrd, Robert W; Everhart, Koyt W; Thomas, Aswathy; Reid, Robert W; Parkin, Isobel A P; Sharpe, Andrew G; Oliver, Rebekah; Guzman, Ivette; Jackson, Eric W

    2014-09-01

    A high-resolution genetic linkage map of B. oleracea was developed from a B. napus SNP array. The work will facilitate genetic and evolutionary studies in Brassicaceae. A broccoli population, VI-158 × BNC, consisting of 150 F2:3 families was used to create a saturated Brassica oleracea (diploid: CC) linkage map using a recently developed rapeseed (Brassica napus) (tetraploid: AACC) Illumina Infinium single nucleotide polymorphism (SNP) array. The map consisted of 547 non-redundant SNP markers spanning 948.1 cM across nine chromosomes with an average interval size of 1.7 cM. As the SNPs are anchored to the genomic reference sequence of the rapid cycling B. oleracea TO1000, we were able to estimate that the map provides 96 % coverage of the diploid genome. Carotenoid analysis of 2 years data identified 3 QTLs on two chromosomes that are associated with up to half of the phenotypic variation associated with the accumulation of total or individual compounds. By searching the genome sequences of the two related diploid species (B. oleracea and B. rapa), we further identified putative carotenoid candidate genes in the region of these QTLs. This is the first description of the use of a B. napus SNP array to rapidly construct high-density genetic linkage maps of one of the constituent diploid species. The unambiguous nature of these markers with regard to genomic sequences provides evidence to the nature of genes underlying the QTL, and demonstrates the value and impact this resource will have on Brassica research.

  13. Mapping and Evaluation of NDVI Trends from Synthetic Time Series Obtained by Blending Landsat and MODIS Data around a Coalfield on the Loess Plateau

    Directory of Open Access Journals (Sweden)

    Kun Wang

    2013-09-01

    Full Text Available The increasingly intensive and extensive coal mining activities on the Loess Plateau pose a threat to the fragile local ecosystems. Quantifying the effects of coal mining activities on environmental conditions is of great interest for restoring and managing the local ecosystems and resources. This paper generates dense NDVI (Normalized Difference Vegetation Index time series between 2000 and 2011 at a spatial resolution of 30 m by blending Landsat and MODIS (Moderate Resolution Imaging Spectroradiometer data using the Spatial and Temporal Adaptive Reflectance Fusion Model (STARFM and further evaluates its capability for mapping vegetation trends around a typical coalfield on the Loss Plateau. Synthetic NDVI images were generated using (1 STARFM-generated NIR (near infrared and red band reflectance data (scheme 1 and (2 Landsat and MODIS NDVI images directly as inputs for STARFM (scheme 2. By comparing the synthetic NDVI images with the corresponding Landsat NDVI, we found that scheme 2 consistently generated better results (0.70 < R2 < 0.76 than scheme 1 (0.56 < R2 < 0.70 in this study area. Trend analysis was then performed with the synthetic dense NDVI time series and the annual maximum NDVI (NDVImax time series. The accuracy of these trends was evaluated by comparing to those from the corresponding MODIS time series, and it was concluded that both the trends from synthetic/MODIS NDVI dense time series and synthetic/MODIS NDVImax time series (2000–2011 were highly consistent. Compared to trends from MODIS time series, trends from synthetic time series are better able to capture fine scale vegetation changes. STARFM-generated synthetic NDVI time series could be used to quantify the effects of mining activities on vegetation, but the test areas should be selected with caution, as the trends derived from synthetic and MODIS time series may be significantly different in some areas.

  14. Development and assessment of 30-meter pine density maps for landscape-level modeling of mountain pine beetle dynamics

    Science.gov (United States)

    Benjamin A. Crabb; James A. Powell; Barbara J. Bentz

    2012-01-01

    Forecasting spatial patterns of mountain pine beetle (MPB) population success requires spatially explicit information on host pine distribution. We developed a means of producing spatially explicit datasets of pine density at 30-m resolution using existing geospatial datasets of vegetation composition and structure. Because our ultimate goal is to model MPB population...

  15. Genomic Characterization of DArT Markers Based on High-Density Linkage Analysis and Physical Mapping to the Eucalyptus Genome

    Science.gov (United States)

    Petroli, César D.; Sansaloni, Carolina P.; Carling, Jason; Steane, Dorothy A.; Vaillancourt, René E.; Myburg, Alexander A.; da Silva, Orzenil Bonfim; Pappas, Georgios Joannis; Kilian, Andrzej; Grattapaglia, Dario

    2012-01-01

    Diversity Arrays Technology (DArT) provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for which no reference

  16. Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome.

    Directory of Open Access Journals (Sweden)

    César D Petroli

    Full Text Available Diversity Arrays Technology (DArT provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for

  17. Drowning--a scientometric analysis and data acquisition of a constant global problem employing density equalizing mapping and scientometric benchmarking procedures.

    Science.gov (United States)

    Groneberg, David A; Schilling, Ute; Scutaru, Cristian; Uibel, Stefanie; Zitnik, Simona; Mueller, Daniel; Klingelhoefer, Doris; Kloft, Beatrix

    2011-10-14

    Drowning is a constant global problem which claims approximately half a million victims worldwide each year, whereas the number of near-drowning victims is considerably higher. Public health strategies to reduce the burden of death are still limited. While research activities in the subject drowning grow constantly, yet there is no scientometric evaluation of the existing literature at the present time. The current study uses classical bibliometric tools and visualizing techniques such as density equalizing mapping to analyse and evaluate the scientific research in the field of drowning. The interpretation of the achieved results is also implemented in the context of the data collection of the WHO. All studies related to drowning and listed in the ISI-Web of Science database since 1900 were identified using the search term "drowning". Implementing bibliometric methods, a constant increase in quantitative markers such as number of publications per state, publication language or collaborations as well as qualitative markers such as citations were observed for research in the field of drowning. The combination with density equalizing mapping exposed different global patterns for research productivity and the total number of drowning deaths and drowning rates respectively. Chart techniques were used to illustrate bi- and multilateral research cooperation. The present study provides the first scientometric approach that visualizes research activity on the subject of drowning. It can be assumed that the scientific approach to this topic will achieve even greater dimensions because of its continuing actuality.

  18. Mapping Charge Carrier Density in Organic Thin-Film Transistors by Time-Resolved Photoluminescence Lifetime Studies

    DEFF Research Database (Denmark)

    Leißner, Till; Jensen, Per Baunegaard With; Liu, Yiming

    2017-01-01

    The device performance of organic transistors is strongly influenced by the charge carrier distribution. A range of factors effect this distribution, including injection barriers at the metal-semiconductor interface, the morphology of the organic film, and charge traps at the dielectric/organic...... interface or at grain boundaries. In our comprehensive experimental and analytical work we demonstrate a method to characterize the charge carrier density in organic thin-film transistors using time-resolved photoluminescence spectroscopy. We developed a numerical model that describes the electrical...... and optical responses consistently. We determined the densities of free and trapped holes at the interface between the organic layer and the SiO2 gate dielectric by comparison to electrical measurements. Furthermore by applying fluorescence lifetime imaging microscopy we determine the local charge carrier...

  19. Mapping of the atomic hydrogen density in combustion processes at atmospheric pressure by two-photon polarization spectroscopy

    International Nuclear Information System (INIS)

    Steiger, A.; Gruetzmacher, K.; Steiger, M.; Gonzalo, A.B.; Rosa, M.I. de la

    2001-01-01

    With laser spectroscopic techniques used so far, quantitative measurements of atomic number densities in flames and other combustion processes at atmospheric pressure yield no satisfying results because high quenching rates remarkably reduce the signal size and the results suffer from large uncertainties. Whereas, two-photon polarization spectroscopy is not limited by quenching, as the polarization signal is a direct measure of the two-photon absorption. This sensitive laser technique with high spatial and temporal resolution has been applied to determine absolute number densities and the kinetic temperatures of atomic hydrogen in flames for the first time. The great potential of this method of measurement comes into its own only in conjunction with laser radiation of highest possible spectral quality, i.e. single-frequency ns-pulses with peak irradiance of up to 1 GW/cm 2 tunable around 243 nm for 1S-2S two-photon transition of atomic hydrogen

  20. Geostatistical analysis of disease data: accounting for spatial support and population density in the isopleth mapping of cancer mortality risk using area-to-point Poisson kriging

    Directory of Open Access Journals (Sweden)

    Goovaerts Pierre

    2006-11-01

    Full Text Available Abstract Background Geostatistical techniques that account for spatially varying population sizes and spatial patterns in the filtering of choropleth maps of cancer mortality were recently developed. Their implementation was facilitated by the initial assumption that all geographical units are the same size and shape, which allowed the use of geographic centroids in semivariogram estimation and kriging. Another implicit assumption was that the population at risk is uniformly distributed within each unit. This paper presents a generalization of Poisson kriging whereby the size and shape of administrative units, as well as the population density, is incorporated into the filtering of noisy mortality rates and the creation of isopleth risk maps. An innovative procedure to infer the point-support semivariogram of the risk from aggregated rates (i.e. areal data is also proposed. Results The novel methodology is applied to age-adjusted lung and cervix cancer mortality rates recorded for white females in two contrasted county geographies: 1 state of Indiana that consists of 92 counties of fairly similar size and shape, and 2 four states in the Western US (Arizona, California, Nevada and Utah forming a set of 118 counties that are vastly different geographical units. Area-to-point (ATP Poisson kriging produces risk surfaces that are less smooth than the maps created by a naïve point kriging of empirical Bayesian smoothed rates. The coherence constraint of ATP kriging also ensures that the population-weighted average of risk estimates within each geographical unit equals the areal data for this unit. Simulation studies showed that the new approach yields more accurate predictions and confidence intervals than point kriging of areal data where all counties are simply collapsed into their respective polygon centroids. Its benefit over point kriging increases as the county geography becomes more heterogeneous. Conclusion A major limitation of choropleth

  1. Geostatistical analysis of disease data: accounting for spatial support and population density in the isopleth mapping of cancer mortality risk using area-to-point Poisson kriging

    Science.gov (United States)

    Goovaerts, Pierre

    2006-01-01

    Background Geostatistical techniques that account for spatially varying population sizes and spatial patterns in the filtering of choropleth maps of cancer mortality were recently developed. Their implementation was facilitated by the initial assumption that all geographical units are the same size and shape, which allowed the use of geographic centroids in semivariogram estimation and kriging. Another implicit assumption was that the population at risk is uniformly distributed within each unit. This paper presents a generalization of Poisson kriging whereby the size and shape of administrative units, as well as the population density, is incorporated into the filtering of noisy mortality rates and the creation of isopleth risk maps. An innovative procedure to infer the point-support semivariogram of the risk from aggregated rates (i.e. areal data) is also proposed. Results The novel methodology is applied to age-adjusted lung and cervix cancer mortality rates recorded for white females in two contrasted county geographies: 1) state of Indiana that consists of 92 counties of fairly similar size and shape, and 2) four states in the Western US (Arizona, California, Nevada and Utah) forming a set of 118 counties that are vastly different geographical units. Area-to-point (ATP) Poisson kriging produces risk surfaces that are less smooth than the maps created by a naïve point kriging of empirical Bayesian smoothed rates. The coherence constraint of ATP kriging also ensures that the population-weighted average of risk estimates within each geographical unit equals the areal data for this unit. Simulation studies showed that the new approach yields more accurate predictions and confidence intervals than point kriging of areal data where all counties are simply collapsed into their respective polygon centroids. Its benefit over point kriging increases as the county geography becomes more heterogeneous. Conclusion A major limitation of choropleth maps is the common biased

  2. Real-time crowd density mapping using a novel sensory fusion model of infrared and visual systems

    OpenAIRE

    Yaseen, S; Al-Habaibeh, A; Su, D; Otham, F

    2013-01-01

    Crowd dynamic management research has seen significant attention in recent years in research and industry in an attempt to improve safety level and management of large scale events and in large public places such as stadiums, theatres, railway stations, subways and other places where high flow of people at high densities is expected. Failure to detect the crowd behaviour at the right time could lead to unnecessary injuries and fatalities. Over the past decades there have been many incidents o...

  3. Spatial Variability of Geriatric Depression Risk in a High-Density City: A Data-Driven Socio-Environmental Vulnerability Mapping Approach.

    Science.gov (United States)

    Ho, Hung Chak; Lau, Kevin Ka-Lun; Yu, Ruby; Wang, Dan; Woo, Jean; Kwok, Timothy Chi Yui; Ng, Edward

    2017-08-31

    Previous studies found a relationship between geriatric depression and social deprivation. However, most studies did not include environmental factors in the statistical models, introducing a bias to estimate geriatric depression risk because the urban environment was found to have significant associations with mental health. We developed a cross-sectional study with a binomial logistic regression to examine the geriatric depression risk of a high-density city based on five social vulnerability factors and four environmental measures. We constructed a socio-environmental vulnerability index by including the significant variables to map the geriatric depression risk in Hong Kong, a high-density city characterized by compact urban environment and high-rise buildings. Crude and adjusted odds ratios (ORs) of the variables were significantly different, indicating that both social and environmental variables should be included as confounding factors. For the comprehensive model controlled by all confounding factors, older adults who were of lower education had the highest geriatric depression risks (OR: 1.60 (1.21, 2.12)). Higher percentage of residential area and greater variation in building height within the neighborhood also contributed to geriatric depression risk in Hong Kong, while average building height had negative association with geriatric depression risk. In addition, the socio-environmental vulnerability index showed that higher scores were associated with higher geriatric depression risk at neighborhood scale. The results of mapping and cross-section model suggested that geriatric depression risk was associated with a compact living environment with low socio-economic conditions in historical urban areas in Hong Kong. In conclusion, our study found a significant difference in geriatric depression risk between unadjusted and adjusted models, suggesting the importance of including environmental factors in estimating geriatric depression risk. We also

  4. Spatial Variability of Geriatric Depression Risk in a High-Density City: A Data-Driven Socio-Environmental Vulnerability Mapping Approach

    Directory of Open Access Journals (Sweden)

    Hung Chak Ho

    2017-08-01

    Full Text Available Previous studies found a relationship between geriatric depression and social deprivation. However, most studies did not include environmental factors in the statistical models, introducing a bias to estimate geriatric depression risk because the urban environment was found to have significant associations with mental health. We developed a cross-sectional study with a binomial logistic regression to examine the geriatric depression risk of a high-density city based on five social vulnerability factors and four environmental measures. We constructed a socio-environmental vulnerability index by including the significant variables to map the geriatric depression risk in Hong Kong, a high-density city characterized by compact urban environment and high-rise buildings. Crude and adjusted odds ratios (ORs of the variables were significantly different, indicating that both social and environmental variables should be included as confounding factors. For the comprehensive model controlled by all confounding factors, older adults who were of lower education had the highest geriatric depression risks (OR: 1.60 (1.21, 2.12. Higher percentage of residential area and greater variation in building height within the neighborhood also contributed to geriatric depression risk in Hong Kong, while average building height had negative association with geriatric depression risk. In addition, the socio-environmental vulnerability index showed that higher scores were associated with higher geriatric depression risk at neighborhood scale. The results of mapping and cross-section model suggested that geriatric depression risk was associated with a compact living environment with low socio-economic conditions in historical urban areas in Hong Kong. In conclusion, our study found a significant difference in geriatric depression risk between unadjusted and adjusted models, suggesting the importance of including environmental factors in estimating geriatric depression risk

  5. Apparent diffusion coefficient maps obtained from high b value diffusion-weighted imaging in the preoperative evaluation of gliomas at 3T: comparison with standard b value diffusion-weighted imaging

    Energy Technology Data Exchange (ETDEWEB)

    Zeng, Qiang; Ling, Chenhan; Zhang, Jianmin [Second Affiliated Hospital of Zhejiang University School of Medicine, Department of Neurosurgery, Hangzhou, Zhejiang (China); Dong, Fei; Jiang, Biao [Second Affiliated Hospital of Zhejiang University School of Medicine, Department of Radiology, Hangzhou, Zhejiang (China); Shi, Feina [Second Affiliated Hospital of Zhejiang University School of Medicine, Department of Neurology, Hangzhou, Zhejiang (China)

    2017-12-15

    To assess whether ADC maps obtained from high b value DWI were more valuable in preoperatively evaluating the grade, Ki-67 index and outcome of gliomas. Sixty-three patients with gliomas, who underwent preoperative multi b value DWI at 3 T, were enrolled. The ADC{sub 1000}, ADC{sub 2000} and ADC{sub 3000} maps were generated. Receiver operating characteristic analyses were conducted to determine the area under the curve (AUC) in differentiating high-grade gliomas (HGG) from low-grade gliomas (LGG). Pearson correlation coefficients (R value) were calculated to investigate the correlation between parameters with the Ki-67 proliferation index. Survival analysis was conducted by using Cox regression. The AUC of the mean ADC{sub 1000} value (0.820) was lower than that of the mean ADC{sub 2000} value (0.847) and mean ADC{sub 3000} value (0.875) in differentiating HGG from LGG. The R value of the mean ADC{sub 1000} value (-0.499) was less negative than that of the mean ADC{sub 2000} value (-0.530) and mean ADC{sub 3000} value (-0.567). The mean ADC{sub 3000} value was an independent prognosis factor for gliomas (p = 0.008), while the mean ADC{sub 1000} and ADC{sub 2000} values were not. ADC maps obtained from high b value DWI might be a better imaging biomarker in the preoperative evaluation of gliomas. (orig.)

  6. Diffusion-Based Density-Equalizing Maps: an Interdisciplinary Approach to Visualizing Homicide Rates and Other Georeferenced Statistical Data

    Science.gov (United States)

    Mazzitello, Karina I.; Candia, Julián

    2012-12-01

    In every country, public and private agencies allocate extensive funding to collect large-scale statistical data, which in turn are studied and analyzed in order to determine local, regional, national, and international policies regarding all aspects relevant to the welfare of society. One important aspect of that process is the visualization of statistical data with embedded geographical information, which most often relies on archaic methods such as maps colored according to graded scales. In this work, we apply nonstandard visualization techniques based on physical principles. We illustrate the method with recent statistics on homicide rates in Brazil and their correlation to other publicly available data. This physics-based approach provides a novel tool that can be used by interdisciplinary teams investigating statistics and model projections in a variety of fields such as economics and gross domestic product research, public health and epidemiology, sociodemographics, political science, business and marketing, and many others.

  7. Mapping axonal density and average diameter using non-monotonic time-dependent gradient-echo MRI

    DEFF Research Database (Denmark)

    Nunes, Daniel; Cruz, Tomás L; Jespersen, Sune N

    2017-01-01

    available in the clinic, or extremely long acquisition schemes to extract information from parameter-intensive models. In this study, we suggest that simple and time-efficient multi-gradient-echo (MGE) MRI can be used to extract the axon density from susceptibility-driven non-monotonic decay in the time...... the quantitative results are compared against ground-truth histology, they seem to reflect the axonal fraction (though with a bias, as evident from Bland-Altman analysis). As well, the extra-axonal fraction can be estimated. The results suggest that our model is oversimplified, yet at the same time evidencing......-dependent signal. We show, both theoretically and with simulations, that a non-monotonic signal decay will occur for multi-compartmental microstructures – such as axons and extra-axonal spaces, which we here used in a simple model for the microstructure – and that, for axons parallel to the main magnetic field...

  8. Cross-recognition of a pit viper (Crotalinae) polyspecific antivenom explored through high-density peptide microarray epitope mapping

    DEFF Research Database (Denmark)

    Engmark, Mikael; Lomonte, Bruno; Gutiérrez, José María

    2017-01-01

    Snakebite antivenom is a 120 years old invention based on polyclonal mixtures of antibodies purified from the blood of hyper-immunized animals. Knowledge on antibody recognition sites (epitopes) on snake venom proteins is limited, but may be used to provide molecular level explanations...... for antivenom cross-reactivity. In turn, this may help guide antivenom development by elucidating immunological biases in existing antivenoms. In this study, we have identified and characterized linear elements of B-cell epitopes from 870 pit viper venom protein sequences by employing a high......-throughput methodology based on custom designed high-density peptide microarrays. By combining data on antibody-peptide interactions with multiple sequence alignments of homologous toxin sequences and protein modelling, we have determined linear elements of antibody binding sites for snake venom metalloproteases (SVMPs...

  9. Identification and mapping of linear antibody epitopes in human serum albumin using high-density Peptide arrays.

    Directory of Open Access Journals (Sweden)

    Lajla Bruntse Hansen

    Full Text Available We have recently developed a high-density photolithographic, peptide array technology with a theoretical upper limit of 2 million different peptides per array of 2 cm(2. Here, we have used this to perform complete and exhaustive analyses of linear B cell epitopes of a medium sized protein target using human serum albumin (HSA as an example. All possible overlapping 15-mers from HSA were synthesized and probed with a commercially available polyclonal rabbit anti-HSA antibody preparation. To allow for identification of even the weakest epitopes and at the same time perform a detailed characterization of key residues involved in antibody binding, the array also included complete single substitution scans (i.e. including each of the 20 common amino acids at each position of each 15-mer peptide. As specificity controls, all possible 15-mer peptides from bovine serum albumin (BSA and from rabbit serum albumin (RSA were included as well. The resulting layout contained more than 200.000 peptide fields and could be synthesized in a single array on a microscope slide. More than 20 linear epitope candidates were identified and characterized at high resolution i.e. identifying which amino acids in which positions were needed, or not needed, for antibody interaction. As expected, moderate cross-reaction with some peptides in BSA was identified whereas no cross-reaction was observed with peptides from RSA. We conclude that high-density peptide microarrays are a very powerful methodology to identify and characterize linear antibody epitopes, and should advance detailed description of individual specificities at the single antibody level as well as serologic analysis at the proteome-wide level.

  10. Identification and mapping of linear antibody epitopes in human serum albumin using high-density Peptide arrays.

    Science.gov (United States)

    Hansen, Lajla Bruntse; Buus, Soren; Schafer-Nielsen, Claus

    2013-01-01

    We have recently developed a high-density photolithographic, peptide array technology with a theoretical upper limit of 2 million different peptides per array of 2 cm(2). Here, we have used this to perform complete and exhaustive analyses of linear B cell epitopes of a medium sized protein target using human serum albumin (HSA) as an example. All possible overlapping 15-mers from HSA were synthesized and probed with a commercially available polyclonal rabbit anti-HSA antibody preparation. To allow for identification of even the weakest epitopes and at the same time perform a detailed characterization of key residues involved in antibody binding, the array also included complete single substitution scans (i.e. including each of the 20 common amino acids) at each position of each 15-mer peptide. As specificity controls, all possible 15-mer peptides from bovine serum albumin (BSA) and from rabbit serum albumin (RSA) were included as well. The resulting layout contained more than 200.000 peptide fields and could be synthesized in a single array on a microscope slide. More than 20 linear epitope candidates were identified and characterized at high resolution i.e. identifying which amino acids in which positions were needed, or not needed, for antibody interaction. As expected, moderate cross-reaction with some peptides in BSA was identified whereas no cross-reaction was observed with peptides from RSA. We conclude that high-density peptide microarrays are a very powerful methodology to identify and characterize linear antibody epitopes, and should advance detailed description of individual specificities at the single antibody level as well as serologic analysis at the proteome-wide level.

  11. Computational neuroanatomy: mapping cell-type densities in the mouse brain, simulations from the Allen Brain Atlas

    Science.gov (United States)

    Grange, Pascal

    2015-09-01

    The Allen Brain Atlas of the adult mouse (ABA) consists of digitized expression profiles of thousands of genes in the mouse brain, co-registered to a common three-dimensional template (the Allen Reference Atlas).This brain-wide, genome-wide data set has triggered a renaissance in neuroanatomy. Its voxelized version (with cubic voxels of side 200 microns) is available for desktop computation in MATLAB. On the other hand, brain cells exhibit a great phenotypic diversity (in terms of size, shape and electrophysiological activity), which has inspired the names of some well-studied cell types, such as granule cells and medium spiny neurons. However, no exhaustive taxonomy of brain cell is available. A genetic classification of brain cells is being undertaken, and some cell types have been chraracterized by their transcriptome profiles. However, given a cell type characterized by its transcriptome, it is not clear where else in the brain similar cells can be found. The ABA can been used to solve this region-specificity problem in a data-driven way: rewriting the brain-wide expression profiles of all genes in the atlas as a sum of cell-type-specific transcriptome profiles is equivalent to solving a quadratic optimization problem at each voxel in the brain. However, the estimated brain-wide densities of 64 cell types published recently were based on one series of co-registered coronal in situ hybridization (ISH) images per gene, whereas the online ABA contains several image series per gene, including sagittal ones. In the presented work, we simulate the variability of cell-type densities in a Monte Carlo way by repeatedly drawing a random image series for each gene and solving the optimization problem. This yields error bars on the region-specificity of cell types.

  12. Synthetic observations of molecular clouds in a galactic centre environment - I. Studying maps of column density and integrated intensity

    Science.gov (United States)

    Bertram, Erik; Glover, Simon C. O.; Clark, Paul C.; Ragan, Sarah E.; Klessen, Ralf S.

    2016-02-01

    We run numerical simulations of molecular clouds, adopting properties similar to those found in the central molecular zone (CMZ) of the Milky Way. For this, we employ the moving mesh code AREPO and perform simulations which account for a simplified treatment of time-dependent chemistry and the non-isothermal nature of gas and dust. We perform simulations using an initial density of n0 = 103 cm-3 and a mass of 1.3 × 105 M⊙. Furthermore, we vary the virial parameter, defined as the ratio of kinetic and potential energy, α = Ekin/|Epot|, by adjusting the velocity dispersion. We set it to α = 0.5, 2.0 and 8.0, in order to analyse the impact of the kinetic energy on our results. We account for the extreme conditions in the CMZ and increase both the interstellar radiation field (ISRF) and the cosmic ray flux (CRF) by a factor of 1000 compared to the values found in the solar neighbourhood. We use the radiative transfer code RADMC-3D to compute synthetic images in various diagnostic lines. These are [C II] at 158 μm, [O I] (145 μm), [O I] (63 μm), 12CO (J = 1 → 0) and 13CO (J = 1 → 0) at 2600 and 2720 μm, respectively. When α is large, the turbulence disperses much of the gas in the cloud, reducing its mean density and allowing the ISRF to penetrate more deeply into the cloud's interior. This significantly alters the chemical composition of the cloud, leading to the dissociation of a significant amount of the molecular gas. On the other hand, when α is small, the cloud remains compact, allowing more of the molecular gas to survive. We show that in each case the atomic tracers accurately reflect most of the physical properties of both the H2 and the total gas of the cloud and that they provide a useful alternative to molecular lines when studying the interstellar medium in the CMZ.

  13. Apocrustacyanin C(1) crystals grown in space and on earth using vapour-diffusion geometry: protein structure refinements and electron-density map comparisons.

    Science.gov (United States)

    Habash, Jarjis; Boggon, Titus J; Raftery, James; Chayen, Naomi E; Zagalsky, Peter F; Helliwell, John R

    2003-07-01

    Models of apocrustacyanin C(1) were refined against X-ray data recorded on Bending Magnet 14 at the ESRF to resolutions of 1.85 and 2 A from a space-grown and an earth-grown crystal, respectively, both using vapour-diffusion crystal-growth geometry. The space crystals were grown in the APCF on the NASA Space Shuttle. The microgravity crystal growth showed a cyclic nature attributed to Marangoni convection, thus reducing the benefits of the microgravity environment, as reported previously [Chayen et al. (1996), Q. Rev. Biophys. 29, 227-278]. A subsequent mosaicity evaluation, also reported previously, showed only a partial improvement in the space-grown crystals over the earth-grown crystals [Snell et al. (1997), Acta Cryst. D53, 231-239], contrary to the case for lysozyme crystals grown in space with liquid-liquid diffusion, i.e. without any major motion during growth [Snell et al. (1995), Acta Cryst. D52, 1099-1102]. In this paper, apocrustacyanin C(1) electron-density maps from the two refined models are now compared. It is concluded that the electron-density maps of the protein and the bound waters are found to be better overall for the structures of apocrustacyanin C(1) studied from the space-grown crystal compared with those from the earth-grown crystal, even though both crystals were grown using vapour-diffusion crystal-growth geometry. The improved residues are on the surface of the protein, with two involved in or nearby crystal lattice-forming interactions, thus linking an improved crystal-growth mechanism to the molecular level. The structural comparison procedures developed should themselves be valuable for evaluating crystal-growth procedures in the future.

  14. Brain dynamics of upstream perceptual processes leading to visual object recognition: a high density ERP topographic mapping study.

    Science.gov (United States)

    Schettino, Antonio; Loeys, Tom; Delplanque, Sylvain; Pourtois, Gilles

    2011-04-01

    Recent studies suggest that visual object recognition is a proactive process through which perceptual evidence accumulates over time before a decision can be made about the object. However, the exact electrophysiological correlates and time-course of this complex process remain unclear. In addition, the potential influence of emotion on this process has not been investigated yet. We recorded high density EEG in healthy adult participants performing a novel perceptual recognition task. For each trial, an initial blurred visual scene was first shown, before the actual content of the stimulus was gradually revealed by progressively adding diagnostic high spatial frequency information. Participants were asked to stop this stimulus sequence as soon as they could correctly perform an animacy judgment task. Behavioral results showed that participants reliably gathered perceptual evidence before recognition. Furthermore, prolonged exploration times were observed for pleasant, relative to either neutral or unpleasant scenes. ERP results showed distinct effects starting at 280 ms post-stimulus onset in distant brain regions during stimulus processing, mainly characterized by: (i) a monotonic accumulation of evidence, involving regions of the posterior cingulate cortex/parahippocampal gyrus, and (ii) true categorical recognition effects in medial frontal regions, including the dorsal anterior cingulate cortex. These findings provide evidence for the early involvement, following stimulus onset, of non-overlapping brain networks during proactive processes eventually leading to visual object recognition. Copyright © 2011 Elsevier Inc. All rights reserved.

