Science.gov

Sample records for density equalizing maps

  1. Density Equalizing Map Projections

    1995-07-01

    A geographic map is mathematically transformed so that the subareas of the map are proportional to a given quantity such as population. In other words, population density is equalized over the entire map. The transformed map can be used as a display tool, or it can be statistically analyzed. For example, cases of disease plotted on the transformed map should be uniformly distributed at random, if disease rates are everywhere equal. Geographic clusters of diseasemore » can be readily identified, and their statistical significance determined, on a density equalized map.« less

  2. Density equalizing map projections: A new algorithm

    SciTech Connect

    Merrill, D.W.; Selvin, S.; Mohr, M.S.

    1992-02-01

    In the study of geographic disease clusters, an alternative to traditional methods based on rates is to analyze case locations on a transformed map in which population density is everywhere equal. Although the analyst`s task is thereby simplified, the specification of the density equalizing map projection (DEMP) itself is not simple and continues to be the subject of considerable research. Here a new DEMP algorithm is described, which avoids some of the difficulties of earlier approaches. The new algorithm (a) avoids illegal overlapping of transformed polygons; (b) finds the unique solution that minimizes map distortion; (c) provides constant magnification over each map polygon; (d) defines a continuous transformation over the entire map domain; (e) defines an inverse transformation; (f) can accept optional constraints such as fixed boundaries; and (g) can use commercially supported minimization software. Work is continuing to improve computing efficiency and improve the algorithm.

  3. Density equalizing map projections: A new algorithm

    SciTech Connect

    Merrill, D.W.; Selvin, S.; Mohr, M.S.

    1992-02-01

    In the study of geographic disease clusters, an alternative to traditional methods based on rates is to analyze case locations on a transformed map in which population density is everywhere equal. Although the analyst's task is thereby simplified, the specification of the density equalizing map projection (DEMP) itself is not simple and continues to be the subject of considerable research. Here a new DEMP algorithm is described, which avoids some of the difficulties of earlier approaches. The new algorithm (a) avoids illegal overlapping of transformed polygons; (b) finds the unique solution that minimizes map distortion; (c) provides constant magnification over each map polygon; (d) defines a continuous transformation over the entire map domain; (e) defines an inverse transformation; (f) can accept optional constraints such as fixed boundaries; and (g) can use commercially supported minimization software. Work is continuing to improve computing efficiency and improve the algorithm.

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

    SciTech Connect

    Merrill, D.W.

    1998-05-01

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

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

    PubMed Central

    Börger, Julia-Annik; Neye, Niko; Scutaru, Cristian; Kreiter, Carolin; Puk, Clemens; Fischer, Tanja C; Groneberg-Kloft, Beatrix

    2008-01-01

    Despite the large amount of experimental studies already conducted on bronchial asthma, further insights into the molecular basics of the disease are required to establish new therapeutic approaches. As a basis for this research different animal models of asthma have been developed in the past years. However, precise bibliometric data on the use of different models do not exist so far. Therefore the present study was conducted to establish a data base of the existing experimental approaches. Density-equalizing algorithms were used and data was retrieved from a Thomson Institute for Scientific Information database. During the period from 1900 to 2006 a number of 3489 filed items were connected to animal models of asthma, the first being published in the year 1968. The studies were published by 52 countries with the US, Japan and the UK being the most productive suppliers, participating in 55.8% of all published items. Analyzing the average citation per item as an indicator for research quality Switzerland ranked first (30.54/item) and New Zealand ranked second for countries with more than 10 published studies. The 10 most productive journals included 4 with a main focus allergy and immunology and 4 with a main focus on the respiratory system. Two journals focussed on pharmacology or pharmacy. In all assigned subject categories examined for a relation to animal models of asthma, immunology ranked first. Assessing numbers of published items in relation to animal species it was found that mice were the preferred species followed by guinea pigs. In summary it can be concluded from density-equalizing calculations that the use of animal models of asthma is restricted to a relatively small number of countries. There are also differences in the use of species. These differences are based on variations in the research focus as assessed by subject category analysis. PMID:18315838

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

    PubMed

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

    2014-09-30

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

  7. MRSA: A Density-Equalizing Mapping Analysis of the Global Research Architecture

    PubMed Central

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

    2014-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) has evolved as an alarming public health thread due to its global spread as hospital and community pathogen. Despite this role, a scientometric analysis has not been performed yet. Therefore, the NewQIS platform was used to conduct a combined density-equalizing mapping and scientometric study. As database, the Web of Science was used, and all entries between 1961 and 2007 were analyzed. In total, 7671 entries were identified. Density equalizing mapping demonstrated a distortion of the world map for the benefit of the USA as leading country with a total output of 2374 publications, followed by the UK (1030) and Japan (862). Citation rate analysis revealed Portugal as leading country with a rate of 35.47 citations per article, followed by New Zealand and Denmark. Country cooperation network analyses showed 743 collaborations with US-UK being most frequent. Network citation analyses indicated the publications that arose from the cooperation of USA and France as well as USA and Japan as the most cited (75.36 and 74.55 citations per collaboration article, respectively). The present study provides the first combined density-equalizing mapping and scientometric analysis of MRSA research. It illustrates the global MRSA research architecture. It can be assumed that this highly relevant topic for public health will achieve even greater dimensions in the future. PMID:25272080

  8. Silicosis: geographic changes in research: an analysis employing density-equalizing mapping

    PubMed Central

    2014-01-01

    Background A critical evaluation of scientific efforts is needed in times of modified evaluation criteria for academic personnel and institutions. Methods Using scientometric benchmark procedures and density-equalizing mapping, we analysed the global scientific efforts on “silicosis” of the last 92 years focusing on geographical changes within the last 30 years, specifying the most productive authors, institutions, countries and the most successful cooperations. Results The USA as the most productive supplier have established their position as center of international cooperation, followed in considerable distance by the United Kingdom, Germany and China. Asian countries, particularly China, catch up and are expected to excel the USA still in this decade. Conclusion The combination of scientometric procedures with density-equalizing mapping reveals a distinct global pattern of research productivity and citation activity. Modified h-index, citationrate and impact factor have to be discussed critically due to distortion by bias of self-citation, language and co-authorship. PMID:24438527

  9. Density equalized map projections: a method for analysing clustering around a fixed point.

    PubMed

    Schulman, J; Selvin, S; Merrill, D W

    1988-04-01

    Cases plotted on a geopolitical map entail difficulties in interpretation and analysis because of variable population density in the study area. Density equalized map projections (DEMPs) eliminate the distribution of the resident population as an interfering influence by transforming map area to be proportional to population. This paper discusses a transformation algorithm, its properties, and develops statistical methods to detect clustering of cases around a fixed point for data plotted on DEMPs. We suggest two numeric methods where exact solutions are too complicated or do not exist. Finally, we illustrate these methods using data from Denver and Jefferson counties in Colorado to investigate whether lung cancer and leukaemia incidence patterns are associated with plutonium exposure from the Rocky Flats plant site. PMID:3368676

  10. Type 2 Diabetes Research Yield, 1951-2012: Bibliometrics Analysis and Density-Equalizing Mapping.

    PubMed

    Geaney, Fiona; Scutaru, Cristian; Kelly, Clare; Glynn, Ronan W; Perry, Ivan J

    2015-01-01

    The objective of this paper is to provide a detailed evaluation of type 2 diabetes mellitus research output from 1951-2012, using large-scale data analysis, bibliometric indicators and density-equalizing mapping. Data were retrieved from the Science Citation Index Expanded database, one of the seven curated databases within Web of Science. Using Boolean operators "OR", "AND" and "NOT", a search strategy was developed to estimate the total number of published items. Only studies with an English abstract were eligible. Type 1 diabetes and gestational diabetes items were excluded. Specific software developed for the database analysed the data. Information including titles, authors' affiliations and publication years were extracted from all files and exported to excel. Density-equalizing mapping was conducted as described by Groenberg-Kloft et al, 2008. A total of 24,783 items were published and cited 476,002 times. The greatest number of outputs were published in 2010 (n=2,139). The United States contributed 28.8% to the overall output, followed by the United Kingdom (8.2%) and Japan (7.7%). Bilateral cooperation was most common between the United States and United Kingdom (n=237). Harvard University produced 2% of all publications, followed by the University of California (1.1%). The leading journals were Diabetes, Diabetologia and Diabetes Care and they contributed 9.3%, 7.3% and 4.0% of the research yield, respectively. In conclusion, the volume of research is rising in parallel with the increasing global burden of disease due to type 2 diabetes mellitus. Bibliometrics analysis provides useful information to scientists and funding agencies involved in the development and implementation of research strategies to address global health issues.

  11. Type 2 Diabetes Research Yield, 1951-2012: Bibliometrics Analysis and Density-Equalizing Mapping

    PubMed Central

    Geaney, Fiona; Scutaru, Cristian; Kelly, Clare; Glynn, Ronan W.; Perry, Ivan J.

    2015-01-01

    The objective of this paper is to provide a detailed evaluation of type 2 diabetes mellitus research output from 1951-2012, using large-scale data analysis, bibliometric indicators and density-equalizing mapping. Data were retrieved from the Science Citation Index Expanded database, one of the seven curated databases within Web of Science. Using Boolean operators "OR", "AND" and "NOT", a search strategy was developed to estimate the total number of published items. Only studies with an English abstract were eligible. Type 1 diabetes and gestational diabetes items were excluded. Specific software developed for the database analysed the data. Information including titles, authors’ affiliations and publication years were extracted from all files and exported to excel. Density-equalizing mapping was conducted as described by Groenberg-Kloft et al, 2008. A total of 24,783 items were published and cited 476,002 times. The greatest number of outputs were published in 2010 (n=2,139). The United States contributed 28.8% to the overall output, followed by the United Kingdom (8.2%) and Japan (7.7%). Bilateral cooperation was most common between the United States and United Kingdom (n=237). Harvard University produced 2% of all publications, followed by the University of California (1.1%). The leading journals were Diabetes, Diabetologia and Diabetes Care and they contributed 9.3%, 7.3% and 4.0% of the research yield, respectively. In conclusion, the volume of research is rising in parallel with the increasing global burden of disease due to type 2 diabetes mellitus. Bibliometrics analysis provides useful information to scientists and funding agencies involved in the development and implementation of research strategies to address global health issues. PMID:26208117

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

    PubMed Central

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

    2015-01-01

    Caesarean section (CS) is a common surgical procedure. Although it has been performed in a modern context for about 100 years, there is no concise analysis of the international architecture of caesarean section research output available so far. Therefore, the present study characterizes the global pattern of the related publications by using the NewQIS (New Quality and Quantity Indices in Science) platform, which combines scientometric methods with density equalizing mapping algorithms. The Web of Science was used as a database. 12,608 publications were identified that originated from 131 countries. The leading nations concerning research activity, overall citations and country-specific h-Index were the USA and the United Kingdom. Relation of the research activity to epidemiologic data indicated that Scandinavian countries including Sweden and Finland were leading the field, whereas, in relation to economic data, countries such as Israel and Ireland led. Semi-qualitative indices such as country-specific citation rates ranked Sweden, Norway and Finland in the top positions. International caesarean section research output continues to grow annually in an era where caesarean section rates increased dramatically over the past decades. With regard to increasing employment of scientometric indicators in performance assessment, these findings should provide useful information for those tasked with the improvement of scientific achievements. PMID:26593932

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

    PubMed Central

    Kusma, Bianca; Scutaru, Cristian; Quarcoo, David; Welte, Tobias; Fischer, Tanja C.; Groneberg-Kloft, Beatrix

    2009-01-01

    Background: Tobacco smoking continues to be a major preventable cause of death and disease and therefore tobacco control research is extremely important. However, research in this area is often hampered by a lack in funding and there is a need for scientometric techniques to display research efforts. Methods: The present study combines classical bibliometric tools with novel scientometric and visualizing techniques in order to analyse and categorise research in the field of tobacco control. Results: All studies related to tobacco control and listed in the ISI database since 1900 were identified by the use of defined search terms. Using bibliometric approaches, a continuous increase in qualitative markers such as collaboration numbers or citations were found for tobacco control research. The combination with density equalizing mapping revealed a distinct global pattern of research productivity and citation activity. Radar chart techniques were used to visualize bi- and multilateral research cooperation and institutional cooperation. Conclusions: The present study supplies a first scientometric approach that visualises research activity in the field of tobacco control. It provides data that can be used for funding policy and the identification of research clusters. PMID:19578464

  14. Use of density equalizing map projections (DEMP) in the analysis of childhood cancer in four California counties

    SciTech Connect

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

    1995-01-01

    In studying geographic disease distributions, one normally compares rates of arbitrarily defined geographic subareas (e.g. census tracts), thereby sacrificing the geographic detail of the original data. The sparser the data, the larger the subareas must be in order to calculate stable rates. This dilemma is avoided with the technique of Density Equalizing Map Projections (DEMP). Boundaries of geographic subregions are adjusted to equalize population density over the entire study area. Case locations plotted on the transformed map should have a uniform distribution if the underlying disease-rates are constant. On the transformed map, the statistical analysis of the observed distribution is greatly simplified. Even for sparse distributions, the statistical significance of a supposed disease cluster can be reliably calculated. The present report describes the first successful application of the DEMP technique to a sizeable ``real-world`` data set of epidemiologic interest. An improved DEMP algorithm [GUSE93, CLOS94] was applied to a data set previously analyzed with conventional techniques [SATA90, REYN91]. The results from the DEMP analysis and a conventional analysis are compared.

  15. 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.

  16. Jarzynski equality for quantum stochastic maps.

    PubMed

    Rastegin, Alexey E; Życzkowski, Karol

    2014-01-01

    Jarzynski equality and related fluctuation theorems can be formulated for various setups. Such an equality was recently derived for nonunitary quantum evolutions described by unital quantum operations, i.e., for completely positive, trace-preserving maps, which preserve the maximally mixed state. We analyze here a more general case of arbitrary quantum operations on finite systems and derive the corresponding form of the Jarzynski equality. It contains a correction term due to nonunitality of the quantum map. Bounds for the relative size of this correction term are established and they are applied for exemplary systems subjected to quantum channels acting on a finite-dimensional Hilbert space.

  17. Jarzynski equality for quantum stochastic maps

    NASA Astrophysics Data System (ADS)

    Rastegin, Alexey E.; Życzkowski, Karol

    2014-01-01

    Jarzynski equality and related fluctuation theorems can be formulated for various setups. Such an equality was recently derived for nonunitary quantum evolutions described by unital quantum operations, i.e., for completely positive, trace-preserving maps, which preserve the maximally mixed state. We analyze here a more general case of arbitrary quantum operations on finite systems and derive the corresponding form of the Jarzynski equality. It contains a correction term due to nonunitality of the quantum map. Bounds for the relative size of this correction term are established and they are applied for exemplary systems subjected to quantum channels acting on a finite-dimensional Hilbert space.

  18. New equal-area map projections for noncircular regions

    USGS Publications Warehouse

    Snyder, John P.

    1988-01-01

    A series of new equal-area map projections has been devised. Called Oblated Equal-Area, its lines of constant distortion follow approximately oval or rectangular paths instead of the circles of the Lambert Azimuthal Equal-Area projection or the straight lines of the Cylindrical Equal-Area projection. The projection series permits design of equal-area maps of oblong regions with less overall distortion of shape and scale than equal-area maps on other projections.

  19. Method for solvent extraction with near-equal density solutions

    DOEpatents

    Birdwell, Joseph F.; Randolph, John D.; Singh, S. Paul

    2001-01-01

    Disclosed is a modified centrifugal contactor for separating solutions of near equal density. The modified contactor has a pressure differential establishing means that allows the application of a pressure differential across fluid in the rotor of the contactor. The pressure differential is such that it causes the boundary between solutions of near-equal density to shift, thereby facilitating separation of the phases. Also disclosed is a method of separating solutions of near-equal density.

  20. All equal-area map projections are created equal, but some are more equal than others

    USGS Publications Warehouse

    Usery, E.L.; Seong, J.C.

    2001-01-01

    High-resolution regional and global raster databases are currently being generated for a variety of environmental and scientific modeling applications. The projection of these data from geographic coordinates to a plane coordinate system is subject to significant areal error. Sources of error include users selecting an inappropriate projection or incorrect parameters for a given projection, algorithmic errors in commercial geographic information system (GIS) software, and errors resulting from the projection of data in the raster format. To assess the latter type of errors, the accuracy of raster projection was analyzed by two methods. First, a set of 12 one-degree by one-degree quadrilaterals placed at various latitudes was projected at several raster resolutions and compared to the projection of a vector representation of the same quadrilaterals. Second, several different raster resolutions of land cover data for Asia were projected and the total areas of 21 land cover categories were tabulated and compared. While equal-area projections are designed to specifically preserve area, the comparison of the results of the one-degree by one-degree quadrilaterals with the common equal area projections (e.g., the Mollweide) indicates a considerable variance in the one-degree area after projection. Similarly, the empirical comparison of land cover areas for Asia among various projections shows that total areas of land cover vary with projection type, raster resolution, and latitude. No single projection is best for all resolutions and all latitudes. While any of the equal-area projections tested are reasonably accurate for most applications with resolutions of eight-kilometer pixels or smaller, significant variances in accuracies appear at larger pixel sizes.

  1. Map Projections and the Visual Detective: How to Tell if a Map Is Equal-Area, Conformal, or Neither

    ERIC Educational Resources Information Center

    Olson, Judy M.

    2006-01-01

    The ability to see whether a map is equal-area, conformal, or neither is useful for looking intelligently at large-area maps. For example, only if a map is equal-area can reliable judgments of relative size be made. If a map is equal-area, latitude-longitude cells are equal in size between a given pair of parallels, the cells between a given pair…

  2. 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.

  3. 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.

  4. 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.

  5. 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. PMID:26331545

  6. Maps of current density using density-functional methods

    NASA Astrophysics Data System (ADS)

    Soncini, A.; Teale, A. M.; Helgaker, T.; de Proft, F.; Tozer, D. J.

    2008-08-01

    The performance of several density-functional theory (DFT) methods for the calculation of current densities induced by a uniform magnetic field is examined. Calculations are performed using the BLYP and KT3 generalized-gradient approximations, together with the B3LYP hybrid functional. For the latter, both conventional and optimized effective potential (OEP) approaches are used. Results are also determined from coupled-cluster singles-and-doubles (CCSD) electron densities by a DFT constrained search procedure using the approach of Wu and Yang (WY). The current densities are calculated within the CTOCD-DZ2 distributed origin approach. Comparisons are made with results from Hartree-Fock (HF) theory. Several small molecules for which correlation is known to be especially important in the calculation of magnetic response properties are considered-namely, O3, CO, PN, and H2CO. As examples of aromatic and antiaromatic systems, benzene and planarized cyclooctatetraene molecules are considered, with specific attention paid to the ring current phenomenon and its Kohn-Sham orbital origin. Finally, the o-benzyne molecule is considered as a computationally challenging case. The HF and DFT induced current maps show qualitative differences, while among the DFT methods the maps show a similar qualitative structure. To assess quantitative differences in the calculated current densities with different methods, the maximal moduli of the induced current densities are compared and integration of the current densities to yield shielding constants is performed. In general, the maximal modulus is reduced in moving from HF to B3LYP and BLYP, and further reduced in moving to KT3, OEP(B3LYP), and WY(CCSD). The latter three methods offer the most accurate shielding constants in comparison with both experimental and ab initio data and hence the more reliable route to DFT calculation of induced current density in molecules.

  7. Some Equal-area, Conformal and Conventional Map Projections: A Tutorial Review

    NASA Astrophysics Data System (ADS)

    Ghaderpour, Ebrahim

    2016-09-01

    Map projections have been widely used in many areas such as geography, oceanography, meteorology, geology, geodesy, photogrammetry and global positioning systems. Understanding different types of map projections is very crucial in these areas. This paper presents a tutorial review of various types of current map projections such as equal-area, conformal and conventional. We present these map projections from a model of the Earth to a flat sheet of paper or map and derive the plotting equations for them in detail. The first fundamental form and the Gaussian fundamental quantities are defined and applied to obtain the plotting equations and distortions in length, shape and size for some of these map projections.

  8. Composite density maps for multivariate trajectories.

    PubMed

    Scheepens, Roeland; Willems, Niels; van de Wetering, Huub; Andrienko, Gennady; Andrienko, Natalia; van Wijk, Jarke J

    2011-12-01

    We consider moving objects as multivariate time-series. By visually analyzing the attributes, patterns may appear that explain why certain movements have occurred. Density maps as proposed by Scheepens et al. [25] are a way to reveal these patterns by means of aggregations of filtered subsets of trajectories. Since filtering is often not sufficient for analysts to express their domain knowledge, we propose to use expressions instead. We present a flexible architecture for density maps to enable custom, versatile exploration using multiple density fields. The flexibility comes from a script, depicted in this paper as a block diagram, which defines an advanced computation of a density field. We define six different types of blocks to create, compose, and enhance trajectories or density fields. Blocks are customized by means of expressions that allow the analyst to model domain knowledge. The versatility of our architecture is demonstrated with several maritime use cases developed with domain experts. Our approach is expected to be useful for the analysis of objects in other domains. PMID:22034373

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

    PubMed Central

    2010-01-01

    Introduction 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. Methods 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. Results 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. Conclusions 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. PMID:21176219

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

    SciTech Connect

    Miyajima, Yoji; Okubo, Satoshi; Abe, Hiroki; Okumura, Hiroki; Fujii, Toshiyuki; Onaka, Susumu; Kato, Masaharu

    2015-06-15

    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.

  11. Evaluating quantitative proton-density-mapping methods.

    PubMed

    Mezer, Aviv; Rokem, Ariel; Berman, Shai; Hastie, Trevor; Wandell, Brian A

    2016-10-01

    Quantitative magnetic resonance imaging (qMRI) aims to quantify tissue parameters by eliminating instrumental bias. We describe qMRI theory, simulations, and software designed to estimate proton density (PD), the apparent local concentration of water protons in the living human brain. First, we show that, in the absence of noise, multichannel coil data contain enough information to separate PD and coil sensitivity, a limiting instrumental bias. Second, we show that, in the presence of noise, regularization by a constraint on the relationship between T1 and PD produces accurate coil sensitivity and PD maps. The ability to measure PD quantitatively has applications in the analysis of in-vivo human brain tissue and enables multisite comparisons between individuals and across instruments. Hum Brain Mapp 37:3623-3635, 2016. © 2016 Wiley Periodicals, Inc.

  12. Evaluating quantitative proton-density-mapping methods.

    PubMed

    Mezer, Aviv; Rokem, Ariel; Berman, Shai; Hastie, Trevor; Wandell, Brian A

    2016-10-01

    Quantitative magnetic resonance imaging (qMRI) aims to quantify tissue parameters by eliminating instrumental bias. We describe qMRI theory, simulations, and software designed to estimate proton density (PD), the apparent local concentration of water protons in the living human brain. First, we show that, in the absence of noise, multichannel coil data contain enough information to separate PD and coil sensitivity, a limiting instrumental bias. Second, we show that, in the presence of noise, regularization by a constraint on the relationship between T1 and PD produces accurate coil sensitivity and PD maps. The ability to measure PD quantitatively has applications in the analysis of in-vivo human brain tissue and enables multisite comparisons between individuals and across instruments. Hum Brain Mapp 37:3623-3635, 2016. © 2016 Wiley Periodicals, Inc. PMID:27273015

  13. Intercalibration of neutral density measurements for mapping the thermosphere

    NASA Astrophysics Data System (ADS)

    Weimer, D. R.; Sutton, E. K.; Mlynczak, M. G.; Hunt, L. A.

    2016-06-01

    This paper describes a technique for mapping exospheric temperatures, derived from neutral density measurements from the Challenging Mini-satellite Payload (CHAMP) and Gravity Recovery and Climate Experiment (GRACE) satellites. The Naval Reasearch Laboratory Mass Spectrometer, Incoherent Scatter Radar Extended Model (NRLMSISE-00) thermosphere model is used for the conversion. Adjustments for each satellite were needed in order for the time-averaged densities to agree with the model. It was necessary to correct for inexact modeling of the annual and semiannual oscillations in the density, as well as the declining densities during the solar minimum. It was found that a time-varying perturbation in the atomic oxygen in the model could produce a good agreement at both altitudes. The time series of this oxygen variation was found to have a very high correlation with independent measurements of CO2 emissions measured with the Sounding of the Atmosphere using Broadband Emission Radiometry (SABER) instrument. The temperature data are averaged on a spherical grid having equal areas in each pixel, avoiding functional fits that would blur finer details. The use of solar magnetic rather than geographic coordinates enhances the auroral ovals. There are strong elevations in the exospheric temperatures in the polar regions, particularly near the dayside cusp. Spatial filtering with spherical wavelets is used to remove statistical fluctuations, although some details are lost. The exospheric temperature maps are well ordered by the nitric oxide emission measurements from SABER. The technique that is described here could be applied to future improvements of empirical density models, having an accuracy and spatial resolution that is not presently available.

  14. 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.

  15. Exact maps in density functional theory for lattice models

    NASA Astrophysics Data System (ADS)

    Dimitrov, Tanja; Appel, Heiko; Fuks, Johanna I.; Rubio, Angel

    2016-08-01

    In the present work, we employ exact diagonalization for model systems on a real-space lattice to explicitly construct the exact density-to-potential and graphically illustrate the complete exact density-to-wavefunction map that underly the Hohenberg-Kohn theorem in density functional theory. Having the explicit wavefunction-to-density map at hand, we are able to construct arbitrary observables as functionals of the ground-state density. We analyze the density-to-potential map as the distance between the fragments of a system increases and the correlation in the system grows. We observe a feature that gradually develops in the density-to-potential map as well as in the density-to-wavefunction map. This feature is inherited by arbitrary expectation values as functional of the ground-state density. We explicitly show the excited-state energies, the excited-state densities, and the correlation entropy as functionals of the ground-state density. All of them show this exact feature that sharpens as the coupling of the fragments decreases and the correlation grows. We denominate this feature as intra-system steepening and discuss how it relates to the well-known inter-system derivative discontinuity. The inter-system derivative discontinuity is an exact concept for coupled subsystems with degenerate ground state. However, the coupling between subsystems as in charge transfer processes can lift the degeneracy. An important conclusion is that for such systems with a near-degenerate ground state, the corresponding cut along the particle number N of the exact density functionals is differentiable with a well-defined gradient near integer particle number.

  16. Exact maps in density functional theory for lattice models

    NASA Astrophysics Data System (ADS)

    Dimitrov, Tanja; Appel, Heiko; Fuks, Johanna I.; Rubio, Angel

    2016-08-01

    In the present work, we employ exact diagonalization for model systems on a real-space lattice to explicitly construct the exact density-to-potential and graphically illustrate the complete exact density-to-wavefunction map that underly the Hohenberg–Kohn theorem in density functional theory. Having the explicit wavefunction-to-density map at hand, we are able to construct arbitrary observables as functionals of the ground-state density. We analyze the density-to-potential map as the distance between the fragments of a system increases and the correlation in the system grows. We observe a feature that gradually develops in the density-to-potential map as well as in the density-to-wavefunction map. This feature is inherited by arbitrary expectation values as functional of the ground-state density. We explicitly show the excited-state energies, the excited-state densities, and the correlation entropy as functionals of the ground-state density. All of them show this exact feature that sharpens as the coupling of the fragments decreases and the correlation grows. We denominate this feature as intra-system steepening and discuss how it relates to the well-known inter-system derivative discontinuity. The inter-system derivative discontinuity is an exact concept for coupled subsystems with degenerate ground state. However, the coupling between subsystems as in charge transfer processes can lift the degeneracy. An important conclusion is that for such systems with a near-degenerate ground state, the corresponding cut along the particle number N of the exact density functionals is differentiable with a well-defined gradient near integer particle number.

  17. 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.

  18. Identification of Secondary Structure Elements in Intermediate Resolution Density Maps

    PubMed Central

    Baker, Matthew L.; Ju, Tao; Chiu, Wah

    2007-01-01

    An increasing number of structural studies of large macromolecular complexes, both in X-ray crystallography and electron cryomicroscopy, have resulted in intermediate resolution (5–10 Å) structures. Despite being limited in resolution, significant structural and functional information may be extractable from these maps. To aid in the analysis and annotation of these complexes, we have developed SSEhunter, a tool for the quantitative detection of α-helices and β-sheets. Based on density skeletonization, local geometry calculations and a template-based search, SSEhunter has been tested and validated on a variety of simulated and authentic subnanometer resolution density maps. The result is a robust, user-friendly approach that allows users to quickly visualize, assess and annotate intermediate resolution density maps. Beyond secondary structure element identification, the skeletonization algorithm in SSEhunter provides secondary structure topology, potentially useful in leading to structural models of individual molecular components directly from the density. PMID:17223528

  19. Using a Mach-Zehnder interferometer to deduce nitrogen density mapping

    NASA Astrophysics Data System (ADS)

    Boudaoud, F.; Lemerini, M.

    2015-07-01

    This work presents an optical method using the Mach-Zehnder interferometer. We especially diagnose a pure nitrogen gas subjected to a point to plane corona discharge, and visualize the density spatial map. The interelectrode distance equals 6 mm and the variation of the optical path has been measured at different pressures: 220 Torr, 400 Torr, and 760 Torr. The interferograms are recorded with a CCD camera, and the numerical analysis of these interferograms is assured by the inverse Abel transformation. The nitrogen density is extracted through the Gladstone-Dale relation. The obtained results are in close agreement with values available in the literature.

  20. Analyses of Subnanometer Resolution Cryo-EM Density Maps

    PubMed Central

    Baker, Matthew L.; Baker, Mariah R.; Hryc, Corey F.; DiMaio, Frank

    2011-01-01

    Today, electron cryomicroscopy (cryo-EM) can routinely achieve subnanometer resolutions of complex macromolecular assemblies. From a density map, one can extract key structural and functional information using a variety of computational analysis tools. At subnanometer resolution, these tools make it possible to isolate individual subunits, identify secondary structures, and accurately fit atomic models. With several cryo-EM studies achieving resolutions beyond 5 Å, computational modeling and feature recognition tools have been employed to construct backbone and atomic models of the protein components directly from a density map. In this chapter, we describe several common classes of computational tools that can be used to analyze and model subnanometer resolution reconstructions from cryo-EM. A general protocol for analyzing subnanometer resolution density maps is presented along with a full description of steps used in analyzing the 4.3 Å resolution structure of Mm-cpn. PMID:20888467

  1. SNP-based high density genetic map and mapping of btwd1 dwarfing gene in barley

    PubMed Central

    Ren, Xifeng; Wang, Jibin; Liu, Lipan; Sun, Genlou; Li, Chengdao; Luo, Hong; Sun, Dongfa

    2016-01-01

    A high-density linkage map is a valuable tool for functional genomics and breeding. A newly developed sequence-based marker technology, restriction site associated DNA (RAD) sequencing, has been proven to be powerful for the rapid discovery and genotyping of genome-wide single nucleotide polymorphism (SNP) markers and for the high-density genetic map construction. The objective of this research was to construct a high-density genetic map of barley using RAD sequencing. 1894 high-quality SNP markers were developed and mapped onto all seven chromosomes together with 68 SSR markers. These 1962 markers constituted a total genetic length of 1375.8 cM and an average of 0.7 cM between adjacent loci. The number of markers within each linkage group ranged from 209 to 396. The new recessive dwarfing gene btwd1 in Huaai 11 was mapped onto the high density linkage maps. The result showed that the btwd1 is positioned between SNP marks 7HL_6335336 and 7_249275418 with a genetic distance of 0.9 cM and 0.7 cM on chromosome 7H, respectively. The SNP-based high-density genetic map developed and the dwarfing gene btwd1 mapped in this study provide critical information for position cloning of the btwd1 gene and molecular breeding of barley. PMID:27530597

  2. SNP-based high density genetic map and mapping of btwd1 dwarfing gene in barley.

    PubMed

    Ren, Xifeng; Wang, Jibin; Liu, Lipan; Sun, Genlou; Li, Chengdao; Luo, Hong; Sun, Dongfa

    2016-01-01

    A high-density linkage map is a valuable tool for functional genomics and breeding. A newly developed sequence-based marker technology, restriction site associated DNA (RAD) sequencing, has been proven to be powerful for the rapid discovery and genotyping of genome-wide single nucleotide polymorphism (SNP) markers and for the high-density genetic map construction. The objective of this research was to construct a high-density genetic map of barley using RAD sequencing. 1894 high-quality SNP markers were developed and mapped onto all seven chromosomes together with 68 SSR markers. These 1962 markers constituted a total genetic length of 1375.8 cM and an average of 0.7 cM between adjacent loci. The number of markers within each linkage group ranged from 209 to 396. The new recessive dwarfing gene btwd1 in Huaai 11 was mapped onto the high density linkage maps. The result showed that the btwd1 is positioned between SNP marks 7HL_6335336 and 7_249275418 with a genetic distance of 0.9 cM and 0.7 cM on chromosome 7H, respectively. The SNP-based high-density genetic map developed and the dwarfing gene btwd1 mapped in this study provide critical information for position cloning of the btwd1 gene and molecular breeding of barley.

  3. SNP-based high density genetic map and mapping of btwd1 dwarfing gene in barley.

    PubMed

    Ren, Xifeng; Wang, Jibin; Liu, Lipan; Sun, Genlou; Li, Chengdao; Luo, Hong; Sun, Dongfa

    2016-01-01

    A high-density linkage map is a valuable tool for functional genomics and breeding. A newly developed sequence-based marker technology, restriction site associated DNA (RAD) sequencing, has been proven to be powerful for the rapid discovery and genotyping of genome-wide single nucleotide polymorphism (SNP) markers and for the high-density genetic map construction. The objective of this research was to construct a high-density genetic map of barley using RAD sequencing. 1894 high-quality SNP markers were developed and mapped onto all seven chromosomes together with 68 SSR markers. These 1962 markers constituted a total genetic length of 1375.8 cM and an average of 0.7 cM between adjacent loci. The number of markers within each linkage group ranged from 209 to 396. The new recessive dwarfing gene btwd1 in Huaai 11 was mapped onto the high density linkage maps. The result showed that the btwd1 is positioned between SNP marks 7HL_6335336 and 7_249275418 with a genetic distance of 0.9 cM and 0.7 cM on chromosome 7H, respectively. The SNP-based high-density genetic map developed and the dwarfing gene btwd1 mapped in this study provide critical information for position cloning of the btwd1 gene and molecular breeding of barley. PMID:27530597

  4. Helicity-Density And Normalized-Helicity Maps Of Flows

    NASA Technical Reports Server (NTRS)

    Degani, David; Levy, Yuval; Seginer, Arnan

    1991-01-01

    Maps of helicity density and normalized helicity useful as graphical representations of important features of three-dimensional flow fields containg vortexes. Emphasize complicated and important parts of flow field, identify vortexes, differentiate between primary and secondary vortexes, indicate sense of swirling motion, locate free singular points, and trace vortex-core streamlines emanating from these points.

