Molecular surface mesh generation by filtering electron density map.

PubMed

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.

Automatically Generated Vegetation Density Maps with LiDAR Survey for Orienteering Purpose

NASA Astrophysics Data System (ADS)

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.

Near equality of ion phase space densities at earth, Jupiter, and Saturn

NASA Technical Reports Server (NTRS)

Cheng, A. F.; Krimigis, S. M.; Armstrong, T. P.

1985-01-01

Energetic-ion phase-space density profiles are strikingly similar in the inner magnetospheres of earth, Jupiter, and Saturn for ions of first adiabatic invariant near 100 MeV/G and small mirror latitudes. Losses occur inside L approximately equal to 7 for Jupiter and Saturn and inside L approximately equal to 5 at earth. At these L values there exist steep plasma-density gradients at all three planets, associated with the Io plasma torus at Jupiter, the Rhea-Dione-Tethys torus at Saturn, and the plasmasphere at earth. Measurements of ion flux-tube contents at Jupiter and Saturn by the low-energy charged-particle experiment show that these are similar (for O ions at L = 5-9) to those at earth (for protons at L = 2-6). Furthermore, the thermal-ion flux-tube contents from Voyager plasma-science data at Jupiter and Saturn are also very nearly equal, and again similar to those at earth, differing by less than a factor of 3 at the respective L values. The near equality of energetic and thermal ion flux-tube contents at earth, Jupiter, and Saturn suggests the possibility of strong physical analogies in the interaction between plasma and energetic particles at the plasma tori/plasma sheets of Jupiter and Saturn and the plasmasphere of earth.

Beyond electronegativity and local hardness: Higher-order equalization criteria for determination of a ground-state electron density.

PubMed

Ayers, Paul W; Parr, Robert G

2008-08-07

Higher-order global softnesses, local softnesses, and softness kernels are defined along with their hardness inverses. The local hardness equalization principle recently derived by the authors is extended to arbitrary order. The resulting hierarchy of equalization principles indicates that the electronegativity/chemical potential, local hardness, and local hyperhardnesses all are constant when evaluated for the ground-state electron density. The new equalization principles can be used to test whether a trial electron density is an accurate approximation to the true ground-state density and to discover molecules with desired reactive properties, as encapsulated by their chemical reactivity indicators.

Model-based local density sharpening of cryo-EM maps

PubMed Central

Jakobi, Arjen J; Wilmanns, Matthias

2017-01-01

Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM structure determination process. Here, we introduce a general procedure for local sharpening of cryo-EM density maps based on prior knowledge of an atomic reference structure. The procedure optimizes contrast of cryo-EM densities by amplitude scaling against the radially averaged local falloff estimated from a windowed reference model. By testing the procedure using six cryo-EM structures of TRPV1, β-galactosidase, γ-secretase, ribosome-EF-Tu complex, 20S proteasome and RNA polymerase III, we illustrate how local sharpening can increase interpretability of density maps in particular in cases of resolution variation and facilitates model building and atomic model refinement. PMID:29058676

Mapping tree density at a global scale

NASA Astrophysics Data System (ADS)

Crowther, T. W.; Glick, H. B.; Covey, K. R.; Bettigole, C.; Maynard, D. S.; Thomas, S. M.; Smith, J. R.; Hintler, G.; Duguid, M. C.; Amatulli, G.; Tuanmu, M.-N.; Jetz, W.; Salas, C.; Stam, C.; Piotto, D.; Tavani, R.; Green, S.; Bruce, G.; Williams, S. J.; Wiser, S. K.; Huber, M. O.; Hengeveld, G. M.; Nabuurs, G.-J.; Tikhonova, E.; Borchardt, P.; Li, C.-F.; Powrie, L. W.; Fischer, M.; Hemp, A.; Homeier, J.; Cho, P.; Vibrans, A. C.; Umunay, P. M.; Piao, S. L.; Rowe, C. W.; Ashton, M. S.; Crane, P. R.; Bradford, M. A.

2015-09-01

The global extent and distribution of forest trees is central to our understanding of the terrestrial biosphere. We provide the first spatially continuous map of forest tree density at a global scale. This map reveals that the global number of trees is approximately 3.04 trillion, an order of magnitude higher than the previous estimate. Of these trees, approximately 1.39 trillion exist in tropical and subtropical forests, with 0.74 trillion in boreal regions and 0.61 trillion in temperate regions. Biome-level trends in tree density demonstrate the importance of climate and topography in controlling local tree densities at finer scales, as well as the overwhelming effect of humans across most of the world. Based on our projected tree densities, we estimate that over 15 billion trees are cut down each year, and the global number of trees has fallen by approximately 46% since the start of human civilization.

Mapping tree density at a global scale.

PubMed

Crowther, T W; Glick, H B; Covey, K R; Bettigole, C; Maynard, D S; Thomas, S M; Smith, J R; Hintler, G; Duguid, M C; Amatulli, G; Tuanmu, M-N; Jetz, W; Salas, C; Stam, C; Piotto, D; Tavani, R; Green, S; Bruce, G; Williams, S J; Wiser, S K; Huber, M O; Hengeveld, G M; Nabuurs, G-J; Tikhonova, E; Borchardt, P; Li, C-F; Powrie, L W; Fischer, M; Hemp, A; Homeier, J; Cho, P; Vibrans, A C; Umunay, P M; Piao, S L; Rowe, C W; Ashton, M S; Crane, P R; Bradford, M A

2015-09-10

The global extent and distribution of forest trees is central to our understanding of the terrestrial biosphere. We provide the first spatially continuous map of forest tree density at a global scale. This map reveals that the global number of trees is approximately 3.04 trillion, an order of magnitude higher than the previous estimate. Of these trees, approximately 1.39 trillion exist in tropical and subtropical forests, with 0.74 trillion in boreal regions and 0.61 trillion in temperate regions. Biome-level trends in tree density demonstrate the importance of climate and topography in controlling local tree densities at finer scales, as well as the overwhelming effect of humans across most of the world. Based on our projected tree densities, we estimate that over 15 billion trees are cut down each year, and the global number of trees has fallen by approximately 46% since the start of human civilization.

Influenza: a scientometric and density-equalizing analysis

PubMed Central

2013-01-01

Background Novel influenza in 2009 caused by H1N1, as well as the seasonal influenza, still are a challenge for the public health sectors worldwide. An increasing number of publications referring to this infectious disease make it difficult to distinguish relevant research output. The current study used scientometric indices for a detailed investigation on influenza related research activity and the method of density equalizing mapping to make the differences of the overall research worldwide obvious. The aim of the study was to compare scientific effort over the time as well as geographical distribution including the cooperation on national and international level. Methods Therefore, publication data was retrieved from Web of Science (WoS) of Thomson Scientific. Subsequently the data was analysed in order to show geographical distributions and the development of the research output over the time. The query retrieved 51,418 publications that are listed in WoS for the time interval from 1900 to 2009. There is a continuous increase in research output and general citation activity especially since 1990. Results The identified all in all 51,418 publications were published by researchers from 151 different countries. Scientists from the USA participate in more than 37 percent of all publications, followed by researchers from the UK and Germany with more than five percent. In addition, the USA is in the focus of international cooperation. In terms of number of publications on influenza, the Journal of Virology ranks first, followed by Vaccine and Virology. The highest impact factor (IF 2009) in this selection can be established for The Lancet (30.75). Robert Webster seems to be the most prolific author contributing the most publications in the field of influenza. Conclusions This study reveals an increasing and wide research interest in influenza. Nevertheless, citation based-declaration of scientific quality should be considered critically due to distortion by self

Mapping Tree Density at the Global Scale

NASA Astrophysics Data System (ADS)

Covey, K. R.; Crowther, T. W.; Glick, H.; Bettigole, C.; Bradford, M.

2015-12-01

The global extent and distribution of forest trees is central to our understanding of the terrestrial biosphere. We provide the first spatially continuous map of forest tree density at a global-scale. This map reveals that the global number of trees is approximately 3.04 trillion, an order of magnitude higher than the previous estimate. Of these trees, approximately 1.39 trillion exist in tropical and subtropical regions, with 0.74, and 0.61 trillion in boreal and temperate regions, respectively. Biome-level trends in tree density demonstrate the importance of climate and topography in controlling local tree densities at finer scales, as well as the overwhelming impact of humans across most of the world. Based on our projected tree densities, we estimate that deforestation is currently responsible for removing over 15 billion trees each year, and the global number of trees has fallen by approximately 46% since the start of human civilization.

[CT pulmonary density mapping: surgical utility].

PubMed

Gavezzoli, D; Caputo, P; Manelli, A; Zuccon, W; Faccini, M; Bonandrini, L

2002-04-01

The present paper considers the technique of CT scan maps of pulmonary isodensity, examining lung density differences as a function of the type of disease and considering their significance for the purposes of refined, useful diagnosis in a surgical context. METHODS. The method is used to examine 3 groups of subjects selected on a clinical/anamnestic basis and a further group already admitted for surgery. For each patient we obtained 2 thoracic density scans during the phase of maximum inspiration and expiration. On each scan we constructed 50 isodensity maps, the equivalent of more than 2500 measurements: the preliminary standard was represented by 100 wide windows to produce total "illumination" of the pulmonary fields. The isodensity windows were then codified differently. Subsequently, the density scans were analysed with the technique of scalar decomposition. The CT scan maps of lung isodensity proved useful for certain lung diseases in which early diagnosis, topographic extent of the pathology and the refined definition of the pathological picture provide important solutions as regards the indication and planning of surgical treatment and for the evaluation of the operative risk and prognosis. We consider that the technique is rapidly performed, not complex and inexpensive and is able to supply detailed information on the lung parenchyma such as to be used not only as a routine technique but also in emergencies.

A high-density genetic map and growth related QTL mapping in bighead carp (Hypophthalmichthys nobilis)

PubMed Central

Fu, Beide; Liu, Haiyang; Yu, Xiaomu; Tong, Jingou

2016-01-01

Growth related traits in fish are controlled by quantitative trait loci (QTL), but no QTL for growth have been detected in bighead carp (Hypophthalmichthys nobilis) due to the lack of high-density genetic map. In this study, an ultra-high density genetic map was constructed with 3,121 SNP markers by sequencing 117 individuals in a F1 family using 2b-RAD technology. The total length of the map was 2341.27 cM, with an average marker interval of 0.75 cM. A high level of genomic synteny between our map and zebrafish was detected. Based on this genetic map, one genome-wide significant and 37 suggestive QTL for five growth-related traits were identified in 6 linkage groups (i.e. LG3, LG11, LG15, LG18, LG19, LG22). The phenotypic variance explained (PVE) by these QTL varied from 15.4% to 38.2%. Marker within the significant QTL region was surrounded by CRP1 and CRP2, which played an important role in muscle cell division. These high-density map and QTL information provided a solid base for QTL fine mapping and comparative genomics in bighead carp. PMID:27345016

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

NASA Astrophysics Data System (ADS)

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.

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

PubMed

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.

Spatial mapping of humeral head bone density.

PubMed

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 < .05. Average apparent bone 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 < .05). Below the anatomic neck, bone density increases from central to peripheral regions, where cortical bone eventually occupies the space (P < .05). In distal slices below the anatomic neck, a higher bone 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.

Evolution of probability densities in stochastic coupled map lattices

NASA Astrophysics Data System (ADS)

Losson, Jérôme; Mackey, Michael C.

1995-08-01

This paper describes the statistical properties of coupled map lattices subjected to the influence of stochastic perturbations. The stochastic analog of the Perron-Frobenius operator is derived for various types of noise. When the local dynamics satisfy rather mild conditions, this equation is shown to possess either stable, steady state solutions (i.e., a stable invariant density) or density limit cycles. Convergence of the phase space densities to these limit cycle solutions explains the nonstationary behavior of statistical quantifiers at equilibrium. Numerical experiments performed on various lattices of tent, logistic, and shift maps with diffusivelike interelement couplings are examined in light of these theoretical results.

Likelihood-based modification of experimental crystal structure electron density maps

DOEpatents

Terwilliger, Thomas C [Sante Fe, NM

2005-04-16

A maximum-likelihood method for improves an electron density map of an experimental crystal structure. A likelihood of a set of structure factors {F.sub.h } is formed for the experimental crystal structure as (1) the likelihood of having obtained an observed set of structure factors {F.sub.h.sup.OBS } if structure factor set {F.sub.h } was correct, and (2) the likelihood that an electron density map resulting from {F.sub.h } is consistent with selected prior knowledge about the experimental crystal structure. The set of structure factors {F.sub.h } is then adjusted to maximize the likelihood of {F.sub.h } for the experimental crystal structure. An improved electron density map is constructed with the maximized structure factors.

Breast cancer research output, 1945-2008: a bibliometric and density-equalizing analysis.

PubMed

Glynn, Ronan W; Scutaru, Cristian; Kerin, Michael J; Sweeney, Karl J

2010-01-01

Breast cancer is the most common form of cancer among women, with an estimated 194,280 new cases diagnosed in the United States in 2009 alone. The primary aim of this work was to provide an in-depth evaluation of research yield in breast cancer from 1945 to 2008, using large-scale data analysis, the employment of bibliometric indicators of production and quality, and density-equalizing mapping. Data were retrieved from the Web of Science (WOS) Science Citation Expanded database; this was searched using the Boolean operator, 'OR', with different terms related to breast cancer, including "breast cancer", "mammary ductal carcinoma" and "breast tumour". Data were then extracted from each file, transferred to Excel charts and visualised as diagrams. Mapping was performed as described by Groneberg-Kloft et al. in 2008. A total of 180,126 breast cancer-associated items were produced over the study period; these had been cited 4,136,224 times. The United States returned the greatest level of output (n = 77,101), followed by the UK (n = 18,357) and Germany (n = 12,529). International cooperation peaked in 2008, with 3,127 entries produced as a result; relationships between the United States and other countries formed the basis for the 10 most common forms of bilateral cooperation. Publications from nations with high levels of international cooperation were associated with greater average citation rates. A total of 4,096 journals published at least one item on breast cancer, although the top 50 most prolific titles together accounted for over 43% (77,517/180,126) of the total output. Breast cancer-associated research output continues to increase annually. In an era when bibliometric indicators are increasingly being employed in performance assessment, these findings should provide useful information for those tasked with improving that performance.

U.S.A. National Surface Rock Density Map - Part 2

NASA Astrophysics Data System (ADS)

Winester, D.

2016-12-01

A map of surface rock densities over the USA has been developed by the NOAA-National Geodetic Survey (NGS) as part of its Gravity for the Redefinition of the American Vertical Datum (GRAV-D) Program. GRAV-D is part of an international effort to generate a North American gravimetric geoid for use as the vertical datum reference surface. As a part of modeling process, it is necessary to eliminate from the observed gravity data the topographic and density effects of all masses above the geoid. However, the long-standing tradition in geoid modeling, which is to use an average rock density (e.g. 2.67 g/cm3), does not adequately represent the variety of lithologies in the USA. The U.S. Geological Survey has assembled a downloadable set of surface geologic formation maps (typically 1:100,000 to 1:500, 000 scale in NAD27) in GIS format. The lithologies were assigned densities typical of their rock type (Part 1) and these variety of densities were then rasterized and averaged over one arc-minute areas. All were then transformed into WGS84 datum. Thin layers of alluvium and some water bodies (interpreted to be less than 40 m thick) have been ignored in deference to underlying rocks. Deep alluvial basins have not been removed, since they represent significant fraction of local mass. The initial assumption for modeling densities will be that the surface rock densities extend down to the geoid. If this results in poor modeling, variable lithologies with depth can be attempted. Initial modeling will use elevations from the SRTM DEM. A map of CONUS densities is presented (denser lithologies are shown brighter). While a visual map at this scale does show detailed features, digital versions are available upon request. Also presented are some pitfalls of using source GIS maps digitized from variable reference sources, including the infamous `state line faults.'

Ellipsoidal terrain correction based on multi-cylindrical equal-area map projection of the reference ellipsoid

NASA Astrophysics Data System (ADS)

Ardalan, A. A.; Safari, A.

2004-09-01

An operational algorithm for computation of terrain correction (or local gravity field modeling) based on application of closed-form solution of the Newton integral in terms of Cartesian coordinates in multi-cylindrical equal-area map projection of the reference ellipsoid is presented. Multi-cylindrical equal-area map projection of the reference ellipsoid has been derived and is described in detail for the first time. Ellipsoidal mass elements with various sizes on the surface of the reference ellipsoid are selected and the gravitational potential and vector of gravitational intensity (i.e. gravitational acceleration) of the mass elements are computed via numerical solution of the Newton integral in terms of geodetic coordinates {λ,ϕ,h}. Four base- edge points of the ellipsoidal mass elements are transformed into a multi-cylindrical equal-area map projection surface to build Cartesian mass elements by associating the height of the corresponding ellipsoidal mass elements to the transformed area elements. Using the closed-form solution of the Newton integral in terms of Cartesian coordinates, the gravitational potential and vector of gravitational intensity of the transformed Cartesian mass elements are computed and compared with those of the numerical solution of the Newton integral for the ellipsoidal mass elements in terms of geodetic coordinates. Numerical tests indicate that the difference between the two computations, i.e. numerical solution of the Newton integral for ellipsoidal mass elements in terms of geodetic coordinates and closed-form solution of the Newton integral in terms of Cartesian coordinates, in a multi-cylindrical equal-area map projection, is less than 1.6×10-8 m2/s2 for a mass element with a cross section area of 10×10 m and a height of 10,000 m. For a mass element with a cross section area of 1×1 km and a height of 10,000 m the difference is less than 1.5×10-4m2/s2. Since 1.5× 10-4 m2/s2 is equivalent to 1.5×10-5m in the vertical

An ultra-high-density bin map facilitates high-throughput QTL mapping of horticultural traits in pepper (Capsicum annuum).

PubMed

Han, Koeun; Jeong, Hee-Jin; Yang, Hee-Bum; Kang, Sung-Min; Kwon, Jin-Kyung; Kim, Seungill; Choi, Doil; Kang, Byoung-Cheorl

2016-04-01

Most agricultural traits are controlled by quantitative trait loci (QTLs); however, there are few studies on QTL mapping of horticultural traits in pepper (Capsicum spp.) due to the lack of high-density molecular maps and the sequence information. In this study, an ultra-high-density map and 120 recombinant inbred lines (RILs) derived from a cross between C. annuum'Perennial' and C. annuum'Dempsey' were used for QTL mapping of horticultural traits. Parental lines and RILs were resequenced at 18× and 1× coverage, respectively. Using a sliding window approach, an ultra-high-density bin map containing 2,578 bins was constructed. The total map length of the map was 1,372 cM, and the average interval between bins was 0.53 cM. A total of 86 significant QTLs controlling 17 horticultural traits were detected. Among these, 32 QTLs controlling 13 traits were major QTLs. Our research shows that the construction of bin maps using low-coverage sequence is a powerful method for QTL mapping, and that the short intervals between bins are helpful for fine-mapping of QTLs. Furthermore, bin maps can be used to improve the quality of reference genomes by elucidating the genetic order of unordered regions and anchoring unassigned scaffolds to linkage groups. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

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

PubMed

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.

Construction of an ultra-high density consensus genetic map, and enhancement of the physical map from genome sequencing in Lupinus angustifolius.

PubMed

Zhou, Gaofeng; Jian, Jianbo; Wang, Penghao; Li, Chengdao; Tao, Ye; Li, Xuan; Renshaw, Daniel; Clements, Jonathan; Sweetingham, Mark; Yang, Huaan

2018-01-01

An ultra-high density genetic map containing 34,574 sequence-defined markers was developed in Lupinus angustifolius. Markers closely linked to nine genes of agronomic traits were identified. A physical map was improved to cover 560.5 Mb genome sequence. Lupin (Lupinus angustifolius L.) is a recently domesticated legume grain crop. In this study, we applied the restriction-site associated DNA sequencing (RADseq) method to genotype an F 9 recombinant inbred line population derived from a wild type × domesticated cultivar (W × D) cross. A high density linkage map was developed based on the W × D population. By integrating sequence-defined DNA markers reported in previous mapping studies, we established an ultra-high density consensus genetic map, which contains 34,574 markers consisting of 3508 loci covering 2399 cM on 20 linkage groups. The largest gap in the entire consensus map was 4.73 cM. The high density W × D map and the consensus map were used to develop an improved physical map, which covered 560.5 Mb of genome sequence data. The ultra-high density consensus linkage map, the improved physical map and the markers linked to genes of breeding interest reported in this study provide a common tool for genome sequence assembly, structural genomics, comparative genomics, functional genomics, QTL mapping, and molecular plant breeding in lupin.

A High-Density Consensus Map of Common Wheat Integrating Four Mapping Populations Scanned by the 90K SNP Array

PubMed Central

Wen, Weie; He, Zhonghu; Gao, Fengmei; Liu, Jindong; Jin, Hui; Zhai, Shengnan; Qu, Yanying; Xia, Xianchun

2017-01-01

A high-density consensus map is a powerful tool for gene mapping, cloning and molecular marker-assisted selection in wheat breeding. The objective of this study was to construct a high-density, single nucleotide polymorphism (SNP)-based consensus map of common wheat (Triticum aestivum L.) by integrating genetic maps from four recombinant inbred line populations. The populations were each genotyped using the wheat 90K Infinium iSelect SNP assay. A total of 29,692 SNP markers were mapped on 21 linkage groups corresponding to 21 hexaploid wheat chromosomes, covering 2,906.86 cM, with an overall marker density of 10.21 markers/cM. Compared with the previous maps based on the wheat 90K SNP chip detected 22,736 (76.6%) of the SNPs with consistent chromosomal locations, whereas 1,974 (6.7%) showed different chromosomal locations, and 4,982 (16.8%) were newly mapped. Alignment of the present consensus map and the wheat expressed sequence tags (ESTs) Chromosome Bin Map enabled assignment of 1,221 SNP markers to specific chromosome bins and 819 ESTs were integrated into the consensus map. The marker orders of the consensus map were validated based on physical positions on the wheat genome with Spearman rank correlation coefficients ranging from 0.69 (4D) to 0.97 (1A, 4B, 5B, and 6A), and were also confirmed by comparison with genetic position on the previously 40K SNP consensus map with Spearman rank correlation coefficients ranging from 0.84 (6D) to 0.99 (6A). Chromosomal rearrangements reported previously were confirmed in the present consensus map and new putative rearrangements were identified. In addition, an integrated consensus map was developed through the combination of five published maps with ours, containing 52,607 molecular markers. The consensus map described here provided a high-density SNP marker map and a reliable order of SNPs, representing a step forward in mapping and validation of chromosomal locations of SNPs on the wheat 90K array. Moreover, it can be

High-Density Genetic Linkage Map Construction and Quantitative Trait Locus Mapping for Hawthorn (Crataegus pinnatifida Bunge).

PubMed

Zhao, Yuhui; Su, Kai; Wang, Gang; Zhang, Liping; Zhang, Jijun; Li, Junpeng; Guo, Yinshan

2017-07-14

Genetic linkage maps are an important tool in genetic and genomic research. In this study, two hawthorn cultivars, Qiujinxing and Damianqiu, and 107 progenies from a cross between them were used for constructing a high-density genetic linkage map using the 2b-restriction site-associated DNA (2b-RAD) sequencing method, as well as for mapping quantitative trait loci (QTL) for flavonoid content. In total, 206,411,693 single-end reads were obtained, with an average sequencing depth of 57× in the parents and 23× in the progeny. After quality trimming, 117,896 high-quality 2b-RAD tags were retained, of which 42,279 were polymorphic; of these, 12,951 markers were used for constructing the genetic linkage map. The map contained 17 linkage groups and 3,894 markers, with a total map length of 1,551.97 cM and an average marker interval of 0.40 cM. QTL mapping identified 21 QTLs associated with flavonoid content in 10 linkage groups, which explained 16.30-59.00% of the variance. This is the first high-density linkage map for hawthorn, which will serve as a basis for fine-scale QTL mapping and marker-assisted selection of important traits in hawthorn germplasm and will facilitate chromosome assignment for hawthorn whole-genome assemblies in the future.

Dislocation density of pure copper processed by accumulative roll bonding and equal-channel angular pressing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miyajima, Yoji, E-mail: miyajima.y.ab@m.titech.ac.jp; Okubo, Satoshi; Abe, Hiroki

The dislocation density of pure copper fabricated by two severe plastic deformation (SPD) processes, i.e., accumulative roll bonding and equal-channel angular pressing, was evaluated using scanning transmission electron microscopy/transmission electron microscopy observations. The dislocation density drastically increased from ~ 10{sup 13} m{sup −} {sup 2} to about 5 × 10{sup 14} m{sup −} {sup 2}, and then saturated, for both SPD processes.

An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio)

PubMed Central

Peng, Wenzhu; Xu, Jian; Zhang, Yan; Feng, Jianxin; Dong, Chuanju; Jiang, Likun; Feng, Jingyan; Chen, Baohua; Gong, Yiwen; Chen, Lin; Xu, Peng

2016-01-01

High density genetic linkage maps are essential for QTL fine mapping, comparative genomics and high quality genome sequence assembly. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,194 SNP markers on 14,146 distinct loci for common carp based on high-throughput genotyping with the carp 250 K single nucleotide polymorphism (SNP) array in a mapping family. The genetic length of the consensus map was 10,595.94 cM with an average locus interval of 0.75 cM and an average marker interval of 0.38 cM. Comparative genomic analysis revealed high level of conserved syntenies between common carp and the closely related model species zebrafish and medaka. The genome scaffolds were anchored to the high-density linkage map, spanning 1,357 Mb of common carp reference genome. QTL mapping and association analysis identified 22 QTLs for growth-related traits and 7 QTLs for sex dimorphism. Candidate genes underlying growth-related traits were identified, including important regulators such as KISS2, IGF1, SMTLB, NPFFR1 and CPE. Candidate genes associated with sex dimorphism were also identified including 3KSR and DMRT2b. The high-density and high-resolution genetic linkage map provides an important tool for QTL fine mapping and positional cloning of economically important traits, and improving common carp genome assembly. PMID:27225429

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

PubMed Central

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

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

PubMed

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.

Terrain Correction on the moving equal area cylindrical map projection of the surface of a reference ellipsoid

NASA Astrophysics Data System (ADS)

Ardalan, A.; Safari, A.; Grafarend, E.

2003-04-01

An operational algorithm for computing the ellipsoidal terrain correction based on application of closed form solution of the Newton integral in terms of Cartesian coordinates in the cylindrical equal area map projected surface of a reference ellipsoid has been developed. As the first step the mapping of the points on the surface of a reference ellipsoid onto the cylindrical equal area map projection of a cylinder tangent to a point on the surface of reference ellipsoid closely studied and the map projection formulas are computed. Ellipsoidal mass elements with various sizes on the surface of the reference ellipsoid is considered and the gravitational potential and the vector of gravitational intensity of these mass elements has been computed via the solution of Newton integral in terms of ellipsoidal coordinates. The geographical cross section areas of the selected ellipsoidal mass elements are transferred into cylindrical equal area map projection and based on the transformed area elements Cartesian mass elements with the same height as that of the ellipsoidal mass elements are constructed. Using the close form solution of the Newton integral in terms of Cartesian coordinates the potential of the Cartesian mass elements are computed and compared with the same results based on the application of the ellipsoidal Newton integral over the ellipsoidal mass elements. The results of the numerical computations show that difference between computed gravitational potential of the ellipsoidal mass elements and Cartesian mass element in the cylindrical equal area map projection is of the order of 1.6 × 10-8m^2/s^2 for a mass element with the cross section size of 10 km × 10 km and the height of 1000 m. For a 1 km × 1 km mass element with the same height, this difference is less than 1.5 × 10-4 m^2}/s^2. The results of the numerical computations indicate that a new method for computing the terrain correction based on the closed form solution of the Newton integral in

FEM: Feature-enhanced map

DOE Office of Scientific and Technical Information (OSTI.GOV)

Afonine, Pavel V.; Moriarty, Nigel W.; Mustyakimov, Marat

A method is presented that modifies a 2 m F obs- D F modelσ A-weighted map such that the resulting map can strengthen a weak signal, if present, and can reduce model bias and noise. The method consists of first randomizing the starting map and filling in missing reflections using multiple methods. This is followed by restricting the map to regions with convincing density and the application of sharpening. The final map is then created by combining a series of histogram-equalized intermediate maps. In the test cases shown, the maps produced in this way are found to have increased interpretabilitymore » and decreased model bias compared with the starting 2 m F obs- D F modelσ A-weighted map.« less

FEM: Feature-enhanced map

DOE PAGES

Afonine, Pavel V.; Moriarty, Nigel W.; Mustyakimov, Marat; ...

2015-02-26

A method is presented that modifies a 2 m F obs- D F modelσ A-weighted map such that the resulting map can strengthen a weak signal, if present, and can reduce model bias and noise. The method consists of first randomizing the starting map and filling in missing reflections using multiple methods. This is followed by restricting the map to regions with convincing density and the application of sharpening. The final map is then created by combining a series of histogram-equalized intermediate maps. In the test cases shown, the maps produced in this way are found to have increased interpretabilitymore » and decreased model bias compared with the starting 2 m F obs- D F modelσ A-weighted map.« less

FEM: feature-enhanced map

PubMed Central

Afonine, Pavel V.; Moriarty, Nigel W.; Mustyakimov, Marat; Sobolev, Oleg V.; Terwilliger, Thomas C.; Turk, Dusan; Urzhumtsev, Alexandre; Adams, Paul D.

2015-01-01

A method is presented that modifies a 2m F obs − D F model σA-weighted map such that the resulting map can strengthen a weak signal, if present, and can reduce model bias and noise. The method consists of first randomizing the starting map and filling in missing reflections using multiple methods. This is followed by restricting the map to regions with convincing density and the application of sharpening. The final map is then created by combining a series of histogram-equalized intermediate maps. In the test cases shown, the maps produced in this way are found to have increased interpretability and decreased model bias compared with the starting 2m F obs − D F model σA-weighted map. PMID:25760612

Local thermodynamic mapping for effective liquid density-functional theory

NASA Technical Reports Server (NTRS)

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.

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

PubMed

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

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

PubMed Central

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

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

PubMed Central

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 been capable of mapping surface charge densities under physiologically relevant conditions. Here, we use a scanning nanopipette setup (scanning ion-conductance microscope) combined with a novel algorithm to investigate the surface conductivity near supported lipid bilayers, and we present a new approach, quantitative surface conductivity microscopy (QSCM), capable of mapping surface charge density with high-quantitative precision and nanoscale resolution. The method is validated through an extensive theoretical analysis of the ionic current at the nanopipette tip, and we demonstrate the capacity of QSCM by mapping the surface charge density of model cationic, anionic and zwitterionic lipids with results accurately matching theoretical values. PMID:27561322

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

NASA Astrophysics Data System (ADS)

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

2016-08-01

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 been capable of mapping surface charge densities under physiologically relevant conditions. Here, we use a scanning nanopipette setup (scanning ion-conductance microscope) combined with a novel algorithm to investigate the surface conductivity near supported lipid bilayers, and we present a new approach, quantitative surface conductivity microscopy (QSCM), capable of mapping surface charge density with high-quantitative precision and nanoscale resolution. The method is validated through an extensive theoretical analysis of the ionic current at the nanopipette tip, and we demonstrate the capacity of QSCM by mapping the surface charge density of model cationic, anionic and zwitterionic lipids with results accurately matching theoretical values.

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

PubMed

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

2016-08-26

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 been capable of mapping surface charge densities under physiologically relevant conditions. Here, we use a scanning nanopipette setup (scanning ion-conductance microscope) combined with a novel algorithm to investigate the surface conductivity near supported lipid bilayers, and we present a new approach, quantitative surface conductivity microscopy (QSCM), capable of mapping surface charge density with high-quantitative precision and nanoscale resolution. The method is validated through an extensive theoretical analysis of the ionic current at the nanopipette tip, and we demonstrate the capacity of QSCM by mapping the surface charge density of model cationic, anionic and zwitterionic lipids with results accurately matching theoretical values.

Construction of a high-density, high-resolution genetic map and its integration with BAC-based physical map in channel catfish

PubMed Central

Li, Yun; Liu, Shikai; Qin, Zhenkui; Waldbieser, Geoff; Wang, Ruijia; Sun, Luyang; Bao, Lisui; Danzmann, Roy G.; Dunham, Rex; Liu, Zhanjiang

2015-01-01

Construction of genetic linkage map is essential for genetic and genomic studies. Recent advances in sequencing and genotyping technologies made it possible to generate high-density and high-resolution genetic linkage maps, especially for the organisms lacking extensive genomic resources. In the present work, we constructed a high-density and high-resolution genetic map for channel catfish with three large resource families genotyped using the catfish 250K single-nucleotide polymorphism (SNP) array. A total of 54,342 SNPs were placed on the linkage map, which to our knowledge had the highest marker density among aquaculture species. The estimated genetic size was 3,505.4 cM with a resolution of 0.22 cM for sex-averaged genetic map. The sex-specific linkage maps spanned a total of 4,495.1 cM in females and 2,593.7 cM in males, presenting a ratio of 1.7 : 1 between female and male in recombination fraction. After integration with the previously established physical map, over 87% of physical map contigs were anchored to the linkage groups that covered a physical length of 867 Mb, accounting for ∼90% of the catfish genome. The integrated map provides a valuable tool for validating and improving the catfish whole-genome assembly and facilitates fine-scale QTL mapping and positional cloning of genes responsible for economically important traits. PMID:25428894

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

PubMed

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.

A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat

PubMed Central

2013-01-01

Background As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning. Results Using a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome. Conclusions Here, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing. PMID:23800011

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

PubMed

Agarwal, Gaurav; Clevenger, Josh; Pandey, Manish K; Wang, Hui; Shasidhar, Yaduru; Chu, Ye; Fountain, Jake C; Choudhary, Divya; Culbreath, Albert K; Liu, Xin; Huang, Guodong; Wang, Xingjun; Deshmukh, Rupesh; Holbrook, C Corley; Bertioli, David J; Ozias-Akins, Peggy; Jackson, Scott A; Varshney, Rajeev K; Guo, Baozhu

2018-04-10

Whole-genome resequencing (WGRS) of mapping populations has facilitated development of high-density genetic maps essential for fine mapping and candidate gene discovery for traits of interest in crop species. Leaf spots, including early leaf spot (ELS) and late leaf spot (LLS), and Tomato spotted wilt virus (TSWV) are devastating diseases in peanut causing significant yield loss. We generated WGRS data on a recombinant inbred line population, developed a SNP-based high-density genetic map, and conducted fine mapping, candidate gene discovery and marker validation for ELS, LLS and TSWV. The first sequence-based high-density map was constructed with 8869 SNPs assigned to 20 linkage groups, representing 20 chromosomes, for the 'T' population (Tifrunner × GT-C20) with a map length of 3120 cM and an average distance of 1.45 cM. The quantitative trait locus (QTL) analysis using high-density genetic map and multiple season phenotyping data identified 35 main-effect QTLs with phenotypic variation explained (PVE) from 6.32% to 47.63%. Among major-effect QTLs mapped, there were two QTLs for ELS on B05 with 47.42% PVE and B03 with 47.38% PVE, two QTLs for LLS on A05 with 47.63% and B03 with 34.03% PVE and one QTL for TSWV on B09 with 40.71% PVE. The epistasis and environment interaction analyses identified significant environmental effects on these traits. The identified QTL regions had disease resistance genes including R-genes and transcription factors. KASP markers were developed for major QTLs and validated in the population and are ready for further deployment in genomics-assisted breeding in peanut. © 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Digital mine claim density map for Federal lands in Montana, 1996

USGS Publications Warehouse

Campbell, Harry W.; Hyndman, Paul C.

1998-01-01

This report describes a digital map and data files generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim information for Federal lands in Montana as of March, 1997. Statewide, 159,704 claims had been recorded with the Bureau of Land Management since 1975. Of those claims, 21,055 (13%) are still actively held while 138,649 (87%) are closed and are no longer held. Montana contains 147,704 sections (usually 1 section equals 1 square mile) in the Public Land Survey System, with 8,569 sections (6%) containing claim data. Of the sections with claim data, 2,192 (26%) contain actively held claims. Only 1.5% of Montana’s sections contains actively held mining claims. The four types of mining claim are lode, placer, mill, and tunnel. A mill claim may be as much as 5 acres or 1/128th (0.78125%) of a square mile. A lode claim, about 20 acres, would cover 1/32nd (3.125%) of a square mile. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. The digital map and data files that are available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller. Campbell (1996) summarized the methodology and GIS techniques that were used to produce the mining claim density map of the Pacific Northwest. Campbell and Hyndman (1997) displayed mining claim information for the Pacific Northwest that used data acquired in 1994. Appendix A of this report lists the attribute data for the digital data files. Appendix B contains the GIS metadata.

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

PubMed

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

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

PubMed Central

Pittiglio, Claudia; Khomenko, Sergei

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

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

PubMed

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 < 0.0001) and in vivo (porcine RA pre-ablation 0.45 ± 0.13 vs. post-ablation 0.78 ± 0.17 points/cm2, P = 0.0008). Increasing chamber geometry was also associated with increased optimal sampling 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

Identification of irrigated crop types from ERTS-1 density contour maps and color infrared aerial photography. [Wyoming

NASA Technical Reports Server (NTRS)

Marrs, R. W.; Evans, M. A.

1974-01-01

The author has identified the following significant results. The crop types of a Great Plains study area were mapped from color infrared aerial photography. Each field was positively identified from field checks in the area. Enlarged (50x) density contour maps were constructed from three ERTS-1 images taken in the summer of 1973. The map interpreted from the aerial photography was compared to the density contour maps and the accuracy of the ERTS-1 density contour map interpretations were determined. Changes in the vegetation during the growing season and harvest periods were detectable on the ERTS-1 imagery. Density contouring aids in the detection of such charges.

Initial Experience With Ultra High-Density Mapping of Human Right Atria.

PubMed

Bollmann, Andreas; Hilbert, Sebastian; John, Silke; Kosiuk, Jedrzej; Hindricks, Gerhard

2016-02-01

Recently, an automatic, high-resolution mapping system has been presented to accurately and quickly identify right atrial geometry and activation patterns in animals, but human data are lacking. This study aims to assess the clinical feasibility and accuracy of high-density electroanatomical mapping of various RA arrhythmias. Electroanatomical maps of the RA (35 partial and 24 complete) were created in 23 patients using a novel mini-basket catheter with 64 electrodes and automatic electrogram annotation. Median acquisition time was 6:43 minutes (0:39-23:05 minutes) with shorter times for partial (4.03 ± 4.13 minutes) than for complete maps (9.41 ± 4.92 minutes). During mapping 3,236 (710-16,306) data points were automatically annotated without manual correction. Maps obtained during sinus rhythm created geometry consistent with CT imaging and demonstrated activation originating at the middle to superior crista terminalis, while maps during CS pacing showed right atrial activation beginning at the infero-septal region. Activation patterns were consistent with cavotricuspid isthmus-dependent atrial flutter (n = 4), complex reentry tachycardia (n = 1), or ectopic atrial tachycardia (n = 2). His bundle and fractionated potentials in the slow pathway region were automatically detected in all patients. Ablation of the cavotricuspid isthmus (n = 9), the atrio-ventricular node (n = 2), atrial ectopy (n = 2), and the slow pathway (n = 3) was successfully and safely performed. RA mapping with this automatic high-density mapping system is fast, feasible, and safe. It is possible to reproducibly identify propagation of atrial activation during sinus rhythm, various tachycardias, and also complex reentrant arrhythmias. © 2015 Wiley Periodicals, Inc.