  15. Detailed deposition density maps constructed by large-scale soil sampling for gamma-ray emitting radioactive nuclides from the Fukushima Dai-ichi Nuclear Power Plant accident.

    Science.gov (United States)

    Saito, Kimiaki; Tanihata, Isao; Fujiwara, Mamoru; Saito, Takashi; Shimoura, Susumu; Otsuka, Takaharu; Onda, Yuichi; Hoshi, Masaharu; Ikeuchi, Yoshihiro; Takahashi, Fumiaki; Kinouchi, Nobuyuki; Saegusa, Jun; Seki, Akiyuki; Takemiya, Hiroshi; Shibata, Tokushi

    2015-01-01

    Soil deposition density maps of gamma-ray emitting radioactive nuclides from the Fukushima Dai-ichi Nuclear Power Plant (NPP) accident were constructed on the basis of results from large-scale soil sampling. In total 10,915 soil samples were collected at 2168 locations. Gamma rays emitted from the samples were measured by Ge detectors and analyzed using a reliable unified method. The determined radioactivity was corrected to that of June 14, 2011 by considering the intrinsic decay constant of each nuclide. Finally the deposition maps were created for (134)Cs, (137)Cs, (131)I, (129m)Te and (110m)Ag. The radioactivity ratio of (134)Cs-(137)Cs was almost constant at 0.91 regardless of the locations of soil sampling. The radioactivity ratios of (131)I and (129m)Te-(137)Cs were relatively high in the regions south of the Fukushima NPP site. Effective doses for 50 y after the accident were evaluated for external and inhalation exposures due to the observed radioactive nuclides. The radiation doses from radioactive cesium were found to be much higher than those from the other radioactive nuclides. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  16. Multisensory representation of frequency across audition and touch: high density electrical mapping reveals early sensory-perceptual coupling.

    Science.gov (United States)

    Butler, John S; Foxe, John J; Fiebelkorn, Ian C; Mercier, Manuel R; Molholm, Sophie

    2012-10-31

    The frequency of environmental vibrations is sampled by two of the major sensory systems, audition and touch, notwithstanding that these signals are transduced through very different physical media and entirely separate sensory epithelia. Psychophysical studies have shown that manipulating frequency in audition or touch can have a significant cross-sensory impact on perceived frequency in the other sensory system, pointing to intimate links between these senses during computation of frequency. In this regard, the frequency of a vibratory event can be thought of as a multisensory perceptual construct. In turn, electrophysiological studies point to temporally early multisensory interactions that occur in hierarchically early sensory regions where convergent inputs from the auditory and somatosensory systems are to be found. A key question pertains to the level of processing at which the multisensory integration of featural information, such as frequency, occurs. Do the sensory systems calculate frequency independently before this information is combined, or is this feature calculated in an integrated fashion during preattentive sensory processing? The well characterized mismatch negativity, an electrophysiological response that indexes preattentive detection of a change within the context of a regular pattern of stimulation, served as our dependent measure. High-density electrophysiological recordings were made in humans while they were presented with separate blocks of somatosensory, auditory, and audio-somatosensory "standards" and "deviants," where the deviant differed in frequency. Multisensory effects were identified beginning at ∼200 ms, with the multisensory mismatch negativity (MMN) significantly different from the sum of the unisensory MMNs. This provides compelling evidence for preattentive coupling between the somatosensory and auditory channels in the cortical representation of frequency.

  17. High Density Linkage Map Construction and QTL Detection for Three Silique-Related Traits in Orychophragmus violaceus Derived Brassica napus Population

    Directory of Open Access Journals (Sweden)

    Yi Yang

    2017-09-01

    Full Text Available Seeds per silique (SS, seed weight (SW, and silique length (SL are important determinant traits of seed yield potential in rapeseed (Brassica napus L., and are controlled by naturally occurring quantitative trait loci (QTLs. Mapping QTLs to narrow chromosomal regions provides an effective means of characterizing the genetic basis of these complex traits. Orychophragmus violaceus is a crucifer with long siliques, many SS, and heavy seeds. A novel B. napus introgression line with many SS was previously selected from multiple crosses (B. rapa ssp. chinesis × O. violaceus × B. napus. In present study, a doubled haploid (DH population with 167 lines was established from a cross between the introgression line and a line with far fewer SS, in order to detect QTLs for silique-related traits. By screening with a Brassica 60K single nucleotide polymorphism (SNP array, a high-density linkage map consisting of 1,153 bins and spanning a cumulative length of 2,209.1 cM was constructed, using 12,602 high-quality polymorphic SNPs in the DH population. The average recombination bin densities of the A and C subgenomes were 1.7 and 2.4 cM, respectively. 45 QTLs were identified for the three traits in all, which explained 4.0–34.4% of the total phenotypic variation; 20 of them were integrated into three unique QTLs by meta-analysis. These unique QTLs revealed a significant positive correlation between SS and SL and a significant negative correlation between SW and SS, and were mapped onto the linkage groups A05, C08, and C09. A trait-by-trait meta-analysis revealed eight, four, and seven consensus QTLs for SS, SW, and SL, respectively, and five major QTLs (cqSS.A09b, cqSS.C09, cqSW.A05, cqSW.C09, and cqSL.C09 were identified. Five, three, and four QTLs for SS, SW, and SL, respectively, might be novel QTLs because of the existence of alien genetic loci for these traits in the alien introgression. Thirty-eight candidate genes underlying nine QTLs for silique

  18. Reward contingencies and the recalibration of task monitoring and reward systems: a high-density electrical mapping study.

    Science.gov (United States)

    Morie, K P; De Sanctis, P; Foxe, J J

    2014-07-25

    Task execution almost always occurs in the context of reward-seeking or punishment-avoiding behavior. As such, ongoing task-monitoring systems are influenced by reward anticipation systems. In turn, when a task has been executed either successfully or unsuccessfully, future iterations of that task will be re-titrated on the basis of the task outcome. Here, we examined the neural underpinnings of the task-monitoring and reward-evaluation systems to better understand how they govern reward-seeking behavior. Twenty-three healthy adult participants performed a task where they accrued points that equated to real world value (gift cards) by responding as rapidly as possible within an allotted timeframe, while success rate was titrated online by changing the duration of the timeframe dependent on participant performance. Informative cues initiated each trial, indicating the probability of potential reward or loss (four levels from very low to very high). We manipulated feedback by first informing participants of task success/failure, after which a second feedback signal indicated actual magnitude of reward/loss. High-density electroencephalography (EEG) recordings allowed for examination of event-related potentials (ERPs) to the informative cues and in turn, to both feedback signals. Distinct ERP components associated with reward cues, task-preparatory and task-monitoring processes, and reward feedback processes were identified. Unsurprisingly, participants displayed increased ERP amplitudes associated with task-preparatory processes following cues that predicted higher chances of reward. They also rapidly updated reward and loss prediction information dependent on task performance after the first feedback signal. Finally, upon reward receipt, initial reward probability was no longer taken into account. Rather, ERP measures suggested that only the magnitude of actual reward or loss was now processed. Reward and task-monitoring processes are clearly dissociable, but

  19. Antagonistic properties of a natural product-Bicuculline with the gamma-aminobutyric acid receptor: studied through electrostatic potential mapping, electronic and vibrational spectra using ab initio and density functional theory.

    Science.gov (United States)

    Srivastava, Anubha; Tandon, Poonam; Jain, Sudha; Asthana, B P

    2011-12-15

    (+)-Bicuculline (hereinafter referred to as bicuculline), a phthalide isoquinoline alkaloid is of current interest as an antagonist of gamma-aminobutyric acid (GABA). Its inhibitor properties have been studied through molecular electrostatic potential (MEP) mapping of this molecule and GABA receptor. The hot site on the potential surface of bicuculline, which is also isosteric with GABA receptor, has been used to interpret the inhibitor property. A systematic quantum chemical study of the possible conformations, their relative stabilities, FT-Raman, FT-IR and UV-vis spectroscopic analysis of bicuculline has been reported. The optimized geometries, wavenumber and intensity of the vibrational bands of all the conformers of bicuculline have been calculated using ab initio Hartree-Fock (HF) and density functional theory (DFT) employing B3LYP functional and 6-311G(d,p) basis set. Mulliken atomic charges, HOMO-LUMO gap ΔE, ionization potential, dipole moments and total energy have also been obtained for the optimized geometries of both the molecules. TD-DFT method is used to calculate the electronic absorption parameters in gas phase as well as in solvent environment using integral equation formalism-polarizable continuum model (IEF-PCM) employing 6-31G basis set and the results thus obtained are compared with the UV absorption spectra. The combination of experimental and calculated results provides an insight into the structural and vibrational spectroscopic properties of bicuculline. Copyright © 2011 Elsevier B.V. All rights reserved.

  20. QTL Mapping of Adult-Plant Resistance to Leaf Rust in the Wheat Cross Zhou 8425B/Chinese Spring Using High-Density SNP Markers

    Directory of Open Access Journals (Sweden)

    Peipei Zhang

    2017-05-01

    Full Text Available Wheat leaf rust is an important disease worldwide. Growing resistant cultivars is an effective means to control the disease. In the present study, 244 recombinant inbred lines from Zhou 8425B/Chinese Spring cross were phenotyped for leaf rust severities during the 2011–2012, 2012–2013, 2013–2014, and 2014–2015 cropping seasons at Baoding, Hebei province, and 2012–2013 and 2013–2014 cropping seasons in Zhoukou, Henan province. The population was genotyped using the high-density Illumina iSelect 90K SNP assay and SSR markers. Inclusive composite interval mapping identified eight QTL, designated as QLr.hebau-2AL, QLr.hebau-2BS, QLr.hebau-3A, QLr.hebau-3BS, QLr.hebau-4AL, QLr.hebau-4B, QLr.hebau-5BL, and QLr.hebau-7DS, respectively. QLr.hebau-2BS, QLr.hebau-3A, QLr.hebau-3BS, and QLr.hebau-5BL were derived from Zhou 8425B, whereas the other four were from Chinese Spring. Three stable QTL on chromosomes 2BS, 4B and 7DS explained 7.5–10.6%, 5.5–24.4%, and 11.2–20.9% of the phenotypic variance, respectively. QLr.hebau-2BS in Zhou 8425B might be the same as LrZH22 in Zhoumai 22; QLr.hebau-4B might be the residual resistance of Lr12, and QLr.hebau-7DS is Lr34. QLr.hebau-2AL, QLr.hebau-3BS, QLr.hebau-4AL, and QLr.hebau-5BL are likely to be novel QTL for leaf rust. These QTL and their closely linked SNP and SSR markers can be used for fine mapping, candidate gene discovery, and marker-assisted selection in wheat breeding.

  1. Dissection of Genetic Factors underlying Wheat Kernel Shape and Size in an Elite × Nonadapted Cross using a High Density SNP Linkage Map

    Directory of Open Access Journals (Sweden)

    Ajay Kumar

    2016-03-01

    Full Text Available Wheat kernel shape and size has been under selection since early domestication. Kernel morphology is a major consideration in wheat breeding, as it impacts grain yield and quality. A population of 160 recombinant inbred lines (RIL, developed using an elite (ND 705 and a nonadapted genotype (PI 414566, was extensively phenotyped in replicated field trials and genotyped using Infinium iSelect 90K assay to gain insight into the genetic architecture of kernel shape and size. A high density genetic map consisting of 10,172 single nucleotide polymorphism (SNP markers, with an average marker density of 0.39 cM/marker, identified a total of 29 genomic regions associated with six grain shape and size traits; ∼80% of these regions were associated with multiple traits. The analyses showed that kernel length (KL and width (KW are genetically independent, while a large number (∼59% of the quantitative trait loci (QTL for kernel shape traits were in common with genomic regions associated with kernel size traits. The most significant QTL was identified on chromosome 4B, and could be an ortholog of major rice grain size and shape gene or . Major and stable loci also were identified on the homeologous regions of Group 5 chromosomes, and in the regions of (6A and (7A genes. Both parental genotypes contributed equivalent positive QTL alleles, suggesting that the nonadapted germplasm has a great potential for enhancing the gene pool for grain shape and size. This study provides new knowledge on the genetic dissection of kernel morphology, with a much higher resolution, which may aid further improvement in wheat yield and quality using genomic tools.

  2. Evaluation of Green-LiDAR Data for Mapping Extent, Density and Height of Aquatic Reed Beds at Lake Chiemsee, Bavaria—Germany

    Directory of Open Access Journals (Sweden)

    Nicolás Corti Meneses

    2017-12-01

    Full Text Available Aquatic reed is an important indicator for the ecological assessment of freshwater lakes. Monitoring is essential to document its expansion or deterioration and decline. The applicability of Green-LiDAR data for the status assessment of aquatic reed beds of Bavarian freshwater lakes was investigated. The study focused on mapping diagnostic structural parameters of aquatic reed beds by exploring 3D data provided by the Green-LiDAR system. Field observations were conducted over 14 different areas of interest along 152 cross-sections. The data indicated the morphologic and phenologic traits of aquatic reed, which were used for validation purposes. For the automatic classification of aquatic reed bed spatial extent, density and height, a rule-based algorithm was developed. LiDAR data allowed for the delimitating of the aquatic reed frontline, as well as shoreline, and therefore an accurate quantification of extents (Hausdorff distance = 5.74 m and RMSE of cross-sections length 0.69 m. The overall accuracy measured for aquatic reed bed density compared to the simultaneously recorded aerial imagery was 96% with a Kappa coefficient of 0.91 and 72% (Kappa = 0.5 compared to field measurements. Digital Surface Models (DSM, calculated from point clouds, similarly showed a high level of agreement in derived heights of flat surfaces (RMSE = 0.1 m and showed an adequate agreement of aquatic reed heights with evenly distributed errors (RMSE = 0.8 m. Compared to field measurements, aerial laser scanning delivered valuable information with no disturbance of the habitat. Analysing data with our classification procedure improved the efficiency, reproducibility, and accuracy of the quantification and monitoring of aquatic reed beds.

  3. Dissection of Genetic Factors underlying Wheat Kernel Shape and Size in an Elite × Nonadapted Cross using a High Density SNP Linkage Map.

    Science.gov (United States)

    Kumar, Ajay; Mantovani, E E; Seetan, R; Soltani, A; Echeverry-Solarte, M; Jain, S; Simsek, S; Doehlert, D; Alamri, M S; Elias, E M; Kianian, S F; Mergoum, M

    2016-03-01

    Wheat kernel shape and size has been under selection since early domestication. Kernel morphology is a major consideration in wheat breeding, as it impacts grain yield and quality. A population of 160 recombinant inbred lines (RIL), developed using an elite (ND 705) and a nonadapted genotype (PI 414566), was extensively phenotyped in replicated field trials and genotyped using Infinium iSelect 90K assay to gain insight into the genetic architecture of kernel shape and size. A high density genetic map consisting of 10,172 single nucleotide polymorphism (SNP) markers, with an average marker density of 0.39 cM/marker, identified a total of 29 genomic regions associated with six grain shape and size traits; ∼80% of these regions were associated with multiple traits. The analyses showed that kernel length (KL) and width (KW) are genetically independent, while a large number (∼59%) of the quantitative trait loci (QTL) for kernel shape traits were in common with genomic regions associated with kernel size traits. The most significant QTL was identified on chromosome 4B, and could be an ortholog of major rice grain size and shape gene or . Major and stable loci also were identified on the homeologous regions of Group 5 chromosomes, and in the regions of (6A) and (7A) genes. Both parental genotypes contributed equivalent positive QTL alleles, suggesting that the nonadapted germplasm has a great potential for enhancing the gene pool for grain shape and size. This study provides new knowledge on the genetic dissection of kernel morphology, with a much higher resolution, which may aid further improvement in wheat yield and quality using genomic tools. Copyright © 2016 Crop Science Society of America.

  4. 2-(2-Chlorobenzoylimino)-1,3-thiazolidine: structure refinement from neutron diffraction data at 113 K and charge density deformation maps

    International Nuclear Information System (INIS)

    Cohen-Addad, C.; Savariault, J.-M.; Lehmann, M.S.

    1981-01-01

    The structure of 2-(2-chlorobenzoylimino)-1,3-thiazolidine, C 10 H 9 ClN 2 OS, has been redetermined by neutron diffraction at 113 K. The space group is P2 1 /c with lattice parameters a = 19.950 (4), b = 7.420 (2), c = 11.566 (3) A, β = 109.10 (3) 0 , Z = 4, Msub(r) = 240.7 and dsub(calc) = 1.52 Mg m -3 . The final R(F 2 ) was 0.045 for 1768 reflections. The structural results show unambiguously that the molecule is found in the imino form with an H atom located near the endocyclic N atom of the thiazolidine group. Based on deformation electron density maps and the interatomic distances it is speculated that the difference in geometry between the two tautomeric forms (imino and amino) is small and that the occurrence of one or the other is strongly dependent on the substituents. A short intramolecular S-O contact of 2.68 A is found and is believed to constitute a very weak bond. (Auth.)

  5. Effect of current density and pH in obtaining the Ni-Fe alloy by electrodeposition; Efeito da densidade de corrente e pH na obtencao da liga Ni-Fe por eletrodeposicao

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Jose Anderson Machado; Raulino, Anamelia de Medeiros Dantas; Raulino, Jose Leonardo Costa; Campos, Ana Regina Nascimento; Prasad, Shiva; Santana, Renato Alexandre Costa de, E-mail: jmo.anderson@gmail.com, E-mail: anameliadantas@yahoo.com.br, E-mail: leonardo.jcr@hotmail.com, E-mail: arncampos@yahoo.com.br, E-mail: prasad@deq.ufcg.edu.br, E-mail: renatoacs@ufcg.edu.br [Universidade Federal de Campina Grande (UFCG), Cuite, PB (Brazil). Lab. de Eletroquimica e Corrosao

    2017-01-15

    Metallic coatings can be applied for different purposes, for example to improve the mechanical, catalytic, anti corrosive properties or simply to improve the decorative appearance. In the work the Fe-Ni alloys have been obtained by electrodeposition process using a simple electrolytic bath containing the reagents, nickel sulfate, iron sulfate and sodium tartrate. A complete experimental design 2{sup 2} , associated with the response surface methodology (RSM) technique was used as optimization tool. Chemical composition, current efficiency, surface morphology and electrochemical corrosion measures were performed. It was observed that a decrease in the pH favored an increase in iron and decrease in nickel contents in the alloy. The iron content influenced the alloy morphology. The best experiment showed an average corrosion resistance 5471.5 Ω.cm² and a corrosion current density 4.814x10{sup -6} A/cm². This experiment presented a composition of 70 wt% Ni and 30 wt% Fe in the alloy and an average deposition current efficiency of 58.7%. (author)

  6. Parcels and Land Ownership, This data set consists of digital map files containing parcel-level cadastral information obtained from property descriptions. Cadastral features contained in the data set include real property boundary lines, rights-of-way boundaries, property dimensions, Published in Not Provided, 1:2400 (1in=200ft) scale, Racine County Government.

    Data.gov (United States)

    NSGIC Local Govt | GIS Inventory — Parcels and Land Ownership dataset current as of unknown. This data set consists of digital map files containing parcel-level cadastral information obtained from...

  7. What and Where in auditory sensory processing: A high-density electrical mapping study of distinct neural processes underlying sound object recognition and sound localization

    Directory of Open Access Journals (Sweden)

    Victoria M Leavitt

    2011-06-01

    Full Text Available Functionally distinct dorsal and ventral auditory pathways for sound localization (where and sound object recognition (what have been described in non-human primates. A handful of studies have explored differential processing within these streams in humans, with highly inconsistent findings. Stimuli employed have included simple tones, noise bursts and speech sounds, with simulated left-right spatial manipulations, and in some cases participants were not required to actively discriminate the stimuli. Our contention is that these paradigms were not well suited to dissociating processing within the two streams. Our aim here was to determine how early in processing we could find evidence for dissociable pathways using better titrated what and where task conditions. The use of more compelling tasks should allow us to amplify differential processing within the dorsal and ventral pathways. We employed high-density electrical mapping using a relatively large and environmentally realistic stimulus set (seven animal calls delivered from seven free-field spatial locations; with stimulus configuration identical across the where and what tasks. Topographic analysis revealed distinct dorsal and ventral auditory processing networks during the where and what tasks with the earliest point of divergence seen during the N1 component of the auditory evoked response, beginning at approximately 100 ms. While this difference occurred during the N1 timeframe, it was not a simple modulation of N1 amplitude as it displayed a wholly different topographic distribution to that of the N1. Global dissimilarity measures using topographic modulation analysis confirmed that this difference between tasks was driven by a shift in the underlying generator configuration. Minimum norm source reconstruction revealed distinct activations that corresponded well with activity within putative dorsal and ventral auditory structures.

  8. Seeing voices: High-density electrical mapping and source-analysis of the multisensory mismatch negativity evoked during the McGurk illusion.

    Science.gov (United States)

    Saint-Amour, Dave; De Sanctis, Pierfilippo; Molholm, Sophie; Ritter, Walter; Foxe, John J

    2007-02-01

    Seeing a speaker's facial articulatory gestures powerfully affects speech perception, helping us overcome noisy acoustical environments. One particularly dramatic illustration of visual influences on speech perception is the "McGurk illusion", where dubbing an auditory phoneme onto video of an incongruent articulatory movement can often lead to illusory auditory percepts. This illusion is so strong that even in the absence of any real change in auditory stimulation, it activates the automatic auditory change-detection system, as indexed by the mismatch negativity (MMN) component of the auditory event-related potential (ERP). We investigated the putative left hemispheric dominance of McGurk-MMN using high-density ERPs in an oddball paradigm. Topographic mapping of the initial McGurk-MMN response showed a highly lateralized left hemisphere distribution, beginning at 175 ms. Subsequently, scalp activity was also observed over bilateral fronto-central scalp with a maximal amplitude at approximately 290 ms, suggesting later recruitment of right temporal cortices. Strong left hemisphere dominance was again observed during the last phase of the McGurk-MMN waveform (350-400 ms). Source analysis indicated bilateral sources in the temporal lobe just posterior to primary auditory cortex. While a single source in the right superior temporal gyrus (STG) accounted for the right hemisphere activity, two separate sources were required, one in the left transverse gyrus and the other in STG, to account for left hemisphere activity. These findings support the notion that visually driven multisensory illusory phonetic percepts produce an auditory-MMN cortical response and that left hemisphere temporal cortex plays a crucial role in this process.

  9. Merging field mapping and numerical simulation to interpret the lithofacies variations from unsteady pyroclastic density currents on uneven terrain: The case of La Fossa di Vulcano (Aeolian Islands, Italy)

    Science.gov (United States)

    Doronzo, Domenico M.; Dellino, Pierfrancesco; Sulpizio, Roberto; Lucchi, Federico

    2017-01-01

    In order to obtain results from computer simulations of explosive volcanic eruptions, one either needs a statistical approach to test a wide range of initial and boundary conditions, or needs using a well-constrained field case study via stratigraphy. Here we followed the second approach, using data obtained from field mapping of the Grotta dei Palizzi 2 pyroclastic deposits (Vulcano Island, Italy) as input for numerical modeling. This case study deals with impulsive phreatomagmatic explosions of La Fossa Cone that generated ash-rich pyroclastic density currents, interacting with the topographic high of the La Fossa Caldera rim. One of the simplifications in dealing with well-sorted ash (one particle size in the model) is to highlight the topographic effects on the same pyroclastic material in an unsteady current. We demonstrate that by merging field data with 3D numerical simulation results it is possible to see key details of the dynamical current-terrain interaction, and to interpret the lithofacies variations of the associated deposits as a function of topography-induced sedimentation (settling) rate. Results suggest that a value of the sedimentation rate lower than 5 kg/m2 s at the bed load can still be sheared by the overlying current, producing tractional structures (laminae) in the deposits. Instead, a sedimentation rate higher than that threshold can preclude the formation of tractional structures, producing thicker massive deposits. We think that the approach used in this study could be applied to other case studies (both for active and ancient volcanoes) to confirm or refine such threshold value of the sedimentation rate, which is to be considered as an upper value as for the limitations of the numerical model.

  10. Construction of a high-density DArTseq SNP-based genetic map and identification of genomic regions with segregation distortion in a genetic population derived from a cross between feral and cultivated-type watermelon.

    Science.gov (United States)

    Ren, Runsheng; Ray, Rumiana; Li, Pingfang; Xu, Jinhua; Zhang, Man; Liu, Guang; Yao, Xiefeng; Kilian, Andrzej; Yang, Xingping

    2015-08-01

    Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is an economically important vegetable crop grown extensively worldwide. To facilitate the identification of agronomically important traits and provide new information for genetic and genomic research on this species, a high-density genetic linkage map of watermelon was constructed using an F2 population derived from a cross between elite watermelon cultivar K3 and wild watermelon germplasm PI 189225. Based on a sliding window approach, a total of 1,161 bin markers representing 3,465 SNP markers were mapped onto 11 linkage groups corresponding to the chromosome pair number of watermelon. The total length of the genetic map is 1,099.2 cM, with an average distance between bins of 1.0 cM. The number of markers in each chromosome varies from 62 in chromosome 07 to 160 in chromosome 05. The length of individual chromosomes ranged between 61.8 cM for chromosome 07 and 140.2 cM for chromosome 05. A total of 616 SNP bin markers showed significant (P watermelon cultivar K3 allele and 103 were skewed toward PI 189225. The number of SNPs and InDels per Mb varied considerably across the segregation distorted regions (SDRs) on each chromosome, and a mixture of dense and sparse SNPs and InDel SDRs coexisted on some chromosomes suggesting that SDRs were randomly distributed throughout the genome. Recombination rates varied greatly among each chromosome, from 2.0 to 4.2 centimorgans per megabase (cM/Mb). An inconsistency was found between the genetic and physical positions on the map for a segment on chromosome 11. The high-density genetic map described in the present study will facilitate fine mapping of quantitative trait loci, the identification of candidate genes, map-based cloning, as well as marker-assisted selection (MAS) in watermelon breeding programs.

  11. From hot rocks to glowing avalanches: Numerical modelling of gravity-induced pyroclastic density currents and hazard maps at the Stromboli volcano (Italy)

    Science.gov (United States)

    Salvatici, Teresa; Di Roberto, Alessio; Di Traglia, Federico; Bisson, Marina; Morelli, Stefano; Fidolini, Francesco; Bertagnini, Antonella; Pompilio, Massimo; Hungr, Oldrich; Casagli, Nicola

    2016-11-01

    Gravity-induced pyroclastic density currents (PDCs) can be produced by the collapse of volcanic crater rims or due to the gravitational instability of materials deposited in proximal areas during explosive activity. These types of PDCs, which are also known as ;glowing avalanches;, have been directly observed, and their deposits have been widely identified on the flanks of several volcanoes that are fed by mafic to intermediate magmas. In this research, the suitability of landslide numerical models for simulating gravity-induced PDCs to provide hazard assessments was tested. This work also presents the results of a back-analysis of three events that occurred in 1906, 1930 and 1944 at the Stromboli volcano by applying a depth-averaged 3D numerical code named DAN-3D. The model assumes a frictional internal rheology and a variable basal rheology (i.e., frictional, Voellmy and plastic). The numerical modelling was able to reproduce the gravity-induced PDCs' extension and deposit thicknesses to an order of magnitude of that reported in the literature. The best results when compared with field data were obtained using a Voellmy model with a frictional coefficient of f = 0.19 and a turbulence parameter ξ = 1000 m s- 1. The results highlight the suitability of this numerical code, which is generally used for landslides, to reproduce the destructive potential of these events in volcanic environments and to obtain information on hazards connected with explosive-related, mass-wasting phenomena in Stromboli Island and at volcanic systems characterized by similar phenomena.

  12. Genome-wide linkage mapping of yield-related traits in three Chinese bread wheat populations using high-density SNP markers.

    Science.gov (United States)

    Li, Faji; Wen, Weie; He, Zhonghu; Liu, Jindong; Jin, Hui; Cao, Shuanghe; Geng, Hongwei; Yan, Jun; Zhang, Pingzhi; Wan, Yingxiu; Xia, Xianchun

    2018-06-01

    We identified 21 new and stable QTL, and 11 QTL clusters for yield-related traits in three bread wheat populations using the wheat 90 K SNP assay. Identification of quantitative trait loci (QTL) for yield-related traits and closely linked molecular markers is important in order to identify gene/QTL for marker-assisted selection (MAS) in wheat breeding. The objectives of the present study were to identify QTL for yield-related traits and dissect the relationships among different traits in three wheat recombinant inbred line (RIL) populations derived from crosses Doumai × Shi 4185 (D × S), Gaocheng 8901 × Zhoumai 16 (G × Z) and Linmai 2 × Zhong 892 (L × Z). Using the available high-density linkage maps previously constructed with the wheat 90 K iSelect single nucleotide polymorphism (SNP) array, 65, 46 and 53 QTL for 12 traits were identified in the three RIL populations, respectively. Among them, 34, 23 and 27 were likely to be new QTL. Eighteen common QTL were detected across two or three populations. Eleven QTL clusters harboring multiple QTL were detected in different populations, and the interval 15.5-32.3 cM around the Rht-B1 locus on chromosome 4BS harboring 20 QTL is an important region determining grain yield (GY). Thousand-kernel weight (TKW) is significantly affected by kernel width and plant height (PH), whereas flag leaf width can be used to select lines with large kernel number per spike. Eleven candidate genes were identified, including eight cloned genes for kernel, heading date (HD) and PH-related traits as well as predicted genes for TKW, spike length and HD. The closest SNP markers of stable QTL or QTL clusters can be used for MAS in wheat breeding using kompetitive allele-specific PCR or semi-thermal asymmetric reverse PCR assays for improvement of GY.

  13. Support for the existence of invertible maps between electronic densities and non-analytic 1-body external potentials in non-relativistic time-dependent quantum mechanics

    Science.gov (United States)

    Mosquera, Martín A.