  5. ESammon: A Computationaly Enhanced Sammon Mapping based on Data Density

    PubMed Central

    Wang, Chanpaul Jin; Fang, Hua; Wang, Honggang

    2016-01-01

    Sammon mapping is a widely used visualization technique to display complex data from high- to low-dimensional space. However, its extensive computational cost may pose potential computational challenges to big data visualization. This paper proposes a computationally-enhanced Sammon mapping (ESammon) by leveraging the characteristics of spatial data density. Unlike the conventional Sammon, ESammon preserves critical pairwise distances between data points in the process of projection, instead of all distances. Specifically, we integrated the Directed-Acyclic-Graph (DAG) based data density characterization method to select the critical distances. The numerical results demonstrated that our ESammon can achieve comparable projection results as the conventional Sammon mapping while reducing the computational cost from O(N2) to O(N).

  6. Characterizing Uncertainty in High-Density Maps from Multiparental Populations

    PubMed Central

    Ahfock, Daniel; Wood, Ian; Stephen, Stuart; Cavanagh, Colin R.

    2014-01-01

    Multiparental populations are of considerable interest in high-density genetic mapping due to their increased levels of polymorphism and recombination relative to biparental populations. However, errors in map construction can have significant impact on QTL discovery in later stages of analysis, and few methods have been developed to quantify the uncertainty attached to the reported order of markers or intermarker distances. Current methods are computationally intensive or limited to assessing uncertainty only for order or distance, but not both simultaneously. We derive the asymptotic joint distribution of maximum composite likelihood estimators for intermarker distances. This approach allows us to construct hypothesis tests and confidence intervals for simultaneously assessing marker-order instability and distance uncertainty. We investigate the effects of marker density, population size, and founder distribution patterns on map confidence in multiparental populations through simulations. Using these data, we provide guidelines on sample sizes necessary to map markers at sub-centimorgan densities with high certainty. We apply these approaches to data from a bread wheat Multiparent Advanced Generation Inter-Cross (MAGIC) population genotyped using the Illumina 9K SNP chip to assess regions of uncertainty and validate them against the recently released pseudomolecule for the wheat chromosome 3B. PMID:25236453

  7. Correlation of peripheral innervation density and dorsal horn map scale.

    PubMed

    Wang, L; Millecchia, R; Brown, P B

    1997-08-01

    Dorsal horn map scale and peripheral innervation density were compared to test a hypothesized linear relationship. In anesthetized cats, low-threshold mechanoreceptive peripheral nerve innervation fields (IFs) were measured by outlining areas of skin from which action potentials could be elicited in cutaneous nerves. The same nerves were processed histologically and used to count myelinated axons. Innervation density for each nerve was calculated as number of axons divided by IF area. Single units were recorded throughout the hindlimb representation, in laminae III and IV. These data, combined with single-unit data from other animals and with cell counts in laminae III and IV, permitted estimation of numbers of cells whose receptive field centers fell in contiguous 1-cm bands from tips of toes to proximal thigh. A similar estimate was performed with the use of the nerve innervation data, so that peripheral innervation densities and map scales for the different 1-cm bands of skin could be compared. Correlation between the two was quite high (r = 0.8), and highly significant (P = 2.5 x 10(-7)). These results are consistent with a proposed developmental model in which map scale, peripheral innervation density, and reciprocal of dorsal horn cell receptive field size are mutually proportional, as a result of developmental mechanisms that produce constant divergence and convergence between primary afferent axons and dorsal horn cells. PMID:9307105

  8. 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

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

    PubMed

    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

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

    PubMed

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

    2016-06-27

    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.

  11. Selective mapping: a strategy for optimizing the construction of high-density linkage maps.

    PubMed Central

    Vision, T J; Brown, D G; Shmoys, D B; Durrett, R T; Tanksley, S D

    2000-01-01

    Historically, linkage mapping populations have consisted of large, randomly selected samples of progeny from a given pedigree or cell lines from a panel of radiation hybrids. We demonstrate that, to construct a map with high genome-wide marker density, it is neither necessary nor desirable to genotype all markers in every individual of a large mapping population. Instead, a reduced sample of individuals bearing complementary recombinational or radiation-induced breakpoints may be selected for genotyping subsequent markers from a large, but sparsely genotyped, mapping population. Choosing such a sample can be reduced to a discrete stochastic optimization problem for which the goal is a sample with breakpoints spaced evenly throughout the genome. We have developed several different methods for selecting such samples and have evaluated their performance on simulated and actual mapping populations, including the Lister and Dean Arabidopsis thaliana recombinant inbred population and the GeneBridge 4 human radiation hybrid panel. Our methods quickly and consistently find much-reduced samples with map resolution approaching that of the larger populations from which they are derived. This approach, which we have termed selective mapping, can facilitate the production of high-quality, high-density genome-wide linkage maps. PMID:10790413

  12. Ligand identification using electron-density map correlations

    SciTech Connect

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

    2007-01-01

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

  13. 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.

  14. Modeling Protein Structures Based on Density Maps at Intermediate Resolutions

    NASA Astrophysics Data System (ADS)

    Ma, Jianpeng

    Structural biology is now in a special era in which increasingly more complex biomolecules are being studied. For many of them, only low- or intermediateresolution density maps (6-10 Å) can be obtained by, for instance, electron cryomicroscopy (cryo-EM) (Bottcher et al., 1997; Conway et al., 1997; DeRosier and Harrison, 1997; Kuhn et al., 2002; Li et al., 2002; Mancini et al., 2000; Zhang et al., 2000; Zhou et al., 2000, 2001a,b). In certain cases, analysis in terms of intermediateresolution density maps is also inevitable in X-ray crystallography as exemplified in the lengthy process of structural determination of the 50S ribosomal subunit that incremented from 9 Å, 5 Å, to 2.4 Å (Ban et al., 1998, 1999, 2000). As a common feature in all these cases, it is usually impossible, with conventional methods, to construct reasonably accurate atomic models from density maps. However, for the purpose of structural analysis, it would still be very helpful if one can build some kind of pseudo-atomic models from the density maps because this will not only facilitate the structural determination to higher resolutions, but also assist further biochemical studies and functional interpretation. For example, significant insights into the architecture and organization of proteins can often be learned if one can roughly locate the major secondary structural elements such as α-helices and β-sheets. This rationale is supported by the fact that the knowledge of protein folds can be obtained primarily from the spatial arrangement of the secondary structural elements independent of the sequence identity of the proteins, as different sequences can have the same fold.

  15. Statistical quality indicators for electron-density maps

    SciTech Connect

    Tickle, Ian J.

    2012-04-01

    A likelihood-based metric for scoring the local agreement of a structure model with the observed electron density is described. The commonly used validation metrics for the local agreement of a structure model with the observed electron density, namely the real-space R (RSR) and the real-space correlation coefficient (RSCC), are reviewed. It is argued that the primary goal of all validation techniques is to verify the accuracy of the model, since precision is an inherent property of the crystal and the data. It is demonstrated that the principal weakness of both of the above metrics is their inability to distinguish the accuracy of the model from its precision. Furthermore, neither of these metrics in their usual implementation indicate the statistical significance of the result. The statistical properties of electron-density maps are reviewed and an improved alternative likelihood-based metric is suggested. This leads naturally to a χ{sup 2} significance test of the difference density using the real-space difference density Z score (RSZD). This is a metric purely of the local model accuracy, as required for effective model validation and structure optimization by practising crystallographers prior to submission of a structure model to the PDB. A new real-space observed density Z score (RSZO) is also proposed; this is a metric purely of the model precision, as a substitute for other precision metrics such as the B factor.

  16. Energy density in small systems equal to the one in heavy-ion collisions

    NASA Astrophysics Data System (ADS)

    Paić, G.; Cuautle, E.

    2016-07-01

    The recent developments in the study of quark-gluon matter at high densities have shown that there are many similarities between the behavior of the observables in light and heavy systems, especially when the light systems are observed at high multiplicities. Contrary to what was previously thought, the small systems do exhibit collective effects that could indicate that small droplets of strongly interacting quark-gluon plasma are possible. The results infer that the energy densities can be computed in light systems in the same way as in heavy systems and hence, the energy density should be considered when comparing systems with different sizes. We review some of the aspects as well as the existing main models and the way to disentangle them using experimental data.

  17. Statistical quality indicators for electron-density maps.

    PubMed

    Tickle, Ian J

    2012-04-01

    The commonly used validation metrics for the local agreement of a structure model with the observed electron density, namely the real-space R (RSR) and the real-space correlation coefficient (RSCC), are reviewed. It is argued that the primary goal of all validation techniques is to verify the accuracy of the model, since precision is an inherent property of the crystal and the data. It is demonstrated that the principal weakness of both of the above metrics is their inability to distinguish the accuracy of the model from its precision. Furthermore, neither of these metrics in their usual implementation indicate the statistical significance of the result. The statistical properties of electron-density maps are reviewed and an improved alternative likelihood-based metric is suggested. This leads naturally to a χ(2) significance test of the difference density using the real-space difference density Z score (RSZD). This is a metric purely of the local model accuracy, as required for effective model validation and structure optimization by practising crystallographers prior to submission of a structure model to the PDB. A new real-space observed density Z score (RSZO) is also proposed; this is a metric purely of the model precision, as a substitute for other precision metrics such as the B factor.

  18. 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.

  19. Mapping Densities in Analogue Laboratory Turbulent Plumes Using Dye Concentration

    NASA Astrophysics Data System (ADS)

    Fisher, M. A.; Kobs-Nawotniak, S. E.

    2014-12-01

    Changing tephra concentration in volcanic eruption columns is difficult to measure in the field due to fluid opacity. The bulk fluid erupted may be higher density than the surrounding atmosphere at the vent and then transition to positive buoyancy through the ingestion and heating of ambient air; thus, the concentration of the plume fluid as it rises is critical to determining whether the material rises in a sustained plume or collapses into a pyroclastic density current. We evaluate the changing concentration of an analogue plume via tracer dye intensity and relate it to plume radius expansion and vent distance. To calibrate our concentration metric, we calculated the density and dye concentration of pre-determined tracer-water mixtures. The density of the solution was directly measured using a micropipette and high precision balance. The calculated density falls within the standard error of the measured density for each step. Five photographs were taken of each concentration using a mounted Ex-FH100 digital camera with identical lighting. Using a MATLAB script, the RGB (Red-Green-Blue) color value was extracted from five pixels located at the same coordinates in each image, confirming that there was no inherent error caused by the camera and that the RGB value was the same across an entire image. We created a color map to convert from the RGB color value of a pixel in an image to its corresponding concentration. This method algorithm can then be applied to an analogue volcanic tank model, using the color variations in the plume eddies to determine the tracer concentration, and thereby density distribution, in the plume.

  20. Density mapping and chemical component calibration development of four-component compacts via terahertz pulsed imaging.

    PubMed

    Palermo, Ryanne; Cogdill, Robert P; Short, Steven M; Drennen, James K; Taday, Philip F

    2008-01-01

    The purpose of this research was to investigate suitable procedures for generating multivariate prediction vectors for quantitative composition and density analysis of intact solid oral dosage forms using terahertz pulsed imaging (TPI) spectroscopy. Both frequency- (absorbance and refractive index) and time-domain data are presented. A set of calibration and prediction samples were created according to a quaternary mixture design with five levels of compaction at each concentration design point. Calibration models were generated by partial least-squares, type II (PLS-2) regression of the TPI spectra against nominal composition and relative density reference measurements. Quantitative frequency-domain composition calibration models were created for all crystalline components (R(2)>0.90), but the calibration models for individual amorphous components (R(2)<0.76) did not perform as well in testing. Combining both amorphous components into a single component variable for regression resulted in lower error statistics and equally good predictions of crystalline components. A non-linear attenuation of time-domain spectra was observed as a function of compaction force, which corresponded to compact density predictions (R(2)=0.948). While refractive index spectra were sensitive to density (R(2)=0.937), the absorbance spectra were not. Surface density maps were prepared based on refractive index calibrations.

  1. Density mapping and chemical component calibration development of four-component compacts via terahertz pulsed imaging.

    PubMed

    Palermo, Ryanne; Cogdill, Robert P; Short, Steven M; Drennen, James K; Taday, Philip F

    2008-01-01

    The purpose of this research was to investigate suitable procedures for generating multivariate prediction vectors for quantitative composition and density analysis of intact solid oral dosage forms using terahertz pulsed imaging (TPI) spectroscopy. Both frequency- (absorbance and refractive index) and time-domain data are presented. A set of calibration and prediction samples were created according to a quaternary mixture design with five levels of compaction at each concentration design point. Calibration models were generated by partial least-squares, type II (PLS-2) regression of the TPI spectra against nominal composition and relative density reference measurements. Quantitative frequency-domain composition calibration models were created for all crystalline components (R(2)>0.90), but the calibration models for individual amorphous components (R(2)<0.76) did not perform as well in testing. Combining both amorphous components into a single component variable for regression resulted in lower error statistics and equally good predictions of crystalline components. A non-linear attenuation of time-domain spectra was observed as a function of compaction force, which corresponded to compact density predictions (R(2)=0.948). While refractive index spectra were sensitive to density (R(2)=0.937), the absorbance spectra were not. Surface density maps were prepared based on refractive index calibrations. PMID:18053671

  2. Mapping surface charge density with a scanning nanopipette

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    Characterisation of the surface charge density (SCD) is important in interface and colloid science, and especially local variations in SCD of biological samples are of keen interest. The surface charge of lipid bilayers governs the uptake of charged particles and guides cell-cell interactions. As the electrostatic potential is screened by high physiological salt concentrations, direct probing of the potential can only be performed at a sub nanometer distance; therefore it was impossible to directly measure the SCD under physiological conditions. Yet the charged surface attracts counter ions leading to an enhanced ionic concentration near the surface, creating a measurable surface conductivity. In this study we measure SCD using a scanning ion-conductance microscope (SICM) setup, where the electrolyte current through a nanopipette is monitored as the pipette is positioned in the vicinity of the sample. We investigate the current dependency of SCD and pipette potential using numerical solutions to Poisson and Nernst-Planck equations and characterise a complex system governed by a multitude of factors such as pipette size, geometry and charge. We then propose an imaging method and prove its feasibility by mapping the surface charge density of phase separated lipid bilayers.

  3. Construction and Analysis of High-Density Linkage Map Using High-Throughput Sequencing Data

    PubMed Central

    Liu, Min; Liu, Hui; Zeng, Huaping; Deng, Dejing; Xin, Huaigen; Song, Jun; Xu, Chunhua; Sun, Xiaowen; Hou, Xilin; Wang, Xiaowu; Zheng, Hongkun

    2014-01-01

    Linkage maps enable the study of important biological questions. The construction of high-density linkage maps appears more feasible since the advent of next-generation sequencing (NGS), which eases SNP discovery and high-throughput genotyping of large population. However, the marker number explosion and genotyping errors from NGS data challenge the computational efficiency and linkage map quality of linkage study methods. Here we report the HighMap method for constructing high-density linkage maps from NGS data. HighMap employs an iterative ordering and error correction strategy based on a k-nearest neighbor algorithm and a Monte Carlo multipoint maximum likelihood algorithm. Simulation study shows HighMap can create a linkage map with three times as many markers as ordering-only methods while offering more accurate marker orders and stable genetic distances. Using HighMap, we constructed a common carp linkage map with 10,004 markers. The singleton rate was less than one-ninth of that generated by JoinMap4.1. Its total map distance was 5,908 cM, consistent with reports on low-density maps. HighMap is an efficient method for constructing high-density, high-quality linkage maps from high-throughput population NGS data. It will facilitate genome assembling, comparative genomic analysis, and QTL studies. HighMap is available at http://highmap.biomarker.com.cn/. PMID:24905985

  4. 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

  5. Optical mapping of fluid density interfaces: Concepts and implementations

    NASA Astrophysics Data System (ADS)

    Zhang, X.; Dabiri, D.; Gharib, M.

    1996-05-01

    Several ideas of color encoding for surface slope measurements are systematically explored and reviewed to develop a new set of fundamental concepts. It is shown that different systems, such as shadowgraphs, Schlieren optics, and our water surface gradient detectors, can also be universally described through the concepts of sun glitter functions, incident light-source encoding, and observer encoding. These concepts provide a more precise way of mathematically formulating and physically interpreting the flow visualization images, thereby providing quantitative results. It is this new system of concepts that uncover the quantitative potential of these optical methods. The measurement abilities of various existing optical systems are thus enhanced from qualitative observation or visualization to the well-defined quantitative measurement. This is a critical step forward. The concepts can also be further extended to measure fluid flows with multiple density layers or flows with continuous density variations. As an example of implementation, the method of measuring a water-surface gradient is extended into a reflective approach of detecting small changes of surface slope at an air-water interface. In this process, fluid surface slopes (surface gradients) are first optically mapped into color space. An array of lenses is used to transform the rays of an optical light source into a series of colored parallel light beams by passing the light through a group of two-dimensional color palettes at the focal planes of the lens array. This system of parallel light beams is used to illuminate a free surface of water. The reflected rays from the free surface are captured by a charge-coupled device color camera located above the surface. The slopes are derived from the color images after the calibration, and surface elevations are obtained by integrating the slopes. This technique is then applied to observe free-surface deformations caused by near-surface turbulence interacting with

  6. 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.

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

    PubMed Central

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

    2016-01-01

    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. PMID:26744365

  8. Task switching: a high-density electrical mapping study.

    PubMed

    Wylie, G R; Javitt, D C; Foxe, J J

    2003-12-01

    Flexibly switching between tasks is one of the paradigmatic functions of so-called "executive control" processes. Neuroimaging studies have implicated both prefrontal and parietal cortical regions in the processing necessary to effectively switch task. Beyond their general involvement in this critical function, however, little is known about the dynamics of processing across frontal and parietal regions. For instance, it remains to be determined to what extent these areas play a role in preparing to switch task before arrival of the stimulus to be acted upon and to what extent they play a role in any switching processes that occur after the stimulus is presented. Here, we used the excellent temporal resolution afforded by high-density mapping of brain potentials to explore the time course of the processes underlying (1) the performance of and (2) the preparation for a switch of task. We detail the contributions of both frontal and parietal processes to these two aspects of the task-switching process. Our data revealed a complex pattern of effects. Most striking was a period of sustained activity over bilateral parietal regions preceding the switch trial. Over frontal regions, activity actually decreased during this same period. Strongest sustained frontal activity was in fact seen for trials on which no switch was required. Further, we find that the first differential activity associated with switching task was over posterior parietal areas (220 ms), whereas over frontal scalp, the first differential activity is found more than 200 ms later. These and other effects are interpreted in terms of a "competition" model in which preparing to switch task is understood as the beginning of a competition between the potentially relevant tasks that is resolved during the switch trial. Our findings are difficult to account for with models that posit a strong role for frontal cortical regions in "reconfiguring" the system during switches of task.

  9. 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.

  10. 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

  11. The mapping of electronic energy distributions using experimental electron density.

    PubMed

    Tsirelson, Vladimir G

    2002-08-01

    It is demonstrated that the approximate kinetic energy density calculated using the second-order gradient expansion with parameters of the multipole model fitted to experimental structure factors reproduces the main features of this quantity in a molecular or crystal position space. The use of the local virial theorem provides an appropriate derivation of approximate potential energy density and electronic energy density from the experimental (model) electron density and its derivatives. Consideration of these functions is not restricted by the critical points in the electron density and provides a comprehensive characterization of bonding in molecules and crystals.

  12. The mapping of electronic energy distributions using experimental electron density.

    PubMed

    Tsirelson, Vladimir G

    2002-08-01

    It is demonstrated that the approximate kinetic energy density calculated using the second-order gradient expansion with parameters of the multipole model fitted to experimental structure factors reproduces the main features of this quantity in a molecular or crystal position space. The use of the local virial theorem provides an appropriate derivation of approximate potential energy density and electronic energy density from the experimental (model) electron density and its derivatives. Consideration of these functions is not restricted by the critical points in the electron density and provides a comprehensive characterization of bonding in molecules and crystals. PMID:12149553

  13. 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.

  14. Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Sea Cucumber Apostichopus japonicus.

    PubMed

    Tian, Meilin; Li, Yangping; Jing, Jing; Mu, Chuang; Du, Huixia; Dou, Jinzhuang; Mao, Junxia; Li, Xue; Jiao, Wenqian; Wang, Yangfan; Hu, Xiaoli; Wang, Shi; Wang, Ruijia; Bao, Zhenmin

    2015-10-06

    Genetic linkage maps are critical and indispensable tools in a wide range of genetic and genomic research. With the advancement of genotyping-by-sequencing (GBS) methods, the construction of a high-density and high-resolution linkage maps has become achievable in marine organisms lacking sufficient genomic resources, such as echinoderms. In this study, high-density, high-resolution genetic map was constructed for a sea cucumber species, Apostichopus japonicus, utilizing the 2b-restriction site-associated DNA (2b-RAD) method. A total of 7839 markers were anchored to the linkage map with the map coverage of 99.57%, to our knowledge, this is the highest marker density among echinoderm species. QTL mapping and association analysis consistently captured one growth-related QTL located in a 5 cM region of linkage group (LG) 5. An annotated candidate gene, retinoblastoma-binding protein 5 (RbBP5), which has been reported to be an important regulator of cell proliferation, was recognized in the QTL region. This linkage map represents a powerful tool for research involving both fine-scale QTL mapping and marker assisted selection (MAS), and will facilitate chromosome assignment and improve the whole-genome assembly of sea cucumber in the future.

  15. Ligand identification using electron-density map correlations.

    PubMed

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

    2007-01-01

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

  16. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  18. Low-density geochemical mapping and the robustness of geochemical patterns

    USGS Publications Warehouse

    Smith, D.B.; Reimann, C.

    2008-01-01

    Geochemical mapping of entire continents and, ultimately, the world is still a challenge for applied geochemists. At sample densities traditionally used for geochemical exploration (1 site per 1-25 km2), geochemical mapping of whole continents is logistically extremely demanding and tremendously expensive. The first low-density geochemical surveys (1 site per 200 km2) were carried out during the late 1960s in Africa. Later surveys conducted in various parts of the world had sample densities ranging from 1 site per 300 km2 to 1 site per 18 000 km2. Although these surveys were deemed successful by the investigators in defining variations in background element content on a regional scale, the scientific community was sceptical that low-density geochemical mapping was possible and would provide useful information. The main area of criticism centred around the concern that at such low sample densities the resulting maps would not be robust, i.e. if the same area were resampled and remapped, different geochemical patterns would emerge. Different examples from the USA, Europe, China and Africa demonstrate that low-density geochemical mapping will result in stable and robust geochemical patterns at the continental scale. Such maps are urgently needed for a wide variety of applications. ?? 2008 AAG/ Geological Society of London.

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

    PubMed

    Ao, Jingqun; Li, Jia; You, Xinxin; Mu, Yinnan; Ding, Yang; Mao, Kaiqiong; Bian, Chao; Mu, Pengfei; Shi, Qiong; Chen, Xinhua

    2015-11-03

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

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

    PubMed Central

    Ao, Jingqun; Li, Jia; You, Xinxin; Mu, Yinnan; Ding, Yang; Mao, Kaiqiong; Bian, Chao; Mu, Pengfei; Shi, Qiong; Chen, Xinhua

    2015-01-01

    High-density genetic maps are essential for genome assembly, comparative genomic analysis and fine mapping of complex traits. In this study, 31,191 single nucleotide polymorphisms (SNPs) evenly distributed across the large yellow croaker (Larimichthys crocea) genome were identified using restriction-site associated DNA sequencing (RAD-seq). Among them, 10,150 high-confidence SNPs were assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 5451.3 cM with an average distance of 0.54 cM between loci. This represents the densest genetic map currently reported for large yellow croaker. Using 2889 SNPs to target specific scaffolds, we assigned 533 scaffolds, comprising 421.44 Mb (62.04%) of the large yellow croaker assembled sequence, to the 24 linkage groups. The mapped assembly scaffolds in large yellow croaker were used for genome synteny analyses against the stickleback (Gasterosteus aculeatus) and medaka (Oryzias latipes). Greater synteny was observed between large yellow croaker and stickleback. This supports the hypothesis that large yellow croaker is more closely related to stickleback than to medaka. Moreover, 1274 immunity-related genes and 195 hypoxia-related genes were mapped to the 24 chromosomes of large yellow croaker. The integration of the high-resolution genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits in large yellow croaker. PMID:26540048

  1. GIS for mapping waterfowl density and distribution from aerial surveys

    USGS Publications Warehouse

    Butler, W.I.; Stehn, R.A.; Balogh, G.R.

    1995-01-01

    We modified standard aerial survey data collection to obtain the geographic location for each waterfowl observation on surveys in Alaska during 1987-1993. Using transect navigation with CPS (global positioning system), data recording on continuously running tapes, and a computer data input program, we located observations with an average deviation along transects of 214 m. The method provided flexibility in survey design and data analysis. Although developed for geese nesting near the coast of the Yukon-Kuskokwim Delta, the methods are widely applicable and were used on other waterfowl surveys in Alaska to map distribution and relative abundance of waterfowl. Accurate location data with GIS analysis and display may improve precision and usefulness of data from any aerial transect survey.

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

    PubMed

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

    2007-04-01

    A microsatellite or simple sequence repeat (SSR) consensus map of barley was constructed by joining six independent genetic maps based on the mapping populations 'Igri x Franka', 'Steptoe x Morex', 'OWB(Rec) x OWB(Dom)', 'Lina x Canada Park', 'L94 x Vada' and 'SusPtrit x Vada'. Segregation data for microsatellite markers from different research groups including SCRI (Bmac, Bmag, EBmac, EBmag, HVGeneName, scsssr), IPK (GBM, GBMS), WUR (GBM), Virginia Polytechnic Institute (HVM), and MPI for Plant Breeding (HVGeneName), generated in above mapping populations, were used in the computer program RECORD to order the markers of the individual linkage data sets. Subsequently, a framework map was constructed for each chromosome by integrating the 496 "bridge markers" common to two or more individual maps with the help of the computer programme JoinMap 3.0. The final map was calculated by following a "neighbours" map approach. The integrated map contained 775 unique microsatellite loci, from 688 primer pairs, ranging from 93 (6H) to 132 (2H) and with an average of 111 markers per linkage group. The genomic DNA-derived SSR marker loci had a higher polymorphism information content value (average 0.61) as compared to the EST/gene-derived SSR loci (average 0.48). The consensus map spans 1,068 cM providing an average density of one SSR marker every 1.38 cM. Such a high-density consensus SSR map provides barley molecular breeding programmes with a better choice regarding the quality of markers and a higher probability of polymorphic markers in an important chromosomal interval. This map also offers the possibilities of thorough alignment for the (future) physical map and implementation in haplotype diversity studies of barley. PMID:17345060

  3. Density-potential mapping in time-dependent density-functional theory

    SciTech Connect

    Maitra, N. T.; Todorov, T. N.; Woodward, C.; Burke, K.

    2010-04-15

    The key questions of uniqueness and existence in time-dependent density-functional theory are usually formulated only for potentials and densities that are analytic in time. Simple examples, standard in quantum mechanics, lead, however, to nonanalyticities. We reformulate these questions in terms of a nonlinear Schroedinger equation with a potential that depends nonlocally on the wave function.

  4. YUP.SCX: coaxing atomic models into medium resolution electron density maps.

    PubMed

    Tan, Robert K-Z; Devkota, Batsal; Harvey, Stephen C

    2008-08-01

    The structures of large macromolecular complexes in different functional states can be determined by cryo-electron microscopy, which yields electron density maps of low to intermediate resolutions. The maps can be combined with high-resolution atomic structures of components of the complex, to produce a model for the complex that is more accurate than the formal resolution of the map. To this end, methods have been developed to dock atomic models into density maps rigidly or flexibly, and to refine a docked model so as to optimize the fit of the atomic model into the map. We have developed a new refinement method called YUP.SCX. The electron density map is converted into a component of the potential energy function to which terms for stereochemical restraints and volume exclusion are added. The potential energy function is then minimized (using simulated annealing) to yield a stereochemically-restrained atomic structure that fits into the electron density map optimally. We used this procedure to construct an atomic model of the 70S ribosome in the pre-accommodation state. Although some atoms are displaced by as much as 33A, they divide themselves into nearly rigid fragments along natural boundaries with smooth transitions between the fragments.

  5. Identifying Components in 3D Density Maps of Protein Nanomachines by Multi-scale Segmentation.

    PubMed

    Pintilie, Grigore; Zhang, Junjie; Chiu, Wah; Gossard, David

    2009-04-01

    Segmentation of density maps obtained using cryo-electron microscopy (cryo-EM) is a challenging task, and is typically accomplished by time-intensive interactive methods. The goal of segmentation is to identify the regions inside the density map that correspond to individual components. We present a multi-scale segmentation method for accomplishing this task that requires very little user interaction. The method uses the concept of scale space, which is created by convolution of the input density map with a Gaussian filter. The latter process smoothes the density map. The standard deviation of the Gaussian filter is varied, with smaller values corresponding to finer scales and larger values to coarser scales. Each of the maps at different scales is segmented using the watershed method, which is very efficient, completely automatic, and does not require the specification of seed points. Some detail is lost in the smoothing process. A sharpening process reintroduces detail into the segmentation at the coarsest scale by using the segmentations at the finer scales. We apply the method to simulated density maps, where the exact segmentation (or ground truth) is known, and rigorously evaluate the accuracy of the resulting segmentations.

  6. Extending stellar density maps of the Orphan Tidal Stream

    NASA Astrophysics Data System (ADS)

    Varilly, Taylor; Carlin, J. L.; Newberg, H. J.; Beaton, R.; Majewski, S. R.

    2014-01-01

    This project involves analyzing data directly off the footprint of the Sloan Digital Sky Survey in order to find the progenitor of the Orphan tidal stream. This stream of stellar debris, known to span distances 20 to 47 kpc from the Sun, is believed to be the remnants of a small dwarf galaxy that is largely disrupted. Images were obtained in the vicinity of this stream from the MOSAIC1.1 camera on the 4-meter Mayall telescope at the Kitt Peak National Observatory. The region observed covers 11 square degrees of sky, approximately 7 square degrees of which have no SDSS data. The area outside the SDSS was selected to explore the increase in density of Orphan stars in this location, discussed in Newberg et al. 2010. The positions and magnitudes of stars outside of the SDSS were calculated and calibrated with both data from the SDSS itself, as well as the USNOB-1 catalog. The resulting Orphan candidates selected from this catalog were used to explore the stellar densities along this stream, providing insight into the nature of its progenitor. This research was supported by NSF grant AST 09-37523.

  7. Construction of a high-density genetic map and QTL mapping for pearl quality-related traits in Hyriopsis cumingii

    PubMed Central

    Bai, Zhi-Yi; Han, Xue-Kai; Liu, Xiao-Jun; Li, Qing-Qing; Li, Jia-Le

    2016-01-01

    A high-density genetic map is essential for quantitative trait locus (QTL) fine mapping. In this study, 4,508 effective single nucleotide polymorphism markers (detected using specific-locus amplified fragment sequencing) and 475 microsatellites were mapped to 19 linkage groups (LGs) using a family with 157 individuals. The map spanned 2,713 cM, with an average of 259 markers and 79 loci per LG and an average inter-marker distance of 1.81 cM. To identify QTLs for pearl quality traits, 26 putatively significant QTLs were detected for 10 traits, including, three for shell width, seven for body weight, two for shell weight, two for margin mantle weight, five for inner mantle weight, and seven for shell nacre colour. Among them, five QTLs associated with shell nacre colour were mapped to LG17 and explained 19.7% to 22.8% of the trait variation; this suggests that some important genes or loci determine shell nacre colour in LG17. The linkage map and mapped QTLs for shell nacre colour would be useful for improving the quality of Hyriopsis cumingii via marker-assisted selection. PMID:27587236

  8. Construction of a high-density genetic map and QTL mapping for pearl quality-related traits in Hyriopsis cumingii.

    PubMed

    Bai, Zhi-Yi; Han, Xue-Kai; Liu, Xiao-Jun; Li, Qing-Qing; Li, Jia-Le

    2016-01-01

    A high-density genetic map is essential for quantitative trait locus (QTL) fine mapping. In this study, 4,508 effective single nucleotide polymorphism markers (detected using specific-locus amplified fragment sequencing) and 475 microsatellites were mapped to 19 linkage groups (LGs) using a family with 157 individuals. The map spanned 2,713 cM, with an average of 259 markers and 79 loci per LG and an average inter-marker distance of 1.81 cM. To identify QTLs for pearl quality traits, 26 putatively significant QTLs were detected for 10 traits, including, three for shell width, seven for body weight, two for shell weight, two for margin mantle weight, five for inner mantle weight, and seven for shell nacre colour. Among them, five QTLs associated with shell nacre colour were mapped to LG17 and explained 19.7% to 22.8% of the trait variation; this suggests that some important genes or loci determine shell nacre colour in LG17. The linkage map and mapped QTLs for shell nacre colour would be useful for improving the quality of Hyriopsis cumingii via marker-assisted selection. PMID:27587236

  9. Breast density mapping based upon system calibration, x-ray techniques, and FFDM images

    NASA Astrophysics Data System (ADS)

    Chen, Biao; Smith, Andrew P.; Jing, Zhenxue; Wu, Tao

    2007-03-01

    Clinical studies have correlated a high breast density to a women's risk of breast cancer. A breast density measurement that can quantitatively depict the volume distribution and percentage of dense tissues in breasts would be very useful for risk factor assessment of breast cancer, and might be more predictive of risks than the common but subjective and coarse 4-point BIRADS scale. This paper proposes to use a neural-network mapping to compute the breast density information based upon system calibration data, x-ray techniques, and Full Field Digital Mammography (FFDM) images. The mapping consists of four modules, namely, system calibration, generator of beam quality, generator of normalized absorption, and a multi-layer feed-forward neural network. As the core of breast density mapping, the network accepts x-ray target/filter combination, normalized x-ray absorption, pixel-wise breast thickness map, and x-ray beam quality during image acquisition as input elements, and exports a pixel-wise breast density distribution and a single breast density percentage for the imaged breast. Training and testing data sets for the design and verification of the network were formulated from calibrated x-ray beam quality, imaging data with a step wedge phantom under a variety x-ray imaging techniques, and nominal breast densities of tissue equivalent materials. The network was trained using a Levenberg-Marquardt algorithm based back-propagation learning method. Various thickness and glandular density phantom studies were performed with clinical x-ray techniques. Preliminary results showed that the neural network mapping is promising in accurately computing glandular density distribution and breast density percentage.