A High Density Consensus Genetic Map of Tetraploid Cotton That Integrates Multiple Component Maps through Molecular Marker Redundancy Check

PubMed Central

Blenda, Anna; Fang, David D.; Rami, Jean-François; Garsmeur, Olivier; Luo, Feng; Lacape, Jean-Marc

2012-01-01

A consensus genetic map of tetraploid cotton was constructed using six high-density maps and after the integration of a sequence-based marker redundancy check. Public cotton SSR libraries (17,343 markers) were curated for sequence redundancy using 90% as a similarity cutoff. As a result, 20% of the markers (3,410) could be considered as redundant with some other markers. The marker redundancy information had been a crucial part of the map integration process, in which the six most informative interspecific Gossypium hirsutum×G. barbadense genetic maps were used for assembling a high density consensus (HDC) map for tetraploid cotton. With redundant markers being removed, the HDC map could be constructed thanks to the sufficient number of collinear non-redundant markers in common between the component maps. The HDC map consists of 8,254 loci, originating from 6,669 markers, and spans 4,070 cM, with an average of 2 loci per cM. The HDC map presents a high rate of locus duplications, as 1,292 markers among the 6,669 were mapped in more than one locus. Two thirds of the duplications are bridging homoeologous AT and DT chromosomes constitutive of allopolyploid cotton genome, with an average of 64 duplications per AT/DT chromosome pair. Sequences of 4,744 mapped markers were used for a mutual blast alignment (BBMH) with the 13 major scaffolds of the recently released Gossypium raimondii genome indicating high level of homology between the diploid D genome and the tetraploid cotton genetic map, with only a few minor possible structural rearrangements. Overall, the HDC map will serve as a valuable resource for trait QTL comparative mapping, map-based cloning of important genes, and better understanding of the genome structure and evolution of tetraploid cotton. PMID:23029214

Topology in Synthetic Column Density Maps for Interstellar Turbulence

NASA Astrophysics Data System (ADS)

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.

Construction of a high-density high-resolution genetic map and its integration with BAC-based physical map in channel catfish

USDA-ARS?s Scientific Manuscript database

Construction of genetic linkage map is essential for genetic and genomic studies. Recent advances in sequencing and genotyping technologies made it possible to generate high-density and high-resolution genetic linkage maps, especially for the organisms lacking extensive genomic resources. In the pre...

In vivo mapping of current density distribution in brain tissues during deep brain stimulation (DBS)

NASA Astrophysics Data System (ADS)

Sajib, Saurav Z. K.; Oh, Tong In; Kim, Hyung Joong; Kwon, Oh In; Woo, Eung Je

2017-01-01

New methods for in vivo mapping of brain responses during deep brain stimulation (DBS) are indispensable to secure clinical applications. Assessment of current density distribution, induced by internally injected currents, may provide an alternative method for understanding the therapeutic effects of electrical stimulation. The current flow and pathway are affected by internal conductivity, and can be imaged using magnetic resonance-based conductivity imaging methods. Magnetic resonance electrical impedance tomography (MREIT) is an imaging method that can enable highly resolved mapping of electromagnetic tissue properties such as current density and conductivity of living tissues. In the current study, we experimentally imaged current density distribution of in vivo canine brains by applying MREIT to electrical stimulation. The current density maps of three canine brains were calculated from the measured magnetic flux density data. The absolute current density values of brain tissues, including gray matter, white matter, and cerebrospinal fluid were compared to assess the active regions during DBS. The resulting current density in different tissue types may provide useful information about current pathways and volume activation for adjusting surgical planning and understanding the therapeutic effects of DBS.

Particle visualization in high-power impulse magnetron sputtering. I. 2D density mapping

DOE Office of Scientific and Technical Information (OSTI.GOV)

Britun, Nikolay, E-mail: nikolay.britun@umons.ac.be; Palmucci, Maria; Konstantinidis, Stephanos

2015-04-28

Time-resolved characterization of an Ar-Ti high-power impulse magnetron sputtering discharge has been performed. This paper deals with two-dimensional density mapping in the discharge volume obtained by laser-induced fluorescence imaging. The time-resolved density evolution of Ti neutrals, singly ionized Ti atoms (Ti{sup +}), and Ar metastable atoms (Ar{sup met}) in the area above the sputtered cathode is mapped for the first time in this type of discharges. The energetic characteristics of the discharge species are additionally studied by Doppler-shift laser-induced fluorescence imaging. The questions related to the propagation of both the neutral and ionized discharge particles, as well as to theirmore » spatial density distributions, are discussed.« less

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

PubMed Central

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

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

PubMed

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

2014-12-01

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.

Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome.

PubMed

Tsai, Hsin Y; Robledo, Diego; Lowe, Natalie R; Bekaert, Michael; Taggart, John B; Bron, James E; Houston, Ross D

2016-07-07

High density linkage maps are useful tools for fine-scale mapping of quantitative trait loci, and characterization of the recombination landscape of a species' genome. Genomic resources for Atlantic salmon (Salmo salar) include a well-assembled reference genome, and high density single nucleotide polymorphism (SNP) arrays. Our aim was to create a high density linkage map, and to align it with the reference genome assembly. Over 96,000 SNPs were mapped and ordered on the 29 salmon linkage groups using a pedigreed population comprising 622 fish from 60 nuclear families, all genotyped with the 'ssalar01' high density SNP array. The number of SNPs per group showed a high positive correlation with physical chromosome length (r = 0.95). While the order of markers on the genetic and physical maps was generally consistent, areas of discrepancy were identified. Approximately 6.5% of the previously unmapped reference genome sequence was assigned to chromosomes using the linkage map. Male recombination rate was lower than females across the vast majority of the genome, but with a notable peak in subtelomeric regions. Finally, using RNA-Seq data to annotate the reference genome, the mapped SNPs were categorized according to their predicted function, including annotation of ∼2500 putative nonsynonymous variants. The highest density SNP linkage map for any salmonid species has been created, annotated, and integrated with the Atlantic salmon reference genome assembly. This map highlights the marked heterochiasmy of salmon, and provides a useful resource for salmonid genetics and genomics research. Copyright © 2016 Tsai et al.

Comparative hi-density intraspecific linkage mapping using three elite populations from common parents

USDA-ARS?s Scientific Manuscript database

High-density linkage maps are fundamental to contemporary organismal research and scientific approaches to genetic improvement, especially in paleopolyploids with exceptionally complex genomes, e.g., Upland cotton (Gossypium hirsutum L., 2n=52). Using 3 full-sib intra-specific mapping populations fr...

Mapping Students' Spoken Conceptions of Equality

ERIC Educational Resources Information Center

Anakin, Megan

2013-01-01

This study expands contemporary theorising about students' conceptions of equality. A nationally representative sample of New Zealand students' were asked to provide a spoken numerical response and an explanation as they solved an arithmetic additive missing number problem. Students' responses were conceptualised as acts of communication and…

Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map.

PubMed

Wang, Linhai; Xia, Qiuju; Zhang, Yanxin; Zhu, Xiaodong; Zhu, Xiaofeng; Li, Donghua; Ni, Xuemei; Gao, Yuan; Xiang, Haitao; Wei, Xin; Yu, Jingyin; Quan, Zhiwu; Zhang, Xiurong

2016-01-05

Sesame is an important high-quality oil seed crop. The sesame genome was de novo sequenced and assembled in 2014 (version 1.0); however, the number of anchored pseudomolecules was higher than the chromosome number (2n = 2x = 26) due to the lack of a high-density genetic map with 13 linkage groups. We resequenced a permanent population consisting of 430 recombinant inbred lines and constructed a genetic map to improve the sesame genome assembly. We successfully anchored 327 scaffolds onto 13 pseudomolecules. The new genome assembly (version 2.0) included 97.5 % of the scaffolds greater than 150 kb in size present in assembly version 1.0 and increased the total pseudomolecule length from 233.7 to 258.4 Mb with 94.3 % of the genome assembled and 97.2 % of the predicted gene models anchored. Based on the new genome assembly, a bin map including 1,522 bins spanning 1090.99 cM was generated and used to identified 41 quantitative trait loci (QTLs) for sesame plant height and 9 for seed coat color. The plant height-related QTLs explained 3-24 % the phenotypic variation (mean value, 8 %), and 29 of them were detected in at least two field trials. Two major loci (qPH-8.2 and qPH-3.3) that contributed 23 and 18 % of the plant height were located in 350 and 928-kb spaces on Chr8 and Chr3, respectively. qPH-3.3, is predicted to be responsible for the semi-dwarf sesame plant phenotype and contains 102 candidate genes. This is the first report of a sesame semi-dwarf locus and provides an interesting opportunity for a plant architecture study of the sesame. For the sesame seed coat color, the QTLs of the color spaces L*, a*, and b* were detected with contribution rates of 3-46 %. qSCb-4.1 contributed approximately 39 % of the b* value and was located on Chr4 in a 199.9-kb space. A list of 32 candidate genes for the locus, including a predicted black seed coat-related gene, was determined by screening the newly anchored genome. This study offers a high-density

16QAM Blind Equalization via Maximum Entropy Density Approximation Technique and Nonlinear Lagrange Multipliers

PubMed Central

Mauda, R.; Pinchas, M.

2014-01-01

Recently a new blind equalization method was proposed for the 16QAM constellation input inspired by the maximum entropy density approximation technique with improved equalization performance compared to the maximum entropy approach, Godard's algorithm, and others. In addition, an approximated expression for the minimum mean square error (MSE) was obtained. The idea was to find those Lagrange multipliers that bring the approximated MSE to minimum. Since the derivation of the obtained MSE with respect to the Lagrange multipliers leads to a nonlinear equation for the Lagrange multipliers, the part in the MSE expression that caused the nonlinearity in the equation for the Lagrange multipliers was ignored. Thus, the obtained Lagrange multipliers were not those Lagrange multipliers that bring the approximated MSE to minimum. In this paper, we derive a new set of Lagrange multipliers based on the nonlinear expression for the Lagrange multipliers obtained from minimizing the approximated MSE with respect to the Lagrange multipliers. Simulation results indicate that for the high signal to noise ratio (SNR) case, a faster convergence rate is obtained for a channel causing a high initial intersymbol interference (ISI) while the same equalization performance is obtained for an easy channel (initial ISI low). PMID:24723813

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

NASA Astrophysics Data System (ADS)

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.

Blood Density Is Nearly Equal to Water Density: A Validation Study of the Gravimetric Method of Measuring Intraoperative Blood Loss

PubMed Central

Vitello, Dominic J.; Ripper, Richard M.; Fettiplace, Michael R.; Weinberg, Guy L.; Vitello, Joseph M.

2015-01-01

Purpose. The gravimetric method of weighing surgical sponges is used to quantify intraoperative blood loss. The dry mass minus the wet mass of the gauze equals the volume of blood lost. This method assumes that the density of blood is equivalent to water (1 gm/mL). This study's purpose was to validate the assumption that the density of blood is equivalent to water and to correlate density with hematocrit. Methods. 50 µL of whole blood was weighed from eighteen rats. A distilled water control was weighed for each blood sample. The averages of the blood and water were compared utilizing a Student's unpaired, one-tailed t-test. The masses of the blood samples and the hematocrits were compared using a linear regression. Results. The average mass of the eighteen blood samples was 0.0489 g and that of the distilled water controls was 0.0492 g. The t-test showed P = 0.2269 and R 2 = 0.03154. The hematocrit values ranged from 24% to 48%. The linear regression R 2 value was 0.1767. Conclusions. The R 2 value comparing the blood and distilled water masses suggests high correlation between the two populations. Linear regression showed the hematocrit was not proportional to the mass of the blood. The study confirmed that the measured density of blood is similar to water. PMID:26464949

Blood Density Is Nearly Equal to Water Density: A Validation Study of the Gravimetric Method of Measuring Intraoperative Blood Loss.

PubMed

Vitello, Dominic J; Ripper, Richard M; Fettiplace, Michael R; Weinberg, Guy L; Vitello, Joseph M

2015-01-01

Purpose. The gravimetric method of weighing surgical sponges is used to quantify intraoperative blood loss. The dry mass minus the wet mass of the gauze equals the volume of blood lost. This method assumes that the density of blood is equivalent to water (1 gm/mL). This study's purpose was to validate the assumption that the density of blood is equivalent to water and to correlate density with hematocrit. Methods. 50 µL of whole blood was weighed from eighteen rats. A distilled water control was weighed for each blood sample. The averages of the blood and water were compared utilizing a Student's unpaired, one-tailed t-test. The masses of the blood samples and the hematocrits were compared using a linear regression. Results. The average mass of the eighteen blood samples was 0.0489 g and that of the distilled water controls was 0.0492 g. The t-test showed P = 0.2269 and R (2) = 0.03154. The hematocrit values ranged from 24% to 48%. The linear regression R (2) value was 0.1767. Conclusions. The R (2) value comparing the blood and distilled water masses suggests high correlation between the two populations. Linear regression showed the hematocrit was not proportional to the mass of the blood. The study confirmed that the measured density of blood is similar to water.

A high-density intraspecific SNP linkage map of pigeonpea (Cajanas cajan L. Millsp.)

PubMed Central

Mandal, Paritra; Bhutani, Shefali; Dutta, Sutapa; Kumawat, Giriraj; Singh, Bikram Pratap; Chaudhary, A. K.; Yadav, Rekha; Gaikwad, K.; Sevanthi, Amitha Mithra; Datta, Subhojit; Raje, Ranjeet S.; Sharma, Tilak R.; Singh, Nagendra Kumar

2017-01-01

Pigeonpea (Cajanus cajan (L.) Millsp.) is a major food legume cultivated in semi-arid tropical regions including the Indian subcontinent, Africa, and Southeast Asia. It is an important source of protein, minerals, and vitamins for nearly 20% of the world population. Due to high carbon sequestration and drought tolerance, pigeonpea is an important crop for the development of climate resilient agriculture and nutritional security. However, pigeonpea productivity has remained low for decades because of limited genetic and genomic resources, and sparse utilization of landraces and wild pigeonpea germplasm. Here, we present a dense intraspecific linkage map of pigeonpea comprising 932 markers that span a total adjusted map length of 1,411.83 cM. The consensus map is based on three different linkage maps that incorporate a large number of single nucleotide polymorphism (SNP) markers derived from next generation sequencing data, using Illumina GoldenGate bead arrays, and genotyping with restriction site associated DNA (RAD) sequencing. The genotyping-by-sequencing enhanced the marker density but was met with limited success due to lack of common markers across the genotypes of mapping population. The integrated map has 547 bead-array SNP, 319 RAD-SNP, and 65 simple sequence repeat (SSR) marker loci. We also show here correspondence between our linkage map and published genome pseudomolecules of pigeonpea. The availability of a high-density linkage map will help improve the anchoring of the pigeonpea genome to its chromosomes and the mapping of genes and quantitative trait loci associated with useful agronomic traits. PMID:28654689

A Comparison of Spatial Analysis Methods for the Construction of Topographic Maps of Retinal Cell Density

PubMed Central

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

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

PubMed

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.

Mercury Slovenian soils: High, medium and low sample density geochemical maps

NASA Astrophysics Data System (ADS)

Gosar, Mateja; Šajn, Robert; Teršič, Tamara

2017-04-01

Regional geochemical survey was conducted in whole territory of Slovenia (20273 km2). High, medium and low sample density surveys were compared. High sample density represented the regional geochemical data set supplemented by local high-density sampling data (irregular grid, n=2835). Medium-density soil sampling was performed in a 5 x 5 km grid (n=817) and low-density geochemical survey was conducted in a sampling grid 25 x 25 km (n=54). Mercury distribution in Slovenian soils was determined with models of mercury distribution in soil using all three data sets. A distinct Hg anomaly in western part of Slovenia is evident on all three models. It is a consequence of 500-years of mining and ore processing in the second largest mercury mine in the world, the Idrija mine. The determined mercury concentrations revealed an important difference between the western and the eastern parts of the country. For the medium scale geochemical mapping is the median value (0.151 mg /kg) for western Slovenia almost 2-fold higher than the median value (0.083 mg/kg) in eastern Slovenia. Besides the Hg median for the western part of Slovenia exceeds the Hg median for European soil by a factor of 4 (Gosar et al., 2016). Comparing these sample density surveys, it was shown that high sampling density allows the identification and characterization of anthropogenic influences on a local scale, while medium- and low-density sampling reveal general trends in the mercury spatial distribution, but are not appropriate for identifying local contamination in industrial regions and urban areas. The resolution of the pattern generated is the best when the high-density survey on a regional scale is supplemented with the geochemical data of the high-density surveys on a local scale. References: Gosar, M, Šajn, R, Teršič, T. Distribution pattern of mercury in the Slovenian soil: geochemical mapping based on multiple geochemical datasets. Journal of geochemical exploration, 2016, 167/38-48.

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

USDA-ARS?s Scientific Manuscript database

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...

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

USDA-ARS?s Scientific Manuscript database

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 ...

Digital mining claim density map for federal lands in Utah: 1996

USGS Publications Warehouse

Hyndman, Paul C.; Campbell, Harry W.

1999-01-01

This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Utah as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate BLM State office. BLM maintains a cumulative computer listing of mining claims in the MCRS database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

Digital mining claim density map for federal lands in California: 1996

USGS Publications Warehouse

Hyndman, Paul C.; Campbell, Harry W.

1999-01-01

This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in California as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate BLM State office. BLM maintains a cumulative computer listing of mining claims in the MCRS database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

Digital mining claim density map for federal lands in Arizona: 1996

USGS Publications Warehouse

Hyndman, Paul C.; Campbell, Harry W.

1999-01-01

This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Arizona as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate BLM State office. BLM maintains a cumulative computer listing of mining claims in the MCRS database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

Statistical parametric mapping of LORETA using high density EEG and individual MRI: application to mismatch negativities in schizophrenia.

PubMed

Park, Hae-Jeong; Kwon, Jun Soo; Youn, Tak; Pae, Ji Soo; Kim, Jae-Jin; Kim, Myung-Sun; Ha, Kyoo-Seob

2002-11-01

We describe a method for the statistical parametric mapping of low resolution electromagnetic tomography (LORETA) using high-density electroencephalography (EEG) and individual magnetic resonance images (MRI) to investigate the characteristics of the mismatch negativity (MMN) generators in schizophrenia. LORETA, using a realistic head model of the boundary element method derived from the individual anatomy, estimated the current density maps from the scalp topography of the 128-channel EEG. From the current density maps that covered the whole cortical gray matter (up to 20,000 points), volumetric current density images were reconstructed. Intensity normalization of the smoothed current density images was used to reduce the confounding effect of subject specific global activity. After transforming each image into a standard stereotaxic space, we carried out statistical parametric mapping of the normalized current density images. We applied this method to the source localization of MMN in schizophrenia. The MMN generators, produced by a deviant tone of 1,200 Hz (5% of 1,600 trials) under the standard tone of 1,000 Hz, 80 dB binaural stimuli with 300 msec of inter-stimulus interval, were measured in 14 right-handed schizophrenic subjects and 14 age-, gender-, and handedness-matched controls. We found that the schizophrenic group exhibited significant current density reductions of MMN in the left superior temporal gyrus and the left inferior parietal gyrus (P < 0. 0005). This study is the first voxel-by-voxel statistical mapping of current density using individual MRI and high-density EEG. Copyright 2002 Wiley-Liss, Inc.

A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna.

PubMed

Dukić, Marinela; Berner, Daniel; Roesti, Marius; Haag, Christoph R; Ebert, Dieter

2016-10-13

Recombination rate is an essential parameter for many genetic analyses. Recombination rates are highly variable across species, populations, individuals and different genomic regions. Due to the profound influence that recombination can have on intraspecific diversity and interspecific divergence, characterization of recombination rate variation emerges as a key resource for population genomic studies and emphasises the importance of high-density genetic maps as tools for studying genome biology. Here we present such a high-density genetic map for Daphnia magna, and analyse patterns of recombination rate across the genome. A F2 intercross panel was genotyped by Restriction-site Associated DNA sequencing to construct the third-generation linkage map of D. magna. The resulting high-density map included 4037 markers covering 813 scaffolds and contigs that sum up to 77 % of the currently available genome draft sequence (v2.4) and 55 % of the estimated genome size (238 Mb). Total genetic length of the map presented here is 1614.5 cM and the genome-wide recombination rate is estimated to 6.78 cM/Mb. Merging genetic and physical information we consistently found that recombination rate estimates are high towards the peripheral parts of the chromosomes, while chromosome centres, harbouring centromeres in D. magna, show very low recombination rate estimates. Due to its high-density, the third-generation linkage map for D. magna can be coupled with the draft genome assembly, providing an essential tool for genome investigation in this model organism. Thus, our linkage map can be used for the on-going improvements of the genome assembly, but more importantly, it has enabled us to characterize variation in recombination rate across the genome of D. magna for the first time. These new insights can provide a valuable assistance in future studies of the genome evolution, mapping of quantitative traits and population genetic studies.

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

PubMed

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.

Classification and assessment of retrieved electron density maps in coherent X-ray diffraction imaging using multivariate analysis.

PubMed

Sekiguchi, Yuki; Oroguchi, Tomotaka; Nakasako, Masayoshi

2016-01-01

Coherent X-ray diffraction imaging (CXDI) is one of the techniques used to visualize structures of non-crystalline particles of micrometer to submicrometer size from materials and biological science. In the structural analysis of CXDI, the electron density map of a sample particle can theoretically be reconstructed from a diffraction pattern by using phase-retrieval (PR) algorithms. However, in practice, the reconstruction is difficult because diffraction patterns are affected by Poisson noise and miss data in small-angle regions due to the beam stop and the saturation of detector pixels. In contrast to X-ray protein crystallography, in which the phases of diffracted waves are experimentally estimated, phase retrieval in CXDI relies entirely on the computational procedure driven by the PR algorithms. Thus, objective criteria and methods to assess the accuracy of retrieved electron density maps are necessary in addition to conventional parameters monitoring the convergence of PR calculations. Here, a data analysis scheme, named ASURA, is proposed which selects the most probable electron density maps from a set of maps retrieved from 1000 different random seeds for a diffraction pattern. Each electron density map composed of J pixels is expressed as a point in a J-dimensional space. Principal component analysis is applied to describe characteristics in the distribution of the maps in the J-dimensional space. When the distribution is characterized by a small number of principal components, the distribution is classified using the k-means clustering method. The classified maps are evaluated by several parameters to assess the quality of the maps. Using the proposed scheme, structure analysis of a diffraction pattern from a non-crystalline particle is conducted in two stages: estimation of the overall shape and determination of the fine structure inside the support shape. In each stage, the most accurate and probable density maps are objectively selected. The validity

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

PubMed Central

2012-01-01

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. PMID:23033896

Digital mining claim density map for federal lands in Nevada: 1996

USGS Publications Warehouse

Hyndman, Paul C.; Campbell, Harry W.

1999-01-01

This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Nevada as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate Bureau of Land Management (BLM) State office. BLM maintains a cumulative computer listing of mining claims in the MCRS database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

Digital mining claim density map for federal lands in Idaho: 1996

USGS Publications Warehouse

Hyndman, Paul C.; Campbell, Harry W.

1999-01-01

This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Idaho as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill and tunnel sites must be recorded at the appropriate Bureau of Land Management (BLM) State office. BLM maintains a cumulative computer listing of mining claims in the Mining Claim Recordation System (MCRS) database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

Digital mining claim density map for federal lands in Wyoming: 1996

USGS Publications Warehouse

Hyndman, Paul C.; Campbell, Harry W.

1999-01-01

This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Wyoming as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate BLM State office. BLM maintains a cumulative computer listing of mining claims in the Mining Claim Recordation System (MCRS) database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

Digital mining claim density map for federal lands in Colorado: 1996

USGS Publications Warehouse

Hyndman, Paul C.; Campbell, Harry W.

1999-01-01

This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Colorado as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate BLM State office. BLM maintains a cumulative computer listing of mining claims in the Mining Claim Recordation System (MCRS) database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

Digital mining claim density map for federal lands in Oregon: 1996

USGS Publications Warehouse

Hyndman, Paul C.; Campbell, Harry W.

1999-01-01

This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Oregon as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill and tunnel sites must be recorded at the appropriate Bureau of Land Management (BLM) State office. BLM maintains a cumulative computer listing of mining claims in the Mining Claim Recordation System (MCRS) database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

Digital mining claim density map for federal lands in Washington: 1996

USGS Publications Warehouse

Hyndman, Paul C.; Campbell, Harry W.

1999-01-01

This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in Washington as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate BLM State office. BLM maintains a cumulative computer listing of mining claims in the Mining Claim Recordation System (MCRS) database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

High-density linkage mapping revealed suppression of recombination at the sex determination locus in papaya.

PubMed Central

Ma, Hao; Moore, Paul H; Liu, Zhiyong; Kim, Minna S; Yu, Qingyi; Fitch, Maureen M M; Sekioka, Terry; Paterson, Andrew H; Ming, Ray

2004-01-01

A high-density genetic map of papaya (Carica papaya L.) was constructed using 54 F(2) plants derived from cultivars Kapoho and SunUp with 1501 markers, including 1498 amplified fragment length polymorphism (AFLP) markers, the papaya ringspot virus coat protein marker, morphological sex type, and fruit flesh color. These markers were mapped into 12 linkage groups at a LOD score of 5.0 and recombination frequency of 0.25. The 12 major linkage groups covered a total length of 3294.2 cM, with an average distance of 2.2 cM between adjacent markers. This map revealed severe suppression of recombination around the sex determination locus with a total of 225 markers cosegregating with sex types. The cytosine bases were highly methylated in this region on the basis of the distribution of methylation-sensitive and -insensitive markers. This high-density genetic map is essential for cloning of specific genes of interest such as the sex determination gene and for the integration of genetic and physical maps of papaya. PMID:15020433

High-density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Siyao; Clark, Lindsay V.; Swaminathan, Kankshita

Miscanthus is a perennial C4 grass that has recently become an important bioenergy crop. The efficiency of breeding improved Miscanthus biomass cultivars could be greatly increased by marker-assisted selection. Thus, a high-density genetic map is critical to Miscanthus improvement. In this study, a mapping population of 261 F1 progeny was developed from a cross between two diploid M. sinensis cultivars, ‘Strictus’ and ‘Kaskade’. High-density genetic maps for the two parents were produced with 3044 newly developed single nucleotide polymorphisms (SNPs) obtained from restriction site-associated DNA sequencing, and 138 previously mapped GoldenGate SNPs. The female parent (‘Strictus’) map spanned 1599 cM,more » with 1989 SNPs on 19 linkage groups, and an average intermarker spacing of 0.8 cM. The length of the male parent (‘Kaskade’) map was 1612 cM, with 1821 SNPs, and an average intermarker spacing of 0.9 cM. The utility of the map was confirmed by locating quantitative trait loci (QTL) for the zebra-striped trait, which was segregating in this population. Three QTL for zebra-striped presence/absence (zb1, zb2 on LG 7, and zb3 on LG 10) and three for zebra-striped intensity (zbi1, zbi2, zbi3 on LGs 7, 10, 3) were identified. Each allele that caused striping was recessive. Incomplete penetrance was observed for each zb QTL, but penetrance was greatest when two or more zb QTL were homozygous for the causative alleles. Similarly, the intensity of striping was greatest when two or more zbi QTL were homozygous for alleles that conferred the trait. Comparative mapping indicated putative correspondence between zb3 and/or zbi2 on LG 10 to previously sequenced genes conferring zebra stripe in maize and rice. These results demonstrate that the new map is useful for identifying marker–trait associations. The mapped markers will become a valuable community resource, facilitating comparisons among studies and the breeding of Miscanthus.« less

High-density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe

DOE PAGES

Liu, Siyao; Clark, Lindsay V.; Swaminathan, Kankshita; ...

2015-05-06

Miscanthus is a perennial C4 grass that has recently become an important bioenergy crop. The efficiency of breeding improved Miscanthus biomass cultivars could be greatly increased by marker-assisted selection. Thus, a high-density genetic map is critical to Miscanthus improvement. In this study, a mapping population of 261 F1 progeny was developed from a cross between two diploid M. sinensis cultivars, ‘Strictus’ and ‘Kaskade’. High-density genetic maps for the two parents were produced with 3044 newly developed single nucleotide polymorphisms (SNPs) obtained from restriction site-associated DNA sequencing, and 138 previously mapped GoldenGate SNPs. The female parent (‘Strictus’) map spanned 1599 cM,more » with 1989 SNPs on 19 linkage groups, and an average intermarker spacing of 0.8 cM. The length of the male parent (‘Kaskade’) map was 1612 cM, with 1821 SNPs, and an average intermarker spacing of 0.9 cM. The utility of the map was confirmed by locating quantitative trait loci (QTL) for the zebra-striped trait, which was segregating in this population. Three QTL for zebra-striped presence/absence (zb1, zb2 on LG 7, and zb3 on LG 10) and three for zebra-striped intensity (zbi1, zbi2, zbi3 on LGs 7, 10, 3) were identified. Each allele that caused striping was recessive. Incomplete penetrance was observed for each zb QTL, but penetrance was greatest when two or more zb QTL were homozygous for the causative alleles. Similarly, the intensity of striping was greatest when two or more zbi QTL were homozygous for alleles that conferred the trait. Comparative mapping indicated putative correspondence between zb3 and/or zbi2 on LG 10 to previously sequenced genes conferring zebra stripe in maize and rice. These results demonstrate that the new map is useful for identifying marker–trait associations. The mapped markers will become a valuable community resource, facilitating comparisons among studies and the breeding of Miscanthus.« less

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

NASA Astrophysics Data System (ADS)

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 < z < 0.098 and cover approximately 1300 deg2 over two long fields. Cross-correlation is detected at a significance of 5.7 σ. The amplitude of the cross-power spectrum is low relative to the expected dark matter power spectrum, assuming a neutral hydrogen (H I) bias and mass density equal to measurements from the ALFALFA survey. The decrement is pronounced and statistically significant at small scales. At k ˜ 1.5 h Mpc-1, the cross-power spectrum is more than a factor of 6 lower than expected, with a significance of 15.3 σ. This decrement indicates a lack of 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.

High-density genetic map construction and comparative genome analysis in asparagus bean.

PubMed

Huang, Haitao; Tan, Huaqiang; Xu, Dongmei; Tang, Yi; Niu, Yisong; Lai, Yunsong; Tie, Manman; Li, Huanxiu

2018-03-19

Genetic maps are a prerequisite for quantitative trait locus (QTL) analysis, marker-assisted selection (MAS), fine gene mapping, and assembly of genome sequences. So far, several asparagus bean linkage maps have been established using various kinds of molecular markers. However, these maps were all constructed by gel- or array-based markers. No maps based on sequencing method have been reported. In this study, an NGS-based strategy, SLAF-seq, was applied to create a high-density genetic map for asparagus bean. Through SLAF library construction and Illumina sequencing of two parents and 100 F2 individuals, a total of 55,437 polymorphic SLAF markers were developed and mined for SNP markers. The map consisted of 5,225 SNP markers in 11 LGs, spanning a total distance of 1,850.81 cM, with an average distance between markers of 0.35 cM. Comparative genome analysis with four other legume species, soybean, common bean, mung bean and adzuki bean showed that asparagus bean is genetically more related to adzuki bean. The results will provide a foundation for future genomic research, such as QTL fine mapping, comparative mapping in pulses, and offer support for assembling asparagus bean genome sequence.

Interfield dysbalances in research input and output benchmarking: Visualisation by density equalizing procedures

PubMed Central

Groneberg-Kloft, Beatrix; Kreiter, Carolin; Welte, Tobias; Fischer, Axel; Quarcoo, David; Scutaru, Cristian

2008-01-01

Background Historical, social and economic reasons can lead to major differences in the allocation of health system resources and research funding. These differences might endanger the progress in diagnostic and therapeutic approaches of socio-economic important diseases. The present study aimed to assess different benchmarking approaches that might be used to analyse these disproportions. Research in two categories was analysed for various output parameters and compared to input parameters. Germany was used as a high income model country. For the areas of cardiovascular and respiratory medicine density equalizing mapping procedures visualized major geographical differences in both input and output markers. Results An imbalance in the state financial input was present with 36 cardiovascular versus 8 respiratory medicine state-financed full clinical university departments at the C4/W3 salary level. The imbalance in financial input is paralleled by an imbalance in overall quantitative output figures: The 36 cardiology chairs published 2708 articles in comparison to 453 articles published by the 8 respiratory medicine chairs in the period between 2002 and 2006. This is a ratio of 75.2 articles per cardiology chair and 56.63 articles per respiratory medicine chair. A similar trend is also present in the qualitative measures. Here, the 2708 cardiology publications were cited 48337 times (7290 times for respiratory medicine) which is an average citation of 17.85 per publication vs. 16.09 for respiratory medicine. The average number of citations per cardiology chair was 1342.69 in contrast to 911.25 citations per respiratory medicine chair. Further comparison of the contribution of the 16 different German states revealed major geographical differences concerning numbers of chairs, published items, total number of citations and average citations. Conclusion Despite similar significances of cardiovascular and respiratory diseases for the global burden of disease, large

Construction of a high-density genetic map for grape using specific length amplified fragment (SLAF) sequencing

PubMed Central

Guo, Yinshan; Xing, Huiyang; Zhao, Yuhui; Liu, Zhendong; Li, Kun; Guo, Xiuwu

2017-01-01

Genetic maps are important tools in plant genomics and breeding. We report a large-scale discovery of single nucleotide polymorphisms (SNPs) using the specific length amplified fragment sequencing (SLAF-seq) technique for the construction of high-density genetic maps for two elite wine grape cultivars, ‘Chardonnay’ and ‘Beibinghong’, and their 130 F1 plants. A total of 372.53 M paired-end reads were obtained after preprocessing. The average sequencing depth was 33.81 for ‘Chardonnay’ (the female parent), 48.20 for ‘Beibinghong’ (the male parent), and 12.66 for the F1 offspring. We detected 202,349 high-quality SLAFs of which 144,972 were polymorphic; 10,042 SNPs were used to construct a genetic map that spanned 1,969.95 cM, with an average genetic distance of 0.23 cM between adjacent markers. This genetic map contains the largest molecular marker number of the grape maps so far reported. We thus demonstrate that SLAF-seq is a promising strategy for the construction of high-density genetic maps; the map that we report here is a good potential resource for QTL mapping of genes linked to major economic and agronomic traits, map-based cloning, and marker-assisted selection of grape. PMID:28746364

Construction of High-Density Genetic Linkage Maps and Mapping of Growth-Related Quantitative Trail Loci in the Japanese Flounder (Paralichthys olivaceus)

PubMed Central

Niu, Yuze; Gao, Fengtao; Zhao, Yongwei; Zhang, Jing; Sun, Jian; Shao, Changwei; Liao, Xiaolin; Wang, Lei; Tian, Yongsheng; Chen, Songlin

2012-01-01

High-density genetic linkage maps were constructed for the Japanese flounder (Paralichthys olivaceus). A total of 1624 microsatellite markers were polymorphic in the reference family. Linkage analysis using JoinMap 4.0 resulted in the mapping of 1487 markers to 24 linkage groups, a result which was consistent with the 24 chromosomes seen in chromosome spreads. The female map was composed of 1257 markers, covering a total of 1663.8 cM with an average interval 1.35 cM between markers. The male map consisted of 1224 markers, spanning 1726.5 cM, with an average interval of 1.44 cM. The genome length in the Japanese flounder was estimated to be 1730.3 cM for the females and 1798.0 cM for the males, a coverage of 96.2% for the female and 96.0% for the male map. The mean recombination at common intervals throughout the genome revealed a slight difference between sexes, i.e. 1.07 times higher in the male than female. High-density genetic linkage maps are very useful for marker-assisted selection (MAS) programs for economically valuable traits in this species and for further evolutionary studies in flatfish and vertebrate species. Furthermore, four quantiative trait loci (QTL) associated with growth traits were mapped on the genetic map. One QTL was identified for body weight on LG 14 f, which explained 14.85% of the total variation of the body weight. Three QTL were identified for body width on LG14f and LG14m, accounting for 16.75%, 13.62% and 13.65% of the total variation in body width, respectively. The additive effects were evident as negative values. There were four QTL for growth traits clustered on LG14, which should prove to be very useful for improving growth traits using molecular MAS. PMID:23209734

Eulerian Mapping Closure Approach for Probability Density Function of Concentration in Shear Flows

NASA Technical Reports Server (NTRS)

He, Guowei; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

The Eulerian mapping closure approach is developed for uncertainty propagation in computational fluid mechanics. The approach is used to study the Probability Density Function (PDF) for the concentration of species advected by a random shear flow. An analytical argument shows that fluctuation of the concentration field at one point in space is non-Gaussian and exhibits stretched exponential form. An Eulerian mapping approach provides an appropriate approximation to both convection and diffusion terms and leads to a closed mapping equation. The results obtained describe the evolution of the initial Gaussian field, which is in agreement with direct numerical simulations.

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

PubMed

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

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

PubMed Central

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

Digital mining claim density map for federal lands in New Mexico: 1996

USGS Publications Warehouse

Hyndman, Paul C.; Campbell, Harry W.

1999-01-01

This report describes a digital map generated by the U.S. Geological Survey (USGS) to provide digital spatial mining claim density information for federal lands in New Mexico as of March 1997. Mining claim data is earth science information deemed to be relevant to the assessment of historic, current, and future ecological, economic, and social systems. There is no paper map included in this Open-File report. In accordance with the Federal Land Policy and Management Act of 1976 (FLPMA), all unpatented mining claims, mill, and tunnel sites must be recorded at the appropriate BLM State office. BLM maintains a cumulative computer listing of mining claims in the MCRS database with locations given by meridian, township, range, and section. A mining claim is considered closed when the claim is relinquished or a formal BLM decision declaring the mining claim null and void has been issued and the appeal period has expired. All other mining claims filed with BLM are considered to be open and actively held. The digital map (figure 1.) with the mining claim density database available in this report are suitable for geographic information system (GIS)-based regional assessments at a scale of 1:100,000 or smaller.

Modeling photo-bleaching kinetics to map local variations in rod rhodopsin density

NASA Astrophysics Data System (ADS)

Ehler, M.; Dobrosotskaya, J.; King, E. J.; Czaja, W.; Bonner, R. F.

2011-03-01

Localized rod photoreceptor and rhodopsin losses have been observed in post mortem histology both in normal aging and in age-related maculopathy. We propose to noninvasively map local rod rhodopsin density through analysis of the brightening of the underlying lipofuscin autofluorescence (LAF) in confocal scanning laser ophthalmoscopy (cSLO) imaging sequences starting in the dark adapted eye. The detected LAF increases as rhodopsin is bleached (time constant ~ 25sec) by the average retinal irradiance of the cSLO 488nm laser beam. We fit parameters of analytical expressions for the kinetics of rhodopsin bleaching that Lamb validated using electroretinogram recordings in human. By performing localized (~ 100μm) kinetic analysis, we create high resolution maps of the rhodopsin density. This new noninvasive imaging and analysis approach appears well-suited for measuring localized changes in the rod photoreceptors and correlating them at high spatial resolution with localized pathological changes of the retinal pigment epithelium (RPE) seen in steady-state LAF images.

Direct mapping of local redox current density on a monolith electrode by laser scanning.

PubMed

Lee, Seung-Woo; Lopez, Jeffrey; Saraf, Ravi F

2013-09-15

An optical method of mapping local redox reaction over a monolith electrode using simple laser scanning is described. As the optical signal is linearly proportional to the maximum redox current that is measured concomitantly by voltammetry, the optical signal quantitatively maps the local redox current density distribution. The method is demonstrated on two types of reactions: (1) a reversible reaction where the redox moieties are ionic, and (2) an irreversible reaction on two different types of enzymes immobilized on the electrode where the reaction moieties are nonionic. To demonstrate the scanning capability, the local redox behavior on a "V-shaped" electrode is studied where the local length scale and, hence, the local current density, is nonuniform. The ability to measure the current density distribution by this method will pave the way for multianalyte analysis on a monolith electrode using a standard three-electrode configuration. The method is called Scanning Electrometer for Electrical Double-layer (SEED). Copyright © 2013 Elsevier B.V. All rights reserved.