    2017-10-01

    Provided the initial state, the Runge-Gross theorem establishes that the time-dependent (TD) external potential of a system of non-relativistic electrons determines uniquely their TD electronic density, and vice versa (up to a constant in the potential). This theorem requires the TD external potential and density to be Taylor-expandable around the initial time of the propagation. This paper presents an extension without this restriction. Given the initial state of the system and evolution of the density due to some TD scalar potential, we show that a perturbative (not necessarily weak) TD potential that induces a non-zero divergence of the external force-density, inside a small spatial subset and immediately after the initial propagation time, will cause a change in the density within that subset, implying that the TD potential uniquely determines the TD density. In this proof, we assume unitary evolution of wavefunctions and first-order differentiability (which does not imply analyticity) in time of the internal and external force-densities, electronic density, current density, and their spatial derivatives over the small spatial subset and short time interval.

  14. Smartphones Based Mobile Mapping Systems

    Directory of Open Access Journals (Sweden)

    A. Al-Hamad

    2014-06-01

    Full Text Available The past 20 years have witnessed an explosive growth in the demand for geo-spatial data. This demand has numerous sources and takes many forms; however, the net effect is an ever-increasing thirst for data that is more accurate, has higher density, is produced more rapidly, and is acquired less expensively. For mapping and Geographic Information Systems (GIS projects, this has been achieved through the major development of Mobile Mapping Systems (MMS. MMS integrate various navigation and remote sensing technologies which allow mapping from moving platforms (e.g. cars, airplanes, boats, etc. to obtain the 3D coordinates of the points of interest. Such systems obtain accuracies that are suitable for all but the most demanding mapping and engineering applications. However, this accuracy doesn't come cheaply. As a consequence of the platform and navigation and mapping technologies used, even an "inexpensive" system costs well over 200 000 USD. Today's mobile phones are getting ever more sophisticated. Phone makers are determined to reduce the gap between computers and mobile phones. Smartphones, in addition to becoming status symbols, are increasingly being equipped with extended Global Positioning System (GPS capabilities, Micro Electro Mechanical System (MEMS inertial sensors, extremely powerful computing power and very high resolution cameras. Using all of these components, smartphones have the potential to replace the traditional land MMS and portable GPS/GIS equipment. This paper introduces an innovative application of smartphones as a very low cost portable MMS for mapping and GIS applications.

  15. Smartphones Based Mobile Mapping Systems

    Science.gov (United States)

    Al-Hamad, A.; El-Sheimy, N.

    2014-06-01

    The past 20 years have witnessed an explosive growth in the demand for geo-spatial data. This demand has numerous sources and takes many forms; however, the net effect is an ever-increasing thirst for data that is more accurate, has higher density, is produced more rapidly, and is acquired less expensively. For mapping and Geographic Information Systems (GIS) projects, this has been achieved through the major development of Mobile Mapping Systems (MMS). MMS integrate various navigation and remote sensing technologies which allow mapping from moving platforms (e.g. cars, airplanes, boats, etc.) to obtain the 3D coordinates of the points of interest. Such systems obtain accuracies that are suitable for all but the most demanding mapping and engineering applications. However, this accuracy doesn't come cheaply. As a consequence of the platform and navigation and mapping technologies used, even an "inexpensive" system costs well over 200 000 USD. Today's mobile phones are getting ever more sophisticated. Phone makers are determined to reduce the gap between computers and mobile phones. Smartphones, in addition to becoming status symbols, are increasingly being equipped with extended Global Positioning System (GPS) capabilities, Micro Electro Mechanical System (MEMS) inertial sensors, extremely powerful computing power and very high resolution cameras. Using all of these components, smartphones have the potential to replace the traditional land MMS and portable GPS/GIS equipment. This paper introduces an innovative application of smartphones as a very low cost portable MMS for mapping and GIS applications.

  16. Estudo da densidade de ligações Cruzadas em géis superabsorventes obtidos do acetato de celulose Study of the crosslinking density in superabsorbent gels obtained from cellulose acetate

    Directory of Open Access Journals (Sweden)

    André M. Senna

    2013-01-01

    :3] and [3:1] PMDA mol/mol of free OH, respectively. A gel was synthesized in excess of 200% of PMDA in relation to free OH groups of the AC. The basis of the Flory-Rehner theory was used for determining crosslinking in the gels. Briefly, the main results showed that the crosslinking density increased proportionally to the amount of PMDA added to the reaction medium. Distinct AFM topographies were obtained for distinct gels, which were also different from the polymer cellulose acetate. This work was motivated by the technological importance of polymers from renewable sources such as cellulose, in which a cellulose derivative was developed with promising application in drug delivery and in adsorption of heavy metals in aqueous systems. The advantage of this cellulose acetate derivative is the use of fewer steps in its synthesis.

  17. Estudo da densidade de ligações Cruzadas em géis superabsorventes obtidos do acetato de celulose Study of the crosslinking density in superabsorbent gels obtained from cellulose acetate

    Directory of Open Access Journals (Sweden)

    André M. Senna

    2012-01-01

    :3] and [3:1] PMDA mol/mol of free OH, respectively. A gel was synthesized in excess of 200% of PMDA in relation to free OH groups of the AC. The basis of the Flory-Rehner theory was used for determining crosslinking in the gels. Briefly, the main results showed that the crosslinking density increased proportionally to the amount of PMDA added to the reaction medium. Distinct AFM topographies were obtained for distinct gels, which were also different from the polymer cellulose acetate. This work was motivated by the technological importance of polymers from renewable sources such as cellulose, in which a cellulose derivative was developed with promising application in drug delivery and in adsorption of heavy metals in aqueous systems. The advantage of this cellulose acetate derivative is the use of fewer steps in its synthesis.

  18. Effective electron-density map improvement and structure validation on a Linux multi-CPU web cluster: The TB Structural Genomics Consortium Bias Removal Web Service.

    Science.gov (United States)

    Reddy, Vinod; Swanson, Stanley M; Segelke, Brent; Kantardjieff, Katherine A; Sacchettini, James C; Rupp, Bernhard

    2003-12-01

    Anticipating a continuing increase in the number of structures solved by molecular replacement in high-throughput crystallography and drug-discovery programs, a user-friendly web service for automated molecular replacement, map improvement, bias removal and real-space correlation structure validation has been implemented. The service is based on an efficient bias-removal protocol, Shake&wARP, and implemented using EPMR and the CCP4 suite of programs, combined with various shell scripts and Fortran90 routines. The service returns improved maps, converted data files and real-space correlation and B-factor plots. User data are uploaded through a web interface and the CPU-intensive iteration cycles are executed on a low-cost Linux multi-CPU cluster using the Condor job-queuing package. Examples of map improvement at various resolutions are provided and include model completion and reconstruction of absent parts, sequence correction, and ligand validation in drug-target structures.

  19. Low-amplitude clustering in low-redshift 21-cm intensity maps cross-correlated with 2dF galaxy densities

    Science.gov (United States)

    Anderson, C. J.; Luciw, N. J.; Li, Y.-C.; Kuo, C. Y.; Yadav, J.; Masui, K. W.; Chang, T.-C.; Chen, X.; Oppermann, N.; Liao, Y.-W.; Pen, U.-L.; Price, D. C.; Staveley-Smith, L.; Switzer, E. R.; Timbie, P. T.; Wolz, L.

    2018-05-01

    We report results from 21-cm intensity maps acquired from the Parkes radio telescope and cross-correlated with galaxy maps from the 2dF galaxy survey. The data span the redshift range 0.057 clustering of neutral hydrogen (H I), a small correlation coefficient between optical galaxies and H I, or some combination of the two. Separating 2dF into red and blue galaxies, we find that red galaxies are much more weakly correlated with H I on k ˜ 1.5 h Mpc-1 scales, suggesting that H I is more associated with blue star-forming galaxies and tends to avoid red galaxies.

  20. SU-E-J-122: The CBCT Dose Calculation Using a Patient Specific CBCT Number to Mass Density Conversion Curve Based On a Novel Image Registration and Organ Mapping Method in Head-And-Neck Radiation Therapy

    International Nuclear Information System (INIS)

    Zhou, J; Lasio, G; Chen, S; Zhang, B; Langen, K; Prado, K; D’Souza, W; Yi, B; Huang, J

    2015-01-01

    Purpose: To develop a CBCT HU correction method using a patient specific HU to mass density conversion curve based on a novel image registration and organ mapping method for head-and-neck radiation therapy. Methods: There are three steps to generate a patient specific CBCT HU to mass density conversion curve. First, we developed a novel robust image registration method based on sparseness analysis to register the planning CT (PCT) and the CBCT. Second, a novel organ mapping method was developed to transfer the organs at risk (OAR) contours from the PCT to the CBCT and corresponding mean HU values of each OAR were measured in both the PCT and CBCT volumes. Third, a set of PCT and CBCT HU to mass density conversion curves were created based on the mean HU values of OARs and the corresponding mass density of the OAR in the PCT. Then, we compared our proposed conversion curve with the traditional Catphan phantom based CBCT HU to mass density calibration curve. Both curves were input into the treatment planning system (TPS) for dose calculation. Last, the PTV and OAR doses, DVH and dose distributions of CBCT plans are compared to the original treatment plan. Results: One head-and-neck cases which contained a pair of PCT and CBCT was used. The dose differences between the PCT and CBCT plans using the proposed method are −1.33% for the mean PTV, 0.06% for PTV D95%, and −0.56% for the left neck. The dose differences between plans of PCT and CBCT corrected using the CATPhan based method are −4.39% for mean PTV, 4.07% for PTV D95%, and −2.01% for the left neck. Conclusion: The proposed CBCT HU correction method achieves better agreement with the original treatment plan compared to the traditional CATPhan based calibration method

  1. SU-E-J-122: The CBCT Dose Calculation Using a Patient Specific CBCT Number to Mass Density Conversion Curve Based On a Novel Image Registration and Organ Mapping Method in Head-And-Neck Radiation Therapy

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, J [University of Maryland School of Medicine, Bel Air, MD (United States); Lasio, G; Chen, S; Zhang, B; Langen, K; Prado, K; D’Souza, W [University of Maryland School of Medicine, Baltimore, MD (United States); Yi, B [Univ. of Maryland School Of Medicine, Baltimore, MD (United States); Huang, J [University of Texas at Arlington, Arlington, TX (United States)

    2015-06-15

    Purpose: To develop a CBCT HU correction method using a patient specific HU to mass density conversion curve based on a novel image registration and organ mapping method for head-and-neck radiation therapy. Methods: There are three steps to generate a patient specific CBCT HU to mass density conversion curve. First, we developed a novel robust image registration method based on sparseness analysis to register the planning CT (PCT) and the CBCT. Second, a novel organ mapping method was developed to transfer the organs at risk (OAR) contours from the PCT to the CBCT and corresponding mean HU values of each OAR were measured in both the PCT and CBCT volumes. Third, a set of PCT and CBCT HU to mass density conversion curves were created based on the mean HU values of OARs and the corresponding mass density of the OAR in the PCT. Then, we compared our proposed conversion curve with the traditional Catphan phantom based CBCT HU to mass density calibration curve. Both curves were input into the treatment planning system (TPS) for dose calculation. Last, the PTV and OAR doses, DVH and dose distributions of CBCT plans are compared to the original treatment plan. Results: One head-and-neck cases which contained a pair of PCT and CBCT was used. The dose differences between the PCT and CBCT plans using the proposed method are −1.33% for the mean PTV, 0.06% for PTV D95%, and −0.56% for the left neck. The dose differences between plans of PCT and CBCT corrected using the CATPhan based method are −4.39% for mean PTV, 4.07% for PTV D95%, and −2.01% for the left neck. Conclusion: The proposed CBCT HU correction method achieves better agreement with the original treatment plan compared to the traditional CATPhan based calibration method.

  2. A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Puccinia hordei and of defence gene homologues

    NARCIS (Netherlands)

    Marcel, T.C.; Varshney, R.K.; Barbieri, M.; Jafary, H.; Kock, de M.J.D.; Graner, A.; Niks, R.E.

    2007-01-01

    A consensus map of barley was constructed based on three reference doubled haploid (DH) populations and three recombinant inbred line (RIL) populations. Several sets of microsatellites were used as bridge markers in the integration of those populations previously genotyped with RFLP or with AFLP

  3. Construction of a genome-anchored, high-density genetic map for melon (Cucumis melo L.) and identification of Fusarium oxysporum f. sp. melonis race 1 resistance QTL.

    Science.gov (United States)

    Branham, Sandra E; Levi, Amnon; Katawczik, Melanie; Fei, Zhangjun; Wechter, W Patrick

    2018-04-01

    Four QTLs and an epistatic interaction were associated with disease severity in response to inoculation with Fusarium oxysporum f. sp. melonis race 1 in a recombinant inbred line population of melon. The USDA Cucumis melo inbred line, MR-1, harbors a wealth of alleles associated with resistance to several major diseases of melon, including powdery mildew, downy mildew, Alternaria leaf blight, and Fusarium wilt. MR-1 was crossed to an Israeli cultivar, Ananas Yok'neam, which is susceptible to all of these diseases, to generate a recombinant inbred line (RIL) population of 172 lines. In this study, the RIL population was genotyped to construct an ultra-dense genetic linkage map with 5663 binned SNPs anchored to the C. melo genome and exhibits the overall high quality of the assembly. The utility of the densely genotyped population was demonstrated through QTL mapping of a well-studied trait, resistance to Fusarium wilt caused by Fusarium oxysporum f. sp. melonis (Fom) race 1. A major QTL co-located with the previously validated resistance gene Fom-2. In addition, three minor QTLs and an epistatic interaction contributing to Fom race 1 resistance were identified. The MR-1 × AY RIL population provides a valuable resource for future QTL mapping studies and marker-assisted selection of disease resistance in melon.

  4. Obtaining the conversion curve of CT numbers to electron density from the effective energy of the CT using the dummy SEFM; Obtencion de la curva de conversion de numeros TC a densidad electronica a partir de la energia efectiva del TC usando el maniqui de la SEFM

    Energy Technology Data Exchange (ETDEWEB)

    Martin-Viera Cueto, J. A.; Garcia Pareja, S.; Benitez Villegas, E. M.; Moreno Saiz, E. M.; Bodineau Gil, C.; Caudepon Moreno, F.

    2011-07-01

    The objective of this work is to obtain the conversion curve of Hounsfield units (A) versus electron densities using a mannequin with different tissue equivalent materials. This provides for the effective energy beam CT and is used to characterize the linear coefficients of absorption of different materials that comprise the dummy.

  5. Saturation of an intra-gene pool linkage map: towards a unified consensus linkage map for fine mapping and synteny analysis in common bean.

    Science.gov (United States)

    Galeano, Carlos H; Fernandez, Andrea C; Franco-Herrera, Natalia; Cichy, Karen A; McClean, Phillip E; Vanderleyden, Jos; Blair, Matthew W

    2011-01-01

    Map-based cloning and fine mapping to find genes of interest and marker assisted selection (MAS) requires good genetic maps with reproducible markers. In this study, we saturated the linkage map of the intra-gene pool population of common bean DOR364 × BAT477 (DB) by evaluating 2,706 molecular markers including SSR, SNP, and gene-based markers. On average the polymorphism rate was 7.7% due to the narrow genetic base between the parents. The DB linkage map consisted of 291 markers with a total map length of 1,788 cM. A consensus map was built using the core mapping populations derived from inter-gene pool crosses: DOR364 × G19833 (DG) and BAT93 × JALO EEP558 (BJ). The consensus map consisted of a total of 1,010 markers mapped, with a total map length of 2,041 cM across 11 linkage groups. On average, each linkage group on the consensus map contained 91 markers of which 83% were single copy markers. Finally, a synteny analysis was carried out using our highly saturated consensus maps compared with the soybean pseudo-chromosome assembly. A total of 772 marker sequences were compared with the soybean genome. A total of 44 syntenic blocks were identified. The linkage group Pv6 presented the most diverse pattern of synteny with seven syntenic blocks, and Pv9 showed the most consistent relations with soybean with just two syntenic blocks. Additionally, a co-linear analysis using common bean transcript map information against soybean coding sequences (CDS) revealed the relationship with 787 soybean genes. The common bean consensus map has allowed us to map a larger number of markers, to obtain a more complete coverage of the common bean genome. Our results, combined with synteny relationships provide tools to increase marker density in selected genomic regions to identify closely linked polymorphic markers for indirect selection, fine mapping or for positional cloning.

  6. Evaluation of the physico-chemical properties of nanocomposites of low density linear polyethylene and organophilic montmorillonite obtained by fusion; Avaliacao das propriedades fisico-quimicas de nanocompositos de polietileno linear de baixa densidade e montmorilonita organofilica obtidos por fusao

    Energy Technology Data Exchange (ETDEWEB)

    Arndt, Aline; Sandrin, Bianca M.; Pezzin, A.P.T., E-mail: anapezzin@yahoo.com.br [Universidade da Regiao de Joinville (UNIVILLE), SC (Brazil); Meier, Marcia M. [Universidade do Estado de Santa Catarina (UESC), Joinville, SC (Brazil). Departamento de Quimica; Balzer, Palova S. [Centro Universitario Unisociesc, Joinville, SC (Brazil). Departamento de Engenharia Mecanica; Tavares, Maria I.B. [Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ (Brazil). Laboratorio de Solucoes em Ralaxometria

    2016-07-01

    In this project they were produced and characterized nanocomposite organoclay applied to linear low density polyethylene in order to improve their physicochemical properties. Samples were produced by means of extrusion and injection process, varying proportions of nanoclay (2; 2.5; 3.0 and 3.5%) in LLDPE. Samples nanocomposites were characterized by TGA, DSC and Flammability test (UL-94). The TGA analysis showed that adding nanoclay increased thermal stability, especially for LLDPE / OMMT2,0 sample increased thermal stability at 4.4%. By DSC it was found that samples with nanoclay incorporation did not affect the Tm of LLDPE, though the increase of nanoclay raised the degree of crystallinity of the samples 52.7% in LLDPE / 2.5 OMMT sample. The flammability results show that the sample LLDPE / OMMT 2.0 showed a decrease of 37.77% in the flame propagation velocity. The NMR showed that the samples up LLDPE / 2.5 OM has an exfoliated nanocomposite formation. (author)

  7. Mapping earthworm communities in Europe

    NARCIS (Netherlands)

    Rutgers, M.; Orgiazzi, A.; Gardi, C.; Römbke, J.; Jansch, S.; Keith, A.; Neilson, R.; Boag, B.; Schmidt, O.; Murchie, A.K.; Blackshaw, R.P.; Pérès, G.; Cluzeau, D.; Guernion, M.; Briones, M.J.I.; Rodeiro, J.; Pineiro, R.; Diaz Cosin, D.J.; Sousa, J.P.; Suhadolc, M.; Kos, I.; Krogh, P.H.; Faber, J.H.; Mulder, C.; Bogte, J.J.; Wijnen, van H.J.; Schouten, A.J.; Zwart, de D.

    2016-01-01

    Existing data sets on earthworm communities in Europe were collected, harmonized, collated, modelled and depicted on a soil biodiversity map. Digital Soil Mapping was applied using multiple regressions relating relatively low density earthworm community data to soil characteristics, land use,

  8. Mapping out Map Libraries

    Directory of Open Access Journals (Sweden)

    Ferjan Ormeling

    2008-09-01

    Full Text Available Discussing the requirements for map data quality, map users and their library/archives environment, the paper focuses on the metadata the user would need for a correct and efficient interpretation of the map data. For such a correct interpretation, knowledge of the rules and guidelines according to which the topographers/cartographers work (such as the kind of data categories to be collected, and the degree to which these rules and guidelines were indeed followed are essential. This is not only valid for the old maps stored in our libraries and archives, but perhaps even more so for the new digital files as the format in which we now have to access our geospatial data. As this would be too much to ask from map librarians/curators, some sort of web 2.0 environment is sought where comments about data quality, completeness and up-to-dateness from knowledgeable map users regarding the specific maps or map series studied can be collected and tagged to scanned versions of these maps on the web. In order not to be subject to the same disadvantages as Wikipedia, where the ‘communis opinio’ rather than scholarship, seems to be decisive, some checking by map curators of this tagged map use information would still be needed. Cooperation between map curators and the International Cartographic Association ( ICA map and spatial data use commission to this end is suggested.

  9. Level densities

    International Nuclear Information System (INIS)

    Ignatyuk, A.V.

    1998-01-01

    For any applications of the statistical theory of nuclear reactions it is very important to obtain the parameters of the level density description from the reliable experimental data. The cumulative numbers of low-lying levels and the average spacings between neutron resonances are usually used as such data. The level density parameters fitted to such data are compiled in the RIPL Starter File for the tree models most frequently used in practical calculations: i) For the Gilber-Cameron model the parameters of the Beijing group, based on a rather recent compilations of the neutron resonance and low-lying level densities and included into the beijing-gc.dat file, are chosen as recommended. As alternative versions the parameters provided by other groups are given into the files: jaeri-gc.dat, bombay-gc.dat, obninsk-gc.dat. Additionally the iljinov-gc.dat, and mengoni-gc.dat files include sets of the level density parameters that take into account the damping of shell effects at high energies. ii) For the backed-shifted Fermi gas model the beijing-bs.dat file is selected as the recommended one. Alternative parameters of the Obninsk group are given in the obninsk-bs.dat file and those of Bombay in bombay-bs.dat. iii) For the generalized superfluid model the Obninsk group parameters included into the obninsk-bcs.dat file are chosen as recommended ones and the beijing-bcs.dat file is included as an alternative set of parameters. iv) For the microscopic approach to the level densities the files are: obninsk-micro.for -FORTRAN 77 source for the microscopical statistical level density code developed in Obninsk by Ignatyuk and coworkers, moller-levels.gz - Moeller single-particle level and ground state deformation data base, moller-levels.for -retrieval code for Moeller single-particle level scheme. (author)

  10. Regularity of optimal transport maps on multiple products of spheres

    OpenAIRE

    Figalli, Alessio; Kim, Young-Heon; McCann, Robert J.

    2010-01-01

    This article addresses regularity of optimal transport maps for cost="squared distance" on Riemannian manifolds that are products of arbitrarily many round spheres with arbitrary sizes and dimensions. Such manifolds are known to be non-negatively cross-curved [KM2]. Under boundedness and non-vanishing assumptions on the transfered source and target densities we show that optimal maps stay away from the cut-locus (where the cost exhibits singularity), and obtain injectivity and continuity of o...

  11. Landslide susceptibility map: from research to application

    Science.gov (United States)

    Fiorucci, Federica; Reichenbach, Paola; Ardizzone, Francesca; Rossi, Mauro; Felicioni, Giulia; Antonini, Guendalina

    2014-05-01

    qualitatively classifying the territory according to slope classes. For the Perugia Municipality the susceptibility map was obtained combining results of statistical multivariate models and landslide density map. In particular, in the first phase a susceptibility zonation was prepared using different single and combined probability statistical multivariate techniques. The zonation was then combined and compared with the landslide density map in order to reclassify the false negative (portion of the territory classified by the model as stable affected by slope failures). The semi-quantitative resulting map was classified in five susceptibility classes. For each class a set of technical regulation was established to manage the territory.

  12. A High-Density SNP Genetic Linkage Map and QTL Analysis of Growth-Related Traits in a Hybrid Family of Oysters (Crassostrea gigas × Crassostrea angulata Using Genotyping-by-Sequencing

    Directory of Open Access Journals (Sweden)

    Jinpeng Wang

    2016-05-01

    Full Text Available Oysters are among the most important species in global aquaculture. Crassostrea gigas, and its subspecies C. angulata, are the major cultured species. To determine the genetic basis of growth-related traits in oysters, we constructed a second-generation linkage map from 3367 single-nucleotide polymorphisms (SNPs based on genotyping-by-sequencing, genotyped from a C. gigas × C. angulata hybrid family. These 3367 SNPs were distributed on 1695 markers, which were assigned to 10 linkage groups. The genetic linkage map had a total length of 1084.3 cM, with an average of 0.8 cM between markers; it thus represents the densest genetic map constructed for oysters to date. Twenty-seven quantitative trait loci (QTL for five growth-related traits were detected. These QTL could explain 4.2–7.7% (mean = 5.4% of the phenotypic variation. In total, 50.8% of phenotypic variance for shell width, 7.7% for mass weight, and 34.1% for soft tissue weight were explained. The detected QTL were distributed among eight linkage groups, and more than half (16 were concentrated within narrow regions in their respective linkage groups. Thirty-eight annotated genes were identified within the QTL regions, two of which are key genes for carbohydrate metabolism. Other genes were found to participate in assembly and regulation of the actin cytoskeleton, signal transduction, and regulation of cell differentiation and development. The newly developed high-density genetic map, and the QTL and candidate genes identified provide a valuable genetic resource and a basis for marker-assisted selection for C. gigas and C. angulata.

  13. Improving the accuracy of S02 column densities and emission rates obtained from upward-looking UV-spectroscopic measurements of volcanic plumes by taking realistic radiative transfer into account

    Science.gov (United States)

    Kern, Christoph; Deutschmann, Tim; Werner, Cynthia; Sutton, A. Jeff; Elias, Tamar; Kelly, Peter J.

    2012-01-01

    Sulfur dioxide (SO2) is monitored using ultraviolet (UV) absorption spectroscopy at numerous volcanoes around the world due to its importance as a measure of volcanic activity and a tracer for other gaseous species. Recent studies have shown that failure to take realistic radiative transfer into account during the spectral retrieval of the collected data often leads to large errors in the calculated emission rates. Here, the framework for a new evaluation method which couples a radiative transfer model to the spectral retrieval is described. In it, absorption spectra are simulated, and atmospheric parameters are iteratively updated in the model until a best match to the measurement data is achieved. The evaluation algorithm is applied to two example Differential Optical Absorption Spectroscopy (DOAS) measurements conducted at Kilauea volcano (Hawaii). The resulting emission rates were 20 and 90% higher than those obtained with a conventional DOAS retrieval performed between 305 and 315 nm, respectively, depending on the different SO2 and aerosol loads present in the volcanic plume. The internal consistency of the method was validated by measuring and modeling SO2 absorption features in a separate wavelength region around 375 nm and comparing the results. Although additional information about the measurement geometry and atmospheric conditions is needed in addition to the acquired spectral data, this method for the first time provides a means of taking realistic three-dimensional radiative transfer into account when analyzing UV-spectral absorption measurements of volcanic SO2 plumes.

  14. A High-Density Genetic Map of Wild Emmer Wheat from the Karaca Dağ Region Provides New Evidence on the Structure and Evolution of Wheat Chromosomes

    Directory of Open Access Journals (Sweden)

    Chad Jorgensen

    2017-10-01

    Full Text Available Wild emmer (Triticum turgidum ssp. dicoccoides is a progenitor of all cultivated wheat grown today. It has been hypothesized that emmer was domesticated in the Karaca Dağ region in southeastern Turkey. A total of 445 recombinant inbred lines of T. turgidum ssp. durum cv. ‘Langdon’ x wild emmer accession PI 428082 from this region was developed and genotyped with the Illumina 90K single nucleotide polymorphism Infinium assay. A genetic map comprising 2,650 segregating markers was constructed. The order of the segregating markers and an additional 8,264 co-segregating markers in the Aegilops tauschii reference genome sequence was used to compare synteny of the tetraploid wheat with the Brachypodium distachyon, rice, and sorghum. These comparisons revealed the presence of 15 structural chromosome rearrangements, in addition to the already known 4A-5A-7B rearrangements. The most common type was an intra-chromosomal translocation in which the translocated segment was short and was translocated only a short distance along the chromosome. A large reciprocal translocation, one small non-reciprocal translocation, and three large and one small paracentric inversions were also discovered. The use of inversions for a phylogeny reconstruction in the Triticum–Aegilops alliance was illustrated. The genetic map was inconsistent with the current model of evolution of the rearranged chromosomes 4A-5A-7B. Genetic diversity in the rearranged chromosome 4A showed that the rearrangements might have been contemporary with wild emmer speciation. A selective sweep was found in the centromeric region of chromosome 4A in Karaca Dağ wild emmer but not in 4A of T. aestivum. The absence of diversity from a large portion of chromosome 4A of wild emmer, believed to be ancestral to all domesticated wheat, is puzzling.

  15. Discovery and fine-mapping of adiposity loci using high density imputation of genome-wide association studies in individuals of African ancestry: African Ancestry Anthropometry Genetics Consortium.