  10. 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

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

    PubMed

    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

  12. 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.

  13. Construction of High-Density Genetic Map in Barley through Restriction-Site Associated DNA Sequencing.

    PubMed

    Zhou, Gaofeng; Zhang, Qisen; Zhang, Xiao-Qi; Tan, Cong; Li, Chengdao

    2015-01-01

    Genetic maps in barley are usually constructed from a limited number of molecular markers such as SSR (simple sequence repeat) and DarT (diversity arrays technology). These markers must be first developed before being used for genotyping. Here, we introduce a new strategy based on sequencing progeny of a doubled haploid population from Baudin × AC Metcalfe to construct a genetic map in barley. About 13,547 polymorphic SNP tags with >93% calling rate were selected to construct the genetic map. A total of 12,998 SNP tags were anchored to seven linkage groups which spanned a cumulative 967.6 cM genetic distance. The high-density genetic map can be used for QTL mapping and the assembly of WGS and BAC contigs. The genetic map was evaluated for its effectiveness and efficiency in QTL mapping and candidate gene identification. A major QTL for plant height was mapped at 105.5 cM on chromosome 3H. This QTL with LOD value of 13.01 explained 44.5% of phenotypic variation. This strategy will enable rapid and efficient establishment of high-density genetic maps in other species. PMID:26182149

  14. Estimation of high-resolution dust column density maps. Empirical model fits

    NASA Astrophysics Data System (ADS)

    Juvela, M.; Montillaud, J.

    2013-09-01

    Context. Sub-millimetre dust emission is an important tracer of column density N of dense interstellar clouds. One has to combine surface brightness information at different spatial resolutions, and specific methods are needed to derive N at a resolution higher than the lowest resolution of the observations. Some methods have been discussed in the literature, including a method (in the following, method B) that constructs the N estimate in stages, where the smallest spatial scales being derived only use the shortest wavelength maps. Aims: We propose simple model fitting as a flexible way to estimate high-resolution column density maps. Our goal is to evaluate the accuracy of this procedure and to determine whether it is a viable alternative for making these maps. Methods: The new method consists of model maps of column density (or intensity at a reference wavelength) and colour temperature. The model is fitted using Markov chain Monte Carlo methods, comparing model predictions with observations at their native resolution. We analyse simulated surface brightness maps and compare its accuracy with method B and the results that would be obtained using high-resolution observations without noise. Results: The new method is able to produce reliable column density estimates at a resolution significantly higher than the lowest resolution of the input maps. Compared to method B, it is relatively resilient against the effects of noise. The method is computationally more demanding, but is feasible even in the analysis of large Herschel maps. Conclusions: The proposed empirical modelling method E is demonstrated to be a good alternative for calculating high-resolution column density maps, even with considerable super-resolution. Both methods E and B include the potential for further improvements, e.g., in the form of better a priori constraints.

  15. 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).

  16. 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.

  17. Likelihood-based modification of experimental crystal structure electron density maps

    DOEpatents

    Terwilliger, Thomas C.

    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.

  18. 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

  19. Neutral density map of Hall thruster plume expansion in a vacuum chamber

    SciTech Connect

    Walker, Mitchell L.R.; Gallimore, Alec D.

    2005-05-15

    A neutral background pressure map of the large vacuum test facility (LVTF) is presented. The LVTF is mapped at cold anode flow rates of 5.25, 10.46, and 14.09 mg/s. In addition, neutral background pressure maps are created at hot anode (i.e., discharge on) flow rates of 5.25 and 10.46 mg/s for discharge voltages of 300 and 500 V, corresponding to P5 Hall thruster operating conditions ranging from 1.5 to 5.0 kW. The chamber pressure is mapped at nominal xenon pumping speeds of 140,000 and 240,000 l/s. The pressure map is performed with a rake consisting of five calibrated Bayard-Alpert hot-cathode ionization gauges. The plume expansion appears to be independent of anode flow rate and facility background pressure. Analysis of axial pressure profiles on the LVTF's centerline shows that the plume pressure decreases from a maximum at the thruster exit plane down to the facility background pressure at approximately 2 m downstream of the exit plane. Comparison of axial pressure profiles on the LVTF's centerline shows that the neutral density is nearly the same for cold flow and hot flow. The study shows that a cold flow neutral density background map accurately characterizes the neutral density in an operating Hall thruster plume.

  20. Mapping the dimensionality, density and topology of data: the growing adaptive neural gas.

    PubMed

    Cselényi, Zsolt

    2005-05-01

    Self-organized maps are commonly applied for tasks of cluster analysis, vector quantization or interpolation. The artificial neural network model introduced in this paper is a hybrid model of the growing neural gas model introduced by Fritzke (Fritzke, in Advances in Neural Information Processing Systems 7, MIT Press, Cambridge MA, 1995) and the adaptive resolution clustering modification for self-organized maps proposed by Firenze (Firenze et al., in International Conference on Artificial Neural Networks, Springer-Verlag, London, 1994). The hybrid model is capable of mapping the distribution, dimensionality and topology of the input data. It has a local performance measure that enables the network to terminate growing in areas of the input space that is mapped by units reaching a performance goal. Therefore the network can accurately map clusters of data appearing on different scales of density. The capabilities of the algorithm are tested using simulated datasets with similar spatial spread but different local density distributions, and a simulated multivariate MR dataset of an anatomical human brain phantom with mild multiple sclerosis lesions. These tests demonstrate the advantages of the model compared to the growing neural gas algorithm when adaptive mapping of areas with low sample density is desirable. PMID:15848269

  1. Spatially mapping the spectral density of a single C60 molecule

    SciTech Connect

    Lu, Xinghua; Grobis, M.; Khoo, K.H.; Louie, Steve G.; Crommie, M.F.

    2002-07-01

    We have used scanning tunneling spectroscopy to spatially map the energy-resolved local density of states of individual C60 molecules on the Ag(100) surface. Spectral maps were obtained for molecular states derived from the C60 HOMO, LUMO, and LUMO + 1 orbitals, revealing new details of the spatially inhomogeneous C60 local electronic structure. Spatial inhomogeneities are explained using ab initio pseudopotential density functional calculations. These calculations emphasize the need for explicitly including the C60-Ag interaction and STM tip trajectory to understand the observed C60 local electronic structure.

  2. 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.

  3. High Density Molecular Linkage Maps of the Tomato and Potato Genomes

    PubMed Central

    Tanksley, S. D.; Ganal, M. W.; Prince, J. P.; de-Vicente, M. C.; Bonierbale, M. W.; Broun, P.; Fulton, T. M.; Giovannoni, J. J.; Grandillo, S.; Martin, G. B.; Messeguer, R.; Miller, J. C.; Miller, L.; Paterson, A. H.; Pineda, O.; Roder, M. S.; Wing, R. A.; Wu, W.; Young, N. D.

    1992-01-01

    High density molecular linkage maps, comprised of more than 1000 markers with an average spacing between markers of approximately 1.2 cM (ca. 900 kb), have been constructed for the tomato and potato genomes. As the two maps are based on a common set of probes, it was possible to determine, with a high degree of precision, the breakpoints corresponding to 5 chromosomal inversions that differentiate the tomato and potato genomes. All of the inversions appear to have resulted from single breakpoints at or near the centromeres of the affected chromosomes, the result being the inversion of entire chromosome arms. While the crossing over rate among chromosomes appears to be uniformly distributed with respect to chromosome size, there is tremendous heterogeneity of crossing over within chromosomes. Regions of the map corresponding to centromeres and centromeric heterochromatin, and in some instances telomeres, experience up to 10-fold less recombination than other areas of the genome. Overall, 28% of the mapped loci reside in areas of putatively suppressed recombination. This includes loci corresponding to both random, single copy genomic clones and transcribed genes (detected with cDNA probes). The extreme heterogeneity of crossing over within chromosomes has both practical and evolutionary implications. Currently tomato and potato are among the most thoroughly mapped eukaryotic species and the availability of high density molecular linkage maps should facilitate chromosome walking, quantitative trait mapping, marker-assisted breeding and evolutionary studies in these two important and well studied crop species. PMID:1360934

  4. X-ray studies of structure defects in recycled aluminum alloy during equal channel angular extrusion: Dislocation density and stored energy

    NASA Astrophysics Data System (ADS)

    Makhlouf, T.; Njah, N.

    2012-02-01

    A recycled aluminum alloy was severely deformed by Equal Channel Angular Extrusion (ECAE) using the processing route Bc, to study the evolution of the micro structure and associated changes of mechanical properties. XRD patterns were analyzed to determine crystallite size, lattice strain and lattice parameter. As a result, ultrafine grains material has been obtained with microstructure showing a mixture of highly strained crystallites. High density of dislocations is achieved as a result of severe plastic deformation through the die. This can explain an important decrease of the lattice parameter observed after the first passage. Changes in mechanical behavior are also reveled after ECAE. This is due to strain hardening. Differential Scanning Calorimetry (DSC) results show overlapped exothermic peaks indicating the succession of the recovery, recrystallization and grain growth phenomena's. Moreover, we demonstrate that the energy stored during ECAE can be related to the dislocation density introduced by severe plastic deformation.

  5. 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

  6. 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

  7. 3D Mapping of Polymer Crosslink Density with Magnetic Resonance Imaging

    SciTech Connect

    Herberg, J L; Gjersing, E L; Chinn, S C; Maxwell, R S

    2005-03-11

    Magnetic Resonance Imaging (MRI) techniques have been used to detect areas of low crosslink density in damaged silicone parts in an effort to develop a QA/QC protocol to be used in the development of new parts. Model materials of varying crosslink density first demonstrated the applicability of the method. Analysis of damaged pads has been shown to be clearly distinguishable by MRI. It is our belief that both the T{sub 2} weighted SPI NMR and the T{sub 2} weighted water/fat suppression MRI experiments can be used to map out the location of different cross-linking densities, ultimately determining the quality or homogeneity in polymers.

  8. Three-dimensional mass density mapping of cellular ultrastructure by ptychographic X-ray nanotomography.

    PubMed

    Diaz, Ana; Malkova, Barbora; Holler, Mirko; Guizar-Sicairos, Manuel; Lima, Enju; Panneels, Valerie; Pigino, Gaia; Bittermann, Anne Greet; Wettstein, Larissa; Tomizaki, Takashi; Bunk, Oliver; Schertler, Gebhard; Ishikawa, Takashi; Wepf, Roger; Menzel, Andreas

    2015-12-01

    We demonstrate absolute quantitative mass density mapping in three dimensions of frozen-hydrated biological matter with an isotropic resolution of 180 nm. As model for a biological system we use Chlamydomonas cells in buffer solution confined in a microcapillary. We use ptychographic X-ray computed tomography to image the entire specimen, including the 18 μm-diameter capillary, thereby providing directly an absolute mass density measurement of biological matter with an uncertainty of about 6%. The resulting maps have sufficient contrast to distinguish cells from the surrounding ice and several organelles of different densities inside the cells. Organelles are identified by comparison with a stained, resin-embedded specimen, which can be compared with established transmission electron microscopy results. For some identified organelles, the knowledge of their elemental composition reduces the uncertainty of their mass density measurement down to 1% with values consistent with previous measurements of dry weight concentrations in thin cellular sections by scanning transmission electron microscopy. With prospects of improving the spatial resolution in the near future, we expect that the capability of non-destructive three-dimensional mapping of mass density in biological samples close to their native state becomes a valuable method for measuring the packing of organic matter on the nanoscale. PMID:26470812

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

    SciTech Connect

    Britun, Nikolay Palmucci, Maria; Konstantinidis, Stephanos; Snyders, Rony

    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 their spatial density distributions, are discussed.

  10. Use of Spatial Variance Information From Remote Sensing Imagery to Map Vegetation Foliage Density

    NASA Astrophysics Data System (ADS)

    Walthall, C. L.; Timlin, D.; Pachepsky, Y.; Dulaney, W.; Daughtry, C.

    2002-12-01

    Maps of foliage density expressed as leaf area index (LAI) are used for natural resources inventories, land surface-atmosphere interaction modeling, and hydrologic modeling. Remote sensing imagery can be used to produce these maps by relating spectral vegetation indexes (SVIs) to LAI calibration samples acquired at selected locations on the surface. This approach traditionally uses ordinary least squares (OLS) relationships between the surface measurements and the SVIs, and does not fully take advantage of the spatial information content of the imagery. Spatial information inherent in a semivariogram of the imagery may provide additional information for mapping LAI patterns. This is demonstrated using a spatially dense sample of corn LAI and calibrated airborne imagery. An LAI map is produced by interpolating surface measurements with a semivariogram from the imagery. The resulting LAI map captures the main spatial features of a LAI map produced by interpolating the surface LAI data with its semivariogram. The image semivariogram approach also provides a product that has less noise characteristic of OLS-based remote sensing methods. The use of the image semivariogram with the surface LAI calibration samples suggests that the spatial domain information can complement spectral information for improving LAI maps especially at high spatial resolution where OLS methods may not perform well.

  11. 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

  12. Retinotopic mapping of adult human visual cortex with high-density diffuse optical tomography

    PubMed Central

    Zeff, Benjamin W.; White, Brian R.; Dehghani, Hamid; Schlaggar, Bradley L.; Culver, Joseph P.

    2007-01-01

    Functional neuroimaging is a vital element of neuroscience and cognitive research and, increasingly, is an important clinical tool. Diffuse optical imaging is an emerging, noninvasive technique with unique portability and hemodynamic contrast capabilities for mapping brain function in young subjects and subjects in enriched or clinical environments. We have developed a high-performance, high-density diffuse optical tomography (DOT) system that overcomes previous limitations and enables superior image quality. We show herein the utility of the DOT system by presenting functional hemodynamic maps of the adult human visual cortex. The functional brain images have a high contrast-to-noise ratio, allowing visualization of individual activations and highly repeatable mapping within and across subjects. With the improved spatial resolution and localization, we were able to image functional responses of 1.7 cm in extent and shifts of <1 cm. Cortical maps of angle and eccentricity in the visual field are consistent with retinotopic studies using functional MRI and positron-emission tomography. These results demonstrate that high-density DOT is a practical and powerful tool for mapping function in the human cortex. PMID:17616584

  13. Osteoarthritis Classification Using Self Organizing Map Based on Gabor Kernel and Contrast-Limited Adaptive Histogram Equalization

    PubMed Central

    Anifah, Lilik; Purnama, I Ketut Eddy; Hariadi, Mochamad; Purnomo, Mauridhi Hery

    2013-01-01

    Localization is the first step in osteoarthritis (OA) classification. Manual classification, however, is time-consuming, tedious, and expensive. The proposed system is designed as decision support system for medical doctors to classify the severity of knee OA. A method has been proposed here to localize a joint space area for OA and then classify it in 4 steps to classify OA into KL-Grade 0, KL-Grade 1, KL-Grade 2, KL-Grade 3 and KL-Grade 4, which are preprocessing, segmentation, feature extraction, and classification. In this proposed system, right and left knee detection was performed by employing the Contrast-Limited Adaptive Histogram Equalization (CLAHE) and the template matching. The Gabor kernel, row sum graph and moment methods were used to localize the junction space area of knee. CLAHE is used for preprocessing step, i.e.to normalize the varied intensities. The segmentation process was conducted using the Gabor kernel, template matching, row sum graph and gray level center of mass method. Here GLCM (contrast, correlation, energy, and homogeinity) features were employed as training data. Overall, 50 data were evaluated for training and 258 data for testing. Experimental results showed the best performance by using gabor kernel with parameters α=8, θ=0, Ψ=[0 π/2], γ=0,8, N=4 and with number of iterations being 5000, momentum value 0.5 and α0=0.6 for the classification process. The run gave classification accuracy rate of 93.8% for KL-Grade 0, 70% for KL-Grade 1, 4% for KL-Grade 2, 10% for KL-Grade 3 and 88.9% for KL-Grade 4. PMID:23525188

  14. Computer controlled techniques for high emission density mapping of thermionic cathodes

    NASA Astrophysics Data System (ADS)

    Gibson, J. W.; Thomas, R. E.

    1985-12-01

    Some of the techniques commonly used (e.g. SLEEP and thermionic emission microscope) for measuring emission or work function uniformity of thermionic cathode surfaces require the use of very low or near zero current densities, thus the cathode is characterized at current densities and temperatures much lower than that of a normally operating cathode. The system reported on here uses a high voltage pulse technique and is capable of measuring emission densities in the range 1 to 80 A/cm 2 at normal cathode operating temperatures. The cathode surface is scanned with an anode having a 0.025 mm aperture whose position is controlled by computer operated stepping motors. The current through the aperture to a collector electrode is measured using a sample-and-hold amplifier. Pulsing and sampling are computer synchronized with the scanning, and data for each pulse are accumulated and can be processed and displayed in several ways using the computer, including a detailed "three-dimensional" map of either the electron emission density or work function variations. The entire surface of the cathode or any portion of it can be mapped in steps as small as 0.001 mm (1μm), but typically steps of 5-100 μm were used. Measurements are presented illustrating the uniformity or nonuniformity of the electron emission densities and work functions for type-B and type-M cathodes.

  15. Multispectral X-ray Imagaing for Core Temperature and Density Maps Retrieval in Direct Drive Implosions

    SciTech Connect

    Tommasini, R; Koch, J A; Izumi, N; Welser, L A; Mancini, R C; Delettrez, J; Regan, S; Smalyuk, V

    2006-04-26

    We report on the experiments aimed at obtaining core temperature and density maps in direct drive implosions at the OMEGA Laser Facility using multi-monochromatic X-ray imagers. These instruments use an array of pinholes and a flat multilayer mirror to provide unique multi-spectral images distributed over a wide spectral range. Using Argon as a dopant in the DD-filled plastic shells produces emission images in the Ar He-b and Ly-b spectral regions. These images allow the retrieval of temperature and density maps of the plasma. We deployed three identical multi-monochromatic X-ray imagers in a quasi-orthogonal line-of-sight configuration to allow tomographic reconstruction of the structure of the imploding core.

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

    PubMed

    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

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

    PubMed

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

    2016-05-26

    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.

  18. 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

  19. A high-density linkage map for Astyanax mexicanus using genotyping-by-sequencing technology.

    PubMed

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

    2015-02-01

    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

  20. On the equivalence between kernel self-organising maps and self-organising mixture density networks.

    PubMed

    Yin, Hujun

    2006-01-01

    The kernel method has become a useful trick and has been widely applied to various learning models to extend their nonlinear approximation and classification capabilities. Such extensions have also recently occurred to the Self-Organising Map (SOM). In this paper, two recently proposed kernel SOMs are reviewed, together with their link to an energy function. The Self-Organising Mixture Network is an extension of the SOM for mixture density modelling. This paper shows that with an isotropic, density-type kernel function, the kernel SOM is equivalent to a homoscedastic Self-Organising Mixture Network, an entropy-based density estimator. This revelation on the one hand explains that kernelising SOM can improve classification performance by acquiring better probability models of the data; but on the other hand it also explains that the SOM already naturally approximates the kernel method.

  1. 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.

  2. 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.; Amara, A.; Réfrégier, A.; Bacon, D.; Becker, M. R.; Bonnett, C.; Carretero, J.; Castander, F. J.; et al

    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 deg2 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 in fourmore » 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

    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 deg2 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 in 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. 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.

  4. 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.

  5. Equal Access.

    ERIC Educational Resources Information Center

    De Patta, Joe

    2003-01-01

    Presents an interview with Stephen McCarthy, co-partner and president of Equal Access ADA Consulting Architects of San Diego, California, about designing schools to naturally integrate compliance with the Americans with Disabilities Act (ADA). (EV)

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. High-resolution Mapping of Linear Antibody Epitopes Using Ultrahigh-density Peptide Microarrays*

    PubMed Central

    Buus, Søren; Rockberg, Johan; Forsström, Björn; Nilsson, Peter; Uhlen, Mathias; Schafer-Nielsen, Claus

    2012-01-01

    Antibodies empower numerous important scientific, clinical, diagnostic, and industrial applications. Ideally, the epitope(s) targeted by an antibody should be identified and characterized, thereby establishing antibody reactivity, highlighting possible cross-reactivities, and perhaps even warning against unwanted (e.g. autoimmune) reactivities. Antibodies target proteins as either conformational or linear epitopes. The latter are typically probed with peptides, but the cost of peptide screening programs tends to prohibit comprehensive specificity analysis. To perform high-throughput, high-resolution mapping of linear antibody epitopes, we have used ultrahigh-density peptide microarrays generating several hundred thousand different peptides per array. Using exhaustive length and substitution analysis, we have successfully examined the specificity of a panel of polyclonal antibodies raised against linear epitopes of the human proteome and obtained very detailed descriptions of the involved specificities. The epitopes identified ranged from 4 to 12 amino acids in size. In general, the antibodies were of exquisite specificity, frequently disallowing even single conservative substitutions. In several cases, multiple distinct epitopes could be identified for the same target protein, suggesting an efficient approach to the generation of paired antibodies. Two alternative epitope mapping approaches identified similar, although not necessarily identical, epitopes. These results show that ultrahigh-density peptide microarrays can be used for linear epitope mapping. With an upper theoretical limit of 2,000,000 individual peptides per array, these peptide microarrays may even be used for a systematic validation of antibodies at the proteomic level. PMID:22984286

  17. High-density interspecific genetic maps of kiwifruit and the identification of sex-specific markers.

    PubMed

    Zhang, Qiong; Liu, Chunyan; Liu, Yifei; VanBuren, Robert; Yao, Xiaohong; Zhong, Caihong; Huang, Hongwen

    2015-10-01

    Kiwifruit (Actinidia chinensis Planchon) is an important specialty fruit crop that suffers from narrow genetic diversity stemming from recent global commercialization and limited cultivar improvement. Here, we present high-density RAD-seq-based genetic maps using an interspecific F1 cross between Actinidia rufa 'MT570001' and A. chinensis 'Guihai No4'. The A. rufa (maternal) map consists of 2,426 single-nucleotide polymorphism (SNP) markers with a total length of 2,651 cM in 29 linkage groups (LGs) corresponding to the 29 chromosomes. The A. chinensis (paternal) map consists of 4,214 SNP markers over 3,142 cM in 29 LGs. Using these maps, we were able to anchor an additional 440 scaffolds from the kiwifruit draft genome assembly. Kiwifruit is functionally dioecious, which presents unique challenges for breeding and production. Three sex-specific simple sequence repeats (SSR) markers can be used to accurately sex type male and female kiwifruit in breeding programmes. The sex-determination region (SDR) in kiwifruit was narrowed to a 1-Mb subtelomeric region on chromosome 25. Localizing the SDR will expedite the discovery of genes controlling carpel abortion in males and pollen sterility in females. PMID:26370666

  18. High-density interspecific genetic maps of kiwifruit and the identification of sex-specific markers.

    PubMed

    Zhang, Qiong; Liu, Chunyan; Liu, Yifei; VanBuren, Robert; Yao, Xiaohong; Zhong, Caihong; Huang, Hongwen

    2015-10-01

    Kiwifruit (Actinidia chinensis Planchon) is an important specialty fruit crop that suffers from narrow genetic diversity stemming from recent global commercialization and limited cultivar improvement. Here, we present high-density RAD-seq-based genetic maps using an interspecific F1 cross between Actinidia rufa 'MT570001' and A. chinensis 'Guihai No4'. The A. rufa (maternal) map consists of 2,426 single-nucleotide polymorphism (SNP) markers with a total length of 2,651 cM in 29 linkage groups (LGs) corresponding to the 29 chromosomes. The A. chinensis (paternal) map consists of 4,214 SNP markers over 3,142 cM in 29 LGs. Using these maps, we were able to anchor an additional 440 scaffolds from the kiwifruit draft genome assembly. Kiwifruit is functionally dioecious, which presents unique challenges for breeding and production. Three sex-specific simple sequence repeats (SSR) markers can be used to accurately sex type male and female kiwifruit in breeding programmes. The sex-determination region (SDR) in kiwifruit was narrowed to a 1-Mb subtelomeric region on chromosome 25. Localizing the SDR will expedite the discovery of genes controlling carpel abortion in males and pollen sterility in females.

  19. Snapshot Image Mapping Spectrometer (IMS) with high sampling density for hyperspectral microscopy

    PubMed Central

    Gao, Liang; Kester, Robert T.; Hagen, Nathan; Tkaczyk, Tomasz S.

    2010-01-01

    A snapshot Image Mapping Spectrometer (IMS) with high sampling density is developed for hyperspectral microscopy, measuring a datacube of dimensions 285 × 285 × 60 (x, y, λ). The spatial resolution is ~0.45 µm with a FOV of 100 × 100 µm2. The measured spectrum is from 450 nm to 650 nm and is sampled by 60 spectral channels with average sampling interval ~3.3 nm. The channel’s spectral resolution is ~8nm. The spectral imaging results demonstrate the potential of the IMS for real-time cellular fluorescence imaging. PMID:20639917

  20. 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.

  1. Herschel-Planck dust optical depth and column density maps. II. Perseus

    NASA Astrophysics Data System (ADS)

    Zari, Eleonora; Lombardi, Marco; Alves, João; Lada, Charles J.; Bouy, Hervé

    2016-03-01

    We present optical depth and temperature maps of the Perseus molecular cloud, obtained combining dust emission data from the Herschel and Planck satellites and 2MASS/NIR dust extinction maps. The maps have a resolution of 36 arcsec in the Herschel regions, and of 5 arcmin elsewhere. The dynamic range of the optical depth map ranges from 1 × 10-2 mag up to 20 mag in the equivalent K-band extinction. We also evaluate the ratio between the 2.2 μm extinction coefficient and the 850 μm opacity. The value we obtain is close to the one found in the Orion B molecular cloud. We show that the cumulative and the differential area function of the data (which is proportional to the probability distribution function of the cloud column density) follow power laws with an index of respectively ≃-2, and ≃-3. We use WISE data to improve current YSO catalogs based mostly on Spitzer data and we build an up-to-date selection of Class I/0 objects. Using this selection, we evaluate the local Schmidt law, ΣYSO ∝ Σgasβ, showing that β = 2.4 ± 0.6. Finally, we show that the area-extinction relation is important for determining the star-formation rate in the cloud, which is in agreement with other recent works. The optical depth and temperature maps (FITS files) are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/587/A106

  2. A high-density genetic map of cucumber derived from Specific Length Amplified Fragment sequencing (SLAF-seq)

    PubMed Central

    Xu, Xuewen; Xu, Ruixue; Zhu, Biyun; Yu, Ting; Qu, Wenqin; Lu, Lu; Xu, Qiang; Qi, Xiaohua; Chen, Xuehao

    2015-01-01

    High-density genetic map provides an essential framework for accurate and efficient genome assembly and QTL fine mapping. Construction of high-density genetic maps appears more feasible since the advent of next-generation sequencing (NGS), which eases SNP discovery and high-throughput genotyping of large population. In this research, a high-density genetic map of cucumber (Cucumis sativus L.) was successfully constructed across an F2 population by a recently developed Specific Length Amplified Fragment sequencing (SLAF-seq) method. In total, 18.69 GB of data containing 93,460,000 paired-end reads were obtained after preprocessing. The average sequencing depth was 44.92 in the D8 (female parent), 42.16 in the Jin5-508 (male parent), and 5.01 in each progeny. 79,092 high-quality SLAFs were detected, of which 6784 SLAFs were polymorphic, and 1892 of the polymorphic markers met the requirements for constructing genetic map. The genetic map spanned 845.87 cm with an average genetic distance of 0.45 cm. It is a reliable linkage map for fine mapping and molecular breeding of cucumber for its high marker density and well-ordered markers. PMID:25610449

  3. Anatomical Mapping and Density of Merkel Cells in Skin and Mucosae of the Dog.

    PubMed

    Ramírez, Gustavo A; Rodríguez, Francisco; Quesada, Óscar; Herráez, Pedro; Fernández, Antonio; Espinosa-de-Los-Monteros, Antonio

    2016-09-01

    Merkel cells (MCs) are specialized cutaneous receptor cells involved with tactile sense. Although the distribution of MCs has been extensively studied in humans and rodents, their precise distribution and density throughout skin in the dog has not previously been determined. Knowledge of their distribution could facilitate understanding of their functions. By using of immunohistochemistry, density, and anatomical mapping of the MCs population in the dog skin was determined. Assessment of the MCs innervation was also achieved. Different patterns were noted in epidermis, hair follicles, or mucosa, including variable-sized clusters, linear or horse-shaped arrangements, and scattered and individualized cells. MCs revealed great variations in density and distribution over the body surface, with the highest numbers in oral mucosa and facial skin. There was no correlation of MCs density with age, sex, type of breed, coat type or pigmentation. Between 41 and 65% of MCs in hairy and glabrous skin and 8-18% of MCs in oral mucosa were in intimate contact with intraepithelial axon terminals. These findings indicate that canine MCs are numerous in sensory receptive areas and may be associated with the tactile sense in the dog. The present article enhances the knowledge of the skin structure in this species. Anat Rec, 299:1157-1164, 2016. © 2016 Wiley Periodicals, Inc. PMID:27341526

  4. Anatomical Mapping and Density of Merkel Cells in Skin and Mucosae of the Dog.

    PubMed

    Ramírez, Gustavo A; Rodríguez, Francisco; Quesada, Óscar; Herráez, Pedro; Fernández, Antonio; Espinosa-de-Los-Monteros, Antonio

    2016-09-01

    Merkel cells (MCs) are specialized cutaneous receptor cells involved with tactile sense. Although the distribution of MCs has been extensively studied in humans and rodents, their precise distribution and density throughout skin in the dog has not previously been determined. Knowledge of their distribution could facilitate understanding of their functions. By using of immunohistochemistry, density, and anatomical mapping of the MCs population in the dog skin was determined. Assessment of the MCs innervation was also achieved. Different patterns were noted in epidermis, hair follicles, or mucosa, including variable-sized clusters, linear or horse-shaped arrangements, and scattered and individualized cells. MCs revealed great variations in density and distribution over the body surface, with the highest numbers in oral mucosa and facial skin. There was no correlation of MCs density with age, sex, type of breed, coat type or pigmentation. Between 41 and 65% of MCs in hairy and glabrous skin and 8-18% of MCs in oral mucosa were in intimate contact with intraepithelial axon terminals. These findings indicate that canine MCs are numerous in sensory receptive areas and may be associated with the tactile sense in the dog. The present article enhances the knowledge of the skin structure in this species. Anat Rec, 299:1157-1164, 2016. © 2016 Wiley Periodicals, Inc.

  5. Creating Protein Models from Electron-Density Maps using Particle-Filtering Methods

    PubMed Central

    Kondrashov, Dmitry A.; Bitto, Eduard; Soni, Ameet; Bingman, Craig A.; Phillips, George N.; Shavlik, Jude W.

    2008-01-01

    Motivation One bottleneck in high-throughput protein crystallography is interpreting an electron-density map; that is, fitting a molecular model to the 3D picture crystallography produces. Previously, we developed Acmi, an algorithm that uses a probabilistic model to infer an accurate protein backbone layout. Here we use a sampling method known as particle filtering to produce a set of all-atom protein models. We use the output of Acmi to guide the particle filter's sampling, producing an accurate, physically feasible set of structures. Results We test our algorithm on ten poor-quality experimental density maps. We show that particle filtering produces accurate all-atom models, resulting in fewer chains, lower sidechain RMS error, and reduced R factor, compared to simply placing the best-matching sidechains on Acmi's trace. We show that our approach produces a more accurate model than three leading methods – Textal, Resolve, and ARP/wARP – in terms of main chain completeness, sidechain identification, and crystallographic R factor. PMID:17933855

  6. Quantitative Autofluorescence and Cell Density Maps of the Human Retinal Pigment Epithelium

    PubMed Central

    Ach, Thomas; Huisingh, Carrie; McGwin, Gerald; Messinger, Jeffrey D.; Zhang, Tianjiao; Bentley, Mark J.; Gutierrez, Danielle B.; Ablonczy, Zsolt; Smith, R. Theodore; Sloan, Kenneth R.; Curcio, Christine A.

    2014-01-01

    Purpose. Lipofuscin (LF) accumulation within RPE cells is considered pathogenic in AMD. To test whether LF contributes to RPE cell loss in aging and to provide a cellular basis for fundus autofluorescence (AF) we created maps of human RPE cell number and histologic AF. Methods. Retinal pigment epithelium–Bruch's membrane flat mounts were prepared from 20 donor eyes (10 ≤ 51 and 10 > 80 years; postmortem: ≤4.2 hours; no retinal pathologies), preserving foveal position. Phalloidin-binding RPE cytoskeleton and LF-AF (488-nm excitation) were imaged at up to 90 predefined positions. Maps were assembled from 83,330 cells in 1470 locations. From Voronoi regions representing each cell, the number of neighbors, cell area, and total AF intensity normalized to an AF standard was determined. Results. Highly variable between individuals, RPE-AF increases significantly with age. A perifoveal ring of high AF mirrors rod photoreceptor topography and fundus-AF. Retinal pigment epithelium cell density peaks at the fovea, independent of age, yet no net RPE cell loss is detectable. The RPE monolayer undergoes considerable lifelong re-modeling. The relationship of cell size and AF, a surrogate for LF concentration, is orderly and linear in both groups. Autofluorescence topography differs distinctly from the topography of age-related rod loss. Conclusions. Digital maps of quantitative AF, cell density, and packing geometry provide metrics for cellular-resolution clinical imaging and model systems. The uncoupling of RPE LF content, cell number, and photoreceptor topography in aging challenges LF's role in AMD. PMID:25034602

  7. 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. PMID:26063584

  8. 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.

  9. High-density genetic linkage mapping in turbot (Scophthalmus maximus L.) based on SNP markers and major sex- and growth-related regions detection.

    PubMed

    Wang, Weiji; Hu, Yulong; Ma, Yu; Xu, Liyong; Guan, Jiantao; Kong, Jie

    2015-01-01

    This paper describes the development of a high density consensus genetic linkage map of a turbot (Scophthalmus maximus L.) family composed of 149 mapping individuals using Single Nucleotide Polymorphisms (SNP) developed using the restriction-site associated DNA (RAD) sequencing technique with the restriction enzyme, PstI. A total of 6,647 SNPs were assigned to 22 linkage groups, which is equal to the number of chromosome pairs in turbot. For the first time, the average marker interval reached 0.3958 cM, which is equal to approximately 0.1203 Mb of the turbot genome. The observed 99.34% genome coverage indicates that the linkage map was genome-wide. A total of 220 Quantitative Traits Locus (QTLs) associated with two body length traits, two body weight traits in different growth periods and sex determination were detected with an LOD > 5.0 in 12 linkage groups (LGs), which explained the corresponding phenotypic variance (R2), ranging from 14.4-100%. Among them, 175 overlapped with linked SNPs, and the remaining 45 were located in regions between contiguous SNPs. According to the QTLs related to growth trait distribution and the changing of LGs during different growth periods, the growth traits are likely controlled by multi-SNPs distributed on several LGs; the effect of these SNPs changed during different growth periods. Most sex-related QTLs were detected at LG 21 with a linkage span of 70.882 cM. Additionally, a small number of QTLs with high feasibility and a narrow R2 distribution were also observed on LG7 and LG14, suggesting that multi LGs or chromosomes might be involved in sex determination. High homology was recorded between LG21 in Cynoglossus semilaevis and turbot. This high-saturated turbot RAD-Seq linkage map is undoubtedly a promising platform for marker assisted selection (MAS) and flatfish genomics research.