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

PubMed Central

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

Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population

PubMed Central

Serin, Elise A. R.; Snoek, L. B.; Nijveen, Harm; Willems, Leo A. J.; Jiménez-Gómez, Jose M.; Hilhorst, Henk W. M.; Ligterink, Wilco

2017-01-01

High-density genetic maps are essential for high resolution mapping of quantitative traits. Here, we present a new genetic map for an Arabidopsis Bayreuth × Shahdara recombinant inbred line (RIL) population, built on RNA-seq data. RNA-seq analysis on 160 RILs of this population identified 30,049 single-nucleotide polymorphisms (SNPs) covering the whole genome. Based on a 100-kbp window SNP binning method, 1059 bin-markers were identified, physically anchored on the genome. The total length of the RNA-seq genetic map spans 471.70 centimorgans (cM) with an average marker distance of 0.45 cM and a maximum marker distance of 4.81 cM. This high resolution genotyping revealed new recombination breakpoints in the population. To highlight the advantages of such high-density map, we compared it to two publicly available genetic maps for the same population, comprising 69 PCR-based markers and 497 gene expression markers derived from microarray data, respectively. In this study, we show that SNP markers can effectively be derived from RNA-seq data. The new RNA-seq map closes many existing gaps in marker coverage, saturating the previously available genetic maps. Quantitative trait locus (QTL) analysis for published phenotypes using the available genetic maps showed increased QTL mapping resolution and reduced QTL confidence interval using the RNA-seq map. The new high-density map is a valuable resource that facilitates the identification of candidate genes and map-based cloning approaches. PMID:29259624

Shape information from a critical point analysis of calculated electron density maps: application to DNA-drug systems

NASA Astrophysics Data System (ADS)

Leherte, L.; Allen, F. H.; Vercauteren, D. P.

1995-04-01

A computational method is described for mapping the volume within the DNA double helix accessible to a groove-binding antibiotic, netropsin. Topological critical point analysis is used to locate maxima in electron density maps reconstructed from crystallographically determined atomic coordinates. The peaks obtained in this way are represented as ellipsoids with axes related to local curvature of the electron density function. Combining the ellipsoids produces a single electron density function which can be probed to estimate effective volumes of the interacting species. Close complementarity between host and ligand in this example shows the method to be a good representation of the electron density function at various resolutions; while at the atomic level the ellipsoid method gives results which are in close agreement with those from the conventional, spherical, van der Waals approach.

Shape information from a critical point analysis of calculated electron density maps: Application to DNA-drug systems

NASA Astrophysics Data System (ADS)

Leherte, Laurence; Allen, Frank H.

1994-06-01

A computational method is described for mapping the volume within the DNA double helix accessible to the groove-binding antibiotic netropsin. Topological critical point analysis is used to locate maxima in electron density maps reconstructed from crystallographically determined atomic coordinates. The peaks obtained in this way are represented as ellipsoids with axes related to local curvature of the electron density function. Combining the ellipsoids produces a single electron density function which can be probed to estimate effective volumes of the interacting species. Close complementarity between host and ligand in this example shows the method to give a good representation of the electron density function at various resolutions. At the atomic level, the ellipsoid method gives results which are in close agreement with those from the conventional spherical van der Waals approach.

Maps and models of density and stiffness within individual Douglas-fir trees

Treesearch

Christine L. Todoroki; Eini C. Lowell; Dennis P. Dykstra; David G. Briggs

2012-01-01

Spatial maps of density and stiffness patterns within individual trees were developed using two methods: (1) measured wood properties of veneer sheets; and (2) mixed effects models, to test the hypothesis that within-tree patterns could be predicted from easily measurable tree variables (height, taper, breast-height diameter, and acoustic velocity). Sample trees...

Construction of a high-density genetic map and the X/Y sex-determining gene mapping in spinach based on large-scale markers developed by specific-locus amplified fragment sequencing (SLAF-seq).

PubMed

Qian, Wei; Fan, Guiyan; Liu, Dandan; Zhang, Helong; Wang, Xiaowu; Wu, Jian; Xu, Zhaosheng

2017-04-04

Cultivated spinach (Spinacia oleracea L.) is one of the most widely cultivated types of leafy vegetable in the world, and it has a high nutritional value. Spinach is also an ideal plant for investigating the mechanism of sex determination because it is a dioecious species with separate male and female plants. Some reports on the sex labeling and localization of spinach in the study of molecular markers have surfaced. However, there have only been two reports completed on the genetic map of spinach. The lack of rich and reliable molecular markers and the shortage of high-density linkage maps are important constraints in spinach research work. In this study, a high-density genetic map of spinach based on the Specific-locus Amplified Fragment Sequencing (SLAF-seq) technique was constructed; the sex-determining gene was also finely mapped. Through bio-information analysis, 50.75 Gb of data in total was obtained, including 207.58 million paired-end reads. Finally, 145,456 high-quality SLAF markers were obtained, with 27,800 polymorphic markers and 4080 SLAF markers were finally mapped onto the genetic map after linkage analysis. The map spanned 1,125.97 cM with an average distance of 0.31 cM between the adjacent marker loci. It was divided into 6 linkage groups corresponding to the number of spinach chromosomes. Besides, the combination of Bulked Segregation Analysis (BSA) with SLAF-seq technology(super-BSA) was employed to generate the linkage markers with the sex-determining gene. Combined with the high-density genetic map of spinach, the sex-determining gene X/Y was located at the position of the linkage group (LG) 4 (66.98 cM-69.72 cM and 75.48 cM-92.96 cM), which may be the ideal region for the sex-determining gene. A high-density genetic map of spinach based on the SLAF-seq technique was constructed with a backcross (BC 1 ) population (which is the highest density genetic map of spinach reported at present). At the same time, the sex-determining gene X/Y was

Genome survey and high-density genetic map construction provide genomic and genetic resources for the Pacific White Shrimp Litopenaeus vannamei

PubMed Central

Yu, Yang; Zhang, Xiaojun; Yuan, Jianbo; Li, Fuhua; Chen, Xiaohan; Zhao, Yongzhen; Huang, Long; Zheng, Hongkun; Xiang, Jianhai

2015-01-01

The Pacific white shrimp Litopenaeus vannamei is the dominant crustacean species in global seafood mariculture. Understanding the genome and genetic architecture is useful for deciphering complex traits and accelerating the breeding program in shrimp. In this study, a genome survey was conducted and a high-density linkage map was constructed using a next-generation sequencing approach. The genome survey was used to identify preliminary genome characteristics and to generate a rough reference for linkage map construction. De novo SNP discovery resulted in 25,140 polymorphic markers. A total of 6,359 high-quality markers were selected for linkage map construction based on marker coverage among individuals and read depths. For the linkage map, a total of 6,146 markers spanning 4,271.43 cM were mapped to 44 sex-averaged linkage groups, with an average marker distance of 0.7 cM. An integration analysis linked 5,885 genome scaffolds and 1,504 BAC clones to the linkage map. Based on the high-density linkage map, several QTLs for body weight and body length were detected. This high-density genetic linkage map reveals basic genomic architecture and will be useful for comparative genomics research, genome assembly and genetic improvement of L. vannamei and other penaeid shrimp species. PMID:26503227

Recurrence quantification analysis applied to spatiotemporal pattern analysis in high-density mapping of human atrial fibrillation.

PubMed

Zeemering, Stef; Bonizzi, Pietro; Maesen, Bart; Peeters, Ralf; Schotten, Ulrich

2015-01-01

Spatiotemporal complexity of atrial fibrillation (AF) patterns is often quantified by annotated intracardiac contact mapping. We introduce a new approach that applies recurrence plot (RP) construction followed by recurrence quantification analysis (RQA) to epicardial atrial electrograms, recorded with a high-density grid of electrodes. In 32 patients with no history of AF (aAF, n=11), paroxysmal AF (PAF, n=12) and persistent AF (persAF, n=9), RPs were constructed using a phase space electrogram embedding dimension equal to the estimated AF cycle length. Spatial information was incorporated by 1) averaging the recurrence over all electrodes, and 2) by applying principal component analysis (PCA) to the matrix of embedded electrograms and selecting the first principal component as a representation of spatial diversity. Standard RQA parameters were computed on the constructed RPs and correlated to the number of fibrillation waves per AF cycle (NW). Averaged RP RQA parameters showed no correlation with NW. Correlations improved when applying PCA, with maximum correlation achieved between RP threshold and NW (RR1%, r=0.68, p <; 0.001) and RP determinism (DET, r=-0.64, p <; 0.001). All studied RQA parameters based on the PCA RP were able to discriminate between persAF and aAF/PAF (DET persAF 0.40 ± 0.11 vs. 0.59 ± 0.14/0.62 ± 0.16, p <; 0.01). RP construction and RQA combined with PCA provide a quick and reliable tool to visualize dynamical behaviour and to assess the complexity of contact mapping patterns in AF.

Transport of phase space densities through tetrahedral meshes using discrete flow mapping

NASA Astrophysics Data System (ADS)

Bajars, Janis; Chappell, David J.; Søndergaard, Niels; Tanner, Gregor

2017-01-01

Discrete flow mapping was recently introduced as an efficient ray based method determining wave energy distributions in complex built up structures. Wave energy densities are transported along ray trajectories through polygonal mesh elements using a finite dimensional approximation of a ray transfer operator. In this way the method can be viewed as a smoothed ray tracing method defined over meshed surfaces. Many applications require the resolution of wave energy distributions in three-dimensional domains, such as in room acoustics, underwater acoustics and for electromagnetic cavity problems. In this work we extend discrete flow mapping to three-dimensional domains by propagating wave energy densities through tetrahedral meshes. The geometric simplicity of the tetrahedral mesh elements is utilised to efficiently compute the ray transfer operator using a mixture of analytic and spectrally accurate numerical integration. The important issue of how to choose a suitable basis approximation in phase space whilst maintaining a reasonable computational cost is addressed via low order local approximations on tetrahedral faces in the position coordinate and high order orthogonal polynomial expansions in momentum space.

Spectral density mapping at multiple magnetic fields suitable for 13C NMR relaxation studies

NASA Astrophysics Data System (ADS)

Kadeřávek, Pavel; Zapletal, Vojtěch; Fiala, Radovan; Srb, Pavel; Padrta, Petr; Přecechtělová, Jana Pavlíková; Šoltésová, Mária; Kowalewski, Jozef; Widmalm, Göran; Chmelík, Josef; Sklenář, Vladimír; Žídek, Lukáš

2016-05-01

Standard spectral density mapping protocols, well suited for the analysis of 15N relaxation rates, introduce significant systematic errors when applied to 13C relaxation data, especially if the dynamics is dominated by motions with short correlation times (small molecules, dynamic residues of macromolecules). A possibility to improve the accuracy by employing cross-correlated relaxation rates and on measurements taken at several magnetic fields has been examined. A suite of protocols for analyzing such data has been developed and their performance tested. Applicability of the proposed protocols is documented in two case studies, spectral density mapping of a uniformly labeled RNA hairpin and of a selectively labeled disaccharide exhibiting highly anisotropic tumbling. Combination of auto- and cross-correlated relaxation data acquired at three magnetic fields was applied in the former case in order to separate effects of fast motions and conformational or chemical exchange. An approach using auto-correlated relaxation rates acquired at five magnetic fields, applicable to anisotropically moving molecules, was used in the latter case. The results were compared with a more advanced analysis of data obtained by interpolation of auto-correlated relaxation rates measured at seven magnetic fields, and with the spectral density mapping of cross-correlated relaxation rates. The results showed that sufficiently accurate values of auto- and cross-correlated spectral density functions at zero and 13C frequencies can be obtained from data acquired at three magnetic fields for uniformly 13C -labeled molecules with a moderate anisotropy of the rotational diffusion tensor. Analysis of auto-correlated relaxation rates at five magnetic fields represents an alternative for molecules undergoing highly anisotropic motions.

FragFit: a web-application for interactive modeling of protein segments into cryo-EM density maps.

PubMed

Tiemann, Johanna K S; Rose, Alexander S; Ismer, Jochen; Darvish, Mitra D; Hilal, Tarek; Spahn, Christian M T; Hildebrand, Peter W

2018-05-21

Cryo-electron microscopy (cryo-EM) is a standard method to determine the three-dimensional structures of molecular complexes. However, easy to use tools for modeling of protein segments into cryo-EM maps are sparse. Here, we present the FragFit web-application, a web server for interactive modeling of segments of up to 35 amino acids length into cryo-EM density maps. The fragments are provided by a regularly updated database containing at the moment about 1 billion entries extracted from PDB structures and can be readily integrated into a protein structure. Fragments are selected based on geometric criteria, sequence similarity and fit into a given cryo-EM density map. Web-based molecular visualization with the NGL Viewer allows interactive selection of fragments. The FragFit web-application, accessible at http://proteinformatics.de/FragFit, is free and open to all users, without any login requirements.

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

PubMed

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 .

Modeling shape and topology of low-resolution density maps of biological macromolecules.

PubMed Central

De-Alarcón, Pedro A; Pascual-Montano, Alberto; Gupta, Amarnath; Carazo, Jose M

2002-01-01

In the present work we develop an efficient way of representing the geometry and topology of volumetric datasets of biological structures from medium to low resolution, aiming at storing and querying them in a database framework. We make use of a new vector quantization algorithm to select the points within the macromolecule that best approximate the probability density function of the original volume data. Connectivity among points is obtained with the use of the alpha shapes theory. This novel data representation has a number of interesting characteristics, such as 1) it allows us to automatically segment and quantify a number of important structural features from low-resolution maps, such as cavities and channels, opening the possibility of querying large collections of maps on the basis of these quantitative structural features; 2) it provides a compact representation in terms of size; 3) it contains a subset of three-dimensional points that optimally quantify the densities of medium resolution data; and 4) a general model of the geometry and topology of the macromolecule (as opposite to a spatially unrelated bunch of voxels) is easily obtained by the use of the alpha shapes theory. PMID:12124252

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

PubMed Central

2012-01-01

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. PMID:22908993

Tree-centric mapping of forest carbon density from airborne laser scanning and hyperspectral data.

PubMed

Dalponte, Michele; Coomes, David A

2016-10-01

Forests are a major component of the global carbon cycle, and accurate estimation of forest carbon stocks and fluxes is important in the context of anthropogenic global change. Airborne laser scanning (ALS) data sets are increasingly recognized as outstanding data sources for high-fidelity mapping of carbon stocks at regional scales.We develop a tree-centric approach to carbon mapping, based on identifying individual tree crowns (ITCs) and species from airborne remote sensing data, from which individual tree carbon stocks are calculated. We identify ITCs from the laser scanning point cloud using a region-growing algorithm and identifying species from airborne hyperspectral data by machine learning. For each detected tree, we predict stem diameter from its height and crown-width estimate. From that point on, we use well-established approaches developed for field-based inventories: above-ground biomasses of trees are estimated using published allometries and summed within plots to estimate carbon density.We show this approach is highly reliable: tests in the Italian Alps demonstrated a close relationship between field- and ALS-based estimates of carbon stocks ( r 2  = 0·98). Small trees are invisible from the air, and a correction factor is required to accommodate this effect.An advantage of the tree-centric approach over existing area-based methods is that it can produce maps at any scale and is fundamentally based on field-based inventory methods, making it intuitive and transparent. Airborne laser scanning, hyperspectral sensing and computational power are all advancing rapidly, making it increasingly feasible to use ITC approaches for effective mapping of forest carbon density also inside wider carbon mapping programs like REDD++.

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

PubMed

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

2017-04-01

White Matter (WM) microstructures, such as axonal density and average diameter, are crucial to the normal function of the Central Nervous System (CNS) as they are closely related with axonal conduction velocities. Conversely, disruptions of these microstructural features may result in severe neurological deficits, suggesting that their noninvasive mapping could be an important step towards diagnosing and following pathophysiology. Whereas diffusion based MRI methods have been proposed to map these features, they typically entail the application of powerful gradients, which are rarely 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-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 were here used as a simple model for the microstructure - and that, for axons parallel to the main magnetic field, the axonal density can be extracted. We then experimentally demonstrate in ex-vivo rat spinal cords that its different tracts - characterized by different microstructures - can be clearly contrasted using the MGE-derived maps. When the quantitative results are compared against ground-truth histology, they 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 a potential and usefulness of the approach to map underlying microstructures using a simple and time-efficient MRI sequence. We further show that a simple general-linear-model can predict the average axonal diameters from the four model parameters, and

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

NASA Astrophysics Data System (ADS)

Nunes, Daniel; Cruz, Tomás L.; Jespersen, Sune N.; Shemesh, Noam

2017-04-01

White Matter (WM) microstructures, such as axonal density and average diameter, are crucial to the normal function of the Central Nervous System (CNS) as they are closely related with axonal conduction velocities. Conversely, disruptions of these microstructural features may result in severe neurological deficits, suggesting that their noninvasive mapping could be an important step towards diagnosing and following pathophysiology. Whereas diffusion based MRI methods have been proposed to map these features, they typically entail the application of powerful gradients, which are rarely 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-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 were here used as a simple model for the microstructure - and that, for axons parallel to the main magnetic field, the axonal density can be extracted. We then experimentally demonstrate in ex-vivo rat spinal cords that its different tracts - characterized by different microstructures - can be clearly contrasted using the MGE-derived maps. When the quantitative results are compared against ground-truth histology, they 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 a potential and usefulness of the approach to map underlying microstructures using a simple and time-efficient MRI sequence. We further show that a simple general-linear-model can predict the average axonal diameters from the four model parameters, and

Construction of a High-Density American Cranberry (Vaccinium macrocarpon Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping

PubMed Central

Schlautman, Brandon; Covarrubias-Pazaran, Giovanny; Diaz-Garcia, Luis; Iorizzo, Massimo; Polashock, James; Grygleski, Edward; Vorsa, Nicholi; Zalapa, Juan

2017-01-01

The American cranberry (Vaccinium macrocarpon Ait.) is a recently domesticated, economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genomic structure and by enabling molecular-assisted breeding strategies. To increase the availability of cranberry genomic resources, genotyping-by-sequencing (GBS) was used to discover and genotype thousands of single nucleotide polymorphisms (SNPs) within three interrelated cranberry full-sib populations. Additional simple sequence repeat (SSR) loci were added to the SNP datasets and used to construct bin maps for the parents of the populations, which were then merged to create the first high-density cranberry composite map containing 6073 markers (5437 SNPs and 636 SSRs) on 12 linkage groups (LGs) spanning 1124 cM. Interestingly, higher rates of recombination were observed in maternal than paternal gametes. The large number of markers in common (mean of 57.3) and the high degree of observed collinearity (mean Pair-wise Spearman rank correlations >0.99) between the LGs of the parental maps demonstrates the utility of GBS in cranberry for identifying polymorphic SNP loci that are transferable between pedigrees and populations in future trait-association studies. Furthermore, the high-density of markers anchored within the component maps allowed identification of segregation distortion regions, placement of centromeres on each of the 12 LGs, and anchoring of genomic scaffolds. Collectively, the results represent an important contribution to the current understanding of cranberry genomic structure and to the availability of molecular tools for future genetic research and breeding efforts in cranberry. PMID:28250016

Construction of a High-Density American Cranberry (Vaccinium macrocarpon Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping.

PubMed

Schlautman, Brandon; Covarrubias-Pazaran, Giovanny; Diaz-Garcia, Luis; Iorizzo, Massimo; Polashock, James; Grygleski, Edward; Vorsa, Nicholi; Zalapa, Juan

2017-04-03

The American cranberry ( Vaccinium macrocarpon Ait.) is a recently domesticated, economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genomic structure and by enabling molecular-assisted breeding strategies. To increase the availability of cranberry genomic resources, genotyping-by-sequencing (GBS) was used to discover and genotype thousands of single nucleotide polymorphisms (SNPs) within three interrelated cranberry full-sib populations. Additional simple sequence repeat (SSR) loci were added to the SNP datasets and used to construct bin maps for the parents of the populations, which were then merged to create the first high-density cranberry composite map containing 6073 markers (5437 SNPs and 636 SSRs) on 12 linkage groups (LGs) spanning 1124 cM. Interestingly, higher rates of recombination were observed in maternal than paternal gametes. The large number of markers in common (mean of 57.3) and the high degree of observed collinearity (mean Pair-wise Spearman rank correlations >0.99) between the LGs of the parental maps demonstrates the utility of GBS in cranberry for identifying polymorphic SNP loci that are transferable between pedigrees and populations in future trait-association studies. Furthermore, the high-density of markers anchored within the component maps allowed identification of segregation distortion regions, placement of centromeres on each of the 12 LGs, and anchoring of genomic scaffolds. Collectively, the results represent an important contribution to the current understanding of cranberry genomic structure and to the availability of molecular tools for future genetic research and breeding efforts in cranberry. Copyright © 2017 Schlautman et al.

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

PubMed Central

2012-01-01

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 and Glycine revealed

A High-Density Linkage Map Reveals Sexual Dimorphism in Recombination Landscapes in Red Deer (Cervus elaphus)

PubMed Central

Johnston, Susan E.; Huisman, Jisca; Ellis, Philip A.; Pemberton, Josephine M.

2017-01-01

High-density linkage maps are an important tool to gain insight into the genetic architecture of traits of evolutionary and economic interest, and provide a resource to characterize variation in recombination landscapes. Here, we used information from the cattle genome and the 50 K Cervine Illumina BeadChip to inform and refine a high-density linkage map in a wild population of red deer (Cervus elaphus). We constructed a predicted linkage map of 38,038 SNPs and a skeleton map of 10,835 SNPs across 34 linkage groups. We identified several chromosomal rearrangements in the deer lineage relative to sheep and cattle, including six chromosome fissions, one fusion, and two large inversions. Otherwise, our findings showed strong concordance with map orders in the cattle genome. The sex-averaged linkage map length was 2739.7 cM and the genome-wide autosomal recombination rate was 1.04 cM/Mb. The female autosomal map length was 1.21 longer than that of males (2767.4 cM vs. 2280.8 cM, respectively). Sex differences in map length were driven by high female recombination rates in peri-centromeric regions, a pattern that is unusual relative to other mammal species. This effect was more pronounced in fission chromosomes that would have had to produce new centromeres. We propose two hypotheses to explain this effect: (1) that this mechanism may have evolved to counteract centromeric drive associated with meiotic asymmetry in oocyte production; and/or (2) that sequence and structural characteristics suppressing recombination in close proximity to the centromere may not have evolved at neo-centromeres. Our study provides insight into how recombination landscapes vary and evolve in mammals, and will provide a valuable resource for studies of evolution, genetic improvement, and population management in red deer and related species. PMID:28667018

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

PubMed Central

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

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

NASA Astrophysics Data System (ADS)

Tanaka, Hiroyuki K. M.

2015-02-01

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 km2. 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.

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

PubMed Central

Tanaka, Hiroyuki K. M.

2015-01-01

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 km2. 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. PMID:25660352

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

PubMed

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.

Comparison of SOM point densities based on different criteria.

PubMed

Kohonen, T

1999-11-15

Point densities of model (codebook) vectors in self-organizing maps (SOMs) are evaluated in this article. For a few one-dimensional SOMs with finite grid lengths and a given probability density function of the input, the numerically exact point densities have been computed. The point density derived from the SOM algorithm turned out to be different from that minimizing the SOM distortion measure, showing that the model vectors produced by the basic SOM algorithm in general do not exactly coincide with the optimum of the distortion measure. A new computing technique based on the calculus of variations has been introduced. It was applied to the computation of point densities derived from the distortion measure for both the classical vector quantization and the SOM with general but equal dimensionality of the input vectors and the grid, respectively. The power laws in the continuum limit obtained in these cases were found to be identical.

Statistical density modification using local pattern matching

DOEpatents

Terwilliger, Thomas C.

2007-01-23

A computer implemented method modifies an experimental electron density map. A set of selected known experimental and model electron density maps is provided and standard templates of electron density are created from the selected experimental and model electron density maps by clustering and averaging values of electron density in a spherical region about each point in a grid that defines each selected known experimental and model electron density maps. Histograms are also created from the selected experimental and model electron density maps that relate the value of electron density at the center of each of the spherical regions to a correlation coefficient of a density surrounding each corresponding grid point in each one of the standard templates. The standard templates and the histograms are applied to grid points on the experimental electron density map to form new estimates of electron density at each grid point in the experimental electron density map.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mashouf, S; University of Toronto, Dept of Radiation Oncology, Toronto, Ontario; Fatemi-Ardekani, A

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 sequencemore » 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.« less

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

NASA Astrophysics Data System (ADS)

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.

Resolution Measurement from a Single Reconstructed Cryo-EM Density Map with Multiscale Spectral Analysis.

PubMed

Yang, Yu-Jiao; Wang, Shuai; Zhang, Biao; Shen, Hong-Bin

2018-06-25

As a relatively new technology to solve the three-dimensional (3D) structure of a protein or protein complex, single-particle reconstruction (SPR) of cryogenic electron microscopy (cryo-EM) images shows much superiority and is in a rapidly developing stage. Resolution measurement in SPR, which evaluates the quality of a reconstructed 3D density map, plays a critical role in promoting methodology development of SPR and structural biology. Because there is no benchmark map in the generation of a new structure, how to realize the resolution estimation of a new map is still an open problem. Existing approaches try to generate a hypothetical benchmark map by reconstructing two 3D models from two halves of the original 2D images for cross-reference, which may result in a premature estimation with a half-data model. In this paper, we report a new self-reference-based resolution estimation protocol, called SRes, that requires only a single reconstructed 3D map. The core idea of SRes is to perform a multiscale spectral analysis (MSSA) on the map through multiple size-variable masks segmenting the map. The MSSA-derived multiscale spectral signal-to-noise ratios (mSSNRs) reveal that their corresponding estimated resolutions will show a cliff jump phenomenon, indicating a significant change in the SSNR properties. The critical point on the cliff borderline is demonstrated to be the right estimator for the resolution of the map.

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

PubMed

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.

1.0 Mm Maps and Radial Density Distributions of Southern Hii/molecular Cloud Complexes

NASA Technical Reports Server (NTRS)

Cheung, L. H.; Frogel, J. A.; Gezar, D. Y.; Hauser, M. G.

1980-01-01

Several 1.0 continuum mapping observations were made of seven southern hemisphere h12/molecular cloud complexes with 65 arcsec resolution. The radial density distribution of the clouds with central luminosity sources was determined observationally. Strong similarities in morphology and general physical conditions were found to exist among all of the southern clouds in the sample.

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

PubMed

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.

Criteria for equality in two entropic inequalities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shirokov, M. E., E-mail: msh@mi.ras.ru

2014-07-31

We obtain a simple criterion for local equality between the constrained Holevo capacity and the quantum mutual information of a quantum channel. This shows that the set of all states for which this equality holds is determined by the kernel of the channel (as a linear map). Applications to Bosonic Gaussian channels are considered. It is shown that for a Gaussian channel having no completely depolarizing components the above characteristics may coincide only at non-Gaussian mixed states and a criterion for the existence of such states is given. All the obtained results may be reformulated as conditions for equality betweenmore » the constrained Holevo capacity of a quantum channel and the input von Neumann entropy. Bibliography: 20 titles. (paper)« less

Landslides density map of S. Miguel Island, Azores archipelago

NASA Astrophysics Data System (ADS)

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.

Symmetry laws improve electronegativity equalization by orders of magnitude and call for a paradigm shift in conceptual density functional theory.

PubMed

von Szentpály, László

2015-03-05

The strict Wigner-Witmer symmetry constraints on chemical bonding are shown to determine the accuracy of electronegativity equalization (ENE) to a high degree. Bonding models employing the electronic chemical potential, μ, as the negative of the ground-state electronegativity, χ(GS), frequently collide with the Wigner-Witmer laws in molecule formation. The violations are presented as the root of the substantially disturbing lack of chemical potential equalization (CPE) in diatomic molecules. For the operational chemical potential, μ(op), the relative deviations from CPE fall between -31% ≤ δμ(op) ≤ +70%. Conceptual density functional theory (cDFT) cannot claim to have operationally (not to mention, rigorously) proven and unified the CPE and ENE principles. The solution to this limitation of cDFT and the symmetry violations is found in substituting μ(op) (i) by Mulliken's valence-state electronegativity, χ(M), for atoms and (ii) its new generalization, the valence-pair-affinity, α(VP), for diatomic molecules. Mulliken's χ(M) is equalized into the α(VP) of the bond, and the accuracy of ENE is orders of magnitude better than that of CPE using μ(op). A paradigm shift replacing the dominance of ground states by emphasizing valence states seems to be in order for conceptual DFT.

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

PubMed Central

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

Some Equalities Are More Equal Than Others: Quality Equality Emerges Later Than Numerical Equality.

PubMed

Sheskin, Mark; Nadal, Amber; Croom, Adam; Mayer, Tanya; Nissel, Jenny; Bloom, Paul

2016-09-01

By age 6, children typically share an equal number of resources between themselves and others. However, fairness involves not merely that each person receive an equal number of resources ("numerical equality") but also that each person receive equal quality resources ("quality equality"). In Study 1, children (N = 87, 3-10 years) typically split four resources "two each" by age 6, but typically monopolized the better two resources until age 10. In Study 2, a new group of 6- to 8-year-olds (N = 32) allocated resources to third parties according to quality equality, indicating that children in this age group understand that fairness requires both types of equality. © 2016 The Authors. Child Development © 2016 Society for Research in Child Development, Inc.

A methodology for mapping forest latent heat flux densities using remote sensing

NASA Technical Reports Server (NTRS)

Pierce, Lars L.; Congalton, Russell G.

1988-01-01

Surface temperatures and reflectances of an upper elevation Sierran mixed conifer forest were monitored using the Thematic Mapper Simulator sensor during the summer of 1985 in order to explore the possibility of using remote sensing to determine the distribution of solar energy on forested watersheds. The results show that the method is capable of quantifying the relative energy allocation relationships between the two cover types defined in the study. It is noted that the method also has the potential to map forest latent heat flux densities.

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

PubMed

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.

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

NASA Astrophysics Data System (ADS)

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.

Functional connectivity density mapping: comparing multiband and conventional EPI protocols.

PubMed

Cohen, Alexander D; Tomasi, Dardo; Shokri-Kojori, Ehsan; Nencka, Andrew S; Wang, Yang

2018-06-01

Functional connectivity density mapping (FCDM) is a newly developed data-driven technique that quantifies the number of local and global functional connections for each voxel in the brain. In this study, we evaluated reproducibility, sensitivity, and specificity of both local functional connectivity density (lFCD) and global functional connectivity density (gFCD). We compared these metrics using the human connectome project (HCP) compatible high-resolution (2 mm isotropic, TR = 0.8 s) multiband (MB), and more typical, lower resolution (3.5 mm isotropic, TR = 2.0 s) single-band (SB) resting state functional MRI (rs-fMRI) acquisitions. Furthermore, in order to be more clinically feasible, only rs-fMRI scans that lasted seven minutes were tested. Subjects were scanned twice within a two-week span. We found sensitivity and specificity increased and reproducibility either increased or did not change for the MB compared to the SB acquisitions. The MB scans also showed improved gray matter/white matter contrast compared to the SB scans. The lFCD and gFCD patterns were similar across MB and SB scans and confined predominantly to gray matter. We also observed a strong spatial correlation of FCD between MB and SB scans indicating the two acquisitions provide similar information. These findings indicate high-resolution MB acquisitions improve the quality of FCD data, and seven minute rs-fMRI scan can provide robust FCD measurements.

A High-Density Linkage Map for Astyanax mexicanus Using Genotyping-by-Sequencing Technology

PubMed Central

Carlson, Brian M.; Onusko, Samuel W.; Gross, Joshua B.

2014-01-01

The Mexican tetra, Astyanax mexicanus, is a unique model system consisting of cave-adapted and surface-dwelling morphotypes that diverged >1 million years (My) ago. This remarkable natural experiment has enabled powerful genetic analyses of cave adaptation. Here, we describe the application of next-generation sequencing technology to the creation of a high-density linkage map. Our map comprises more than 2200 markers populating 25 linkage groups constructed from genotypic data generated from a single genotyping-by-sequencing project. We leveraged emergent genomic and transcriptomic resources to anchor hundreds of anonymous Astyanax markers to the genome of the zebrafish (Danio rerio), the most closely related model organism to our study species. This facilitated the identification of 784 distinct connections between our linkage map and the Danio rerio genome, highlighting several regions of conserved genomic architecture between the two species despite ∼150 My of divergence. Using a Mendelian cave-associated trait as a proof-of-principle, we successfully recovered the genomic position of the albinism locus near the gene Oca2. Further, our map successfully informed the positions of unplaced Astyanax genomic scaffolds within particular linkage groups. This ability to identify the relative location, orientation, and linear order of unaligned genomic scaffolds will facilitate ongoing efforts to improve on the current early draft and assemble future versions of the Astyanax physical genome. Moreover, this improved linkage map will enable higher-resolution genetic analyses and catalyze the discovery of the genetic basis for cave-associated phenotypes. PMID:25520037

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

PubMed

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.

A High-Density Genetic Map of Tetraploid Salix matsudana Using Specific Length Amplified Fragment Sequencing (SLAF-seq)

PubMed Central

Li, Min; Li, Yujuan; Wang, Ying; Ma, Xiangjian; Zhang, Yuan; Tan, Feng; Wu, Rongling

2016-01-01

As a salt-tolerant arbor tree species, Salix matsudana plays an important role in afforestation and greening in the coastal areas of China. To select superior Salix varieties that adapt to wide saline areas, it is of paramount importance to understand and identify the mechanisms of salt-tolerance at the level of the whole genome. Here, we describe a high-density genetic linkage map of S. matsudana that represents a good coverage of the Salix genome. An intraspecific F1 hybrid population was established by crossing the salt-sensitive “Yanjiang” variety as the female parent with the salt-tolerant “9901” variety as the male parent. This population, along with its parents, was genotyped by specific length amplified fragment sequencing (SLAF-seq), leading to 277,333 high-quality SLAF markers. By marker analysis, we found that both the parents and offspring were tetraploid. The mean sequencing depth was 53.20-fold for “Yanjiang”, 47.41-fold for “9901”, and 11.02-fold for the offspring. Of the SLAF markers detected, 42,321 are polymorphic with sufficient quality for map construction. The final genetic map was constructed using 6,737 SLAF markers, covering 38 linkage groups (LGs). The genetic map spanned 5,497.45 cM in length, with an average distance of 0.82 cM. As a first high-density genetic map of S. matsudana constructed from salt tolerance-varying varieties, this study will provide a foundation for mapping quantitative trait loci that modulate salt tolerance and resistance in Salix and provide important references for molecular breeding of this important forest tree. PMID:27327501

Active Free Surface Density Maps

NASA Astrophysics Data System (ADS)

Çelen, S.

2016-10-01

Percolation problems were occupied to many physical problems after their establishment in 1957 by Broadbent and Hammersley. They can be used to solve complex systems such as bone remodeling. Volume fraction method was adopted to set some algorithms in the literature. However, different rate of osteoporosis could be observed for different microstructures which have the same mass density, mechanical stimuli, hormonal stimuli and nutrition. Thus it was emphasized that the bone might have identical porosity with different specific surfaces. Active free surface density of bone refers the used total area for its effective free surface. The purpose of this manuscript is to consolidate a mathematical approach which can be called as “active free surface density maps” for different surface patterns and derive their formulations. Active free surface density ratios were calculated for different Archimedean lattice models according to Helmholtz free energy and they were compared with their site and bond percolation thresholds from the background studies to derive their potential probability for bone remodeling.

Construction of a high density SNP linkage map of kelp (Saccharina japonica) by sequencing Taq I site associated DNA and mapping of a sex determining locus.

PubMed

Zhang, Ning; Zhang, Linan; Tao, Ye; Guo, Li; Sun, Juan; Li, Xia; Zhao, Nan; Peng, Jie; Li, Xiaojie; Zeng, Liang; Chen, Jinsa; Yang, Guanpin

2015-03-15

Kelp (Saccharina japonica) has been intensively cultured in China for almost a century. Its genetic improvement is comparable with that of rice. However, the development of its molecular tools is extremely limited, thus its genes, genetics and genomics. Kelp performs an alternative life cycle during which sporophyte generation alternates with gametophyte generation. The gametophytes of kelp can be cloned and crossed. Due to these characteristics, kelp may serve as a reference for the biological and genetic studies of Volvox, mosses and ferns. We constructed a high density single nucleotide polymorphism (SNP) linkage map for kelp by restriction site associated DNA (RAD) sequencing. In total, 4,994 SNP-containing physical (tag-defined) RAD loci were mapped on 31 linkage groups. The map expanded a total genetic distance of 1,782.75 cM, covering 98.66% of the expected (1,806.94 cM). The length of RAD tags (85 bp) was extended to 400-500 bp with Miseq method, offering us an easiness of developing SNP chips and shifting SNP genotyping to a high throughput track. The number of linkage groups was in accordance with the documented with cytological methods. In addition, we identified a set of microsatellites (99 in total) from the extended RAD tags. A gametophyte sex determining locus was mapped on linkage group 2 in a window about 9.0 cM in width, which was 2.66 cM up to marker_40567 and 6.42 cM down to marker_23595. A high density SNP linkage map was constructed for kelp, an intensively cultured brown alga in China. The RAD tags were also extended so that a SNP chip could be developed. In addition, a set of microsatellites were identified among mapped loci, and a gametophyte sex determining locus was mapped. This map will facilitate the genetic studies of kelp including for example the evaluation of germplasm and the decipherment of the genetic bases of economic traits.

A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shirasawa, Kenta; Tanaka, Masaru; Takahata, Yasuhiro

Sweetpotato (Ipomoea batatas) is an autohexaploid species with 90 chromosomes (2n = 6x = 90) and a basic chromosome number of 15, and is therefore regarded as one of the most challenging species for high-density genetic map construction. Here, we used single nucleotide polymorphisms (SNPs) identified by double-digest restriction site-associated DNA sequencing based on next-generation sequencing technology to construct a map for sweetpotato. We then aligned the sequence reads onto the reference genome sequence of I. trifida, a likely diploid ancestor of sweetpotato, to detect SNPs. In addition, to simplify analysis of the complex genetic mode of autohexaploidy, we usedmore » an S1 mapping population derived from self-pollination of a single parent. As a result, 28,087 double-simplex SNPs showing a Mendelian segregation ratio in the S1 progeny could be mapped onto 96 linkage groups (LGs), covering a total distance of 33,020.4 cM. Based on the positions of the SNPs on the I. trifida genome, the LGs were classified into 15 groups, each with roughly six LGs and six small extra groups. The molecular genetic techniques used in this study are applicable to high-density mapping of other polyploid plant species, including important crops.« less

A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas)

DOE PAGES

Shirasawa, Kenta; Tanaka, Masaru; Takahata, Yasuhiro; ...

2017-03-10

Sweetpotato (Ipomoea batatas) is an autohexaploid species with 90 chromosomes (2n = 6x = 90) and a basic chromosome number of 15, and is therefore regarded as one of the most challenging species for high-density genetic map construction. Here, we used single nucleotide polymorphisms (SNPs) identified by double-digest restriction site-associated DNA sequencing based on next-generation sequencing technology to construct a map for sweetpotato. We then aligned the sequence reads onto the reference genome sequence of I. trifida, a likely diploid ancestor of sweetpotato, to detect SNPs. In addition, to simplify analysis of the complex genetic mode of autohexaploidy, we usedmore » an S1 mapping population derived from self-pollination of a single parent. As a result, 28,087 double-simplex SNPs showing a Mendelian segregation ratio in the S1 progeny could be mapped onto 96 linkage groups (LGs), covering a total distance of 33,020.4 cM. Based on the positions of the SNPs on the I. trifida genome, the LGs were classified into 15 groups, each with roughly six LGs and six small extra groups. The molecular genetic techniques used in this study are applicable to high-density mapping of other polyploid plant species, including important crops.« less

Mapping wood density globally using remote sensing and climatological data

NASA Astrophysics Data System (ADS)

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.