    Science.gov (United States)

    Ng, Maggie C Y; Graff, Mariaelisa; Lu, Yingchang; Justice, Anne E; Mudgal, Poorva; Liu, Ching-Ti; Young, Kristin; Yanek, Lisa R; Feitosa, Mary F; Wojczynski, Mary K; Rand, Kristin; Brody, Jennifer A; Cade, Brian E; Dimitrov, Latchezar; Duan, Qing; Guo, Xiuqing; Lange, Leslie A; Nalls, Michael A; Okut, Hayrettin; Tajuddin, Salman M; Tayo, Bamidele O; Vedantam, Sailaja; Bradfield, Jonathan P; Chen, Guanjie; Chen, Wei-Min; Chesi, Alessandra; Irvin, Marguerite R; Padhukasahasram, Badri; Smith, Jennifer A; Zheng, Wei; Allison, Matthew A; Ambrosone, Christine B; Bandera, Elisa V; Bartz, Traci M; Berndt, Sonja I; Bernstein, Leslie; Blot, William J; Bottinger, Erwin P; Carpten, John; Chanock, Stephen J; Chen, Yii-Der Ida; Conti, David V; Cooper, Richard S; Fornage, Myriam; Freedman, Barry I; Garcia, Melissa; Goodman, Phyllis J; Hsu, Yu-Han H; Hu, Jennifer; Huff, Chad D; Ingles, Sue A; John, Esther M; Kittles, Rick; Klein, Eric; Li, Jin; McKnight, Barbara; Nayak, Uma; Nemesure, Barbara; Ogunniyi, Adesola; Olshan, Andrew; Press, Michael F; Rohde, Rebecca; Rybicki, Benjamin A; Salako, Babatunde; Sanderson, Maureen; Shao, Yaming; Siscovick, David S; Stanford, Janet L; Stevens, Victoria L; Stram, Alex; Strom, Sara S; Vaidya, Dhananjay; Witte, John S; Yao, Jie; Zhu, Xiaofeng; Ziegler, Regina G; Zonderman, Alan B; Adeyemo, Adebowale; Ambs, Stefan; Cushman, Mary; Faul, Jessica D; Hakonarson, Hakon; Levin, Albert M; Nathanson, Katherine L; Ware, Erin B; Weir, David R; Zhao, Wei; Zhi, Degui; Arnett, Donna K; Grant, Struan F A; Kardia, Sharon L R; Oloapde, Olufunmilayo I; Rao, D C; Rotimi, Charles N; Sale, Michele M; Williams, L Keoki; Zemel, Babette S; Becker, Diane M; Borecki, Ingrid B; Evans, Michele K; Harris, Tamara B; Hirschhorn, Joel N; Li, Yun; Patel, Sanjay R; Psaty, Bruce M; Rotter, Jerome I; Wilson, James G; Bowden, Donald W; Cupples, L Adrienne; Haiman, Christopher A; Loos, Ruth J F; North, Kari E

    2017-04-01

    Genome-wide association studies (GWAS) have identified >300 loci associated with measures of adiposity including body mass index (BMI) and waist-to-hip ratio (adjusted for BMI, WHRadjBMI), but few have been identified through screening of the African ancestry genomes. We performed large scale meta-analyses and replications in up to 52,895 individuals for BMI and up to 23,095 individuals for WHRadjBMI from the African Ancestry Anthropometry Genetics Consortium (AAAGC) using 1000 Genomes phase 1 imputed GWAS to improve coverage of both common and low frequency variants in the low linkage disequilibrium African ancestry genomes. In the sex-combined analyses, we identified one novel locus (TCF7L2/HABP2) for WHRadjBMI and eight previously established loci at P African ancestry individuals. An additional novel locus (SPRYD7/DLEU2) was identified for WHRadjBMI when combined with European GWAS. In the sex-stratified analyses, we identified three novel loci for BMI (INTS10/LPL and MLC1 in men, IRX4/IRX2 in women) and four for WHRadjBMI (SSX2IP, CASC8, PDE3B and ZDHHC1/HSD11B2 in women) in individuals of African ancestry or both African and European ancestry. For four of the novel variants, the minor allele frequency was low (African ancestry sex-combined and sex-stratified analyses, 26 BMI loci and 17 WHRadjBMI loci contained ≤ 20 variants in the credible sets that jointly account for 99% posterior probability of driving the associations. The lead variants in 13 of these loci had a high probability of being causal. As compared to our previous HapMap imputed GWAS for BMI and WHRadjBMI including up to 71,412 and 27,350 African ancestry individuals, respectively, our results suggest that 1000 Genomes imputation showed modest improvement in identifying GWAS loci including low frequency variants. Trans-ethnic meta-analyses further improved fine mapping of putative causal variants in loci shared between the African and European ancestry populations.

  16. Obtaining of inulin acetate

    OpenAIRE

    Khusenov, Arslonnazar; Rakhmanberdiev, Gappar; Rakhimov, Dilshod; Khalikov, Muzaffar

    2014-01-01

    In the article first obtained inulin ester inulin acetate, by etherification of inulin with acetic anhydride has been exposed. Obtained product has been studied using elementary analysis and IR spectroscopy.

  17. Reduction of density-modification bias by β correction

    International Nuclear Information System (INIS)

    Skubák, Pavol; Pannu, Navraj S.

    2011-01-01

    A cross-validation-based method for bias reduction in ‘classical’ iterative density modification of experimental X-ray crystallography maps provides significantly more accurate phase-quality estimates and leads to improved automated model building. Density modification often suffers from an overestimation of phase quality, as seen by escalated figures of merit. A new cross-validation-based method to address this estimation bias by applying a bias-correction parameter ‘β’ to maximum-likelihood phase-combination functions is proposed. In tests on over 100 single-wavelength anomalous diffraction data sets, the method is shown to produce much more reliable figures of merit and improved electron-density maps. Furthermore, significantly better results are obtained in automated model building iterated with phased refinement using the more accurate phase probability parameters from density modification

  18. Densities of carbon foils

    International Nuclear Information System (INIS)

    Stoner, J.O. Jr.

    1991-01-01

    The densities of arc-evaporated carbon target foils have been measured by several methods. The density depends upon the method used to measure it; for the same surface density, values obtained by different measurement techniques may differ by fifty percent or more. The most reliable density measurements are by flotation, yielding a density of 2.01±0.03 g cm -3 , and interferometric step height with the surface density known from auxiliary measurements, yielding a density of 2.61±0.4 g cm -3 . The difference between these density values mayy be due in part to the compressive stresses that carbon films have while still on their substrates, uncertainties in the optical calibration of surface densities of carbon foils, and systematic errors in step-height measurements. Mechanical thickness measurements by micrometer caliper are unreliable due to nonplanarity of these foils. (orig.)

  19. TU-AB-BRA-03: Atlas-Based Algorithms with Local Registration-Goodness Weighting for MRI-Driven Electron Density Mapping

    Energy Technology Data Exchange (ETDEWEB)

    Farjam, R; Tyagi, N [Memorial Sloan-Kettering Cancer Center, New York, NY (United States); Veeraraghavan, H; Apte, A; Zakian, K; Deasy, J [Memorial Sloan Kettering Cancer Center, New York, NY (United States); Hunt, M [Mem Sloan-Kettering Cancer Center, New York, NY (United States)

    2016-06-15

    Purpose: To develop image-analysis algorithms to synthesize CT with accurate electron densities for MR-only radiotherapy of head & neck (H&N) and pelvis anatomies. Methods: CT and 3T-MRI (Philips, mDixon sequence) scans were randomly selected from a pool of H&N (n=11) and pelvis (n=12) anatomies to form an atlas. All MRIs were pre-processed to eliminate scanner and patient-induced intensity inhomogeneities and standardize their intensity histograms. CT and MRI for each patient were then co-registered to construct CT-MRI atlases. For more accurate CT-MR fusion, bone intensities in CT were suppressed to improve the similarity between CT and MRI. For a new patient, all CT-MRI atlases are deformed onto the new patients’ MRI initially. A newly-developed generalized registration error (GRE) metric was then calculated as a measure of local registration accuracy. The synthetic CT value at each point is a 1/GRE-weighted average of CTs from all CT-MR atlases. For evaluation, the mean absolute error (MAE) between the original and synthetic CT (generated in a leave-one-out scheme) was computed. The planning dose from the original and synthetic CT was also compared. Results: For H&N patients, MAE was 67±9, 114±22, and 116±9 HU over the entire-CT, air and bone regions, respectively. For pelvis anatomy, MAE was 47±5 and 146±14 for the entire and bone regions. In comparison with MIRADA medical, an FDA-approved registration tool, we found that our proposed registration strategy reduces MAE by ∼30% and ∼50% over the entire and bone regions, respectively. GRE-weighted strategy further lowers MAE by ∼15% to ∼40%. Our primary dose calculation also showed highly consistent results between the original and synthetic CT. Conclusion: We’ve developed a novel image-analysis technique to synthesize CT for H&N and pelvis anatomies. Our proposed image fusion strategy and GRE metric help generate more accurate synthetic CT using locally more similar atlases (Support: Philips

  20. TU-AB-BRA-03: Atlas-Based Algorithms with Local Registration-Goodness Weighting for MRI-Driven Electron Density Mapping

    International Nuclear Information System (INIS)

    Farjam, R; Tyagi, N; Veeraraghavan, H; Apte, A; Zakian, K; Deasy, J; Hunt, M

    2016-01-01

    Purpose: To develop image-analysis algorithms to synthesize CT with accurate electron densities for MR-only radiotherapy of head & neck (H&N) and pelvis anatomies. Methods: CT and 3T-MRI (Philips, mDixon sequence) scans were randomly selected from a pool of H&N (n=11) and pelvis (n=12) anatomies to form an atlas. All MRIs were pre-processed to eliminate scanner and patient-induced intensity inhomogeneities and standardize their intensity histograms. CT and MRI for each patient were then co-registered to construct CT-MRI atlases. For more accurate CT-MR fusion, bone intensities in CT were suppressed to improve the similarity between CT and MRI. For a new patient, all CT-MRI atlases are deformed onto the new patients’ MRI initially. A newly-developed generalized registration error (GRE) metric was then calculated as a measure of local registration accuracy. The synthetic CT value at each point is a 1/GRE-weighted average of CTs from all CT-MR atlases. For evaluation, the mean absolute error (MAE) between the original and synthetic CT (generated in a leave-one-out scheme) was computed. The planning dose from the original and synthetic CT was also compared. Results: For H&N patients, MAE was 67±9, 114±22, and 116±9 HU over the entire-CT, air and bone regions, respectively. For pelvis anatomy, MAE was 47±5 and 146±14 for the entire and bone regions. In comparison with MIRADA medical, an FDA-approved registration tool, we found that our proposed registration strategy reduces MAE by ∼30% and ∼50% over the entire and bone regions, respectively. GRE-weighted strategy further lowers MAE by ∼15% to ∼40%. Our primary dose calculation also showed highly consistent results between the original and synthetic CT. Conclusion: We’ve developed a novel image-analysis technique to synthesize CT for H&N and pelvis anatomies. Our proposed image fusion strategy and GRE metric help generate more accurate synthetic CT using locally more similar atlases (Support: Philips

  1. Unique Microstructural Changes in the Brain Associated with Urological Chronic Pelvic Pain Syndrome (UCPPS Revealed by Diffusion Tensor MRI, Super-Resolution Track Density Imaging, and Statistical Parameter Mapping: A MAPP Network Neuroimaging Study.

    Directory of Open Access Journals (Sweden)

    Davis Woodworth

    Full Text Available Studies have suggested chronic pain syndromes are associated with neural reorganization in specific regions associated with perception, processing, and integration of pain. Urological chronic pelvic pain syndrome (UCPPS represents a collection of pain syndromes characterized by pelvic pain, namely Chronic Prostatitis/Chronic Pelvic Pain Syndrome (CP/CPPS and Interstitial Cystitis/Painful Bladder Syndrome (IC/PBS, that are both poorly understood in their pathophysiology, and treated ineffectively. We hypothesized patients with UCPPS may have microstructural differences in the brain compared with healthy control subjects (HCs, as well as patients with irritable bowel syndrome (IBS, a common gastrointestinal pain disorder. In the current study we performed population-based voxel-wise DTI and super-resolution track density imaging (TDI in a large, two-center sample of phenotyped patients from the multicenter cohort with UCPPS (N = 45, IBS (N = 39, and HCs (N = 56 as part of the MAPP Research Network. Compared with HCs, UCPPS patients had lower fractional anisotropy (FA, lower generalized anisotropy (GA, lower track density, and higher mean diffusivity (MD in brain regions commonly associated with perception and integration of pain information. Results also showed significant differences in specific anatomical regions in UCPPS patients when compared with IBS patients, consistent with microstructural alterations specific to UCPPS. While IBS patients showed clear sex related differences in FA, MD, GA, and track density consistent with previous reports, few such differences were observed in UCPPS patients. Heat maps illustrating the correlation between specific regions of interest and various pain and urinary symptom scores showed clustering of significant associations along the cortico-basal ganglia-thalamic-cortical loop associated with pain integration, modulation, and perception. Together, results suggest patients with UCPPS have extensive

  2. Polycrystal model of the mechanical behavior of a Mo–TiC30vol.% metal–ceramic composite using a three-dimensional microstructure map obtained by dual beam focused ion beam scanning electron microscopy

    International Nuclear Information System (INIS)

    Cédat, D.; Fandeur, O.; Rey, C.; Raabe, D.

    2012-01-01

    The mechanical behavior of a Mo–TiC 30vol.% ceramic–metal composite was investigated over a wide temperature range (25–700 °C). High-energy X-ray tomography was used to reveal percolation of the hard titanium carbide phase through the composite. Using a polycrystal approach for a two-phase material, finite-element simulations were performed on a real three-dimensional (3-D) aggregate of the material. The 3-D microstructure, used as the starting configuration for the predictions, was obtained by serial sectioning in a dual beam focused ion beam scanning electron microscope coupled to an electron backscattered diffraction system. The 3-D aggregate consists of a molybdenum matrix and a percolating TiC skeleton. As for most body-centered cubic (bcc) metals, the molybdenum matrix phase is characterized by a change in plasticity mechanism with temperature. We used a polycrystal model for bcc materials which was extended to two phases (TiC and Mo). The model parameters of the matrix were determined from experiments on pure molydenum. For all temperatures investigated the TiC particles were considered to be brittle. Gradual damage to the TiC particles was treated, based on an accumulative failure law that is approximated by evolution of the apparent particle elastic stiffness. The model enabled us to determine the evolution of the local mechanical fields with deformation and temperature. We showed that a 3-D aggregate representing the actual microstructure of the composite is required to understand the local and global mechanical properties of the composite studied.

  3. Ergodicity of polygonal slap maps

    International Nuclear Information System (INIS)

    Del Magno, Gianluigi; Pedro Gaivão, José; Lopes Dias, João; Duarte, Pedro

    2014-01-01

    Polygonal slap maps are piecewise affine expanding maps of the interval obtained by projecting the sides of a polygon along their normals onto the perimeter of the polygon. These maps arise in the study of polygonal billiards with non-specular reflection laws. We study the absolutely continuous invariant probabilities (acips) of the slap maps for several polygons, including regular polygons and triangles. We also present a general method for constructing polygons with slap maps with more than one ergodic acip. (paper)

  4. Analysis of multiplex gene expression maps obtained by voxelation

    OpenAIRE

    An, L; Xie, H; Chin, MH; Obradovic, Z; Smith, DJ; Megalooikonomou, V

    2009-01-01

    Abstract Background Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological disease. Researchers have previously used voxelation in combination with microarrays for acquisition of genome-wide atlases of expression patterns in the mouse brain. On the other hand, some work has been performed on studying gene functions, without taking into account the location information of a gene's expression in a mouse brain. In this paper, we presen...

  5. Road density

    Data.gov (United States)

    U.S. Environmental Protection Agency — Road density is generally highly correlated with amount of developed land cover. High road densities usually indicate high levels of ecological disturbance. More...

  6. Statistical density modification using local pattern matching

    International Nuclear Information System (INIS)

    Terwilliger, Thomas C.

    2003-01-01

    Statistical density modification can make use of local patterns of density found in protein structures to improve crystallographic phases. A method for improving crystallographic phases is presented that is based on the preferential occurrence of certain local patterns of electron density in macromolecular electron-density maps. The method focuses on the relationship between the value of electron density at a point in the map and the pattern of density surrounding this point. Patterns of density that can be superimposed by rotation about the central point are considered equivalent. Standard templates are created from experimental or model electron-density maps by clustering and averaging local patterns of electron density. The clustering is based on correlation coefficients after rotation to maximize the correlation. Experimental or model maps are also used to create histograms relating the value of electron density at the central point to the correlation coefficient of the density surrounding this point with each member of the set of standard patterns. These histograms are then used to estimate the electron density at each point in a new experimental electron-density map using the pattern of electron density at points surrounding that point and the correlation coefficient of this density to each of the set of standard templates, again after rotation to maximize the correlation. The method is strengthened by excluding any information from the point in question from both the templates and the local pattern of density in the calculation. A function based on the origin of the Patterson function is used to remove information about the electron density at the point in question from nearby electron density. This allows an estimation of the electron density at each point in a map, using only information from other points in the process. The resulting estimates of electron density are shown to have errors that are nearly independent of the errors in the original map using

  7. Maximum entropy reconstruction of spin densities involving non uniform prior

    International Nuclear Information System (INIS)

    Schweizer, J.; Ressouche, E.; Papoular, R.J.; Zheludev, A.I.

    1997-01-01

    Diffraction experiments give microscopic information on structures in crystals. A method which uses the concept of maximum of entropy (MaxEnt), appears to be a formidable improvement in the treatment of diffraction data. This method is based on a bayesian approach: among all the maps compatible with the experimental data, it selects that one which has the highest prior (intrinsic) probability. Considering that all the points of the map are equally probable, this probability (flat prior) is expressed via the Boltzman entropy of the distribution. This method has been used for the reconstruction of charge densities from X-ray data, for maps of nuclear densities from unpolarized neutron data as well as for distributions of spin density. The density maps obtained by this method, as compared to those resulting from the usual inverse Fourier transformation, are tremendously improved. In particular, any substantial deviation from the background is really contained in the data, as it costs entropy compared to a map that would ignore such features. However, in most of the cases, before the measurements are performed, some knowledge exists about the distribution which is investigated. It can range from the simple information of the type of scattering electrons to an elaborate theoretical model. In these cases, the uniform prior which considers all the different pixels as equally likely, is too weak a requirement and has to be replaced. In a rigorous bayesian analysis, Skilling has shown that prior knowledge can be encoded into the Maximum Entropy formalism through a model m(rvec r), via a new definition for the entropy given in this paper. In the absence of any data, the maximum of the entropy functional is reached for ρ(rvec r) = m(rvec r). Any substantial departure from the model, observed in the final map, is really contained in the data as, with the new definition, it costs entropy. This paper presents illustrations of model testing

  8. A method for age-matched OCT angiography deviation mapping in the assessment of disease- related changes to the radial peripapillary capillaries.

    Science.gov (United States)

    Pinhas, Alexander; Linderman, Rachel; Mo, Shelley; Krawitz, Brian D; Geyman, Lawrence S; Carroll, Joseph; Rosen, Richard B; Chui, Toco Y

    2018-01-01

    To present a method for age-matched deviation mapping in the assessment of disease-related changes to the radial peripapillary capillaries (RPCs). We reviewed 4.5x4.5mm en face peripapillary OCT-A scans of 133 healthy control eyes (133 subjects, mean 41.5 yrs, range 11-82 yrs) and 4 eyes with distinct retinal pathologies, obtained using spectral-domain optical coherence tomography angiography. Statistical analysis was performed to evaluate the impact of age on RPC perfusion densities. RPC density group mean and standard deviation maps were generated for each decade of life. Deviation maps were created for the diseased eyes based on these maps. Large peripapillary vessel (LPV; noncapillary vessel) perfusion density was also studied for impact of age. Average healthy RPC density was 42.5±1.47%. ANOVA and pairwise Tukey-Kramer tests showed that RPC density in the ≥60yr group was significantly lower compared to RPC density in all younger decades of life (pDeviation mapping enabled us to quantitatively and visually elucidate the significance of RPC density changes in disease. It is important to consider changes that occur with aging when analyzing RPC and LPV density changes in disease. RPC density, coupled with age-matched deviation mapping techniques, represents a potentially clinically useful method in detecting changes to peripapillary perfusion in disease.

  9. Lung density

    DEFF Research Database (Denmark)

    Garnett, E S; Webber, C E; Coates, G

    1977-01-01

    The density of a defined volume of the human lung can be measured in vivo by a new noninvasive technique. A beam of gamma-rays is directed at the lung and, by measuring the scattered gamma-rays, lung density is calculated. The density in the lower lobe of the right lung in normal man during quiet...... breathing in the sitting position ranged from 0.25 to 0.37 g.cm-3. Subnormal values were found in patients with emphsema. In patients with pulmonary congestion and edema, lung density values ranged from 0.33 to 0.93 g.cm-3. The lung density measurement correlated well with the findings in chest radiographs...... but the lung density values were more sensitive indices. This was particularly evident in serial observations of individual patients....

  10. Genome-wide identification of QTL for seed yield and yield-related traits and construction of a high-density consensus map for QTL comparison in Brassica napus

    Directory of Open Access Journals (Sweden)

    Weiguo eZhao

    2016-01-01

    Full Text Available Seed yield (SY is the most important trait in rapeseed, which was determined by multiple seed yield-related traits (SYRTs and also easily subject to environmental influence. Lots of quantitative trait loci (QTL for SY and SYRTs were reported in Brassica napus. However, no studies have focused on SY and seven agronomic traits affecting SY simultaneous. Genome-wide QTL analysis for SY and seven SYRTs in eight environments was conducted in a doubled haploid population containing 348 lines. Totally, 18 and 208 QTLs for SY and SYRTs were observed, respectively, and then these QTLs were integrated into 144 consensus QTLs by a meta-analysis. Three major QTLs for SY were observed, including cqSY-C6-2 and cqSY-C6-3 that expressed stably in winter cultivation area for three years and cqSY-A2-2 only expressed in spring rapeseed area. Trait-by-trait meta-analysis revealed that the 144 consensus QTLs were integrated into 72 pleiotropic unique QTLs. Among them, all the unique QTLs affected SY, except for uq-A6-1, including uq.A2-3, uq.C1-2, uq.C1-3, uq.C6-1, uq.C6-5 and uq.C6-6 could also affect more than two SYRTs. According to high density consensus map construction and QTL comparison from literature, 36 QTLs from five populations were co-localized with QTLs identified in this study. In addition, 13 orthologs genes were observed, including five each genes for SY and SW, one each gene for BY, BH and PH, respectively. The genomic information of these QTLs would be valuable in hybrid cultivar breeding, and be helpful to analyze QTL expression in different environments.

  11. Two-mode Gaussian density matrices and squeezing of photons

    International Nuclear Information System (INIS)

    Tucci, R.R.

    1992-01-01

    In this paper, the authors generalize to 2-mode states the 1-mode state results obtained in a previous paper. The authors study 2-mode Gaussian density matrices. The authors find a linear transformation which maps the two annihilation operators, one for each mode, into two new annihilation operators that are uncorrelated and unsqueezed. This allows the authors to express the density matrix as a product of two 1-mode density matrices. The authors find general conditions under which 2-mode Gaussian density matrices become pure states. Possible pure states include the 2-mode squeezed pure states commonly mentioned in the literature, plus other pure states never mentioned before. The authors discuss the entropy and thermodynamic laws (Second Law, Fundamental Equation, and Gibbs-Duhem Equation) for the 2-mode states being considered

  12. Surface Snow Density of East Antarctica Derived from In-Situ Observations

    Science.gov (United States)

    Tian, Y.; Zhang, S.; Du, W.; Chen, J.; Xie, H.; Tong, X.; Li, R.

    2018-04-01

    Models based on physical principles or semi-empirical parameterizations have used to compute the firn density, which is essential for the study of surface processes in the Antarctic ice sheet. However, parameterization of surface snow density is often challenged by the description of detailed local characterization. In this study we propose to generate a surface density map for East Antarctica from all the filed observations that are available. Considering that the observations are non-uniformly distributed around East Antarctica, obtained by different methods, and temporally inhomogeneous, the field observations are used to establish an initial density map with a grid size of 30 × 30 km2 in which the observations are averaged at a temporal scale of five years. We then construct an observation matrix with its columns as the map grids and rows as the temporal scale. If a site has an unknown density value for a period, we will set it to 0 in the matrix. In order to construct the main spatial and temple information of surface snow density matrix we adopt Empirical Orthogonal Function (EOF) method to decompose the observation matrix and only take first several lower-order modes, because these modes already contain most information of the observation matrix. However, there are a lot of zeros in the matrix and we solve it by using matrix completion algorithm, and then we derive the time series of surface snow density at each observation site. Finally, we can obtain the surface snow density by multiplying the modes interpolated by kriging with the corresponding amplitude of the modes. Comparative analysis have done between our surface snow density map and model results. The above details will be introduced in the paper.

  13. Computational methods for constructing protein structure models from 3D electron microscopy maps.

    Science.gov (United States)

    Esquivel-Rodríguez, Juan; Kihara, Daisuke

    2013-10-01

    Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided. Copyright © 2013 Elsevier Inc. All rights reserved.

  14. Report for fiscal 1982 on comprehensive survey for nationwide geothermal resources. Preparation of lineament density maps - radar image analyses - in north-eastern area; 1982 nendo zenkoku chinetsu shigen sogo chosa hokokusho. Lineament mitsudozu sakusei (radar gazo kaiseki (Tohoku chiiki))

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1983-03-01

    Geological structure analysis maps and lineament maps were prepared on the north-eastern area and parts of the ancillary areas thereof by analyzing radar images of a 1 to 200,000 scale. With regard to the geological structures, analyses were performed by using as the original data the north look radar images for the three special geothermal areas to have prepared the geological structure analysis maps. The analysis of the radar images identified ground bed boundary lines in more detail than in the existing geological maps, and new discoveries were made available on faults. The lineament maps were compiled by implanting into respectively corresponding topographic maps the 24 N-S lineament maps made by the west look radar images for the whole surveyed areas, and the 16 E-W lineament maps made by the north look radar images for the special geothermal areas. Based on the clarity and characteristics deciphered on the images, the lineaments were classified into the major, minor, and subtle lineaments, which were indicated on the lineament maps. The lineaments were digitized by positions of the edge points, and the histograms and statistical tables were prepared by computer processing. (NEDO)

  15. Mapping earthworm communities in Europe

    DEFF Research Database (Denmark)

    Rutgers, Michiel; Orgiazzi, Alberto; Gardi, Ciro

    Existing data sets on earthworm communities in Europe were collected, harmonized, modelled and depicted on a soil biodiversity map of Europe. Digital Soil Mapping was applied using multiple regressions relating relatively low density earthworm community data to soil characteristics, land use...

  16. Cosmic string induced CMB maps

    International Nuclear Information System (INIS)

    Landriau, M.; Shellard, E. P. S.

    2011-01-01

    We compute maps of CMB temperature fluctuations seeded by cosmic strings using high resolution simulations of cosmic strings in a Friedmann-Robertson-Walker universe. We create full-sky, 18 deg. and 3 deg. CMB maps, including the relevant string contribution at each resolution from before recombination to today. We extract the angular power spectrum from these maps, demonstrating the importance of recombination effects. We briefly discuss the probability density function of the pixel temperatures, their skewness, and kurtosis.

  17. Redox potential distribution of an organic-rich contaminated site obtained by the inversion of self-potential data

    Science.gov (United States)

    Abbas, M.; Jardani, A.; Soueid Ahmed, A.; Revil, A.; Brigaud, L.; Bégassat, Ph.; Dupont, J. P.

    2017-11-01

    Mapping the redox potential of shallow aquifers impacted by hydrocarbon contaminant plumes is important for the characterization and remediation of such contaminated sites. The redox potential of groundwater is indicative of the biodegradation of hydrocarbons and is important in delineating the shapes of contaminant plumes. The self-potential method was used to reconstruct the redox potential of groundwater associated with an organic-rich contaminant plume in northern France. The self-potential technique is a passive technique consisting in recording the electrical potential distribution at the surface of the Earth. A self-potential map is essentially the sum of two contributions, one associated with groundwater flow referred to as the electrokinetic component, and one associated with redox potential anomalies referred to as the electroredox component (thermoelectric and diffusion potentials are generally negligible). A groundwater flow model was first used to remove the electrokinetic component from the observed self-potential data. Then, a residual self-potential map was obtained. The source current density generating the residual self-potential signals is assumed to be associated with the position of the water table, an interface characterized by a change in both the electrical conductivity and the redox potential. The source current density was obtained through an inverse problem by minimizing a cost function including a data misfit contribution and a regularizer. This inversion algorithm allows the determination of the vertical and horizontal components of the source current density taking into account the electrical conductivity distribution of the saturated and non-saturated zones obtained independently by electrical resistivity tomography. The redox potential distribution was finally determined from the inverted residual source current density. A redox map was successfully built and the estimated redox potential values correlated well with in

  18. Powder densification maps in Selective Laser Sintering

    International Nuclear Information System (INIS)

    Bourell, D.; Wohlert, M.; Harlan, N.; Beaman, J.; Das, S.

    2002-01-01

    Selective Laser Sintering (SLS) is a manufacturing process in which a part is produced without the need for part-specific tooling. It competes effectively with other manufacturing processes when part geometry is complex and the production run is not large. Traditionally, this was limited to prototype production, although tooling applications are now appearing. This paper describes several applications of powder densification maps to advance solutions in direct SLS of metallic and ceramic powders. Time-dependent plasticity issues arise in pre-processing of powder to make it suitable for SLS and in post-processing of SLS parts to obtain desired density. (Abstract Copyright [2002], Wiley Periodicals, Inc.)

  19. Density of liquid Ytterbium

    International Nuclear Information System (INIS)

    Stankus, S.V.; Basin, A.S.

    1983-01-01

    Results are presented for measurements of the density of metallic ytterbium in the liquid state and at the liquid-solid phase transition. Based on the numerical data obtained, the coefficient of thermal expansion βZ of the liquid and the density discontinuity on melting deltarho/sub m/ are calculated. The magnitudes of βZ and deltarho/sub m/ for the heavy lanthanides are compared

  20. Low Bone Density

    Science.gov (United States)

    ... Density Exam/Testing › Low Bone Density Low Bone Density Low bone density is when your bone density ... people with normal bone density. Detecting Low Bone Density A bone density test will determine whether you ...

  1. Topographic mapping

    Science.gov (United States)

    ,

    2008-01-01

    The U.S. Geological Survey (USGS) produced its first topographic map in 1879, the same year it was established. Today, more than 100 years and millions of map copies later, topographic mapping is still a central activity for the USGS. The topographic map remains an indispensable tool for government, science, industry, and leisure. Much has changed since early topographers traveled the unsettled West and carefully plotted the first USGS maps by hand. Advances in survey techniques, instrumentation, and design and printing technologies, as well as the use of aerial photography and satellite data, have dramatically improved mapping coverage, accuracy, and efficiency. Yet cartography, the art and science of mapping, may never before have undergone change more profound than today.