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

    PubMed Central

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

    2016-01-01

    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. PMID:27194803

  11. BCL::EM-Fit: rigid body fitting of atomic structures into density maps using geometric hashing and real space refinement.

    PubMed

    Woetzel, Nils; Lindert, Steffen; Stewart, Phoebe L; Meiler, Jens

    2011-09-01

    Cryo-electron microscopy (cryoEM) can visualize large macromolecular assemblies at resolutions often below 10Å and recently as good as 3.8-4.5 Å. These density maps provide important insights into the biological functioning of molecular machineries such as viruses or the ribosome, in particular if atomic-resolution crystal structures or models of individual components of the assembly can be placed into the density map. The present work introduces a novel algorithm termed BCL::EM-Fit that accurately fits atomic-detail structural models into medium resolution density maps. In an initial step, a "geometric hashing" algorithm provides a short list of likely placements. In a follow up Monte Carlo/Metropolis refinement step, the initial placements are optimized by their cross correlation coefficient. The resolution of density maps for a reliable fit was determined to be 10 Å or better using tests with simulated density maps. The algorithm was applied to fitting of capsid proteins into an experimental cryoEM density map of human adenovirus at a resolution of 6.8 and 9.0 Å, and fitting of the GroEL protein at 5.4 Å. In the process, the handedness of the cryoEM density map was unambiguously identified. The BCL::EM-Fit algorithm offers an alternative to the established Fourier/Real space fitting programs. BCL::EM-Fit is free for academic use and available from a web server or as downloadable binary file at http://www.meilerlab.org.

  12. BCL::EM-Fit: Rigid body fitting of atomic structures into density maps using geometric hashing and real space refinement

    PubMed Central

    Woetzel, Nils; Lindert, Steffen; Stewart, Phoebe L.; Meiler, Jens

    2011-01-01

    Cryo-Electron Microscopy can visualize large macromolecular assemblies at resolutions often below 10 Å and recently as good as 3.8–4.5 Å. These density maps provide important insights into the biological functioning of molecular machineries such as viruses or the ribosome, in particular if atomic-resolution crystal structures or models of individual components of the assembly can be placed into the density map. The present work introduces a novel algorithm termed BCL::EM-Fit that accurately fits atomic-detail structural models into medium resolution density maps. In an initial step, a “geometric hashing” algorithm provides a short list of likely placements. In a follow up Monte Carlo/Metropolis refinement step, the initial placements are optimized by their cross correlation coefficient. The resolution of density maps for a reliable fit was determined to be 10 Å or better using tests with simulated density maps. The algorithm was applied to fitting of capsid proteins into an experimental cryoEM density map of human adenovirus at a resolution of 6.8 and 9.0 Å, and fitting of the GroEL protein at 5.4 Å. In the process, the handedness of the cryoEM density map was unambiguously identified. The BCL::EM-Fit algorithm offers an alternative to the established Fourier/Real space fitting programs. BCL::EM-Fit is free for academic use and available from a webserver or as downloadable binary file at http://www.meilerlab.org. PMID:21565271

  13. 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

  14. 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.

  15. 'Risky places?': mapping gambling machine density and socio-economic deprivation.

    PubMed

    Wardle, Heather; Keily, Ruth; Astbury, Gaynor; Reith, Gerda

    2014-03-01

    The aims of this project were to map the location and density of gambling machines in Britain; to explore whether geographic areas with higher densities of machines exist and to examine the socio-economic characteristics of these areas relative to others. Using geospatial analysis of premises records, we identified 8861 Machine Zones which were areas with a 400 meter radius around gambling machine venue and 384 High Density Machine Zones (HDMZ) with 1 or more gambling machine per hectare. There was a significant correlation between machine density and socio-economic deprivation. HDMZs had greater levels of income deprivation, more economically inactive people and a younger age profile than other areas; 37 % of those living in HDMZs were economically inactive compared with 33 % of those in non-machine areas. HDMZs were in seaside locations but also New Towns or satellite towns to major urban areas. Area affluence explains some of this pattern; of the New Towns with HDMZs, 78 % were in New Towns with a high proportion of low income areas. We therefore concluded that the distribution of gambling machines in Great Britain, in line with other international jurisdictions, displays a significant association with areas of socio-economic deprivation. The profile of the resident population living in HDMZs mirrors the profile of those most at-risk of experiencing harm from gambling. This spatial pattern has important implications for assessing the relationship between gambling availability and gambling-related harm, and for the future development of policy, harm-prevention and treatment strategies. PMID:23242474

  16. Calibrated and completeness-corrected optical stellar density maps of the northern Galactic plane

    NASA Astrophysics Data System (ADS)

    Farnhill, H. J.; Drew, J. E.; Barentsen, G.; González-Solares, E. A.

    2016-03-01

    Following on from the second release of calibrated photometry from IPHAS, the INT/WFC Photometric Hα Survey of the Northern Galactic Plane, we present incompleteness-corrected stellar density maps in the r and i photometric bands. These have been computed to a range of limiting magnitudes reaching to 20th magnitude in r and 19th in i (Vega system), and with different angular resolutions - the highest resolution available being 1 arcmin2. The maps obtained cover 94 per cent of the 1800 square degree IPHAS footprint, spanning the Galactic latitude range, -5° < b < +5°, north of the celestial equator. The corrections for incompleteness, due to confusion and sensitivity loss at the faint limit, have been deduced by the method of artificial source injection. The presentation of this method is preceded by a discussion of other more approximate methods of determining completeness. Our method takes full account of position-dependent seeing and source ellipticity in the survey data base. The application of the star counts to testing reddened Galactic disc models is previewed by a comparison with predicted counts along three constant-longitude cuts at ℓ ≃ 30°, 90° and 175°: some overprediction of the most heavily reddened ℓ ≃ 30° counts is found, alongside good agreement at ℓ ≃ 90° and 175°.

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

    PubMed Central

    Gaur, Rashmi; Chattopadhyay, Debasis; Jain, Mukesh; Parida, Swarup K.; Bhatia, Sabhyata

    2015-01-01

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

  18. High-Density Genetic Mapping with Interspecific Hybrids of Two Sea Urchins, Strongylocentrotus nudus and S. intermedius, by RAD Sequencing.

    PubMed

    Zhou, Zunchun; Liu, Shikai; Dong, Ying; Gao, Shan; Chen, Zhong; Jiang, Jingwei; Yang, Aifu; Sun, Hongjuan; Guan, Xiaoyan; Jiang, Bei; Wang, Bai

    2015-01-01

    Sea urchins have long been used as research model organisms for developmental biology and evolutionary studies. Some of them are also important aquaculture species in East Asia. In this work, we report the construction of RAD-tag based high-density genetic maps by genotyping F1 interspecific hybrids derived from a crossing between a female sea urchin Strongylocentrotus nudus and a male Strongylocentrotus intermedius. With polymorphisms present in these two wild individuals, we constructed a female meiotic map containing 3,080 markers for S. nudus, and a male meiotic map for S. intermedius which contains 1,577 markers. Using the linkage maps, we were able to anchor a total of 1,591 scaffolds (495.9 Mb) accounting for 60.8% of the genome assembly of Strongylocentrotus purpuratus. A genome-wide scan resulted in the identification of one putative QTL for body size which spanned from 25.3 cM to 30.3 cM. This study showed the efficiency of RAD-Seq based high-density genetic map construction using F1 progenies for species with no prior genomic information. The genetic maps are essential for QTL mapping and are useful as framework to order and orientate contiguous scaffolds from sea urchin genome assembly. The integration of the genetic map with genome assembly would provide an unprecedented opportunity to conduct QTL analysis, comparative genomics, and population genetics studies.

  19. Directly mapping the surface charge density of lipid bilayers under physiological conditions

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    The surface charge density of lipid bilayers governs the cellular uptake of charged particles and guides cell-cell and cell-surface interactions. Direct probing of the potential requires sub nanometer distances as the electrostatic potential is screened by high physiological salt concentrations. This prevented direct measurement of the SCD under physiological conditions. In this study we investigate supported bilayers of lipid mixtures that form domains of distinct surface charges, submerged in 150mM NaCl. We use a scanning ion-conductance microscope (SICM) setup to measure the ionic current through a nanopipette as the pipette is scanned several nanometers above the sample. The charged headgroups of the lipids attract counter ions leading to a charge dependent enhancement of the ion concentration near the surface. This creates a measurable change of conductivity in the vicinity of the surface. As the dependency of the current on the SCD and pipette potential is non-trivial we characterized it using numerical solutions to Poisson and Nernst-Planck equations. Based on the simulation results we propose an imaging method. We confirm feasibility of the proposed method by experimentally mapping the local surface charge density of phase separated lipid bilayers.

  20. EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps.

    PubMed

    Lindert, Steffen; Alexander, Nathan; Wötzel, Nils; Karakaş, Mert; Stewart, Phoebe L; Meiler, Jens

    2012-03-01

    Electron density maps of membrane proteins or large macromolecular complexes are frequently only determined at medium resolution between 4 Å and 10 Å, either by cryo-electron microscopy or X-ray crystallography. In these density maps, the general arrangement of secondary structure elements (SSEs) is revealed, whereas their directionality and connectivity remain elusive. We demonstrate that the topology of proteins with up to 250 amino acids can be determined from such density maps when combined with a computational protein folding protocol. Furthermore, we accurately reconstruct atomic detail in loop regions and amino acid side chains not visible in the experimental data. The EM-Fold algorithm assembles the SSEs de novo before atomic detail is added using Rosetta. In a benchmark of 27 proteins, the protocol consistently and reproducibly achieves models with root mean square deviation values <3 Å.

  1. A detailed RFLP map of Sorghum bicolor x S. propinquum, suitable for high-density mapping, suggests ancestral duplication of Sorghum chromosomes or chromosomal segments.

    PubMed

    Chittenden, L M; Schertz, K F; Lin, Y R; Wing, R A; Paterson, A H

    1994-03-01

    The first "complete" genetic linkage map of Sorghum section Sorghum is described, comprised of ten linkage groups putatively corresponding to the ten gametic chromosomes of S. bicolor and S. propinquum. The map includes 276 RFLP loci, predominately detected by PstI-digested S. bicolor genomic probes, segregating in 56 F2 progeny of a cross between S. bicolor and S. propinquum. Although prior cytological evidence suggests that the genomes of these species are largely homosequential, a high level of molecular divergence is evidenced by the abundant RFLP and RAPD polymorphisms, the marked deviations from Mendelian segregation in many regions of the genome, and several species-specific DNA probes. The remarkable level of DNA polymorphism between these species will facilitate development of a high-density genetic map. Further, the high level of DNA polymorphism permitted mapping of multiple loci for 21 (8.2%) DNA probes. Linkage relationships among eight (38%) of these probes suggest ancestral duplication of three genomic regions. Mapping of 13 maize genomic clones in this cross was consistent with prior results. Mapping of heterologous cDNAs from rice and oat suggests that it may be feasible to extend comparative mapping to these distantly-related species, and to ultimately generate a detailed description of chromosome rearrangements among cultivated Gramineae. Limited investigation of a small number of RFLPs showed several alleles common to S. bicolor and S. Halepense ("johnson-grass"), but few alleles common to S. propinquum and S. halepense, raising questions about the origin of S. halepense.

  2. Identification and High-Density Mapping of Gene-Rich Regions in Chromosome Group 1 of Wheat

    PubMed Central

    Gill, K. S.; Gill, B. S.; Endo, T. R.; Taylor, T.

    1996-01-01

    We studied the distribution of genes and recombination in wheat (Triticum aestivum) group 1 chromosomes by comparing high-density physical and genetic maps. Physical maps of chromosomes 1A, 1B, and 1D were generated by mapping 50 DNA markers on 56 single-break deletion lines. A consensus physical map was compared with the 1D genetic map of Triticum tauschii (68 markers) and a Triticeae group 1 consensus map (288 markers) to generate a cytogenetic ladder map (CLM). Most group 1 markers (86%) were present in five clusters that encompassed only 10% of the group 1 chromosome. This distribution may reflect that of genes because more than half of the probes were cDNA clones and 30% were PstI genomic. All 14 agronomically important genes in group 1 chromosomes were present in these clusters. Most recombination occurred in gene-cluster regions. Markers fell at an average distance of 244 kb in these regions. The CLM involving the Triticeae consensus genetic map revealed that the above distribution of genes and recombination is the same in other Triticeae species. Because of a significant number of common markers, our CLM can be used for comparative mapping and to estimate physical distances among markers in many Poaceae species including rice and maize. PMID:8978071

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

    SciTech Connect

    Mashouf, S; Fatemi-Ardekani, A; Song, W

    2015-06-15

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

  4. Mapping

    ERIC Educational Resources Information Center

    Kinney, Douglas M.; McIntosh, Willard L.

    1978-01-01

    Geologic mapping in the United States increased by about one-quarter in the past year. Examinations of mapping trends were in the following categories: (1) Mapping at scales of 1:100, 000; (2) Metric-scale base maps; (3) International mapping, and (4) Planetary mapping. (MA)

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

    SciTech Connect

    Mohamadizadeh, A.; Zarei-Hanzaki, A.; Abedi, H.R.; Mehtonen, S.; Porter, D.

    2015-09-15

    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 different 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 initiation

  6. 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

  7. A SNP Based High-Density Linkage Map of Apis cerana Reveals a High Recombination Rate Similar to Apis mellifera

    PubMed Central

    Huang, Zachary Y.; Wu, Xiao Bo; Zhu, Yong Qiang; Zheng, Hua Jun; Zeng, Zhi Jiang

    2013-01-01

    Background The Eastern honey bee, Apis cerana Fabricius, is distributed in southern and eastern Asia, from India and China to Korea and Japan and southeast to the Moluccas. This species is also widely kept for honey production besides Apis mellifera. Apis cerana is also a model organism for studying social behavior, caste determination, mating biology, sexual selection, and host-parasite interactions. Few resources are available for molecular research in this species, and a linkage map was never constructed. A linkage map is a prerequisite for quantitative trait loci mapping and for analyzing genome structure. We used the Chinese honey bee, Apis cerana cerana to construct the first linkage map in the Eastern honey bee. Results F2 workers (N = 103) were genotyped for 126,990 single nucleotide polymorphisms (SNPs). After filtering low quality and those not passing the Mendel test, we obtained 3,000 SNPs, 1,535 of these were informative and used to construct a linkage map. The preliminary map contains 19 linkage groups, we then mapped the 19 linkage groups to 16 chromosomes by comparing the markers to the genome of A. mellfiera. The final map contains 16 linkage groups with a total of 1,535 markers. The total genetic distance is 3,942.7 centimorgans (cM) with the largest linkage group (180 loci) measuring 574.5 cM. Average marker interval for all markers across the 16 linkage groups is 2.6 cM. Conclusion We constructed a high density linkage map for A. c. cerana with 1,535 markers. Because the map is based on SNP markers, it will enable easier and faster genotyping assays than randomly amplified polymorphic DNA or microsatellite based maps used in A. mellifera. PMID:24130775

  8. Fine mapping QTL for resistance to VNN disease using a high-density linkage map in Asian seabass.

    PubMed

    Liu, Peng; Wang, Le; Wong, Sek-Man; Yue, Gen Hua

    2016-08-24

    Asian seabass has suffered from viral nervous necrosis (VNN) disease. Our previous study has mapped quantitative trait loci (QTL) for resistance to VNN disease. To fine map these QTL and identify causative genes, we identified 6425 single nucleotide polymorphisms (SNPs) from 85 dead and 94 surviving individuals. Combined with 155 microsatellites, we constructed a genetic map consisting of 24 linkage groups (LGs) containing 3000 markers, with an average interval of 1.27 cM. We mapped one significant and three suggestive QTL with phenotypic variation explained (PVE) of 8.3 to 11.0%, two significant and two suggestive QTL with PVE of 7.8 to 10.9%, for resistance in three LGs and survival time in four LGs, respectively. Further analysis one QTL with the largest effect identified protocadherin alpha-C 2-like (Pcdhac2) as the possible candidate gene. Association study in 43 families with 1127 individuals revealed a 6 bp insertion-deletion was significantly associated with disease resistance. qRT-PCR showed the expression of Pcdhac2 was significantly induced in the brain, muscle and skin after nervous necrosis virus (NNV) infection. Our results could facilitate marker-assisted selection (MAS) for resistance to NNV in Asian seabass and set up the basis for functional analysis of the potential causative gene for resistance.

  9. Fine mapping QTL for resistance to VNN disease using a high-density linkage map in Asian seabass.

    PubMed

    Liu, Peng; Wang, Le; Wong, Sek-Man; Yue, Gen Hua

    2016-01-01

    Asian seabass has suffered from viral nervous necrosis (VNN) disease. Our previous study has mapped quantitative trait loci (QTL) for resistance to VNN disease. To fine map these QTL and identify causative genes, we identified 6425 single nucleotide polymorphisms (SNPs) from 85 dead and 94 surviving individuals. Combined with 155 microsatellites, we constructed a genetic map consisting of 24 linkage groups (LGs) containing 3000 markers, with an average interval of 1.27 cM. We mapped one significant and three suggestive QTL with phenotypic variation explained (PVE) of 8.3 to 11.0%, two significant and two suggestive QTL with PVE of 7.8 to 10.9%, for resistance in three LGs and survival time in four LGs, respectively. Further analysis one QTL with the largest effect identified protocadherin alpha-C 2-like (Pcdhac2) as the possible candidate gene. Association study in 43 families with 1127 individuals revealed a 6 bp insertion-deletion was significantly associated with disease resistance. qRT-PCR showed the expression of Pcdhac2 was significantly induced in the brain, muscle and skin after nervous necrosis virus (NNV) infection. Our results could facilitate marker-assisted selection (MAS) for resistance to NNV in Asian seabass and set up the basis for functional analysis of the potential causative gene for resistance. PMID:27555039

  10. Fine mapping QTL for resistance to VNN disease using a high-density linkage map in Asian seabass

    PubMed Central

    Liu, Peng; Wang, Le; Wong, Sek-Man; Yue, Gen Hua

    2016-01-01

    Asian seabass has suffered from viral nervous necrosis (VNN) disease. Our previous study has mapped quantitative trait loci (QTL) for resistance to VNN disease. To fine map these QTL and identify causative genes, we identified 6425 single nucleotide polymorphisms (SNPs) from 85 dead and 94 surviving individuals. Combined with 155 microsatellites, we constructed a genetic map consisting of 24 linkage groups (LGs) containing 3000 markers, with an average interval of 1.27 cM. We mapped one significant and three suggestive QTL with phenotypic variation explained (PVE) of 8.3 to 11.0%, two significant and two suggestive QTL with PVE of 7.8 to 10.9%, for resistance in three LGs and survival time in four LGs, respectively. Further analysis one QTL with the largest effect identified protocadherin alpha-C 2-like (Pcdhac2) as the possible candidate gene. Association study in 43 families with 1127 individuals revealed a 6 bp insertion-deletion was significantly associated with disease resistance. qRT-PCR showed the expression of Pcdhac2 was significantly induced in the brain, muscle and skin after nervous necrosis virus (NNV) infection. Our results could facilitate marker-assisted selection (MAS) for resistance to NNV in Asian seabass and set up the basis for functional analysis of the potential causative gene for resistance. PMID:27555039

  11. A High-Density Genetic Linkage Map for Cucumber (Cucumis sativus L.): Based on Specific Length Amplified Fragment (SLAF) Sequencing and QTL Analysis of Fruit Traits in Cucumber.

    PubMed

    Zhu, Wen-Ying; Huang, Long; Chen, Long; Yang, Jian-Tao; Wu, Jia-Ni; Qu, Mei-Ling; Yao, Dan-Qing; Guo, Chun-Li; Lian, Hong-Li; He, Huan-Le; Pan, Jun-Song; Cai, Run

    2016-01-01

    High-density genetic linkage map plays an important role in genome assembly and quantitative trait loci (QTL) fine mapping. Since the coming of next-generation sequencing, makes the structure of high-density linkage maps much more convenient and practical, which simplifies SNP discovery and high-throughput genotyping. In this research, a high-density linkage map of cucumber was structured using specific length amplified fragment sequencing, using 153 F2 populations of S1000 × S1002. The high-density genetic map composed 3,057 SLAFs, including 4,475 SNP markers on seven chromosomes, and spanned 1061.19 cM. The average genetic distance is 0.35 cM. Based on this high-density genome map, QTL analysis was performed on two cucumber fruit traits, fruit length and fruit diameter. There are 15 QTLs for the two fruit traits were detected.

  12. A High-Density Genetic Linkage Map for Cucumber (Cucumis sativus L.): Based on Specific Length Amplified Fragment (SLAF) Sequencing and QTL Analysis of Fruit Traits in Cucumber.

    PubMed

    Zhu, Wen-Ying; Huang, Long; Chen, Long; Yang, Jian-Tao; Wu, Jia-Ni; Qu, Mei-Ling; Yao, Dan-Qing; Guo, Chun-Li; Lian, Hong-Li; He, Huan-Le; Pan, Jun-Song; Cai, Run

    2016-01-01

    High-density genetic linkage map plays an important role in genome assembly and quantitative trait loci (QTL) fine mapping. Since the coming of next-generation sequencing, makes the structure of high-density linkage maps much more convenient and practical, which simplifies SNP discovery and high-throughput genotyping. In this research, a high-density linkage map of cucumber was structured using specific length amplified fragment sequencing, using 153 F2 populations of S1000 × S1002. The high-density genetic map composed 3,057 SLAFs, including 4,475 SNP markers on seven chromosomes, and spanned 1061.19 cM. The average genetic distance is 0.35 cM. Based on this high-density genome map, QTL analysis was performed on two cucumber fruit traits, fruit length and fruit diameter. There are 15 QTLs for the two fruit traits were detected. PMID:27148281

  13. A High-Density Genetic Linkage Map for Cucumber (Cucumis sativus L.): Based on Specific Length Amplified Fragment (SLAF) Sequencing and QTL Analysis of Fruit Traits in Cucumber

    PubMed Central

    Zhu, Wen-Ying; Huang, Long; Chen, Long; Yang, Jian-Tao; Wu, Jia-Ni; Qu, Mei-Ling; Yao, Dan-Qing; Guo, Chun-Li; Lian, Hong-Li; He, Huan-Le; Pan, Jun-Song; Cai, Run

    2016-01-01

    High-density genetic linkage map plays an important role in genome assembly and quantitative trait loci (QTL) fine mapping. Since the coming of next-generation sequencing, makes the structure of high-density linkage maps much more convenient and practical, which simplifies SNP discovery and high-throughput genotyping. In this research, a high-density linkage map of cucumber was structured using specific length amplified fragment sequencing, using 153 F2 populations of S1000 × S1002. The high-density genetic map composed 3,057 SLAFs, including 4,475 SNP markers on seven chromosomes, and spanned 1061.19 cM. The average genetic distance is 0.35 cM. Based on this high-density genome map, QTL analysis was performed on two cucumber fruit traits, fruit length and fruit diameter. There are 15 QTLs for the two fruit traits were detected. PMID:27148281

  14. Construction of a high-density microsatellite genetic linkage map and mapping of sexual and growth-related traits in half-smooth tongue sole (Cynoglossus semilaevis).

    PubMed

    Song, Wentao; Li, Yangzhen; Zhao, Yongwei; Liu, Yang; Niu, Yuze; Pang, Renyi; Miao, Guidong; Liao, Xiaolin; Shao, Changwei; Gao, Fengtao; Chen, Songlin

    2012-01-01

    High-density genetic linkage maps of half-smooth tongue sole were developed with 1007 microsatellite markers, two SCAR markers and an F1 family containing 94. The female map was composed of 828 markers in 21 linkage groups, covering a total of 1447.3 cM, with an average interval 1.83 cM between markers. The male map consisted of 794 markers in 21 linkage groups, spanning 1497.5 cM, with an average interval of 1.96 cM. The female and male maps had 812 and 785 unique positions, respectively. The genome length of half-smooth tongue sole was estimated to be 1527.7 cM for the females and 1582.1 cM for the males. Based on estimations of the map lengths, the female and male maps covered 94.74 and 94.65% of the genome, respectively. The consensus map was composed of 1007 microsatellite markers and two SCAR markers in 21 linkage groups, covering a total of 1624 cM with an average interval of 1.67 cM. Furthermore, 159 sex-linked SSR markers were identified. Five sex-linked microsatellite markers were confirmed in their association with sex in a large number of individuals selected from different families. These sex-linked markers were mapped on the female map LG1f with zero recombination. Two QTLs that were identified for body weight, designated as We-1 and We-2, accounted for 26.39% and 10.60% of the phenotypic variation. Two QTLs for body width, designated Wi-1 and Wi-2, were mapped in LG4f and accounted for 14.33% and 12.83% of the phenotypic variation, respectively. Seven sex-related loci were mapped in LG1f, LG14f and LG1m by CIM, accounting for 12.5-25.2% of the trait variation. The results should prove to be very useful for improving growth traits using molecular MAS.

  15. Developing a Penetrometer-Based Mapping System for Visualizing Silage Bulk Density from the Bunker Silo Face.

    PubMed

    Li, Menghua; Jungbluth, Kerstin H; Sun, Yurui; Cheng, Qiang; Maack, Christian; Buescher, Wolfgang; Lin, Jianhui; Zhou, Haiyang; Wang, Zhongyi

    2016-07-05

    For silage production, high bulk density (BD) is critical to minimize aerobic deterioration facilitated by oxygen intrusion. To precisely assess packing quality for bunker silos, there is a desire to visualize the BD distribution within the silage. In this study, a penetrometer-based mapping system was developed. The data processing included filtering of the penetration friction component (PFC) out of the penetration resistance (PR), transfer of the corrected penetration resistance (PRc) to BD, incorporation of Kriged interpolation for data expansion and map generation. The experiment was conducted in a maize bunker silo (width: 8 m, middle height: 3 m). The BD distributions near the bunker silo face were represented using two map groups, one related to horizontal- and the other to vertical-density distribution patterns. We also presented a comparison between the map-based BD results and core sampling data. Agreement between the two measurement approaches (RMSE = 19.175 kg·m(-3)) demonstrates that the developed penetrometer mapping system may be beneficial for rapid assessment of aerobic deterioration potential in bunker silos.

  16. Developing a Penetrometer-Based Mapping System for Visualizing Silage Bulk Density from the Bunker Silo Face

    PubMed Central

    Li, Menghua; Jungbluth, Kerstin H.; Sun, Yurui; Cheng, Qiang; Maack, Christian; Buescher, Wolfgang; Lin, Jianhui; Zhou, Haiyang; Wang, Zhongyi

    2016-01-01

    For silage production, high bulk density (BD) is critical to minimize aerobic deterioration facilitated by oxygen intrusion. To precisely assess packing quality for bunker silos, there is a desire to visualize the BD distribution within the silage. In this study, a penetrometer-based mapping system was developed. The data processing included filtering of the penetration friction component (PFC) out of the penetration resistance (PR), transfer of the corrected penetration resistance (PRc) to BD, incorporation of Kriged interpolation for data expansion and map generation. The experiment was conducted in a maize bunker silo (width: 8 m, middle height: 3 m). The BD distributions near the bunker silo face were represented using two map groups, one related to horizontal- and the other to vertical-density distribution patterns. We also presented a comparison between the map-based BD results and core sampling data. Agreement between the two measurement approaches (RMSE = 19.175 kg·m−3) demonstrates that the developed penetrometer mapping system may be beneficial for rapid assessment of aerobic deterioration potential in bunker silos. PMID:27399703

  17. Developing a Penetrometer-Based Mapping System for Visualizing Silage Bulk Density from the Bunker Silo Face.

    PubMed

    Li, Menghua; Jungbluth, Kerstin H; Sun, Yurui; Cheng, Qiang; Maack, Christian; Buescher, Wolfgang; Lin, Jianhui; Zhou, Haiyang; Wang, Zhongyi

    2016-01-01

    For silage production, high bulk density (BD) is critical to minimize aerobic deterioration facilitated by oxygen intrusion. To precisely assess packing quality for bunker silos, there is a desire to visualize the BD distribution within the silage. In this study, a penetrometer-based mapping system was developed. The data processing included filtering of the penetration friction component (PFC) out of the penetration resistance (PR), transfer of the corrected penetration resistance (PRc) to BD, incorporation of Kriged interpolation for data expansion and map generation. The experiment was conducted in a maize bunker silo (width: 8 m, middle height: 3 m). The BD distributions near the bunker silo face were represented using two map groups, one related to horizontal- and the other to vertical-density distribution patterns. We also presented a comparison between the map-based BD results and core sampling data. Agreement between the two measurement approaches (RMSE = 19.175 kg·m(-3)) demonstrates that the developed penetrometer mapping system may be beneficial for rapid assessment of aerobic deterioration potential in bunker silos. PMID:27399703

  18. High-density genetic linkage map construction and QTL mapping of grain shape and size in the wheat population Yanda1817 × Beinong6.

    PubMed

    Wu, Qiu-Hong; Chen, Yong-Xing; Zhou, Sheng-Hui; Fu, Lin; Chen, Jiao-Jiao; Xiao, Yao; Zhang, Dong; Ouyang, Shu-Hong; Zhao, Xiao-Jie; Cui, Yu; Zhang, De-Yun; Liang, Yong; Wang, Zhen-Zhong; Xie, Jing-Zhong; Qin, Jin-Xia; Wang, Guo-Xin; Li, De-Lin; Huang, Yin-Lian; Yu, Mei-Hua; Lu, Ping; Wang, Li-Li; Wang, Ling; Wang, Hao; Dang, Chen; Li, Jie; Zhang, Yan; Peng, Hui-Ru; Yuan, Cheng-Guo; You, Ming-Shan; Sun, Qi-Xin; Wang, Ji-Rui; Wang, Li-Xin; Luo, Ming-Cheng; Han, Jun; Liu, Zhi-Yong

    2015-01-01

    High-density genetic linkage maps are necessary for precisely mapping quantitative trait loci (QTLs) controlling grain shape and size in wheat. By applying the Infinium iSelect 9K SNP assay, we have constructed a high-density genetic linkage map with 269 F 8 recombinant inbred lines (RILs) developed between a Chinese cornerstone wheat breeding parental line Yanda1817 and a high-yielding line Beinong6. The map contains 2431 SNPs and 128 SSR & EST-SSR markers in a total coverage of 3213.2 cM with an average interval of 1.26 cM per marker. Eighty-eight QTLs for thousand-grain weight (TGW), grain length (GL), grain width (GW) and grain thickness (GT) were detected in nine ecological environments (Beijing, Shijiazhuang and Kaifeng) during five years between 2010-2014 by inclusive composite interval mapping (ICIM) (LOD ≥ 2.5). Among which, 17 QTLs for TGW were mapped on chromosomes 1A, 1B, 2A, 2B, 3A, 3B, 3D, 4A, 4D, 5A, 5B and 6B with phenotypic variations ranging from 2.62% to 12.08%. Four stable QTLs for TGW could be detected in five and seven environments, respectively. Thirty-two QTLs for GL were mapped on chromosomes 1B, 1D, 2A, 2B, 2D, 3B, 3D, 4A, 4B, 4D, 5A, 5B, 6B, 7A and 7B, with phenotypic variations ranging from 2.62% to 44.39%. QGl.cau-2A.2 can be detected in all the environments with the largest phenotypic variations, indicating that it is a major and stable QTL. For GW, 12 QTLs were identified with phenotypic variations range from 3.69% to 12.30%. We found 27 QTLs for GT with phenotypic variations ranged from 2.55% to 36.42%. In particular, QTL QGt.cau-5A.1 with phenotypic variations of 6.82-23.59% was detected in all the nine environments. Moreover, pleiotropic effects were detected for several QTL loci responsible for grain shape and size that could serve as target regions for fine mapping and marker assisted selection in wheat breeding programs.

  19. Ultrahigh-density linkage map for cultivated cucumber (Cucumis sativus L.) using a single-nucleotide polymorphism genotyping array.

    PubMed

    Rubinstein, Mor; Katzenellenbogen, Mark; Eshed, Ravit; Rozen, Ada; Katzir, Nurit; Colle, Marivi; Yang, Luming; Grumet, Rebecca; Weng, Yiqun; Sherman, Amir; Ophir, Ron

    2015-01-01

    Genotyping arrays are tools for high-throughput genotyping, which is beneficial in constructing saturated genetic maps and therefore high-resolution mapping of complex traits. Since the report of the first cucumber genome draft, genetic maps have been constructed mainly based on simple-sequence repeats (SSRs) or on combinations of SSRs and sequence-related amplified polymorphism (SRAP). In this study, we developed the first cucumber genotyping array consisting of 32,864 single-nucleotide polymorphisms (SNPs). These markers cover the cucumber genome with a median interval of ~2 Kb and have expected genotype calls in parents/F1 hybridizations as a training set. The training set was validated with Fluidigm technology and showed 96% concordance with the genotype calls in the parents/F1 hybridizations. Application of the genotyping array was illustrated by constructing a 598.7 cM genetic map based on a '9930' × 'Gy14' recombinant inbred line (RIL) population comprised of 11,156 SNPs. Marker collinearity between the genetic map and reference genomes of the two parents was estimated at R2 = 0.97. We also used the array-derived genetic map to investigate chromosomal rearrangements, regional recombination rate, and specific regions with segregation distortions. Finally, 82% of the linkage-map bins were polymorphic in other cucumber variants, suggesting that the array can be applied for genotyping in other lines. The genotyping array presented here, together with the genotype calls of the parents/F1 hybridizations as a training set, should be a powerful tool in future studies with high-throughput cucumber genotyping. An ultrahigh-density linkage map constructed by this genotyping array on RIL population may be invaluable for assembly improvement, and for mapping important cucumber QTLs.