Flood Detection/Monitoring Using Adjustable Histogram Equalization Technique

PubMed Central

Riaz, Muhammad Mohsin; Ghafoor, Abdul

2014-01-01

Flood monitoring technique using adjustable histogram equalization is proposed. The technique overcomes the limitations (overenhancement, artifacts, and unnatural look) of existing technique by adjusting the contrast of images. The proposed technique takes pre- and postimages and applies different processing steps for generating flood map without user interaction. The resultant flood maps can be used for flood monitoring and detection. Simulation results show that the proposed technique provides better output quality compared to the state of the art existing technique. PMID:24558332

A High Density Consensus Map of Rye (Secale cereale L.) Based on DArT Markers

PubMed Central

Myśków, Beata; Stojałowski, Stefan; Heller-Uszyńska, Katarzyna; Góralska, Magdalena; Brągoszewski, Piotr; Uszyński, Grzegorz; Kilian, Andrzej; Rakoczy-Trojanowska, Monika

2011-01-01

Background Rye (Secale cereale L.) is an economically important crop, exhibiting unique features such as outstanding resistance to biotic and abiotic stresses and high nutrient use efficiency. This species presents a challenge to geneticists and breeders due to its large genome containing a high proportion of repetitive sequences, self incompatibility, severe inbreeding depression and tissue culture recalcitrance. The genomic resources currently available for rye are underdeveloped in comparison with other crops of similar economic importance. The aim of this study was to create a highly saturated, multilocus linkage map of rye via consensus mapping, based on Diversity Arrays Technology (DArT) markers. Methodology/Principal Findings Recombinant inbred lines (RILs) from 5 populations (564 in total) were genotyped using DArT markers and subjected to linkage analysis using Join Map 4.0 and Multipoint Consensus 2.2 software. A consensus map was constructed using a total of 9703 segregating markers. The average chromosome map length ranged from 199.9 cM (2R) to 251.4 cM (4R) and the average map density was 1.1 cM. The integrated map comprised 4048 loci with the number of markers per chromosome ranging from 454 for 7R to 805 for 4R. In comparison with previously published studies on rye, this represents an eight-fold increase in the number of loci placed on a consensus map and a more than two-fold increase in the number of genetically mapped DArT markers. Conclusions/Significance Through the careful choice of marker type, mapping populations and the use of software packages implementing powerful algorithms for map order optimization, we produced a valuable resource for rye and triticale genomics and breeding, which provides an excellent starting point for more in-depth studies on rye genome organization. PMID:22163026

Dynamical density delay maps: simple, new method for visualising the behaviour of complex systems

PubMed Central

2014-01-01

Background Physiologic signals, such as cardiac interbeat intervals, exhibit complex fluctuations. However, capturing important dynamical properties, including nonstationarities may not be feasible from conventional time series graphical representations. Methods We introduce a simple-to-implement visualisation method, termed dynamical density delay mapping (“D3-Map” technique) that provides an animated representation of a system’s dynamics. The method is based on a generalization of conventional two-dimensional (2D) Poincaré plots, which are scatter plots where each data point, x(n), in a time series is plotted against the adjacent one, x(n + 1). First, we divide the original time series, x(n) (n = 1,…, N), into a sequence of segments (windows). Next, for each segment, a three-dimensional (3D) Poincaré surface plot of x(n), x(n + 1), h[x(n),x(n + 1)] is generated, in which the third dimension, h, represents the relative frequency of occurrence of each (x(n),x(n + 1)) point. This 3D Poincaré surface is then chromatised by mapping the relative frequency h values onto a colour scheme. We also generate a colourised 2D contour plot from each time series segment using the same colourmap scheme as for the 3D Poincaré surface. Finally, the original time series graph, the colourised 3D Poincaré surface plot, and its projection as a colourised 2D contour map for each segment, are animated to create the full “D3-Map.” Results We first exemplify the D3-Map method using the cardiac interbeat interval time series from a healthy subject during sleeping hours. The animations uncover complex dynamical changes, such as transitions between states, and the relative amount of time the system spends in each state. We also illustrate the utility of the method in detecting hidden temporal patterns in the heart rate dynamics of a patient with atrial fibrillation. The videos, as well as the source code, are made publicly available. Conclusions Animations

Talbot-Lau x-ray deflectometry phase-retrieval methods for electron density diagnostics in high-energy density experiments.

PubMed

Valdivia, Maria Pia; Stutman, Dan; Stoeckl, Christian; Mileham, Chad; Begishev, Ildar A; Bromage, Jake; Regan, Sean P

2018-01-10

Talbot-Lau x-ray interferometry uses incoherent x-ray sources to measure refraction index changes in matter. These measurements can provide accurate electron density mapping through phase retrieval. An adaptation of the interferometer has been developed in order to meet the specific requirements of high-energy density experiments. This adaptation is known as a moiré deflectometer, which allows for single-shot capabilities in the form of interferometric fringe patterns. The moiré x-ray deflectometry technique requires a set of object and reference images in order to provide electron density maps, which can be costly in the high-energy density environment. In particular, synthetic reference phase images obtained ex situ through a phase-scan procedure, can provide a feasible solution. To test this procedure, an object phase map was retrieved from a single-shot moiré image obtained from a plasma-produced x-ray source. A reference phase map was then obtained from phase-stepping measurements using a continuous x-ray tube source in a small laboratory setting. The two phase maps were used to retrieve an electron density map. A comparison of the moiré and phase-stepping phase-retrieval methods was performed to evaluate single-exposure plasma electron density mapping for high-energy density and other transient plasma experiments. It was found that a combination of phase-retrieval methods can deliver accurate refraction angle mapping. Once x-ray backlighter quality is optimized, the ex situ method is expected to deliver electron density mapping with improved resolution. The steps necessary for improved diagnostic performance are discussed.

High-Density SNP Map Construction and QTL Identification for the Apetalous Character in Brassica napus L.

PubMed Central

Wang, Xiaodong; Yu, Kunjiang; Li, Hongge; Peng, Qi; Chen, Feng; Zhang, Wei; Chen, Song; Hu, Maolong; Zhang, Jiefu

2015-01-01

The apetalous genotype is a morphological ideotype for increasing seed yield and should be of considerable agricultural use; however, only a few studies have focused on the genetic control of this trait in Brassica napus. In the present study, a recombinant inbred line, the AH population, containing 189 individuals was derived from a cross between an apetalous line ‘APL01’ and a normally petalled variety ‘Holly’. The Brassica 60 K Infinium BeadChip Array harboring 52,157 single nucleotide polymorphism (SNP) markers was used to genotype the AH individuals. A high-density genetic linkage map was constructed based on 2,755 bins involving 11,458 SNPs and 57 simple sequence repeats, and was used to identify loci associated with petalous degree (PDgr). The linkage map covered 2,027.53 cM, with an average marker interval of 0.72 cM. The AH map had good collinearity with the B. napus reference genome, indicating its high quality and accuracy. After phenotypic analyses across five different experiments, a total of 19 identified quantitative trait loci (QTLs) distributed across chromosomes A3, A5, A6, A9 and C8 were obtained, and these QTLs were further integrated into nine consensus QTLs by a meta-analysis. Interestingly, the major QTL qPD.C8-2 was consistently detected in all five experiments, and qPD.A9-2 and qPD.C8-3 were stably expressed in four experiments. Comparative mapping between the AH map and the B. napus reference genome suggested that there were 328 genes underlying the confidence intervals of the three steady QTLs. Based on the Gene Ontology assignments of 52 genes to the regulation of floral development in published studies, 146 genes were considered as potential candidate genes for PDgr. The current study carried out a QTL analysis for PDgr using a high-density SNP map in B. napus, providing novel targets for improving seed yield. These results advanced our understanding of the genetic control of PDgr regulation in B. napus. PMID:26779193

High-Density SNP Map Construction and QTL Identification for the Apetalous Character in Brassica napus L.

PubMed

Wang, Xiaodong; Yu, Kunjiang; Li, Hongge; Peng, Qi; Chen, Feng; Zhang, Wei; Chen, Song; Hu, Maolong; Zhang, Jiefu

2015-01-01

The apetalous genotype is a morphological ideotype for increasing seed yield and should be of considerable agricultural use; however, only a few studies have focused on the genetic control of this trait in Brassica napus. In the present study, a recombinant inbred line, the AH population, containing 189 individuals was derived from a cross between an apetalous line 'APL01' and a normally petalled variety 'Holly'. The Brassica 60 K Infinium BeadChip Array harboring 52,157 single nucleotide polymorphism (SNP) markers was used to genotype the AH individuals. A high-density genetic linkage map was constructed based on 2,755 bins involving 11,458 SNPs and 57 simple sequence repeats, and was used to identify loci associated with petalous degree (PDgr). The linkage map covered 2,027.53 cM, with an average marker interval of 0.72 cM. The AH map had good collinearity with the B. napus reference genome, indicating its high quality and accuracy. After phenotypic analyses across five different experiments, a total of 19 identified quantitative trait loci (QTLs) distributed across chromosomes A3, A5, A6, A9 and C8 were obtained, and these QTLs were further integrated into nine consensus QTLs by a meta-analysis. Interestingly, the major QTL qPD.C8-2 was consistently detected in all five experiments, and qPD.A9-2 and qPD.C8-3 were stably expressed in four experiments. Comparative mapping between the AH map and the B. napus reference genome suggested that there were 328 genes underlying the confidence intervals of the three steady QTLs. Based on the Gene Ontology assignments of 52 genes to the regulation of floral development in published studies, 146 genes were considered as potential candidate genes for PDgr. The current study carried out a QTL analysis for PDgr using a high-density SNP map in B. napus, providing novel targets for improving seed yield. These results advanced our understanding of the genetic control of PDgr regulation in B. napus.

VizieR Online Data Catalog: EBHIS spectra and HI column density maps (Winkel+, 2016)

NASA Astrophysics Data System (ADS)

Winkel, B.; Kerp, J.; Floeer, L.; Kalberla, P. M. W.; Ben Bekhti, N.; Keller, R.; Lenz, D.

2015-11-01

The EBHIS 1st data release comprises 21-cm neutral atomic hydrogen data of the Milky Way (-600km/smap projections, CAR, SIN, and SFL; see world-coordinate-system, WCS, references: Greisen & Calabretta, 2002A&A...395.1061G Calabretta & Greisen, 2002A&A...395.1077C Greisen et al., 2006A&A...446..747G Note, size in longitude is 20° in absolute coordinates for CAR projection, and true-angular size for SIN and SFL projections. (2) FITS binary tables containing lists of spectra sampled on a HealPIX grid (nside=1024, Galactic coordinates, Ring indexing scheme, Gorski et al., 2005ApJ...622..759G). To make handling of the data easier, the table is split into smaller files. Each of these contains spectra belonging to one of the 192 base/parent pixels of the nside=4 pixelization. For convenience, the binary tables also contain EQ2000 and Galactic coordinate positions for each individual spectrum, as well as the associated HealPIX index. Furthermore, we provide the full northern-sky HI column density distribution, both, in a (1) HealPIX-grid binary table (nside=1024, Galactic coordinates, Ring indexing scheme) (2) Standard FITS 2D image in ZEA-projection (zenith equal area). (6 data files).

Density Visualization

ERIC Educational Resources Information Center

Keiter, Richard L.; Puzey, Whitney L.; Blitz, Erin A.

2006-01-01

Metal rods of high purity for many elements are now commercially available and may be used to construct a display of relative densities. We have constructed a display with nine metal rods (Mg, Al, Ti, V, Fe, Cu, Ag, Pb, and W) of equal mass whose densities vary from 1.74 to 19.3 g cm[superscript -3]. The relative densities of the metals may be…

A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding

USDA-ARS?s Scientific Manuscript database

Consensus linkage maps are important tools in crop genomics. We have assembled a high-density tetraploid wheat consensus map by integrating 13 datasets from independent biparental populations involving durum wheat cultivars (Triticum turgidum ssp. durum), cultivated emmer (T. turgidum ssp. dicoccum...

Polder maps: Improving OMIT maps by excluding bulk solvent

DOE PAGES

Liebschner, Dorothee; Afonine, Pavel V.; Moriarty, Nigel W.; ...

2017-02-01

The crystallographic maps that are routinely used during the structure-solution workflow are almost always model-biased because model information is used for their calculation. As these maps are also used to validate the atomic models that result from model building and refinement, this constitutes an immediate problem: anything added to the model will manifest itself in the map and thus hinder the validation. OMIT maps are a common tool to verify the presence of atoms in the model. The simplest way to compute an OMIT map is to exclude the atoms in question from the structure, update the corresponding structure factorsmore » and compute a residual map. It is then expected that if these atoms are present in the crystal structure, the electron density for the omitted atoms will be seen as positive features in this map. This, however, is complicated by the flat bulk-solvent model which is almost universally used in modern crystallographic refinement programs. This model postulates constant electron density at any voxel of the unit-cell volume that is not occupied by the atomic model. Consequently, if the density arising from the omitted atoms is weak then the bulk-solvent model may obscure it further. A possible solution to this problem is to prevent bulk solvent from entering the selected OMIT regions, which may improve the interpretative power of residual maps. This approach is called a polder (OMIT) map. Polder OMIT maps can be particularly useful for displaying weak densities of ligands, solvent molecules, side chains, alternative conformations and residues both in terminal regions and in loops. As a result, the tools described in this manuscript have been implemented and are available in PHENIX.« less

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

PubMed

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.

A High-Density Genetic Map with Array-Based Markers Facilitates Structural and Quantitative Trait Locus Analyses of the Common Wheat Genome

PubMed Central

Iehisa, Julio Cesar Masaru; Ohno, Ryoko; Kimura, Tatsuro; Enoki, Hiroyuki; Nishimura, Satoru; Okamoto, Yuki; Nasuda, Shuhei; Takumi, Shigeo

2014-01-01

The large genome and allohexaploidy of common wheat have complicated construction of a high-density genetic map. Although improvements in the throughput of next-generation sequencing (NGS) technologies have made it possible to obtain a large amount of genotyping data for an entire mapping population by direct sequencing, including hexaploid wheat, a significant number of missing data points are often apparent due to the low coverage of sequencing. In the present study, a microarray-based polymorphism detection system was developed using NGS data obtained from complexity-reduced genomic DNA of two common wheat cultivars, Chinese Spring (CS) and Mironovskaya 808. After design and selection of polymorphic probes, 13,056 new markers were added to the linkage map of a recombinant inbred mapping population between CS and Mironovskaya 808. On average, 2.49 missing data points per marker were observed in the 201 recombinant inbred lines, with a maximum of 42. Around 40% of the new markers were derived from genic regions and 11% from repetitive regions. The low number of retroelements indicated that the new polymorphic markers were mainly derived from the less repetitive region of the wheat genome. Around 25% of the mapped sequences were useful for alignment with the physical map of barley. Quantitative trait locus (QTL) analyses of 14 agronomically important traits related to flowering, spikes, and seeds demonstrated that the new high-density map showed improved QTL detection, resolution, and accuracy over the original simple sequence repeat map. PMID:24972598

Improving the Accuracy of Mapping Urban Vegetation Carbon Density by Combining Shadow Remove, Spectral Unmixing Analysis and Spatial Modeling

NASA Astrophysics Data System (ADS)

Qie, G.; Wang, G.; Wang, M.

2016-12-01

Mixed pixels and shadows due to buildings in urban areas impede accurate estimation and mapping of city vegetation carbon density. In most of previous studies, these factors are often ignored, which thus result in underestimation of city vegetation carbon density. In this study we presented an integrated methodology to improve the accuracy of mapping city vegetation carbon density. Firstly, we applied a linear shadow remove analysis (LSRA) on remotely sensed Landsat 8 images to reduce the shadow effects on carbon estimation. Secondly, we integrated a linear spectral unmixing analysis (LSUA) with a linear stepwise regression (LSR), a logistic model-based stepwise regression (LMSR) and k-Nearest Neighbors (kNN), and utilized and compared the integrated models on shadow-removed images to map vegetation carbon density. This methodology was examined in Shenzhen City of Southeast China. A data set from a total of 175 sample plots measured in 2013 and 2014 was used to train the models. The independent variables statistically significantly contributing to improving the fit of the models to the data and reducing the sum of squared errors were selected from a total of 608 variables derived from different image band combinations and transformations. The vegetation fraction from LSUA was then added into the models as an important independent variable. The estimates obtained were evaluated using a cross-validation method. Our results showed that higher accuracies were obtained from the integrated models compared with the ones using traditional methods which ignore the effects of mixed pixels and shadows. This study indicates that the integrated method has great potential on improving the accuracy of urban vegetation carbon density estimation. Key words: Urban vegetation carbon, shadow, spectral unmixing, spatial modeling, Landsat 8 images

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

NASA Astrophysics Data System (ADS)

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.

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

USDA-ARS?s Scientific Manuscript database

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...

PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps.

PubMed

Kuzu, Guray; Keskin, Ozlem; Nussinov, Ruth; Gursoy, Attila

2016-10-01

The structures of protein assemblies are important for elucidating cellular processes at the molecular level. Three-dimensional electron microscopy (3DEM) is a powerful method to identify the structures of assemblies, especially those that are challenging to study by crystallography. Here, a new approach, PRISM-EM, is reported to computationally generate plausible structural models using a procedure that combines crystallographic structures and density maps obtained from 3DEM. The predictions are validated against seven available structurally different crystallographic complexes. The models display mean deviations in the backbone of <5 Å. PRISM-EM was further tested on different benchmark sets; the accuracy was evaluated with respect to the structure of the complex, and the correlation with EM density maps and interface predictions were evaluated and compared with those obtained using other methods. PRISM-EM was then used to predict the structure of the ternary complex of the HIV-1 envelope glycoprotein trimer, the ligand CD4 and the neutralizing protein m36.

High-Density Linkage Map Construction and Mapping of Salt-Tolerant QTLs at Seedling Stage in Upland Cotton Using Genotyping by Sequencing (GBS).

PubMed

Diouf, Latyr; Pan, Zhaoe; He, Shou-Pu; Gong, Wen-Fang; Jia, Yin Hua; Magwanga, Richard Odongo; Romy, Kimbembe Romesh Eric; Or Rashid, Harun; Kirungu, Joy Nyangasi; Du, Xiongming

2017-12-05

Over 6% of agricultural land is affected by salinity. It is becoming obligatory to use saline soils, so growing salt-tolerant plants is a priority. To gain an understanding of the genetic basis of upland cotton tolerance to salinity at seedling stage, an intra-specific cross was developed from CCRI35, tolerant to salinity, as female with Nan Dan (NH), sensitive to salinity, as the male. A genetic map of 5178 SNP markers was developed from 277 F 2:3 populations. The map spanned 4768.098 cM, with an average distance of 0.92 cM. A total of 66 QTLs for 10 traits related to salinity were detected in three environments (0, 110, and 150 mM salt treatment). Only 14 QTLs were consistent, accounting for 2.72% to 9.87% of phenotypic variation. Parental contributions were found to be in the ratio of 3:1, 10 QTLs from the sensitive and four QTLs from the resistant parent. Five QTLs were located in A t and nine QTLs in the D t sub-genome. Moreover, eight clusters were identified, in which 12 putative key genes were found to be related to salinity. The GBS-SNPs-based genetic map developed is the first high-density genetic map that has the potential to provide deeper insights into upland cotton salinity tolerance. The 12 key genes found in this study could be used for QTL fine mapping and cloning for further studies.

A high density linkage map of the ancestral diploid strawberry F. iinumae using SNP markers from the ISTRAW90 array and GBS

USDA-ARS?s Scientific Manuscript database

Fragaria iinumae is recognized as an ancestor of the octoploid strawberry species, including the cultivated strawberry, Fragaria ×ananassa. Here we report the construction of the first high density linkage map for F. iinumae. The map is based on two high-throughput techniques of single nucleotide p...

Construction of a high-density genetic map and lint percentage and cottonseed nutrient trait QTL identification in upland cotton (Gossypium hirsutum L.).

PubMed

Liu, Dexin; Liu, Fang; Shan, Xiaoru; Zhang, Jian; Tang, Shiyi; Fang, Xiaomei; Liu, Xueying; Wang, Wenwen; Tan, Zhaoyun; Teng, Zhonghua; Zhang, Zhengsheng; Liu, Dajun

2015-10-01

Upland cotton plays a critical role not only in the textile industry, but also in the production of important secondary metabolites, such as oil and proteins. Construction of a high-density linkage map and identifying yield and seed trait quantitative trail loci (QTL) are prerequisites for molecular marker-assisted selective breeding projects. Here, we update a high-density upland cotton genetic map from recombinant inbred lines. A total of 25,313 SSR primer pairs were screened for polymorphism between Yumian 1 and T586, and 1712 SSR primer pairs were used to genotype the mapping population and construct a map. An additional 1166 loci have been added to our previously published map with 509 SSR markers. The updated genetic map spans a total recombinant length of 3338.2 cM and contains 1675 SSR loci and nine morphological markers, with an average interval of 1.98 cM between adjacent markers. Green lint (Lg) mapped on chromosome 15 in a previous report is mapped in an interval of 2.6 cM on chromosome 21. Based on the map and phenotypic data from multiple environments, 79 lint percentage and seed nutrient trait QTL are detected. These include 8 lint percentage, 13 crude protein, 15 crude oil, 8 linoleic, 10 oleic, 13 palmitic, and 12 stearic acid content QTL. They explain 3.5-62.7 % of the phenotypic variation observed. Four morphological markers identified have a major impact on lint percentage and cottonseed nutrients traits. In this study, our genetic map provides new sights into the tetraploid cotton genome. Furthermore, the stable QTL and morphological markers could be used for fine-mapping and map-based cloning.

Quantification of mammographic masking risk with volumetric breast density maps: how to select women for supplemental screening

NASA Astrophysics Data System (ADS)

Holland, Katharina; van Gils, Carla H.; Wanders, Johanna OP; Mann, Ritse M.; Karssemeijer, Nico

2016-03-01

The sensitivity of mammograms is low for women with dense breasts, since cancers may be masked by dense tissue. In this study, we investigated methods to identify women with density patterns associated with a high masking risk. Risk measures are derived from volumetric breast density maps. We used the last negative screening mammograms of 93 women who subsequently presented with an interval cancer (IC), and, as controls, 930 randomly selected normal screening exams from women without cancer. Volumetric breast density maps were computed from the mammograms, which provide the dense tissue thickness at each location. These were used to compute absolute and percentage glandular tissue volume. We modeled the masking risk for each pixel location using the absolute and percentage dense tissue thickness and we investigated the effect of taking the cancer location probability distribution (CLPD) into account. For each method, we selected cases with the highest masking measure (by thresholding) and computed the fraction of ICs as a function of the fraction of controls selected. The latter can be interpreted as the negative supplemental screening rate (NSSR). Between the models, when incorporating CLPD, no significant differences were found. In general, the methods performed better when CLPD was included. At higher NSSRs some of the investigated masking measures had a significantly higher performance than volumetric breast density. These measures may therefore serve as an alternative to identify women with a high risk for a masked cancer.

Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps.

PubMed

DiMaio, F; Chiu, W

2016-01-01

Electron cryo-microscopy (cryoEM) has advanced dramatically to become a viable tool for high-resolution structural biology research. The ultimate outcome of a cryoEM study is an atomic model of a macromolecule or its complex with interacting partners. This chapter describes a variety of algorithms and software to build a de novo model based on the cryoEM 3D density map, to optimize the model with the best stereochemistry restraints and finally to validate the model with proper protocols. The full process of atomic structure determination from a cryoEM map is described. The tools outlined in this chapter should prove extremely valuable in revealing atomic interactions guided by cryoEM data. © 2016 Elsevier Inc. All rights reserved.

On contribution of known atomic partial charges of protein backbone in electrostatic potential density maps.

PubMed

Wang, Jimin

2017-06-01

Partial charges of atoms in a molecule and electrostatic potential (ESP) density for that molecule are known to bear a strong correlation. In order to generate a set of point-field force field parameters for molecular dynamics, Kollman and coworkers have extracted atomic partial charges for each of all 20 amino acids using restrained partial charge-fitting procedures from theoretical ESP density obtained from condensed-state quantum mechanics. The magnitude of atomic partial charges for neutral peptide backbone they have obtained is similar to that of partial atomic charges for ionized carboxylate side chain atoms. In this study, the effect of these known atomic partial charges on ESP is examined using computer simulations and compared with the experimental ESP density recently obtained for proteins using electron microscopy. It is found that the observed ESP density maps are most consistent with the simulations that include atomic partial charges of protein backbone. Therefore, atomic partial charges are integral part of atomic properties in protein molecules and should be included in model refinement. © 2017 The Protein Society.

On contribution of known atomic partial charges of protein backbone in electrostatic potential density maps

PubMed Central

2017-01-01

Abstract Partial charges of atoms in a molecule and electrostatic potential (ESP) density for that molecule are known to bear a strong correlation. In order to generate a set of point‐field force field parameters for molecular dynamics, Kollman and coworkers have extracted atomic partial charges for each of all 20 amino acids using restrained partial charge‐fitting procedures from theoretical ESP density obtained from condensed‐state quantum mechanics. The magnitude of atomic partial charges for neutral peptide backbone they have obtained is similar to that of partial atomic charges for ionized carboxylate side chain atoms. In this study, the effect of these known atomic partial charges on ESP is examined using computer simulations and compared with the experimental ESP density recently obtained for proteins using electron microscopy. It is found that the observed ESP density maps are most consistent with the simulations that include atomic partial charges of protein backbone. Therefore, atomic partial charges are integral part of atomic properties in protein molecules and should be included in model refinement. PMID:28370507

Mapping Mangrove Density from Rapideye Data in Central America

NASA Astrophysics Data System (ADS)

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.

A high-density genetic map with array-based markers facilitates structural and quantitative trait locus analyses of the common wheat genome.

PubMed

Iehisa, Julio Cesar Masaru; Ohno, Ryoko; Kimura, Tatsuro; Enoki, Hiroyuki; Nishimura, Satoru; Okamoto, Yuki; Nasuda, Shuhei; Takumi, Shigeo

2014-10-01

The large genome and allohexaploidy of common wheat have complicated construction of a high-density genetic map. Although improvements in the throughput of next-generation sequencing (NGS) technologies have made it possible to obtain a large amount of genotyping data for an entire mapping population by direct sequencing, including hexaploid wheat, a significant number of missing data points are often apparent due to the low coverage of sequencing. In the present study, a microarray-based polymorphism detection system was developed using NGS data obtained from complexity-reduced genomic DNA of two common wheat cultivars, Chinese Spring (CS) and Mironovskaya 808. After design and selection of polymorphic probes, 13,056 new markers were added to the linkage map of a recombinant inbred mapping population between CS and Mironovskaya 808. On average, 2.49 missing data points per marker were observed in the 201 recombinant inbred lines, with a maximum of 42. Around 40% of the new markers were derived from genic regions and 11% from repetitive regions. The low number of retroelements indicated that the new polymorphic markers were mainly derived from the less repetitive region of the wheat genome. Around 25% of the mapped sequences were useful for alignment with the physical map of barley. Quantitative trait locus (QTL) analyses of 14 agronomically important traits related to flowering, spikes, and seeds demonstrated that the new high-density map showed improved QTL detection, resolution, and accuracy over the original simple sequence repeat map. © The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Evaluation of normal swallowing functions by using dynamic high-density surface electromyography maps.

PubMed

Zhu, Mingxing; Yu, Bin; Yang, Wanzhang; Jiang, Yanbing; Lu, Lin; Huang, Zhen; Chen, Shixiong; Li, Guanglin

2017-11-21

Swallowing is a continuous process with substantive interdependencies among different muscles, and it plays a significant role in our daily life. The aim of this study was to propose a novel technique based on high-density surface electromyography (HD sEMG) for the evaluation of normal swallowing functions. A total of 96 electrodes were placed on the front neck to acquire myoelectric signals from 12 healthy subjects while they were performing different swallowing tasks. HD sEMG energy maps were constructed based on the root mean square values to visualize muscular activities during swallowing. The effects of different volumes, viscosities, and head postures on the normal swallowing process were systemically investigated by using the energy maps. The results showed that the HD sEMG energy maps could provide detailed spatial and temporal properties of the muscle electrical activity, and visualize the muscle contractions that closely related to the swallowing function. The energy maps also showed that the swallowing time and effort was also explicitly affected by the volume and viscosity of the bolus. The concentration of the muscular activities shifted to the opposite side when the subjects turned their head to either side. The proposed method could provide an alternative method to physiologically evaluate the dynamic characteristics of normal swallowing and had the advantage of providing a full picture of how different muscle activities cooperate in time and location. The findings from this study suggested that the HD sEMG technique might be a useful tool for fast screening and objective assessment of swallowing disorders or dysphagia.

Mapping the Baby Universe

NASA Technical Reports Server (NTRS)

Wanjek, Christopher

2003-01-01

In June, NASA plans to launch the Microwave Anisotropy Probe (MAP) to survey the ancient radiation in unprecedented detail. MAP will map slight temperature fluctuations within the microwave background that vary by only 0.00001 C across a chilly radiation that now averages 2.73 C above absolute zero. The temperature differences today point back to density differences in the fiery baby universe, in which there was a little more matter here and a little less matter there. Areas of slightly enhanced density had stronger gravity than low-density areas. The high-density areas pulled back on the background radiation, making it appear slightly cooler in those directions.

Low density, resorcinol-formaldehyde aerogels

DOEpatents

Pekala, R.W.

1988-05-26

The polycondensation of resorcinol with formaldehyde under alkaline conditions results in the formation of surface functionalized polymer ''clusters''. The covalent crosslinking of these ''clusters'' produces gels which when processed under supercritical conditions, produce low density, organic aerogels (density less than or equal to100 mg/cc; cell size less than or equal to0.1 microns). The aerogels are transparent,dark red in color and consist of interconnected colloidal-like particles with diameters of about 100 A/degree/. These aerogels may be further carbonized to form low density carbon foams with cell size of about 0.1 micron. 1 fig., 1 tab.

Portable cosmic particle detectors for subsurface density mapping

NASA Astrophysics Data System (ADS)

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

Implementation of a new algorithm for Density Equalizing Map Projections (DEMP)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Close, E.R.; Merrill, D.W.; Holmes, H.H.

The purpose of the PAREP (Populations at Risk to Environmental Pollution) Project at Lawrence Berkeley National Laboratory (LBNL), an ongoing Department of Energy (DOE) project since 1978, is to develop resources (data, computing techniques, and biostatistical methodology) applicable to DOE`s needs. Specifically, the PAREP project has developed techniques for statistically analyzing disease distributions in the vicinity of supposed environmental hazards. Such techniques can be applied to assess the health risks in populations residing near DOE installations, provided adequate small-area health data are available. The FY 1994 task descriptions for the PAREP project were determined in discussions at LBNL on 11/2/93.more » The FY94 PAREP Work Authorization specified three major tasks: a prototype small area study, a feasibility study for obtaining small-area data, and preservation of the PAREP data archive. The complete FY94 work plan, and the subtasks accomplished to date, were included in the Cumulative FY94 progress report.« less

A variable-density absorption event in NGC 3227 mapped with Suzaku and Swift

NASA Astrophysics Data System (ADS)

Beuchert, T.; Markowitz, A. G.; Krauß, F.; Miniutti, G.; Longinotti, A. L.; Guainazzi, M.; de La Calle Pérez, I.; Malkan, M.; Elvis, M.; Miyaji, T.; Hiriart, D.; López, J. M.; Agudo, I.; Dauser, T.; Garcia, J.; Kreikenbohm, A.; Kadler, M.; Wilms, J.

2015-12-01

Context. The morphology of the circumnuclear gas accreting onto supermassive black holes in Seyfert galaxies remains a topic of much debate. As the innermost regions of active galactic nuclei (AGN) are spatially unresolved, X-ray spectroscopy, and in particular line-of-sight absorption variability, is a key diagnostic to map out the distribution of gas. Aims: Observations of variable X-ray absorption in multiple Seyferts and over a wide range of timescales indicate the presence of clumps/clouds of gas within the circumnuclear material. Eclipse events by clumps transiting the line of sight allow us to explore the properties of the clumps over a wide range of radial distances from the optical/UV broad line region (BLR) to beyond the dust sublimation radius. Time-resolved absorption events have been extremely rare so far, but suggest a range of density profiles across Seyferts. We resolve a weeks-long absorption event in the Seyfert NGC 3227. Methods: We examine six Suzaku and 12 Swift observations from a 2008 campaign spanning five weeks. We use a model accounting for the complex spectral interplay of three absorbers with different levels of ionization. We perform time-resolved spectroscopy to discern the absorption variability behavior. We also examine the IR to X-ray spectral energy distribution (SED) to test for reddening by dust. Results: The 2008 absorption event is due to moderately-ionized (log ξ ~ 1.2-1.4) gas covering 90% of the line of sight. We resolve the density profile to be highly irregular, in contrast to a previous symmetric and centrally-peaked event mapped with RXTE in the same object. The UV data do not show significant reddening, suggesting that the cloud is dust-free. Conclusions: The 2008 campaign has revealed a transit by a filamentary, moderately-ionized cloud of variable density that is likely located in the BLR, and possibly part of a disk wind.

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

NASA Astrophysics Data System (ADS)

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.

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

NASA Astrophysics Data System (ADS)

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.

Edge Density Imaging: Mapping the Anatomic Embedding of the Structural Connectome Within the White Matter of the Human Brain

PubMed Central

Owen, Julia P.; Chang, Yi-Shin; Mukherjee, Pratik

2015-01-01

The structural connectome has emerged as a powerful tool to characterize the network architecture of the human brain and shows great potential for generating important new biomarkers for neurologic and psychiatric disorders. The edges of the cerebral graph traverse white matter to interconnect cortical and subcortical nodes, although the anatomic embedding of these edges is generally overlooked in the literature. Mapping the paths of the connectome edges could elucidate the relative importance of individual white matter tracts to the overall network topology of the brain and also lead to a better understanding of the effect of regionally-specific white matter pathology on cognition and behavior. In this work, we introduce edge density imaging (EDI), which maps the number of network edges that pass through every white matter voxel. Test-retest analysis shows good to excellent reliability for edge density (ED) measurements, with consistent results using different cortical and subcortical parcellation schemes and different diffusion MR imaging acquisition parameters. We also demonstrate that ED yields complementary information to both traditional and emerging voxel-wise metrics of white matter microstructure and connectivity, including fractional anisotropy, track density, fiber orientation dispersion and neurite density. Our results demonstrate spatially ordered variations of ED throughout the white matter, notably including greater ED in posterior than anterior cerebral white matter. The EDI framework is employed to map the white matter regions that are enriched with pathways connecting rich club nodes and also those with high densities of intra-modular and inter-modular edges. We show that periventricular white matter has particularly high ED and high densities of rich club edges, which is significant for diseases in which these areas are selectively affected, ranging from white matter injury of prematurity in infants to leukoaraiosis in the elderly. Using edge

Construction of Ultradense Linkage Maps with Lep-MAP2: Stickleback F2 Recombinant Crosses as an Example

PubMed Central

Rastas, Pasi; Calboli, Federico C. F.; Guo, Baocheng; Shikano, Takahito; Merilä, Juha

2016-01-01

High-density linkage maps are important tools for genome biology and evolutionary genetics by quantifying the extent of recombination, linkage disequilibrium, and chromosomal rearrangements across chromosomes, sexes, and populations. They provide one of the best ways to validate and refine de novo genome assemblies, with the power to identify errors in assemblies increasing with marker density. However, assembly of high-density linkage maps is still challenging due to software limitations. We describe Lep-MAP2, a software for ultradense genome-wide linkage map construction. Lep-MAP2 can handle various family structures and can account for achiasmatic meiosis to gain linkage map accuracy. Simulations show that Lep-MAP2 outperforms other available mapping software both in computational efficiency and accuracy. When applied to two large F2-generation recombinant crosses between two nine-spined stickleback (Pungitius pungitius) populations, it produced two high-density (∼6 markers/cM) linkage maps containing 18,691 and 20,054 single nucleotide polymorphisms. The two maps showed a high degree of synteny, but female maps were 1.5–2 times longer than male maps in all linkage groups, suggesting genome-wide recombination suppression in males. Comparison with the genome sequence of the three-spined stickleback (Gasterosteus aculeatus) revealed a high degree of interspecific synteny with a low frequency (<5%) of interchromosomal rearrangements. However, a fairly large (ca. 10 Mb) translocation from autosome to sex chromosome was detected in both maps. These results illustrate the utility and novel features of Lep-MAP2 in assembling high-density linkage maps, and their usefulness in revealing evolutionarily interesting properties of genomes, such as strong genome-wide sex bias in recombination rates. PMID:26668116

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

NASA Astrophysics Data System (ADS)

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

Inter-track interference mitigation with two-dimensional variable equalizer for bit patterned media recording

NASA Astrophysics Data System (ADS)

Wang, Yao; Vijaya Kumar, B. V. K.

2017-05-01

The increased track density in bit patterned media recording (BPMR) causes increased inter-track interference (ITI), which degrades the bit error rate (BER) performance. In order to mitigate the effect of the ITI, signals from multiple tracks can be equalized by a 2D equalizer with 1D target. Usually, the 2D fixed equalizer coefficients are obtained by using a pseudo-random bit sequence (PRBS) for training. In this study, a 2D variable equalizer is proposed, where various sets of 2D equalizer coefficients are predetermined and stored for different ITI patterns besides the usual PRBS training. For data detection, as the ITI patterns are unknown in the first global iteration, the main and adjacent tracks are equalized with the conventional 2D fixed equalizer, detected with Bahl-Cocke-Jelinek-Raviv (BCJR) detector and decoded with low-density parity-check (LDPC) decoder. Then using the estimated bit information from main and adjacent tracks, the ITI pattern for each island of the main track can be estimated and the corresponding 2D variable equalizers are used to better equalize the bits on the main track. This process is executed iteratively by feeding back the main track information. Simulation results indicate that for both single-track and two-track detection, the proposed 2D variable equalizer can achieve better BER and frame error rate (FER) compared to that with the 2D fixed equalizer.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, C.; Pujol, A.; Gaztañaga, E.

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 amore » $$\\sim$$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.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, C.; Pujol, A.; Gaztañaga, E.

We measure the redshift evolution of galaxy bias for a magnitude-limited galaxy sample by combining the galaxy density maps and weak lensing shear maps for a ~116 deg 2 area of the Dark Energy Survey (DES) Science Verification (SV) data. This method was first developed in Amara et al. and later re-examined in a companion paper 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 i < 22.5 galaxy sample. We find the galaxy bias and 1σ error bars inmore » four photometric redshift bins to be 1.12 ± 0.19 (z = 0.2–0.4), 0.97 ± 0.15 (z = 0.4–0.6), 1.38 ± 0.39 (z = 0.6–0.8), and 1.45 ± 0.56 (z = 0.8–1.0). These measurements are consistent at the 2σ level with measurements on the same data set using galaxy clustering and cross-correlation of galaxies with cosmic microwave background lensing, with most of the redshift bins consistent within the 1σ error bars. In addition, our method provides the only σ8 independent constraint among the three. We forward model the main observational effects using mock galaxy catalogues 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. Moreover, 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.« less

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

DOE PAGES

Chang, C.; Pujol, A.; Gaztañaga, E.; ...

2016-04-15

We measure the redshift evolution of galaxy bias for a magnitude-limited galaxy sample by combining the galaxy density maps and weak lensing shear maps for a ~116 deg 2 area of the Dark Energy Survey (DES) Science Verification (SV) data. This method was first developed in Amara et al. and later re-examined in a companion paper 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 i < 22.5 galaxy sample. We find the galaxy bias and 1σ error bars inmore » four photometric redshift bins to be 1.12 ± 0.19 (z = 0.2–0.4), 0.97 ± 0.15 (z = 0.4–0.6), 1.38 ± 0.39 (z = 0.6–0.8), and 1.45 ± 0.56 (z = 0.8–1.0). These measurements are consistent at the 2σ level with measurements on the same data set using galaxy clustering and cross-correlation of galaxies with cosmic microwave background lensing, with most of the redshift bins consistent within the 1σ error bars. In addition, our method provides the only σ8 independent constraint among the three. We forward model the main observational effects using mock galaxy catalogues 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. Moreover, 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.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kashiwagi, Toshiya; Suto, Yasushi; Taruya, Atsushi

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.more » 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.« less

Functional mapping of the pelvic floor and sphincter muscles from high-density surface EMG recordings.

PubMed

Peng, Yun; He, Jinbao; Khavari, Rose; Boone, Timothy B; Zhang, Yingchun

2016-11-01

Knowledge of the innervation of pelvic floor and sphincter muscles is of great importance to understanding the pathophysiology of female pelvic floor dysfunctions. This report presents our high-density intravaginal and intrarectal electromyography (EMG) probes and a comprehensive innervation zone (IZ) imaging technique based on high-density EMG readings to characterize the IZ distribution. Both intravaginal and intrarectal probes are covered with a high-density surface electromyography electrode grid (8 × 8). Surface EMG signals were acquired in ten healthy women performing maximum voluntary contractions of their pelvic floor. EMG decomposition was performed to separate motor-unit action potentials (MUAPs) and then localize their IZs. High-density surface EMG signals were successfully acquired over the vaginal and rectal surfaces. The propagation patterns of muscle activity were clearly visualized for multiple muscle groups of the pelvic floor and anal sphincter. During each contraction, up to 218 and 456 repetitions of motor units were detected by the vaginal and rectal probes, respectively. MUAPs were separated with their IZs identified at various orientations and depths. The proposed probes are capable of providing a comprehensive mapping of IZs of the pelvic floor and sphincter muscles. They can be employed as diagnostic and preventative tools in clinical practices.