  2. Navigating 3D electron microscopy maps with EM-SURFER.

    Science.gov (United States)

    Esquivel-Rodríguez, Juan; Xiong, Yi; Han, Xusi; Guang, Shuomeng; Christoffer, Charles; Kihara, Daisuke

    2015-05-30

    The Electron Microscopy DataBank (EMDB) is growing rapidly, accumulating biological structural data obtained mainly by electron microscopy and tomography, which are emerging techniques for determining large biomolecular complex and subcellular structures. Together with the Protein Data Bank (PDB), EMDB is becoming a fundamental resource of the tertiary structures of biological macromolecules. To take full advantage of this indispensable resource, the ability to search the database by structural similarity is essential. However, unlike high-resolution structures stored in PDB, methods for comparing low-resolution electron microscopy (EM) density maps in EMDB are not well established. We developed a computational method for efficiently searching low-resolution EM maps. The method uses a compact fingerprint representation of EM maps based on the 3D Zernike descriptor, which is derived from a mathematical series expansion for EM maps that are considered as 3D functions. The method is implemented in a web server named EM-SURFER, which allows users to search against the entire EMDB in real-time. EM-SURFER compares the global shapes of EM maps. Examples of search results from different types of query structures are discussed. We developed EM-SURFER, which retrieves structurally relevant matches for query EM maps from EMDB within seconds. The unique capability of EM-SURFER to detect 3D shape similarity of low-resolution EM maps should prove invaluable in structural biology.

  3. Measurement of loose powder density

    International Nuclear Information System (INIS)

    Akhtar, S.; Ali, A.; Haider, A.; Farooque, M.

    2011-01-01

    Powder metallurgy is a conventional technique for making engineering articles from powders. Main objective is to produce final products with the highest possible uniform density, which depends on the initial loose powder characteristics. Producing, handling, characterizing and compacting materials in loose powder form are part of the manufacturing processes. Density of loose metallic or ceramic powder is an important parameter for die design. Loose powder density is required for calculating the exact mass of powder to fill the die cavity for producing intended green density of the powder compact. To fulfill this requirement of powder metallurgical processing, a loose powder density meter as per ASTM standards is designed and fabricated for measurement of density. The density of free flowing metallic powders can be determined using Hall flow meter funnel and density cup of 25 cm/sup 3/ volume. Density of metal powders like cobalt, manganese, spherical bronze and pure iron is measured and results are obtained with 99.9% accuracy. (author)

  4. The effect of respiratory induced density variations on non-TOF PET quantitation in the lung

    Science.gov (United States)

    Holman, Beverley F.; Cuplov, Vesna; Hutton, Brian F.; Groves, Ashley M.; Thielemans, Kris

    2016-04-01

    Accurate PET quantitation requires a matched attenuation map. Obtaining matched CT attenuation maps in the thorax is difficult due to the respiratory cycle which causes both motion and density changes. Unlike with motion, little attention has been given to the effects of density changes in the lung on PET quantitation. This work aims to explore the extent of the errors caused by pulmonary density attenuation map mismatch on dynamic and static parameter estimates. Dynamic XCAT phantoms were utilised using clinically relevant 18F-FDG and 18F-FMISO time activity curves for all organs within the thorax to estimate the expected parameter errors. The simulations were then validated with PET data from 5 patients suffering from idiopathic pulmonary fibrosis who underwent PET/Cine-CT. The PET data were reconstructed with three gates obtained from the Cine-CT and the average Cine-CT. The lung TACs clearly displayed differences between true and measured curves with error depending on global activity distribution at the time of measurement. The density errors from using a mismatched attenuation map were found to have a considerable impact on PET quantitative accuracy. Maximum errors due to density mismatch were found to be as high as 25% in the XCAT simulation. Differences in patient derived kinetic parameter estimates and static concentration between the extreme gates were found to be as high as 31% and 14%, respectively. Overall our results show that respiratory associated density errors in the attenuation map affect quantitation throughout the lung, not just regions near boundaries. The extent of this error is dependent on the activity distribution in the thorax and hence on the tracer and time of acquisition. Consequently there may be a significant impact on estimated kinetic parameters throughout the lung.

  5. The effect of respiratory induced density variations on non-TOF PET quantitation in the lung

    International Nuclear Information System (INIS)

    Holman, Beverley F; Cuplov, Vesna; Hutton, Brian F; Groves, Ashley M; Thielemans, Kris

    2016-01-01

    Accurate PET quantitation requires a matched attenuation map. Obtaining matched CT attenuation maps in the thorax is difficult due to the respiratory cycle which causes both motion and density changes. Unlike with motion, little attention has been given to the effects of density changes in the lung on PET quantitation. This work aims to explore the extent of the errors caused by pulmonary density attenuation map mismatch on dynamic and static parameter estimates. Dynamic XCAT phantoms were utilised using clinically relevant 18 F-FDG and 18 F-FMISO time activity curves for all organs within the thorax to estimate the expected parameter errors. The simulations were then validated with PET data from 5 patients suffering from idiopathic pulmonary fibrosis who underwent PET/Cine-CT. The PET data were reconstructed with three gates obtained from the Cine-CT and the average Cine-CT. The lung TACs clearly displayed differences between true and measured curves with error depending on global activity distribution at the time of measurement. The density errors from using a mismatched attenuation map were found to have a considerable impact on PET quantitative accuracy. Maximum errors due to density mismatch were found to be as high as 25% in the XCAT simulation. Differences in patient derived kinetic parameter estimates and static concentration between the extreme gates were found to be as high as 31% and 14%, respectively. Overall our results show that respiratory associated density errors in the attenuation map affect quantitation throughout the lung, not just regions near boundaries. The extent of this error is dependent on the activity distribution in the thorax and hence on the tracer and time of acquisition. Consequently there may be a significant impact on estimated kinetic parameters throughout the lung. (paper)

  6. TRACING H2 COLUMN DENSITY WITH ATOMIC CARBON (C I) AND CO ISOTOPOLOGS

    International Nuclear Information System (INIS)

    Lo, N.; Bronfman, L.; Cunningham, M. R.; Jones, P. A.; Lowe, V.; Cortes, P. C.; Simon, R.; Fissel, L.; Novak, G.

    2014-01-01

    We present the first results of neutral carbon ([C I] 3 P 1 - 3 P 0 at 492 GHz) and carbon monoxide ( 13 CO, J = 1-0) mapping in the Vela Molecular Ridge cloud C (VMR-C) and the G333 giant molecular cloud complexes with the NANTEN2 and Mopra telescopes. For the four regions mapped in this work, we find that [C I] has very similar spectral emission profiles to 13 CO, with comparable line widths. We find that [C I] has an opacity of 0.1-1.3 across the mapped region while the [C I]/ 13 CO peak brightness temperature ratio is between 0.2 and 0.8. The [C I] column density is an order of magnitude lower than that of 13 CO. The H 2 column density derived from [C I] is comparable to values obtained from 12 CO. Our maps show that C I is preferentially detected in gas with low temperatures (below 20 K), which possibly explains the comparable H 2 column density calculated from both tracers (both C I and 12 CO underestimate column density), as a significant amount of the C I in the warmer gas is likely in the higher energy state transition ([C I] 3 P 2 - 3 P 1 at 810 GHz), and thus it is likely that observations of both the above [C I] transitions are needed in order to recover the total H 2 column density

  7. Universal map for cellular automata

    International Nuclear Information System (INIS)

    García-Morales, V.

    2012-01-01

    A universal map is derived for all deterministic 1D cellular automata (CAs) containing no freely adjustable parameters and valid for any alphabet size and any neighborhood range (including non-symmetrical neighborhoods). The map can be extended to an arbitrary number of dimensions and topologies and to arbitrary order in time. Specific CA maps for the famous Conway's Game of Life and Wolfram's 256 elementary CAs are given. An induction method for CAs, based in the universal map, allows mathematical expressions for the orbits of a wide variety of elementary CAs to be systematically derived. -- Highlights: ► A universal map is derived for all deterministic 1D cellular automata (CA). ► The map is generalized to 2D for Von Neumann, Moore and hexagonal neighborhoods. ► A map for all Wolfram's 256 elementary CAs is derived. ► A map for Conway's “Game of Life” is obtained.

  8. Compositional cokriging for mapping the probability risk of groundwater contamination by nitrates.

    Science.gov (United States)

    Pardo-Igúzquiza, Eulogio; Chica-Olmo, Mario; Luque-Espinar, Juan A; Rodríguez-Galiano, Víctor

    2015-11-01

    Contamination by nitrates is an important cause of groundwater pollution and represents a potential risk to human health. Management decisions must be made using probability maps that assess the nitrate concentration potential of exceeding regulatory thresholds. However these maps are obtained with only a small number of sparse monitoring locations where the nitrate concentrations have been measured. It is therefore of great interest to have an efficient methodology for obtaining those probability maps. In this paper, we make use of the fact that the discrete probability density function is a compositional variable. The spatial discrete probability density function is estimated by compositional cokriging. There are several advantages in using this approach: (i) problems of classical indicator cokriging, like estimates outside the interval (0,1) and order relations, are avoided; (ii) secondary variables (e.g. aquifer parameters) can be included in the estimation of the probability maps; (iii) uncertainty maps of the probability maps can be obtained; (iv) finally there are modelling advantages because the variograms and cross-variograms of real variables that do not have the restrictions of indicator variograms and indicator cross-variograms. The methodology was applied to the Vega de Granada aquifer in Southern Spain and the advantages of the compositional cokriging approach were demonstrated. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Timed bisimulation and open maps

    DEFF Research Database (Denmark)

    Hune, Thomas; Nielsen, Mogens

    1998-01-01

    of timed bisimulation. Thus the abstract results from the theory of open maps apply, e.g. the existence of canonical models and characteristic logics. Here, we provide an alternative proof of decidability of bisimulation for finite timed transition systems in terms of open maps, and illustrate the use......Open maps have been used for defining bisimulations for a range of models, but none of these have modelled real-time. We define a category of timed transition systems, and use the general framework of open maps to obtain a notion of bisimulation. We show this to be equivalent to the standard notion...... of open maps in presenting bisimulations....

  10. Participatory Maps

    DEFF Research Database (Denmark)

    Salovaara-Moring, Inka

    2016-01-01

    practice. In particular, mapping environmental damage, endangered species, and human-made disasters has become one focal point for environmental knowledge production. This type of digital map has been highlighted as a processual turn in critical cartography, whereas in related computational journalism...... of a geo-visualization within information mapping that enhances embodiment in the experience of the information. InfoAmazonia is defined as a digitally created map-space within which journalistic practice can be seen as dynamic, performative interactions between journalists, ecosystems, space, and species...

  11. Divergence from, and Convergence to, Uniformity of Probability Density Quantiles

    Directory of Open Access Journals (Sweden)

    Robert G. Staudte

    2018-04-01

    Full Text Available We demonstrate that questions of convergence and divergence regarding shapes of distributions can be carried out in a location- and scale-free environment. This environment is the class of probability density quantiles (pdQs, obtained by normalizing the composition of the density with the associated quantile function. It has earlier been shown that the pdQ is representative of a location-scale family and carries essential information regarding shape and tail behavior of the family. The class of pdQs are densities of continuous distributions with common domain, the unit interval, facilitating metric and semi-metric comparisons. The Kullback–Leibler divergences from uniformity of these pdQs are mapped to illustrate their relative positions with respect to uniformity. To gain more insight into the information that is conserved under the pdQ mapping, we repeatedly apply the pdQ mapping and find that further applications of it are quite generally entropy increasing so convergence to the uniform distribution is investigated. New fixed point theorems are established with elementary probabilistic arguments and illustrated by examples.

  12. Histogram specification as a method of density modification

    International Nuclear Information System (INIS)

    Harrison, R.W.

    1988-01-01

    A new method for improving the quality and extending the resolution of Fourier maps is described. The method is based on a histogram analysis of the electron density. The distribution of electron density values in the map is forced to be 'ideal'. The 'ideal' distribution is assumed to be Gaussian. The application of the method to improve the electron density map for the protein Acinetobacter asparaginase, which is a tetrameric enzyme of molecular weight 140000 daltons, is described. (orig.)

  13. Probing topological relations between high-density and low-density regions of 2MASS with hexagon cells

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Yongfeng [American Physical Society, San Diego, CA (United States); Xiao, Weike, E-mail: yongfeng.wu@maine.edu [Department of Astronautics Engineering, Harbin Institute of Technology, P.O. Box 345, Heilongjiang Province 150001 (China)

    2014-02-01

    We introduced a new two-dimensional (2D) hexagon technique for probing the topological structure of the universe in which we mapped regions of the sky with high and low galaxy densities onto a 2D lattice of hexagonal unit cells. We defined filled cells as corresponding to high-density regions and empty cells as corresponding to low-density regions. The numbers of filled cells and empty cells were kept the same by controlling the size of the cells. By analyzing the six sides of each hexagon, we could obtain and compare the statistical topological properties of high-density and low-density regions of the universe in order to have a better understanding of the evolution of the universe. We applied this hexagonal method to Two Micron All Sky Survey data and discovered significant topological differences between the high-density and low-density regions. Both regions had significant (>5σ) topological shifts from both the binomial distribution and the random distribution.

  14. Concept Mapping

    Science.gov (United States)

    Technology & Learning, 2005

    2005-01-01

    Concept maps are graphical ways of working with ideas and presenting information. They reveal patterns and relationships and help students to clarify their thinking, and to process, organize and prioritize. Displaying information visually--in concept maps, word webs, or diagrams--stimulates creativity. Being able to think logically teaches…

  15. Smoothing densities under shape constraints

    OpenAIRE

    Davies, Paul Laurie; Meise, Monika

    2009-01-01

    In Davies and Kovac (2004) the taut string method was proposed for calculating a density which is consistent with the data and has the minimum number of peaks. The main disadvantage of the taut string density is that it is piecewise constant. In this paper a procedure is presented which gives a smoother density by minimizing the total variation of a derivative of the density subject to the number, positions and heights of the local extreme values obtained from the taut string density. 2...

  16. Quantitative measurements of localized density variations in cylindrical tablets using X-ray microtomography.

    Science.gov (United States)

    Busignies, Virginie; Leclerc, Bernard; Porion, Patrice; Evesque, Pierre; Couarraze, Guy; Tchoreloff, Pierre

    2006-08-01

    Direct compaction is a complex process that results in a density distribution inside the tablets which is often heterogeneous. Therefore, the density variations may affect the compact properties. A quantitative analysis of this phenomenon is still lacking. Recently, X-ray microtomography has been successfully used in pharmaceutical development to study qualitatively the impact of tablet shape and break-line in the density of pharmaceutical tablets. In this study, we evaluate the density profile in microcrystalline cellulose (Vivapur 12) compacts obtained at different mean porosity (ranging from 7.7% to 33.5%) using X-ray tomography technique. First, the validity of the Beer-Lambert law is studied. Then, density calibration is performed and density maps of cylindrical tablets are obtained and visualized using a process with colour-scale calibration plot which is explained. As expected, important heterogeneity in density is observed and quantified. The higher densities in peripheral region were particularly investigated and appraised in regard to the lower densities observed in the middle of the tablet. The results also underlined that in the case of pharmaceutical tablets, it is important to differentiate the mechanical properties representative of the total volume tablet and the mechanical properties that only characterize the tablet surface like the Brinell hardness measurements.

  17. Distinguishability notion based on Wootters statistical distance: Application to discrete maps

    Science.gov (United States)

    Gomez, Ignacio S.; Portesi, M.; Lamberti, P. W.

    2017-08-01

    We study the distinguishability notion given by Wootters for states represented by probability density functions. This presents the particularity that it can also be used for defining a statistical distance in chaotic unidimensional maps. Based on that definition, we provide a metric d ¯ for an arbitrary discrete map. Moreover, from d ¯ , we associate a metric space with each invariant density of a given map, which results to be the set of all distinguished points when the number of iterations of the map tends to infinity. Also, we give a characterization of the wandering set of a map in terms of the metric d ¯ , which allows us to identify the dissipative regions in the phase space. We illustrate the results in the case of the logistic and the circle maps numerically and analytically, and we obtain d ¯ and the wandering set for some characteristic values of their parameters. Finally, an extension of the metric space associated for arbitrary probability distributions (not necessarily invariant densities) is given along with some consequences. The statistical properties of distributions given by histograms are characterized in terms of the cardinal of the associated metric space. For two conjugate variables, the uncertainty principle is expressed in terms of the diameters of the associated metric space with those variables.

  18. Conceptual maps as evaluation strategy

    Directory of Open Access Journals (Sweden)

    Dionísio Borsato

    2007-03-01

    Full Text Available The following work shows the conceptual map as an evaluation tool. In this study, an opening text was used as a previous organizer, with a theme related to the students’ daily lives. The developed activity consisted in elaborating conceptual maps before and after the experimental works. The evaluation was applied to 21 students of the 1st grade and 22 of the 3rd grade of High School. The elaborated maps were scored according to hierarchy, propositions, linking words, cross linking and examples. The classification of the maps elaborated before and after the experimental activity, was obtained having as a parameter, a referential conceptual map. In this classification many differences were observed between the first and second maps of both grades and among the groups. The elaboration of conceptual maps showed great potential as evaluation resources.

  19. Transfer maps and projection formulas

    OpenAIRE

    Tabuada, Goncalo

    2010-01-01

    Transfer maps and projection formulas are undoubtedly one of the key tools in the development and computation of (co)homology theories. In this note we develop an unified treatment of transfer maps and projection formulas in the non-commutative setting of dg categories. As an application, we obtain transfer maps and projection formulas in algebraic K-theory, cyclic homology, topological cyclic homology, and other scheme invariants.

  20. Symplectic maps for accelerator lattices

    International Nuclear Information System (INIS)

    Warnock, R.L.; Ruth, R.; Gabella, W.

    1988-05-01

    We describe a method for numerical construction of a symplectic map for particle propagation in a general accelerator lattice. The generating function of the map is obtained by integrating the Hamilton-Jacobi equation as an initial-value problem on a finite time interval. Given the generating function, the map is put in explicit form by means of a Fourier inversion technique. We give an example which suggests that the method has promise. 9 refs., 9 figs

  1. Fission level densities

    International Nuclear Information System (INIS)

    Maslov, V.M.

    1998-01-01

    Fission level densities (or fissioning nucleus level densities at fission saddle deformations) are required for statistical model calculations of actinide fission cross sections. Back-shifted Fermi-Gas Model, Constant Temperature Model and Generalized Superfluid Model (GSM) are widely used for the description of level densities at stable deformations. These models provide approximately identical level density description at excitations close to the neutron binding energy. It is at low excitation energies that they are discrepant, while this energy region is crucial for fission cross section calculations. A drawback of back-shifted Fermi gas model and traditional constant temperature model approaches is that it is difficult to include in a consistent way pair correlations, collective effects and shell effects. Pair, shell and collective properties of nucleus do not reduce just to the renormalization of level density parameter a, but influence the energy dependence of level densities. These effects turn out to be important because they seem to depend upon deformation of either equilibrium or saddle-point. These effects are easily introduced within GSM approach. Fission barriers are another key ingredients involved in the fission cross section calculations. Fission level density and barrier parameters are strongly interdependent. This is the reason for including fission barrier parameters along with the fission level densities in the Starter File. The recommended file is maslov.dat - fission barrier parameters. Recent version of actinide fission barrier data obtained in Obninsk (obninsk.dat) should only be considered as a guide for selection of initial parameters. These data are included in the Starter File, together with the fission barrier parameters recommended by CNDC (beijing.dat), for completeness. (author)

  2. Obtaining of ceramics biphasic dense and porous

    International Nuclear Information System (INIS)

    Pallone, E.M.J.A.; Rigo, E.C.S.; Fraga, A.F.

    2010-01-01

    Among the bioceramic hydroxyapatite (HAP) and beta-tricalcium phosphate (beta-TCP) are materials commonly used in biomedical field. Their combined properties result in a material with absorbable and at the same time with bioactive surface. Called biphasic ceramics such materials respond more quickly when exposed to physiological environment. In this work, powders of HAP/beta-TCP were obtained by chemical precipitation. After obtaining the post-phase was added at a ratio of 0, 15% and 30w% aqueous solutions of corn starch in order to obtain porous bodies. After mixing the resulting solutions were dried, resigned in tablet form and sintered at 1300 deg C. The initial powder was characterized by X-ray diffraction with Rietveld refinement to quantify the phases present. Bodies-of-evidence has been characterized by calculating the bulk density, X-ray diffraction (XRD), scanning electron microscopy and diametral compression. (author)

  3. Mapping racism.

    Science.gov (United States)

    Moss, Donald B

    2006-01-01

    The author uses the metaphor of mapping to illuminate a structural feature of racist thought, locating the degraded object along vertical and horizontal axes. These axes establish coordinates of hierarchy and of distance. With the coordinates in place, racist thought begins to seem grounded in natural processes. The other's identity becomes consolidated, and parochialism results. The use of this kind of mapping is illustrated via two patient vignettes. The author presents Freud's (1905, 1927) views in relation to such a "mapping" process, as well as Adorno's (1951) and Baldwin's (1965). Finally, the author conceptualizes the crucial status of primitivity in the workings of racist thought.

  4. Quantal density-functional theory in the presence of a magnetic field

    International Nuclear Information System (INIS)

    Yang Tao; Pan Xiaoyin; Sahni, Viraht

    2011-01-01

    We generalize the quantal density-functional theory (QDFT) of electrons in the presence of an external electrostatic field E(r)=-∇v(r) to include an external magnetostatic field B(r)=∇xA(r), where (v(r),A(r)) are the respective scalar and vector potentials. The generalized QDFT, valid for nondegenerate ground and excited states, is the mapping from the interacting system of electrons to a model of noninteracting fermions with the same density ρ(r) and physical current density j(r), and from which the total energy can be obtained. The properties (ρ(r),j(r)) constitute the basic quantum-mechanical variables because, as proved previously, for a nondegenerate ground state they uniquely determine the potentials (v(r),A(r)). The mapping to the noninteracting system is arbitrary in that the model fermions may be either in their ground or excited state. The theory is explicated by application to a ground state of the exactly solvable (two-dimensional) Hooke's atom in a magnetic field, with the mapping being to a model system also in its ground state. The majority of properties of the model are obtained in closed analytical or semianalytical form. A comparison with the corresponding mapping from a ground state of the (three-dimensional) Hooke's atom in the absence of a magnetic field is also made.

  5. Genetic Mapping

    Science.gov (United States)

    ... greatly advanced genetics research. The improved quality of genetic data has reduced the time required to identify a ... cases, a matter of months or even weeks. Genetic mapping data generated by the HGP's laboratories is freely accessible ...

  6. All Hazard Hotspots/Population Density

    Indian Academy of Sciences (India)

    This map shows hotspots of humanitarian risk for floods, cyclones, and drought overlaying a population density gradient. Blue areas with striped overlay represent areas of high population density that are also risk hotspots. These are at higher risk of future population displacement as a result of climate hazards.

  7. Spectral Properties of Chaotic Signals Generated by the Bernoulli Map

    Directory of Open Access Journals (Sweden)

    Rafael A. da Costa

    2014-11-01

    Full Text Available In the last decades, the use of chaotic signals as broadband carriers has been considered in Telecommunications. Despite the relevance of the frequency domain analysis in this field, there are few studies that are concerned with spectral properties of chaotic signals. Bearing this in mind, this paper aims the characterization of the power spectral density (PSD of chaotic orbits generated by Bernoulli maps. We obtain analytic expressions for autocorrelation sequence, PSD and essential bandwidth for chaotic orbits generated by this map as function of the family parameter and Lyapunov exponent. Moreover, we verify that analytical expressions match numerical results. We conclude that the power of the generated orbits is concentrated in low frequencies for all parameters values. Besides, it is possible to obtain chaotic narrowband signals.

  8. Generalized Models from Beta(p, 2) Densities with Strong Allee Effect: Dynamical Approach

    OpenAIRE

    Aleixo, Sandra M.; Rocha, J. Leonel

    2012-01-01

    A dynamical approach to study the behaviour of generalized populational growth models from Beta(p, 2) densities, with strong Allee effect, is presented. The dynamical analysis of the respective unimodal maps is performed using symbolic dynamics techniques. The complexity of the correspondent discrete dynamical systems is measured in terms of topological entropy. Different populational dynamics regimes are obtained when the intrinsic growth rates are modified: extinction, bistability, chaotic ...

  9. Density limit in ASDEX discharges with peaked density profiles

    International Nuclear Information System (INIS)

    Staebler, A.; Niedermeyer, H.; Loch, R.; Mertens, V.; Mueller, E.R.; Soeldner, F.X.; Wagner, F.

    1989-01-01

    Results concerning the density limit in OH and NI-heated ASDEX discharges with the usually observed broad density profiles have been reported earlier: In ohmic discharges with high q a (q-cylindrical is used throughout this paper) the Murakami parameter (n e R/B t ) is a good scaling parameter. At the high densities edge cooling is observed causing the plasma to shrink until an m=2-instability terminates the discharge. When approaching q a =2 the density limit is no longer proportional to I p ; a minimum exists in n e,max (q a ) at q a ∼2.15. With NI-heating the density limit increases less than proportional to the heating power; the behaviour during the pre-disruptive phase is rather similar to the one of OH discharges. There are specific operating regimes on ASDEX leading to discharges with strongly peaked density profiles: the improved ohmic confinement regime, counter neutral injection, and multipellet injection. These regimes are characterized by enhanced energy and particle confinement. The operational limit in density for these discharges is, therefore, of great interest having furthermore in mind that high central densities are favourable in achieving high fusion yields. In addition, further insight into the mechanisms of the density limit observed in tokamaks may be obtained by comparing plasmas with rather different density profiles at their maximum attainable densities. 7 refs., 2 figs

  10. Anisotropic dynamic mass density for fluidsolid composites

    KAUST Repository

    Wu, Ying; Mei, Jun; Sheng, Ping

    2012-01-01

    By taking the low frequency limit of multiple-scattering theory, we obtain the dynamic effective mass density of fluidsolid composites with a two-dimensional rectangular lattice structure. The anisotropic mass density can be described by an angle

  11. Density functional theory and parallel processing

    International Nuclear Information System (INIS)

    Ward, R.C.; Geist, G.A.; Butler, W.H.

    1987-01-01

    The authors demonstrate a method for obtaining the ground state energies and charge densities of a system of atoms described within density functional theory using simulated annealing on a parallel computer

  12. Some Characterizations of Open, Closed, and Continuous Mappings

    Directory of Open Access Journals (Sweden)

    Navpreet Singh Noorie

    2008-01-01

    Full Text Available We obtain new characterizations of open maps in terms of closures, of closed maps in terms of interiors, and of continuous maps in terms of interiors. Further open (closed onto maps ∶→ are described in terms of images under of certain closed (open sets in . Continuity of (onto maps is also characterized in terms of saturated sets.

  13. Construction of a dense genetic linkage map and mapping quantitative trait loci for economic traits of a doubled haploid population of Pyropia haitanensis (Bangiales, Rhodophyta).

    Science.gov (United States)

    Xu, Yan; Huang, Long; Ji, Dehua; Chen, Changsheng; Zheng, Hongkun; Xie, Chaotian

    2015-09-21

    Pyropia haitanensis is one of the most economically important mariculture crops in China. A high-density genetic map has not been published yet and quantitative trait locus (QTL) mapping has not been undertaken for P. haitanensis because of a lack of sufficient molecular markers. Specific length amplified fragment sequencing (SLAF-seq) was developed recently for large-scale, high resolution de novo marker discovery and genotyping. In this study, SLAF-seq was used to obtain mass length polymorphic markers to construct a high-density genetic map for P. haitanensis. In total, 120.33 Gb of data containing 75.21 M pair-end reads was obtained after sequencing. The average coverage for each SLAF marker was 75.50-fold in the male parent, 74.02-fold in the female parent, and 6.14-fold average in each double haploid individual. In total, 188,982 SLAFs were detected, of which 6731 were length polymorphic SLAFs that could be used to construct a genetic map. The final map included 4550 length polymorphic markers that were combined into 740 bins on five linkage groups, with a length of 874.33 cM and an average distance of 1.18 cM between adjacent bins. This map was used for QTL mapping to identify chromosomal regions associated with six economically important traits: frond length, width, thickness, fresh weight, growth rates of frond length and growth rates of fresh weight. Fifteen QTLs were identified for these traits. The value of phenotypic variance explained by an individual QTL ranged from 9.59 to 16.61 %, and the confidence interval of each QTL ranged from 0.97 cM to 16.51 cM. The first high-density genetic linkage map for P. haitanensis was constructed, and fifteen QTLs associated with six economically important traits were identified. The results of this study not only provide a platform for gene and QTL fine mapping, map-based gene isolation, and molecular breeding for P. haitanensis, but will also serve as a reference for positioning sequence scaffolds on a physical

  14. Individualized volume CT dose index determined by cross-sectional area and mean density of the body to achieve uniform image noise of contrast-enhanced pediatric chest CT obtained at variable kV levels and with combined tube current modulation

    International Nuclear Information System (INIS)

    Goo, Hyun Woo

    2011-01-01

    A practical body-size adaptive protocol providing uniform image noise at various kV levels is not available for pediatric CT. To develop a practical contrast-enhanced pediatric chest CT protocol providing uniform image noise by using an individualized volume CT dose index (CTDIvol) determined by the cross-sectional area and density of the body at variable kV levels and with combined tube current modulation. A total of 137 patients (mean age, 7.6 years) underwent contrast-enhanced pediatric chest CT based on body weight. From the CTDIvol, image noise, and area and mean density of the cross-section at the lung base in the weight-based group, the best fit equation was estimated with a very high correlation coefficient (γ 2 = 0.86, P 2 vs. 326.3 ± 124.8 cm 2 ), mean density (-212.9 ± 53.1 HU vs. -221.1 ± 56.3 HU), and image noise (13.8 ± 2.3 vs. 13.6 ± 1.7 HU) between the weight-based and the CTDIvol groups (P > 0.05). Contrast-enhanced pediatric chest CT with the CTDIvol determined individually by the cross-sectional area and density of the body provides more uniform noise and better dose adaptation to body habitus than does weight-based CT at variable kV levels and with combined tube current modulation. (orig.)