  20. Ultrahigh-Density Linkage Map for Cultivated Cucumber (Cucumis sativus L.) Using a Single-Nucleotide Polymorphism Genotyping Array

    PubMed Central

    Rubinstein, Mor; Katzenellenbogen, Mark; Eshed, Ravit; Rozen, Ada; Katzir, Nurit; Colle, Marivi; Yang, Luming; Grumet, Rebecca; Weng, Yiqun; Sherman, Amir; Ophir, Ron

    2015-01-01

    Genotyping arrays are tools for high-throughput genotyping, which is beneficial in constructing saturated genetic maps and therefore high-resolution mapping of complex traits. Since the report of the first cucumber genome draft, genetic maps have been constructed mainly based on simple-sequence repeats (SSRs) or on combinations of SSRs and sequence-related amplified polymorphism (SRAP). In this study, we developed the first cucumber genotyping array consisting of 32,864 single-nucleotide polymorphisms (SNPs). These markers cover the cucumber genome with a median interval of ~2 Kb and have expected genotype calls in parents/F1 hybridizations as a training set. The training set was validated with Fluidigm technology and showed 96% concordance with the genotype calls in the parents/F1 hybridizations. Application of the genotyping array was illustrated by constructing a 598.7 cM genetic map based on a ‘9930’ × ‘Gy14’ recombinant inbred line (RIL) population comprised of 11,156 SNPs. Marker collinearity between the genetic map and reference genomes of the two parents was estimated at R2 = 0.97. We also used the array-derived genetic map to investigate chromosomal rearrangements, regional recombination rate, and specific regions with segregation distortions. Finally, 82% of the linkage-map bins were polymorphic in other cucumber variants, suggesting that the array can be applied for genotyping in other lines. The genotyping array presented here, together with the genotype calls of the parents/F1 hybridizations as a training set, should be a powerful tool in future studies with high-throughput cucumber genotyping. An ultrahigh-density linkage map constructed by this genotyping array on RIL population may be invaluable for assembly improvement, and for mapping important cucumber QTLs. PMID:25874931

  1. The Double-Reduction Landscape in Tetraploid Potato as Revealed by a High-Density Linkage Map.

    PubMed

    Bourke, Peter M; Voorrips, Roeland E; Visser, Richard G F; Maliepaard, Chris

    2015-11-01

    The creation of genetic linkage maps in polyploid species has been a long-standing problem for which various approaches have been proposed. In the case of autopolyploids, a commonly used simplification is that random bivalents form during meiosis. This leads to relatively straightforward estimation of recombination frequencies using maximum likelihood, from which a genetic map can be derived. However, autopolyploids such as tetraploid potato (Solanum tuberosum L.) may exhibit additional features, such as double reduction, not normally encountered in diploid or allopolyploid species. In this study, we produced a high-density linkage map of tetraploid potato and used it to identify regions of double reduction in a biparental mapping population. The frequency of multivalents required to produce this degree of double reduction was determined through simulation. We also determined the effect that multivalents or preferential pairing between homologous chromosomes has on linkage mapping. Low levels of multivalents or preferential pairing do not adversely affect map construction when highly informative marker types and phases are used. We reveal the double-reduction landscape in tetraploid potato, clearly showing that this phenomenon increases with distance from the centromeres. PMID:26377683

  2. Rapidly calculated density functional theory (DFT) relaxed Iso-potential Phi Si Maps: Beta-cellobiose

    Technology Transfer Automated Retrieval System (TEKTRAN)

    New cellobiose Phi-H/Si-H maps are rapidly generated using a mixed basis set DFT method, found to achieve a high level of confidence while reducing computer resources dramatically. Relaxed iso-potential maps are made for different conformational states of cellobiose, showing how glycosidic bond dihe...

  3. Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing

    PubMed Central

    Tong, Chunfa; Li, Huogen; Wang, Ying; Li, Xuran; Ou, Jiajia; Wang, Deyuan; Xu, Houxi; Ma, Chao; Lang, Xianye; Liu, Guangxin; Zhang, Bo; Shi, Jisen

    2016-01-01

    Although numerous linkage maps have been constructed in the genus Populus, they are typically sparse and thus have limited applications due to low throughput of traditional molecular markers. Restriction-site associated DNA sequencing (RADSeq) technology allows us to identify a large number of single nucleotide polymorphisms (SNP) across genomes of many individuals in a fast and cost-effective way, and makes it possible to construct high-density genetic linkage maps. We performed RADSeq for 299 progeny and their two parents in an F1 hybrid population generated by crossing the female Populus deltoides ‘I-69’ and male Populus simonii ‘L3’. A total of 2,545 high quality SNP markers were obtained and two parent-specific linkage maps were constructed. The female genetic map contained 1601 SNPs and 20 linkage groups, spanning 4,249.12 cM of the genome with an average distance of 2.69 cM between adjacent markers, while the male map consisted of 940 SNPs and also 20 linkage groups with a total length of 3,816.24 cM and an average marker interval distance of 4.15 cM. Finally, our analysis revealed that synteny and collinearity are highly conserved between the parental linkage maps and the reference genome of P. trichocarpa. We demonstrated that RAD sequencing is a powerful technique capable of rapidly generating a large number of SNPs for constructing genetic maps in outbred forest trees. The high-quality linkage maps constructed here provided reliable genetic resources to facilitate locating quantitative trait loci (QTLs) that control growth and wood quality traits in the hybrid population. PMID:26964097

  4. Development of a high density integrated reference genetic linkage map for the multinational Brassica rapa Genome Sequencing Project.

    PubMed

    Li, Xiaonan; Ramchiary, Nirala; Choi, Su Ryun; Van Nguyen, Dan; Hossain, Md Jamil; Yang, Hyeon Kook; Lim, Yong Pyo

    2010-11-01

    We constructed a high-density Brassica rapa integrated linkage map by combining a reference genetic map of 78 doubled haploid lines derived from Chiifu-401-42 × Kenshin (CKDH) and a new map of 190 F2 lines derived from Chiifu-401-42 × rapid cycling B. rapa (CRF2). The integrated map contains 1017 markers and covers 1262.0 cM of the B. rapa genome, with an average interlocus distance of 1.24 cM. High similarity of marker order and position was observed among the linkage groups of the maps with few short-distance inversions. In total, 155 simple sequence repeat (SSR) markers, anchored to 102 new bacterial artificial chromosomes (BACs) and 146 intron polymorphic (IP) markers were mapped in the integrated map, which would be helpful to align the sequenced BACs in the ongoing multinational Brassica rapa Genome Sequencing Project (BrGSP). Further, comparison of the B. rapa consensus map with the 10 B. juncea A-genome linkage groups by using 98 common IP markers showed high-degree colinearity between the A-genome linkage groups, except for few markers showing inversion or translocation. Suggesting that chromosomes are highly conserved between these Brassica species, although they evolved independently after divergence. The sequence information coming out of BrGSP would be useful for B. juncea breeding. and the identified Arabidopsis chromosomal blocks and known quantitative trait loci (QTL) information of B. juncea could be applied to improve other Brassica crops including B. rapa.

  5. Spatial Mapping of Macular Pigment Optical Density and Its Relationship to Contrast Sensitivity and Glare Disability

    NASA Astrophysics Data System (ADS)

    Putnam, Christopher

    This dissertation explored the relationship of the macular pigment optical density (MPOD) spatial profile with measures of contrast sensitivity (CS), glare disability (GD), relative glare disability (RGD) and intraocular light scatter. A novel device capable of measuring MPOD across the central 160 of retina along 8 principle meridians using customized heterochromatic flicker photometry (cHFP) at eccentricities of 00, 20, 40, 60 and 80 was built. MPOD was calculated as both discrete and integrated values at all measured retinal loci. CS was measured using vertical grating stimuli of 3, 6 and 9 cycles per degree (cpd) also presented at 00, 20, 4 0, 60 and 80 eccentricity. GD was calculated as a difference in CS between glare and no glare conditions (CSNo Glare - CSGlare) using the same vertical grating stimuli presented at the same eccentricities. RGD [(CSNo Glare - CSGlare) / CSNo Glare] was calculated to isolate the glare attenuation effects of MPOD by controlling for CS variability among the subject sample. Intraocular scatter was assessed through a direct compensation method using a commercially available device. Statistical analyses of the discrete and integrated MPOD associations with CS, GD, RGD and intraocular scatter were evaluated. The cHFP identified reliable MPOD spatial distribution maps demonstrating a 1 st order exponential decay curve as a function of increasing eccentricity. Foveal MPOD revealed the highest correlation coefficients with RGD using 9cpd stimuli. These results are consistent with the glare attenuation effects of MP at higher spatial frequencies. Further support may be seen from the significant correlations found between corresponding parafoveal MPOD measures and both GD and RGD at 20 and 40 of eccentricity using 9cpd stimuli with greater MPOD being associated with less glare disability. All calculated measures of foveal MPOD shared similar significant correlation coefficients with both GD and RGD using 6cpd and 9cpd stimuli. Discrete

  6. Traveling wave solutions of density-dependent nonlinear reaction-diffusion equation via the extended generalized Riccati equation mapping method

    NASA Astrophysics Data System (ADS)

    Kengne, Emmanuel; Saydé, Michel; Ben Hamouda, Fathi; Lakhssassi, Ahmed

    2013-11-01

    Analytical entire traveling wave solutions to the 1+1 density-dependent nonlinear reaction-diffusion equation via the extended generalized Riccati equation mapping method are presented in this paper. This equation can be regarded as an extension case of the Fisher-Kolmogoroff equation, which is used for studying insect and animal dispersal with growth dynamics. The analytical solutions are then used to investigate the effect of equation parameters on the population distribution.

  7. 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

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

    PubMed

    Zhang, Jian; Yuan, Huwei; 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.

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

    PubMed

    Zhang, Jian; Yuan, Huwei; 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

  10. The Effect of Noise in Dust Emission Maps on the Derivation of Column Density, Temperature, and Emissivity Spectral Index

    NASA Astrophysics Data System (ADS)

    Schnee, S.; Kauffmann, J.; Goodman, A.; Bertoldi, F.

    2007-03-01

    We have mapped the central 10'×10' of the dense core TMC-1C at 450, 850, and 1200 μm using SCUBA on the James Clerk Maxwell Telescope and MAMBO on the IRAM 30 m telescope. We show that although one can, in principle, use images at these wavelengths to map the emissivity spectral index, temperature, and column density independently, noise and calibration errors would have to be less than ~2% to accurately derive these three quantities from a set of three emission maps. Because our data are not this free of errors, we use our emission maps to fit the dust temperature and column density assuming a constant value of the emissivity spectral index and explore the effects of noise on the derived physical parameters. We find that the derived extinction values for TMC-1C are large for a starless core (~80 mag AV) and the derived temperatures are low (~6 K) in the densest regions of the core, using our derived value of β=1.8.

  11. Mapping.

    ERIC Educational Resources Information Center

    Kinney, Douglas M.; McIntosh, Willard L.

    1979-01-01

    The area of geological mapping in the United States in 1978 increased greatly over that reported in 1977; state geological maps were added for California, Idaho, Nevada, and Alaska last year. (Author/BB)

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

    PubMed

    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.

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

    PubMed

    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

  14. 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.

  15. 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

  16. Genome Wide SSR High Density Genetic Map Construction from an Interspecific Cross of Gossypium hirsutum × Gossypium tomentosum.

    PubMed

    Khan, Muhammad K R; Chen, Haodong; Zhou, Zhongli; Ilyas, Muhammad K; Wang, Xingxing; Cai, Xiaoyan; Wang, Chunying; Liu, Fang; Wang, Kunbo

    2016-01-01

    A high density genetic map was constructed using F2 population derived from an interspecific cross of G. hirsutum × G. tomentosum. The map consisted of 3093 marker loci distributed across all the 26 chromosomes and covered 4365.3 cM of cotton genome with an average inter-marker distance of 1.48 cM. The maximum length of chromosome was 218.38 cM and the minimum was 122.09 cM with an average length of 167.90 cM. A sub-genome covers more genetic distance (2189.01 cM) with an average inter loci distance of 1.53 cM than D sub-genome which covers a length of 2176.29 cM with an average distance of 1.43 cM. There were 716 distorted loci in the map accounting for 23.14% and most distorted loci were distributed on D sub-genome (25.06%), which were more than on A sub-genome (21.23%). In our map 49 segregation hotspots (SDR) were distributed across the genome with more on D sub-genome as compared to A genome. Two post-polyploidization reciprocal translocations of "A2/A3 and A4/A5" were suggested by seven pairs of duplicate loci. The map constructed through these studies is one of the three densest genetic maps in cotton however; this is the first dense genome wide SSR interspecific genetic map between G. hirsutum and G. tomentosum. PMID:27148280

  17. Genome Wide SSR High Density Genetic Map Construction from an Interspecific Cross of Gossypium hirsutum × Gossypium tomentosum.

    PubMed

    Khan, Muhammad K R; Chen, Haodong; Zhou, Zhongli; Ilyas, Muhammad K; Wang, Xingxing; Cai, Xiaoyan; Wang, Chunying; Liu, Fang; Wang, Kunbo

    2016-01-01

    A high density genetic map was constructed using F2 population derived from an interspecific cross of G. hirsutum × G. tomentosum. The map consisted of 3093 marker loci distributed across all the 26 chromosomes and covered 4365.3 cM of cotton genome with an average inter-marker distance of 1.48 cM. The maximum length of chromosome was 218.38 cM and the minimum was 122.09 cM with an average length of 167.90 cM. A sub-genome covers more genetic distance (2189.01 cM) with an average inter loci distance of 1.53 cM than D sub-genome which covers a length of 2176.29 cM with an average distance of 1.43 cM. There were 716 distorted loci in the map accounting for 23.14% and most distorted loci were distributed on D sub-genome (25.06%), which were more than on A sub-genome (21.23%). In our map 49 segregation hotspots (SDR) were distributed across the genome with more on D sub-genome as compared to A genome. Two post-polyploidization reciprocal translocations of "A2/A3 and A4/A5" were suggested by seven pairs of duplicate loci. The map constructed through these studies is one of the three densest genetic maps in cotton however; this is the first dense genome wide SSR interspecific genetic map between G. hirsutum and G. tomentosum.

  18. 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.

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

    PubMed Central

    Šimková, Hana; Svensson, Jan T; Condamine, Pascal; Hřibová, Eva; Suchánková, Pavla; Bhat, Prasanna R; Bartoš, Jan; Šafář, Jan; Close, Timothy J; Doležel, Jaroslav

    2008-01-01

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

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

    SciTech Connect

    Kashiwagi, Toshiya; Suto, Yasushi; Taruya, Atsushi; Yahata, Kazuhiro; Kayo, Issha; Nishimichi, Takahiro

    2015-02-01

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

  1. High-density genetic map construction and identification of a locus controlling weeping trait in an ornamental woody plant (Prunus mume Sieb. et Zucc)

    PubMed Central

    Zhang, Jie; Zhang, Qixiang; Cheng, Tangren; Yang, Weiru; Pan, Huitang; Zhong, Junjun; Huang, Long; Liu, Enze

    2015-01-01

    High-density genetic map is a valuable tool for fine mapping locus controlling a specific trait especially for perennial woody plants. In this study, we firstly constructed a high-density genetic map of mei (Prunus mume) using SLAF markers, developed by specific locus amplified fragment sequencing (SLAF-seq). The linkage map contains 8,007 markers, with a mean marker distance of 0.195 cM, making it the densest genetic map for the genus Prunus. Though weeping trees are used worldwide as landscape plants, little is known about weeping controlling gene(s) (Pl). To test the utility of the high-density genetic map, we did fine-scale mapping of this important ornamental trait. In total, three statistic methods were performed progressively based on the result of inheritance analysis. Quantitative trait loci (QTL) analysis initially revealed that a locus on linkage group 7 was strongly responsible for weeping trait. Mutmap-like strategy and extreme linkage analysis were then applied to fine map this locus within 1.14 cM. Bioinformatics analysis of the locus identified some candidate genes. The successful localization of weeping trait strongly indicates that the high-density map constructed using SLAF markers is a worthy reference for mapping important traits for woody plants. PMID:25776277

  2. High-density genetic map construction and identification of a locus controlling weeping trait in an ornamental woody plant (Prunus mume Sieb. et Zucc).

    PubMed

    Zhang, Jie; Zhang, Qixiang; Cheng, Tangren; Yang, Weiru; Pan, Huitang; Zhong, Junjun; Huang, Long; Liu, Enze

    2015-06-01

    High-density genetic map is a valuable tool for fine mapping locus controlling a specific trait especially for perennial woody plants. In this study, we firstly constructed a high-density genetic map of mei (Prunus mume) using SLAF markers, developed by specific locus amplified fragment sequencing (SLAF-seq). The linkage map contains 8,007 markers, with a mean marker distance of 0.195 cM, making it the densest genetic map for the genus Prunus. Though weeping trees are used worldwide as landscape plants, little is known about weeping controlling gene(s) (Pl). To test the utility of the high-density genetic map, we did fine-scale mapping of this important ornamental trait. In total, three statistic methods were performed progressively based on the result of inheritance analysis. Quantitative trait loci (QTL) analysis initially revealed that a locus on linkage group 7 was strongly responsible for weeping trait. Mutmap-like strategy and extreme linkage analysis were then applied to fine map this locus within 1.14 cM. Bioinformatics analysis of the locus identified some candidate genes. The successful localization of weeping trait strongly indicates that the high-density map constructed using SLAF markers is a worthy reference for mapping important traits for woody plants.

  3. High-density linkage mapping and distribution of segregation distortion regions in the oak genome

    PubMed Central

    Bodénès, Catherine; Chancerel, Emilie; Ehrenmann, François; Kremer, Antoine; Plomion, Christophe

    2016-01-01

    We developed the densest single-nucleotide polymorphism (SNP)-based linkage genetic map to date for the genus Quercus. An 8k gene-based SNP array was used to genotype more than 1,000 full-sibs from two intraspecific and two interspecific full-sib families of Quercus petraea and Quercus robur. A high degree of collinearity was observed between the eight parental maps of the two species. A composite map was then established with 4,261 SNP markers spanning 742 cM over the 12 linkage groups (LGs) of the oak genome. Nine genomic regions from six LGs displayed highly significant distortions of segregation. Two main hypotheses concerning the mechanisms underlying segregation distortion are discussed: genetic load vs. reproductive barriers. Our findings suggest a predominance of pre-zygotic to post-zygotic barriers. PMID:27013549

  4. 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.

  5. A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome.

    PubMed

    Yu, John Z; Kohel, Russell J; Fang, David D; Cho, Jaemin; Van Deynze, Allen; Ulloa, Mauricio; Hoffman, Steven M; Pepper, Alan E; Stelly, David M; Jenkins, Johnie N; Saha, Sukumar; Kumpatla, Siva P; Shah, Manali R; Hugie, William V; Percy, Richard G

    2012-01-01

    Genetic linkage maps play fundamental roles in understanding genome structure, explaining genome formation events during evolution, and discovering the genetic bases of important traits. A high-density cotton (Gossypium spp.) genetic map was developed using representative sets of simple sequence repeat (SSR) and the first public set of single nucleotide polymorphism (SNP) markers to genotype 186 recombinant inbred lines (RILs) derived from an interspecific cross between Gossypium hirsutum L. (TM-1) and G. barbadense L. (3-79). The genetic map comprised 2072 loci (1825 SSRs and 247 SNPs) and covered 3380 centiMorgan (cM) of the cotton genome (AD) with an average marker interval of 1.63 cM. The allotetraploid cotton genome produced equivalent recombination frequencies in its two subgenomes (At and Dt). Of the 2072 loci, 1138 (54.9%) were mapped to 13 At-subgenome chromosomes, covering 1726.8 cM (51.1%), and 934 (45.1%) mapped to 13 Dt-subgenome chromosomes, covering 1653.1 cM (48.9%). The genetically smallest homeologous chromosome pair was Chr. 04 (A04) and 22 (D04), and the largest was Chr. 05 (A05) and 19 (D05). Duplicate loci between and within homeologous chromosomes were identified that facilitate investigations of chromosome translocations. The map augments evidence of reciprocal rearrangement between ancestral forms of Chr. 02 and 03 versus segmental homeologs 14 and 17 as centromeric regions show homeologous between Chr. 02 (A02) and 17 (D02), as well as between Chr. 03 (A03) and 14 (D03). This research represents an important foundation for studies on polyploid cottons, including germplasm characterization, gene discovery, and genome sequence assembly. PMID:22384381

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

    PubMed

    Guajardo, Verónica; Solís, Simón; Sagredo, Boris; Gainza, Felipe; Muñoz, Carlos; Gasic, Ksenija; Hinrichsen, Patricio

    2015-01-01

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

  7. 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

  8. 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. PMID:27572730

  9. 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.

  10. 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

  11. Image of Fomalhaut Dust Ring at 350 Microns: The Relative Column Density Map Shows Pericenter-Apocenter Asymmetry

    NASA Technical Reports Server (NTRS)

    Marsh, K. A.; Velusamy, T.; Dowell, C. D.; Grogan, K.; Beichman, C. A.

    2005-01-01

    We have imaged the circumstellar disk of Fomalhaut at 350 mm wavelength, using SHARC II (Submillimeter High Angular Resolution Camera II) at the Caltech Submillimeter Observatory. The spatial resolution of the raw images (9") has been enhanced by a factor of 3 using the HiRes deconvolution procedure. We find that at this wavelength and signal-to-noise ratio (approx.12), the observed morphology is that of a simple inclined ring (i approx. 70 deg), with little or no other apparent structure--this is the first observation that shows clearly the ring morphology of the disk. We have combined our 350 mm data with Spitzer Space Telescope images at 24, 70, and 160 mm in order to estimate the two-dimensional spatial variation of relative column density ("tau map") using our DISKFIT procedure. The tau map is based on the following physical assumptions: (1) the wavelength variation of opacity is the same throughout the disk, (2) the radial variation of dust temperature is dictated by the energy balance of individual grains in the stellar radiation field, and (3) the vertical scale height of the disk follows a power-law radial variation. The results confirm the ringlike morphology but also show that the geometric center is displaced from the star by about 8 AU and that the ring has an apocentric enhancement of approximately 14% in integrated column density. If we interpret the displacement in terms of elliptical orbital motion due to gravitational perturbation by an unseen planet, then the implied forced eccentricity is 0.06; dynamical modeling then predicts an apocentric density enhancement consistent with that inferred from the tau map.

  12. Mapping of the cometary plasma density around comet CG/67P at perihelion.

    NASA Astrophysics Data System (ADS)

    Pierre, H.; Eriksson, A. I.; Edberg, N. J. T.; Béghin, C.; Décréau, P.; Grard, R.; Hamelin, M.; Johansson, E. P. G.; Johansson, F.; Lebreton, J. P.; Mazelle, C. X.; Odelstad, E.; Randriamboarison, O.; Schmidt, W.; Wattieaux, G.; Winterhalter, D.; Vallières, X.; Vigren, E.; Glassmeier, K. H.; Goetz, C.; Koenders, C.; Richter, I.; Volwerk, M.; Burch, J. L.; Broiles, T. W.; Goldstein, R.; Mandt, K.; Mokashi, P.; Nilsson, H.; Stenberg Wieser, G.; Carr, C.; Cupido, E.; Galand, M. F.; Matteini, L.; Nemeth, Z.; Szego, K.; Vallat, C.; Schwartz, S. J.

    2015-12-01

    In August 2015, comet 67P/Churyumov-Gerasimenko, target of the ESA's Rosetta mission, reached its perihelion at 1.3 AU from the Sun. The Rosetta Plasma Consortium (RPC) onboard the Rosetta spacecraft offers a unique opportunity to analyze the plasma environment during this period. Combining observations from the Mutual Impedance probe (RPC-MIP) and the Langmuir probes (RPC-LAP), we estimate the cometary plasma density. We will present its spatial distribution around the comet when close to perihelion. Combined Mutual impedance and Langmuir probes density measurements are also compared to the density derived from particle measurements (RPC-ICA and RPC-IES). In addition, we will focus on localised, strong variations of the cometary plasma density over short timescales (~ minutes to seconds) observed during this period. These strong plasma density enhancements are interpreted taken into account the electron energy spectrum measured by the Ion and Electron Spectrometer (RPC-IES). Possible correlations of these plasma enhancements with variations in the magnetic field direction measured from the Magnetometer (RPC-MAG) will be discussed.

  13. VizieR Online Data Catalog: Perseus dust optical depth and column density maps (Zari+, 2016)

    NASA Astrophysics Data System (ADS)

    Zari, E.; Lombardi, M.; Alves, J.; Lada, C.; Bouy, H.

    2015-11-01

    We present optical depth and temperature maps of the Perseus Molecular Cloud, created combining Planck and Herschel data. The maps were obtained using Herschel SPIRE 250um, SPIRE 350um, SPIRE 500um, and, where available, PACS 160um data. The file planckherschelfit.fits reports the results of a full SED fit (with free parameters the optical depth and the temperature), at the SPIRE 500um resolution (36-arcsec). The file planckherschelfit2-a.fits uses the temperature from planckherschelfit.fits and the flux at SPIRE 250um to infer the optical depth with a resolution of 18 arcsec. Finally, the catalogue of Class I/0 protostars reports WISE magnitudes for the sources used to estimate the Schmidt law. (3 data files).

  14. 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

  15. 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.

  16. 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. PMID:26779193

  17. Mapping Brucellosis Increases Relative to Elk Density Using Hierarchical Bayesian Models

    PubMed Central

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

    2010-01-01

    The relationship between host density and parasite transmission is central to the effectiveness of many disease management strategies. Few studies, however, have empirically estimated this relationship particularly in large mammals. We applied hierarchical Bayesian methods to a 19-year dataset of over 6400 brucellosis tests of adult female elk (Cervus elaphus) in northwestern Wyoming. Management captures that occurred from January to March were over two times more likely to be seropositive than hunted elk that were killed in September to December, while accounting for site and year effects. Areas with supplemental feeding grounds for elk had higher seroprevalence in 1991 than other regions, but by 2009 many areas distant from the feeding grounds were of comparable seroprevalence. The increases in brucellosis seroprevalence were correlated with elk densities at the elk management unit, or hunt area, scale (mean 2070 km2; range  = [95–10237]). The data, however, could not differentiate among linear and non-linear effects of host density. Therefore, control efforts that focus on reducing elk densities at a broad spatial scale were only weakly supported. Additional research on how a few, large groups within a region may be driving disease dynamics is needed for more targeted and effective management interventions. Brucellosis appears to be expanding its range into new regions and elk populations, which is likely to further complicate the United States brucellosis eradication program. This study is an example of how the dynamics of host populations can affect their ability to serve as disease reservoirs. PMID:20428240

  18. Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Btau_4.0 and UMD3.1 are two distinct cattle reference genome assemblies. In our previous study using the low density BovineSNP50 array, we reported a copy number variation (CNV) analysis on Btau_4.0 with 521 animals of 21 cattle breeds, yielding 682 CNV regions with a total length of 139.8 megabases...

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

    USGS Publications Warehouse

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

    2010-01-01

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

  20. Mapping Human Population Density in and Around New Hapmshire's Loon Lakes: A Comparison of Dasymetric Methods

    EPA Science Inventory

    The impact of anthropogenic stressors on ecosystems is directly related to the pattern of human population density across the landscape; thus, accurate information on the distribution of human populations is critical for associating the impact of human population and ecological r...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  3. Development of high-density linkage map and tagging leaf spot resistance in pearl millet using genotyping-by-sequencing markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pearl millet is an important forage and grain crop in many parts of the world. Genome mapping studies are a prerequisite for tagging agronomically important traits. Genotyping-by-Sequencing (GBS) markers can be used to build high density linkage maps even in species lacking a reference genome. A re...

  4. FEM: Feature-enhanced map

    SciTech Connect

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

    2015-02-26

    A method is presented that modifies a 2mFobs-DFmodelσA-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 2mFobs-DFmodelσA-weighted map.

  5. FEM: Feature-enhanced map

    DOE PAGES

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

    2015-02-26

    A method is presented that modifies a 2mFobs-DFmodelσA-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 themore » starting 2mFobs-DFmodelσA-weighted map.« less

  6. 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

  7. Construction of the first high-density genetic linkage map of Salvia miltiorrhiza using specific length amplified fragment (SLAF) sequencing

    PubMed Central

    Liu, Tian; Guo, Linlin; Pan, Yuling; Zhao, Qi; Wang , Jianhua; Song, Zhenqiao

    2016-01-01

    Salvia miltiorrhiza is an important medicinal crop in traditional Chinese medicine (TCM). Knowledge of its genetic foundation is limited because sufficient molecular markers have not been developed, and therefore a high-density genetic linkage map is incomplete. Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-throughput strategy for large-scale SNP (Single Nucleotide Polymorphisms) discovery and genotyping based on next generation sequencing (NGS). In this study, genomic DNA extracted from two parents and their 96 F1 individuals was subjected to high-throughput sequencing and SLAF library construction. A total of 155.96 Mb of data containing 155,958,181 pair-end reads were obtained after preprocessing. The average coverage of each SLAF marker was 83.43-fold for the parents compared with 10.36-fold for the F1 offspring. The final linkage map consists of 5,164 SLAFs in 8 linkage groups (LGs) and spans 1,516.43 cM, with an average distance of 0.29 cM between adjacent markers. The results will not only provide a platform for mapping quantitative trait loci but also offer a critical new tool for S. miltiorrhiza biotechnology and comparative genomics as well as a valuable reference for TCM studies. PMID:27040179

  8. Surface Current Density Mapping for Identification of Gastric Slow Wave Propagation

    PubMed Central

    Bradshaw, L. A.; Cheng, L. K.; Richards, W. O.; Pullan, A. J.

    2009-01-01

    The magnetogastrogram records clinically relevant parameters of the electrical slow wave of the stomach noninvasively. Besides slow wave frequency, gastric slow wave propagation velocity is a potentially useful clinical indicator of the state of health of gastric tissue, but it is a difficult parameter to determine from noninvasive bioelectric or biomagnetic measurements. We present a method for computing the surface current density (SCD) from multichannel magnetogastrogram recordings that allows computation of the propagation velocity of the gastric slow wave. A moving dipole source model with hypothetical as well as realistic biomagnetometer parameters demonstrates that while a relatively sparse array of magnetometer sensors is sufficient to compute a single average propagation velocity, more detailed information about spatial variations in propagation velocity requires higher density magnetometer arrays. Finally, the method is validated with simultaneous MGG and serosal EMG measurements in a porcine subject. PMID:19403355

  9. Land use mapping using edge density texture measures on Thematic Mapper simulator data

    NASA Technical Reports Server (NTRS)

    Hlavka, C. A.

    1985-01-01

    Texture analysis was performed as part of an investigation of the information content of Thematic Mapper (TM) imagery. High altitude aircraft scanner imagery from the Airborne Thematic Mapper (ATM) instrument was acquired over central California and used to simulate TM data. Edge density texture images were constructed by computation of proportions of edge pixels in a 31 x 31 moving window on a near infrared ATM band. A training technique was employed to select computational parameters to maximize the difference between edge density measurements in urban and in rural areas. The results of classification of the texture images showed that urban and rural areas could be distinguished with texture alone, indicating that inclusion of texture in automated classification procedures could significantly improve their accuracy.

  10. Enhanced magnetic flux density mapping using coherent steady state equilibrium signal in MREIT

    NASA Astrophysics Data System (ADS)

    Jeong, Woo Chul; Lee, Mun Bae; Sajib, Saurav Z. K.; Kim, Hyung Joong; Kwon, Oh In; Woo, Eung Je

    2016-03-01

    Measuring the z-component of magnetic flux density B = (Bx, By, Bz) induced by transversally injected current, magnetic resonance electrical impedance tomography (MREIT) aims to visualize electrical property (current density and/or conductivity distribution) in a three-dimensional imaging object. For practical implementations of MREIT technique, it is critical to reduce injection of current pulse within safety requirements. With the goal of minimizing the noise level in measured Bz data, we propose a new method to enhance the measure Bz data using steady-state coherent gradient multi-echo (SSC-GME) MR pulse sequence combining with injection current nonlinear encoding (ICNE) method in MREIT, where the ICNE technique injects current during a readout gradient to maximize the signal intensity of phase signal including Bz. The total phase offset in SSC-GME includes additional magnetic flux density due to the injected current, which is different from the phase signal for the conventional spoiled MR pulse sequence. We decompose the magnetization precession phase from the total phase offset including Bz and optimize Bz data using the steady-state equilibrium signal. Results from a real phantom experiment including different kinds of anomalies demonstrated that the proposed method enhanced Bz comparing to a conventional spoiled pulse sequence.

  11. 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

  12. Forget about equality.

    PubMed

    Powers, Madison

    1996-06-01

    Justice is widely thought to consist in equality. For many theorists, the central question has been: Equality of what? The author argues that the ideal of equality distorts practical reasoning and has deeply counterintuitive implications. Moreover, an alternative view of distributive justice can give a better account of what egalitarians should care about than can any of the competing ideals of equality.