A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits

PubMed Central

Wenzl, Peter; Li, Haobing; Carling, Jason; Zhou, Meixue; Raman, Harsh; Paul, Edie; Hearnden, Phillippa; Maier, Christina; Xia, Ling; Caig, Vanessa; Ovesná, Jaroslava; Cakir, Mehmet; Poulsen, David; Wang, Junping; Raman, Rosy; Smith, Kevin P; Muehlbauer, Gary J; Chalmers, Ken J; Kleinhofs, Andris; Huttner, Eric; Kilian, Andrzej

2006-01-01

Background Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers. Results The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 ± 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 ± 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits. Conclusion Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding

Equality in Education: An Equality of Condition Perspective

ERIC Educational Resources Information Center

Lynch, Kathleen; Baker, John

2005-01-01

Transforming schools into truly egalitarian institutions requires a holistic and integrated approach. Using a robust conception of "equality of condition", we examine key dimensions of equality that are central to both the purposes and processes of education: equality in educational and related resources; equality of respect and recognition;…

Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.

PubMed Central

Hulse-Kemp, Amanda M.; Lemm, Jana; Plieske, Joerg; Ashrafi, Hamid; Buyyarapu, Ramesh; Fang, David D.; Frelichowski, James; Giband, Marc; Hague, Steve; Hinze, Lori L.; Kochan, Kelli J.; Riggs, Penny K.; Scheffler, Jodi A.; Udall, Joshua A.; Ulloa, Mauricio; Wang, Shirley S.; Zhu, Qian-Hao; Bag, Sumit K.; Bhardwaj, Archana; Burke, John J.; Byers, Robert L.; Claverie, Michel; Gore, Michael A.; Harker, David B.; Islam, Md S.; Jenkins, Johnie N.; Jones, Don C.; Lacape, Jean-Marc; Llewellyn, Danny J.; Percy, Richard G.; Pepper, Alan E.; Poland, Jesse A.; Mohan Rai, Krishan; Sawant, Samir V.; Singh, Sunil Kumar; Spriggs, Andrew; Taylor, Jen M.; Wang, Fei; Yourstone, Scott M.; Zheng, Xiuting; Lawley, Cindy T.; Ganal, Martin W.; Van Deynze, Allen; Wilson, Iain W.; Stelly, David M.

2015-01-01

High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection, and studying patterns of genomic diversity among cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intraspecific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum L. and 17,954 putative interspecific SNP markers for use with crosses of other cotton species with G. hirsutum. The SNPs on the array were developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense L., G. tomentosum Nuttal × Seemann, G. mustelinum Miers × Watt, G. armourianum Kearny, and G. longicalyx J.B. Hutchinson and Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F2 mapping populations, one intraspecific and one interspecific, and 3,533 SNP markers were co-occurring in both maps. The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii Ulbrich reference genome sequence. The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community. PMID:25908569

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

PubMed

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.

Quantifying volcanic hazard at Campi Flegrei caldera (Italy) with uncertainty assessment: 2. Pyroclastic density current invasion maps

NASA Astrophysics Data System (ADS)

Neri, Augusto; Bevilacqua, Andrea; Esposti Ongaro, Tomaso; Isaia, Roberto; Aspinall, Willy P.; Bisson, Marina; Flandoli, Franco; Baxter, Peter J.; Bertagnini, Antonella; Iannuzzi, Enrico; Orsucci, Simone; Pistolesi, Marco; Rosi, Mauro; Vitale, Stefano

2015-04-01

Campi Flegrei (CF) is an example of an active caldera containing densely populated settlements at very high risk of pyroclastic density currents (PDCs). We present here an innovative method for assessing background spatial PDC hazard in a caldera setting with probabilistic invasion maps conditional on the occurrence of an explosive event. The method encompasses the probabilistic assessment of potential vent opening positions, derived in the companion paper, combined with inferences about the spatial density distribution of PDC invasion areas from a simplified flow model, informed by reconstruction of deposits from eruptions in the last 15 ka. The flow model describes the PDC kinematics and accounts for main effects of topography on flow propagation. Structured expert elicitation is used to incorporate certain sources of epistemic uncertainty, and a Monte Carlo approach is adopted to produce a set of probabilistic hazard maps for the whole CF area. Our findings show that, in case of eruption, almost the entire caldera is exposed to invasion with a mean probability of at least 5%, with peaks greater than 50% in some central areas. Some areas outside the caldera are also exposed to this danger, with mean probabilities of invasion of the order of 5-10%. Our analysis suggests that these probability estimates have location-specific uncertainties which can be substantial. The results prove to be robust with respect to alternative elicitation models and allow the influence on hazard mapping of different sources of uncertainty, and of theoretical and numerical assumptions, to be quantified.

Mapping the conduction band edge density of states of γ-In2Se3 by diffuse reflectance spectra

NASA Astrophysics Data System (ADS)

Kumar, Pradeep; Vedeshwar, Agnikumar G.

2018-03-01

It is demonstrated that the measured diffuse reflectance spectra of γ-In2Se3 can be used to map the conduction band edge density of states through Kubelka-Munk analysis. The Kubelka-Munk function derived from the measured spectra almost mimics the calculated density of states in the vicinity of conduction band edge. The calculation of density of states was carried out using first-principles approach yielding the structural, electronic, and optical properties. The calculations were carried out implementing various functionals and only modified Tran and Blaha (TB-MBJ) results tally closest with the experimental result of band gap. The electronic and optical properties were calculated using FP-LAPW + lo approach based on the Density Functional Theory formalism implementing only TB-mBJ functional. The electron and hole effective masses have been calculated as me * = 0.25 m 0 and mh * = 1.11 m 0 , respectively. The optical properties clearly indicate the anisotropic nature of γ-In2Se3.

Mapping out the QCD phase transition in multiparticle production

NASA Astrophysics Data System (ADS)

Kabana, Sonja; Minkowski, Peter

2001-04-01

We analyse multiparticle production in a thermal framework for seven central nucleus + nucleus collisions, e+ + e- annihilation into hadrons on the Z resonance and four hadronic reactions p + p and p + pbar with partial centrality selection), with centre of mass energies ranging from √(s) = 2.6 GeV (per nucleon pair) to 1.8 TeV. Thermodynamic parameters at chemical freeze-out (temperature and baryon and strangeness fugacities) are obtained from appropriate fits, generally improving in quality for reactions subjected to centrality cuts. All systems with non-vanishing fugacities are extrapolated along trajectories of equal energy density, density and entropy density to zero fugacities. The so-obtained temperatures extrapolated to zero fugacities as a function of initial energy density ɛin universally show a strong rise followed by a saturating limit of Tlim = 155 +/- 6 +/- 20 MeV. We interpret this behaviour as mapping out the boundary between quark gluon plasma and hadronic phases. The ratio of strange antiquarks to light ones as a function of the initial energy density ɛin shows the same behaviour as the temperature, saturating at a value of 0.365 +/- 0.033 +/- 0.07. No distinctive feature of `strangeness enhancement' is seen for heavy ion collisions relative to hadronic and leptonic reactions, when compared at the same initial energy density.

Development and deployment of a high-density linkage map identified quantitative trait loci for plant height in peanut (Arachis hypogaea L.).

PubMed

Huang, Li; Ren, Xiaoping; Wu, Bei; Li, Xinping; Chen, Weigang; Zhou, Xiaojing; Chen, Yuning; Pandey, Manish K; Jiao, Yongqing; Luo, Huaiyong; Lei, Yong; Varshney, Rajeev K; Liao, Boshou; Jiang, Huifang

2016-12-20

Plant height is one of the most important architecture traits in crop plants. In peanut, the genetic basis of plant height remains ambiguous. In this context, we genotyped a recombinant inbred line (RIL) population with 140 individuals developed from a cross between two peanut varieties varying in plant height, Zhonghua 10 and ICG 12625. Genotyping data was generated for 1,175 SSR and 42 transposon polymorphic markers and a high-density genetic linkage map was constructed with 1,219 mapped loci covering total map length of 2,038.75 cM i.e., accounted for nearly 80% of the peanut genome. Quantitative trait locus (QTL) analysis using genotyping and phenotyping data for three environments identified 8 negative-effect QTLs and 10 positive-effect QTLs for plant height. Among these QTLs, 8 QTLs had a large contribution to plant height that explained ≥10% phenotypic variation. Two major-effect consensus QTLs namely cqPHA4a and cqPHA4b were identified with stable performance across three environments. Further, the allelic recombination of detected QTLs proved the existence of the phenomenon of transgressive segregation for plant height in the RIL population. Therefore, this study not only successfully reported a high-density genetic linkage map of peanut and identified genomic region controlling plant height but also opens opportunities for further gene discovery and molecular breeding for plant height in peanut.

Scanning micro-Hall probe mapping of magnetic flux distributions and current densities in YBa2Cu3O7 thin films

NASA Technical Reports Server (NTRS)

Xing, W.; Heinrich, B.; Zhou, HU; Fife, A. A.; Cragg, A. R.; Grant, P. D.

1995-01-01

Mapping of the magnetic flux density B(sub z) (perpendicular to the film plane) for a YBa2Cu3O7 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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ren, S; Tianjin University, Tianjin; Hara, W

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)more » 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.« less

The construction of a high-density linkage map for identifying SNP markers that are tightly linked to a nuclear-recessive major gene for male sterility in Cryptomeria japonica D. Don

PubMed Central

2012-01-01

Background High-density linkage maps facilitate the mapping of target genes and the construction of partial linkage maps around target loci to develop markers for marker-assisted selection (MAS). MAS is quite challenging in conifers because of their large, complex, and poorly-characterized genomes. Our goal was to construct a high-density linkage map to facilitate the identification of markers that are tightly linked to a major recessive male-sterile gene (ms1) for MAS in C. japonica, a species that is important in Japanese afforestation but which causes serious social pollinosis problems. Results We constructed a high-density saturated genetic linkage map for C. japonica using expressed sequence-derived co-dominant single nucleotide polymorphism (SNP) markers, most of which were genotyped using the GoldenGate genotyping assay. A total of 1261 markers were assigned to 11 linkage groups with an observed map length of 1405.2 cM and a mean distance between two adjacent markers of 1.1 cM; the number of linkage groups matched the basic chromosome number in C. japonica. Using this map, we located ms1 on the 9th linkage group and constructed a partial linkage map around the ms1 locus. This enabled us to identify a marker (hrmSNP970_sf) that is closely linked to the ms1 gene, being separated from it by only 0.5 cM. Conclusions Using the high-density map, we located the ms1 gene on the 9th linkage group and constructed a partial linkage map around the ms1 locus. The map distance between the ms1 gene and the tightly linked marker was only 0.5 cM. The identification of markers that are tightly linked to the ms1 gene will facilitate the early selection of male-sterile trees, which should expedite C. japonica breeding programs aimed at alleviating pollinosis problems without harming productivity. PMID:22424262

FAINT EXTENDED OH EMISSION FROM THE LOCAL INTERSTELLAR MEDIUM IN THE DIRECTION l Almost-Equal-To 108 Degree-Sign , b Almost-Equal-To 5 Degree-Sign

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allen, Ronald J.; Rodriguez, Monica Ivette; Black, John H.

We have mapped faint 1667 OH line emission (T{sub A} Almost-Equal-To 20-40 mK in our Almost-Equal-To 30' beam) along many lines of sight in the Galaxy covering an area of Almost-Equal-To 4 Degree-Sign Multiplication-Sign 4 Degree-Sign in the general direction of l Almost-Equal-To 108 Degree-Sign , b Almost-Equal-To 5 Degree-Sign . The OH emission is widespread, similar in extent to the local H I (r {approx}< 2 kpc) both in space and in velocity. The OH profile amplitudes show a good general correlation with those of H I in spectral channels of Almost-Equal-To 1 km s{sup -1}; this relation ismore » described by T{sub A} (OH) Almost-Equal-To 1.50 Multiplication-Sign 10{sup -4} T{sub B} (H I) for values of T{sub B} (H I) {approx}< 60-70 K. Beyond this the H I line appears to 'saturate', and few values are recorded above Almost-Equal-To 90 K. However, the OH brightness continues to rise, by a further factor Almost-Equal-To 3. The OH velocity profiles show multiple features with widths typically 2-3 km s{sup -1}, but less than 10% of these features are associated with CO(1-0) emission in existing surveys of the area smoothed to comparable resolution.« less

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

PubMed Central

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. PMID:27749938

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

PubMed

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.

Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping.

PubMed

Covarrubias-Pazaran, Giovanny; Diaz-Garcia, Luis; Schlautman, Brandon; Deutsch, Joseph; Salazar, Walter; Hernandez-Ochoa, Miguel; Grygleski, Edward; Steffan, Shawn; Iorizzo, Massimo; Polashock, James; Vorsa, Nicholi; Zalapa, Juan

2016-06-13

The application of genotyping by sequencing (GBS) approaches, combined with data imputation methodologies, is narrowing the genetic knowledge gap between major and understudied, minor crops. GBS is an excellent tool to characterize the genomic structure of recently domesticated (~200 years) and understudied species, such as cranberry (Vaccinium macrocarpon Ait.), by generating large numbers of markers for genomic studies such as genetic mapping. We identified 10842 potentially mappable single nucleotide polymorphisms (SNPs) in a cranberry pseudo-testcross population wherein 5477 SNPs and 211 short sequence repeats (SSRs) were used to construct a high density linkage map in cranberry of which a total of 4849 markers were mapped. Recombination frequency, linkage disequilibrium (LD), and segregation distortion at the genomic level in the parental and integrated linkage maps were characterized for first time in cranberry. SSR markers, used as the backbone in the map, revealed high collinearity with previously published linkage maps. The 4849 point map consisted of twelve linkage groups spanning 1112 cM, which anchored 2381 nuclear scaffolds accounting for ~13 Mb of the estimated 470 Mb cranberry genome. Bin mapping identified 592 and 672 unique bins in the parentals and a total of 1676 unique marker positions in the integrated map. Synteny analyses comparing the order of anchored cranberry scaffolds to their homologous positions in kiwifruit, grape, and coffee genomes provided initial evidence of homology between cranberry and closely related species. GBS data was used to rapidly saturate the cranberry genome with markers in a pseudo-testcross population. Collinearity between the present saturated genetic map and previous cranberry SSR maps suggests that the SNP locations represent accurate marker order and chromosome structure of the cranberry genome. SNPs greatly improved current marker genome coverage, which allowed for genome-wide structure investigations such

Symplectic Propagation of the Map, Tangent Map and Tangent Map Derivative through Quadrupole and Combined-Function Dipole Magnets without Truncation

NASA Astrophysics Data System (ADS)

Bruhwiler, D. L.; Cary, J. R.; Shasharina, S.

1998-04-01

The MAPA accelerator modeling code symplectically advances the full nonlinear map, tangent map and tangent map derivative through all accelerator elements. The tangent map and its derivative are nonlinear generalizations of Browns first- and second-order matrices(K. Brown, SLAC-75, Rev. 4 (1982), pp. 107-118.), and they are valid even near the edges of the dynamic aperture, which may be beyond the radius of convergence for a truncated Taylor series. In order to avoid truncation of the map and its derivatives, the Hamiltonian is split into pieces for which the map can be obtained analytically. Yoshidas method(H. Yoshida, Phys. Lett. A 150 (1990), pp. 262-268.) is then used to obtain a symplectic approximation to the map, while the tangent map and its derivative are appropriately composed at each step to obtain them with equal accuracy. We discuss our splitting of the quadrupole and combined-function dipole Hamiltonians and show that typically few steps are required for a high-energy accelerator.

A predator equalizes rate of capture of a schooling prey in a patchy environment.

PubMed

Vijayan, Sundararaj; Kotler, Burt P; Abramsky, Zvika

2017-05-01

Prey individuals are often distributed heterogeneously in the environment, and their abundances and relative availabilities vary among patches. A foraging predator should maximize energetic gains by selectively choosing patches with higher prey density. However, catching behaviorally responsive and group-forming prey in patchy environments can be a challenge for predators. First, they have to identify the profitable patches, and second, they must manage the prey's sophisticated anti-predator behavior. Thus, the forager and its prey have to continuously adjust their behavior to that of their opponent. Given these conditions, the foraging predator's behavior should be dynamic with time in terms of foraging effort and prey capture rates across different patches. Theoretically, the allocation of its time among patches of behaviorally responsive prey should be such that it equalizes its prey capture rates across patches through time. We tested this prediction in a model system containing a predator (little egret) and group-forming prey (common gold fish) in two sets of experiments in which (1) patches (pools) contained equal numbers of prey, or in which (2) patches contained unequal densities of prey. The egret equalized the prey capture rate through time in both equal and different density experiments. Copyright © 2017 Elsevier B.V. All rights reserved.

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

Treesearch

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...

Map projections for global and continental data sets and an analysis of pixel distortion caused by reprojection

USGS Publications Warehouse

Steinwand, Daniel R.; Hutchinson, John A.; Snyder, J.P.

1995-01-01

In global change studies the effects of map projection properties on data quality are apparent, and the choice of projection is significant. To aid compilers of global and continental data sets, six equal-area projections were chosen: the interrupted Goode Homolosine, the interrupted Mollweide, the Wagner IV, and the Wagner VII for global maps; the Lambert Azimuthal Equal-Area for hemisphere maps; and the Oblated Equal-Area and the Lambert Azimuthal Equal-Area for continental maps. Distortions in small-scale maps caused by reprojection, and the additional distortions incurred when reprojecting raster images, were quantified and graphically depicted. For raster images, the errors caused by the usual resampling methods (pixel brightness level interpolation) were responsible for much of the additional error where the local resolution and scale change were the greatest.

Mapping Bone Mineral Density Obtained by Quantitative Computed Tomography to Bone Volume Fraction

NASA Technical Reports Server (NTRS)

Pennline, James A.; Mulugeta, Lealem

2017-01-01

Methods for relating or mapping estimates of volumetric Bone Mineral Density (vBMD) obtained by Quantitative Computed Tomography to Bone Volume Fraction (BVF) are outlined mathematically. The methods are based on definitions of bone properties, cited experimental studies and regression relations derived from them for trabecular bone in the proximal femur. Using an experimental range of values in the intertrochanteric region obtained from male and female human subjects, age 18 to 49, the BVF values calculated from four different methods were compared to the experimental average and numerical range. The BVF values computed from the conversion method used data from two sources. One source provided pre bed rest vBMD values in the intertrochanteric region from 24 bed rest subject who participated in a 70 day study. Another source contained preflight vBMD values from 18 astronauts who spent 4 to 6 months on the ISS. To aid the use of a mapping from BMD to BVF, the discussion includes how to formulate them for purpose of computational modeling. An application of the conversions would be used to aid in modeling of time varying changes in vBMD as it relates to changes in BVF via bone remodeling and/or modeling.

Construction of a high-density linkage map and mapping quantitative trait loci for somatic embryogenesis using leaf petioles as explants in upland cotton (Gossypium hirsutum L.).

PubMed

Xu, Zhenzhen; Zhang, Chaojun; Ge, Xiaoyang; Wang, Ni; Zhou, Kehai; Yang, Xiaojie; Wu, Zhixia; Zhang, Xueyan; Liu, Chuanliang; Yang, Zuoren; Li, Changfeng; Liu, Kun; Yang, Zhaoen; Qian, Yuyuan; Li, Fuguang

2015-07-01

The first high-density linkage map was constructed to identify quantitative trait loci (QTLs) for somatic embryogenesis (SE) in cotton ( Gossypium hirsutum L.) using leaf petioles as explants. Cotton transformation is highly limited by only a few regenerable genotypes and the lack of understanding of the genetic and molecular basis of somatic embryogenesis (SE) in cotton (Gossypium hirsutum L.). To construct a more saturated linkage map and further identify quantitative trait loci (QTLs) for SE using leaf petioles as explants, a high embryogenesis frequency line (W10) from the commercial Chinese cotton cultivar CRI24 was crossed with TM-1, a genetic standard upland cotton with no embryogenesis frequency. The genetic map spanned 2300.41 cM in genetic distance and contained 411 polymorphic simple sequence repeat (SSR) loci. Of the 411 mapped loci, 25 were developed from unigenes identified for SE in our previous study. Six QTLs for SE were detected by composite interval mapping method, each explaining 6.88-37.07% of the phenotypic variance. Single marker analysis was also performed to verify the reliability of QTLs detection, and the SSR markers NAU3325 and DPL0209 were detected by the two methods. Further studies on the relatively stable and anchoring QTLs/markers for SE in an advanced population of W10 × TM-1 and other cross combinations with different SE abilities may shed light on the genetic and molecular mechanism of SE in cotton.

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

PubMed

Shi, Yuan Yuan; Sun, Liang Xian; Huang, Zachary Y; Wu, Xiao Bo; Zhu, Yong Qiang; Zheng, Hua Jun; Zeng, Zhi Jiang

2013-01-01

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. 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. 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.

The Development of a High Density Linkage Map for Black Tiger Shrimp (Penaeus monodon) Based on cSNPs

PubMed Central

Baranski, Matthew; Gopikrishna, Gopalapillay; Robinson, Nicholas A.; Katneni, Vinaya Kumar; Shekhar, Mudagandur S.; Shanmugakarthik, Jayakani; Jothivel, Sarangapani; Gopal, Chavali; Ravichandran, Pitchaiyappan; Kent, Matthew; Arnyasi, Mariann; Ponniah, Alphis G.

2014-01-01

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. PMID:24465553

Earth mapping - aerial or satellite imagery comparative analysis

NASA Astrophysics Data System (ADS)

Fotev, Svetlin; Jordanov, Dimitar; Lukarski, Hristo

Nowadays, solving the tasks for revision of existing map products and creation of new maps requires making a choice of the land cover image source. The issue of the effectiveness and cost of the usage of aerial mapping systems versus the efficiency and cost of very-high resolution satellite imagery is topical [1, 2, 3, 4]. The price of any remotely sensed image depends on the product (panchromatic or multispectral), resolution, processing level, scale, urgency of task and on whether the needed image is available in the archive or has to be requested. The purpose of the present work is: to make a comparative analysis between the two approaches for mapping the Earth having in mind two parameters: quality and cost. To suggest an approach for selection of the map information sources - airplane-based or spacecraft-based imaging systems with very-high spatial resolution. Two cases are considered: area that equals approximately one satellite scene and area that equals approximately the territory of Bulgaria.

Implementation of digital equality comparator circuit on memristive memory crossbar array using material implication logic

NASA Astrophysics Data System (ADS)

Haron, Adib; Mahdzair, Fazren; Luqman, Anas; Osman, Nazmie; Junid, Syed Abdul Mutalib Al

2018-03-01

One of the most significant constraints of Von Neumann architecture is the limited bandwidth between memory and processor. The cost to move data back and forth between memory and processor is considerably higher than the computation in the processor itself. This architecture significantly impacts the Big Data and data-intensive application such as DNA analysis comparison which spend most of the processing time to move data. Recently, the in-memory processing concept was proposed, which is based on the capability to perform the logic operation on the physical memory structure using a crossbar topology and non-volatile resistive-switching memristor technology. This paper proposes a scheme to map digital equality comparator circuit on memristive memory crossbar array. The 2-bit, 4-bit, 8-bit, 16-bit, 32-bit, and 64-bit of equality comparator circuit are mapped on memristive memory crossbar array by using material implication logic in a sequential and parallel method. The simulation results show that, for the 64-bit word size, the parallel mapping exhibits 2.8× better performance in total execution time than sequential mapping but has a trade-off in terms of energy consumption and area utilization. Meanwhile, the total crossbar area can be reduced by 1.2× for sequential mapping and 1.5× for parallel mapping both by using the overlapping technique.

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

PubMed Central

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. PMID:29259608

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

PubMed

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.

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

PubMed

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.

High-density genetic map construction and QTLs identification for plant height in white jute (Corchorus capsularis L.) using specific locus amplified fragment (SLAF) sequencing.

PubMed

Tao, Aifen; Huang, Long; Wu, Guifen; Afshar, Reza Keshavarz; Qi, Jianmin; Xu, Jiantang; Fang, Pingping; Lin, Lihui; Zhang, Liwu; Lin, Peiqing

2017-05-08

Genetic mapping and quantitative trait locus (QTL) detection are powerful methodologies in plant improvement and breeding. White jute (Corchorus capsularis L.) is an important industrial raw material fiber crop because of its elite characteristics. However, construction of a high-density genetic map and identification of QTLs has been limited in white jute due to a lack of sufficient molecular markers. The specific locus amplified fragment sequencing (SLAF-seq) strategy combines locus-specific amplification and high-throughput sequencing to carry out de novo single nuclear polymorphism (SNP) discovery and large-scale genotyping. In this study, SLAF-seq was employed to obtain sufficient markers to construct a high-density genetic map for white jute. Moreover, with the development of abundant markers, genetic dissection of fiber yield traits such as plant height was also possible. Here, we present QTLs associated with plant height that were identified using our newly constructed genetic linkage groups. An F 8 population consisting of 100 lines was developed. In total, 69,446 high-quality SLAFs were detected of which 5,074 SLAFs were polymorphic; 913 polymorphic markers were used for the construction of a genetic map. The average coverage for each SLAF marker was 43-fold in the parents, and 9.8-fold in each F 8 individual. A linkage map was constructed that contained 913 SLAFs on 11 linkage groups (LGs) covering 1621.4 cM with an average density of 1.61 cM per locus. Among the 11 LGs, LG1 was the largest with 210 markers, a length of 406.34 cM, and an average distance of 1.93 cM between adjacent markers. LG11 was the smallest with only 25 markers, a length of 29.66 cM, and an average distance of 1.19 cM between adjacent markers. 'SNP_only' markers accounted for 85.54% and were the predominant markers on the map. QTL mapping based on the F 8 phenotypes detected 11 plant height QTLs including one major effect QTL across two cultivation locations, with each QTL

Estimation of dislocations density and distribution of dislocations during ECAP-Conform process

NASA Astrophysics Data System (ADS)

Derakhshan, Jaber Fakhimi; Parsa, Mohammad Habibi; Ayati, Vahid; Jafarian, Hamidreza

2018-01-01

Dislocation density of coarse grain aluminum AA1100 alloy (140 µm) that was severely deformed by Equal Channel Angular Pressing-Conform (ECAP-Conform) are studied at various stages of the process by electron backscattering diffraction (EBSD) method. The geometrically necessary dislocations (GNDs) density and statistically stored dislocations (SSDs) densities were estimate. Then the total dislocations densities are calculated and the dislocation distributions are presented as the contour maps. Estimated average dislocations density for annealed of about 2×1012 m-2 increases to 4×1013 m-2 at the middle of the groove (135° from the entrance), and they reach to 6.4×1013 m-2 at the end of groove just before ECAP region. Calculated average dislocations density for one pass severely deformed Al sample reached to 6.2×1014 m-2. At micrometer scale the behavior of metals especially mechanical properties largely depend on the dislocation density and dislocation distribution. So, yield stresses at different conditions were estimated based on the calculated dislocation densities. Then estimated yield stresses were compared with experimental results and good agreements were found. Although grain size of material did not clearly change, yield stress shown intensive increase due to the development of cell structure. A considerable increase in dislocations density in this process is a good justification for forming subgrains and cell structures during process which it can be reason of increasing in yield stress.

Genotyping by Sequencing Using Specific Allelic Capture to Build a High-Density Genetic Map of Durum Wheat

PubMed Central

Holtz, Yan; Ardisson, Morgane; Ranwez, Vincent; Besnard, Alban; Leroy, Philippe; Poux, Gérard; Roumet, Pierre; Viader, Véronique; Santoni, Sylvain; David, Jacques

2016-01-01

Targeted sequence capture is a promising technology which helps reduce costs for sequencing and genotyping numerous genomic regions in large sets of individuals. Bait sequences are designed to capture specific alleles previously discovered in parents or reference populations. We studied a set of 135 RILs originating from a cross between an emmer cultivar (Dic2) and a recent durum elite cultivar (Silur). Six thousand sequence baits were designed to target Dic2 vs. Silur polymorphisms discovered in a previous RNAseq study. These baits were exposed to genomic DNA of the RIL population. Eighty percent of the targeted SNPs were recovered, 65% of which were of high quality and coverage. The final high density genetic map consisted of more than 3,000 markers, whose genetic and physical mapping were consistent with those obtained with large arrays. PMID:27171472

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

PubMed

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.

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

PubMed Central

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. PMID:28644843

Variants for HDL-C, LDL-C, and triglycerides identified from admixture mapping and fine-mapping analysis in African American families.

PubMed

Shetty, Priya B; Tang, Hua; Feng, Tao; Tayo, Bamidele; Morrison, Alanna C; Kardia, Sharon L R; Hanis, Craig L; Arnett, Donna K; Hunt, Steven C; Boerwinkle, Eric; Rao, Dabeeru C; Cooper, Richard S; Risch, Neil; Zhu, Xiaofeng

2015-02-01

Admixture mapping of lipids was followed-up by family-based association analysis to identify variants for cardiovascular disease in African Americans. The present study conducted admixture mapping analysis for total cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides. The analysis was performed in 1905 unrelated African American subjects from the National Heart, Lung and Blood Institute's Family Blood Pressure Program (FBPP). Regions showing admixture evidence were followed-up with family-based association analysis in 3556 African American subjects from the FBPP. The admixture mapping and family-based association analyses were adjusted for age, age(2), sex, body mass index, and genome-wide mean ancestry to minimize the confounding caused by population stratification. Regions that were suggestive of local ancestry association evidence were found on chromosomes 7 (low-density lipoprotein cholesterol), 8 (high-density lipoprotein cholesterol), 14 (triglycerides), and 19 (total cholesterol and triglycerides). In the fine-mapping analysis, 52 939 single-nucleotide polymorphisms (SNPs) were tested and 11 SNPs (8 independent SNPs) showed nominal significant association with high-density lipoprotein cholesterol (2 SNPs), low-density lipoprotein cholesterol (4 SNPs), and triglycerides (5 SNPs). The family data were used in the fine-mapping to identify SNPs that showed novel associations with lipids and regions, including genes with known associations for cardiovascular disease. This study identified regions on chromosomes 7, 8, 14, and 19 and 11 SNPs from the fine-mapping analysis that were associated with high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides for further studies of cardiovascular disease in African Americans. © 2014 American Heart Association, Inc.

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.

PubMed

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

Integrated platform for genome-wide screening and construction of high-density genetic interaction maps in mammalian cells

PubMed Central

Kampmann, Martin; Bassik, Michael C.; Weissman, Jonathan S.

2013-01-01

A major challenge of the postgenomic era is to understand how human genes function together in normal and disease states. In microorganisms, high-density genetic interaction (GI) maps are a powerful tool to elucidate gene functions and pathways. We have developed an integrated methodology based on pooled shRNA screening in mammalian cells for genome-wide identification of genes with relevant phenotypes and systematic mapping of all GIs among them. We recently demonstrated the potential of this approach in an application to pathways controlling the susceptibility of human cells to the toxin ricin. Here we present the complete quantitative framework underlying our strategy, including experimental design, derivation of quantitative phenotypes from pooled screens, robust identification of hit genes using ultra-complex shRNA libraries, parallel measurement of tens of thousands of GIs from a single double-shRNA experiment, and construction of GI maps. We describe the general applicability of our strategy. Our pooled approach enables rapid screening of the same shRNA library in different cell lines and under different conditions to determine a range of different phenotypes. We illustrate this strategy here for single- and double-shRNA libraries. We compare the roles of genes for susceptibility to ricin and Shiga toxin in different human cell lines and reveal both toxin-specific and cell line-specific pathways. We also present GI maps based on growth and ricin-resistance phenotypes, and we demonstrate how such a comparative GI mapping strategy enables functional dissection of physical complexes and context-dependent pathways. PMID:23739767

Using specific length amplified fragment sequencing to construct the high-density genetic map for Vitis (Vitis vinifera L. × Vitis amurensis Rupr.).

PubMed

Guo, Yinshan; Shi, Guangli; Liu, Zhendong; Zhao, Yuhui; Yang, Xiaoxu; Zhu, Junchi; Li, Kun; Guo, Xiuwu

2015-01-01

In this study, 149 F1 plants from the interspecific cross between 'Red Globe' (Vitis vinifera L.) and 'Shuangyou' (Vitis amurensis Rupr.) and the parent were used to construct a molecular genetic linkage map by using the specific length amplified fragment sequencing technique. DNA sequencing generated 41.282 Gb data consisting of 206,411,693 paired-end reads. The average sequencing depths were 68.35 for 'Red Globe,' 63.65 for 'Shuangyou,' and 8.01 for each progeny. In all, 115,629 high-quality specific length amplified fragments were detected, of which 42,279 were polymorphic. The genetic map was constructed using 7,199 of these polymorphic markers. These polymorphic markers were assigned to 19 linkage groups; the total length of the map was 1929.13 cm, with an average distance of 0.28 cm between each maker. To our knowledge, the genetic maps constructed in this study contain the largest number of molecular markers. These high-density genetic maps might form the basis for the fine quantitative trait loci mapping and molecular-assisted breeding of grape.

Measurement of carbon nanotube microstructure relative density by optical attenuation and observation of size-dependent variations.

PubMed

Park, Sei Jin; Schmidt, Aaron J; Bedewy, Mostafa; Hart, A John

2013-07-21

Engineering the density of carbon nanotube (CNT) forest microstructures is vital to applications such as electrical interconnects, micro-contact probes, and thermal interface materials. For CNT forests on centimeter-scale substrates, weight and volume can be used to calculate density. However, this is not suitable for smaller samples, including individual microstructures, and moreover does not enable mapping of spatial density variations within the forest. We demonstrate that the relative mass density of individual CNT microstructures can be measured by optical attenuation, with spatial resolution equaling the size of the focused spot. For this, a custom optical setup was built to measure the transmission of a focused laser beam through CNT microstructures. The transmittance was correlated with the thickness of the CNT microstructures by Beer-Lambert-Bouguer law to calculate the attenuation coefficient. We reveal that the density of CNT microstructures grown by CVD can depend on their size, and that the overall density of arrays of microstructures is affected significantly by run-to-run process variations. Further, we use the technique to quantify the change in CNT microstructure density due to capillary densification. This is a useful and accessible metrology technique for CNTs in future microfabrication processes, and will enable direct correlation of density to important properties such as stiffness and electrical conductivity.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xing, W.; Heinrich, B.; Zhou, H.

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 willmore » be shown.« less

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

PubMed Central

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

Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea

PubMed Central

Kujur, Alice; Upadhyaya, Hari D.; Shree, Tanima; Bajaj, Deepak; Das, Shouvik; Saxena, Maneesha S.; Badoni, Saurabh; Kumar, Vinod; Tripathi, Shailesh; Gowda, C. L. L.; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K.; Parida, Swarup K.

2015-01-01

We discovered 26785 and 16573 high-quality SNPs differentiating two parental genotypes of a RIL mapping population using reference desi and kabuli genome-based GBS assay. Of these, 3625 and 2177 SNPs have been integrated into eight desi and kabuli chromosomes, respectively in order to construct ultra-high density (0.20–0.37 cM) intra-specific chickpea genetic linkage maps. One of these constructed high-resolution genetic map has potential to identify 33 major genomic regions harbouring 35 robust QTLs (PVE: 17.9–39.7%) associated with three agronomic traits, which were mapped within <1 cM mean marker intervals on desi chromosomes. The extended LD (linkage disequilibrium) decay (~15 cM) in chromosomes of genetic maps have encouraged us to use a rapid integrated approach (comparative QTL mapping, QTL-region specific haplotype/LD-based trait association analysis, expression profiling and gene haplotype-based association mapping) rather than a traditional QTL map-based cloning method to narrow-down one major seed weight (SW) robust QTL region. It delineated favourable natural allelic variants and superior haplotype-containing one seed-specific candidate embryo defective gene regulating SW in chickpea. The ultra-high-resolution genetic maps, QTLs/genes and alleles/haplotypes-related genomic information generated and integrated strategy for rapid QTL/gene identification developed have potential to expedite genomics-assisted breeding applications in crop plants, including chickpea for their genetic enhancement. PMID:25942004

36 CFR 254.12 - Value equalization; cash equalization waiver.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 36 Parks, Forests, and Public Property 2 2010-07-01 2010-07-01 false Value equalization; cash... AGRICULTURE LANDOWNERSHIP ADJUSTMENTS Land Exchanges § 254.12 Value equalization; cash equalization waiver. (a..., either with or without adjustments of relative values as compensation for various costs, the parties to...

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, H; Lee, Y; Ruschin, M

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.more » 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

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

NASA Astrophysics Data System (ADS)

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.

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

NASA Technical Reports Server (NTRS)

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.

A population-based tissue probability map-driven level set method for fully automated mammographic density estimations.

PubMed

Kim, Youngwoo; Hong, Byung Woo; Kim, Seung Ja; Kim, Jong Hyo

2014-07-01

A major challenge when distinguishing glandular tissues on mammograms, especially for area-based estimations, lies in determining a boundary on a hazy transition zone from adipose to glandular tissues. This stems from the nature of mammography, which is a projection of superimposed tissues consisting of different structures. In this paper, the authors present a novel segmentation scheme which incorporates the learned prior knowledge of experts into a level set framework for fully automated mammographic density estimations. The authors modeled the learned knowledge as a population-based tissue probability map (PTPM) that was designed to capture the classification of experts' visual systems. The PTPM was constructed using an image database of a selected population consisting of 297 cases. Three mammogram experts extracted regions for dense and fatty tissues on digital mammograms, which was an independent subset used to create a tissue probability map for each ROI based on its local statistics. This tissue class probability was taken as a prior in the Bayesian formulation and was incorporated into a level set framework as an additional term to control the evolution and followed the energy surface designed to reflect experts' knowledge as well as the regional statistics inside and outside of the evolving contour. A subset of 100 digital mammograms, which was not used in constructing the PTPM, was used to validate the performance. The energy was minimized when the initial contour reached the boundary of the dense and fatty tissues, as defined by experts. The correlation coefficient between mammographic density measurements made by experts and measurements by the proposed method was 0.93, while that with the conventional level set was 0.47. The proposed method showed a marked improvement over the conventional level set method in terms of accuracy and reliability. This result suggests that the proposed method successfully incorporated the learned knowledge of the experts

System Transversal Equalizer.

DTIC Science & Technology

The report describes the implementation, theory of operation, and performance of an adjustable, 48 tap, surface wave transversal equalizer designed...for the Rome Air Development Center, Floyd Site Radar. The transversal equalizer achieves equalization of system distortion by an array of fixed taps...which provide leading and lagging echoes of the main signal. Equalization is achieved by the introduction of an equal but oppositely phased echo of

Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing

PubMed Central

Nunes, José de Ribamar da Silva; Liu, Shikai; Pértille, Fábio; Perazza, Caio Augusto; Villela, Priscilla Marqui Schmidt; de Almeida-Val, Vera Maria Fonseca; Hilsdorf, Alexandre Wagner Silva; Liu, Zhanjiang; Coutinho, Luiz Lehmann

2017-01-01

Colossoma macropomum, or tambaqui, is the largest native Characiform species found in the Amazon and Orinoco river basins, yet few resources for genetic studies and the genetic improvement of tambaqui exist. In this study, we identified a large number of single-nucleotide polymorphisms (SNPs) for tambaqui and constructed a high-resolution genetic linkage map from a full-sib family of 124 individuals and their parents using the genotyping by sequencing method. In all, 68,584 SNPs were initially identified using minimum minor allele frequency (MAF) of 5%. Filtering parameters were used to select high-quality markers for linkage analysis. We selected 7,734 SNPs for linkage mapping, resulting in 27 linkage groups with a minimum logarithm of odds (LOD) of 8 and maximum recombination fraction of 0.35. The final genetic map contains 7,192 successfully mapped markers that span a total of 2,811 cM, with an average marker interval of 0.39 cM. Comparative genomic analysis between tambaqui and zebrafish revealed variable levels of genomic conservation across the 27 linkage groups which allowed for functional SNP annotations. The large-scale SNP discovery obtained here, allowed us to build a high-density linkage map in tambaqui, which will be useful to enhance genetic studies that can be applied in breeding programs. PMID:28387238

StructMap: Elastic Distance Analysis of Electron Microscopy Maps for Studying Conformational Changes.