  15. Machine learning-based dual-energy CT parametric mapping.

    Science.gov (United States)

    Su, Kuan-Hao; Kuo, Jung-Wen; Jordan, David W; Van Hedent, Steven; Klahr, Paul; Wei, Zhouping; Al Helo, Rose; Liang, Fan; Qian, Pengjiang; Pereira, Gisele C; Rassouli, Negin; Gilkeson, Robert C; Traughber, Bryan J; Cheng, Chee-Wai; Muzic, Raymond F

    2018-05-22

    The aim is to develop and evaluate machine learning methods for generating quantitative parametric maps of effective atomic number (Zeff), relative electron densitye), mean excitation energy (Ix), and relative stopping power (RSP) from clinical dual-energy CT data. The maps could be used for material identification and radiation dose calculation. Machine learning methods of historical centroid (HC), random forest (RF), and artificial neural networks (ANN) were used to learn the relationship between dual-energy CT input data and ideal output parametric maps calculated for phantoms from the known compositions of 13 tissue substitutes. After training and model selection steps, the machine learning predictors were used to generate parametric maps from independent phantom and patient input data. Precision and accuracy were evaluated using the ideal maps. This process was repeated for a range of exposure doses, and performance was compared to that of the clinically-used dual-energy, physics-based method which served as the reference. The machine learning methods generated more accurate and precise parametric maps than those obtained using the reference method. Their performance advantage was particularly evident when using data from the lowest exposure, one-fifth of a typical clinical abdomen CT acquisition. The RF method achieved the greatest accuracy. In comparison, the ANN method was only 1% less accurate but had much better computational efficiency than RF, being able to produce parametric maps in 15 seconds. Machine learning methods outperformed the reference method in terms of accuracy and noise tolerance when generating parametric maps, encouraging further exploration of the techniques. Among the methods we evaluated, ANN is the most suitable for clinical use due to its combination of accuracy, excellent low-noise performance, and computational efficiency. . © 2018 Institute of Physics and Engineering in

  16. Level density of 57Co

    International Nuclear Information System (INIS)

    Mishra, V.; Boukharouba, N.; Brient, C.E.; Grimes, S.M.; Pedroni, R.S.

    1994-01-01

    Levels in 57 Co have been studied in the region of resolved levels (E 57 Fe(p,n) 57 Co neutron spectrum with resolution ΔE∼5 keV. Seventeen previously unknown levels are located. Level density parameters in the continuum region are deduced from thick target measurements of the same reaction and additional level density information is deduced from Ericson fluctuation studies of the reaction 56 Fe(p,n) 56 Co. A set of level density parameters is found which describes the level density of 57 Co at energies up to 14 MeV. Efforts to obtain level density information from the 56 Fe(d,n) 57 Co reaction were unsuccessful, but estimates of the fraction of the deuteron absorption cross section corresponding to compound nucleus formation are obtained

  17. Processing of hydroxyapatite obtained by combustion synthesis

    International Nuclear Information System (INIS)

    Canillas, M.; Rivero, R.; García-Carrodeguas, R.; Barba, F.; Rodríguez, M.A.

    2017-01-01

    One of the reasons of implants failure are the stress forces appearing in the material–tissue interface due to the differences between their mechanical properties. For this reason, similar mechanical properties to the surrounding tissue are desirable. The synthesis of hydroxyapatite by solution combustion method and its processing have been studied in order to obtain fully dense ceramic bodies with improved mechanical strength. Combustion synthesis provides nanostructured powders characterized by a high surface area to facilitate the following sintering. Moreover, synthesis was conducted in aqueous and oxidizing media. Oxidizing media improve homogenization and increase the energy released during combustion. It gives rise to particles whose morphology and size suggest lower surface energies compared with aqueous media. The obtained powders were sintered by using a controlled sintering rate schedule. Lower surfaces energies minimize the shrinkage during sintering and relative densities measurements and diametral compression test confirm improved densification and consequently mechanical properties. [es

  18. Processing of hydroxyapatite obtained by combustion synthesis

    Directory of Open Access Journals (Sweden)

    M. Canillas

    2017-09-01

    Full Text Available One of the reasons of implants failure are the stress forces appearing in the material–tissue interface due to the differences between their mechanical properties. For this reason, similar mechanical properties to the surrounding tissue are desirable. The synthesis of hydroxyapatite by solution combustion method and its processing have been studied in order to obtain fully dense ceramic bodies with improved mechanical strength. Combustion synthesis provides nanostructured powders characterized by a high surface area to facilitate the following sintering. Moreover, synthesis was conducted in aqueous and oxidizing media. Oxidizing media improve homogenization and increase the energy released during combustion. It gives rise to particles whose morphology and size suggest lower surface energies compared with aqueous media. The obtained powders were sintered by using a controlled sintering rate schedule. Lower surfaces energies minimize the shrinkage during sintering and relative densities measurements and diametral compression test confirm improved densification and consequently mechanical properties.

  19. Synchronizability of coupled PWL maps

    International Nuclear Information System (INIS)

    Polynikis, A.; Di Bernardo, M.; Hogan, S.J.

    2009-01-01

    In this paper we discuss the phenomenon of synchronization of chaotic systems in the case of coupled piecewise linear (PWL) continuous and discontinuous one-dimensional maps. We present numerical results for two examples of coupled systems consisting of two PWL maps. We illustrate how the coupled system can achieve synchronization and discuss the nature of the bifurcation that occurs at a critical value of the coupling strength. We then determine this critical coupling using linear stability analysis. We discuss the effects of variation of the parameters of the PWL maps on the critical coupling and present different bifurcation scenarios obtained for different sets of values of these parameters. Finally, we discuss an extension of our work to the synchronizability of networks consisting of two or more PWL maps. We show how the synchronizability of a network of PWL maps can be improved by tuning the map parameters.

  20. Projective mapping

    DEFF Research Database (Denmark)

    Dehlholm, Christian; Brockhoff, Per B.; Bredie, Wender Laurentius Petrus

    2012-01-01

    by the practical testing environment. As a result of the changes, a reasonable assumption would be to question the consequences caused by the variations in method procedures. Here, the aim is to highlight the proven or hypothetic consequences of variations of Projective Mapping. Presented variations will include...... instructions and influence heavily the product placements and the descriptive vocabulary (Dehlholm et.al., 2012b). The type of assessors performing the method influences results with an extra aspect in Projective Mapping compared to more analytical tests, as the given spontaneous perceptions are much dependent......Projective Mapping (Risvik et.al., 1994) and its Napping (Pagès, 2003) variations have become increasingly popular in the sensory field for rapid collection of spontaneous product perceptions. It has been applied in variations which sometimes are caused by the purpose of the analysis and sometimes...

  1. Affective Maps

    DEFF Research Database (Denmark)

    Salovaara-Moring, Inka

    . In particular, mapping environmental damage, endangered species, and human made disasters has become one of the focal point of affective knowledge production. These ‘more-than-humangeographies’ practices include notions of species, space and territory, and movement towards a new political ecology. This type...... of digital cartographies has been highlighted as the ‘processual turn’ in critical cartography, whereas in related computational journalism it can be seen as an interactive and iterative process of mapping complex and fragile ecological developments. This paper looks at computer-assisted cartography as part...

  2. Graphene mobility mapping

    DEFF Research Database (Denmark)

    Buron, Jonas Christian Due; Pizzocchero, Filippo; Jepsen, Peter Uhd

    2015-01-01

    Carrier mobility and chemical doping level are essential figures of merit for graphene, and large-scale characterization of these properties and their uniformity is a prerequisite for commercialization of graphene for electronics and electrodes. However, existing mapping techniques cannot directly...... assess these vital parameters in a non-destructive way. By deconvoluting carrier mobility and density from non-contact terahertz spectroscopic measurements of conductance in graphene samples with terahertz-transparent backgates, we are able to present maps of the spatial variation of both quantities over...... graphene indicates dominance by charged scatterers. Unexpectedly, significant variations in mobility rather than doping are the cause of large conductance inhomogeneities, highlighting the importance of statistical approaches when assessing large-area graphene transport properties....

  3. Super liquid density target designs

    International Nuclear Information System (INIS)

    Pan, Y.L.; Bailey, D.S.

    1976-01-01

    The success of laser fusion depends on obtaining near isentropic compression of fuel to very high densities and igniting this fuel. To date, the results of laser fusion experiments have been based mainly on the exploding pusher implosion of fusion capsules consisting of thin glass microballoons (wall thickness of less than 1 micron) filled with low density DT gas (initial density of a few mg/cc). Maximum DT densities of a few tenths of g/cc and temperatures of a few keV have been achieved in these experiments. We will discuss the results of LASNEX target design calculations for targets which: (a) can compress fuel to much higher densities using the capabilities of existing Nd-glass systems at LLL; (b) allow experimental measurement of the peak fuel density achieved

  4. High density dispersion fuel

    International Nuclear Information System (INIS)

    Hofman, G.L.

    1996-01-01

    A fuel development campaign that results in an aluminum plate-type fuel of unlimited LEU burnup capability with an uranium loading of 9 grams per cm 3 of meat should be considered an unqualified success. The current worldwide approved and accepted highest loading is 4.8 g cm -3 with U 3 Si 2 as fuel. High-density uranium compounds offer no real density advantage over U 3 Si 2 and have less desirable fabrication and performance characteristics as well. Of the higher-density compounds, U 3 Si has approximately a 30% higher uranium density but the density of the U 6 X compounds would yield the factor 1.5 needed to achieve 9 g cm -3 uranium loading. Unfortunately, irradiation tests proved these peritectic compounds have poor swelling behavior. It is for this reason that the authors are turning to uranium alloys. The reason pure uranium was not seriously considered as a dispersion fuel is mainly due to its high rate of growth and swelling at low temperatures. This problem was solved at least for relatively low burnup application in non-dispersion fuel elements with small additions of Si, Fe, and Al. This so called adjusted uranium has nearly the same density as pure α-uranium and it seems prudent to reconsider this alloy as a dispersant. Further modifications of uranium metal to achieve higher burnup swelling stability involve stabilization of the cubic γ phase at low temperatures where normally α phase exists. Several low neutron capture cross section elements such as Zr, Nb, Ti and Mo accomplish this in various degrees. The challenge is to produce a suitable form of fuel powder and develop a plate fabrication procedure, as well as obtain high burnup capability through irradiation testing

  5. MAP user's manual copyright

    International Nuclear Information System (INIS)

    Pillsbury, R.D. Jr.

    1991-12-01

    The program MITMAP represents a set of general purpose, two- dimensional, finite element programs for the calculation of magnetic fields. It consists of the program MAP and MAP2DJ. The two programs are used to solve different electromagnetic problems, but they have a common set of subrountines for pre- and postprocessing. Originally separate programs, they have been combined to make modification easier. The manuals, however, will remain separate. The program MAP is described in this manual. MAP is applicable to the class of problems with two-dimensional-planar or axisymmetric - geometries, in which the current density and the magnetic vector potential have only a single nonvanishing component. The single component is associated with the direction that is perpendicular to the plane of the problem and is invariant with respect to that direction. Maxwell's equations can be reduced to a solver diffusion equation in terms of the single, nonvanishing component of the magnetic vector potential for planar problems and to a single component of a vector potential for planar problems and to a single component of a vector diffusion equation for axisymmetric problems. The magnetic permeability appears in the governing equation. The permeability may be a function of the magnetic flux density. In addition, any electrically conducting material present will have eddy currents induced by a time varying magnetic field. These eddy currents must be included in the solution process. This manual provides a description of the structure of the input data and output for the program. There are several example problems presented that illustrate the major program features. Appendices are included that contain a derivation of the governing equations and the application of the finite element method to the solution of the equations

  6. A COSMIC MICROWAVE BACKGROUND LENSING MASS MAP AND ITS CORRELATION WITH THE COSMIC INFRARED BACKGROUND

    Energy Technology Data Exchange (ETDEWEB)

    Holder, G. P.; De Haan, T.; Dobbs, M. A.; Dudley, J. [Department of Physics, McGill University, Montreal, Quebec H3A 2T8 (Canada); Viero, M. P.; Bock, J. [California Institute of Technology, Pasadena, CA 91125 (United States); Zahn, O. [Berkeley Center for Cosmological Physics, Department of Physics, University of California, and Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Aird, K. A. [University of Chicago, Chicago, IL 60637 (United States); Benson, B. A.; Bhattacharya, S.; Bleem, L. E.; Carlstrom, J. E.; Chang, C. L.; Crawford, T. M.; Crites, A. T. [Kavli Institute for Cosmological Physics, University of Chicago, Chicago, IL 60637 (United States); Brodwin, M. [Department of Physics and Astronomy, University of Missouri, Kansas City, MO 64110 (United States); Cho, H-M. [NIST Quantum Devices Group, Boulder, CO 80305 (United States); Conley, A. [Center for Astrophysics and Space Astronomy, University of Colorado, Boulder, CO 80309 (United States); George, E. M. [Department of Physics, University of California, Berkeley, CA 94720 (United States); Halverson, N. W. [Department of Astrophysical and Planetary Sciences and Department of Physics, University of Colorado, Boulder, CO 80309 (United States); and others

    2013-07-01

    We use a temperature map of the cosmic microwave background (CMB) obtained using the South Pole Telescope at 150 GHz to construct a map of the gravitational convergence to z {approx} 1100, revealing the fluctuations in the projected mass density. This map shows individual features that are significant at the {approx}4{sigma} level, providing the first image of CMB lensing convergence. We cross-correlate this map with Herschel/SPIRE maps covering 90 deg{sup 2} at wavelengths of 500, 350, and 250 {mu}m. We show that these submillimeter (submm) wavelength maps are strongly correlated with the lensing convergence map, with detection significances in each of the three submm bands ranging from 6.7{sigma} to 8.8{sigma}. We fit the measurement of the cross power spectrum assuming a simple constant bias model and infer bias factors of b = 1.3-1.8, with a statistical uncertainty of 15%, depending on the assumed model for the redshift distribution of the dusty galaxies that are contributing to the Herschel/SPIRE maps.

  7. Energetic map

    International Nuclear Information System (INIS)

    2012-01-01

    This report explains the energetic map of Uruguay as well as the different systems that delimits political frontiers in the region. The electrical system importance is due to the electricity, oil and derived , natural gas, potential study, biofuels, wind and solar energy

  8. Necklace maps

    NARCIS (Netherlands)

    Speckmann, B.; Verbeek, K.A.B.

    2010-01-01

    Statistical data associated with geographic regions is nowadays globally available in large amounts and hence automated methods to visually display these data are in high demand. There are several well-established thematic map types for quantitative data on the ratio-scale associated with regions:

  9. Participatory maps

    DEFF Research Database (Denmark)

    Salovaara-Moring, Inka

    towards a new political ecology. This type of digital cartographies has been highlighted as the ‘processual turn’ in critical cartography, whereas in related computational journalism it can be seen as an interactive and iterative process of mapping complex and fragile ecological developments. This paper...

  10. Effects of melt-temperature on limiting current density in Al electrodeposition and morphology of Al electrodeposits obtained from ambient temperature type molten salt; Joongata yoyuen kara no denki aluminium mekki no genkai denryu mitsudo oyobi denseki keitai ni oyobosu mekki ekion no eikyo

    Energy Technology Data Exchange (ETDEWEB)

    Shimizu, T.; Tatano, M.; Uchida, Y. [Nisshin Steel Co. Ltd., Tokyo (Japan)

    1996-03-31

    Some of more important electrolytic solutions for Al electrodeposition are organic solvents, high-temperature type molten salts and low-temperature type molten salts having a melting point of 30{degree}C or lower, such as ethylmethylimidazolium chloride (EMIC). This study uses a molten salt of AlCl3-EMIC as the low-temperature type solution for high-speed electrodeposition. Discussed herein are the effects of melt temperature on limiting current density in Al electrodeposition and Al electrodeposit morphology. Limiting current density increases as melt temperature increases at any AlCl3 concentration used in this study. The AlCl3 concentration that gives the maximum limiting current density shifts from 64 to 67mol% at a melt temperature of 120{degree}C. A dense, smooth Al electrodeposited film results at a melt temperature of 100{degree}C or lower, but the electrodeposited grains become coarser as melt temperature increases. Melt temperature can be increased to 140{degree}C to secure a smooth electrodeposited film, showing possibility of 2 times faster electrodeposition than the conventional one. 21 refs., 12 figs., 1 tab.

  11. Chemical bonding in view of electron charge density and kinetic energy density descriptors.

    Science.gov (United States)

    Jacobsen, Heiko

    2009-05-01

    Stalke's dilemma, stating that different chemical interpretations are obtained when one and the same density is interpreted either by means of natural bond orbital (NBO) and subsequent natural resonance theory (NRT) application or by the quantum theory of atoms in molecules (QTAIM), is reinvestigated. It is shown that within the framework of QTAIM, the question as to whether for a given molecule two atoms are bonded or not is only meaningful in the context of a well-defined reference geometry. The localized-orbital-locator (LOL) is applied to map out patterns in covalent bonding interaction, and produces results that are consistent for a variety of reference geometries. Furthermore, LOL interpretations are in accord with NBO/NRT, and assist in an interpretation in terms of covalent bonding. 2008 Wiley Periodicals, Inc.

  12. Experimental results obtained at GANIL

    International Nuclear Information System (INIS)

    Borrel, V.

    1993-01-01

    A review of experimental results obtained at GANIL on the study of nuclear structure and nuclear reactions with secondary radioactive beams is presented. Mass measurements by means of the GANIL cyclotrons are described. The possibilities of GANIL/LISE3 for the production and separation of radioactive beams are illustrated through a large variety of experiments. (author). 19 refs., 8 figs

  13. Individualized volume CT dose index determined by cross-sectional area and mean density of the body to achieve uniform image noise of contrast-enhanced pediatric chest CT obtained at variable kV levels and with combined tube current modulation

    Energy Technology Data Exchange (ETDEWEB)

    Goo, Hyun Woo [University of Ulsan College of Medicine, Department of Radiology and Research Institute of Radiology, Asan Medical Center, Seoul (Korea, Republic of)

    2011-07-15

    A practical body-size adaptive protocol providing uniform image noise at various kV levels is not available for pediatric CT. To develop a practical contrast-enhanced pediatric chest CT protocol providing uniform image noise by using an individualized volume CT dose index (CTDIvol) determined by the cross-sectional area and density of the body at variable kV levels and with combined tube current modulation. A total of 137 patients (mean age, 7.6 years) underwent contrast-enhanced pediatric chest CT based on body weight. From the CTDIvol, image noise, and area and mean density of the cross-section at the lung base in the weight-based group, the best fit equation was estimated with a very high correlation coefficient ({gamma}{sup 2} = 0.86, P < 0.001). For the next study, 177 patients (mean age, 7.9 years; the CTDIvol group) underwent contrast-enhanced pediatric chest CT with the CTDIvol determined individually by the best fit equation. CTDIvol values on the dose report after CT scanning, noise differences from the target noise, areas, and mean densities were compared between these two groups. The CTDIvol values (mean{+-}standard deviation, 1.6 {+-} 0.7 mGy) and the noise differences from the target noise (1.1 {+-} 0.9 HU) of the CTDIvol group were significantly lower than those of the weight-based group (2.0 {+-} 1.0 mGy, 1.8 {+-} 1.4 HU) (P < 0.001). In contrast, no statistically significant difference was found in area (317.0 {+-} 136.8 cm{sup 2} vs. 326.3 {+-} 124.8 cm{sup 2}), mean density (-212.9 {+-} 53.1 HU vs. -221.1 {+-} 56.3 HU), and image noise (13.8 {+-} 2.3 vs. 13.6 {+-} 1.7 HU) between the weight-based and the CTDIvol groups (P > 0.05). Contrast-enhanced pediatric chest CT with the CTDIvol determined individually by the cross-sectional area and density of the body provides more uniform noise and better dose adaptation to body habitus than does weight-based CT at variable kV levels and with combined tube current modulation. (orig.)

  14. High-density mapping of the MHC identifies a shared role for HLA-DRB1*01:03 in inflammatory bowel diseases and heterozygous advantage in ulcerative colitis

    DEFF Research Database (Denmark)

    Goyette, Philippe; Boucher, Gabrielle; Mallon, Dermot

    2015-01-01

    high-density SNP typing of the MHC in >32,000 individuals with IBD, implicating multiple HLA alleles, with a primary role for HLA-DRB1*01:03 in both Crohn's disease and ulcerative colitis. Noteworthy differences were observed between these diseases, including a predominant role for class II HLA......Genome-wide association studies of the related chronic inflammatory bowel diseases (IBD) known as Crohn's disease and ulcerative colitis have shown strong evidence of association to the major histocompatibility complex (MHC). This region encodes a large number of immunological candidates, including...

  15. MIMIC: An Innovative Methodology for Determining Mobile Laser Scanning System Point Density

    Directory of Open Access Journals (Sweden)

    Conor Cahalane

    2014-08-01

    Full Text Available Understanding how various Mobile Mapping System (MMS laser hardware configurations and operating parameters exercise different influence on point density is important for assessing system performance, which in turn facilitates system design and MMS benchmarking. Point density also influences data processing, as objects that can be recognised using automated algorithms generally require a minimum point density. Although obtaining the necessary point density impacts on hardware costs, survey time and data storage requirements, a method for accurately and rapidly assessing MMS performance is lacking for generic MMSs. We have developed a method for quantifying point clouds collected by an MMS with respect to known objects at specified distances using 3D surface normals, 2D geometric formulae and line drawing algorithms. These algorithms were combined in a system called the Mobile Mapping Point Density Calculator (MIMIC and were validated using point clouds captured by both a single scanner and a dual scanner MMS. Results from MIMIC were promising: when considering the number of scan profiles striking the target, the average error equated to less than 1 point per scan profile. These tests highlight that MIMIC is capable of accurately calculating point density for both single and dual scanner MMSs.

  16. Study on magnetic field mapping within cylindrical center volume of general magnet

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Li; Lee, Sang Jin [Uiduk University, Gyeongju (Korea, Republic of)

    2016-06-15

    For the magnetic field analysis or design, it is important to know the behavior of the magnetic field in an interesting space. Magnetic field mapping becomes a useful tool for the study of magnetic field. In this paper, a numerical way for mapping the magnetic field within the cylindrical center volume of magnet is presented, based on the solution of the Laplace's equation in the cylindrical coordinate system. The expression of the magnetic field can be obtained by the magnetic flux density, which measured in the mapped volume. According to the form of the expression, the measurement points are arranged with the parallel cylindrical line (PCL) method. As example, the magnetic flux density generated by an electron cyclotron resonance ion source (ECRIS) magnet and a quadrupole magnet were mapped using the PCL method, respectively. The mapping results show the PCL arrangement method is feasible and convenience to map the magnetic field within a cylindrical center volume generated by the general magnet.

  17. Integrated genetic linkage map of cultivated peanut by three RIL populations

    Institute of Scientific and Technical Information of China (English)

    Yanbin Song; Huifang Jiang; Huaiyong Luo; Li Huang; Yuning Chen; Weigang Chen; Nian Liu; Xiaoping Ren; Bolun Yu; Jianbin Guo

    2017-01-01

    High-density and precise genetic linkage map is fundamental to detect quanti-tative trait locus (QTL) of agronomic and quality related traits in cultivated peanut (Arachis hypogaea L.). In this study, three linkage maps from three RIL (recombinant inbred line) populations were used to construct an integrated map. A total of 2,069 SSR and transposon markers were anchored on the high-density integrated map which covered 2,231.53 cM with 20 linkage groups. Totally, 92 QTLs correlating with pod length (PL), pod width (PW), hun-dred pods weight (HPW) and plant height (PH) from above RIL populations were mapped on it. Seven intervals were found to harbor QTLs controlling the same traits in different pop-ulations, including one for PL, three for PW, two for HPW, and one for PH. Besides, QTLs controlling different traits in different populations were found to be overlapped in four inter-vals. Interval on A05 contains 17 QTLs for different traits from two RIL populations. New markers were added to these intervals to detect QTLs with narrow confidential intervals. Results obtained in this study may facilitate future genomic researches such as QTL study, fine mapping, positional cloning and marker-assisted selection (MAS) in peanut.

  18. Calculation of dose absorbed for the verification of the calibration curves UH-Density electronic relative obtained with various mannequins; Calculo de dosis absorbida para la verificacion de las curvas de calibracion UH-Densidad electronica relativa obtenidas con distintos maniquies

    Energy Technology Data Exchange (ETDEWEB)

    Perez Alvarez, M. E.; Sena Espinel, E. de; Delgado Aparicio, J. M.; Martin Rincon, C.; Garcia Repiso, S.; Ramos Pacho, J. A.; Verde Velasco, J. M.; Gomez Gonzalez, N.; Cons Perez, N.; Saez Beltran, M.

    2013-07-01

    In order to discern with what calibration curve is obtained a more accurate dosimetry distribution, dose measurements are carried out on the treatment unit and the values found are evaluated. (Author)

  19. Large Scale Landform Mapping Using Lidar DEM

    Directory of Open Access Journals (Sweden)

    Türkay Gökgöz

    2015-08-01

    Full Text Available In this study, LIDAR DEM data was used to obtain a primary landform map in accordance with a well-known methodology. This primary landform map was generalized using the Focal Statistics tool (Majority, considering the minimum area condition in cartographic generalization in order to obtain landform maps at 1:1000 and 1:5000 scales. Both the primary and the generalized landform maps were verified visually with hillshaded DEM and an orthophoto. As a result, these maps provide satisfactory visuals of the landforms. In order to show the effect of generalization, the area of each landform in both the primary and the generalized maps was computed. Consequently, landform maps at large scales could be obtained with the proposed methodology, including generalization using LIDAR DEM.

  20. Geopolymer obtained from coal ash

    International Nuclear Information System (INIS)

    Conte, V.; Bissari, E.S.; Uggioni, E.; Bernardin, A.M.

    2011-01-01

    Geopolymers are three-dimensional alumino silicates that can be rapidly formed at low temperature from naturally occurring aluminosilicates with a structure similar to zeolites. In this work coal ash (Tractebel Energy) was used as source of aluminosilicate according a full factorial design in eight formulations with three factors (hydroxide type and concentration and temperature) and two-levels. The ash was dried and hydroxide was added according type and concentration. The geopolymer was poured into cylindrical molds, cured (14 days) and subjected to compression test. The coal ash from power plants belongs to the Si-Al system and thus can easily form geopolymers. The compression tests showed that it is possible to obtain samples with strength comparable to conventional Portland cement. As a result, temperature and molarity are the main factors affecting the compressive strength of the obtained geopolymer. (author)

  1. Truncated States Obtained by Iteration

    International Nuclear Information System (INIS)

    Cardoso, W. B.; Almeida, N. G. de

    2008-01-01

    We introduce the concept of truncated states obtained via iterative processes (TSI) and study its statistical features, making an analogy with dynamical systems theory (DST). As a specific example, we have studied TSI for the doubling and the logistic functions, which are standard functions in studying chaos. TSI for both the doubling and logistic functions exhibit certain similar patterns when their statistical features are compared from the point of view of DST

  2. Geochemical mapping study of Panjang island

    International Nuclear Information System (INIS)

    Sutisna; Sumardjo

    2010-01-01

    Impact of industrial and regional development are not only related to an improvement of socio-economic, but also to an environmental conservation and sustainable. This impact could be observed on a change of geochemical mapping before and after an operational of the industry. In the relation with a regional development and resources utilization, the geochemical mapping have been done in the aim to know a resources and an elemental distribution at Panjang island. In this research, ko-Instrumental Neutron Activation Analysis (k_0-INAA) have been applied in an elemental quantification on the geochemical mapping. Pencuplikan of geochemical sample have been carried out by using a grid systematic method with a sample density of about 10 sample per square kilometre involved 85 pencuplikan point. The geochemical sample of sediment and soil have been provided as a dry weight of 100 mesh. Internal quality control have done by using a number of Standard Reference Materials obtained from US. Geological Survey. Fifteen elements of Sc, Co, In, Rb, Mo, Ba, Ce, Nd, Eu, La, Yb, Th, U, lr and Hf contained in standard materials have been evaluated. The analysis result show that a relative standard deviation less than 11 %, except for Mo (13 %) and lr (26 %). Fourteen elements of Al, Br, Ca, Co, Eu, Fe, La, U, Na, Ce, Mn, As, Sc and Th have been mapped and presented in this paper. The major elements of Ca, Al and Fe, and minor elements of Mn, U and Sc are distributed at all region. The lanthanide elements of La, Ce and Eu have vary concentration and could be found at the middle to the north of the island. (author)

  3. MAPPING INNOVATION

    DEFF Research Database (Denmark)

    Thuesen, Christian Langhoff; Koch, Christian

    2011-01-01

    By adopting a theoretical framework from strategic niche management research (SNM) this paper presents an analysis of the innovation system of the Danish Construction industry. The analysis shows a multifaceted landscape of innovation around an existing regime, built around existing ways of working...... and developed over generations. The regime is challenged from various niches and the socio-technical landscape through trends as globalization. Three niches (Lean Construction, BIM and System Deliveries) are subject to a detailed analysis showing partly incompatible rationales and various degrees of innovation...... potential. The paper further discusses how existing policymaking operates in a number of tensions one being between government and governance. Based on the concepts from SNM the paper introduces an innovation map in order to support the development of meta-governance policymaking. By mapping some...

  4. Mapping filmmaking

    DEFF Research Database (Denmark)

    Gilje, Øystein; Frølunde, Lisbeth; Lindstrand, Fredrik

    2010-01-01

    This chapter concerns mapping patterns in regards to how young filmmakers (age 15 – 20) in the Scandinavian countries learn about filmmaking. To uncover the patterns, we present portraits of four young filmmakers who participated in the Scandinavian research project Making a filmmaker. The focus ...... is on their learning practices and how they create ‘learning paths’ in relation to resources in diverse learning contexts, whether formal, non-formal and informal contexts.......This chapter concerns mapping patterns in regards to how young filmmakers (age 15 – 20) in the Scandinavian countries learn about filmmaking. To uncover the patterns, we present portraits of four young filmmakers who participated in the Scandinavian research project Making a filmmaker. The focus...