  13. Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS)

    PubMed Central

    Pootakham, Wirulda; Ruang-Areerate, Panthita; Jomchai, Nukoon; Sonthirod, Chutima; Sangsrakru, Duangjai; Yoocha, Thippawan; Theerawattanasuk, Kanikar; Nirapathpongporn, Kanlaya; Romruensukharom, Phayao; Tragoonrung, Somvong; Tangphatsornruang, Sithichoke

    2015-01-01

    Construction of linkage maps is crucial for genetic studies and marker-assisted breeding programs. Recent advances in next generation sequencing technologies allow for the generation of high-density linkage maps, especially in non-model species lacking extensive genomic resources. Here, we constructed a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis), the sole commercial producer of high-quality natural rubber. We applied a genotyping-by-sequencing (GBS) technique to simultaneously discover and genotype single nucleotide polymorphism (SNP) markers in two rubber tree populations. A total of 21,353 single nucleotide substitutions were identified, 55% of which represented transition events. GBS-based genetic maps of populations P and C comprised 1704 and 1719 markers and encompassed 2041 cM and 1874 cM, respectively. The average marker densities of these two maps were one SNP in 1.23–1.25 cM. A total of 1114 shared SNP markers were used to merge the two component maps. An integrated linkage map consisted of 2321 markers and spanned the cumulative length of 2052 cM. The composite map showed a substantial improvement in marker density, with one SNP marker in every 0.89 cM. To our knowledge, this is the most saturated genetic map in rubber tree to date. This integrated map allowed us to anchor 28,965 contigs, covering 135 Mb or 12% of the published rubber tree genome. We demonstrated that GBS is a robust and cost-effective approach for generating a common set of genome-wide SNP data suitable for constructing integrated linkage maps from multiple populations in a highly heterozygous agricultural species. PMID:26074933

  14. High-Density Genetic Mapping Identifies New Major Loci for Tolerance to Low-Phosphorus Stress in Soybean

    PubMed Central

    Zhang, Dan; Li, Hongyan; Wang, Jinshe; Zhang, Hengyou; Hu, Zhenbin; Chu, Shanshan; Lv, Haiyan; Yu, Deyue

    2016-01-01

    Phosphorus (P) is essential for all living cells and organisms, and low-P stress represents a major constraint on plant growth and yield worldwide. Soybean is an important economical resource of protein and oil for human and animals, and soybean is also a high-P demand species that is sensitive to low-P stress, which is considered a major constraint on soybean production. However, P efficiency is an important complex quantitative trait involving multiple genes, and the mechanisms underlying soybean P efficiency are largely unknown. Here, we reported the construction of a high-density genetic map using a specific-locus amplified fragment sequencing (SLAF-seq) strategy in soybean. This map, spanning 3020.59 cM in length, contained 6159 markers on 20 chromosomes, with an average distance of 0.49 cM between adjacent markers. Based on this map, 20 loci, including eight novel loci, associated with P efficiency-related traits were identified across multiple years and treatments. The confidence intervals of almost all QTLs were refined significantly, and the accuracy of this map was evidenced by coincident detections of the previously identified P efficiency-related genes GmACP1 and GmPT1. Notably, a highly significant novel QTL located on chromosome 4, q4-2, was identified across traits, years and treatments. Several candidate genes, such as a pectin methylesterase-encoding gene (Glyma.04G214000) and a protein kinase gene (Glyma.13G161900), with significantly differential expression upon low-P stress were considered as promising candidates involved in regulating soybean P efficiency. Markers that tightly associated with P efficiency could be used for marker-assisted selection in a soybean P efficient breeding program. Further, dissection of these QTLs will facilitate gene cloning underlying P efficiency in soybean, and increase our understanding of efficient use of P in enhancing crop yield. PMID:27065041

  15. High-density mapping suggests cytoplasmic male sterility with two restorer genes in almond × peach progenies

    PubMed Central

    Donoso, José Manuel; Eduardo, Iban; Picañol, Roger; Batlle, Ignasi; Howad, Werner; Aranzana, María José; Arús, Pere

    2015-01-01

    Peach (Prunus persica) and almond (Prunus dulcis) are two sexually compatible species that produce fertile offspring. Almond, a highly polymorphic species, is a potential source of new genes for peach that has a strongly eroded gene pool. Here we describe the genetics of a male sterile phenotype that segregated in two almond (‘Texas’) × peach (‘Earlygold’) progenies: an F2 (T×E) and a backcross one (T1E) to the ‘Earlygold’ parent. High-density maps were developed using a 9k peach SNP chip and 135 simple-sequence repeats. Three highly syntenic and collinear maps were obtained: one for the F2 (T×E) and two for the backcross, T1E (for the hybrid) and E (for ‘Earlygold’). A major reduction of recombination was observed in the interspecific maps (T×E and T1E) compared to the intraspecific parent (E). The E map also had extensive monomorphic genomic regions suggesting the presence of large DNA fragments identical by descent. Our data for the male sterility character were consistent with the existence of cytoplasmic male sterility, where individuals having the almond cytoplasm required the almond allele in at least one of two independent restorer genes, Rf1 and Rf2, to be fertile. The restorer genes were located in a 3.4 Mbp fragment of linkage group 2 (Rf1) and 1.4 Mbp of linkage group 6 (Rf2). Both fragments contained several genes coding for pentatricopeptide proteins, demonstrated to be responsible for restoring fertility in other species. The implications of these results for using almond as a source of novel variability in peach are discussed. PMID:26504569

  16. High-density mapping suggests cytoplasmic male sterility with two restorer genes in almond × peach progenies.

    PubMed

    Donoso, José Manuel; Eduardo, Iban; Picañol, Roger; Batlle, Ignasi; Howad, Werner; Aranzana, María José; Arús, Pere

    2015-01-01

    Peach (Prunus persica) and almond (Prunus dulcis) are two sexually compatible species that produce fertile offspring. Almond, a highly polymorphic species, is a potential source of new genes for peach that has a strongly eroded gene pool. Here we describe the genetics of a male sterile phenotype that segregated in two almond ('Texas') × peach ('Earlygold') progenies: an F2 (T×E) and a backcross one (T1E) to the 'Earlygold' parent. High-density maps were developed using a 9k peach SNP chip and 135 simple-sequence repeats. Three highly syntenic and collinear maps were obtained: one for the F2 (T×E) and two for the backcross, T1E (for the hybrid) and E (for 'Earlygold'). A major reduction of recombination was observed in the interspecific maps (T×E and T1E) compared to the intraspecific parent (E). The E map also had extensive monomorphic genomic regions suggesting the presence of large DNA fragments identical by descent. Our data for the male sterility character were consistent with the existence of cytoplasmic male sterility, where individuals having the almond cytoplasm required the almond allele in at least one of two independent restorer genes, Rf1 and Rf2, to be fertile. The restorer genes were located in a 3.4 Mbp fragment of linkage group 2 (Rf1) and 1.4 Mbp of linkage group 6 (Rf2). Both fragments contained several genes coding for pentatricopeptide proteins, demonstrated to be responsible for restoring fertility in other species. The implications of these results for using almond as a source of novel variability in peach are discussed.

  17. High-density genetic map of the BRCA1 region of chromosome 17q12-q21

    SciTech Connect

    Anderson, L.A.; Friedman, L.; Lynch, E.; King, M.C. ); Osborne-Lawrence, S.; Bowcock, A. ); Weissenbach, J. )

    1993-09-01

    To facilitate the positional cloning of the breast-ovarian cancer gene BRCA1, the authors constructed a high-density genetic map of the 8.3-cM interval between D17S250 and GIP on chromosome 17q12-q21. Markers were mapped by linkage in the CEPH and in extended kindreds in the breast cancer series. The map comprises 33 ordered polymorphisms, including 12 genes and 21 anonymous markers, yielding an average of one polymorphism every 250 kb. Twenty-five of the markers are PCR-based systems. The order of polymorphic genes and markers is cen-D17S250-D17S518-HER2-THRA1-RARA-D17S80-KRT10-[D17S800-D17S857]-GAS-D17S856-EDH17B-D17S855-D17S859-D17S858-[PPY-D17S78]-D17S183-EPB3-D17S579-D17S509-[D17S508-D17S190 = D17S810]-D17S791-[D17S181 = D17S806]-D17S797-HOX2B-GP3A-[D17S507 = GIP]-qter. BRCA1 lies in the middle of the interval, between THRA1 and D17S183. Markers from this map can be used to determine whether cancer is linked to BRCA1 in families, to evaluate whether tumors have lost heterozygosity at loci in the region, and to identify probes for characterizing chromosomal rearrangements from patients and from tumors. 21 refs., 1 fig., 3 tabs.

  18. 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

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

    PubMed

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

    2015-10-27

    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.

  20. High-density genetic linkage map construction and identification of fruit-related QTLs in pear using SNP and SSR markers.

    PubMed

    Wu, Jun; Li, Lei-Ting; Li, Meng; Khan, M Awais; Li, Xiu-Gen; Chen, Hui; Yin, Hao; Zhang, Shao-Ling

    2014-11-01

    Pear (Pyrus spp) is an important fruit crop, grown in all temperate regions of the world, with global production ranked after grape and apples among deciduous tree crops. A high-density linkage map is a valuable tool for fine mapping quantitative trait loci (QTL) and map-based gene cloning. In this study, we firstly constructed a high-density linkage map of pear using SNPs integrated with SSRs, developed by the rapid and robust technology of restriction-associated DNA sequencing (RADseq). The linkage map consists of 3143 SNP markers and 98 SSRs, 3241 markers in total, spanning 2243.4 cM, with an average marker distance of 0.70 cM. Anchoring SSRs were able to anchor seventeen linkage groups to their corresponding chromosomes. Based on this high-density integrated pear linkage map and two years of fruit phenotyping, a total of 32 potential QTLs for 11 traits, including length of pedicel (LFP), single fruit weight (SFW), soluble solid content (SSC), transverse diameter (TD), vertical diameter (VD), calyx status (CS), flesh colour (FC), juice content (JC), number of seeds (NS), skin colour (SC), and skin smooth (SS), were identified and positioned on the genetic map. Among them, some important fruit-related traits have for the first time been identified, such as calyx status, length of pedicel, and flesh colour, and reliable localization of QTLs were verified repeatable. This high-density linkage map of pear is a worthy reference for mapping important fruit traits, QTL identification, and comparison and combination of different genetic maps.

  1. Quantification of Pathologic Air Trapping in Lung Transplant Patients Using CT Density Mapping: Comparison with Other CT Air Trapping Measures.

    PubMed

    Solyanik, Olga; Hollmann, Patrick; Dettmer, Sabine; Kaireit, Till; Schaefer-Prokop, Cornelia; Wacker, Frank; Vogel-Claussen, Jens; Shin, Hoen-oh

    2015-01-01

    To determine whether density mapping (DM) is more accurate for detection and quantification of pathologic air trapping (pAT) in patients after lung transplantation compared to other CT air trapping measures. One-hundred forty-seven lung and heart-lung transplant recipients underwent CT-examinations at functional residual capacity (FRC) and total lung capacity (TLC) and PFT six months after lung transplantation. Quantification of air trapping was performed with the threshold-based method in expiration (EXP), density mapping (DM) and the expiratory to inspiratory ratio of the mean lung density (E/I-ratio MLD). A non-rigid registration of inspiration-expiration CT-data with a following voxel-to-voxel mapping was carried out for DM. Systematic variation of attenuation ranges was performed for EXP and DM and correlated with the ratio of residual volume to total lung capacity (RV/TLC) by Spearman rank correlation test. AT was considered pathologic if RV/TLC was above the 95th percentile of the predicted upper limit of normal values. Receiver operating characteristic (ROC) analysis was performed. The optimal attenuation range for the EXP method was from -790 HU to -950 HU (EXP(-790 to -950HU)) (r = 0.524, p<0.001) to detect air trapping. Within the segmented lung parenchyma, AT was best defined as voxel difference less than 80 HU between expiration and registered inspiration using the DM method. DM correlated best with RV/TLC (r = 0.663, p<0.001). DM and E/I-ratio MLD showed a larger AUC (0.78; 95% CI 0.69-0.86; 0.76, 95% CI 0.67-0.85) than EXP(-790 HU to -950 HU) (0.71, 95% CI 0.63-0.78). DM and E/I-ratio MLD showed better correlation with RV/TLC and are more suited quantitative CT-methods to detect pAT in lung transplant patients than the EXP(-790HU to -950HU).

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

    PubMed

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

    2012-12-01

    Using the Immunochip custom SNP array, which was designed for dense genotyping of 186 loci identified through genome-wide association studies (GWAS), we analyzed 11,475 individuals with rheumatoid arthritis (cases) of European ancestry and 15,870 controls for 129,464 markers. We combined these data in a meta-analysis with GWAS data from additional independent cases (n = 2,363) and controls (n = 17,872). We identified 14 new susceptibility loci, 9 of which were associated with rheumatoid arthritis overall and five of which were specifically associated with disease that was positive for anticitrullinated peptide antibodies, bringing the number of confirmed rheumatoid arthritis risk loci in individuals of European ancestry to 46. We refined the peak of association to a single gene for 19 loci, identified secondary independent effects at 6 loci and identified association to low-frequency variants at 4 loci. Bioinformatic analyses generated strong hypotheses for the causal SNP at seven loci. This study illustrates the advantages of dense SNP mapping analysis to inform subsequent functional investigations.

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

    PubMed

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

    2012-12-01

    Using the Immunochip custom SNP array, which was designed for dense genotyping of 186 loci identified through genome-wide association studies (GWAS), we analyzed 11,475 individuals with rheumatoid arthritis (cases) of European ancestry and 15,870 controls for 129,464 markers. We combined these data in a meta-analysis with GWAS data from additional independent cases (n = 2,363) and controls (n = 17,872). We identified 14 new susceptibility loci, 9 of which were associated with rheumatoid arthritis overall and five of which were specifically associated with disease that was positive for anticitrullinated peptide antibodies, bringing the number of confirmed rheumatoid arthritis risk loci in individuals of European ancestry to 46. We refined the peak of association to a single gene for 19 loci, identified secondary independent effects at 6 loci and identified association to low-frequency variants at 4 loci. Bioinformatic analyses generated strong hypotheses for the causal SNP at seven loci. This study illustrates the advantages of dense SNP mapping analysis to inform subsequent functional investigations. PMID:23143596

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

    PubMed Central

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

    2012-01-01

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

  5. Doppler Spectrometry for Ultrafast Temporal Mapping of Density Dynamics in Laser-Induced Plasmas

    SciTech Connect

    Mondal, S.; Lad, Amit D.; Ahmed, Saima; Narayanan, V.; Pasley, J.; Rajeev, P. P.; Robinson, A. P. L.; Kumar, G. Ravindra

    2010-09-03

    We present high resolution measurements of the ultrafast temporal dynamics of the critical surface in moderately overdense, hot plasma by using two-color, pump-probe Doppler spectrometry. Our measurements clearly capture the initial inward motion of the plasma inside the critical surface of the pump laser which is followed by outward expansion. The measured instantaneous velocity and acceleration profiles are very well reproduced by a hybrid simulation that uses a 1D electromagnetic particle-in-cell simulation for the initial evolution and a hydrodynamics simulation for the later times. The combination of high temporal resolution and dynamic range in our measurements clearly provides quantitative unraveling of the dynamics in this important region, enabling this as a powerful technique to obtain ultrafast snapshots of plasma density and temperature profiles for providing benchmarks for simulations.

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

    PubMed

    Maccaferri, Marco; Ricci, Andrea; Salvi, Silvio; Milner, Sara Giulia; Noli, Enrico; Martelli, Pier Luigi; Casadio, Rita; Akhunov, Eduard; Scalabrin, Simone; Vendramin, Vera; Ammar, Karim; Blanco, Antonio; Desiderio, Francesca; Distelfeld, Assaf; Dubcovsky, Jorge; Fahima, Tzion; Faris, Justin; Korol, Abraham; Massi, Andrea; Mastrangelo, Anna Maria; Morgante, Michele; Pozniak, Curtis; N'Diaye, Amidou; Xu, Steven; Tuberosa, Roberto

    2015-06-01

    Consensus linkage maps are important tools in crop genomics. We have assembled a high-density tetraploid wheat consensus map by integrating 13 data sets from independent biparental populations involving durum wheat cultivars (Triticum turgidum ssp. durum), cultivated emmer (T. turgidum ssp. dicoccum) and their ancestor (wild emmer, T. turgidum ssp. dicoccoides). The consensus map harboured 30 144 markers (including 26 626 SNPs and 791 SSRs) half of which were present in at least two component maps. The final map spanned 2631 cM of all 14 durum wheat chromosomes and, differently from the individual component maps, all markers fell within the 14 linkage groups. Marker density per genetic distance unit peaked at centromeric regions, likely due to a combination of low recombination rate in the centromeric regions and even gene distribution along the chromosomes. Comparisons with bread wheat indicated fewer regions with recombination suppression, making this consensus map valuable for mapping in the A and B genomes of both durum and bread wheat. Sequence similarity analysis allowed us to relate mapped gene-derived SNPs to chromosome-specific transcripts. Dense patterns of homeologous relationships have been established between the A- and B-genome maps and between nonsyntenic homeologous chromosome regions as well, the latter tracing to ancient translocation events. The gene-based homeologous relationships are valuable to infer the map location of homeologs of target loci/QTLs. Because most SNP and SSR markers were previously mapped in bread wheat, this consensus map will facilitate a more effective integration and exploitation of genes and QTL for wheat breeding purposes. PMID:25424506

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

    PubMed

    Maccaferri, Marco; Ricci, Andrea; Salvi, Silvio; Milner, Sara Giulia; Noli, Enrico; Martelli, Pier Luigi; Casadio, Rita; Akhunov, Eduard; Scalabrin, Simone; Vendramin, Vera; Ammar, Karim; Blanco, Antonio; Desiderio, Francesca; Distelfeld, Assaf; Dubcovsky, Jorge; Fahima, Tzion; Faris, Justin; Korol, Abraham; Massi, Andrea; Mastrangelo, Anna Maria; Morgante, Michele; Pozniak, Curtis; N'Diaye, Amidou; Xu, Steven; Tuberosa, Roberto

    2015-06-01

    Consensus linkage maps are important tools in crop genomics. We have assembled a high-density tetraploid wheat consensus map by integrating 13 data sets from independent biparental populations involving durum wheat cultivars (Triticum turgidum ssp. durum), cultivated emmer (T. turgidum ssp. dicoccum) and their ancestor (wild emmer, T. turgidum ssp. dicoccoides). The consensus map harboured 30 144 markers (including 26 626 SNPs and 791 SSRs) half of which were present in at least two component maps. The final map spanned 2631 cM of all 14 durum wheat chromosomes and, differently from the individual component maps, all markers fell within the 14 linkage groups. Marker density per genetic distance unit peaked at centromeric regions, likely due to a combination of low recombination rate in the centromeric regions and even gene distribution along the chromosomes. Comparisons with bread wheat indicated fewer regions with recombination suppression, making this consensus map valuable for mapping in the A and B genomes of both durum and bread wheat. Sequence similarity analysis allowed us to relate mapped gene-derived SNPs to chromosome-specific transcripts. Dense patterns of homeologous relationships have been established between the A- and B-genome maps and between nonsyntenic homeologous chromosome regions as well, the latter tracing to ancient translocation events. The gene-based homeologous relationships are valuable to infer the map location of homeologs of target loci/QTLs. Because most SNP and SSR markers were previously mapped in bread wheat, this consensus map will facilitate a more effective integration and exploitation of genes and QTL for wheat breeding purposes.

  8. A high-density SNP Map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12.

    PubMed

    Talukder, Zahirul I; Gong, Li; Hulke, Brent S; Pegadaraju, Venkatramana; Song, Qijian; Schultz, Quentin; Qi, Lili

    2014-01-01

    A high-resolution genetic map of sunflower was constructed by integrating SNP data from three F2 mapping populations (HA 89/RHA 464, B-line/RHA 464, and CR 29/RHA 468). The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers derived from RAD tag sequencing and 118 publicly available SSR markers distributed in 17 linkage groups, corresponding to the haploid chromosome number of sunflower. The maximum interval between markers in the consensus map is 12.37 cM and the average distance is 0.28 cM between adjacent markers. Despite a few short-distance inversions in marker order, the consensus map showed high levels of collinearity among individual maps with an average Spearman's rank correlation coefficient of 0.972 across the genome. The order of the SSR markers on the consensus map was also in agreement with the order of the individual map and with previously published sunflower maps. Three individual and one consensus maps revealed the uneven distribution of markers across the genome. Additionally, we performed fine mapping and marker validation of the rust resistance gene R12, providing closely linked SNP markers for marker-assisted selection of this gene in sunflower breeding programs. This high resolution consensus map will serve as a valuable tool to the sunflower community for studying marker-trait association of important agronomic traits, marker assisted breeding, map-based gene cloning, and comparative mapping.

  9. Executive Dysfunction and Reward Dysregulation: A High-Density Electrical Mapping Study in Cocaine Abusers

    PubMed Central

    Morie, Kristen P.; De Sanctis, Pierfilippo; Garavan, Hugh; Foxe, John J.

    2015-01-01

    Executive function deficits and reward dysregulation, which mainly manifests as anhedonia, are well documented in drug abusers. We investigated specific aspects of executive function (inhibitory control and cognitive control), as well as anhedonia, in a cohort of current cocaine abusers in order to ascertain to what extent these factors are associated with more severe drug dependence. Participants filled out questionnaires relating to anhedonia and their addiction history. Participants also performed a response inhibition task while high-density event-related potentials (ERPs) were recorded. Electrophysiological responses to successful inhibitions (N2/P3 components) and to commission errors (ERN/Pe components) were compared between 23 current users of cocaine and 27 non-using controls. A regression model was performed to determine the association of our measures of reward dysregulation and executive function with addiction severity. As expected, cocaine users performed more poorly than controls on the inhibitory control task and showed significant electrophysiological differences. They were also generally more anhedonic than controls. Higher levels of anhedonia were associated with more severe substance use, whereas the level of executive dysfunction was not associated with more severe substance use. However, N2 amplitude was associated with duration of drug use. Further, inhibitory control and anhedonia were correlated, but only in controls. These data suggest that while executive dysfunction characterizes drug abuse, it is anhedonia, independent of executive dysfunction, that is most strongly associated with more severe use. PMID:24911989

  10. A High-Density Genetic Map Identifies a Novel Major QTL for Boron Efficiency in Oilseed Rape (Brassica napus L.)

    PubMed Central

    Wang, Xiaohua; Zhao, Hua; Shi, Lei; Xu, Fangsen

    2014-01-01

    Low boron (B) seriously limits the growth of oilseed rape (Brassica napus L.), a high B demand species that is sensitive to low B conditions. Significant genotypic variations in response to B deficiency have been observed among B. napus cultivars. To reveal the genetic basis for B efficiency in B. napus, quantitative trait loci (QTLs) for the plant growth traits, B uptake traits and the B efficiency coefficient (BEC) were analyzed using a doubled haploid (DH) population derived from a cross between a B-efficient parent, Qingyou 10, and a B-inefficient parent, Westar 10. A high-density genetic map was constructed based on single nucleotide polymorphisms (SNPs) assayed using Brassica 60 K Infinium BeadChip Array, simple sequence repeats (SSRs) and amplified fragment length polymorphisms (AFLPs). The linkage map covered a total length of 2139.5 cM, with 19 linkage groups (LGs) and an average distance of 1.6 cM between adjacent markers. Based on hydroponic evaluation of six B efficiency traits measured in three separate repeated trials, a total of 52 QTLs were identified, accounting for 6.14–46.27% of the phenotypic variation. A major QTL for BEC, qBEC-A3a, was co-located on A3 with other QTLs for plant growth and B uptake traits under low B stress. Using a subset of substitution lines, qBEC-A3a was validated and narrowed down to the interval between CNU384 and BnGMS436. The results of this study provide a novel major locus located on A3 for B efficiency in B. napus that will be suitable for fine mapping and marker-assisted selection breeding for B efficiency in B. napus. PMID:25375356

  11. High-density interspecific genetic linkage mapping provides insights into genomic incompatibility between channel catfish and blue catfish.

    PubMed

    Liu, S; Li, Y; Qin, Z; Geng, X; Bao, L; Kaltenboeck, L; Kucuktas, H; Dunham, R; Liu, Z

    2016-02-01

    Catfish is the leading aquaculture species in the United States. The interspecific hybrid catfish produced by mating female channel catfish with male blue catfish outperform both of their parent species in a number of traits. However, mass production of the hybrids has been difficult because of reproductive isolation. Investigations of genome structure and organization of the hybrids provide insights into the genetic basis for maintenance of species divergence in the face of gene flow, thereby helping develop strategies for introgression and efficient production of the hybrids for aquaculture. In this study, we constructed a high-density genetic linkage map using the hybrid catfish system with the catfish 250K SNP array. A total of 26,238 SNPs were mapped to 29 linkage groups, with 12,776 unique marker positions. The linkage map spans approximately 3240 cM with an average intermarker distance of 0.25 cM. A fraction of markers (986 of 12,776) exhibited significant deviation from the expected Mendelian ratio of segregation, and they were clustered in major genomic blocks across 15 LGs, most notably LG9 and LG15. The distorted markers exhibited significant bias for maternal alleles among the backcross progenies, suggesting strong selection against the blue catfish alleles. The clustering of distorted markers within genomic blocks should lend insights into speciation as marked by incompatibilities between the two species. Such findings should also have profound implications for understanding the genomic evolution of closely related species as well as the introgression of hybrid production programs in aquaculture. PMID:26537786

  12. A high-density SSR genetic map constructed from a F2 population of Gossypium hirsutum and Gossypium darwinii.

    PubMed

    Chen, Haodong; Khan, M Kashif Riaz; Zhou, Zhongli; Wang, Xingxing; Cai, Xiaoyan; Ilyas, M Kashif; Wang, Chunying; Wang, Yuhong; Li, Yuqiang; Liu, Fang; Wang, Kunbo

    2015-12-15

    The cultivated allotetraploid species Gossypium hirsutum, accounts for 90% of the world cotton production, has narrow genetic basis that's why its yield, quality or stress resistance breeding is stagnant. It is therefore, essential to explore desirable genes from Gossypium darwinii which has enviable traits such as high fiber fineness, drought tolerance, fusarium and verticillium resistance. We used G. darwinii as primary plant materials in this study not only to enrich the genetic diversity of exiting germplasm but also to better understand its genome structure. An interspecific high density linkage map of allotetraploid cotton was constructed using F2 population (G. hirsutum×G. darwinii). The map was based entirely on genome-wide simple sequence repeat (SSR) markers. A total of 2763 markers were mapped in 26 linkage groups (chromosomes) covering a genome length of 4176.7cM with an average inter-locus distance of 1.5cM. The length of the chromosomes ranged from 84.7 to 238.5cM with an average length of 160.6cM. At subgenome length was 2160.7cM with an average distance of 1.6cM, where as Dt genome length was 2016cM with an average distance of 1.4cM. There were 601 distorted SSR loci. Less number of segregation distortion loci were located in At subgenome than in Dt subgenome. Two post-polyploidization reciprocal translocations of "A2/A3 and A4/A5" were suggested by 44 pairs of duplicate loci.

  13. High-density interspecific genetic linkage mapping provides insights into genomic incompatibility between channel catfish and blue catfish.

    PubMed

    Liu, S; Li, Y; Qin, Z; Geng, X; Bao, L; Kaltenboeck, L; Kucuktas, H; Dunham, R; Liu, Z

    2016-02-01

    Catfish is the leading aquaculture species in the United States. The interspecific hybrid catfish produced by mating female channel catfish with male blue catfish outperform both of their parent species in a number of traits. However, mass production of the hybrids has been difficult because of reproductive isolation. Investigations of genome structure and organization of the hybrids provide insights into the genetic basis for maintenance of species divergence in the face of gene flow, thereby helping develop strategies for introgression and efficient production of the hybrids for aquaculture. In this study, we constructed a high-density genetic linkage map using the hybrid catfish system with the catfish 250K SNP array. A total of 26,238 SNPs were mapped to 29 linkage groups, with 12,776 unique marker positions. The linkage map spans approximately 3240 cM with an average intermarker distance of 0.25 cM. A fraction of markers (986 of 12,776) exhibited significant deviation from the expected Mendelian ratio of segregation, and they were clustered in major genomic blocks across 15 LGs, most notably LG9 and LG15. The distorted markers exhibited significant bias for maternal alleles among the backcross progenies, suggesting strong selection against the blue catfish alleles. The clustering of distorted markers within genomic blocks should lend insights into speciation as marked by incompatibilities between the two species. Such findings should also have profound implications for understanding the genomic evolution of closely related species as well as the introgression of hybrid production programs in aquaculture.

  14. Ultra-High Density, Transcript-Based Genetic Maps of Pepper Define Recombination in the Genome and Synteny Among Related Species

    PubMed Central

    Hill, Theresa; Ashrafi, Hamid; Chin-Wo, Sebastian Reyes; Stoffel, Kevin; Truco, Maria-Jose; Kozik, Alexander; Michelmore, Richard; Van Deynze, Allen

    2015-01-01

    Our ability to assemble complex genomes and construct ultradense genetic maps now allows the determination of recombination rates, translocations, and the extent of genomic collinearity between populations, species, and genera. We developed two ultradense genetic linkage maps for pepper from single-position polymorphisms (SPPs) identified de novo with a 30,173 unigene pepper genotyping array. The Capsicum frutescens × C. annuum interspecific and the C. annuum intraspecific genetic maps were constructed comprising 16,167 and 3,878 unigene markers in 2108 and 783 genetic bins, respectively. Accuracies of marker groupings and orders are validated by the high degree of collinearity between the two maps. Marker density was sufficient to locate the chromosomal breakpoint resulting in the P1/P8 translocation between C. frutescens and C. annuum to a single bin. The two maps aligned to the pepper genome showed varying marker density along the chromosomes. There were extensive chromosomal regions with suppressed recombination and reduced intraspecific marker density. These regions corresponded to the pronounced nonrecombining pericentromeric regions in tomato, a related Solanaceous species. Similar to tomato, the extent of reduced recombination appears to be more pronounced in pepper than in other plant species. Alignment of maps with the tomato and potato genomes shows the presence of previously known translocations and a translocation event that was not observed in previous genetic maps of pepper. PMID:26355020

  15. Ultra-High Density, Transcript-Based Genetic Maps of Pepper Define Recombination in the Genome and Synteny Among Related Species.

    PubMed

    Hill, Theresa; Ashrafi, Hamid; Chin-Wo, Sebastian Reyes; Stoffel, Kevin; Truco, Maria-Jose; Kozik, Alexander; Michelmore, Richard; Van Deynze, Allen

    2015-09-08

    Our ability to assemble complex genomes and construct ultradense genetic maps now allows the determination of recombination rates, translocations, and the extent of genomic collinearity between populations, species, and genera. We developed two ultradense genetic linkage maps for pepper from single-position polymorphisms (SPPs) identified de novo with a 30,173 unigene pepper genotyping array. The Capsicum frutescens × C. annuum interspecific and the C. annuum intraspecific genetic maps were constructed comprising 16,167 and 3,878 unigene markers in 2108 and 783 genetic bins, respectively. Accuracies of marker groupings and orders are validated by the high degree of collinearity between the two maps. Marker density was sufficient to locate the chromosomal breakpoint resulting in the P1/P8 translocation between C. frutescens and C. annuum to a single bin. The two maps aligned to the pepper genome showed varying marker density along the chromosomes. There were extensive chromosomal regions with suppressed recombination and reduced intraspecific marker density. These regions corresponded to the pronounced nonrecombining pericentromeric regions in tomato, a related Solanaceous species. Similar to tomato, the extent of reduced recombination appears to be more pronounced in pepper than in other plant species. Alignment of maps with the tomato and potato genomes shows the presence of previously known translocations and a translocation event that was not observed in previous genetic maps of pepper.

  16. 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.

  17. 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…

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

    PubMed Central

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

    2015-01-01

    Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx. PMID:25760616

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

    SciTech Connect

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

    2015-03-01

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

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

    PubMed

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

    2015-03-01

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

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

    PubMed Central

    Guajardo, Verónica; Solís, Simón; Sagredo, Boris; Gainza, Felipe; Muñoz, Carlos; Gasic, Ksenija; Hinrichsen, Patricio

    2015-01-01

    Linkage maps are valuable tools in genetic and genomic studies. For sweet cherry, linkage maps have been constructed using mainly microsatellite markers (SSRs) and, recently, using single nucleotide polymorphism markers (SNPs) from a cherry 6K SNP array. Genotyping-by-sequencing (GBS), a new methodology based on high-throughput sequencing, holds great promise for identification of high number of SNPs and construction of high density linkage maps. In this study, GBS was used to identify SNPs from an intra-specific sweet cherry cross. A total of 8,476 high quality SNPs were selected for mapping. The physical position for each SNP was determined using the peach genome, Peach v1.0, as reference, and a homogeneous distribution of markers along the eight peach scaffolds was obtained. On average, 65.6% of the SNPs were present in genic regions and 49.8% were located in exonic regions. In addition to the SNPs, a group of SSRs was also used for construction of linkage maps. Parental and consensus high density maps were constructed by genotyping 166 siblings from a ‘Rainier’ x ‘Rivedel’ (Ra x Ri) cross. Using Ra x Ri population, 462, 489 and 985 markers were mapped into eight linkage groups in ‘Rainier’, ‘Rivedel’ and the Ra x Ri map, respectively, with 80% of mapped SNPs located in genic regions. Obtained maps spanned 549.5, 582.6 and 731.3 cM for ‘Rainier’, ‘Rivedel’ and consensus maps, respectively, with an average distance of 1.2 cM between adjacent markers for both ‘Rainier’ and ‘Rivedel’ maps and of 0.7 cM for Ra x Ri map. High synteny and co-linearity was observed between obtained maps and with Peach v1.0. These new high density linkage maps provide valuable information on the sweet cherry genome, and serve as the basis for identification of QTLs and genes relevant for the breeding of the species. PMID:26011256

  2. A high-density SNP map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A high-resolution genetic map of sunflower was constructed by integrating SNP data from three F2 mapping populations (HA 89/ RHA 464, B-line/ RHA 464, and CR 29/ RHA 468). The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers derived from RAD tag sequencing and 1...

  3. Denoising of high-resolution single-particle electron-microscopy density maps by their approximation using three-dimensional Gaussian functions.

    PubMed

    Jonić, S; Vargas, J; Melero, R; Gómez-Blanco, J; Carazo, J M; Sorzano, C O S

    2016-06-01

    Cryo-electron microscopy (cryo-EM) of frozen-hydrated preparations of isolated macromolecular complexes is the method of choice to obtain the structure of complexes that cannot be easily studied by other experimental methods due to their flexibility or large size. An increasing number of macromolecular structures are currently being obtained at subnanometer resolution but the interpretation of structural details in such EM-derived maps is often difficult because of noise at these high-frequency signal components that reduces their contrast. In this paper, we show that the method for EM density-map approximation using Gaussian functions can be used for denoising of single-particle EM maps of high (typically subnanometer) resolution. We show its denoising performance using simulated and experimental EM density maps of several complexes.

  4. Integrating soil map delineations properties and land use into soil carbon density assessment at regional scale (Emilia Romagna, Italy)

    NASA Astrophysics Data System (ADS)

    Ungaro, F.; Calzolari, C.

    2009-04-01

    Accurate estimates of soil organic carbon (SOC) at regional scale are important to estimate the potential of soils as C reservoir. Different approaches can be used resulting in different degree of uncertainty associated to the estimates (Ungaro et al, 2005). Among the major source of uncertainty, land use, soil variability and bulk density for the reference depth are those with the greater influence on the final SOC stock estimation (Meersman, 2007). In order to reconstruct the spatial patterns of SOC at the landscape scale and to reduce the uncertainty associated to SOC stock estimates, an hybrid approach has been developed, combining the properties of the delineations of the regional 1:50.000 soil map with a geostatistical procedure (sequential Gaussian simulation). In the alluvial plain area of Emilia Romagna (10,734 km2) in Northern Italy, the available spatially explicit soil data (17,652 horizons from 3,302 profiles,), from 237 soil typological units, have been referred to 13 soil functional groups, divided in 42 subgroups. Based on the main geomorphic and pedogenetic processes, the soil functional groups and subgroups are defined in terms of top-soil textural classes (texture family), drainage class, slope, presence of organic materials (O horizons), flooding occurrence, origin of the parent material and presence of limestone. In order to take into account the influence of land use, the observations within each functional group have been further divided according to the different agricultural districts of the plain, characterized by different dominant land uses. The SOC density (Mg ha-1) of the 100 cm reference depth has been calculated as a weighed sum of the values calculated for each horizon., using a set of locally calibrated pedotransfer functions (Ungaro, 2007) whose inputs beside organic C are the sand, silt, and clay textural fractions The average values of each soil functional (sub)group of each district were used to assign a SOC density (Mg ha-1

  5. Improving the Accuracy of Fitted Atomic Models in Cryo-EM Density Maps of Protein Assemblies Using Evolutionary Information from Aligned Homologous Proteins.