PubMed

Sanchez Sorzano, Carlos Oscar; Alvarez-Cabrera, Ana Lucia; Kazemi, Mohsen; Carazo, Jose María; Jonić, Slavica

2016-04-26

Single-particle electron microscopy (EM) has been shown to be very powerful for studying structures and associated conformational changes of macromolecular complexes. In the context of analyzing conformational changes of complexes, distinct EM density maps obtained by image analysis and three-dimensional (3D) reconstruction are usually analyzed in 3D for interpretation of structural differences. However, graphic visualization of these differences based on a quantitative analysis of elastic transformations (deformations) among density maps has not been done yet due to a lack of appropriate methods. Here, we present an approach that allows such visualization. This approach is based on statistical analysis of distances among elastically aligned pairs of EM maps (one map is deformed to fit the other map), and results in visualizing EM maps as points in a lower-dimensional distance space. The distances among points in the new space can be analyzed in terms of clusters or trajectories of points related to potential conformational changes. The results of the method are shown with synthetic and experimental EM maps at different resolutions. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Using specific length amplified fragment sequencing to construct the high-density genetic map for Vitis (Vitis vinifera L. × Vitis amurensis Rupr.)

PubMed Central

Guo, Yinshan; Shi, Guangli; Liu, Zhendong; Zhao, Yuhui; Yang, Xiaoxu; Zhu, Junchi; Li, Kun; Guo, Xiuwu

2015-01-01

In this study, 149 F1 plants from the interspecific cross between ‘Red Globe’ (Vitis vinifera L.) and ‘Shuangyou’ (Vitis amurensis Rupr.) and the parent were used to construct a molecular genetic linkage map by using the specific length amplified fragment sequencing technique. DNA sequencing generated 41.282 Gb data consisting of 206,411,693 paired-end reads. The average sequencing depths were 68.35 for ‘Red Globe,’ 63.65 for ‘Shuangyou,’ and 8.01 for each progeny. In all, 115,629 high-quality specific length amplified fragments were detected, of which 42,279 were polymorphic. The genetic map was constructed using 7,199 of these polymorphic markers. These polymorphic markers were assigned to 19 linkage groups; the total length of the map was 1929.13 cm, with an average distance of 0.28 cm between each maker. To our knowledge, the genetic maps constructed in this study contain the largest number of molecular markers. These high-density genetic maps might form the basis for the fine quantitative trait loci mapping and molecular-assisted breeding of grape. PMID:26089826

Visualizing the Logistic Map with a Microcontroller

ERIC Educational Resources Information Center

Serna, Juan D.; Joshi, Amitabh

2012-01-01

The logistic map is one of the simplest nonlinear dynamical systems that clearly exhibits the route to chaos. In this paper, we explore the evolution of the logistic map using an open-source microcontroller connected to an array of light-emitting diodes (LEDs). We divide the one-dimensional domain interval [0,1] into ten equal parts, an associate…

TSPmap, a tool making use of traveling salesperson problem solvers in the efficient and accurate construction of high-density genetic linkage maps.

PubMed

Monroe, J Grey; Allen, Zachariah A; Tanger, Paul; Mullen, Jack L; Lovell, John T; Moyers, Brook T; Whitley, Darrell; McKay, John K

2017-01-01

Recent advances in nucleic acid sequencing technologies have led to a dramatic increase in the number of markers available to generate genetic linkage maps. This increased marker density can be used to improve genome assemblies as well as add much needed resolution for loci controlling variation in ecologically and agriculturally important traits. However, traditional genetic map construction methods from these large marker datasets can be computationally prohibitive and highly error prone. We present TSPmap , a method which implements both approximate and exact Traveling Salesperson Problem solvers to generate linkage maps. We demonstrate that for datasets with large numbers of genomic markers (e.g. 10,000) and in multiple population types generated from inbred parents, TSPmap can rapidly produce high quality linkage maps with low sensitivity to missing and erroneous genotyping data compared to two other benchmark methods, JoinMap and MSTmap . TSPmap is open source and freely available as an R package. With the advancement of low cost sequencing technologies, the number of markers used in the generation of genetic maps is expected to continue to rise. TSPmap will be a useful tool to handle such large datasets into the future, quickly producing high quality maps using a large number of genomic markers.

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

PubMed Central

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

Improving experimental phases for strong reflections prior to density modification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uervirojnangkoorn, Monarin; Hilgenfeld, Rolf; Terwilliger, Thomas C.

Experimental phasing of diffraction data from macromolecular crystals involves deriving phase probability distributions. These distributions are often bimodal, making their weighted average, the centroid phase, improbable, so that electron-density maps computed using centroid phases are often non-interpretable. Density modification brings in information about the characteristics of electron density in protein crystals. In successful cases, this allows a choice between the modes in the phase probability distributions, and the maps can cross the borderline between non-interpretable and interpretable. Based on the suggestions by Vekhter [Vekhter (2005), Acta Cryst. D 61, 899–902], the impact of identifying optimized phases for a small numbermore » of strong reflections prior to the density-modification process was investigated while using the centroid phase as a starting point for the remaining reflections. A genetic algorithm was developed that optimizes the quality of such phases using the skewness of the density map as a target function. Phases optimized in this way are then used in density modification. In most of the tests, the resulting maps were of higher quality than maps generated from the original centroid phases. In one of the test cases, the new method sufficiently improved a marginal set of experimental SAD phases to enable successful map interpretation. Lastly, a computer program, SISA, has been developed to apply this method for phase improvement in macromolecular crystallography.« less

Improving experimental phases for strong reflections prior to density modification

DOE PAGES

Uervirojnangkoorn, Monarin; Hilgenfeld, Rolf; Terwilliger, Thomas C.; ...

2013-09-20

Experimental phasing of diffraction data from macromolecular crystals involves deriving phase probability distributions. These distributions are often bimodal, making their weighted average, the centroid phase, improbable, so that electron-density maps computed using centroid phases are often non-interpretable. Density modification brings in information about the characteristics of electron density in protein crystals. In successful cases, this allows a choice between the modes in the phase probability distributions, and the maps can cross the borderline between non-interpretable and interpretable. Based on the suggestions by Vekhter [Vekhter (2005), Acta Cryst. D 61, 899–902], the impact of identifying optimized phases for a small numbermore » of strong reflections prior to the density-modification process was investigated while using the centroid phase as a starting point for the remaining reflections. A genetic algorithm was developed that optimizes the quality of such phases using the skewness of the density map as a target function. Phases optimized in this way are then used in density modification. In most of the tests, the resulting maps were of higher quality than maps generated from the original centroid phases. In one of the test cases, the new method sufficiently improved a marginal set of experimental SAD phases to enable successful map interpretation. Lastly, a computer program, SISA, has been developed to apply this method for phase improvement in macromolecular crystallography.« less

Gaussian-input Gaussian mixture model for representing density maps and atomic models.

PubMed

Kawabata, Takeshi

2018-07-01

A new Gaussian mixture model (GMM) has been developed for better representations of both atomic models and electron microscopy 3D density maps. The standard GMM algorithm employs an EM algorithm to determine the parameters. It accepted a set of 3D points with weights, corresponding to voxel or atomic centers. Although the standard algorithm worked reasonably well; however, it had three problems. First, it ignored the size (voxel width or atomic radius) of the input, and thus it could lead to a GMM with a smaller spread than the input. Second, the algorithm had a singularity problem, as it sometimes stopped the iterative procedure due to a Gaussian function with almost zero variance. Third, a map with a large number of voxels required a long computation time for conversion to a GMM. To solve these problems, we have introduced a Gaussian-input GMM algorithm, which considers the input atoms or voxels as a set of Gaussian functions. The standard EM algorithm of GMM was extended to optimize the new GMM. The new GMM has identical radius of gyration to the input, and does not suddenly stop due to the singularity problem. For fast computation, we have introduced a down-sampled Gaussian functions (DSG) by merging neighboring voxels into an anisotropic Gaussian function. It provides a GMM with thousands of Gaussian functions in a short computation time. We also have introduced a DSG-input GMM: the Gaussian-input GMM with the DSG as the input. This new algorithm is much faster than the standard algorithm. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

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

PubMed Central

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

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.

PubMed

Ulloa, Mauricio; Hulse-Kemp, Amanda M; De Santiago, Luis M; Stelly, David M; Burke, John J

2017-01-01

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, especially in paleopolyploids with exceptionally complex genomes, eg, upland cotton ( Gossypium hirsutum L., "2n = 52"). Three independently developed intraspecific upland mapping populations were analyzed to generate 3 high-density genetic linkage single-nucleotide polymorphism (SNP) maps and a consensus map using the CottonSNP63K array. The populations consisted of a previously reported F 2 , a recombinant inbred line (RIL), and reciprocal RIL population, from "Phytogen 72" and "Stoneville 474" cultivars. The cluster file provided 7417 genotyped SNP markers, resulting in 26 linkage groups corresponding to the 26 chromosomes (c) of the allotetraploid upland cotton (AD) 1 arisen from the merging of 2 genomes ("A" Old World and "D" New World). Patterns of chromosome-specific recombination were largely consistent across mapping populations. The high-density genetic consensus map included 7244 SNP markers that spanned 3538 cM and comprised 3824 SNP bins, of which 1783 and 2041 were in the A t and D t subgenomes with 1825 and 1713 cM map lengths, respectively. Subgenome average distances were nearly identical, indicating that subgenomic differences in bin number arose due to the high numbers of SNPs on the D t subgenome. Examination of expected recombination frequency or crossovers (COs) on the chromosomes within each population of the 2 subgenomes revealed that COs were also not affected by the SNPs or SNP bin number in these subgenomes. Comparative alignment analyses identified historical ancestral A t -subgenomic translocations of c02 and c03, as well as of c04 and c05. The consensus map SNP sequences aligned with high congruency to the NBI assembly of Gossypium hirsutum . However, the genomic comparisons revealed evidence of additional

Are consistent equal-weight particle filters possible?

NASA Astrophysics Data System (ADS)

van Leeuwen, P. J.

2017-12-01

Particle filters are fully nonlinear data-assimilation methods that could potentially change the way we do data-assimilation in highly nonlinear high-dimensional geophysical systems. However, the standard particle filter in which the observations come in by changing the relative weights of the particles is degenerate. This means that one particle obtains weight one, and all other particles obtain a very small weight, effectively meaning that the ensemble of particles reduces to that one particle. For over 10 years now scientists have searched for solutions to this problem. One obvious solution seems to be localisation, in which each part of the state only sees a limited number of observations. However, for a realistic localisation radius based on physical arguments, the number of observations is typically too large, and the filter is still degenerate. Another route taken is trying to find proposal densities that lead to more similar particle weights. There is a simple proof, however, that shows that there is an optimum, the so-called optimal proposal density, and that optimum will lead to a degenerate filter. On the other hand, it is easy to come up with a counter example of a particle filter that is not degenerate in high-dimensional systems. Furthermore, several particle filters have been developed recently that claim to have equal or equivalent weights. In this presentation I will show how to construct a particle filter that is never degenerate in high-dimensional systems, and how that is still consistent with the proof that one cannot do better than the optimal proposal density. Furthermore, it will be shown how equal- and equivalent-weights particle filters fit within this framework. This insight will then lead to new ways to generate particle filters that are non-degenerate, opening up the field of nonlinear filtering in high-dimensional systems.

Dissection of the genetic architecture underlying the plant density response by mapping plant height-related traits in maize (Zea mays L.).

PubMed

Ku, Lixia; Zhang, Liangkun; Tian, Zhiqiang; Guo, Shulei; Su, Huihui; Ren, Zhenzhen; Wang, Zhiyong; Li, Guohui; Wang, Xiaobo; Zhu, Yuguang; Zhou, Jinlong; Chen, Yanhui

2015-08-01

Plant height is one of the most heritable traits in maize (Zea mays L.). Understanding the genetic control of plant height is important for elucidating the molecular mechanisms that regulate maize development. To investigate the genetic basis of the plant height response to density in maize, we evaluated the effects of two different plant densities (60,000 and 120,000 plant/hm(2)) on three plant height-related traits (plant height, ear height, and ear height-to-plant height ratio) using four sets of recombinant inbred line populations. The phenotypes observed under the two-plant density treatments indicated that high plant density increased the phenotypic performance values of the three measured traits. Twenty-three quantitative trait loci (QTLs) were detected under the two-plant density treatments, and five QTL clusters were located. Nine QTLs were detected under the low plant density treatment, and seven QTLs were detected under the high plant density treatment. Our results suggested that plant height may be controlled mainly by a common set of genes that could be influenced by additional genetic mechanisms when the plants were grown under high plant density. Fine mapping for genetic regions of the stable QTLs across different plant density environments may provide additional information about their different responses to density. The results presented here provide useful information for further research and will help to reveal the molecular mechanisms related to plant height in response to density.

High-density genetic maps for loci involved in nuclear male sterility (NMS1) and sporophytic self-incompatibility (S-locus) in chicory (Cichorium intybus L., Asteraceae).

PubMed

Gonthier, Lucy; Blassiau, Christelle; Mörchen, Monika; Cadalen, Thierry; Poiret, Matthieu; Hendriks, Theo; Quillet, Marie-Christine

2013-08-01

High-density genetic maps were constructed for loci involved in nuclear male sterility (NMS1-locus) and sporophytic self-incompatibility (S-locus) in chicory (Cichorium intybus L.). The mapping population consisted of 389 F1' individuals derived from a cross between two plants, K28 (male-sterile) and K59 (pollen-fertile), both heterozygous at the S-locus. This F1' mapping population segregated for both male sterility (MS) and strong self-incompatibility (SI) phenotypes. Phenotyping F1' individuals for MS allowed us to map the NMS1-locus to linkage group (LG) 5, while controlled diallel and factorial crosses to identify compatible/incompatible phenotypes mapped the S-locus to LG2. To increase the density of markers around these loci, bulked segregant analysis was used. Bulks and parental plants K28 and K59 were screened using amplified fragment length polymorphism (AFLP) analysis, with a complete set of 256 primer combinations of EcoRI-ANN and MseI-CNN. A total of 31,000 fragments were generated, of which 2,350 showed polymorphism between K59 and K28. Thirteen AFLP markers were identified close to the NMS1-locus and six in the vicinity of the S-locus. From these AFLP markers, eight were transformed into sequence-characterized amplified region (SCAR) markers and of these five showed co-dominant polymorphism. The chromosomal regions containing the NMS1-locus and the S-locus were each confined to a region of 0.8 cM. In addition, we mapped genes encoding proteins similar to S-receptor kinase, the female determinant of sporophytic SI in the Brasicaceae, and also markers in the vicinity of the putative S-locus of sunflower, but none of these genes or markers mapped close to the chicory S-locus.

Development of a 63K SNP array for Gossypium and high-density mapping of intra- and inter-specific populations of cotton (G. hirsutum L.)

USDA-ARS?s Scientific Manuscript database

High-throughput genotyping arrays provide a standardized resource for crop research communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), candidate marker and quantitative trait loci (QTL) ide...

BM-Map: Bayesian Mapping of Multireads for Next-Generation Sequencing Data

PubMed Central

Ji, Yuan; Xu, Yanxun; Zhang, Qiong; Tsui, Kam-Wah; Yuan, Yuan; Norris, Clift; Liang, Shoudan; Liang, Han

2011-01-01

Summary Next-generation sequencing (NGS) technology generates millions of short reads, which provide valuable information for various aspects of cellular activities and biological functions. A key step in NGS applications (e.g., RNA-Seq) is to map short reads to correct genomic locations within the source genome. While most reads are mapped to a unique location, a significant proportion of reads align to multiple genomic locations with equal or similar numbers of mismatches; these are called multireads. The ambiguity in mapping the multireads may lead to bias in downstream analyses. Currently, most practitioners discard the multireads in their analysis, resulting in a loss of valuable information, especially for the genes with similar sequences. To refine the read mapping, we develop a Bayesian model that computes the posterior probability of mapping a multiread to each competing location. The probabilities are used for downstream analyses, such as the quantification of gene expression. We show through simulation studies and RNA-Seq analysis of real life data that the Bayesian method yields better mapping than the current leading methods. We provide a C++ program for downloading that is being packaged into a user-friendly software. PMID:21517792

Adaptive image contrast enhancement using generalizations of histogram equalization.

PubMed

Stark, J A

2000-01-01

This paper proposes a scheme for adaptive image-contrast enhancement based on a generalization of histogram equalization (HE). HE is a useful technique for improving image contrast, but its effect is too severe for many purposes. However, dramatically different results can be obtained with relatively minor modifications. A concise description of adaptive HE is set out, and this framework is used in a discussion of past suggestions for variations on HE. A key feature of this formalism is a "cumulation function," which is used to generate a grey level mapping from the local histogram. By choosing alternative forms of cumulation function one can achieve a wide variety of effects. A specific form is proposed. Through the variation of one or two parameters, the resulting process can produce a range of degrees of contrast enhancement, at one extreme leaving the image unchanged, at another yielding full adaptive equalization.

A High-Density Admixture Map for Disease Gene Discovery in African Americans

PubMed Central

Smith, Michael W. ; Patterson, Nick ; Lautenberger, James A. ; Truelove, Ann L. ; McDonald, Gavin J. ; Waliszewska, Alicja ; Kessing, Bailey D. ; Malasky, Michael J. ; Scafe, Charles ; Le, Ernest ; De Jager, Philip L. ; Mignault, Andre A. ; Yi, Zeng ; de Thé, Guy ; Essex, Myron ; Sankalé, Jean-Louis ; Moore, Jason H. ; Poku, Kwabena ; Phair, John P. ; Goedert, James J. ; Vlahov, David ; Williams, Scott M. ; Tishkoff, Sarah A. ; Winkler, Cheryl A. ; De La Vega, Francisco M. ; Woodage, Trevor ; Sninsky, John J. ; Hafler, David A. ; Altshuler, David ; Gilbert, Dennis A. ; O’Brien, Stephen J. ; Reich, David 

2004-01-01

Admixture mapping (also known as “mapping by admixture linkage disequilibrium,” or MALD) provides a way of localizing genes that cause disease, in admixed ethnic groups such as African Americans, with ∼100 times fewer markers than are required for whole-genome haplotype scans. However, it has not been possible to perform powerful scans with admixture mapping because the method requires a dense map of validated markers known to have large frequency differences between Europeans and Africans. To create such a map, we screened through databases containing ∼450,000 single-nucleotide polymorphisms (SNPs) for which frequencies had been estimated in African and European population samples. We experimentally confirmed the frequencies of the most promising SNPs in a multiethnic panel of unrelated samples and identified 3,011 as a MALD map (1.2 cM average spacing). We estimate that this map is ∼70% informative in differentiating African versus European origins of chromosomal segments. This map provides a practical and powerful tool, which is freely available without restriction, for screening for disease genes in African American patient cohorts. The map is especially appropriate for those diseases that differ in incidence between the parental African and European populations. PMID:15088270

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chojnowski, Grzegorz, E-mail: gchojnowski@genesilico.pl; Waleń, Tomasz; University of Warsaw, Banacha 2, 02-097 Warsaw

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 ismore » 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.« less

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

PubMed

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 .

High-density genetic linkage map construction by F2 populations and QTL analysis of early-maturity traits in upland cotton (Gossypium hirsutum L.).

PubMed

Li, Libei; Zhao, Shuqi; Su, Junji; Fan, Shuli; Pang, Chaoyou; Wei, Hengling; Wang, Hantao; Gu, Lijiao; Zhang, Chi; Liu, Guoyuan; Yu, Dingwei; Liu, Qibao; Zhang, Xianlong; Yu, Shuxun

2017-01-01

Due to China's rapidly increasing population, the total arable land area has dramatically decreased; as a consequence, the competition for farming land allocated for grain and cotton production has become fierce. Therefore, to overcome the existing contradiction between cotton grain and fiber production and the limited farming land, development of early-maturing cultivars is necessary. In this research, a high-density linkage map of upland cotton was constructed using genotyping by sequencing (GBS) to discover single nucleotide polymorphism (SNP) markers associated with early maturity in 170 F2 individuals derived from a cross between LU28 and ZHONG213. The high-density genetic map, which was composed of 3978 SNP markers across the 26 cotton chromosomes, spanned 2480 cM with an average genetic distance of 0.62 cM. Collinearity analysis showed that the genetic map was of high quality and accurate and agreed well with the Gossypium hirsutum reference genome. Based on this high-density linkage map, QTL analysis was performed on cotton early-maturity traits, including FT, FBP, WGP, NFFB, HNFFB and PH. A total 47 QTLs for the six traits were detected; each of these QTLs explained between 2.61% and 32.57% of the observed phenotypic variation. A major region controlling early-maturity traits in Gossypium hirsutum was identified for FT, FBP, WGP, NFFB and HNFFB on chromosome D03. QTL analyses revealed that phenotypic variation explained (PVE) ranged from 10.42% to 32.57%. Two potential candidate genes, Gh_D03G0885 and Gh_D03G0922, were predicted in a stable QTL region and had higher expression levels in the early-maturity variety ZHONG213 than in the late-maturity variety LU28. However, further evidence is required for functional validation. This study could provide useful information for the dissection of early-maturity traits and guide valuable genetic loci for molecular-assisted selection (MAS) in cotton breeding.

High-density genetic linkage map construction by F2 populations and QTL analysis of early-maturity traits in upland cotton (Gossypium hirsutum L.)

PubMed Central

Li, Libei; Zhao, Shuqi; Su, Junji; Fan, Shuli; Pang, Chaoyou; Wei, Hengling; Wang, Hantao; Gu, Lijiao; Zhang, Chi; Liu, Guoyuan; Yu, Dingwei; Liu, Qibao; Zhang, Xianlong

2017-01-01

Due to China’s rapidly increasing population, the total arable land area has dramatically decreased; as a consequence, the competition for farming land allocated for grain and cotton production has become fierce. Therefore, to overcome the existing contradiction between cotton grain and fiber production and the limited farming land, development of early-maturing cultivars is necessary. In this research, a high-density linkage map of upland cotton was constructed using genotyping by sequencing (GBS) to discover single nucleotide polymorphism (SNP) markers associated with early maturity in 170 F2 individuals derived from a cross between LU28 and ZHONG213. The high-density genetic map, which was composed of 3978 SNP markers across the 26 cotton chromosomes, spanned 2480 cM with an average genetic distance of 0.62 cM. Collinearity analysis showed that the genetic map was of high quality and accurate and agreed well with the Gossypium hirsutum reference genome. Based on this high-density linkage map, QTL analysis was performed on cotton early-maturity traits, including FT, FBP, WGP, NFFB, HNFFB and PH. A total 47 QTLs for the six traits were detected; each of these QTLs explained between 2.61% and 32.57% of the observed phenotypic variation. A major region controlling early-maturity traits in Gossypium hirsutum was identified for FT, FBP, WGP, NFFB and HNFFB on chromosome D03. QTL analyses revealed that phenotypic variation explained (PVE) ranged from 10.42% to 32.57%. Two potential candidate genes, Gh_D03G0885 and Gh_D03G0922, were predicted in a stable QTL region and had higher expression levels in the early-maturity variety ZHONG213 than in the late-maturity variety LU28. However, further evidence is required for functional validation. This study could provide useful information for the dissection of early-maturity traits and guide valuable genetic loci for molecular-assisted selection (MAS) in cotton breeding. PMID:28809947

Reframing Inclusive Education: Educational Equality as Capability Equality

ERIC Educational Resources Information Center

Terzi, Lorella

2014-01-01

In this paper, I argue that rethinking questions of inclusive education in the light of the value of educational equality--specifically conceived as capability equality, or genuine opportunities to achieve educational functionings--adds some important insights to the current debate on inclusive education. First, it provides a cohesive value…

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

PubMed

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

2017-06-01

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. • The original brain CT template achieved successful normalization of brain morphology. • Postmortem changes in the brain were independent of sex. • Cortical GM density decreased rapidly after death. • WM and deep GM densities increased following cortical GM density change. • SPM could be useful for assessment of whole brain postmortem changes.

Microwave Transversal Equalizer.

DTIC Science & Technology

1980-05-01

AD-AO?7 603 EATONCORP MELVILLE NY AIL DIV F/6 9/5 MICROWAVE TRANSVERSAL EQUALIZER .(U) MAY 80 J WOLCZOK. 6 KANISCHAK F 3 0602-T8-C-0352 UNCLASSIFIED... Equalizer (MTE) Side-lobe distortion Equalization II Automation ABSTRACT (Continue on revere side It necesary and identify by block numb.r) A...Microwave Transversal Equalizer has been designed, fabricated, and installed at RADC and is capable of reducing side-lobe distortion levels of -18 dBm to

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

PubMed

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

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

PubMed Central

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

Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.).

PubMed

Zhang, Zhen; Shang, Haihong; Shi, Yuzhen; Huang, Long; Li, Junwen; Ge, Qun; Gong, Juwu; Liu, Aiying; Chen, Tingting; Wang, Dan; Wang, Yanling; Palanga, Koffi Kibalou; Muhammad, Jamshed; Li, Weijie; Lu, Quanwei; Deng, Xiaoying; Tan, Yunna; Song, Weiwu; Cai, Juan; Li, Pengtao; Rashid, Harun or; Gong, Wankui; Yuan, Youlu

2016-04-11

Upland Cotton (Gossypium hirsutum) is one of the most important worldwide crops it provides natural high-quality fiber for the industrial production and everyday use. Next-generation sequencing is a powerful method to identify single nucleotide polymorphism markers on a large scale for the construction of a high-density genetic map for quantitative trait loci mapping. In this research, a recombinant inbred lines population developed from two upland cotton cultivars 0-153 and sGK9708 was used to construct a high-density genetic map through the specific locus amplified fragment sequencing method. The high-density genetic map harbored 5521 single nucleotide polymorphism markers which covered a total distance of 3259.37 cM with an average marker interval of 0.78 cM without gaps larger than 10 cM. In total 18 quantitative trait loci of boll weight were identified as stable quantitative trait loci and were detected in at least three out of 11 environments and explained 4.15-16.70 % of the observed phenotypic variation. In total, 344 candidate genes were identified within the confidence intervals of these stable quantitative trait loci based on the cotton genome sequence. These genes were categorized based on their function through gene ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis and eukaryotic orthologous groups analysis. This research reported the first high-density genetic map for Upland Cotton (Gossypium hirsutum) with a recombinant inbred line population using single nucleotide polymorphism markers developed by specific locus amplified fragment sequencing. We also identified quantitative trait loci of boll weight across 11 environments and identified candidate genes within the quantitative trait loci confidence intervals. The results of this research would provide useful information for the next-step work including fine mapping, gene functional analysis, pyramiding breeding of functional genes as well as marker-assisted selection.

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

PubMed

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.

Game of Life on the Equal Degree Random Lattice

NASA Astrophysics Data System (ADS)

Shao, Zhi-Gang; Chen, Tao

2010-12-01

An effective matrix method is performed to build the equal degree random (EDR) lattice, and then a cellular automaton game of life on the EDR lattice is studied by Monte Carlo (MC) simulation. The standard mean field approximation (MFA) is applied, and then the density of live cells is given ρ=0.37017 by MFA, which is consistent with the result ρ=0.37±0.003 by MC simulation.

Topographic maps: Tools for planning

USGS Publications Warehouse

Kaufman, George A.

1980-01-01

Topographic maps are a detailed record of a land area, giving geographic positions and elevations for both natural and man-made features. They show the shape of the land the mountains, valleys, and plains by means of brown contour lines (lines of equal elevation above sea level). In steep mountainous areas, contours are closely spaced; in flatter areas, they are far apart. The elevation of any point on the map can be estimated by referring to the elevations of the contour lines above and below it.

Temperature as a third dimension in column-density mapping of dusty astrophysical structures associated with star formation

NASA Astrophysics Data System (ADS)

Marsh, K. A.; Whitworth, A. P.; Lomax, O.

2015-12-01

We present point process mapping (PPMAP), a Bayesian procedure that uses images of dust continuum emission at multiple wavelengths to produce resolution-enhanced image cubes of differential column density as a function of dust temperature and position. PPMAP is based on the generic `point process formalism, whereby the system of interest (in this case, a dusty astrophysical structure such as a filament or pre-stellar core) is represented by a collection of points in a suitably defined state space. It can be applied to a variety of observational data, such as Herschel images, provided only that the image intensity is delivered by optically thin dust in thermal equilibrium. PPMAP takes full account of the instrumental point-spread functions and does not require all images to be degraded to the same resolution. We present the results of testing using simulated data for a pre-stellar core and a fractal turbulent cloud, and demonstrate its performance with real data from the Herschel infrared Galactic Plane Survey (Hi-GAL). Specifically, we analyse observations of a large filamentary structure in the CMa OB1 giant molecular cloud. Histograms of differential column density indicate that the warm material (T ≳ 13 K) is distributed lognormally, consistent with turbulence, but the column densities of the cooler material are distributed as a high-density tail, consistent with the effects of self-gravity. The results illustrate the potential of PPMAP to aid in distinguishing between different physical components along the line of sight in star-forming clouds, and aid the interpretation of the associated Probability distribution functions (PDFs) of column density.

Interspecies synteny mapping identifies a quantitative trait locus for bone mineral density on human chromosome Xp22.

PubMed

Parsons, Claire A; Mroczkowski, H Joel; McGuigan, Fiona E A; Albagha, Omar M E; Manolagas, Stavros; Reid, David M; Ralston, Stuart H; Shmookler Reis, Robert J

2005-11-01

Bone mineral density (BMD) is a complex trait with a strong genetic component and an important predictor of osteoporotic fracture risk. Here we report the use of a cross-species strategy to identify genes that regulate BMD, proceeding from quantitative trait mapping in mice to association mapping of the syntenic region in the human genome. We identified a quantitative trait locus (QTL) on the mouse X-chromosome for post-maturity change in spine BMD in a cross of SAMP6 and AKR/J mice and conducted association mapping of the syntenic region on human chromosome Xp22. We studied 76 single nucleotide polymorphisms (SNP) from the human region in two sets of DNA pools prepared from individuals with lumbar spine-BMD (LS-BMD) values falling into the top and bottom 13th percentiles of a population-based study of 3100 post-menopausal women. This procedure identified a region of significant association for two adjacent SNP (rs234494 and rs234495) within the Xp22 locus (P<0.001). Individual genotyping for rs234494 in the BMD pools confirmed the presence of an association for alleles (P=0.018) and genotypes (P=0.008). Analysis of rs234494 and rs234495 in 1053 women derived from the same population who were not selected for BMD values showed an association with LS-BMD for rs234495 (P=0.01) and for haplotypes defined by both SNP (P=0.002). Our study illustrates that interspecies synteny can be used to identify and refine QTL for complex traits and represents the first example where a human QTL for BMD regulation has been mapped using this approach.

A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species.

PubMed

Di Pierro, Erica A; Gianfranceschi, Luca; Di Guardo, Mario; Koehorst-van Putten, Herma Jj; Kruisselbrink, Johannes W; Longhi, Sara; Troggio, Michela; Bianco, Luca; Muranty, Hélène; Pagliarani, Giulia; Tartarini, Stefano; Letschka, Thomas; Lozano Luis, Lidia; Garkava-Gustavsson, Larisa; Micheletti, Diego; Bink, Marco Cam; Voorrips, Roeland E; Aziz, Ebrahimi; Velasco, Riccardo; Laurens, François; van de Weg, W Eric

2016-01-01

Quantitative trait loci (QTL) mapping approaches rely on the correct ordering of molecular markers along the chromosomes, which can be obtained from genetic linkage maps or a reference genome sequence. For apple ( Malus domestica Borkh), the genome sequence v1 and v2 could not meet this need; therefore, a novel approach was devised to develop a dense genetic linkage map, providing the most reliable marker-loci order for the highest possible number of markers. The approach was based on four strategies: (i) the use of multiple full-sib families, (ii) the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism (SNP) markers, (iii) the construction of a single backcross-type data set including all families, and (iv) a two-step map generation procedure based on the sequential inclusion of markers. The map comprises 15 417 SNP markers, clustered in 3 K HaploBlock markers spanning 1 267 cM, with an average distance between adjacent markers of 0.37 cM and a maximum distance of 3.29 cM. Moreover, chromosome 5 was oriented according to its homoeologous chromosome 10. This map was useful to improve the apple genome sequence, design the Axiom Apple 480 K SNP array and perform multifamily-based QTL studies. Its collinearity with the genome sequences v1 and v3 are reported. To our knowledge, this is the shortest published SNP map in apple, while including the largest number of markers, families and individuals. This result validates our methodology, proving its value for the construction of integrated linkage maps for any outbreeding species.

A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species

PubMed Central

Di Pierro, Erica A; Gianfranceschi, Luca; Di Guardo, Mario; Koehorst-van Putten, Herma JJ; Kruisselbrink, Johannes W; Longhi, Sara; Troggio, Michela; Bianco, Luca; Muranty, Hélène; Pagliarani, Giulia; Tartarini, Stefano; Letschka, Thomas; Lozano Luis, Lidia; Garkava-Gustavsson, Larisa; Micheletti, Diego; Bink, Marco CAM; Voorrips, Roeland E; Aziz, Ebrahimi; Velasco, Riccardo; Laurens, François; van de Weg, W Eric

2016-01-01

Quantitative trait loci (QTL) mapping approaches rely on the correct ordering of molecular markers along the chromosomes, which can be obtained from genetic linkage maps or a reference genome sequence. For apple (Malus domestica Borkh), the genome sequence v1 and v2 could not meet this need; therefore, a novel approach was devised to develop a dense genetic linkage map, providing the most reliable marker-loci order for the highest possible number of markers. The approach was based on four strategies: (i) the use of multiple full-sib families, (ii) the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism (SNP) markers, (iii) the construction of a single backcross-type data set including all families, and (iv) a two-step map generation procedure based on the sequential inclusion of markers. The map comprises 15 417 SNP markers, clustered in 3 K HaploBlock markers spanning 1 267 cM, with an average distance between adjacent markers of 0.37 cM and a maximum distance of 3.29 cM. Moreover, chromosome 5 was oriented according to its homoeologous chromosome 10. This map was useful to improve the apple genome sequence, design the Axiom Apple 480 K SNP array and perform multifamily-based QTL studies. Its collinearity with the genome sequences v1 and v3 are reported. To our knowledge, this is the shortest published SNP map in apple, while including the largest number of markers, families and individuals. This result validates our methodology, proving its value for the construction of integrated linkage maps for any outbreeding species. PMID:27917289

Science EQUALS Success.

ERIC Educational Resources Information Center

Cobb, Kitty B., Ed.; Conwell, Catherine R., Ed.

The purpose of the EQUALS programs is to increase the interest and awareness that females and minorities have concerning mathematics and science related careers. This book, produced by an EQUALS program in North Carolina, contains 35 hands-on, discovery science activities that center around four EQUALS processes--problem solving, cooperative…

Equality Matters: The Critical Implications of Precisely Defining Equality

ERIC Educational Resources Information Center

Faulkner, Valerie; Walkowiak, Temple; Cain, Chris; Lee, Carrie

2016-01-01

Equality is such an important concept for children to develop. In this article it is argued that a precise definition is needed to ensure that students are provided with a consistent "picture" of what it is that equality really means.

Speech processing using conditional observable maximum likelihood continuity mapping

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hogden, John; Nix, David

A computer implemented method enables the recognition of speech and speech characteristics. Parameters are initialized of first probability density functions that map between the symbols in the vocabulary of one or more sequences of speech codes that represent speech sounds and a continuity map. Parameters are also initialized of second probability density functions that map between the elements in the vocabulary of one or more desired sequences of speech transcription symbols and the continuity map. The parameters of the probability density functions are then trained to maximize the probabilities of the desired sequences of speech-transcription symbols. A new sequence ofmore » speech codes is then input to the continuity map having the trained first and second probability function parameters. A smooth path is identified on the continuity map that has the maximum probability for the new sequence of speech codes. The probability of each speech transcription symbol for each input speech code can then be output.« less

Building perceptual color maps for visualizing interval data

NASA Astrophysics Data System (ADS)

Kalvin, Alan D.; Rogowitz, Bernice E.; Pelah, Adar; Cohen, Aron

2000-06-01

In visualization, a 'color map' maps a range of data values onto a scale of colors. However, unless a color map is e carefully constructed, visual artifacts can be produced. This problem has stimulated considerable interest in creating perceptually based color maps, that is, color maps where equal steps in data value are perceived as equal steps in the color map [Robertson (1988); Pizer (1981); Green (1992); Lefkowitz and Herman, 1992)]. In Rogowitz and Treinish, (1996, 1998) and in Bergman, Treinish and Rogowitz, (1995), we demonstrated that color maps based on luminance or saturation could be good candidates for satisfying this requirement. This work is based on the seminal work of S.S. Stevens (1966), who measured the perceived magnitude of different magnitudes of physical stimuli. He found that for many physical scales, including luminance (cd/m2) and saturation (the 'redness' of a long-wavelength light source), equal ratios in stimulus value produced equal ratios in perceptual magnitude. He interpreted this as indicating that there exists in human cognition a common scale for representing magnitude, and we scale the effects of different physical stimuli to this internal scale. In Rogowitz, Kalvin, Pelahb and Cohen (1999), we used a psychophysical technique to test this hypothesis as it applies to the creation of perceptually uniform color maps. We constructed color maps as trajectories through three-color spaces, a common computer graphics standard (uncalibrated HSV), a common perceptually-based engineering standard for creating visual stimuli (L*a*b*), and a space commonly used in the graphic arts (Munsell). For each space, we created color scales that varied linearly in hue, saturation, or luminance and measured the detectability of increments in hue, saturation or luminance for each of these color scales. We measured the amplitude of the just-detectable Gaussian increments at 20 different values along the range of each color map. For all three color spaces

Hot deformation characterization of duplex low-density steel through 3D processing map development

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mohamadizadeh, A.; Zarei-Hanzaki, A., E-mail: zareih@ut.ac.ir; Abedi, H.R.

The high temperature deformation behavior of duplex low-density Fe–18Mn–8Al–0.8C steel was investigated at temperatures in the range of 600–1000 °C. The primary constitutive analysis indicated that the Zener–Hollomon parameter, which represents the coupled effects of temperature and strain rate, significantly varies with the amount of deformation. Accordingly, the 3D processing maps were developed considering the effect of strain and were used to determine the safe and unsafe deformation conditions in association with the microstructural evolution. The deformation at efficiency domain I (900–1100 °C\\10{sup −} {sup 2}–10{sup −} {sup 3} s{sup −} {sup 1}) was found to be safe at differentmore » strains due to the occurrence of dynamic recrystallization in austenite. The safe efficiency domain II (700–900 °C\\1–10{sup −} {sup 1} s{sup −} {sup 1}), which appeared at logarithmic strain of 0.4, was characterized by deformation induced ferrite formation. Scanning electron microscopy revealed that the microband formation and crack initiation at ferrite\\austenite interphases were the main causes of deformation instability at 600–800 °C\\10{sup −} {sup 2}–10{sup −} {sup 3} s{sup −} {sup 1}. The degree of instability was found to decrease by increasing the strain due to the uniformity of microbanded structure obtained at higher strains. The shear band formation at 900–1100 °C\\1–10{sup −} {sup 1} s{sup −} {sup 1} was verified by electron backscattered diffraction. The local dynamic recrystallization of austenite and the deformation induced ferrite formation were observed within shear-banded regions as the results of flow localization. - Graphical abstract: Display Omitted - Highlights: • The 3D processing map is developed for duplex low-density Fe–Mn–Al–C steel. • The efficiency domains shrink, expand or appear with increasing strain. • The occurrence of DRX and DIFF increases the power efficiency. • Crack

The warm and cold neutral phase in the local interstellar medium at absolute value of B greater than or equal to 10 deg

NASA Astrophysics Data System (ADS)

Poppel, W. G. L.; Marronetti, P.; Benaglia, P.