  5. Glassceramics obtained from industrial waste

    Energy Technology Data Exchange (ETDEWEB)

    Cimdins, R.; Rozenstrauha, I.; Berzina, L. [Riga Technical University, Faculty of Chemical Technology, Biomaterials R and D Laboratory, 14/24 Azenes St., LV-1048 Riga (Latvia); Bossert, J.; Buecker, M. [Technisches Institut Materialwissenschaft, Friedrich-Schiller Universitaet, Loebdegraben 32, 07743 Jena (Germany)

    2000-06-01

    Large areas of Latvia are contaminated with industrial waste: metallurgical slag, fly-ash, etching refuse, peat, and coal ash as well as glass waste which often contain dangerous substances. From the environmental point of view this waste should be neutralised. As this waste also contains valuable chemical compounds, it can be considered as a raw material for the generation of new materials. One method of utilisation is to produce recycled materials - street plates, decorative tiles, or floor tiles. Dense sintered glassceramics with a water uptake of 0.34-3.23 wt.%, a final density of 2.93-3.05 g/cm{sup 3}, and a bending strength of 80-96 MPa have been created from industrial waste. The mast chemically durable glassceramics contained clay additions. Thus, the material containing only waste had a durability (mass loss) of 3.02% in 0.1 N HCl, while the composition containing 30% clay addition had a durability of 0.2% in 0.1 N HCl.

  6. Plasticity characteristic obtained by indentation

    International Nuclear Information System (INIS)

    Milman, Yu V

    2008-01-01

    A dimensionless parameter δ H = ε p /ε t (where ε p and ε t are the average values of plastic and total deformation of material on the contact area indenter-specimen) may be used as the plasticity characteristic of materials, which made it possible to characterize the plasticity of materials that are brittle in standard mechanical tests. δ H may be calculated from the values of microhardness HM, Young's modulus E and Poisson's ratio ν. In instrumented indentation the plasticity characteristic δ A = A p /A t (A p and A t are the work of plastic and total deformation during indentation) may be calculated. δ A ∼ δ H for materials with δ H > 0.5, i.e. for all metals and the majority of ceramic materials. In this case, the theoretical equation δ A ∼ δ H = 1-10.2 · (1 - ν - 2ν 2 )(HM/E) is satisfied in experiments with the Berkovich indenter. The influence of the temperature and structural parameters (dislocation density and grain size including nanostructured materials) on δ H is discussed

  7. Obtaining zircaloy powder through hydriding

    International Nuclear Information System (INIS)

    Dupim, Ivaldete da Silva; Moreira, Joao M.L.

    2009-01-01

    Zirconium alloys are good options for the metal matrix in dispersion fuels for power reactors due to their low thermal neutron absorption cross-section, good corrosion resistance, good mechanical strength and high thermal conductivity. A necessary step for obtaining such fuels is producing Zr alloy powder for the metal matrix composite material. This article presents results from the Zircaloy-4 hydrogenation tests with the purpose to embrittle the alloy as a first step for comminuting. Several hydrogenation tests were performed and studied through thermogravimetric analysis. They included H 2 pressures of 25 and 50 kPa and temperatures ranging between from 20 to 670 deg C. X-ray diffraction analysis showed in the hydrogenated samples the predominant presence of ZrH 2 and some ZrO 2 . Some kinetics parameters for the Zircaloy-4 hydrogenation reaction were obtained: the time required to reach the equilibrium state at the dwell temperature was about 100 minutes; the hydrogenation rate during the heating process from 20 to 670 deg C was about 21 mg/h, and at constant temperature of 670 deg C, the hydride rate was about 1.15 mg/h. The hydrogenation rate is largest during the heating process and most of it occurs during this period. After hydrogenated, the samples could easily be comminuted indicating that this is a possible technology to obtain Zircaloy powder. The results show that only few minutes of hydrogenation are necessary to reach the hydride levels required for comminuting the Zircaloy. The final hydride stoichiometry was between 2.7 and 2.8 H for each Zr atom in the sample (author)

  8. The density of cement phases

    International Nuclear Information System (INIS)

    Balonis, M.; Glasser, F.P.

    2009-01-01

    The densities of principal crystalline phases occurring in Portland cement are critically assessed and tabulated, in some cases with addition of new data. A reliable and self-consistent density set for crystalline phases was obtained by calculating densities from crystallographic data and unit cell contents. Independent laboratory work was undertaken to synthesize major AFm and AFt cement phases, determine their unit cell parameters and compare the results with those recorded in the literature. Parameters were refined from powder diffraction patterns using CELREF 2 software. A density value is presented for each phase, showing literature sources, in some cases describing limitations on the data, and the weighting attached to numerical values where an averaging process was used for accepted data. A brief discussion is made of the consequences of the packing of water to density changes in AFm and AFt structures.

  9. Assessment and Mapping of Forest Parcel Sizes

    Science.gov (United States)

    Brett J. Butler; Susan L. King

    2005-01-01

    A method for analyzing and mapping forest parcel sizes in the Northeastern United States is presented. A decision tree model was created that predicts forest parcel size from spatially explicit predictor variables: population density, State, percentage forest land cover, and road density. The model correctly predicted parcel size for 60 percent of the observations in a...

  10. Generating a Danish raster-based topsoil property map combining choropleth maps and point information

    DEFF Research Database (Denmark)

    Greve, Mogens H.; Greve, Mette B.; Bøcher, Peder K.

    2007-01-01

    The Danish environmental authorities have posed a soil type dependent restriction on the application of nitrogen. The official Danish soil map is a choropleth topsoil map classifying the agricultural land into eight classes. The use of the soil map has shown that the maps have serious...... classification flaws. The objective of this work is to compile a continuous national topsoil texture map to replace the old topsoil map. Approximately 45,000 point samples were interpolated using ordinary kriging in 250 m x 250 m cells. To reduce variability and to obtain more homogeneous strata, the samples...... were stratified according to landscape types. Five new soil texture maps were compiled; one for each of the five textural classes, and a new categorical soil type map was compiled using the old classification system. Both the old choropleth map and the new continuous soil maps were compared to 354...

  11. AUTOMATED ASSESSMENT OF EPIDERMAL THICKNESS AND VASCULAR DENSITY OF PORT WINE STAINS OCT IMAGE

    Directory of Open Access Journals (Sweden)

    CHENGMING WANG

    2014-01-01

    Full Text Available Optical coherence tomography (OCT enables in vivo imaging of port wine stains (PWS lesions. The knowledge of vascular structure and epidermal thickness (ET of PWS may aid the objective diagnosis and optimal treatment. To obtain the structural parameters more rapidly and avoid user intervention, an automated algorithm of energy map is introduced based on intensity and edge information to extract the skin surface using dynamic programming method. Subsequently, an averaged A-scan analysis is performed to obtain the mean ET and the relative intensity of dermis indicating the corresponding vascular density. This approach is currently successfully applied in clinical diagnosis and shows promising guidance and assessment of PDT treatment.

  12. THE TURBULENCE SPECTRUM OF MOLECULAR CLOUDS IN THE GALACTIC RING SURVEY: A DENSITY-DEPENDENT PRINCIPAL COMPONENT ANALYSIS CALIBRATION

    International Nuclear Information System (INIS)

    Roman-Duval, Julia; Jackson, James; Federrath, Christoph; Klessen, Ralf S.; Brunt, Christopher; Heyer, Mark

    2011-01-01

    Turbulence plays a major role in the formation and evolution of molecular clouds. Observationally, turbulent velocities are convolved with the density of an observed region. To correct for this convolution, we investigate the relation between the turbulence spectrum of model clouds, and the statistics of their synthetic observations obtained from principal component analysis (PCA). We apply PCA to spectral maps generated from simulated density and velocity fields, obtained from hydrodynamic simulations of supersonic turbulence, and from fractional Brownian motion (fBm) fields with varying velocity, density spectra, and density dispersion. We examine the dependence of the slope of the PCA pseudo-structure function, α PCA , on intermittency, on the turbulence velocity (β v ) and density (β n ) spectral indexes, and on density dispersion. We find that PCA is insensitive to β n and to the log-density dispersion σ s , provided σ s ≤ 2. For σ s > 2, α PCA increases with σ s due to the intermittent sampling of the velocity field by the density field. The PCA calibration also depends on intermittency. We derive a PCA calibration based on fBm structures with σ s ≤ 2 and apply it to 367 13 CO spectral maps of molecular clouds in the Galactic Ring Survey. The average slope of the PCA structure function, (α PCA ) = 0.62 ± 0.2, is consistent with the hydrodynamic simulations and leads to a turbulence velocity exponent of (β v ) = 2.06 ± 0.6 for a non-intermittent, low density dispersion flow. Accounting for intermittency and density dispersion, the coincidence between the PCA slope of the GRS clouds and the hydrodynamic simulations suggests β v ≅ 1.9, consistent with both Burgers and compressible intermittent turbulence.

  13. Density dependent hadron field theory

    International Nuclear Information System (INIS)

    Fuchs, C.; Lenske, H.; Wolter, H.H.

    1995-01-01

    A fully covariant approach to a density dependent hadron field theory is presented. The relation between in-medium NN interactions and field-theoretical meson-nucleon vertices is discussed. The medium dependence of nuclear interactions is described by a functional dependence of the meson-nucleon vertices on the baryon field operators. As a consequence, the Euler-Lagrange equations lead to baryon rearrangement self-energies which are not obtained when only a parametric dependence of the vertices on the density is assumed. It is shown that the approach is energy-momentum conserving and thermodynamically consistent. Solutions of the field equations are studied in the mean-field approximation. Descriptions of the medium dependence in terms of the baryon scalar and vector density are investigated. Applications to infinite nuclear matter and finite nuclei are discussed. Density dependent coupling constants obtained from Dirac-Brueckner calculations with the Bonn NN potentials are used. Results from Hartree calculations for energy spectra, binding energies, and charge density distributions of 16 O, 40,48 Ca, and 208 Pb are presented. Comparisons to data strongly support the importance of rearrangement in a relativistic density dependent field theory. Most striking is the simultaneous improvement of charge radii, charge densities, and binding energies. The results indicate the appearance of a new ''Coester line'' in the nuclear matter equation of state

  14. Acid Deposition Maps in Spain

    International Nuclear Information System (INIS)

    Artinano, B.; Cabal, H.; Garcia, C.

    1998-01-01

    Animal and monthly deposition velocity and total sulfur deposition maps have been performed for the peninsular Spain for 1992 by using the inferential method. To do this, updated databases with high space and time resolution, for land uses (CORINE) and meteorological information from analysis modelling for the same year, have been utilized. The final result are deposition maps in a 5x5 Km 2 grid which allow to assess the methodology used in Europe to obtain the maps of excedances over the critical loads of pollutants. (Author) 32 refs

  15. A Dense Brown Trout (Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity

    Science.gov (United States)

    Leitwein, Maeva; Guinand, Bruno; Pouzadoux, Juliette; Desmarais, Erick; Berrebi, Patrick; Gagnaire, Pierre-Alexandre

    2017-01-01

    High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmo trutta), a socioeconomically important species heavily impacted by human activities. A total of 3977 ddRAD markers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombination distances obtained from two family crosses. Performing map comparison between S. trutta and its sister species, S. salar, revealed extensive chromosomal rearrangements. Strikingly, all of the fusion and fission events that occurred after the S. salar/S. trutta speciation happened in the Atlantic salmon branch, whereas the brown trout remained closer to the ancestral chromosome structure. Using the strongly conserved synteny within chromosome arms, we aligned the brown trout linkage map to the Atlantic salmon genome sequence to estimate the local recombination rate in S. trutta at 3721 loci. A significant positive correlation between recombination rate and within-population nucleotide diversity (π) was found, indicating that selection constrains variation at linked neutral sites in brown trout. This new high-density linkage map provides a useful genomic resource for future aquaculture, conservation, and eco-evolutionary studies in brown trout. PMID:28235829

  16. A Dense Brown Trout (Salmo trutta Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity

    Directory of Open Access Journals (Sweden)

    Maeva Leitwein

    2017-04-01

    Full Text Available High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmo trutta, a socioeconomically important species heavily impacted by human activities. A total of 3977 ddRAD markers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombination distances obtained from two family crosses. Performing map comparison between S. trutta and its sister species, S. salar, revealed extensive chromosomal rearrangements. Strikingly, all of the fusion and fission events that occurred after the S. salar/S. trutta speciation happened in the Atlantic salmon branch, whereas the brown trout remained closer to the ancestral chromosome structure. Using the strongly conserved synteny within chromosome arms, we aligned the brown trout linkage map to the Atlantic salmon genome sequence to estimate the local recombination rate in S. trutta at 3721 loci. A significant positive correlation between recombination rate and within-population nucleotide diversity (π was found, indicating that selection constrains variation at linked neutral sites in brown trout. This new high-density linkage map provides a useful genomic resource for future aquaculture, conservation, and eco-evolutionary studies in brown trout.

  17. Mapping Resilience

    DEFF Research Database (Denmark)

    Carruth, Susan

    2015-01-01

    by planners when aiming to construct resilient energy plans. It concludes that a graphical language has the potential to be a significant tool, flexibly facilitating cross-disciplinary communication and decision-making, while emphasising that its role is to support imaginative, resilient planning rather than...... the relationship between resilience and energy planning, suggesting that planning in, and with, time is a core necessity in this domain. It then reviews four examples of graphically mapping with time, highlighting some of the key challenges, before tentatively proposing a graphical language to be employed...

  18. Mapping of

    Directory of Open Access Journals (Sweden)

    Sayed M. Arafat

    2014-06-01

    Full Text Available Land cover map of North Sinai was produced based on the FAO-Land Cover Classification System (LCCS of 2004. The standard FAO classification scheme provides a standardized system of classification that can be used to analyze spatial and temporal land cover variability in the study area. This approach also has the advantage of facilitating the integration of Sinai land cover mapping products to be included with the regional and global land cover datasets. The total study area is covering a total area of 20,310.4 km2 (203,104 hectare. The landscape classification was based on SPOT4 data acquired in 2011 using combined multispectral bands of 20 m spatial resolution. Geographic Information System (GIS was used to manipulate the attributed layers of classification in order to reach the maximum possible accuracy. GIS was also used to include all necessary information. The identified vegetative land cover classes of the study area are irrigated herbaceous crops, irrigated tree crops and rain fed tree crops. The non-vegetated land covers in the study area include bare rock, bare soils (stony, very stony and salt crusts, loose and shifting sands and sand dunes. The water bodies were classified as artificial perennial water bodies (fish ponds and irrigated canals and natural perennial water bodies as lakes (standing. The artificial surfaces include linear and non-linear features.

  19. Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.

    Directory of Open Access Journals (Sweden)

    Shokeen Bhumika

    2011-02-01

    Full Text Available Abstract Background Chickpea (Cicer arietinum L. is an economically important cool season grain legume crop that is valued for its nutritive seeds having high protein content. However, several biotic and abiotic stresses and the low genetic variability in the chickpea genome have continuously hindered the chickpea molecular breeding programs. STMS (Sequence Tagged Microsatellite Sites markers which are preferred for the construction of saturated linkage maps in several crop species, have also emerged as the most efficient and reliable source for detecting allelic diversity in chickpea. However, the number of STMS markers reported in chickpea is still limited and moreover exhibit low rates of both inter and intraspecific polymorphism, thereby limiting the positions of the SSR markers especially on the intraspecific linkage maps of chickpea. Hence, this study was undertaken with the aim of developing additional STMS markers and utilizing them for advancing the genetic linkage map of chickpea which would have applications in QTL identification, MAS and for de novo assembly of high throughput whole genome sequence data. Results A microsatellite enriched library of chickpea (enriched for (GT/CAn and (GA/CTn repeats was constructed from which 387 putative microsatellite containing clones were identified. From these, 254 STMS primers were designed of which 181 were developed as functional markers. An intraspecific mapping population of chickpea, [ICCV-2 (single podded × JG-62 (double podded] and comprising of 126 RILs, was genotyped for mapping. Of the 522 chickpea STMS markers (including the double-podding trait, screened for parental polymorphism, 226 (43.3% were polymorphic in the parents and were used to genotype the RILs. At a LOD score of 3.5, eight linkage groups defining the position of 138 markers were obtained that spanned 630.9 cM with an average marker density of 4.57 cM. Further, based on the common loci present between the current map

  20. Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Gaur, Rashmi; Sethy, Niroj K; Choudhary, Shalu; Shokeen, Bhumika; Gupta, Varsha; Bhatia, Sabhyata

    2011-02-17

    Chickpea (Cicer arietinum L.) is an economically important cool season grain legume crop that is valued for its nutritive seeds having high protein content. However, several biotic and abiotic stresses and the low genetic variability in the chickpea genome have continuously hindered the chickpea molecular breeding programs. STMS (Sequence Tagged Microsatellite Sites) markers which are preferred for the construction of saturated linkage maps in several crop species, have also emerged as the most efficient and reliable source for detecting allelic diversity in chickpea. However, the number of STMS markers reported in chickpea is still limited and moreover exhibit low rates of both inter and intraspecific polymorphism, thereby limiting the positions of the SSR markers especially on the intraspecific linkage maps of chickpea. Hence, this study was undertaken with the aim of developing additional STMS markers and utilizing them for advancing the genetic linkage map of chickpea which would have applications in QTL identification, MAS and for de novo assembly of high throughput whole genome sequence data. A microsatellite enriched library of chickpea (enriched for (GT/CA)n and (GA/CT)n repeats) was constructed from which 387 putative microsatellite containing clones were identified. From these, 254 STMS primers were designed of which 181 were developed as functional markers. An intraspecific mapping population of chickpea, [ICCV-2 (single podded) × JG-62 (double podded)] and comprising of 126 RILs, was genotyped for mapping. Of the 522 chickpea STMS markers (including the double-podding trait, screened for parental polymorphism, 226 (43.3%) were polymorphic in the parents and were used to genotype the RILs. At a LOD score of 3.5, eight linkage groups defining the position of 138 markers were obtained that spanned 630.9 cM with an average marker density of 4.57 cM. Further, based on the common loci present between the current map and the previously published chickpea

  1. Histogram specification as a method of density modification

    Energy Technology Data Exchange (ETDEWEB)

    Harrison, R.W.

    1988-12-01

    A new method for improving the quality and extending the resolution of Fourier maps is described. The method is based on a histogram analysis of the electron density. The distribution of electron density values in the map is forced to be 'ideal'. The 'ideal' distribution is assumed to be Gaussian. The application of the method to improve the electron density map for the protein Acinetobacter asparaginase, which is a tetrameric enzyme of molecular weight 140000 daltons, is described.

  2. Clinical evaluation of coronary territory map by using unfolded map of Tl-201 myocardial SPECT

    International Nuclear Information System (INIS)

    Uehara, Toshiisa; Nishimura, Tsunehiko; Katafuchi, Tetsuro; Yamagami, Hidetoshi; Kumita, Shinichirou; Hayashida, Kohei; Hayashi, Makoto

    1990-01-01

    Coronary territory map was developed on unfolded map of exercise Tl-201 myocardial SPECT. Each coronary territory was determined by summing the each unfolded map of 54 cases of single vessel disease respectively, and standardizing with normal pattern obtained from normal patients. The diagnostic accuracy of coronary territory map to identify the diseased coronary artery was analyzed in 104 clinical cases and was compared with that of planar and SPECT visual diagnosis, simple unfolded map (raw map) and extent and severity map. The results were as follows. (1) Territory map showed excellent diagnostic accuracy in single or double vessel disease, especially in diagnosis of left circumflex coronary artery lesion. (2) In triple vessel disease, the diagnostic accuracy of territory map or other unfolded maps was 30% at best, and was inferior to planar or SPECT visual analysis. The cause of this inferiority seemed that the quantitatively analyzed map had no information about the degree of Tl-uptake into lung or myocardium, which give useful information in visual diagnosis. (3) The diagnostic agreement ratio in two observers was the highest in territory map diagnosis, so that the territory map diagnosis seemed to be the most objective one. (4) The unfolded map diagnosis with apical display obtained from long-axis tomogram was useful to diagnose left anteior descending coronary (LAD) lesion, which improve not only the sensitivity of LAD but also specificity of right coronary artery single vessel disease. (author)

  3. Drugs obtained by biotechnology processing

    Directory of Open Access Journals (Sweden)

    Hugo Almeida

    2011-06-01

    Full Text Available In recent years, the number of drugs of biotechnological origin available for many different diseases has increased exponentially, including different types of cancer, diabetes mellitus, infectious diseases (e.g. AIDS Virus / HIV as well as cardiovascular, neurological, respiratory, and autoimmune diseases, among others. The pharmaceutical industry has used different technologies to obtain new and promising active ingredients, as exemplified by the fermentation technique, recombinant DNA technique and the hybridoma technique. The expiry of the patents of the first drugs of biotechnological origin and the consequent emergence of biosimilar products, have posed various questions to health authorities worldwide regarding the definition, framework, and requirements for authorization to market such products.Nos últimos anos, tem aumentado exponencialmente o número de fármacos de origem biotecnológica ao dispor das mais diversas patologias, entre elas destacam-se, os diferentes tipos de cancêr, as doenças infecciosas (ex. vírus AIDS/HIV, as doenças autoimunes, as doenças cardiovasculares, a Diabetes Mellitus, as doenças neurológicas, as doenças respiratórias, entre outras. A indústria farmacêutica tem recorrido a diferentes tecnologias para a obtenção de novos e promissores princípios ativos, como são exemplo a fermentação, a técnica de DNA Recombinante, a técnica de hidridoma, entre outras. A queda das patentes dos primeiros fármacos de origem biotecnológica e o consequente aparecimento dos produtos biossimilares têm colocado diferentes questões às autoridades de saúde mundiais, sobre a definição, enquadramento e exigências para a autorização de entrada no mercado deste tipo de produtos.

  4. Mineral density volume gradients in normal and diseased human tissues.

    Directory of Open Access Journals (Sweden)

    Sabra I Djomehri

    Full Text Available Clinical computed tomography provides a single mineral density (MD value for heterogeneous calcified tissues containing early and late stage pathologic formations. The novel aspect of this study is that, it extends current quantitative methods of mapping mineral density gradients to three dimensions, discretizes early and late mineralized stages, identifies elemental distribution in discretized volumes, and correlates measured MD with respective calcium (Ca to phosphorus (P and Ca to zinc (Zn elemental ratios. To accomplish this, MD variations identified using polychromatic radiation from a high resolution micro-computed tomography (micro-CT benchtop unit were correlated with elemental mapping obtained from a microprobe X-ray fluorescence (XRF using synchrotron monochromatic radiation. Digital segmentation of tomograms from normal and diseased tissues (N=5 per group; 40-60 year old males contained significant mineral density variations (enamel: 2820-3095 mg/cc, bone: 570-1415 mg/cc, cementum: 1240-1340 mg/cc, dentin: 1480-1590 mg/cc, cementum affected by periodontitis: 1100-1220 mg/cc, hypomineralized carious dentin: 345-1450 mg/cc, hypermineralized carious dentin: 1815-2740 mg/cc, and dental calculus: 1290-1770 mg/cc. A plausible linear correlation between segmented MD volumes and elemental ratios within these volumes was established, and Ca/P ratios for dentin (1.49, hypomineralized dentin (0.32-0.46, cementum (1.51, and bone (1.68 were observed. Furthermore, varying Ca/Zn ratios were distinguished in adapted compared to normal tissues, such as in bone (855-2765 and in cementum (595-990, highlighting Zn as an influential element in prompting observed adaptive properties. Hence, results provide insights on mineral density gradients with elemental concentrations and elemental footprints that in turn could aid in elucidating mechanistic processes for pathologic formations.

  5. Mineral Density Volume Gradients in Normal and Diseased Human Tissues

    Science.gov (United States)

    Djomehri, Sabra I.; Candell, Susan; Case, Thomas; Browning, Alyssa; Marshall, Grayson W.; Yun, Wenbing; Lau, S. H.; Webb, Samuel; Ho, Sunita P.

    2015-01-01

    Clinical computed tomography provides a single mineral density (MD) value for heterogeneous calcified tissues containing early and late stage pathologic formations. The novel aspect of this study is that, it extends current quantitative methods of mapping mineral density gradients to three dimensions, discretizes early and late mineralized stages, identifies elemental distribution in discretized volumes, and correlates measured MD with respective calcium (Ca) to phosphorus (P) and Ca to zinc (Zn) elemental ratios. To accomplish this, MD variations identified using polychromatic radiation from a high resolution micro-computed tomography (micro-CT) benchtop unit were correlated with elemental mapping obtained from a microprobe X-ray fluorescence (XRF) using synchrotron monochromatic radiation. Digital segmentation of tomograms from normal and diseased tissues (N=5 per group; 40-60 year old males) contained significant mineral density variations (enamel: 2820-3095mg/cc, bone: 570-1415mg/cc, cementum: 1240-1340mg/cc, dentin: 1480-1590mg/cc, cementum affected by periodontitis: 1100-1220mg/cc, hypomineralized carious dentin: 345-1450mg/cc, hypermineralized carious dentin: 1815-2740mg/cc, and dental calculus: 1290-1770mg/cc). A plausible linear correlation between segmented MD volumes and elemental ratios within these volumes was established, and Ca/P ratios for dentin (1.49), hypomineralized dentin (0.32-0.46), cementum (1.51), and bone (1.68) were observed. Furthermore, varying Ca/Zn ratios were distinguished in adapted compared to normal tissues, such as in bone (855-2765) and in cementum (595-990), highlighting Zn as an influential element in prompting observed adaptive properties. Hence, results provide insights on mineral density gradients with elemental concentrations and elemental footprints that in turn could aid in elucidating mechanistic processes for pathologic formations. PMID:25856386

  6. Rapid myelin water content mapping on clinical MR systems

    International Nuclear Information System (INIS)

    Tonkova, Vyara; Arhelger, Volker; Schenk, Jochen; Neeb, Heiko; Koblenz Univ.

    2012-01-01

    We present an algorithm for the fast mapping of myelin water content using standard multiecho gradient echo acquisitions of the human brain. The method extents a previously published approach for the simultaneous measurement of brain T 1 , T * 2 and total water content. Employing the multiexponential T * 2 decay signal of myelinated tissue, myelin water content was measured based on the quantification of two water pools ('myelin water' and 'rest') with different relaxation times. As the existing protocol was focussed on the fast mapping of quantitative MR parameters with whole brain coverage in clinically relevant measurement times, the sampling density of the T * 2 curve was compromised to 10 echo times with a T Emax of approx. 40 ms. Therefore, pool amplitudes were determined using a quadratic optimisation approach. The optimisation was constrained by including a priori knowledge about brain water pools. All constraints were optimised in a simulation study to minimise systematic error sources given the incomplete knowledge about the real pool-specific relaxation properties. Based on the simulation results, whole brain in vivo myelin water content maps were acquired in 10 healthy controls and one subject with multiple sclerosis. The in vivo results obtained were consistent with previous reports which demonstrates that a simultaneous whole brain mapping of T 1 , T * 2 , total and myelin water content is feasible on almost any modern MR scanner in less than 10 minutes. (orig.)

  7. A comparative study of density functional and density functional tight binding calculations of defects in graphene

    Energy Technology Data Exchange (ETDEWEB)

    Zobelli, Alberto [Laboratoire de Physique des Solides, Univ. Paris Sud, CNRS UMR, Orsay (France); Ivanovskaya, Viktoria; Wagner, Philipp; Yaya, Abu; Ewels, Chris P. [Institut des Materiaux Jean Rouxel (IMN), CNRS UMR, University of Nantes (France); Suarez-Martinez, Irene [Nanochemistry Research Institute, Curtin University of Technology, Perth, Western Australia (Australia)

    2012-02-15

    The density functional tight binding approach (DFTB) is well adapted for the study of point and line defects in graphene based systems. After briefly reviewing the use of DFTB in this area, we present a comparative study of defect structures, energies, and dynamics between DFTB results obtained using the dftb+ code, and density functional results using the localized Gaussian orbital code, AIMPRO. DFTB accurately reproduces structures and energies for a range of point defect structures such as vacancies and Stone-Wales defects in graphene, as well as various unfunctionalized and hydroxylated graphene sheet edges. Migration barriers for the vacancy and Stone-Wales defect formation barriers are accurately reproduced using a nudged elastic band approach. Finally we explore the potential for dynamic defect simulations using DFTB, taking as an example electron irradiation damage in graphene. DFTB-MD derived sputtering energy threshold map for a carbon atom in a graphene plane. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  8. Automated structure solution, density modification and model building.

    Science.gov (United States)

    Terwilliger, Thomas C

    2002-11-01

    The approaches that form the basis of automated structure solution in SOLVE and RESOLVE are described. The use of a scoring scheme to convert decision making in macromolecular structure solution to an optimization problem has proven very useful and in many cases a single clear heavy-atom solution can be obtained and used for phasing. Statistical density modification is well suited to an automated approach to structure solution because the method is relatively insensitive to choices of numbers of cycles and solvent content. The detection of non-crystallographic symmetry (NCS) in heavy-atom sites and checking of potential NCS operations against the electron-density map has proven to be a reliable method for identification of NCS in most cases. Automated model building beginning with an FFT-based search for helices and sheets has been successful in automated model building for maps with resolutions as low as 3 A. The entire process can be carried out in a fully automatic fashion in many cases.

  9. Towards mapping the Dioscorea genome

    International Nuclear Information System (INIS)

    Terauchi, R.; Kahl, G.