    PubMed

    Rakesh, Ramachandran; Srinivasan, Narayanaswamy

    2016-01-01

    Cryo-Electron Microscopy (cryo-EM) has become an important technique to obtain structural insights into large macromolecular assemblies. However the resolution of the density maps do not allow for its interpretation at atomic level. Hence they are combined with high resolution structures along with information from other experimental or bioinformatics techniques to obtain pseudo-atomic models. Here, we describe the use of evolutionary conservation of residues as obtained from protein structures and alignments of homologous proteins to detect errors in the fitting of atomic structures as well as improve accuracy of the protein-protein interfacial regions in the cryo-EM density maps.

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

    PubMed

    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

    2015-05-05

    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.

  7. Constructing a high-density linkage map for Gossypium hirsutum × Gossypium barbadense and identifying QTLs for lint percentage.

    PubMed

    Shi, Yuzhen; Li, Wentan; Li, Aiguo; Ge, Ruihua; Zhang, Baocai; Li, Junzhi; Liu, Guangping; Li, Junwen; Liu, Aiying; Shang, Haihong; Gong, Juwu; Gong, Wankui; Yang, Zemao; Tang, Feiyü; Liu, Zhi; Zhu, Weiping; Jiang, Jianxiong; Yu, Xiaonan; Wang, Tao; Wang, Wei; Chen, Tingting; Wang, Kunbo; Zhang, Zhengsheng; Yuan, Youlu

    2015-05-01

    To introgress the good fiber quality and yield from Gossypium barbadense into a commercial Upland cotton variety, a high-density simple sequence repeat (SSR) genetic linkage map was developed from a BC1 F1 population of Gossypium hirsutum × Gossypium barbadense. The map comprised 2,292 loci and covered 5115.16 centiMorgan (cM) of the cotton AD genome, with an average marker interval of 2.23 cM. Of the marker order for 1,577 common loci on this new map, 90.36% agrees well with the marker order on the D genome sequence genetic map. Compared with five published high-density SSR genetic maps, 53.14% of marker loci were newly discovered in this map. Twenty-six quantitative trait loci (QTLs) for lint percentage (LP) were identified on nine chromosomes. Nine stable or common QTLs could be used for marker-assisted selection. Fifty percent of the QTLs were from G. barbadense and increased LP by 1.07%-2.41%. These results indicated that the map could be used for screening chromosome substitution segments from G. barbadense in the Upland cotton background, identifying QTLs or genes from G. barbadense, and further developing the gene pyramiding effect for improving fiber yield and quality.

  8. High-density linkage mapping aided by transcriptomics documents ZW sex determination system in the Chinese mitten crab Eriocheir sinensis

    PubMed Central

    Cui, Z; Hui, M; Liu, Y; Song, C; Li, X; Li, Y; Liu, L; Shi, G; Wang, S; Li, F; Zhang, X; Liu, C; Xiang, J; Chu, K H

    2015-01-01

    The sex determination system in crabs is believed to be XY-XX from karyotypy, but centromeres could not be identified in some chromosomes and their morphology is not completely clear. Using quantitative trait locus mapping of the gender phenotype, we revealed a ZW-ZZ sex determination system in Eriocheir sinensis and presented a high-density linkage map covering ~98.5% of the genome, with 73 linkage groups corresponding to the haploid chromosome number. All sex-linked markers in the family we used were located on a single linkage group, LG60, and sex linkage was confirmed by genome-wide association studies (GWAS). Forty-six markers detected by GWAS were heterozygous and segregated only in the female parent. The female LG60 was thus the putative W chromosome, with the homologous male LG60 as the Z chromosome. The putative Z and W sex chromosomes were identical in size and carried many homologous loci. Sex ratio (5:1) skewing towards females in induced triploids using unrelated animals also supported a ZW-ZZ system. Transcriptome data were used to search for candidate sex-determining loci, but only one LG60 gene was identified as an ankyrin-2 gene. Double sex- and mab3-related transcription factor 1 (Dmrt1), a Z-linked gene in birds, was located on a putative autosome. With complete genome sequencing and transcriptomic data, more genes on putative sex chromosomes will be characterised, thus leading towards a comprehensive understanding of the sex determination and differentiation mechanisms of E. sinensis, and decapod crustaceans in general. PMID:25873149

  9. A Complex Recombination Pattern in the Genome of Allotetraploid Brassica napus as Revealed by a High-Density Genetic Map

    PubMed Central

    Yi, Bin; Fan, Chuchuan; Edwards, David; Batley, Jacqueline; Zhou, Yongming

    2014-01-01

    Polyploidy plays a crucial role in plant evolution. Brassica napus (2n = 38, AACC), the most important oil crop in the Brassica genus, is an allotetraploid that originated through natural doubling of chromosomes after the hybridization of its progenitor species, B. rapa (2n = 20, AA) and B. oleracea (2n = 18, CC). A better understanding of the evolutionary relationship between B. napus and B. rapa, B. oleracea, as well as Arabidopsis, which has a common ancestor with these three species, will provide valuable information about the generation and evolution of allopolyploidy. Based on a high-density genetic map with single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers, we performed a comparative genomic analysis of B. napus with Arabidopsis and its progenitor species B. rapa and B. oleracea. Based on the collinear relationship of B. rapa and B. oleracea in the B. napus genetic map, the B. napus genome was found to consist of 70.1% of the skeleton components of the chromosomes of B. rapa and B. oleracea, with 17.7% of sequences derived from reciprocal translocation between homoeologous chromosomes between the A- and C-genome and 3.6% of sequences derived from reciprocal translocation between non-homologous chromosomes at both intra- and inter-genomic levels. The current study thus provides insights into the formation and evolution of the allotetraploid B. napus genome, which will allow for more accurate transfer of genomic information from B. rapa, B. oleracea and Arabidopsis to B. napus. PMID:25356735

  10. A complex recombination pattern in the genome of allotetraploid Brassica napus as revealed by a high-density genetic map.

    PubMed

    Cai, Guangqin; Yang, Qingyong; Yi, Bin; Fan, Chuchuan; Edwards, David; Batley, Jacqueline; Zhou, Yongming

    2014-01-01

    Polyploidy plays a crucial role in plant evolution. Brassica napus (2n = 38, AACC), the most important oil crop in the Brassica genus, is an allotetraploid that originated through natural doubling of chromosomes after the hybridization of its progenitor species, B. rapa (2n = 20, AA) and B. oleracea (2n = 18, CC). A better understanding of the evolutionary relationship between B. napus and B. rapa, B. oleracea, as well as Arabidopsis, which has a common ancestor with these three species, will provide valuable information about the generation and evolution of allopolyploidy. Based on a high-density genetic map with single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers, we performed a comparative genomic analysis of B. napus with Arabidopsis and its progenitor species B. rapa and B. oleracea. Based on the collinear relationship of B. rapa and B. oleracea in the B. napus genetic map, the B. napus genome was found to consist of 70.1% of the skeleton components of the chromosomes of B. rapa and B. oleracea, with 17.7% of sequences derived from reciprocal translocation between homoeologous chromosomes between the A- and C-genome and 3.6% of sequences derived from reciprocal translocation between non-homologous chromosomes at both intra- and inter-genomic levels. The current study thus provides insights into the formation and evolution of the allotetraploid B. napus genome, which will allow for more accurate transfer of genomic information from B. rapa, B. oleracea and Arabidopsis to B. napus.

  11. A complex recombination pattern in the genome of allotetraploid Brassica napus as revealed by a high-density genetic map.

    PubMed

    Cai, Guangqin; Yang, Qingyong; Yi, Bin; Fan, Chuchuan; Edwards, David; Batley, Jacqueline; Zhou, Yongming

    2014-01-01

    Polyploidy plays a crucial role in plant evolution. Brassica napus (2n = 38, AACC), the most important oil crop in the Brassica genus, is an allotetraploid that originated through natural doubling of chromosomes after the hybridization of its progenitor species, B. rapa (2n = 20, AA) and B. oleracea (2n = 18, CC). A better understanding of the evolutionary relationship between B. napus and B. rapa, B. oleracea, as well as Arabidopsis, which has a common ancestor with these three species, will provide valuable information about the generation and evolution of allopolyploidy. Based on a high-density genetic map with single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers, we performed a comparative genomic analysis of B. napus with Arabidopsis and its progenitor species B. rapa and B. oleracea. Based on the collinear relationship of B. rapa and B. oleracea in the B. napus genetic map, the B. napus genome was found to consist of 70.1% of the skeleton components of the chromosomes of B. rapa and B. oleracea, with 17.7% of sequences derived from reciprocal translocation between homoeologous chromosomes between the A- and C-genome and 3.6% of sequences derived from reciprocal translocation between non-homologous chromosomes at both intra- and inter-genomic levels. The current study thus provides insights into the formation and evolution of the allotetraploid B. napus genome, which will allow for more accurate transfer of genomic information from B. rapa, B. oleracea and Arabidopsis to B. napus. PMID:25356735

  12. VizieR Online Data Catalog: HI4PI spectra and column density maps (HI4PI team+, 2016)

    NASA Astrophysics Data System (ADS)

    Hi4PI Collaboration; Ben Bekhti, N.; Floeer, L.; Keller, R.; Kerp, J.; Lenz, D.; Winkel, B.; Bailin, J.; Calabretta, M. R.; Dedes, L.; Ford, H. A.; Gibson, B. K.; Haud, U.; Janowiecki, S.; Kalberla, P. M. W.; Lockman, F. J.; McClure-Griffiths, N. M.; Murphy, T.; Nakanishi, H.; Pisano, D. J.; Staveley-Smith, L.

    2016-09-01

    The HI4PI data release comprises 21-cm neutral atomic hydrogen data of the Milky Way (-600km/s0°; -470km/smap projections, AIT, CAR, MOL, 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 (2) Smaller FITS data cubes, each having a size of about 20x20 sq.deg. For convenience, we provide four different map projections, CAR, SFL, SIN, and TAN (again see WCS references). Note, size in longitude is 20° in absolute coordinates for CAR projection, and 20° true-angular size for SFL, SIN, and TAN projections. Again, Equatorial and Galactic coordinate systems are provided. (3) 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-sky HI column density distribution, both, in a (1) HealPIX-grid binary table (nside=1024, Galactic coordinates, Ring indexing scheme), and (2) Standard FITS 2D images in four map projections, AIT, CAR, MOL, and SFL. Various velocity intervals were applied to calculate NHI. Equatorial and Galactic coordinate systems are provided. (16 data files).

  13. Vegetation mapping from medium-density discrete echo Airborne Laser Scanning data: a case study of the Lake Balaton wetlands

    NASA Astrophysics Data System (ADS)

    Zlinszky, A.; Mücke, W.; Lehner, H.; Briese, C.; Pfeifer, N.

    2012-04-01

    also the main vegetation genera and the health of the dominant species. The decision tree algorithm was set up on the basis of a signature analysis comparing the histograms of each ALS-derived variable within the ground truth areas, and separating the classes based on histogram differences. This has proven robust enough to work across the full study area, and artefacts were relatively easy to recognize and understand. Classification accuracies produced by this study are between 60% and 92%, with an overall accuracy of 83% for all categories. While this is clearly below the maximum accuracy achievable by hyperspectral surveys of small areas, it is comparable to many passive multispectral or fused passive multispectral and ALS vegetation surveys and also the accuracies of ALS-based forest monitoring. Since the method itself is not specific for wetlands, it is believed that such an approach could provide valid vegetation classification results in other areas. As shown by this case study, medium-density discrete echo ALS datasets similar to those collected during European region-wide surveys can successfully be used to map vegetation classes relevant for ecology and conservation.

  14. 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.

  15. A highly recombined, high-density, eight-founder wheat MAGIC map reveals extensive segregation distortion and genomic locations of introgression segments.

    PubMed

    Gardner, Keith A; Wittern, Lukas M; Mackay, Ian J

    2016-06-01

    Multiparent Advanced Generation Intercross (MAGIC) mapping populations offer unique opportunities and challenges for marker and QTL mapping in crop species. We have constructed the first eight-parent MAGIC genetic map for wheat, comprising 18 601 SNP markers. We validated the accuracy of our map against the wheat genome sequence and found an improvement in accuracy compared to published genetic maps. Our map shows a notable increase in precision resulting from the three generations of intercrossing required to create the population. This is most pronounced in the pericentromeric regions of the chromosomes. Sixteen percent of mapped markers exhibited segregation distortion (SD) with many occurring in long (>20 cM) blocks. Some of the longest and most distorted blocks were collinear with noncentromeric high-marker-density regions of the genome, suggesting they were candidates for introgression fragments introduced into the bread wheat gene pool from other grass species. We investigated two of these linkage blocks in detail and found strong evidence that one on chromosome 4AL, showing SD against the founder Robigus, is an interspecific introgression fragment. The completed map is available from http://www.niab.com/pages/id/326/Resources.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  17. 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…

  18. 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…

  19. Equality, Innovation and Diversity.

    ERIC Educational Resources Information Center

    Smith, Janet

    1999-01-01

    Offers some ideas concerning promotion of gender equality and diversity within European Union-funded programs and activities. Reviews efforts since the 1970s to foster equal access in European schools and universities, examines some principles of innovation and entrepreneurship, and considers stages in diversity policy development. (DB)

  20. Early Understanding of Equality

    ERIC Educational Resources Information Center

    Leavy, Aisling; Hourigan, Mairéad; McMahon, Áine

    2013-01-01

    Quite a bit of the arithmetic in elementary school contains elements of algebraic reasoning. After researching and testing a number of instructional strategies with Irish third graders, these authors found effective methods for cultivating a relational concept of equality in third-grade students. Understanding equality is fundamental to algebraic…

  1. Integer Equal Flows

    SciTech Connect

    Meyers, C A; Schulz, A S

    2009-01-07

    The integer equal flow problem is an NP-hard network flow problem, in which all arcs in given sets R{sub 1}, ..., R{sub {ell}} must carry equal flow. We show this problem is effectively inapproximable, even if the cardinality of each set R{sub k} is two. When {ell} is fixed, it is solvable in polynomial time.

  2. Searching for Equality.

    ERIC Educational Resources Information Center

    Giese, James; Miller, Barbara

    1987-01-01

    Offers an activity designed to illustrate the historical context of current legal questions relating to equal rights. The activity shows how the definition of equality has been expanded as a result of the continuous hard work of individuals and civil rights groups. (JDH)

  3. A High-Density SNP-Based Linkage Map of the Chicken Genome Reveals Sequence Features Correlated With Recombination Rate

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The resolution of the widely used chicken consensus linkage map was highly enlarged by genotyping a total of 12,945 SNPs on the three existing mapping populations in chicken; the Wageningen (WU), East Lansing (EL) and Uppsala (UPP) mapping populations. A total of 8608 SNPs could be included on the m...

  4. Enhancing the Contrast of ApoB to Locate the Surface Components in the 3D Density Map of Human LDL

    PubMed Central

    Liu, Yuhang; Atkinson, David

    2010-01-01

    A 26Å resolution map of the structure of human LDL was obtained from cryo-EM and single particle image reconstruction. The structure showed a discoidal shaped LDL particle with high-density regions mainly distributed at the edge of the particle and low-density regions at the flat surface that covers the core region. To determine the chemical components that correspond to these density regions and to delineate the distribution of protein and phospholipid located at the particle surface at the resolution of the map, we used Mono-Sulfo-NHS-Undecagold labeling to increase preferentially the contrast of the apoB protein component on the LDL particle. In the 3D maps from the image reconstruction of the undecagold labeled LDL particles, the high-density region from the undecagold label was distributed mainly at the edge of the particle and lower density regions were found at the flat surfaces that cover the neutral lipid core. This suggests that apoB mainly encircles LDL at the edge of the particle and the phospholipid monolayers are located at the flat surfaces, which are parallel to the cholesterol ester layers in the core and may interact with the core lipid layers through the acyl-chains. PMID:21029740

  5. Construction of a High-Density Genetic Map Based on Large-Scale Marker Development in Mango Using Specific-Locus Amplified Fragment Sequencing (SLAF-seq).

    PubMed

    Luo, Chun; Shu, Bo; Yao, Quangsheng; Wu, Hongxia; Xu, Wentian; Wang, Songbiao

    2016-01-01

    Genetic maps are particularly important and valuable tools for quantitative trait locus (QTL) mapping and marker assisted selection (MAS) of plant with desirable traits. In this study, 173 F1 plants from a cross between Mangifera indica L. "Jin-Hwang" and M. indica L. "Irwin" and their parent plants were subjected to high-throughput sequencing and specific-locus amplified fragment (SLAF) library construction. After preprocessing, 66.02 Gb of raw data containing 330.64 M reads were obtained. A total of 318,414 SLAFs were detected, of which 156,368 were polymorphic. Finally, 6594 SLAFs were organized into a linkage map consisting of 20 linkage groups (LGs). The total length of the map was 3148.28 cM and the average distance between adjacent markers was 0.48 cM. This map could be considered, to our knowledge, the first high-density genetic map of mango, and might form the basis for fine QTL mapping and MAS of mango. PMID:27625670

  6. Construction of a High-Density Genetic Map Based on Large-Scale Marker Development in Mango Using Specific-Locus Amplified Fragment Sequencing (SLAF-seq)

    PubMed Central

    Luo, Chun; Shu, Bo; Yao, Quangsheng; Wu, Hongxia; Xu, Wentian; Wang, Songbiao

    2016-01-01

    Genetic maps are particularly important and valuable tools for quantitative trait locus (QTL) mapping and marker assisted selection (MAS) of plant with desirable traits. In this study, 173 F1 plants from a cross between Mangifera indica L. “Jin-Hwang” and M. indica L. “Irwin” and their parent plants were subjected to high-throughput sequencing and specific-locus amplified fragment (SLAF) library construction. After preprocessing, 66.02 Gb of raw data containing 330.64 M reads were obtained. A total of 318,414 SLAFs were detected, of which 156,368 were polymorphic. Finally, 6594 SLAFs were organized into a linkage map consisting of 20 linkage groups (LGs). The total length of the map was 3148.28 cM and the average distance between adjacent markers was 0.48 cM. This map could be considered, to our knowledge, the first high-density genetic map of mango, and might form the basis for fine QTL mapping and MAS of mango. PMID:27625670

  7. Construction of a High-Density Genetic Map Based on Large-Scale Marker Development in Mango Using Specific-Locus Amplified Fragment Sequencing (SLAF-seq)

    PubMed Central

    Luo, Chun; Shu, Bo; Yao, Quangsheng; Wu, Hongxia; Xu, Wentian; Wang, Songbiao

    2016-01-01

    Genetic maps are particularly important and valuable tools for quantitative trait locus (QTL) mapping and marker assisted selection (MAS) of plant with desirable traits. In this study, 173 F1 plants from a cross between Mangifera indica L. “Jin-Hwang” and M. indica L. “Irwin” and their parent plants were subjected to high-throughput sequencing and specific-locus amplified fragment (SLAF) library construction. After preprocessing, 66.02 Gb of raw data containing 330.64 M reads were obtained. A total of 318,414 SLAFs were detected, of which 156,368 were polymorphic. Finally, 6594 SLAFs were organized into a linkage map consisting of 20 linkage groups (LGs). The total length of the map was 3148.28 cM and the average distance between adjacent markers was 0.48 cM. This map could be considered, to our knowledge, the first high-density genetic map of mango, and might form the basis for fine QTL mapping and MAS of mango.

  8. Equalization in redundant channels

    NASA Technical Reports Server (NTRS)

    Tulpule, Bhalchandra R. (Inventor); Collins, Robert E. (Inventor); Cominelli, Donald F. (Inventor); O'Neill, Richard D. (Inventor)

    1988-01-01

    A miscomparison between a channel's configuration data base and a voted system configuration data base in a redundant channel system having identically operating, frame synchronous channels triggers autoequalization of the channel's historical signal data bases in a hierarchical, chronological manner with that of a correctly operating channel. After equalization, symmetrization of the channel's configuration data base with that of the system permits upgrading of the previously degraded channel to full redundancy. An externally provided equalization command, e.g., manually actuated, can also trigger equalization.

  9. 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

  10. Happiness as Educational Equality

    ERIC Educational Resources Information Center

    McCord, Arline Sakuma

    1974-01-01

    A review of six monographs in the American Sociological Association Rose Monograph Series that examine attitudes toward self as they relate to the pervasiveness of American values concerning happiness and equality of opportunity. (EH)

  11. IPS observations of heliospheric density structures associated with active regions

    NASA Technical Reports Server (NTRS)

    Hick, P.; Jackson, B. V.; Altrock, R.; Woan, G.; Slater, G.

    1996-01-01

    Interplanetary scintillation (IPS) measurements of the 'disturbance factor' g, obtained with the Cambridge (UK) array can be used to explore the heliospheric density structure. We have used these data to construct synoptic (Carrington) maps, representing the large-scale enhancements of the g-factor in the inner heliosphere. These maps emphasize the stable corotating, rather than the transient heliospheric density enhancements. We have compared these maps with Carrington maps of Fe XIV observations National Solar Observatory ((NSO), Sacramento Peak) and maps based on Yohkoh Soft X-Ray Telescope (SXT) X-ray observations. Our results indicate that the regions of enhanced g tend to map to active regions rather than the current sheet. The implication is that act ve regions are the dominant source of the small-scale (approximately equal 200 km) density variations present in the quiet solar wind.

  12. Genetic Dissection of Yield and Its Component Traits Using High-Density Composite Map of Wheat Chromosome 3A: Bridging Gaps between QTLs and Underlying Genes

    PubMed Central

    Rustgi, Sachin; Shafqat, Mustafa N.; Kumar, Neeraj; Baenziger, P. Stephen; Ali, M. Liakat; Dweikat, Ismail; Campbell, B. Todd; Gill, Kulvinder Singh

    2013-01-01

    Earlier we identified wheat (Triticum aestivum L.) chromosome 3A as a major determinant of grain yield and its component traits. In the present study, a high-density genetic linkage map of 81 chromosome 3A-specific markers was developed to increase the precision of previously identified yield component QTLs, and to map QTLs for biomass-related traits. Many of the previously identified QTLs for yield and its component traits were confirmed and were localized to narrower intervals. Four novel QTLs one each for shoot biomass (Xcfa2262-Xbcd366), total biomass (wPt2740-Xcfa2076), kernels/spike (KPS) (Xwmc664-Xbarc67), and Pseudocercosporella induced lodging (PsIL) were also detected. The major QTLs identified for grain yield (GY), KPS, grain volume weight (GVWT) and spikes per square meter (SPSM) respectively explained 23.2%, 24.2%, 20.5% and 20.2% of the phenotypic variation. Comparison of the genetic map with the integrated physical map allowed estimation of recombination frequency in the regions of interest and suggested that QTLs for grain yield detected in the marker intervals Xcdo549-Xbarc310 and Xpsp3047-Xbarc356 reside in the high-recombination regions, thus should be amenable to map-based cloning. On the other hand, QTLs for KPS and SPSM flanked by markers Xwmc664 and Xwmc489 mapped in the low-recombination region thus are not suitable for map-based cloning. Comparisons with the rice (Oryza sativa L.) genomic DNA sequence identified 11 candidate genes (CGs) for yield and yield related QTLs of which chromosomal location of two (CKX2 and GID2-like) was confirmed using wheat aneuploids. This study provides necessary information to perform high-resolution mapping for map-based cloning and for CG-based cloning of yield QTLs. PMID:23894667

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

    PubMed

    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

    2015-04-22

    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.

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

    PubMed

    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

    2015-06-01

    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

  15. 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

  16. High-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using Genotyping-by-Sequencing (GBS)

    PubMed Central

    Verma, Subodh; Gupta, Shefali; Bandhiwal, Nitesh; Kumar, Tapan; Bharadwaj, Chellapilla; Bhatia, Sabhyata

    2015-01-01

    This study reports the use of Genotyping-by-Sequencing (GBS) for large-scale SNP discovery and simultaneous genotyping of recombinant inbred lines (RILs) of an intra-specific mapping population of chickpea contrasting for seed traits. A total of 119,672 raw SNPs were discovered, which after stringent filtering revealed 3,977 high quality SNPs of which 39.5% were present in genic regions. Comparative analysis using physically mapped marker loci revealed a higher degree of synteny with Medicago in comparison to soybean. The SNP genotyping data was utilized to construct one of the most saturated intra-specific genetic linkage maps of chickpea having 3,363 mapped positions including 3,228 SNPs on 8 linkage groups spanning 1006.98 cM at an average inter marker distance of 0.33 cM. The map was utilized to identify 20 quantitative trait loci (QTLs) associated with seed traits accounting for phenotypic variations ranging from 9.97% to 29.71%. Analysis of the genomic sequence corresponding to five robust QTLs led to the identification of 684 putative candidate genes whose expression profiling revealed that 101 genes exhibited seed specific expression. The integrated approach utilizing the identified QTLs along with the available genome and transcriptome could serve as a platform for candidate gene identification for molecular breeding of chickpea. PMID:26631981

  17. High-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using Genotyping-by-Sequencing (GBS).

    PubMed

    Verma, Subodh; Gupta, Shefali; Bandhiwal, Nitesh; Kumar, Tapan; Bharadwaj, Chellapilla; Bhatia, Sabhyata

    2015-01-01

    This study reports the use of Genotyping-by-Sequencing (GBS) for large-scale SNP discovery and simultaneous genotyping of recombinant inbred lines (RILs) of an intra-specific mapping population of chickpea contrasting for seed traits. A total of 119,672 raw SNPs were discovered, which after stringent filtering revealed 3,977 high quality SNPs of which 39.5% were present in genic regions. Comparative analysis using physically mapped marker loci revealed a higher degree of synteny with Medicago in comparison to soybean. The SNP genotyping data was utilized to construct one of the most saturated intra-specific genetic linkage maps of chickpea having 3,363 mapped positions including 3,228 SNPs on 8 linkage groups spanning 1006.98 cM at an average inter marker distance of 0.33 cM. The map was utilized to identify 20 quantitative trait loci (QTLs) associated with seed traits accounting for phenotypic variations ranging from 9.97% to 29.71%. Analysis of the genomic sequence corresponding to five robust QTLs led to the identification of 684 putative candidate genes whose expression profiling revealed that 101 genes exhibited seed specific expression. The integrated approach utilizing the identified QTLs along with the available genome and transcriptome could serve as a platform for candidate gene identification for molecular breeding of chickpea.

  18. A high-density genetic linkage map of a black spruce (Picea mariana) × red spruce (Picea rubens) interspecific hybrid.

    PubMed

    Kang, Bum-Yong; Major, John E; Rajora, Om P

    2011-02-01

    Genetic maps provide an important genomic resource of basic and applied significance. Spruce (Picea) has a very large genome size (between 0.85 × 1010 and 2.4 × 1010 bp; 8.5-24.0 pg/1C, a mean of 17.7 pg/1C ). We have constructed a near-saturated genetic linkage map for an interspecific backcross (BC1) hybrid of black spruce (BS; Picea mariana (Mill.) B.S.P.) and red spruce (RS; Picea rubens Sarg.), using selectively amplified microsatellite polymorphic loci (SAMPL) markers. A total of 2284 SAMPL markers were resolved using 31 SAMPL-MseI selective nucleotide primer combinations. Of these, 1216 SAMPL markers showing Mendelian segregation were mapped, whereas 1068 (46.8%) SAMPL fragments showed segregation distortion at α = 0.05. Maternal, paternal, and consensus maps consistently coalesced into 12 linkage groups, corresponding to the haploid chromosome number (1n = 1x = 12) of 12 in the genus Picea. The maternal BS map consisted of 814 markers distributed over 12 linkage groups, covering 1670 cM, with a mean map distance of 2.1 cM between adjacent markers. The paternal BS × RS map consisted of 773 markers distributed over 12 linkage groups, covering 1563 cM, with a mean map distance of 2.0 cM between adjacent markers. The consensus interspecific hybrid BC1 map consisted of 1216 markers distributed over 12 linkage groups, covering 1865 cM (98% genome coverage), with a mean map distance of 1.5 cM between adjacent markers. The genetic map reported here provides an important genomic resource in Picea, Pinaceae, and conifers.

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

    PubMed

    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.

  20. 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

  1. 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

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

    SciTech Connect

    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 will be shown.

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

    SciTech Connect

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

    1995-04-01

    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.

  4. 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.

  5. An ultra-high-density map as a community resource for discerning the genetic basis of quantitative traits in maize

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this study, we generated a linkage map containing 1,151,856 high quality SNPs between Mo17 and B73, which were verified in the maize intermated B73'×'Mo17 (IBM) Syn10 population. This resource is an excellent complement to existing maize genetic maps available in an online database (iPlant, http:...

  6. Mapping SOC content and bulk density of a disturbed peatland relict with electromagnetic induction and DEM data

    NASA Astrophysics Data System (ADS)

    Altdorff, Daniel; Bechtold, Michel; van der Kruk, Jan; Tiemeyer, Bärbel; von Hebel, Christian; Huisman, Johan Alexander

    2014-05-01

    Peatlands represent a huge storage of soil organic carbon (SOC), and there is considerable interest to assess the total amount of carbon stored in these ecosystems. However, reliable field-scale information about peat properties, particularly SOC content and bulk density (BD) necessary to estimate C stocks, remains difficult to obtain. A potential way to acquire information on these properties and its spatial variation is the non-invasive mapping of easily recordable physical variables that correlate with peat properties, such as bulk electrical conductivity (ECa) measured with electromagnetic induction (EMI). However, ECa depends on a range of soil properties, including BD, soil and water chemistry, and water content, and thus results often show complex and site-specific relationships. Therefore, a reliable prediction of SOC and BD from ECa data is not necessarily given. In this study, we aim to explore the usefulness of Multiple Linear Regression (MLR) models to predict the peat soil properties SOC and BD from multi-offset EMI and high-resolution DEM data. The quality of the MLR models is assessed by cross-validation. We use data from a medium-scale disturbed peat relict (approximately 35ha) in Northern Germany. The potential explanatory variables considered in MLR were: EMI data of six different integral depths (approximately 0.25, 0.5, 0.6, 0.9, 1, and 1.80 m), their vertical heterogeneity, as well as several topographical variables extracted from the DEM. Ground truth information for SOC, BD content and peat layer thickness was obtained from 34 soil cores of 1 m depth. Each core was divided into several 5 to 20 cm thick layers so that integral information of the upper 0.25, 0.5, and 1 m as well as from the total peat layer was obtained. For cross-validation of results, we clustered the 34 soil cores into 4 classes using K-means clustering and selected 8 cores for validation from the clusters with a probability that depended on the size of the cluster. With the

  7. Micro-Brillouin spectroscopy mapping of the residual density field induced by Vickers indentation in a soda-lime silicate glass

    NASA Astrophysics Data System (ADS)

    Tran, H.; Clément, S.; Vialla, R.; Vandembroucq, D.; Rufflé, B.

    2012-06-01

    High-resolution Brillouin scattering is used to achieve 3-dimensional maps of the longitudinal acoustic mode frequency shift in soda-lime silicate glasses subject to Vickers indentations. Assuming that residual stress-induced effects are simply proportional to density changes, residual densification fields are obtained. The density gradient is nearly isotropic, confirming earlier optical observations made on a similar glass. The results show that Brillouin micro-spectroscopy opens the way to a fully quantitative comparison of experimental data with predictions of mechanical models for the identification of a constitutive law.

  8. Transhumanism and moral equality.

    PubMed

    Wilson, James

    2007-10-01

    Conservative thinkers such as Francis Fukuyama have produced a battery of objections to the transhumanist project of fundamentally enhancing human capacities. This article examines one of these objections, namely that by allowing some to greatly extend their capacities, we will undermine the fundamental moral equality of human beings. I argue that this objection is groundless: once we understand the basis for human equality, it is clear that anyone who now has sufficient capacities to count as a person from the moral point of view will continue to count as one even if others are fundamentally enhanced; and it is mistaken to think that a creature which had even far greater capacities than an unenhanced human being should count as more than an equal from the moral point of view.

  9. 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…

  10. 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

  11. High-dynamic-range extinction mapping of infrared dark clouds. Dependence of density variance with sonic Mach number in molecular clouds

    NASA Astrophysics Data System (ADS)

    Kainulainen, J.; Tan, J. C.

    2013-01-01

    Context. Measuring the mass distribution of infrared dark clouds (IRDCs) over the wide dynamic range of their column densities is a fundamental obstacle in determining the initial conditions of high-mass star formation and star cluster formation. Aims: We present a new technique to derive high-dynamic-range, arcsecond-scale resolution column density data for IRDCs and demonstrate the potential of such data in measuring the density variance - sonic Mach number relation in molecular clouds. Methods: We combine near-infrared data from the UKIDSS/Galactic Plane Survey with mid-infrared data from the Spitzer/GLIMPSE survey to derive dust extinction maps for a sample of ten IRDCs. We then examine the linewidths of the IRDCs using 13CO line emission data from the FCRAO/Galactic Ring Survey and derive a column density - sonic Mach number relation for them. For comparison, we also examine the relation in a sample of nearby molecular clouds. Results: The presented column density mapping technique provides a very capable, temperature independent tool for mapping IRDCs over the column density range equivalent to AV ≃ 1-100 mag at a resolution of 2″. Using the data provided by the technique, we present the first direct measurement of the relationship between the column density dispersion, σN/⟨N⟩, and sonic Mach number, ℳs, in molecular clouds. We detect correlation between the variables with about 3-σ confidence. We derive the relation σN/⟨N⟩ ≈ (0.047 ± 0.016)ℳs, which is suggestive of the correlation coefficient between the volume density and sonic Mach number, σρ/⟨ρ⟩ ≈ (0.20-0.22+0.37)ℳs, in which the quoted uncertainties indicate the 3-σ range. When coupled with the results of recent numerical works, the existence of the correlation supports the picture of weak correlation between the magnetic field strength and density in molecular clouds (i.e., B ∝ ρ0.5). While our results remain suggestive because of the small number of clouds in our

  12. Equality and Academic Subjects

    ERIC Educational Resources Information Center

    Hardarson, Atli

    2013-01-01

    A recent national curriculum guide for upper secondary schools in my home country, Iceland, requires secondary schools to work towards equality and five other overarching aims. This requirement raises questions about to what extent secondary schools have to change their curricula in order to approach these aims or work towards them in an adequate…

  13. Equal Opportunity in Employment

    ERIC Educational Resources Information Center

    Bullock, Paul

    This book focuses on discrimination in employment, defined as the denial of equal opportunity in the labor market to qualified persons on the basis of race, color, religion, national origin, age, sex, or any other factor not related to their individual qualifications for work. The average nonwhite college graduate can expect to earn less during…

  14. Education and Economic Equality

    ERIC Educational Resources Information Center

    Thurow, Lester C.