1994-07-01

We made a systematic separation of both the neutral phases using the atlases of 21-cm profiles of Heiles & Habing (1974) and Colomb et al. (1980), complemented with other data. First, we fitted the emission of the warm neutral medium (WNM) by means of a broad Gaussian curve (velocity dispersion sigma approximately 10-14 km/s). We derived maps of the column densities NWH and the radial velocities VW of the WNM. Its overall distribution appears to be very inhomogeneous with a large hole in the range b greater than or equal to +50 deg. However, if the hole is excluded, the mean latitude-profiles admit a rough cosec absolute value of b-fit common to both hemispheres. A kinematical analysis of VW for the range 10 deg less than or equal to absolute value of b less than or equal to 40 deg indicates a mean differential rotation with a small nodal deviation. At absolute value of b greater than 50 deg VW is negative, with larger values and discontinuities in the north. On the mean, sigma increases for absolute value of b decreasing, as is expected from differential rotation. From a statistical study of the peaks of the residual profiles we derived some characteristics of the cold neutral medium (CNM). The latter is generally characterized by a single component of sigma approximately 2-6 km/s. Additionally we derived the sky-distribution of the column densities NCH and the radial velocities VC of the CNM within bins of 1.2 deg sec b x 1 deg in l, b. Furthermore, we focused on the characteristics of Linblad's feature A of cool gas by considering the narrow ridge of local H I, which appears in the b-V contour maps at fixed l (e.g. Schoeber 1976). The ridge appears to be the main component of the CNM. We suggest a scenario for the formulation and evolution of the Gould belt system of stars and gas on the basis of an explosive event within a shingle of cold dense gas tilted to the galactic plane. The scenario appears to be consistent with the results found for both the neutral

Improving experimental phases for strong reflections prior to density modification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uervirojnangkoorn, Monarin; University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck; Hilgenfeld, Rolf, E-mail: hilgenfeld@biochem.uni-luebeck.de

A genetic algorithm has been developed to optimize the phases of the strongest reflections in SIR/SAD data. This is shown to facilitate density modification and model building in several test cases. Experimental phasing of diffraction data from macromolecular crystals involves deriving phase probability distributions. These distributions are often bimodal, making their weighted average, the centroid phase, improbable, so that electron-density maps computed using centroid phases are often non-interpretable. Density modification brings in information about the characteristics of electron density in protein crystals. In successful cases, this allows a choice between the modes in the phase probability distributions, and the mapsmore » can cross the borderline between non-interpretable and interpretable. Based on the suggestions by Vekhter [Vekhter (2005 ▶), Acta Cryst. D61, 899–902], the impact of identifying optimized phases for a small number of strong reflections prior to the density-modification process was investigated while using the centroid phase as a starting point for the remaining reflections. A genetic algorithm was developed that optimizes the quality of such phases using the skewness of the density map as a target function. Phases optimized in this way are then used in density modification. In most of the tests, the resulting maps were of higher quality than maps generated from the original centroid phases. In one of the test cases, the new method sufficiently improved a marginal set of experimental SAD phases to enable successful map interpretation. A computer program, SISA, has been developed to apply this method for phase improvement in macromolecular crystallography.« less

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

PubMed Central

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

SOMKE: kernel density estimation over data streams by sequences of self-organizing maps.

PubMed

Cao, Yuan; He, Haibo; Man, Hong

2012-08-01

In this paper, we propose a novel method SOMKE, for kernel density estimation (KDE) over data streams based on sequences of self-organizing map (SOM). In many stream data mining applications, the traditional KDE methods are infeasible because of the high computational cost, processing time, and memory requirement. To reduce the time and space complexity, we propose a SOM structure in this paper to obtain well-defined data clusters to estimate the underlying probability distributions of incoming data streams. The main idea of this paper is to build a series of SOMs over the data streams via two operations, that is, creating and merging the SOM sequences. The creation phase produces the SOM sequence entries for windows of the data, which obtains clustering information of the incoming data streams. The size of the SOM sequences can be further reduced by combining the consecutive entries in the sequence based on the measure of Kullback-Leibler divergence. Finally, the probability density functions over arbitrary time periods along the data streams can be estimated using such SOM sequences. We compare SOMKE with two other KDE methods for data streams, the M-kernel approach and the cluster kernel approach, in terms of accuracy and processing time for various stationary data streams. Furthermore, we also investigate the use of SOMKE over nonstationary (evolving) data streams, including a synthetic nonstationary data stream, a real-world financial data stream and a group of network traffic data streams. The simulation results illustrate the effectiveness and efficiency of the proposed approach.

Characterization of Three Maize Bacterial Artificial Chromosome Libraries toward Anchoring of the Physical Map to the Genetic Map Using High-Density Bacterial Artificial Chromosome Filter Hybridization1

PubMed Central

Yim, Young-Sun; Davis, Georgia L.; Duru, Ngozi A.; Musket, Theresa A.; Linton, Eric W.; Messing, Joachim W.; McMullen, Michael D.; Soderlund, Carol A.; Polacco, Mary L.; Gardiner, Jack M.; Coe, Edward H.

2002-01-01

Three maize (Zea mays) bacterial artificial chromosome (BAC) libraries were constructed from inbred line B73. High-density filter sets from all three libraries, made using different restriction enzymes (HindIII, EcoRI, and MboI, respectively), were evaluated with a set of complex probes including the185-bp knob repeat, ribosomal DNA, two telomere-associated repeat sequences, four centromere repeats, the mitochondrial genome, a multifragment chloroplast DNA probe, and bacteriophage λ. The results indicate that the libraries are of high quality with low contamination by organellar and λ-sequences. The use of libraries from multiple enzymes increased the chance of recovering each region of the genome. Ninety maize restriction fragment-length polymorphism core markers were hybridized to filters of the HindIII library, representing 6× coverage of the genome, to initiate development of a framework for anchoring BAC contigs to the intermated B73 × Mo17 genetic map and to mark the bin boundaries on the physical map. All of the clones used as hybridization probes detected at least three BACs. Twenty-two single-copy number core markers identified an average of 7.4 ± 3.3 positive clones, consistent with the expectation of six clones. This information is integrated into fingerprinting data generated by the Arizona Genomics Institute to assemble the BAC contigs using fingerprint contig and contributed to the process of physical map construction. PMID:12481051

Thresholding histogram equalization.

PubMed

Chuang, K S; Chen, S; Hwang, I M

2001-12-01

The drawbacks of adaptive histogram equalization techniques are the loss of definition on the edges of the object and overenhancement of noise in the images. These drawbacks can be avoided if the noise is excluded in the equalization transformation function computation. A method has been developed to separate the histogram into zones, each with its own equalization transformation. This method can be used to suppress the nonanatomic noise and enhance only certain parts of the object. This method can be combined with other adaptive histogram equalization techniques. Preliminary results indicate that this method can produce images with superior contrast.

Volume and density changes of biological fluids with temperature

NASA Technical Reports Server (NTRS)

Hinghofer-Szalkay, H.

1985-01-01

The thermal expansion of human blood, plasma, ultrafiltrate, and erythrocycte concentration at temperatures in the range of 4-48 C is studied. The mechanical oscillator technique which has an accuracy of 1 x 10 to the -5 th g/ml is utilized to measure fluid density. The relationship between thermal expansion, density, and temperature is analyzed. The study reveals that: (1) thermal expansion increases with increasing temperature; (2) the magnitude of the increase declines with increasing temperature; (3) thermal expansion increases with density at temperatures below 40 C; and (4) the thermal expansion of intracellular fluid is greater than that of extracellular fluid in the temperature range of 4-10 C, but it is equal at temperatures greater than or equal to 40 C.

Native protein mapping and visualization of protein interactions in the area of human plasma high-density lipoprotein by combining nondenaturing micro 2DE and quantitative LC-MS/MS.

PubMed

Jin, Ya; Bu, Shujie; Zhang, Jun; Yuan, Qi; Manabe, Takashi; Tan, Wen

2014-07-01

A human plasma sample was subjected to nondenaturing micro 2DE and a gel area (5 mm × 18 mm) that includes high-density lipoprotein (HDL) was cut into 1 mm × 1 mm squares, then the proteins in the 90 gel pieces were analyzed by quantitative LC-MS/MS. Grid-cutting of the gel was employed to; (i) ensure the total analysis of the proteins in the area, (ii) standardize the conditions of analysis by LC-MS/MS, (iii) reconstruct the protein distribution patterns from the quantity data. Totally 154 proteins were assigned in the 90 gel pieces and the quantity distribution of each was reconstructed as a color density pattern (a native protein map). The map of apolipoprotein (Apo) A-I showed a wide apparent mass distribution characteristic to HDL and was compared with the maps of the other 153 proteins. Eleven proteins showed maps of wide distribution that overlapped with the map of Apo A-I, and all have been reported to be the components of HDL. Further, seven minor proteins associated with HDL were detected at the gel positions of high Apo A-I quantity. These results for the first time visualized the localization of HDL apolipoproteins on a nondenaturing 2DE gel and strongly suggested their interactions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.).

PubMed

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

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.

PubMed

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.

Changing Concepts of Educational Equality

ERIC Educational Resources Information Center

Cropley, A. J.

1976-01-01

States that if educational equality is defined, not in terms of equal learning facilities and equally well qualified teachers, but in terms of equal outcomes, equality has not been achieved. True equality implies recognition of learning as life-long process, for the purpose of self-fulfillment. (Author/RW)

Hotspot detection in pancreatic neuroendocrine tumors: density approximation by α-shape maps

NASA Astrophysics Data System (ADS)

Niazi, M. K. K.; Hartman, Douglas J.; Pantanowitz, Liron; Gurcan, Metin N.

2016-03-01

The grading of neuroendocrine tumors of the digestive system is dependent on accurate and reproducible assessment of the proliferation with the tumor, either by counting mitotic figures or counting Ki-67 positive nuclei. At the moment, most pathologists manually identify the hotspots, a practice which is tedious and irreproducible. To better help pathologists, we present an automatic method to detect all potential hotspots in neuroendocrine tumors of the digestive system. The method starts by segmenting Ki-67 positive nuclei by entropy based thresholding, followed by detection of centroids for all Ki-67 positive nuclei. Based on geodesic distance, approximated by the nuclei centroids, we compute two maps: an amoeba map and a weighted amoeba map. These maps are later combined to generate the heat map, the segmentation of which results in the hotspots. The method was trained on three and tested on nine whole slide images of neuroendocrine tumors. When evaluated by two expert pathologists, the method reached an accuracy of 92.6%. The current method does not discriminate between tumor, stromal and inflammatory nuclei. The results show that α-shape maps may represent how hotspots are perceived.

Urban-scale mapping of PM2.5 distribution via data fusion between high-density sensor network and MODIS Aerosol Optical Depth

NASA Astrophysics Data System (ADS)

Ba, Yu Tao; xian Liu, Bao; Sun, Feng; Wang, Li hua; Tang, Yu jia; Zhang, Da wei

2017-04-01

High-resolution mapping of PM2.5 is the prerequisite for precise analytics and subsequent anti-pollution interventions. Considering the large variances of particulate distribution, urban-scale mapping is challenging either with ground-based fixed stations, with satellites or via models. In this study, a dynamic fusion method between high-density sensor network and MODIS Aerosol Optical Depth (AOD) was introduced. The sensor network was deployed in Beijing ( > 1000 fixed monitors across 16000 km2 area) to provide raw observations with high temporal resolution (sampling interval < 1 hour), high spatial resolution in flat areas ( < 1 km), and low spatial resolution in mountainous areas ( > 5 km). The MODIS AOD was calibrated to provide distribution map with low temporal resolution (daily) and moderate spatial resolution ( = 3 km). By encoding the data quality and defects (e.g. could, reflectance, abnormal), a hybrid interpolation procedure with cross-validation generated PM2.5 distribution with both high temporal and spatial resolution. Several no-pollutant and high-pollution periods were tested to validate the proposed fusion method for capturing the instantaneous patterns of PM2.5 emission.

Pyroclastic density current hazard maps at Campi Flegrei caldera (Italy): the effects of event scale, vent location and time forecasts.

NASA Astrophysics Data System (ADS)

Bevilacqua, Andrea; Neri, Augusto; Esposti Ongaro, Tomaso; Isaia, Roberto; Flandoli, Franco; Bisson, Marina

2016-04-01

Today hundreds of thousands people live inside the Campi Flegrei caldera (Italy) and in the adjacent part of the city of Naples making a future eruption of such volcano an event with huge consequences. Very high risks are associated with the occurrence of pyroclastic density currents (PDCs). Mapping of background or long-term PDC hazard in the area is a great challenge due to the unknown eruption time, scale and vent location of the next event as well as the complex dynamics of the flow over the caldera topography. This is additionally complicated by the remarkable epistemic uncertainty on the eruptive record, affecting the time of past events, the location of vents as well as the PDCs areal extent estimates. First probability maps of PDC invasion were produced combining a vent-opening probability map, statistical estimates concerning the eruptive scales and a Cox-type temporal model including self-excitement effects, based on the eruptive record of the last 15 kyr. Maps were produced by using a Monte Carlo approach and adopting a simplified inundation model based on the "box model" integral approximation tested with 2D transient numerical simulations of flow dynamics. In this presentation we illustrate the independent effects of eruption scale, vent location and time of forecast of the next event. Specific focus was given to the remarkable differences between the eastern and western sectors of the caldera and their effects on the hazard maps. The analysis allowed to identify areas with elevated probabilities of flow invasion as a function of the diverse assumptions made. With the quantification of some sources of uncertainty in relation to the system, we were also able to provide mean and percentile maps of PDC hazard levels.

Density and Reproductive Success of California Towhees

Treesearch

Kathryn L. Purcell; Jared Verner

1998-01-01

Models of habitat selection commonly asume that higher-quality source habitats will be occupied at higher densities than sink habitats. We examined an apparent sink habitat for California Towhees (Pipilo crissalis) in which densities are greater than in nearby source habitats. We estimated territory density using spot-mapping and monitored nests of towhees in grazed...

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

PubMed Central

Lau, Kevin Ka-Lun; Yu, Ruby; Wang, Dan; Kwok, Timothy Chi Yui; Ng, Edward

2017-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2014-06-01

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.

Electron density and gas density measurements in a millimeter-wave discharge

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schaub, S. C., E-mail: sschaub@mit.edu; Hummelt, J. S.; Guss, W. C.

2016-08-15

Electron density and neutral gas density have been measured in a non-equilibrium air breakdown plasma using optical emission spectroscopy and two-dimensional laser interferometry, respectively. A plasma was created with a focused high frequency microwave beam in air. Experiments were run with 110 GHz and 124.5 GHz microwaves at powers up to 1.2 MW. Microwave pulses were 3 μs long at 110 GHz and 2.2 μs long at 124.5 GHz. Electron density was measured over a pressure range of 25 to 700 Torr as the input microwave power was varied. Electron density was found to be close to the critical density, where the collisional plasma frequency is equal tomore » the microwave frequency, over the pressure range studied and to vary weakly with input power. Neutral gas density was measured over a pressure range from 150 to 750 Torr at power levels high above the threshold for initiating breakdown. The two-dimensional structure of the neutral gas density was resolved. Intense, localized heating was found to occur hundreds of nanoseconds after visible plasma formed. This heating led to neutral gas density reductions of greater than 80% where peak plasma densities occurred. Spatial structure and temporal dynamics of gas heating at atmospheric pressure were found to agree well with published numerical simulations.« less

A consensus linkage map of lentil based on DArT markers from three RIL mapping populations.

PubMed

Ates, Duygu; Aldemir, Secil; Alsaleh, Ahmad; Erdogmus, Semih; Nemli, Seda; Kahriman, Abdullah; Ozkan, Hakan; Vandenberg, Albert; Tanyolac, Bahattin

2018-01-01

Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including "CDC Redberry" x "ILL7502" (LR8), "ILL8006" x "CDC Milestone" (LR11) and "PI320937" x "Eston" (LR39). The lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4). The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps. This high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data.

Muscle Activity Map Reconstruction from High Density Surface EMG Signals With Missing Channels Using Image Inpainting and Surface Reconstruction Methods.

PubMed

Ghaderi, Parviz; Marateb, Hamid R

2017-07-01

The aim of this study was to reconstruct low-quality High-density surface EMG (HDsEMG) signals, recorded with 2-D electrode arrays, using image inpainting and surface reconstruction methods. It is common that some fraction of the electrodes may provide low-quality signals. We used variety of image inpainting methods, based on partial differential equations (PDEs), and surface reconstruction methods to reconstruct the time-averaged or instantaneous muscle activity maps of those outlier channels. Two novel reconstruction algorithms were also proposed. HDsEMG signals were recorded from the biceps femoris and brachial biceps muscles during low-to-moderate-level isometric contractions, and some of the channels (5-25%) were randomly marked as outliers. The root-mean-square error (RMSE) between the original and reconstructed maps was then calculated. Overall, the proposed Poisson and wave PDE outperformed the other methods (average RMSE 8.7 μV rms ± 6.1 μV rms and 7.5 μV rms ± 5.9 μV rms ) for the time-averaged single-differential and monopolar map reconstruction, respectively. Biharmonic Spline, the discrete cosine transform, and the Poisson PDE outperformed the other methods for the instantaneous map reconstruction. The running time of the proposed Poisson and wave PDE methods, implemented using a Vectorization package, was 4.6 ± 5.7 ms and 0.6 ± 0.5 ms, respectively, for each signal epoch or time sample in each channel. The proposed reconstruction algorithms could be promising new tools for reconstructing muscle activity maps in real-time applications. Proper reconstruction methods could recover the information of low-quality recorded channels in HDsEMG signals.

High density genetic linkage map and bin mapping for disease resistance QTLs in peanut

USDA-ARS?s Scientific Manuscript database

Mapping and identification of QTLs are important for efficient marker-assisted breeding and for analysis of the molecular mechanisms regulating traits. Diseases, such as early and late leaf spots, Tomato spotted wilt virus (TSWV), cause significant loses to peanut growers. Our goal is to develop a h...

Prior-knowledge-based spectral mixture analysis for impervious surface mapping

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Jinshui; He, Chunyang; Zhou, Yuyu

2014-01-03

In this study, we developed a prior-knowledge-based spectral mixture analysis (PKSMA) to map impervious surfaces by using endmembers derived separately for high- and low-density urban regions. First, an urban area was categorized into high- and low-density urban areas, using a multi-step classification method. Next, in high-density urban areas that were assumed to have only vegetation and impervious surfaces (ISs), the Vegetation-Impervious model (V-I) was used in a spectral mixture analysis (SMA) with three endmembers: vegetation, high albedo, and low albedo. In low-density urban areas, the Vegetation-Impervious-Soil model (V-I-S) was used in an SMA analysis with four endmembers: high albedo, lowmore » albedo, soil, and vegetation. The fraction of IS with high and low albedo in each pixel was combined to produce the final IS map. The root mean-square error (RMSE) of the IS map produced using PKSMA was about 11.0%, compared to 14.52% using four-endmember SMA. Particularly in high-density urban areas, PKSMA (RMSE = 6.47%) showed better performance than four-endmember (15.91%). The results indicate that PKSMA can improve IS mapping compared to traditional SMA by using appropriately selected endmembers and is particularly strong in high-density urban areas.« less

Potential Stream Density in Mid-Atlantic U.S. Watersheds

PubMed Central

Elmore, Andrew J.; Julian, Jason P.; Guinn, Steven M.; Fitzpatrick, Matthew C.

2013-01-01

Stream network density exerts a strong influence on ecohydrologic processes in watersheds, yet existing stream maps fail to capture most headwater streams and therefore underestimate stream density. Furthermore, discrepancies between mapped and actual stream length vary between watersheds, confounding efforts to understand the impacts of land use on stream ecosystems. Here we report on research that predicts stream presence from coupled field observations of headwater stream channels and terrain variables that were calculated both locally and as an average across the watershed upstream of any location on the landscape. Our approach used maximum entropy modeling (MaxEnt), a robust method commonly implemented to model species distributions that requires information only on the presence of the entity of interest. In validation, the method correctly predicts the presence of 86% of all 10-m stream segments and errors are low (<1%) for catchments larger than 10 ha. We apply this model to the entire Potomac River watershed (37,800 km2) and several adjacent watersheds to map stream density and compare our results with the National Hydrography Dataset (NHD). We find that NHD underestimates stream density by up to 250%, with errors being greatest in the densely urbanized cities of Washington, DC and Baltimore, MD and in regions where the NHD has never been updated from its original, coarse-grain mapping. This work is the most ambitious attempt yet to map stream networks over a large region and will have lasting implications for modeling and conservation efforts. PMID:24023704

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

PubMed

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.

Material and Optical Densities

ERIC Educational Resources Information Center

Gluck, Paul

2007-01-01

The bending of a laser beam in a medium with a density and refractive index gradient in the same direction has been described previously. When a transparent container is half filled with a salt or sugar solution and an equal amount of water is floated on top of it, then diffusion will create a concentration gradient from top to bottom. A laser…

Design and characterization of a mapping device optimized to collect XRD patterns from highly inhomogeneous and low density powder samples

NASA Astrophysics Data System (ADS)

D'Elia, A.; Cibin, G.; Robbins, P. E.; Maggi, V.; Marcelli, A.

2017-11-01

We report on the development of a device designed to improve X-ray Powder Diffraction data acquisition through mapping coupled to a rotational motion of the sample. The device and procedures developed aim at overcoming the experimental issues that accompany the analysis of inhomogeneous samples, such as powders, dust or aerosols deposited on a flat substrate. Introducing the mapping of the substrate on which powders are deposited and at the same time the rotation, we may overcome drawbacks associated to inhomogeneous distributions such as ring-like patterns due to the coffee stain effect generated by the evaporation of a solution. Experimental data have been collected from powders of a NIST standard soil sample (11 μg) and from an airborne dust extracted from deep ice cores in Antarctica (9.6 μg). Both particulate samples have been deposited on polycarbonate membranes from ultra-dilute solutions. Data show that this approach makes possible to collect XRD patterns useful to identify mineral fractions present in these low density samples.

Metrics for comparison of crystallographic maps

DOE PAGES

Urzhumtsev, Alexandre; Afonine, Pavel V.; Lunin, Vladimir Y.; ...

2014-10-01

Numerical comparison of crystallographic contour maps is used extensively in structure solution and model refinement, analysis and validation. However, traditional metrics such as the map correlation coefficient (map CC, real-space CC or RSCC) sometimes contradict the results of visual assessment of the corresponding maps. This article explains such apparent contradictions and suggests new metrics and tools to compare crystallographic contour maps. The key to the new methods is rank scaling of the Fourier syntheses. The new metrics are complementary to the usual map CC and can be more helpful in map comparison, in particular when only some of their aspects,more » such as regions of high density, are of interest.« less

A consensus linkage map of lentil based on DArT markers from three RIL mapping populations

PubMed Central

Ates, Duygu; Aldemir, Secil; Alsaleh, Ahmad; Erdogmus, Semih; Nemli, Seda; Kahriman, Abdullah; Ozkan, Hakan; Vandenberg, Albert

2018-01-01

Background Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. Materials and methods A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including “CDC Redberry” x “ILL7502” (LR8), “ILL8006” x “CDC Milestone” (LR11) and “PI320937” x “Eston” (LR39). Results The lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4). The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps. Conclusion This high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data. PMID:29351563

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

PubMed Central

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carr, J. K.; Roy, S.; Skinner, J. L.

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 andmore » 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.« less

The North American upper mantle: density, composition, and evolution

USGS Publications Warehouse

Mooney, Walter D.; Kaban, Mikhail K.

2010-01-01

The upper mantle of North America has been well studied using various seismic methods. Here we investigate the density structure of the North American (NA) upper mantle based on the integrative use of the gravity field and seismic data. The basis of our study is the removal of the gravitational effect of the crust to determine the mantle gravity anomalies. The effect of the crust is removed in three steps by subtracting the gravitational contributions of (1) topography and bathymetry, (2) low-density sedimentary accumulations, and (3) the three-dimensional density structure of the crystalline crust as determined by seismic observations. Information regarding sedimentary accumulations, including thickness and density, are taken from published maps and summaries of borehole measurements of densities; the seismic structure of the crust is based on a recent compilation, with layer densities estimated from P-wave velocities. The resultant mantle gravity anomaly map shows a pronounced negative anomaly (−50 to −400 mGal) beneath western North America and the adjacent oceanic region and positive anomalies (+50 to +350 mGal) east of the NA Cordillera. This pattern reflects the well-known division of North America into the stable eastern region and the tectonically active western region. The close correlation of large-scale features of the mantle anomaly map with those of the topographic map indicates that a significant amount of the topographic uplift in western NA is due to buoyancy in the hot upper mantle, a conclusion supported by previous investigations. To separate the contributions of mantle temperature anomalies from mantle compositional anomalies, we apply an additional correction to the mantle anomaly map for the thermal structure of the uppermost mantle. The thermal model is based on the conversion of seismic shear-wave velocities to temperature and is consistent with mantle temperatures that are independently estimated from heat flow and heat production data

Equality Hypocrisy, Inconsistency, and Prejudice: The Unequal Application of the Universal Human Right to Equality.

PubMed

Abrams, Dominic; Houston, Diane M; Van de Vyver, Julie; Vasiljevic, Milica

2015-02-01

In Western culture, there appears to be widespread endorsement of Article 1 of the Universal Declaration of Human Rights (which stresses equality and freedom). But do people really apply their equality values equally, or are their principles and application systematically discrepant, resulting in equality hypocrisy? The present study, conducted with a representative national sample of adults in the United Kingdom ( N = 2,895), provides the first societal test of whether people apply their value of "equality for all" similarly across multiple types of status minority (women, disabled people, people aged over 70, Blacks, Muslims, and gay people). Drawing on theories of intergroup relations and stereotyping we examined, relation to each of these groups, respondents' judgments of how important it is to satisfy their particular wishes, whether there should be greater or reduced equality of employment opportunities, and feelings of social distance. The data revealed a clear gap between general equality values and responses to these specific measures. Respondents prioritized equality more for "paternalized" groups (targets of benevolent prejudice: women, disabled, over 70) than others (Black people, Muslims, and homosexual people), demonstrating significant inconsistency. Respondents who valued equality more, or who expressed higher internal or external motivation to control prejudice, showed greater consistency in applying equality. However, even respondents who valued equality highly showed significant divergence in their responses to paternalized versus nonpaternalized groups, revealing a degree of hypocrisy. Implications for strategies to promote equality and challenge prejudice are discussed.

Equality Hypocrisy, Inconsistency, and Prejudice: The Unequal Application of the Universal Human Right to Equality

PubMed Central

2015-01-01

In Western culture, there appears to be widespread endorsement of Article 1 of the Universal Declaration of Human Rights (which stresses equality and freedom). But do people really apply their equality values equally, or are their principles and application systematically discrepant, resulting in equality hypocrisy? The present study, conducted with a representative national sample of adults in the United Kingdom (N = 2,895), provides the first societal test of whether people apply their value of “equality for all” similarly across multiple types of status minority (women, disabled people, people aged over 70, Blacks, Muslims, and gay people). Drawing on theories of intergroup relations and stereotyping we examined, relation to each of these groups, respondents’ judgments of how important it is to satisfy their particular wishes, whether there should be greater or reduced equality of employment opportunities, and feelings of social distance. The data revealed a clear gap between general equality values and responses to these specific measures. Respondents prioritized equality more for “paternalized” groups (targets of benevolent prejudice: women, disabled, over 70) than others (Black people, Muslims, and homosexual people), demonstrating significant inconsistency. Respondents who valued equality more, or who expressed higher internal or external motivation to control prejudice, showed greater consistency in applying equality. However, even respondents who valued equality highly showed significant divergence in their responses to paternalized versus nonpaternalized groups, revealing a degree of hypocrisy. Implications for strategies to promote equality and challenge prejudice are discussed. PMID:25914516

THE PHASE COHERENCE OF INTERSTELLAR DENSITY FLUCTUATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burkhart, Blakesley; Lazarian, A.

2016-08-10

Studies of MHD turbulence often investigate the Fourier power spectrum to provide information on the nature of the turbulence cascade. However, the Fourier power spectrum only contains the Fourier amplitudes and rejects all information regarding the Fourier phases. Here, we investigate the utility of two statistical diagnostics for recovering information on Fourier phases in ISM column density maps: the averaged amplitudes of the bispectrum and the phase coherence index (PCI), a new phase technique for the ISM. We create three-dimensional density and two-dimensional column density maps using a set of simulations of isothermal ideal MHD turbulence with a wide rangemore » of sonic and Alfvénic Mach numbers. We find that the bispectrum averaged along different angles with respect to either the k {sub 1} or k {sub 2} axis is primarily sensitive to the sonic Mach number while averaging the bispectral amplitudes over different annuli is sensitive to both the sonic and Alfvénic Mach numbers. The PCI of density suggests that the most correlated phases occur in supersonic sub-Alfvénic turbulence and near the shock scale. This suggests that nonlinear interactions with correlated phases are strongest in shock-dominated regions, in agreement with findings from the solar wind. Our results suggest that the phase information contained in the bispectrum and PCI can be used to find the turbulence parameters in column density maps.« less

Equalizer reduces SNP bias in Affymetrix microarrays.

PubMed

Quigley, David

2015-07-30

Gene expression microarrays measure the levels of messenger ribonucleic acid (mRNA) in a sample using probe sequences that hybridize with transcribed regions. These probe sequences are designed using a reference genome for the relevant species. However, most model organisms and all humans have genomes that deviate from their reference. These variations, which include single nucleotide polymorphisms, insertions of additional nucleotides, and nucleotide deletions, can affect the microarray's performance. Genetic experiments comparing individuals bearing different population-associated single nucleotide polymorphisms that intersect microarray probes are therefore subject to systemic bias, as the reduction in binding efficiency due to a technical artifact is confounded with genetic differences between parental strains. This problem has been recognized for some time, and earlier methods of compensation have attempted to identify probes affected by genome variants using statistical models. These methods may require replicate microarray measurement of gene expression in the relevant tissue in inbred parental samples, which are not always available in model organisms and are never available in humans. By using sequence information for the genomes of organisms under investigation, potentially problematic probes can now be identified a priori. However, there is no published software tool that makes it easy to eliminate these probes from an annotation. I present equalizer, a software package that uses genome variant data to modify annotation files for the commonly used Affymetrix IVT and Gene/Exon platforms. These files can be used by any microarray normalization method for subsequent analysis. I demonstrate how use of equalizer on experiments mapping germline influence on gene expression in a genetic cross between two divergent mouse species and in human samples significantly reduces probe hybridization-induced bias, reducing false positive and false negative findings. The

EnviroAtlas - Paterson, NJ - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Fresno, CA - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Woodbine, IA - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Phoenix, AZ - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Pittsburgh, PA - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Milwaukee, WI - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Austin, TX - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Cleveland, OH - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Portland, ME - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Portland, OR - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Durham, NC - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Tampa, FL - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Memphis, TN - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

Why the Equal Rights Amendment?

ERIC Educational Resources Information Center

Denmark, Florence L.

The Equal Rights Amendment proposes to ensure constitutional protection against all legislative sex discrimination. "Separate but Equal" standards, be they legal, social or psychological, are inevitably incompatable with equal protection under the law and act as a barrier to each individual's freedom for self determination. Equal rights,…

Americans misperceive racial economic equality.

PubMed

Kraus, Michael W; Rucker, Julian M; Richeson, Jennifer A

2017-09-26

The present research documents the widespread misperception of race-based economic equality in the United States. Across four studies ( n = 1,377) sampling White and Black Americans from the top and bottom of the national income distribution, participants overestimated progress toward Black-White economic equality, largely driven by estimates of greater current equality than actually exists according to national statistics. Overestimates of current levels of racial economic equality, on average, outstripped reality by roughly 25% and were predicted by greater belief in a just world and social network racial diversity (among Black participants). Whereas high-income White respondents tended to overestimate racial economic equality in the past, Black respondents, on average, underestimated the degree of past racial economic equality. Two follow-up experiments further revealed that making societal racial discrimination salient increased the accuracy of Whites' estimates of Black-White economic equality, whereas encouraging Whites to anchor their estimates on their own circumstances increased their tendency to overestimate current racial economic equality. Overall, these findings suggest a profound misperception of and unfounded optimism regarding societal race-based economic equality-a misperception that is likely to have any number of important policy implications.

A density functional approach to ferrogels

NASA Astrophysics Data System (ADS)

Cremer, P.; Heinen, M.; Menzel, A. M.; Löwen, H.

2017-07-01

Ferrogels consist of magnetic colloidal particles embedded in an elastic polymer matrix. As a consequence, their structural and rheological properties are governed by a competition between magnetic particle-particle interactions and mechanical matrix elasticity. Typically, the particles are permanently fixed within the matrix, which makes them distinguishable by their positions. Over time, particle neighbors do not change due to the fixation by the matrix. Here we present a classical density functional approach for such ferrogels. We map the elastic matrix-induced interactions between neighboring colloidal particles distinguishable by their positions onto effective pairwise interactions between indistinguishable particles similar to a ‘pairwise pseudopotential’. Using Monte-Carlo computer simulations, we demonstrate for one-dimensional dipole-spring models of ferrogels that this mapping is justified. We then use the pseudopotential as an input into classical density functional theory of inhomogeneous fluids and predict the bulk elastic modulus of the ferrogel under various conditions. In addition, we propose the use of an ‘external pseudopotential’ when one switches from the viewpoint of a one-dimensional dipole-spring object to a one-dimensional chain embedded in an infinitely extended bulk matrix. Our mapping approach paves the way to describe various inhomogeneous situations of ferrogels using classical density functional concepts of inhomogeneous fluids.

Saturn's ionosphere: Inferred electron densities

NASA Technical Reports Server (NTRS)

Kaiser, M. L.; Desch, M. D.; Connerney, J. E. P.

1983-01-01

During the two Voyager encounters with Saturn, radio bursts were detected which appear to have originated from atmospheric lightning storms. Although these bursts generally extended over frequencies from as low as 100 kHz to the upper detection limit of the instrument, 40 MHz, they often exhibited a sharp but variable low frequency cutoff below which bursts were not detected. We interpret the variable low-frequency extent of these bursts to be due to the reflection of the radio waves as they propagate through an ionosphere which varies with local time. We obtain estimates of electron densities at a variety of latitude and local time locations. These compare well with the dawn and dusk densitis measured by the Pioneer 11 Voyager Radio Science investigations, and with model predictions for dayside densities. However, we infer a two-order-of-magnitude diurnal variation of electron density, which had not been anticipated by theoretical models of Saturn's ionosphere, and an equally dramatic extinction of ionospheric electron density by Saturn's rings.

Students’ misconception on equal sign

NASA Astrophysics Data System (ADS)

Kusuma, N. F.; Subanti, S.; Usodo, B.

2018-04-01

Equivalence is a very general relation in mathematics. The focus of this article is narrowed specifically to an equal sign in the context of equations. The equal sign is a symbol of mathematical equivalence. Studies have found that many students do not have a deep understanding of equivalence. Students often misinterpret the equal sign as an operational rather than a symbol of mathematical equivalence. This misinterpretation of the equal sign will be label as a misconception. It is important to discuss and must resolve immediately because it can lead to the problems in students’ understanding. The purpose of this research is to describe students’ misconception about the meaning of equal sign on equal matrices. Descriptive method was used in this study involving five students of Senior High School in Boyolali who were taking Equal Matrices course. The result of this study shows that all of the students had the misconception about the meaning of the equal sign. They interpret the equal sign as an operational symbol rather than a symbol of mathematical equivalence. Students merely solve the problem only single way, which is a computational method, so that students stuck in a monotonous way of thinking and unable to develop their creativity.

Density of Primitive Pythagorean Triples

ERIC Educational Resources Information Center

Killen, Duncan A.

2004-01-01

Based on the properties of a Primitive Pythagorean Triple (PPT), a computer program was written to generate, print, and count all PPTs greater than or equal to I[subscript x], where I[subscript x] is an arbitrarily chosen integer. The Density of Primitive Pythagorean Triples may be defined as the ratio of the number of PPTs whose hypotenuse is…

Equal Pay for Equal Work in Academic Obstetrics and Gynecology.

PubMed

Eichelberger, Kacey Y

2018-02-01

The most compelling data suggest women in academic obstetrics and gynecology earn approximately $36,000 less than male colleagues per year in regression models correcting for commonly cited explanatory variables. Although residual confounding may exist, academic departments in the United States should consider rigorous examination of their own internal metrics around salary to ensure gender-neutral compensation, commonly referred to as equal pay for equal work.

Effects of habitat map generalization in biodiversity assessment

NASA Technical Reports Server (NTRS)

Stoms, David M.

1992-01-01

Species richness is being mapped as part of an inventory of biological diversity in California (i.e., gap analysis). Species distributions are modeled with a GIS on the basis of maps of each species' preferred habitats. Species richness is then tallied in equal-area sampling units. A GIS sensitivity analysis examined the effects of the level of generalization of the habitat map on the predicted distribution of species richness in the southern Sierra Nevada. As the habitat map was generalized, the number of habitat types mapped within grid cells tended to decrease with a corresponding decline in numbers of species predicted. Further, the ranking of grid cells in order of predicted numbers of species changed dramatically between levels of generalization. Areas predicted to be of greatest conservation value on the basis of species richness may therefore be sensitive to GIS data resolution.

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

PubMed Central

Pan, Lei; Wang, Nian; Wu, Zhihua; Guo, Rui; Yu, Xiaolu; Zheng, Yu; Xia, Qiuju; Gui, Songtao; Chen, Chanyou

2017-01-01

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. PMID:28936219

A sequencing-based linkage map of cucumber

USDA-ARS?s Scientific Manuscript database

Genetic maps are important tools for molecular breeding, gene cloning, and study of meiotic recombination. In cucumber (Cucumis sativus L.), the marker density, resolution and genome coverage of previously developed genetic maps using PCR-based molecular markers are relatively low. In this study we ...

Mapping Air Population

NASA Astrophysics Data System (ADS)

Peterson, Michael P.; Hunt, Paul; Weiß, Konrad

2018-05-01

"Air population" refers to the total number of people flying above the earth at any point in time. The total number of passengers can then be estimated by multiplying the number of seats for each aircraft by the current seat occupancy rate. Using this method, the estimated air population is determined by state for the airspace over the United States. In the interactive, real-time mapping system, maps are provided to show total air population, the density of air population (air population / area of state), and the ratio of air population to ground population.

Surface Snow Density of East Antarctica Derived from In-Situ Observations

NASA Astrophysics Data System (ADS)

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.

Mapping auditory nerve firing density using high-level compound action potentials and high-pass noise masking a

PubMed Central

Earl, Brian R.; Chertoff, Mark E.

2012-01-01

Future implementation of regenerative treatments for sensorineural hearing loss may be hindered by the lack of diagnostic tools that specify the target(s) within the cochlea and auditory nerve for delivery of therapeutic agents. Recent research has indicated that the amplitude of high-level compound action potentials (CAPs) is a good predictor of overall auditory nerve survival, but does not pinpoint the location of neural damage. A location-specific estimate of nerve pathology may be possible by using a masking paradigm and high-level CAPs to map auditory nerve firing density throughout the cochlea. This initial study in gerbil utilized a high-pass masking paradigm to determine normative ranges for CAP-derived neural firing density functions using broadband chirp stimuli and low-frequency tonebursts, and to determine if cochlear outer hair cell (OHC) pathology alters the distribution of neural firing in the cochlea. Neural firing distributions for moderate-intensity (60 dB pSPL) chirps were affected by OHC pathology whereas those derived with high-level (90 dB pSPL) chirps were not. These results suggest that CAP-derived neural firing distributions for high-level chirps may provide an estimate of auditory nerve survival that is independent of OHC pathology. PMID:22280596

Use of total electron content data to analyze ionosphere electron density gradients

NASA Astrophysics Data System (ADS)

Nava, B.; Radicella, S. M.; Leitinger, R.; Coïsson, P.