    1998-01-01

    Yams are important starchy tuber crops in (sub-) tropical countries of the world. Despite their importance in the regional economy, no serious attempt has been made toward their improvement. In order to obtain basic knowledge of the genetics of yams, we are trying to establish a linkage map of a wild yam species, Dioscorea tokoro. So far, six allozyme markers, six STMS markers and twenty AFLP markers have been identified. They will be used for linkage mapping of a population comprising 80 progeny obtained from a controlled cross. (author)

  10. The response analysis of fractional-order stochastic system via generalized cell mapping method.

    Science.gov (United States)

    Wang, Liang; Xue, Lili; Sun, Chunyan; Yue, Xiaole; Xu, Wei

    2018-01-01

    This paper is concerned with the response of a fractional-order stochastic system. The short memory principle is introduced to ensure that the response of the system is a Markov process. The generalized cell mapping method is applied to display the global dynamics of the noise-free system, such as attractors, basins of attraction, basin boundary, saddle, and invariant manifolds. The stochastic generalized cell mapping method is employed to obtain the evolutionary process of probability density functions of the response. The fractional-order ϕ 6 oscillator and the fractional-order smooth and discontinuous oscillator are taken as examples to give the implementations of our strategies. Studies have shown that the evolutionary direction of the probability density function of the fractional-order stochastic system is consistent with the unstable manifold. The effectiveness of the method is confirmed using Monte Carlo results.

  11. Strange distributionally chaotic triangular maps

    International Nuclear Information System (INIS)

    Paganoni, L.; Smital, J.

    2005-01-01

    The notion of distributional chaos was introduced by Schweizer, Smital [Measures of chaos and a spectral decompostion of dynamical systems on the interval. Trans. Amer. Math. Soc. 344;1994:737-854] for continuous maps of the interval. For continuous maps of a compact metric space three mutually nonequivalent versions of distributional chaos, DC1-DC3, can be considered. In this paper we study distributional chaos in the class T m of triangular maps of the square which are monotone on the fibres; such maps must have zero topological entropy. The main results: (i) There is an F-bar T m such that F-bar DC2 and F vertical bar Rec(F)-bar DC3. (ii) If no ω-limit set of an F-bar T m contains two minimal subsets then F-bar DC1. This completes recent results obtained by Forti et al. [Dynamics of homeomorphisms on minimal sets generated by triangular mappings. Bull Austral Math Soc 59;1999:1-20], Smital, Stefankova [Distributional chaos for triangular maps, Chaos, Solitons and Fractals 21;2004:1125-8], and Balibrea et al. [The three versions of distributional chaos. Chaos, Solitons and Fractals 23;2005:1581-3]. The paper contributes to the solution of a long-standing open problem by Sharkovsky concerning classification of triangular maps

  12. Mapping the brain

    International Nuclear Information System (INIS)

    Begley, S.; Wright, L.; Church, V.; Hager, M.

    1992-01-01

    With powerful new technologies such as positron tomography and superconducting quantum interference device that peer through the skull and see the brain at work, neuroscientists seek the wellsprings of thoughts and emotions, the genesis of intelligence and language. A functional map of the brain is thus obtained and its challenge is to move beyond brain structure to create a detailed diagram of which part do what. For that the brain's cartographers rely on a variety of technologies such as positron tomography and superconducting quantum interference devices. Their performances and uses are briefly reviewed. ills

  13. Soviet contributions towards MAP/WINE

    Science.gov (United States)

    Rapoport, Z. Ts.; Kazimirovsky, E. S.

    In the winter of 1983/1984, the research institutes of the Soviet Union took an active part in the accomplishment of the project ``Winter in Northern Europe'' of the Middle Atmosphere Program (MAP/WINE). Different methods were used to measure temperature, direction and velocity of wind, turbulence, electron density in the lower ionosphere, and radio wave absorption. The study of the stratospheric warmings and the related changes in the mesosphere and lower ionosphere was considered of special importance. The analysis of the obtained data has shown, in particular, that during stratospheric warmings the westerly wind in wintertime becomes weaker and even reverses. At the same time period the electron density and the radio wave absorption in the lower ionosphere are often reduced. It is also observed that the high absorption zones move from west to east. These results confirm the concept about the role of the cyclonic circumpolar vortex in the transport of the auroral air to temperate latitudes and about the appearance of conditions for the winter anomalous radio wave absorption.

  14. Mapping the universe.

    Science.gov (United States)

    Geller, M J; Huchra, J P

    1989-11-17

    Maps of the galaxy distribution in the nearby universe reveal large coherent structures. The extent of the largest features is limited only by the size of the survey. Voids with a density typically 20 percent of the mean and with diameters of 5000 km s(-1) are present in every survey large enough to contain them. Many galaxies lie in thin sheet-like structures. The largest sheet detected so far is the "Great Wall" with a minimum extent of 60 h(-1) Mpc x 170 h(-1) Mpc, where h is the Hubble constant in units of 100 km s(-1) Mpc(-1). The frequent occurrence of these structures is one of several serious challenges to our current understanding of the origin and evolution of the large-scale distribution of matter in the universe.

  15. Ground penetrating radar evaluation of new pavement density.

    Science.gov (United States)

    2015-02-01

    The objective of this project was to map pavement surface density variations using dielectric : measurements from ground penetrating radar (GPR). The work was carried out as part of an : Asphalt Intelligent Compaction demonstration project on SR 539 ...

  16. Landslide susceptibility mapping using AHP method and GIS in the peninsula of Tangier (Rif-northern morocco

    Directory of Open Access Journals (Sweden)

    Ait Brahim L

    2018-01-01

    Full Text Available The peninsula of Tangier (Northern Morocco is submitted to a significant number of landslides each year due to its lithological, structural and morphological complexity; which cause a lot of damage to the road network and other related infrastructure. The main objective of this study is to create a landslide indexed susceptibility map of Tangier peninsula, by using AHP (Analytical Hierarchical Processes model to calculate each factor’s weight. The work is made via GIS by using an ArcGIS AHP extension. In the current research, First of all, the four main types of landslides were identified and mapped from existing documents, works and new data which came from either remote sensing or fieldwork. Lithology, land use, slope, hypsometry, exposure, fault density and drainage network density were used as main parameters controlling the occurrence of the selected landslides. Then, afterward, each parameter is classified into a number of significant classes based on their relative influence on gravitational movement genesis. The validity of the susceptibility zoning map which is obtained through linear summation of indexed maps was tested and cross-checked by inventoried and studied landslides. The obtained landslide susceptibility map constitutes a powerful decision-making tool in land-use planning, i.e. New highways, secondary highways, railways, etc. within the national development program in the Northern provinces. It is a necessary step for the landslides hazard assessment in the Tangier peninsula in northern Morocco.

  17. Density Distribution Sunflower Plots

    Directory of Open Access Journals (Sweden)

    William D. Dupont

    2003-01-01

    Full Text Available Density distribution sunflower plots are used to display high-density bivariate data. They are useful for data where a conventional scatter plot is difficult to read due to overstriking of the plot symbol. The x-y plane is subdivided into a lattice of regular hexagonal bins of width w specified by the user. The user also specifies the values of l, d, and k that affect the plot as follows. Individual observations are plotted when there are less than l observations per bin as in a conventional scatter plot. Each bin with from l to d observations contains a light sunflower. Other bins contain a dark sunflower. In a light sunflower each petal represents one observation. In a dark sunflower, each petal represents k observations. (A dark sunflower with p petals represents between /2-pk k and /2+pk k observations. The user can control the sizes and colors of the sunflowers. By selecting appropriate colors and sizes for the light and dark sunflowers, plots can be obtained that give both the overall sense of the data density distribution as well as the number of data points in any given region. The use of this graphic is illustrated with data from the Framingham Heart Study. A documented Stata program, called sunflower, is available to draw these graphs. It can be downloaded from the Statistical Software Components archive at http://ideas.repec.org/c/boc/bocode/s430201.html . (Journal of Statistical Software 2003; 8 (3: 1-5. Posted at http://www.jstatsoft.org/index.php?vol=8 .

  18. U3O8 obtained from metallic uranium

    International Nuclear Information System (INIS)

    Lopez, Marisol; Gonzalez, Alfredo; Pasqualini, Enrique E.

    2003-01-01

    Enriched uranium oxide, U 3 O 8 , used as nuclear powder in MTR's, can be obtained by direct oxidation of metallic uranium at 800 C degrees. Maximum density, 8.2 gr/cm 3 , is achieved after grinding and a high temperature treatment at 1400 C degrees. All the process is highly controllable and performed in dry environments. (author)

  19. Imaginary time density-density correlations for two-dimensional electron gases at high density

    Energy Technology Data Exchange (ETDEWEB)

    Motta, M.; Galli, D. E. [Dipartimento di Fisica, Università degli Studi di Milano, Via Celoria 16, 20133 Milano (Italy); Moroni, S. [IOM-CNR DEMOCRITOS National Simulation Center and SISSA, Via Bonomea 265, 34136 Trieste (Italy); Vitali, E. [Department of Physics, College of William and Mary, Williamsburg, Virginia 23187-8795 (United States)

    2015-10-28

    We evaluate imaginary time density-density correlation functions for two-dimensional homogeneous electron gases of up to 42 particles in the continuum using the phaseless auxiliary field quantum Monte Carlo method. We use periodic boundary conditions and up to 300 plane waves as basis set elements. We show that such methodology, once equipped with suitable numerical stabilization techniques necessary to deal with exponentials, products, and inversions of large matrices, gives access to the calculation of imaginary time correlation functions for medium-sized systems. We discuss the numerical stabilization techniques and the computational complexity of the methodology and we present the limitations related to the size of the systems on a quantitative basis. We perform the inverse Laplace transform of the obtained density-density correlation functions, assessing the ability of the phaseless auxiliary field quantum Monte Carlo method to evaluate dynamical properties of medium-sized homogeneous fermion systems.

  20. Digital radioisotope moisture-density meter

    International Nuclear Information System (INIS)

    Bychvarov, N.; Vankov, I.; Dimitrov, L.

    1982-01-01

    The primary information from the detectors of a combined radioisotope moisture-density meter is obtained as pulses, their counting rate being functionally dependent on the humidity per unit volume and the wet density. However, most practical cases demand information on the moisture per unit weight and the mass density of the dry skeleton. The paper describes how the proposed electronic circuit processes the input primary information to obtain the moisture in weight % and the mass density of the dry skeleton in g/cm 3 . (authors)

  1. The application of GBS markers for extending the dense genetic map of rye (Secale cereale L.) and the localization of the Rfc1 gene restoring male fertility in plants with the C source of sterility-inducing cytoplasm.

    Science.gov (United States)

    Milczarski, Paweł; Hanek, Monika; Tyrka, Mirosław; Stojałowski, Stefan

    2016-11-01

    Genotyping by sequencing (GBS) is an efficient method of genotyping in numerous plant species. One of the crucial steps toward the application of GBS markers in crop improvement is anchoring them on particular chromosomes. In rye (Secale cereale L.), chromosomal localization of GBS markers has not yet been reported. In this paper, the application of GBS markers generated by the DArTseq platform for extending the high-density map of rye is presented. Additionally, their application is used for the localization of the Rfc1 gene that restores male fertility in plants with the C source of sterility-inducing cytoplasm. The total number of markers anchored on the current version of the map is 19,081, of which 18,132 were obtained from the DArTseq platform. Numerous markers co-segregated within the studied mapping population, so, finally, only 3397 unique positions were located on the map of all seven rye chromosomes. The total length of the map is 1593 cM and the average distance between markers is 0.47 cM. In spite of the resolution of the map being not very high, it should be a useful tool for further studies of the Secale cereale genome because of the presence on this map of numerous GBS markers anchored for the first time on rye chromosomes. The Rfc1 gene was located on high-density maps of the long arm of the 4R chromosome obtained for two mapping populations. Genetic maps were composed of DArT, DArTseq, and PCR-based markers. Consistent mapping results were obtained and DArTs tightly linked to the Rfc1 gene were successfully applied for the development of six new PCR-based markers useful in marker-assisted selection.

  2. Spatially resolved determination of the short-circuit current density of silicon solar cells via lock-in thermography

    International Nuclear Information System (INIS)

    Fertig, Fabian; Greulich, Johannes; Rein, Stefan

    2014-01-01

    We present a spatially resolved method to determine the short-circuit current density of crystalline silicon solar cells by means of lock-in thermography. The method utilizes the property of crystalline silicon solar cells that the short-circuit current does not differ significantly from the illuminated current under moderate reverse bias. Since lock-in thermography images locally dissipated power density, this information is exploited to extract values of spatially resolved current density under short-circuit conditions. In order to obtain an accurate result, one or two illuminated lock-in thermography images and one dark lock-in thermography image need to be recorded. The method can be simplified in a way that only one image is required to generate a meaningful short-circuit current density map. The proposed method is theoretically motivated, and experimentally validated for monochromatic illumination in comparison to the reference method of light-beam induced current.

  3. Evaluation of biodiesel obtained from cottonseed oil

    Energy Technology Data Exchange (ETDEWEB)

    Rashid, Umer [Department of Chemistry and Biochemistry, University of Agriculture, Faisalabad-38040 (Pakistan); Department of Industrial Chemistry, Government College University, Faisalabad-38000 (Pakistan); Anwar, Farooq [Department of Chemistry and Biochemistry, University of Agriculture, Faisalabad-38040 (Pakistan); Knothe, Gerhard [United States Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL 61604 (United States)

    2009-09-15

    Esters from vegetable oils have attracted a great deal of interest as substitutes for petrodiesel to reduce dependence on imported petroleum and provide a fuel with more benign environmental properties. In this work biodiesel was prepared from cottonseed oil by transesterification with methanol, using sodium hydroxide, potassium hydroxide, sodium methoxide and potassium methoxide as catalysts. A series of experiments were conducted in order to evaluate the effects of reaction variables such as methanol/oil molar ratio (3:1-15:1), catalyst concentration (0.25-1.50%), temperature (25-65 C), and stirring intensity (180-600 rpm) to achieve the maximum yield and quality. The optimized variables of 6:1 methanol/oil molar ratio (mol/mol), 0.75% sodium methoxide concentration (wt.%), 65 C reaction temperature, 600 rpm agitation speed and 90 min reaction time offered the maximum methyl ester yield (96.9%). The obtained fatty acid methyl esters (FAME) were analyzed by gas chromatography (GC) and {sup 1}H NMR spectroscopy. The fuel properties of cottonseed oil methyl esters (COME), cetane number, kinematic viscosity, oxidative stability, lubricity, cloud point, pour point, cold filter plugging point, flash point, ash content, sulfur content, acid value, copper strip corrosion value, density, higher heating value, methanol content, free and bound glycerol were determined and are discussed in the light of biodiesel standards such as ASTM D6751 and EN 14214. (author)

  4. Human Mind Maps

    Science.gov (United States)

    Glass, Tom

    2016-01-01

    When students generate mind maps, or concept maps, the maps are usually on paper, computer screens, or a blackboard. Human Mind Maps require few resources and little preparation. The main requirements are space where students can move around and a little creativity and imagination. Mind maps can be used for a variety of purposes, and Human Mind…

  5. Laboratory Density Functionals

    OpenAIRE

    Giraud, B. G.

    2007-01-01

    We compare several definitions of the density of a self-bound system, such as a nucleus, in relation with its center-of-mass zero-point motion. A trivial deconvolution relates the internal density to the density defined in the laboratory frame. This result is useful for the practical definition of density functionals.

  6. Fractional equations of kicked systems and discrete maps

    International Nuclear Information System (INIS)

    Tarasov, Vasily E; Zaslavsky, George M

    2008-01-01

    Starting from kicked equations of motion with derivatives of non-integer orders, we obtain 'fractional' discrete maps. These maps are generalizations of well-known universal, standard, dissipative, kicked damped rotator maps. The main property of the suggested fractional maps is a long-term memory. The memory effects in the fractional discrete maps mean that their present state evolution depends on all past states with special forms of weights. These forms are represented by combinations of power-law functions

  7. Trace maps of general substitutional sequences

    International Nuclear Information System (INIS)

    Kolar, M.; Nori, F.

    1990-01-01

    It is shown that for arbitrary n, there exists a trace map for any n-letter substitutional sequence. Trace maps are explicitly obtained for the well-known circle and Rudin-Shapiro sequences which can be defined by means of substitution rules on three and four letters, respectively. The properties of the two trace maps and their consequences for various spectral properties are briefly discussed

  8. Electron densities in planetary nebulae

    International Nuclear Information System (INIS)

    Stanghellini, L.; Kaler, J.B.

    1989-01-01

    Electron densities for 146 planetary nebulae have been obtained for analyzing a large sample of forbidden lines by interpolating theoretical curves obtained from solutions of the five-level atoms using up-to-date collision strengths and transition probabilities. Electron temperatures were derived from forbidden N II and/or forbidden O III lines or were estimated from the He II 4686 A line strengths. The forbidden O II densities are generally lower than those from forbidden Cl III by an average factor of 0.65. For data sets in which forbidden O II and forbidden S II were observed in common, the forbidden O II values drop to 0.84 that of the forbidden S II, implying that the outermost parts of the nebulae might have elevated densities. The forbidden Cl II and forbidden Ar IV densities show the best correlation, especially where they have been obtained from common data sets. The data give results within 30 percent of one another, assuming homogeneous nebulae. 106 refs

  9. Maps & minds : mapping through the ages

    Science.gov (United States)

    ,

    1984-01-01

    Throughout time, maps have expressed our understanding of our world. Human affairs have been influenced strongly by the quality of maps available to us at the major turning points in our history. "Maps & Minds" traces the ebb and flow of a few central ideas in the mainstream of mapping. Our expanding knowledge of our cosmic neighborhood stems largely from a small number of simple but grand ideas, vigorously pursued.

  10. Lunar Map Catalog

    Data.gov (United States)

    National Aeronautics and Space Administration — The Lunar Map Catalog includes various maps of the moon's surface, including Apollo landing sites; earthside, farside, and polar charts; photography index maps; zone...

  11. Baby Brain Map

    Science.gov (United States)

    ... a Member Home Resources & Services Professional Resource Baby Brain Map Mar 17, 2016 The Brain Map was adapted in 2006 by ZERO TO ... supports Adobe Flash Player. To view the Baby Brain Map, please visit this page on a browser ...

  12. Snapshots for Semantic Maps

    National Research Council Canada - National Science Library

    Nielsen, Curtis W; Ricks, Bob; Goodrich, Michael A; Bruemmer, David; Few, Doug; Walton, Miles

    2004-01-01

    .... Semantic maps are a relatively new approach to information presentation. Semantic maps provide more detail about an environment than typical maps because they are augmented by icons or symbols that provide meaning for places or objects of interest...

  13. A unifying probabilistic Bayesian approach to derive electron density from MRI for radiation therapy treatment planning

    International Nuclear Information System (INIS)

    Gudur, Madhu Sudhan Reddy; Hara, Wendy; Le, Quynh-Thu; Wang, Lei; Xing, Lei; Li, Ruijiang

    2014-01-01

    MRI significantly improves the accuracy and reliability of target delineation in radiation therapy for certain tumors due to its superior soft tissue contrast compared to CT. A treatment planning process with MRI as the sole imaging modality will eliminate systematic CT/MRI co-registration errors, reduce cost and radiation exposure, and simplify clinical workflow. However, MRI lacks the key electron density information necessary for accurate dose calculation and generating reference images for patient setup. The purpose of this work is to develop a unifying method to derive electron density from standard T1-weighted MRI. We propose to combine both intensity and geometry information into a unifying probabilistic Bayesian framework for electron density mapping. For each voxel, we compute two conditional probability density functions (PDFs) of electron density given its: (1) T1-weighted MRI intensity, and (2) geometry in a reference anatomy, obtained by deformable image registration between the MRI of the atlas and test patient. The two conditional PDFs containing intensity and geometry information are combined into a unifying posterior PDF, whose mean value corresponds to the optimal electron density value under the mean-square error criterion. We evaluated the algorithm’s accuracy of electron density mapping and its ability to detect bone in the head for eight patients, using an additional patient as the atlas or template. Mean absolute HU error between the estimated and true CT, as well as receiver operating characteristics for bone detection (HU > 200) were calculated. The performance was compared with a global intensity approach based on T1 and no density correction (set whole head to water). The proposed technique significantly reduced the errors in electron density estimation, with a mean absolute HU error of 126, compared with 139 for deformable registration (p = 2  ×  10 −4 ), 283 for the intensity approach (p = 2  ×  10 −6 ) and 282

  14. Cannabis publication analysis using density-equalising mapping ...

    African Journals Online (AJOL)

    University, Berlin, Germany. Conclusion. ... this time could therefore be illustrated accurately, and it was possible to .... Thirty-one per cent of Dutch and 25% of German cannabis ..... Glowniak J. History, structure, and function of the Internet.

  15. Cannabis publication analysis using density-equalising mapping ...

    African Journals Online (AJOL)

    class C drug, causing widespread concern among health care workers and the ... 'Coffee shops are tolerated in the attempt to keep young people, who experiment with ... LaGuardia,4 in which he stated that cannabis consumption leads to tolerance ..... Consciousness under the influence of Cannabis indica. Science. 1893 ...

  16. Subsurface density mapping of the earth with cosmic ray muons

    Energy Technology Data Exchange (ETDEWEB)

    Tanaka, Hiroyuki K.M. [Earthquake Research Institute, The University of Tokyo, 113-0032 Tokyo (Japan)

    2013-10-15

    Since its original discovery by Wilhelm Conrad Rontgen in 1895, one of the directions of researchers pursued was an application of x-ray radiography to larger objects, while the advent of high voltage x-ray tubes allowed radiographs of industrial objects to be produced in a reasonable amount of time. In spite of the great motivation we have to survey the earth's interior, we now know that x rays are not sufficiently penetrative to successfully target geophysical objects. Our current knowledge about the cross sections of the muon with matter solves the problem about this x-ray's inspectable size limit. These particles do not interact strongly with matter, and those with relativistic momentum travel long distances penetrating deep into rock. By tracking the ray paths of the muon after passing through the object, the method gives researchers the ability to study the earth in new ways. The purpose of this article is to review recent progress in probing the earth's interior with muons.

  17. Cannabis publication analysis using density-equalising mapping ...

    African Journals Online (AJOL)

    Background. Cannabis has been a topic of political and medical controversy in many countries over the past century. Although many publications on this topic are available, there is currently no comprehensive evaluation of global research activities in the field. Objective. This study was conducted in order to provide a ...

  18. Random unitary maps for quantum state reconstruction

    International Nuclear Information System (INIS)

    Merkel, Seth T.; Riofrio, Carlos A.; Deutsch, Ivan H.; Flammia, Steven T.

    2010-01-01

    We study the possibility of performing quantum state reconstruction from a measurement record that is obtained as a sequence of expectation values of a Hermitian operator evolving under repeated application of a single random unitary map, U 0 . We show that while this single-parameter orbit in operator space is not informationally complete, it can be used to yield surprisingly high-fidelity reconstruction. For a d-dimensional Hilbert space with the initial observable in su(d), the measurement record lacks information about a matrix subspace of dimension ≥d-2 out of the total dimension d 2 -1. We determine the conditions on U 0 such that the bound is saturated, and show they are achieved by almost all pseudorandom unitary matrices. When we further impose the constraint that the physical density matrix must be positive, we obtain even higher fidelity than that predicted from the missing subspace. With prior knowledge that the state is pure, the reconstruction will be perfect (in the limit of vanishing noise) and for arbitrary mixed states, the fidelity is over 0.96, even for small d, and reaching F>0.99 for d>9. We also study the implementation of this protocol based on the relationship between random matrices and quantum chaos. We show that the Floquet operator of the quantum kicked top provides a means of generating the required type of measurement record, with implications on the relationship between quantum chaos and information gain.

  19. Density dependence of the nuclear energy-density functional

    Science.gov (United States)

    Papakonstantinou, Panagiota; Park, Tae-Sun; Lim, Yeunhwan; Hyun, Chang Ho

    2018-01-01

    Background: The explicit density dependence in the coupling coefficients entering the nonrelativistic nuclear energy-density functional (EDF) is understood to encode effects of three-nucleon forces and dynamical correlations. The necessity for the density-dependent coupling coefficients to assume the form of a preferably small fractional power of the density ρ is empirical and the power is often chosen arbitrarily. Consequently, precision-oriented parametrizations risk overfitting in the regime of saturation and extrapolations in dilute or dense matter may lose predictive power. Purpose: Beginning with the observation that the Fermi momentum kF, i.e., the cubic root of the density, is a key variable in the description of Fermi systems, we first wish to examine if a power hierarchy in a kF expansion can be inferred from the properties of homogeneous matter in a domain of densities, which is relevant for nuclear structure and neutron stars. For subsequent applications we want to determine a functional that is of good quality but not overtrained. Method: For the EDF, we fit systematically polynomial and other functions of ρ1 /3 to existing microscopic, variational calculations of the energy of symmetric and pure neutron matter (pseudodata) and analyze the behavior of the fits. We select a form and a set of parameters, which we found robust, and examine the parameters' naturalness and the quality of resulting extrapolations. Results: A statistical analysis confirms that low-order terms such as ρ1 /3 and ρ2 /3 are the most relevant ones in the nuclear EDF beyond lowest order. It also hints at a different power hierarchy for symmetric vs. pure neutron matter, supporting the need for more than one density-dependent term in nonrelativistic EDFs. The functional we propose easily accommodates known or adopted properties of nuclear matter near saturation. More importantly, upon extrapolation to dilute or asymmetric matter, it reproduces a range of existing microscopic

  20. The Thermal Entropy Density of Spacetime

    Directory of Open Access Journals (Sweden)

    Rongjia Yang

    2013-01-01

    Full Text Available Introducing the notion of thermal entropy density via the first law of thermodynamics and assuming the Einstein equation as an equation of thermal state, we obtain the thermal entropy density of any arbitrary spacetime without assuming a temperature or a horizon. The results confirm that there is a profound connection between gravity and thermodynamics.

  1. Polarizable Density Embedding Coupled Cluster Method

    DEFF Research Database (Denmark)

    Hršak, Dalibor; Olsen, Jógvan Magnus Haugaard; Kongsted, Jacob

    2018-01-01

    by an embedding potential consisting of a set of fragment densities obtained from calculations on isolated fragments with a quantum-chemistry method such as Hartree-Fock (HF) or Kohn-Sham density functional theory (KS-DFT) and dressed with a set of atom-centered anisotropic dipole-dipole polarizabilities...

  2. Liquid fuel obtain from polypropylene (PP-5) and high density polyethylene (HDPE-2) waste plastics mixture

    Energy Technology Data Exchange (ETDEWEB)

    Sarker, Moinuddin; Rashid, Mohammad Mamunor; Rahman, Md. Sadikur; Molla, Mohammed [Department of Research and Development, Natural State Research Inc, Stamford, (United States)

    2011-07-01

    Plastics are made by combination of small based molecules to form monomers. The monomers are then joined together by chemical polymerization mechanism to form polymers also known as plastics. These plastics contain various elements such as carbon, hydrogen, oxygen, nitrogen, chlorine and sul fur. The use of plastics is vastly expanded and it is being used in every sector of the world. However, using plastics does have a negative aspect, after use they end up in our landfill as waste causing numerous health and environmental problems. Landfill waste plastics release harmful gases due to the presence of carbon, chlorine and sul fur in them into the atmosphere causing climates to change drastically, equivalent to the effects of greenhouse gases (GHG) emission. To overcome these environmental issues, scientists have already developed many methods to converting these waste plastics into energy and fuel . We developed one new methods thermal cracking conversion to convert these waste plastics into usable liquid fuel . Thermal cracking conversion is a process to shorten the long chain hydrocarbons to produce liquid fuel in the absence of a catalyst. The thermal degradation process of the waste plastics long chain hydrocarbon to makes short chain hydrocarbon fuel. The fuel produced has been analyzed and tested according to standard methods. Key words: fuel , hydrocarbon, waste plastic, thermal degradation, conversion, GC/MS.

  3. Liquid fuel obtain from polypropylene (PP-5) and high density polyethylene (HDPE-2) waste plastics mixture

    International Nuclear Information System (INIS)

    Sarker, Moinuddin; Rashid, Mohammad Mamunor; Rahman, Md. Sadikur; Molla, Mohammed

    2011-01-01

    Plastics are made by combination of small based molecules to form monomers. The monomers are then joined together by chemical polymerization mechanism to form polymers also known as plastics. These plastics contain various elements such as carbon, hydrogen, oxygen, nitrogen, chlorine and sul fur. The use of plastics is vastly expanded and it is being used in every sector of the world. However, using plastics does have a negative aspect, after use they end up in our landfill as waste causing numerous health and environmental problems. Landfill waste plastics release harmful gases due to the presence of carbon, chlorine and sul fur in them into the atmosphere causing climates to change drastically, equivalent to the effects of greenhouse gases (GHG) emission. To overcome these environmental issues, scientists have already developed many methods to converting these waste plastics into energy and fuel . We developed one new methods thermal cracking conversion to convert these waste plastics into usable liquid fuel . Thermal cracking conversion is a process to shorten the long chain hydrocarbons to produce liquid fuel in the absence of a catalyst. The thermal degradation process of the waste plastics long chain hydrocarbon to makes short chain hydrocarbon fuel. The fuel produced has been analyzed and tested according to standard methods. Key words: fuel , hydrocarbon, waste plastic, thermal degradation, conversion, GC/MS

  4. Sperm fractions obtained following density gradient centrifugation in human ejaculates show differences in sperm DNA longevity

    Directory of Open Access Journals (Sweden)

    Jaime Gosálvez

    2014-06-01

    Conclusion: 1 Unnecessary incubation of spermatozoa prior to artificial insemination or in vitro fertilization, should be avoided, since sperm DNA longevity is significantly reduced after ex vivo sperm handling and 2 Although sperm selection by DCG significantly reduces the baseline levels of SDF of sperm in Fraction 3, sperm DNA longevity in this fraction was ultimately lower following 24 h incubation when compared to sperm recovered from non-centrifuged NSS.

  5. A bijection for tri-cellular maps

    DEFF Research Database (Denmark)

    Han, Hillary Siwei; Reidys, Christian

    2013-01-01

    In this paper we give a bijective proof f