In the presence of electron density gradients the thin shell approximation for the ionosphere, used together with a simple mapping function to convert slant total electron content (TEC) to vertical TEC, could lead to TEC conversion errors. These "mapping function errors" can therefore be used to detect the electron density gradients in the ionosphere. In the present work GPS derived slant TEC data have been used to investigate the effects of the electron density gradients in the middle and low latitude ionosphere under geomagnetic quiet and disturbed conditions. In particular the data corresponding to the geographic area of the American Sector for the days 5-7 April 2000 have been used to perform a complete analysis of mapping function errors based on the "coinciding pierce point technique". The results clearly illustrate the electron density gradient effects according to the locations considered and to the actual levels of disturbance of the ionosphere. In addition, the possibility to assess an ionospheric shell height able to minimize the mapping function errors has been verified.

Americans misperceive racial economic equality

PubMed Central

Kraus, Michael W.; Rucker, Julian M.; Richeson, Jennifer A.

2017-01-01

The present research documents the widespread misperception of race-based economic equality in the United States. Across four studies (n = 1,377) sampling White and Black Americans from the top and bottom of the national income distribution, participants overestimated progress toward Black–White economic equality, largely driven by estimates of greater current equality than actually exists according to national statistics. Overestimates of current levels of racial economic equality, on average, outstripped reality by roughly 25% and were predicted by greater belief in a just world and social network racial diversity (among Black participants). Whereas high-income White respondents tended to overestimate racial economic equality in the past, Black respondents, on average, underestimated the degree of past racial economic equality. Two follow-up experiments further revealed that making societal racial discrimination salient increased the accuracy of Whites’ estimates of Black–White economic equality, whereas encouraging Whites to anchor their estimates on their own circumstances increased their tendency to overestimate current racial economic equality. Overall, these findings suggest a profound misperception of and unfounded optimism regarding societal race-based economic equality—a misperception that is likely to have any number of important policy implications. PMID:28923915

EQUAL PAY FACTS.

ERIC Educational Resources Information Center

Women's Bureau (DOL), Washington, DC.

EQUAL PAY MEANS PAYMENT OF "RATE OF THE JOB" WITHOUT REGARD TO SEX. EQUAL PAY LAWS WERE ENACTED IN 29 STATES FROM 1919 TO 1965. FOUR ADDITIONAL STATES HAVE FAIR EMPLOYMENT PRACTICES LAWS. SUPPORT FOR SUCH LEGISLATION HAS COME FROM WOMEN'S AND CIVIC ORGANIZATIONS, AFL-CIO, AND THE PRESIDENT'S AND STATE COMMISSIONS ON THE STATUS OF WOMEN. THE…

Shell stability and conditions analyzed using a new method of extracting shell areal density maps from spectrally resolved images of direct-drive inertial confinement fusion implosions

DOE PAGES

Johns, H. M.; Mancini, R. C.; Nagayama, T.; ...

2016-01-25

In warm target direct-drive inertial confinement fusion implosion experiments performed at the OMEGA laser facility, plastic micro-balloons doped with a titanium tracer layer in the shell and filled with deuterium gas were imploded using a low-adiabat shaped laser pulse. Continuum radiation emitted in the core is transmitted through the tracer layer and the resulting spectrum recorded with a gated multi-monochromatic x-ray imager (MMI). Titanium K-shell line absorption spectra observed in the data are due to transitions in L-shell titanium ions driven by the backlighting continuum. The MMI data consist of an array of spectrally resolved images of the implosion. Thesemore » 2-D space-resolved titanium spectral features constrain the plasma conditions and areal density of the titanium doped region of the shell. The MMI data were processed to obtain narrow-band images and space resolved spectra of titanium spectral features. Shell areal density maps, ρL(x,y), extracted using a new method using both narrow-band images and space resolved spectra are confirmed to be consistent within uncertainties. We report plasma conditions in the titanium-doped region of electron temperature (Te) = 400 ± 28 eV, electron number density (N e) = 8.5 × 10 24 ± 2.5 × 10 24 cm –3, and average areal density = 86 ± 7 mg/cm 2. Fourier analysis of areal density maps reveals shell modulations caused by hydrodynamic instability growth near the fuel-shell interface in the deceleration phase. We observe significant structure in modes l = 2–9, dominated by l = 2. We extract a target breakup fraction of 7.1 ± 1.5% from our Fourier analysis. Furthermore, a new method for estimating mix width is evaluated against existing literature and our target breakup fraction. We estimate a mix width of 10.5 ±1 μm.« less

EnviroAtlas - New York, NY - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Green Bay, WI - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - Des Moines, IA - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

EnviroAtlas - New Bedford, MA - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

Mapping the Frozen Void

NASA Astrophysics Data System (ADS)

Suutarinen, Aleksi; Fraser, Helen

2013-07-01

Reactions on the surfaces of dust grains play a vital role in the overall chemistry of interstellar matter. These grains become covered by icy layers, which are the largest molecular reservoir in the interstellar medium. Given this, it is surprising that the effect ice has on the overall chain of reactions is poorly characterized. One step on the path of gaining better understanding here is to develop methods of figuring out how much ice is present in these clouds, the links between ice components, and synergy between the ices and gas phase molecules. We do this by examining the absorption spectra of ices on lines of sight towards several stars behind clouds of interstellar matter. From these we can reconstruct spatial maps of the ice distribution on scales of as little as 1000 AU, as a test of the chemical variation within a cloud. By overlapping the ice data with other maps of the same region (gas emission, temperature, density etc) we create combined maps to reveal the astrochemistry of star-forming regions and pre-stellar cores. In this poster we present the continuing results of our ice mapping programme, using data from the AKARI satellite, specifically in slitless spectroscopy observations in the NIR. In this region the key ice features encompass H2O, CO and CO2. The maps illustrate the power of our dedicated AKARI data reduction pipeline, and the novelty of our observing programme. We also detail the next steps' in our ice mapping research. The method is being expanded to include the full 10'x10' AKARI field of view, taking account of image distortion induced by the dispersing optics. These maps are then combined with exiting gas-phase observations and SCUBA maps. The latest attempts at this are shown here. What is clear already is that it is difficult to predict ice abundances from factors such as extinction or gas density alone, and that ice formation and evolution can vary hugely over even very small astronomical scales.

Friedberg-Lee model at finite temperature and density

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mao Hong; CCAST; Yao Minjie

2008-06-15

The Friedberg-Lee model is studied at finite temperature and density. By using the finite temperature field theory, the effective potential of the Friedberg-Lee model and the bag constant B(T) and B(T,{mu}) have been calculated at different temperatures and densities. It is shown that there is a critical temperature T{sub C}{approx_equal}106.6 MeV when {mu}=0 MeV and a critical chemical potential {mu}{approx_equal}223.1 MeV for fixing the temperature at T=50 MeV. We also calculate the soliton solutions of the Friedberg-Lee model at finite temperature and density. It turns out that when T{<=}T{sub C} (or {mu}{<=}{mu}{sub C}), there is a bag constant B(T) [ormore » B(T,{mu})] and the soliton solutions are stable. However, when T>T{sub C} (or {mu}>{mu}{sub C}) the bag constant B(T)=0 MeV [or B(T,{mu})=0 MeV] and there is no soliton solution anymore, therefore, the confinement of quarks disappears quickly.« less

Preliminary Mapping of the Western Corn Rootworm (Diabrotica virgifera virgifera) Genome and Quantitative Trait Locus (QTL) Interval Mapping for Growth

USDA-ARS?s Scientific Manuscript database

Preliminary investigations into the organization of the western corn rootworm (Diabrotica virgifera virgifera; WCR) genome have resulted in low to moderate density gender-specific maps constructed from progeny of a backcrossed, short-diapause WCR family. Maps were based upon variation at microsatel...

Equality and Economy

ERIC Educational Resources Information Center

Brink, Chris

2012-01-01

The two big events in higher education during 2010 were the implementation of the Equality Act, and the introduction of a new dispensation on fees and funding. The former is intended to promote equality, the latter is premised on the need for economy. In this article, the author focuses on the effect of the latter on the former. He considers this…

The statistics of primordial density fluctuations

NASA Astrophysics Data System (ADS)

Barrow, John D.; Coles, Peter

1990-05-01

The statistical properties of the density fluctuations produced by power-law inflation are investigated. It is found that, even the fluctuations present in the scalar field driving the inflation are Gaussian, the resulting density perturbations need not be, due to stochastic variations in the Hubble parameter. All the moments of the density fluctuations are calculated, and is is argued that, for realistic parameter choices, the departures from Gaussian statistics are small and would have a negligible effect on the large-scale structure produced in the model. On the other hand, the model predicts a power spectrum with n not equal to 1, and this could be good news for large-scale structure.

Averaged kick maps: less noise, more signal…and probably less bias

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pražnikar, Jure; Afonine, Pavel V.; Gunčar, Gregor

2009-09-01

Averaged kick maps are the sum of a series of individual kick maps, where each map is calculated from atomic coordinates modified by random shifts. These maps offer the possibility of an improved and less model-biased map interpretation. Use of reliable density maps is crucial for rapid and successful crystal structure determination. Here, the averaged kick (AK) map approach is investigated, its application is generalized and it is compared with other map-calculation methods. AK maps are the sum of a series of kick maps, where each kick map is calculated from atomic coordinates modified by random shifts. As such, theymore » are a numerical analogue of maximum-likelihood maps. AK maps can be unweighted or maximum-likelihood (σ{sub A}) weighted. Analysis shows that they are comparable and correspond better to the final model than σ{sub A} and simulated-annealing maps. The AK maps were challenged by a difficult structure-validation case, in which they were able to clarify the problematic region in the density without the need for model rebuilding. The conclusion is that AK maps can be useful throughout the entire progress of crystal structure determination, offering the possibility of improved map interpretation.« less

CRISM Multispectral and Hyperspectral Mapping Data - A Global Data Set for Hydrated Mineral Mapping

NASA Astrophysics Data System (ADS)

Seelos, F. P.; Hash, C. D.; Murchie, S. L.; Lim, H.

2017-12-01

The Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) is a visible through short-wave infrared hyperspectral imaging spectrometer (VNIR S-detector: 364-1055 nm; IR L-detector: 1001-3936 nm; 6.55 nm sampling) that has been in operation on the Mars Reconnaissance Orbiter (MRO) since 2006. Over the course of the MRO mission, CRISM has acquired 290,000 individual mapping observation segments (mapping strips) with a variety of observing modes and data characteristics (VNIR/IR; 100/200 m/pxl; multi-/hyper-spectral band selection) over a wide range of observing conditions (atmospheric state, observation geometry, instrument state). CRISM mapping data coverage density varies primarily with latitude and secondarily due to seasonal and operational considerations. The aggregate global IR mapping data coverage currently stands at 85% ( 80% at the equator with 40% repeat sampling), which is sufficient spatial sampling density to support the assembly of empirically optimized radiometrically consistent mapping mosaic products. The CRISM project has defined a number of mapping mosaic data products (e.g. Multispectral Reduced Data Record (MRDR) map tiles) with varying degrees of observation-specific processing and correction applied prior to mosaic assembly. A commonality among the mosaic products is the presence of inter-observation radiometric discrepancies which are traceable to variable observation circumstances or associated atmospheric/photometric correction residuals. The empirical approach to radiometric reconciliation leverages inter-observation spatial overlaps and proximal relationships to construct a graph that encodes the mosaic structure and radiometric discrepancies. The graph theory abstraction allows the underling structure of the msaic to be evaluated and the corresponding optimization problem configured so it is well-posed. Linear and non-linear least squares optimization is then employed to derive a set of observation- and wavelength- specific model

Mapping from Space - Ontology Based Map Production Using Satellite Imageries

NASA Astrophysics Data System (ADS)

Asefpour Vakilian, A.; Momeni, M.

2013-09-01

Determination of the maximum ability for feature extraction from satellite imageries based on ontology procedure using cartographic feature determination is the main objective of this research. Therefore, a special ontology has been developed to extract maximum volume of information available in different high resolution satellite imageries and compare them to the map information layers required in each specific scale due to unified specification for surveying and mapping. ontology seeks to provide an explicit and comprehensive classification of entities in all sphere of being. This study proposes a new method for automatic maximum map feature extraction and reconstruction of high resolution satellite images. For example, in order to extract building blocks to produce 1 : 5000 scale and smaller maps, the road networks located around the building blocks should be determined. Thus, a new building index has been developed based on concepts obtained from ontology. Building blocks have been extracted with completeness about 83%. Then, road networks have been extracted and reconstructed to create a uniform network with less discontinuity on it. In this case, building blocks have been extracted with proper performance and the false positive value from confusion matrix was reduced by about 7%. Results showed that vegetation cover and water features have been extracted completely (100%) and about 71% of limits have been extracted. Also, the proposed method in this article had the ability to produce a map with largest scale possible from any multi spectral high resolution satellite imagery equal to or smaller than 1 : 5000.

Mapping from Space - Ontology Based Map Production Using Satellite Imageries

NASA Astrophysics Data System (ADS)

Asefpour Vakilian, A.; Momeni, M.

2013-09-01

Determination of the maximum ability for feature extraction from satellite imageries based on ontology procedure using cartographic feature determination is the main objective of this research. Therefore, a special ontology has been developed to extract maximum volume of information available in different high resolution satellite imageries and compare them to the map information layers required in each specific scale due to unified specification for surveying and mapping. ontology seeks to provide an explicit and comprehensive classification of entities in all sphere of being. This study proposes a new method for automatic maximum map feature extraction and reconstruction of high resolution satellite images. For example, in order to extract building blocks to produce 1 : 5000 scale and smaller maps, the road networks located around the building blocks should be determined. Thus, a new building index has been developed based on concepts obtained from ontology. Building blocks have been extracted with completeness about 83 %. Then, road networks have been extracted and reconstructed to create a uniform network with less discontinuity on it. In this case, building blocks have been extracted with proper performance and the false positive value from confusion matrix was reduced by about 7 %. Results showed that vegetation cover and water features have been extracted completely (100 %) and about 71 % of limits have been extracted. Also, the proposed method in this article had the ability to produce a map with largest scale possible from any multi spectral high resolution satellite imagery equal to or smaller than 1 : 5000.

Mapping seabird sensitivity to offshore wind farms.

PubMed

Bradbury, Gareth; Trinder, Mark; Furness, Bob; Banks, Alex N; Caldow, Richard W G; Hume, Duncan

2014-01-01

We present a Geographic Information System (GIS) tool, SeaMaST (Seabird Mapping and Sensitivity Tool), to provide evidence on the use of sea areas by seabirds and inshore waterbirds in English territorial waters, mapping their relative sensitivity to offshore wind farms. SeaMaST is a freely available evidence source for use by all connected to the offshore wind industry and will assist statutory agencies in assessing potential risks to seabird populations from planned developments. Data were compiled from offshore boat and aerial observer surveys spanning the period 1979-2012. The data were analysed using distance analysis and Density Surface Modelling to produce predicted bird densities across a grid covering English territorial waters at a resolution of 3 km×3 km. Coefficients of Variation were estimated for each grid cell density, as an indication of confidence in predictions. Offshore wind farm sensitivity scores were compiled for seabird species using English territorial waters. The comparative risks to each species of collision with turbines and displacement from operational turbines were reviewed and scored separately, and the scores were multiplied by the bird density estimates to produce relative sensitivity maps. The sensitivity maps reflected well the amassed distributions of the most sensitive species. SeaMaST is an important new tool for assessing potential impacts on seabird populations from offshore development at a time when multiple large areas of development are proposed which overlap with many seabird species' ranges. It will inform marine spatial planning as well as identifying priority areas of sea usage by marine birds. Example SeaMaST outputs are presented.

A high-resolution optical measurement system for rapid acquisition of radiation flux density maps

NASA Astrophysics Data System (ADS)

Thelen, Martin; Raeder, Christian; Willsch, Christian; Dibowski, Gerd

2017-06-01

To identify the power and flux density of concentrated solar radiation the Institute of Solar Research at the German Aerospace Center (DLR - Deutsches Zentrum für Luft-und Raumfahrt e. V.) has used the camera-based measurement system FATMES (Flux and Temperature Measurement System) since 1995. The disadvantages of low resolution, difficult handling and poor computing power required a revision of the existing measurement system. The measurement system FMAS (Flux Mapping Acquisition system) is equipped with state-of-the-art-hardware, is compatible with computers off-the-shelf and is programmed in LabView. The expenditure of time for an image evaluation is reduced by the factor 60 compared to FATMES. The new measurement system is no longer associated with the facilities Solar Furnace and High Flux Solar Simulator at the DLR in Cologne but is also applicable as a mobile system. The data and the algorithms are transparent throughout the complete process. The measurement accuracy of FMAS is determined to at most ±3 % until now. The error of measurement of FATMES is at least 2 % higher according to the conducted comparison tests.

Mapping the Influence of Prior Tectonism on Seismicity in the Central and Eastern US

NASA Astrophysics Data System (ADS)

Boyd, O. S.; Levandowski, W.; Ramirez-Guzman, L.; Zellman, M.; Briggs, R.

2015-12-01

From the Atlantic margin to the Rockies, most earthquakes in the central and eastern U.S. occur in ancient tectonic zones, yet many such features have been historically quiescent. If all intraplate stress were transferred from plate boundaries or bases, the stress field would be broadly uniform, with all well-oriented faults equally likely to slip. But faults are not the only product of tectonism; intrusions, metamorphism, or any number of other alterations may modify crustal and/or upper mantle density, leaving behind lithostatic pressure gradients that can locally elevate or reduce stress on faults. With data provided by Earthscope, we are working to map lithospheric density across the U.S. and to quantify gravitational body-forces using analytical and finite-element methods. Regional-scale 3D models show that gravitational forces focus seismicity and reorient principal stress both in the New Madrid seismic zone and the western Great Plains. Sedimentary fill and low elevation encourage Reelfoot Rift-normal contraction, yet along-strike variations in lower crustal density rotate body-forces beneath New Madrid to interfere constructively with far-field compression, augmenting differential stress by 5-10 MPa. On the plains of SE Colorado and SE Wyoming, the Cheraw and Wheatland/Whalen faults collocate with multiply reactivated Proterozoic sutures, enigmatic Quaternary extension, and focused seismicity with regionally anomalous NW-SE moment tensor T-axes. Earthscope data help reveal anomalously buoyant lower crust beneath each suture -­- which we hypothesize reflects hydration by Farallon slab-derived fluids that have preferentially migrated along ancient fracture networks -- that generates 10 MPa of localized suture-normal tension, consistent with geomorphic strain- and seismic stress-indicators. As continent-wide seismic models emerge from Earthscope data, we will continue to map regions where inherited structures encourage intraplate seismicity.

Evaluation of Techniques Used to Estimate Cortical Feature Maps

PubMed Central

Katta, Nalin; Chen, Thomas L.; Watkins, Paul V.; Barbour, Dennis L.

2011-01-01

Functional properties of neurons are often distributed nonrandomly within a cortical area and form topographic maps that reveal insights into neuronal organization and interconnection. Some functional maps, such as in visual cortex, are fairly straightforward to discern with a variety of techniques, while other maps, such as in auditory cortex, have resisted easy characterization. In order to determine appropriate protocols for establishing accurate functional maps in auditory cortex, artificial topographic maps were probed under various conditions, and the accuracy of estimates formed from the actual maps was quantified. Under these conditions, low-complexity maps such as sound frequency can be estimated accurately with as few as 25 total samples (e.g., electrode penetrations or imaging pixels) if neural responses are averaged together. More samples are required to achieve the highest estimation accuracy for higher complexity maps, and averaging improves map estimate accuracy even more than increasing sampling density. Undersampling without averaging can result in misleading map estimates, while undersampling with averaging can lead to the false conclusion of no map when one actually exists. Uniform sample spacing only slightly improves map estimation over nonuniform sample spacing typical of serial electrode penetrations. Tessellation plots commonly used to visualize maps estimated using nonuniform sampling are always inferior to linearly interpolated estimates, although differences are slight at higher sampling densities. Within primary auditory cortex, then, multiunit sampling with at least 100 samples would likely result in reasonable feature map estimates for all but the highest complexity maps and the highest variability that might be expected. PMID:21889537

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

PubMed

Yang, Yi; Shen, Yusen; Li, Shunda; Ge, Xianhong; Li, Zaiyun

2017-01-01

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

A proteome-scale map of the human interactome network

PubMed Central

Rolland, Thomas; Taşan, Murat; Charloteaux, Benoit; Pevzner, Samuel J.; Zhong, Quan; Sahni, Nidhi; Yi, Song; Lemmens, Irma; Fontanillo, Celia; Mosca, Roberto; Kamburov, Atanas; Ghiassian, Susan D.; Yang, Xinping; Ghamsari, Lila; Balcha, Dawit; Begg, Bridget E.; Braun, Pascal; Brehme, Marc; Broly, Martin P.; Carvunis, Anne-Ruxandra; Convery-Zupan, Dan; Corominas, Roser; Coulombe-Huntington, Jasmin; Dann, Elizabeth; Dreze, Matija; Dricot, Amélie; Fan, Changyu; Franzosa, Eric; Gebreab, Fana; Gutierrez, Bryan J.; Hardy, Madeleine F.; Jin, Mike; Kang, Shuli; Kiros, Ruth; Lin, Guan Ning; Luck, Katja; MacWilliams, Andrew; Menche, Jörg; Murray, Ryan R.; Palagi, Alexandre; Poulin, Matthew M.; Rambout, Xavier; Rasla, John; Reichert, Patrick; Romero, Viviana; Ruyssinck, Elien; Sahalie, Julie M.; Scholz, Annemarie; Shah, Akash A.; Sharma, Amitabh; Shen, Yun; Spirohn, Kerstin; Tam, Stanley; Tejeda, Alexander O.; Trigg, Shelly A.; Twizere, Jean-Claude; Vega, Kerwin; Walsh, Jennifer; Cusick, Michael E.; Xia, Yu; Barabási, Albert-László; Iakoucheva, Lilia M.; Aloy, Patrick; De Las Rivas, Javier; Tavernier, Jan; Calderwood, Michael A.; Hill, David E.; Hao, Tong; Roth, Frederick P.; Vidal, Marc

2014-01-01

SUMMARY Just as reference genome sequences revolutionized human genetics, reference maps of interactome networks will be critical to fully understand genotype-phenotype relationships. Here, we describe a systematic map of ~14,000 high-quality human binary protein-protein interactions. At equal quality, this map is ~30% larger than what is available from small-scale studies published in the literature in the last few decades. While currently available information is highly biased and only covers a relatively small portion of the proteome, our systematic map appears strikingly more homogeneous, revealing a “broader” human interactome network than currently appreciated. The map also uncovers significant inter-connectivity between known and candidate cancer gene products, providing unbiased evidence for an expanded functional cancer landscape, while demonstrating how high quality interactome models will help “connect the dots” of the genomic revolution. PMID:25416956

Saturn's ionosphere - Inferred electron densities

NASA Technical Reports Server (NTRS)

Kaiser, M. L.; Desch, M. D.; Connerney, J. E. P.

1984-01-01

During the two Voyager encounters with Saturn, radio bursts were detected which appear to have originated from atmospheric lightning storms. Although these bursts generally extended over frequencies from as low as 100 kHz to the upper detection limit of the instrument, 40 MHz, they often exhibited a sharp but variable low frequency cutoff below which bursts were not detected. We interpret the variable low-frequency extent of these bursts to be due to the reflection of the radio waves as they propagate through an ionosphere which varies with local time. We obtain estimates of electron densities at a variety of latitude and local time locations. These compare well with the dawn and dusk densities measured by the Pioneer 11 Voyager Radio Science investigations, and with model predictions for dayside densities. However, we infer a two-order-of-magnitude diurnal variation of electron density, which had not been anticipated by theoretical models of Saturn's ionosphere, and an equally dramatic extinction of ionospheric electron density by Saturn's rings. Previously announced in STAR as N84-17102

Individual Component Map of Rotatory Strength (ICM-RS) and Rotatory Strength Density (RSD) plots as analysis tools of circular dicroism spectra of complex systems.

PubMed

Chang, Le; Baseggio, Oscar; Sementa, Luca; Cheng, Daojian; Fronzoni, Giovanna; Toffoli, Daniele; Aprà, Edoardo; Stener, Mauro; Fortunelli, Alessandro

2018-06-13

We introduce Individual Component Maps of Rotatory Strength (ICM-RS) and Rotatory Strength Density (RSD) plots as analysis tools of chiro-optical linear response spectra deriving from time-dependent density functional theory (TDDFT) simulations. ICM-RS and RSD allow one to visualize the origin of chiro-optical response in momentum or real space, including signed contributions and therefore highlighting cancellation terms that are ubiquitous in chirality phenomena, and should be especially useful in analyzing the spectra of complex systems. As test cases, we use ICM-RS and RSD to analyze circular dichroism spectra of selected (Ag-Au)30(SR)18 monolayer-protected metal nanoclusters, showing the potential of the proposed tools to derive insight and understanding, and eventually rational design, in chiro-optical studies of complex systems.

Field Line Mapping of the Polar Cap Neutral Density Anomaly

NASA Astrophysics Data System (ADS)

Sutton, E. K.; Lin, C. S.; Huang, C. Y.; Cooke, D. L.

2016-12-01

Polar cap neutral density anomaly (PCNDA) events of localized density enhancement with a half size around 700-1000 km had been frequently detected by CHAMP satellite at around 400 km during major magnetic storms with Dst < -100 nT. Density enhancement is probably produced via Joule heating of the thermosphere when a significant amount of energy is deposited in the polar cap. We have identified 12 PCNDA events measured by CHAMP during two major magnetic storms including one initiated by a large solar wind pressure pulse. Their density anomaly locations are found to scatter randomly within the polar circle of 80o magnetic latitude in the geomagnetic coordinate. However after transformed to the Geocentric Solar Wind (GSW) coordinates, their locations become aligned in the direction of solar wind velocity. To better understand the polar cap energy deposition we trace magnetic field lines to the magnetosphere up to 30 earth radii from the ionosphere at 400 km using the data-based Tsyganenko T95 and TS05 magnetic field models. Field line tracing is performed in the GSW coordinate along the CHAMP orbit as well as for the whole polar cap. Each traced magnetic field line is classified into one of the three categories, (1) magnetosphere closed field line (MC) crossing the equatorial plane within 30 earth radii, (2) open field line connected to the magnetopause (MP), or (3) open field line connected to the magnetotail lobe (MT). For nine PCNDA events among the 10 events that we are able to conduct tracing, field lines originated from the density anomaly regions are classified as MT. Only one outlier event in association with a very large IMF BZ is classified as MP. Furthermore the separation angle between the density anomaly peak and the MP-MT field line separation point at 400 km on the X- and Z-axes meridian plane varies from -4o to 16o. Based on these results we speculate that convective electric fields and field aligned currents in the ionosphere might be enhanced near

EnviroAtlas - Minneapolis/St. Paul, MN - Estimated Intersection Density of Walkable Roads

EPA Pesticide Factsheets

This EnviroAtlas dataset estimates the intersection density of walkable roads within a 750 meter radius of any given 10 meter pixel in the community. Intersections are defined as any point where 3 or more roads meet and density is calculated using kernel density, where closer intersections are weighted higher than further intersections. Intersection density is highly correlated with walking for transportation. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as downloadable data (https://edg.epa.gov/data/Public/ORD/EnviroAtlas) or as an EnviroAtlas map service. Additional descriptive information about each attribute in this dataset can be found in its associated EnviroAtlas Fact Sheet (https://www.epa.gov/enviroatlas/enviroatlas-fact-sheets).

Use of Total Electron Content data to analyze ionosphere electron density gradients

NASA Astrophysics Data System (ADS)

Nava, B.; Radicella, S. M.; Leitinger, R.; Coisson, P.

In presence of electron density gradients the thin shell approximation for the ionosphere used together with a simple mapping function to convert slant Total Electron Content TEC to vertical TEC could lead to TEC conversion errors Therefore these mapping function errors can be used to identify the effects of the electron density gradients in the ionosphere In the present work high precision GPS derived slant TEC data have been used to investigate the effects of the electron density gradients in the middle and low latitude ionosphere under geomagnetic quiet and disturbed conditions In particular the data corresponding to the geographic area of the American sector for the days 5-7 April 2000 have been used to perform a complete analysis of mapping function errors based on the coinciding pierce point technique The results clearly illustrate the electron density gradient effects according to the locations considered and to the actual levels of disturbance of the ionosphere

Equality in Sport for Women.

ERIC Educational Resources Information Center

Geadelmann, Patricia L.; And Others

Essays concerning multiple aspects of integrating the concept of professional equality between the sexes into the field of sport are presented. The abstract idea of sexual equality is examined, and methods for determining the degree of equality present in given working situations are set forth. A discussion of the laws, enforcing agencies, and…

Lod scores for gene mapping in the presence of marker map uncertainty.

PubMed

Stringham, H M; Boehnke, M

2001-07-01

Multipoint lod scores are typically calculated for a grid of locus positions, moving the putative disease locus across a fixed map of genetic markers. Changing the order of a set of markers and/or the distances between the markers can make a substantial difference in the resulting lod score curve and the location and height of its maximum. The typical approach of using the best maximum likelihood marker map is not easily justified if other marker orders are nearly as likely and give substantially different lod score curves. To deal with this problem, we propose three weighted multipoint lod score statistics that make use of information from all plausible marker orders. In each of these statistics, the information conditional on a particular marker order is included in a weighted sum, with weight equal to the posterior probability of that order. We evaluate the type 1 error rate and power of these three statistics on the basis of results from simulated data, and compare these results to those obtained using the best maximum likelihood map and the map with the true marker order. We find that the lod score based on a weighted sum of maximum likelihoods improves on using only the best maximum likelihood map, having a type 1 error rate and power closest to that of using the true marker order in the simulation scenarios we considered. Copyright 2001 Wiley-Liss, Inc.

High and low density development in Puerto Rico

Treesearch

William A. Gould; Sebastian Martinuzzi; Olga M. Ramos Gonzalez

2008-01-01

This map shows the distribution of high and low density developed lands in Puerto Rico (Martinuzzi et al. 2007). The map was created using a mosaic of Landsat ETM+ images that range from the years 2000 to 2003. The developed land cover was classified using the Iterative Self-Organizing Data Analysis Technique (ISODATA) unsupervised classification (ERDAS 2003)....

ERTS-1 image enhancement by optically combining density slices

NASA Technical Reports Server (NTRS)

Tapper, G. O.; Pease, R. W.

1973-01-01

The technique of density slicing using a photographic film and its application to enhancement of ERTS-1 imagery has proved to be useful for mapping varigated areal phenomena and provides a useful supplement ot the I2S MiniAddcol viewing system. The intial experiments conducted with this film were encouraging, and indicated that this technique of density slicing using readily accessible darkroom facilities and simple darkroom procedures allows rapid, accurate, and facile interpretation of certain areal phenomena to be made from the imagery. The distribution of the tree yucca, Yucca brevifolia Jaegeriana, in the eastern Mojave Desert of Southern California and southern Nevada was used as an example to test the accuracy of the technique for mapping purposes. The distribution was mapped at a relatively high level of accuracy.

Quantum Entanglement and Reduced Density Matrices

NASA Astrophysics Data System (ADS)

Purwanto, Agus; Sukamto, Heru; Yuwana, Lila

2018-05-01

We investigate entanglement and separability criteria of multipartite (n-partite) state by examining ranks of its reduced density matrices. Firstly, we construct the general formula to determine the criterion. A rank of origin density matrix always equals one, meanwhile ranks of reduced matrices have various ranks. Next, separability and entanglement criterion of multipartite is determined by calculating ranks of reduced density matrices. In this article we diversify multipartite state criteria into completely entangled state, completely separable state, and compound state, i.e. sub-entangled state and sub-entangledseparable state. Furthermore, we also shorten the calculation proposed by the previous research to determine separability of multipartite state and expand the methods to be able to differ multipartite state based on criteria above.

Genetic Diversity and Human Equality.

ERIC Educational Resources Information Center

Dobzhansky, Theodosius

The idea of equality often, if not frequently, bogs down in confusion and apparent contradictions; equality is confused with identity, and diversity with inequality. It would seem that the easiest way to discredit the idea of equality is to show that people are innately, genetically, and, therefore, irremediably diverse and unlike. The snare is,…

EqualChance: Addressing Intra-set Write Variation to Increase Lifetime of Non-volatile Caches

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mittal, Sparsh; Vetter, Jeffrey S

To address the limitations of SRAM such as high-leakage and low-density, researchers have explored use of non-volatile memory (NVM) devices, such as ReRAM (resistive RAM) and STT-RAM (spin transfer torque RAM) for designing on-chip caches. A crucial limitation of NVMs, however, is that their write endurance is low and the large intra-set write variation introduced by existing cache management policies may further exacerbate this problem, thereby reducing the cache lifetime significantly. We present EqualChance, a technique to increase cache lifetime by reducing intra-set write variation. EqualChance works by periodically changing the physical cache-block location of a write-intensive data item withinmore » a set to achieve wear-leveling. Simulations using workloads from SPEC CPU2006 suite and HPC (high-performance computing) field show that EqualChance improves the cache lifetime by 4.29X. Also, its implementation overhead is small, and it incurs very small performance and energy loss.« less

Mapping Seabird Sensitivity to Offshore Wind Farms

PubMed Central

Bradbury, Gareth; Trinder, Mark; Furness, Bob; Banks, Alex N.; Caldow, Richard W. G.; Hume, Duncan

2014-01-01

We present a Geographic Information System (GIS) tool, SeaMaST (Seabird Mapping and Sensitivity Tool), to provide evidence on the use of sea areas by seabirds and inshore waterbirds in English territorial waters, mapping their relative sensitivity to offshore wind farms. SeaMaST is a freely available evidence source for use by all connected to the offshore wind industry and will assist statutory agencies in assessing potential risks to seabird populations from planned developments. Data were compiled from offshore boat and aerial observer surveys spanning the period 1979–2012. The data were analysed using distance analysis and Density Surface Modelling to produce predicted bird densities across a grid covering English territorial waters at a resolution of 3 km×3 km. Coefficients of Variation were estimated for each grid cell density, as an indication of confidence in predictions. Offshore wind farm sensitivity scores were compiled for seabird species using English territorial waters. The comparative risks to each species of collision with turbines and displacement from operational turbines were reviewed and scored separately, and the scores were multiplied by the bird density estimates to produce relative sensitivity maps. The sensitivity maps reflected well the amassed distributions of the most sensitive species. SeaMaST is an important new tool for assessing potential impacts on seabird populations from offshore development at a time when multiple large areas of development are proposed which overlap with many seabird species’ ranges. It will inform marine spatial planning as well as identifying priority areas of sea usage by marine birds. Example SeaMaST outputs are presented. PMID:25210739

Co-operation of digital nonlinear equalizers and soft-decision LDPC FEC in nonlinear transmission.

PubMed

Tanimura, Takahito; Oda, Shoichiro; Hoshida, Takeshi; Aoki, Yasuhiko; Tao, Zhenning; Rasmussen, Jens C

2013-12-30

We experimentally and numerically investigated the characteristics of 128 Gb/s dual polarization - quadrature phase shift keying signals received with two types of nonlinear equalizers (NLEs) followed by soft-decision (SD) low-density parity-check (LDPC) forward error correction (FEC). Successful co-operation among SD-FEC and NLEs over various nonlinear transmissions were demonstrated by optimization of parameters for NLEs.

Distinguishability notion based on Wootters statistical distance: Application to discrete maps

NASA Astrophysics Data System (ADS)

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.

Right ventricular outflow tract high-density endocardial unipolar voltage mapping in patients with Brugada syndrome: evidence for electroanatomical abnormalities.

PubMed

Letsas, Konstantinos P; Efremidis, Michael; Vlachos, Konstantinos; Georgopoulos, Stamatis; Karamichalakis, Nikolaos; Asvestas, Dimitrios; Valkanas, Kosmas; Korantzopoulos, Panagiotis; Liu, Tong; Sideris, Antonios

2017-05-02

Epicardial structural abnormalities at the right ventricular outflow tract (RVOT) may provide the arrhythmia substrate in Brugada syndrome (BrS). Electroanatomical endocardial unipolar voltage mapping is an emerging tool that accurately identifies epicardial abnormalities in different clinical settings. This study investigated whether endocardial unipolar voltage mapping of the RVOT detects electroanatomical abnormalities in patients with BrS. Ten asymptomatic patients (8 males, 34.5 ± 11.2 years) with spontaneous type 1 ECG pattern of BrS and negative late gadolinium enhancement-cardiac magnetic resonance imaging (LGE-c-MRI) underwent high-density endocardial electroanatomical mapping (>800 points). Using a cut-off of 1 mV and 4 mV for normal bipolar and unipolar voltage, respectively, derived from 20 control patients without structural heart disease established by LGE-c-MRI, the extend of low-voltage areas within the RVOT was estimated using a specific calculation software. The mean RVOT area presenting low-voltage bipolar signals in BrS patients was 3.4 ± 1.7 cm2 (range 1.5-7 cm2). A significantly greater area of abnormal unipolar signals was identified (12.6 ± 4.6 cm2 [range 7-22 cm2], P: 0.001). Both bipolar and unipolar electroanatomical abnormalities were mainly located at the free wall of the RVOT. The mean RVOT activation time was significantly prolonged in BrS patients compared to control population (86.4 ± 16.5 vs. 63.4 ± 9.7 ms, P < 0.001). Isochronal mapping demonstrated lines of conduction slowing within the RVOT in 8/10 BrS patients. Wide areas of endocardial unipolar voltage abnormalities that possibly reflect epicardial structural abnormalities are identified at the RVOT of BrS patients. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2017. For permissions, please email: journals.permissions@oup.com.

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

Treesearch

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

2017-01-01

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...

Local breast density assessment using reacquired mammographic images.

PubMed

García, Eloy; Diaz, Oliver; Martí, Robert; Diez, Yago; Gubern-Mérida, Albert; Sentís, Melcior; Martí, Joan; Oliver, Arnau

2017-08-01

The aim of this paper is to evaluate the spatial glandular volumetric tissue distribution as well as the density measures provided by Volpara™ using a dataset composed of repeated pairs of mammograms, where each pair was acquired in a short time frame and in a slightly changed position of the breast. We conducted a retrospective analysis of 99 pairs of repeatedly acquired full-field digital mammograms from 99 different patients. The commercial software Volpara™ Density Maps (Volpara Solutions, Wellington, New Zealand) is used to estimate both the global and the local glandular tissue distribution in each image. The global measures provided by Volpara™, such as breast volume, volume of glandular tissue, and volumetric breast density are compared between the two acquisitions. The evaluation of the local glandular information is performed using histogram similarity metrics, such as intersection and correlation, and local measures, such as statistics from the difference image and local gradient correlation measures. Global measures showed a high correlation (breast volume R=0.99, volume of glandular tissue R=0.94, and volumetric breast density R=0.96) regardless the anode/filter material. Similarly, histogram intersection and correlation metric showed that, for each pair, the images share a high degree of information. Regarding the local distribution of glandular tissue, small changes in the angle of view do not yield significant differences in the glandular pattern, whilst changes in the breast thickness between both acquisition affect the spatial parenchymal distribution. This study indicates that Volpara™ Density Maps is reliable in estimating the local glandular tissue distribution and can be used for its assessment and follow-up. Volpara™ Density Maps is robust to small variations of the acquisition angle and to the beam energy, although divergences arise due to different breast compression conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

Isostatic gravity map with simplified geology of the Los Angeles 30 x 60 minute quadrangle

USGS Publications Warehouse

Wooley, R.J.; Yerkes, R.F.; Langenheim, V.E.; Chuang, F.C.

2003-01-01

This isostatic residual gravity map is part of the Southern California Areal Mapping Project (SCAMP) and is intended to promote further understanding of the geology in the Los Angeles 30 x 60 minute quadrangle, California, by serving as a basis for geophysical interpretations and by supporting both geological mapping and topical (especially earthquake) studies. Local spatial variations in the Earth's gravity field (after various corrections for elevation, terrain, and deep crustal structure explained below) reflect the lateral variation in density in the mid- to upper crust. Densities often can be related to rock type, and abrupt spatial changes in density commonly mark lithologic boundaries. The map shows contours of isostatic gravity overlain on a simplified geology including faults and rock types. The map is draped over shaded-relief topography to show landforms.

Oregon Cascades Play Fairway Analysis: Faults and Heat Flow maps

DOE Data Explorer

Adam Brandt

2015-11-15

This submission includes a fault map of the Oregon Cascades and backarc, a probability map of heat flow, and a fault density probability layer. More extensive metadata can be found within each zip file.