    1972-01-01

    Argues that the present reliance on education as the ultimate policy for curing all problems, economic and social, is unwarranted at best and in all probability, ineffective. Suggests that any time a consensus emerges on the need for more equality, it can be at least partly achieved by making a frontal attack on wage differentials. (RJ)

  15. EQUALS Investigations: Remote Rulers.

    ERIC Educational Resources Information Center

    Mayfield, Karen; Whitlow, Robert

    EQUALS is a teacher education program that helps elementary and secondary educators acquire methods and materials to attract minority and female students to mathematics. It supports a problem-solving approach to mathematics which has students working in groups, uses active assessment methods, and incorporates a broad mathematics curriculum…

  16. Equality of Fitness Centers

    ERIC Educational Resources Information Center

    Swoyer, Jesse O.

    2008-01-01

    The author, who has been a personal trainer for the past ten years, recently realized that all fitness centers are not equal. In February, he was able to participate in the grand opening of the Center for Independent Living of Central PA (CILCP), a fitness center that is designed to accommodate persons with disabilities living in the Central…

  17. Granting Each Equal Access.

    ERIC Educational Resources Information Center

    Walling, Linda Lucas

    1992-01-01

    Summarizes federal legislation regarding equal access for students with disabilities and discusses environmental barriers to accessibility in the library media center. Solutions to these design problems are suggested in the following areas: material formats and space requirements; the physical setting, including furniture, floor coverings,…

  18. Equality of Educational Opportunity.

    ERIC Educational Resources Information Center

    Cross, K. Patricia

    A consideration of the use of the phrase "equality of educational opportunity" and of the educational models used to attempt its implementation suggest the following recommendations. If education is to devise learning models that will maximize individual potential and aid in matching human abilities to the work required by societies, then (1) we…

  19. Defining Equality in Education

    ERIC Educational Resources Information Center

    Benson, Ronald E.

    1977-01-01

    Defines equality of education in three areas: 1) by the degree of integration of school systems; 2) by a comparison of material resources and assets in education; and 3) by the effects of schooling as measured by the mean scores of groups on standardized tests. Available from: College of Education, 107 Quadrangle, Iowa State University, Ames, Iowa…

  20. Equality Versus Inequality.

    ERIC Educational Resources Information Center

    Dahl, Robert A.

    1996-01-01

    Argues that political equality and democracy are attainable only through the distribution of access to political resources and the willingness to use them. Discusses the broad philosophical and sociological components that contribute to a system marked by advantage and inequalities, as well as opportunities for opposition and resistance. (MJP)

  1. Construction of an integrated high density simple sequence repeat linkage map in cultivated strawberry (Fragaria × ananassa) and its applicability.

    PubMed

    Isobe, Sachiko N; Hirakawa, Hideki; Sato, Shusei; Maeda, Fumi; Ishikawa, Masami; Mori, Toshiki; Yamamoto, Yuko; Shirasawa, Kenta; Kimura, Mitsuhiro; Fukami, Masanobu; Hashizume, Fujio; Tsuji, Tomoko; Sasamoto, Shigemi; Kato, Midori; Nanri, Keiko; Tsuruoka, Hisano; Minami, Chiharu; Takahashi, Chika; Wada, Tsuyuko; Ono, Akiko; Kawashima, Kumiko; Nakazaki, Naomi; Kishida, Yoshie; Kohara, Mitsuyo; Nakayama, Shinobu; Yamada, Manabu; Fujishiro, Tsunakazu; Watanabe, Akiko; Tabata, Satoshi

    2013-02-01

    The cultivated strawberry (Fragaria × ananassa) is an octoploid (2n = 8x = 56) of the Rosaceae family whose genomic architecture is still controversial. Several recent studies support the AAA'A'BBB'B' model, but its complexity has hindered genetic and genomic analysis of this important crop. To overcome this difficulty and to assist genome-wide analysis of F. × ananassa, we constructed an integrated linkage map by organizing a total of 4474 of simple sequence repeat (SSR) markers collected from published Fragaria sequences, including 3746 SSR markers [Fragaria vesca expressed sequence tag (EST)-derived SSR markers] derived from F. vesca ESTs, 603 markers (F. × ananassa EST-derived SSR markers) from F. × ananassa ESTs, and 125 markers (F. × ananassa transcriptome-derived SSR markers) from F. × ananassa transcripts. Along with the previously published SSR markers, these markers were mapped onto five parent-specific linkage maps derived from three mapping populations, which were then assembled into an integrated linkage map. The constructed map consists of 1856 loci in 28 linkage groups (LGs) that total 2364.1 cM in length. Macrosynteny at the chromosome level was observed between the LGs of F. × ananassa and the genome of F. vesca. Variety distinction on 129 F. × ananassa lines was demonstrated using 45 selected SSR markers.

  2. High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea

    PubMed Central

    Gaur, Rashmi; Jeena, Ganga; Shah, Niraj; Gupta, Shefali; Pradhan, Seema; Tyagi, Akhilesh K; Jain, Mukesh; Chattopadhyay, Debasis; Bhatia, Sabhyata

    2015-01-01

    This study presents genome-wide discovery of SNPs through next generation sequencing of the genome of Cicer reticulatum. Mapping of the C. reticulatum sequenced reads onto the draft genome assembly of C. arietinum (desi chickpea) resulted in identification of 842,104 genomic SNPs which were utilized along with an additional 36,446 genic SNPs identified from transcriptome sequences of the aforementioned varieties. Two new chickpea Oligo Pool All (OPAs) each having 3,072 SNPs were designed and utilized for SNP genotyping of 129 Recombinant Inbred Lines (RILs). Using Illumina GoldenGate Technology genotyping data of 5,041 SNPs were generated and combined with the 1,673 marker data from previously published studies, to generate a high resolution linkage map. The map comprised of 6698 markers distributed on eight linkage groups spanning 1083.93 cM with an average inter-marker distance of 0.16 cM. Utility of the present map was demonstrated for improving the anchoring of the earlier reported draft genome sequence of desi chickpea by ~30% and that of kabuli chickpea by 18%. The genetic map reported in this study represents the most dense linkage map of chickpea , with the potential to facilitate efficient anchoring of the draft genome sequences of desi as well as kabuli chickpea varieties. PMID:26303721

  3. High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea.

    PubMed

    Gaur, Rashmi; Jeena, Ganga; Shah, Niraj; Gupta, Shefali; Pradhan, Seema; Tyagi, Akhilesh K; Jain, Mukesh; Chattopadhyay, Debasis; Bhatia, Sabhyata

    2015-01-01

    This study presents genome-wide discovery of SNPs through next generation sequencing of the genome of Cicer reticulatum. Mapping of the C. reticulatum sequenced reads onto the draft genome assembly of C. arietinum (desi chickpea) resulted in identification of 842,104 genomic SNPs which were utilized along with an additional 36,446 genic SNPs identified from transcriptome sequences of the aforementioned varieties. Two new chickpea Oligo Pool All (OPAs) each having 3,072 SNPs were designed and utilized for SNP genotyping of 129 Recombinant Inbred Lines (RILs). Using Illumina GoldenGate Technology genotyping data of 5,041 SNPs were generated and combined with the 1,673 marker data from previously published studies, to generate a high resolution linkage map. The map comprised of 6698 markers distributed on eight linkage groups spanning 1083.93 cM with an average inter-marker distance of 0.16 cM. Utility of the present map was demonstrated for improving the anchoring of the earlier reported draft genome sequence of desi chickpea by ~30% and that of kabuli chickpea by 18%. The genetic map reported in this study represents the most dense linkage map of chickpea , with the potential to facilitate efficient anchoring of the draft genome sequences of desi as well as kabuli chickpea varieties.

  4. Identification and High-Density Mapping of Gene-Rich Regions in Chromosome Group 5 of Wheat

    PubMed Central

    Gill, K. S.; Gill, B. S.; Endo, T. R.; Boyko, E. V.

    1996-01-01

    The distribution of genes and recombination in the wheat genome was studied by comparing physical maps with the genetic linkage maps. The physical maps were generated by mapping 80 DNA and two phenotypic markers on an array of 65 deletion lines for homoeologous group 5 chromosomes. The genetic maps were constructed for chromosome 5B in wheat and 5D in Triticum tauschii. No marker mapped in the proximal 20% chromosome region surrounding the centromere. More than 60% of the long arm markers were present in three major clusters that physically encompassed <18% of the arm. Because 48% of the markers were cDNA clones and the distributions of the cDNA and genomic clones were similar, the marker distribution may represent the distribution of genes. The gene clusters were identified and allocated to very small chromosome regions because of a higher number of deletions in their surrounding regions. The recombination was suppressed in the centromeric regions and mainly occurred in the gene-rich regions. The bp/cM estimates varied from 118 kb for gene-rich regions to 22 Mb for gene-poor regions. The wheat genes present in these clusters are, therefore, amenable to molecular manipulations parallel to the plants with smaller genomes like rice. PMID:8725245

  5. 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.

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

    SciTech Connect

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

    2014-06-14

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

  7. High-density sex-specific linkage maps of a European tree frog (Hyla arborea) identify the sex chromosome without information on offspring sex.

    PubMed

    Brelsford, A; Dufresnes, C; Perrin, N

    2016-02-01

    Identifying homology between sex chromosomes of different species is essential to understanding the evolution of sex determination. Here, we show that the identity of a homomorphic sex chromosome pair can be established using a linkage map, without information on offspring sex. By comparing sex-specific maps of the European tree frog Hyla arborea, we find that the sex chromosome (linkage group 1) shows a threefold difference in marker number between the male and female maps. In contrast, the number of markers on each autosome is similar between the two maps. We also find strongly conserved synteny between H. arborea and Xenopus tropicalis across 200 million years of evolution, suggesting that the rate of chromosomal rearrangement in anurans is low. Finally, we show that recombination in males is greatly reduced at the centers of large chromosomes, consistent with previous cytogenetic findings. Our research shows the importance of high-density linkage maps for studies of recombination, chromosomal rearrangement and the genetic architecture of ecologically or economically important traits. PMID:26374238

  8. Contrast enhancement via texture region based histogram equalization

    NASA Astrophysics Data System (ADS)

    Singh, Kuldeep; Vishwakarma, Dinesh K.; Singh Walia, Gurjit; Kapoor, Rajiv

    2016-08-01

    This paper presents two novel contrast enhancement approaches using texture regions-based histogram equalization (HE). In HE-based contrast enhancement methods, the enhanced image often contains undesirable artefacts because an excessive number of pixels in the non-textured areas heavily bias the histogram. The novel idea presented in this paper is to suppress the impact of pixels in non-textured areas and to exploit texture features for the computation of histogram in the process of HE. The first algorithm named as Dominant Orientation-based Texture Histogram Equalization (DOTHE), constructs the histogram of the image using only those image patches having dominant orientation. DOTHE categories image patches into smooth, dominant or non-dominant orientation patches by using the image variance and singular value decomposition algorithm and utilizes only dominant orientation patches in the process of HE. The second method termed as Edge-based Texture Histogram Equalization, calculates significant edges in the image and constructs the histogram using the grey levels present in the neighbourhood of edges. The cumulative density function of the histogram formed from texture features is mapped on the entire dynamic range of the input image to produce the contrast-enhanced image. Subjective as well as objective performance assessment of proposed methods is conducted and compared with other existing HE methods. The performance assessment in terms of visual quality, contrast improvement index, entropy and measure of enhancement reveals that the proposed methods outperform the existing HE methods.

  9. Freedom, equality, race.

    PubMed

    Ferguson, Jeffrey B

    2011-01-01

    This essay explores come of the reasons for the continuing power of racial categorization in our era, and thus offers some friendly amendments to the more optimistic renderings of the term post-racial. Focusing mainly on the relationship between black and white Americans, it argues that the widespread embrace of universal values of freedom and equality, which most regard as antidotes to racial exclusion, actually reinforce it. The internal logic of these categories requires the construction of the "other." In America, where freedom and equality still stand at the contested center of collective identity, a history of racial oppression informs the very meaning of these terms. Thus the irony: much of the effort exerted to transcend race tends to fuel continuing division. PMID:21469393

  10. Mapping the energy density of shaped waves in scattering media onto a complete set of diffusion modes.

    PubMed

    Ojambati, Oluwafemi S; Mosk, Allard P; Vellekoop, Ivo M; Lagendijk, Ad; Vos, Willem L

    2016-08-01

    We study the energy density of shaped waves inside a quasi-1D disordered waveguide. We find that the spatial energy density of optimally shaped waves, when expanded in the complete set of eigenfunctions of the diffusion equation, is well described by considering only a few of the lowest eigenfunctions. Taking into account only the fundamental eigenfunction, the total internal energy inside the sample is underestimated by only 2%. The spatial distribution of the shaped energy density is very similar to the fundamental eigenfunction, up to a cosine distance of about 0.01. We obtain the energy density of transmission eigenchannels inside the sample by numerical simulation of the scattering matrix. Computing the transmission-averaged energy density over all transmission channels yields the ensemble averaged energy density of shaped waves. From the averaged energy density, we reconstruct its spatial distribution using the eigenfunctions of the diffusion equation. The results of our study have exciting applications in controlled biomedical imaging, efficient light harvesting in solar cells, enhanced energy conversion in solid-state lighting, and low threshold random lasers. PMID:27505816

  11. Mapping the energy density of shaped waves in scattering media onto a complete set of diffusion modes.

    PubMed

    Ojambati, Oluwafemi S; Mosk, Allard P; Vellekoop, Ivo M; Lagendijk, Ad; Vos, Willem L

    2016-08-01

    We study the energy density of shaped waves inside a quasi-1D disordered waveguide. We find that the spatial energy density of optimally shaped waves, when expanded in the complete set of eigenfunctions of the diffusion equation, is well described by considering only a few of the lowest eigenfunctions. Taking into account only the fundamental eigenfunction, the total internal energy inside the sample is underestimated by only 2%. The spatial distribution of the shaped energy density is very similar to the fundamental eigenfunction, up to a cosine distance of about 0.01. We obtain the energy density of transmission eigenchannels inside the sample by numerical simulation of the scattering matrix. Computing the transmission-averaged energy density over all transmission channels yields the ensemble averaged energy density of shaped waves. From the averaged energy density, we reconstruct its spatial distribution using the eigenfunctions of the diffusion equation. The results of our study have exciting applications in controlled biomedical imaging, efficient light harvesting in solar cells, enhanced energy conversion in solid-state lighting, and low threshold random lasers.

  12. Lemurs in a complex landscape: mapping species density in subtropical dry forests of southwestern Madagascar using data at multiple levels.

    PubMed

    Axel, Anne C; Maurer, Brian A

    2011-01-01

    The study of southern dry forest lemurs has been largely restricted to small reserves; yet, the majority of the region's lemur populations reside outside protected areas. Lemur catta and Propithecus verreauxi occupy the same forests but have different dietary preferences. This study assessed L. catta and P. verreauxi population densities across a 3-km dry forest gradient (1,539 ha) in southern Madagascar. The study was designed to allow lemur densities to be related to particular forest types. A particular aim of this study was to collect lemur data in both protected and unprotected areas. Density estimates were calculated using point transect distance sampling in a study area that contained the Beza Mahafaly Special Reserve and the adjacent disturbed forests. The highest densities recorded for each species were in the protected area where the two species were most segregated in their distribution, with L. catta density highest in gallery forest type and P. verreauxi density highest in dry deciduous. Densities of both species varied widely outside the protected area, but P. verreauxi density was more uniform than was L. catta. Results of this study indicate that patterns of lemur density in protected areas are not representative of patterns in disturbed forests; this also suggests that we cannot fully understand the ecological constraints facing primate species by studying them only in protected areas. This research highlights the value of pairing the study of landscape-level patterns of species distribution with both local ground-level ecological interpretations and broad-scale satellite data; information from only one level may give an incomplete view of the community.

  13. 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.

  14. Construction of high-density genetic linkage map and identification of flowering-time QTLs in orchardgrass using SSRs and SLAF-seq

    PubMed Central

    Zhao, Xinxin; Huang, Linkai; Zhang, Xinquan; Wang, Jianping; Yan, Defei; Li, Ji; Tang, Lu; Li, Xiaolong; Shi, Tongwei

    2016-01-01

    Orchardgrass (Dactylis glomerata L.) is one of the most economically important perennial, cool-season forage species grown and pastured worldwide. High-density genetic linkage mapping is a valuable and effective method for exploring complex quantitative traits. In this study, we developed 447,177 markers based on SLAF-seq and used them to perform a comparative genomics analysis. Perennial ryegrass sequences were the most similar (5.02%) to orchardgrass sequences. A high-density linkage map of orchardgrass was constructed using 2,467 SLAF markers and 43 SSRs, which were distributed on seven linkage groups spanning 715.77 cM. The average distance between adjacent markers was 0.37 cM. Based on phenotyping in four environments, 11 potentially significant quantitative trait loci (QTLs) for two target traits–heading date (HD) and flowering time (FT)–were identified and positioned on linkage groups LG1, LG3, and LG5. Significant QTLs explained 8.20–27.00% of the total phenotypic variation, with the LOD ranging from 3.85–12.21. Marker167780 and Marker139469 were associated with FT and HD at the same location (Ya’an) over two different years. The utility of SLAF markers for rapid generation of genetic maps and QTL analysis has been demonstrated for heading date and flowering time in a global forage grass. PMID:27389619

  15. 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;…

  16. The First High-Density Genetic Map Construction in Tree Peony (Paeonia Sect. Moutan) using Genotyping by Specific-Locus Amplified Fragment Sequencing

    PubMed Central

    Cai, Changfu; Cheng, Fang-Yun; Wu, Jing; Zhong, Yuan; Liu, Gaixiu

    2015-01-01

    Genetic linkage maps, permitting the elucidation of genome structure, are one of most powerful genomic tools to accelerate marker-assisted breeding. However, due to a lack of sufficient user-friendly molecular markers, no genetic linkage map has been developed for tree peonies (Paeonia Sect. Moutan), a group of important horticultural plants worldwide. Specific-locus amplified fragment sequencing (SLAF-seq) is a recent molecular marker development technology that enable the large-scale discovery and genotyping of sequence-based marker in genome-wide. In this study, we performed SLAF sequencing of an F1 population, derived from the cross P. ostti ‘FenDanBai’ × P. × suffruticosa ‘HongQiao’, to identify sufficient high-quality markers for the construction of high-density genetic linkage map in tree peonies. After SLAF sequencing, a total of 78 Gb sequencing data and 285,403,225 pair-end reads were generated. We detected 309,198 high-quality SLAFs from these data, of which 85,124 (27.5%) were polymorphic. Subsequently, 3518 of the polymorphic markers, which were successfully encoded in to Mendelian segregation types, and were in conformity with the criteria of high-quality markers, were defined as effective markers and used for genetic linkage mapping. Finally, we constructed an integrated genetic map, which comprised 1189 markers on the five linkage groups, and spanned 920.699 centiMorgans (cM) with an average inter-marker distance of 0.774 cM. There were 1115 ‘SNP-only’ markers, 18 ‘InDel-only’ markers, and 56 ‘SNP&InDel’ markers on the map. Among these markers, 450 (37.85%) showed significant segregation distortion (P < 0.05). In conclusion, this investigation reported the first large-scale marker development and high-density linkage map construction for tree peony. The results of this study will serve as a solid foundation not only for marker-assisted breeding, but also for genome sequence assembly for tree peony. PMID:26010095

  17. The First High-Density Genetic Map Construction in Tree Peony (Paeonia Sect. Moutan) using Genotyping by Specific-Locus Amplified Fragment Sequencing.

    PubMed

    Cai, Changfu; Cheng, Fang-Yun; Wu, Jing; Zhong, Yuan; Liu, Gaixiu

    2015-01-01

    Genetic linkage maps, permitting the elucidation of genome structure, are one of most powerful genomic tools to accelerate marker-assisted breeding. However, due to a lack of sufficient user-friendly molecular markers, no genetic linkage map has been developed for tree peonies (Paeonia Sect. Moutan), a group of important horticultural plants worldwide. Specific-locus amplified fragment sequencing (SLAF-seq) is a recent molecular marker development technology that enable the large-scale discovery and genotyping of sequence-based marker in genome-wide. In this study, we performed SLAF sequencing of an F1 population, derived from the cross P. ostti 'FenDanBai' × P. × suffruticosa 'HongQiao', to identify sufficient high-quality markers for the construction of high-density genetic linkage map in tree peonies. After SLAF sequencing, a total of 78 Gb sequencing data and 285,403,225 pair-end reads were generated. We detected 309,198 high-quality SLAFs from these data, of which 85,124 (27.5%) were polymorphic. Subsequently, 3518 of the polymorphic markers, which were successfully encoded in to Mendelian segregation types, and were in conformity with the criteria of high-quality markers, were defined as effective markers and used for genetic linkage mapping. Finally, we constructed an integrated genetic map, which comprised 1189 markers on the five linkage groups, and spanned 920.699 centiMorgans (cM) with an average inter-marker distance of 0.774 cM. There were 1115 'SNP-only' markers, 18 'InDel-only' markers, and 56 'SNP&InDel' markers on the map. Among these markers, 450 (37.85%) showed significant segregation distortion (P < 0.05). In conclusion, this investigation reported the first large-scale marker development and high-density linkage map construction for tree peony. The results of this study will serve as a solid foundation not only for marker-assisted breeding, but also for genome sequence assembly for tree peony.

  18. A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cotton genome complexity was investigated with a saturated molecular genetic map that combined several sets of microsatellites or simple sequence repeats (SSR) and the first major public set of single nucleotide polymorphism (SNP) markers in cotton genomes (Gossypium spp.), and that was constructed ...

  19. 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.; Mayes, D. C.; Tommasini, R.; Smalyuk, V. A.; Regan, S. P.; Delettrez, J. A.

    2016-01-25

    In warm target direct-drive ICF implosion experiments performed at the OMEGA laser facility, plastic microballoons 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. These 2-D space-resolvedmore » 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±28eV, electron number density (Ne) = 8.5x1024±2.5x1024 cm-3, and average areal density <ρR> = 86±7mg/cm2. 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. 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±1μm.« less

  20. 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

    NASA Astrophysics Data System (ADS)

    Johns, H. M.; Mancini, R. C.; Nagayama, T.; Mayes, D. C.; Tommasini, R.; Smalyuk, V. A.; Regan, S. P.; Delettrez, J. A.

    2016-01-01

    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. These 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 (Ne) = 8.5 × 1024 ± 2.5 × 1024 cm-3, and average areal density <ρR> = 86 ± 7 mg/cm2. 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. 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.

  1. Non-destructive mapping of doping and structural composition of MOVPE-grown high current density resonant tunnelling diodes through photoluminescence spectroscopy

    NASA Astrophysics Data System (ADS)

    Jacobs, K. J. P.; Stevens, B. J.; Mukai, T.; Ohnishi, D.; Hogg, R. A.

    2015-05-01

    We report on photoluminescence (PL) characterisation of metal-organic vapour phase epitaxy (MOVPE) grown high current density (~700 kA/cm2) InGaAs/AlAs/InP based resonant tunnelling diodes (RTDs) for terahertz emission. The PL mapping we describe allows important information about doping level and uniformity, ternary alloy composition and uniformity, and uniformity of quantum well thickness to be deduced. PL as a function of doping concentration is studied for InGaAs test layers at low temperatures and correlated to secondary-ion mass spectroscopy (SIMS) and electrochemical capacitance-voltage (eCV) profiling to provide non-destructive mapping of doping over the wafer. For the RTD structures, we utilise eCV as a selective etch tool to identify the origin of low temperature PL emission from the quantum well (QW) and the highly doped contact layers. PL mapping of the RTD wafer at low temperatures is shown to allow the assessment of variations in InGaAs alloy composition and QW thickness. Details of the growth process are discussed and confirmed using high resolution X-ray diffraction (HRXRD) crystallography. The rapid non-destructive characterisation and wafer mapping of these structures promises a route to future growth optimisation of such structures.

  2. Gate-control efficiency and interface state density evaluated from capacitance-frequency-temperature mapping for GaN-based metal-insulator-semiconductor devices

    SciTech Connect

    Shih, Hong-An; Kudo, Masahiro; Suzuki, Toshi-kazu

    2014-11-14

    We present an analysis method for GaN-based metal-insulator-semiconductor (MIS) devices by using capacitance-frequency-temperature (C-f-T) mapping to evaluate the gate-control efficiency and the interface state density, both exhibiting correlations with the linear-region intrinsic transconductance. The effectiveness of the method was exemplified by application to AlN/AlGaN/GaN MIS devices to elucidate the properties of AlN-AlGaN interfaces depending on their formation processes. Using the C-f-T mapping, we extract the gate-bias-dependent activation energy with its derivative giving the gate-control efficiency, from which we evaluate the AlN-AlGaN interface state density through the Lehovec equivalent circuit in the DC limit. It is shown that the gate-control efficiency and the interface state density have correlations with the linear-region intrinsic transconductance, all depending on the interface formation processes. In addition, we give characterization of the AlN-AlGaN interfaces by using X-ray photoelectron spectroscopy, in relation with the results of the analysis.

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

    PubMed

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

    2015-07-01

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

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

    PubMed Central

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

    2015-01-01

    Reference panels from the 1000 Genomes (1000G) Project Consortium provide near complete coverage of common and low-frequency genetic variation with minor allele frequency ≥0.5% across European ancestry populations. Within the European Network for Genetic and Genomic Epidemiology (ENGAGE) Consortium, we have undertaken the first large-scale meta-analysis of genome-wide association studies (GWAS), supplemented by 1000G imputation, for four quantitative glycaemic and obesity-related traits, in up to 87,048 individuals of European ancestry. We identified two loci for body mass index (BMI) at genome-wide significance, and two for fasting glucose (FG), none of which has been previously reported in larger meta-analysis efforts to combine GWAS of European ancestry. Through conditional analysis, we also detected multiple distinct signals of association mapping to established loci for waist-hip ratio adjusted for BMI (RSPO3) and FG (GCK and G6PC2). The index variant for one association signal at the G6PC2 locus is a low-frequency coding allele, H177Y, which has recently been demonstrated to have a functional role in glucose regulation. Fine-mapping analyses revealed that the non-coding variants most likely to drive association signals at established and novel loci were enriched for overlap with enhancer elements, which for FG mapped to promoter and transcription factor binding sites in pancreatic islets, in particular. Our study demonstrates that 1000G imputation and genetic fine-mapping of common and low-frequency variant association signals at GWAS loci, integrated with genomic annotation in relevant tissues, can provide insight into the functional and regulatory mechanisms through which their effects on glycaemic and obesity-related traits are mediated. PMID:26132169

  5. Mapping the genome of meta-generalized gradient approximation density functionals: The search for B97M-V

    SciTech Connect

    Mardirossian, Narbe; Head-Gordon, Martin

    2015-02-21

    A meta-generalized gradient approximation density functional paired with the VV10 nonlocal correlation functional is presented. The functional form is selected from more than 10{sup 10} choices carved out of a functional space of almost 10{sup 40} possibilities. Raw data come from training a vast number of candidate functional forms on a comprehensive training set of 1095 data points and testing the resulting fits on a comprehensive primary test set of 1153 data points. Functional forms are ranked based on their ability to reproduce the data in both the training and primary test sets with minimum empiricism, and filtered based on a set of physical constraints and an often-overlooked condition of satisfactory numerical precision with medium-sized integration grids. The resulting optimal functional form has 4 linear exchange parameters, 4 linear same-spin correlation parameters, and 4 linear opposite-spin correlation parameters, for a total of 12 fitted parameters. The final density functional, B97M-V, is further assessed on a secondary test set of 212 data points, applied to several large systems including the coronene dimer and water clusters, tested for the accurate prediction of intramolecular and intermolecular geometries, verified to have a readily attainable basis set limit, and checked for grid sensitivity. Compared to existing density functionals, B97M-V is remarkably accurate for non-bonded interactions and very satisfactory for thermochemical quantities such as atomization energies, but inherits the demonstrable limitations of existing local density functionals for barrier heights.

  6. Mapping the genome of meta-generalized gradient approximation density functionals: The search for B97M-V

    NASA Astrophysics Data System (ADS)

    Mardirossian, Narbe; Head-Gordon, Martin

    2015-02-01

    A meta-generalized gradient approximation density functional paired with the VV10 nonlocal correlation functional is presented. The functional form is selected from more than 1010 choices carved out of a functional space of almost 1040 possibilities. Raw data come from training a vast number of candidate functional forms on a comprehensive training set of 1095 data points and testing the resulting fits on a comprehensive primary test set of 1153 data points. Functional forms are ranked based on their ability to reproduce the data in both the training and primary test sets with minimum empiricism, and filtered based on a set of physical constraints and an often-overlooked condition of satisfactory numerical precision with medium-sized integration grids. The resulting optimal functional form has 4 linear exchange parameters, 4 linear same-spin correlation parameters, and 4 linear opposite-spin correlation parameters, for a total of 12 fitted parameters. The final density functional, B97M-V, is further assessed on a secondary test set of 212 data points, applied to several large systems including the coronene dimer and water clusters, tested for the accurate prediction of intramolecular and intermolecular geometries, verified to have a readily attainable basis set limit, and checked for grid sensitivity. Compared to existing density functionals, B97M-V is remarkably accurate for non-bonded interactions and very satisfactory for thermochemical quantities such as atomization energies, but inherits the demonstrable limitations of existing local density functionals for barrier heights.

  7. Criteria for equality in two entropic inequalities

    SciTech Connect

    Shirokov, M. E.

    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 between the constrained Holevo capacity of a quantum channel and the input von Neumann entropy. Bibliography: 20 titles. (paper)

  8. Mapping the genome of meta-generalized gradient approximation density functionals: the search for B97M-V.

    PubMed

    Mardirossian, Narbe; Head-Gordon, Martin

    2015-02-21

    A meta-generalized gradient approximation density functional paired with the VV10 nonlocal correlation functional is presented. The functional form is selected from more than 10(10) choices carved out of a functional space of almost 10(40) possibilities. Raw data come from training a vast number of candidate functional forms on a comprehensive training set of 1095 data points and testing the resulting fits on a comprehensive primary test set of 1153 data points. Functional forms are ranked based on their ability to reproduce the data in both the training and primary test sets with minimum empiricism, and filtered based on a set of physical constraints and an often-overlooked condition of satisfactory numerical precision with medium-sized integration grids. The resulting optimal functional form has 4 linear exchange parameters, 4 linear same-spin correlation parameters, and 4 linear opposite-spin correlation parameters, for a total of 12 fitted parameters. The final density functional, B97M-V, is further assessed on a secondary test set of 212 data points, applied to several large systems including the coronene dimer and water clusters, tested for the accurate prediction of intramolecular and intermolecular geometries, verified to have a readily attainable basis set limit, and checked for grid sensitivity. Compared to existing density functionals, B97M-V is remarkably accurate for non-bonded interactions and very satisfactory for thermochemical quantities such as atomization energies, but inherits the demonstrable limitations of existing local density functionals for barrier heights. PMID:25702006

  9. Precision Mapping of Laser-Driven Magnetic Fields and Their Evolution in High-Energy-Density Plasmas

    NASA Astrophysics Data System (ADS)

    Gao, L.; Nilson, P. M.; Igumenshchev, I. V.; Haines, M. G.; Froula, D. H.; Betti, R.; Meyerhofer, D. D.

    2015-05-01

    The magnetic fields generated at the surface of a laser-irradiated planar solid target are mapped using ultrafast proton radiography. Thick (50 μ m ) plastic foils are irradiated with 4-kJ, 2.5-ns laser pulses focused to an intensity of 4 ×1014 W /cm2 . The data show magnetic fields concentrated at the edge of the laser-focal region, well within the expanding coronal plasma. The magnetic-field spatial distribution is tracked and shows good agreement with 2D resistive magnetohydrodynamic simulations using the code draco when the Biermann battery source, fluid and Nernst advection, resistive magnetic diffusion, and Righi-Leduc heat flow are included.

  10. Precision mapping of laser-driven magnetic fields and their evolution in high-energy-density plasmas

    SciTech Connect

    Gao, L.; Nilson, P. M.; Igumenshchev, I. V.; Haines, M. G.; Froula, D. H.; Betti, R.; Meyerhofer, D. D.

    2015-05-29

    The magnetic fields generated at the surface of a laser-irradiated planar solid target are mapped using ultrafast proton radiography. Thick (50 μm) plastic foils are irradiated with 4-kJ, 2.5-ns laser pulses focused to an intensity of 4 x 10¹⁴ W/cm². The data show magnetic fields concentrated at the edge of the laser-focal region, well within the expanding coronal plasma. The magnetic-field spatial distribution is tracked and shows good agreement with 2D resistive magnetohydrodynamic simulations using the code DRACO when the Biermann battery source, fluid and Nernst advection, resistive magnetic diffusion, and Righi-Leduc heat flow are included.

  11. Precision mapping of laser-driven magnetic fields and their evolution in high-energy-density plasmas.

    PubMed

    Gao, L; Nilson, P M; Igumenshchev, I V; Haines, M G; Froula, D H; Betti, R; Meyerhofer, D D

    2015-05-29

    The magnetic fields generated at the surface of a laser-irradiated planar solid target are mapped using ultrafast proton radiography. Thick (50  μm) plastic foils are irradiated with 4-kJ, 2.5-ns laser pulses focused to an intensity of 4×10^{14}  W/cm^{2}. The data show magnetic fields concentrated at the edge of the laser-focal region, well within the expanding coronal plasma. The magnetic-field spatial distribution is tracked and shows good agreement with 2D resistive magnetohydrodynamic simulations using the code draco when the Biermann battery source, fluid and Nernst advection, resistive magnetic diffusion, and Righi-Leduc heat flow are included. PMID:26066442

  12. An Atlas-Based Electron Density Mapping Method for Magnetic Resonance Imaging (MRI)-Alone Treatment Planning and Adaptive MRI-Based Prostate Radiation Therapy

    SciTech Connect

    Dowling, Jason A.; Lambert, Jonathan; Parker, Joel; Salvado, Olivier; Fripp, Jurgen; Capp, Anne; Wratten, Chris; Denham, James W.; Greer, Peter B.

    2012-05-01

    Purpose: Prostate radiation therapy dose planning directly on magnetic resonance imaging (MRI) scans would reduce costs and uncertainties due to multimodality image registration. Adaptive planning using a combined MRI-linear accelerator approach will also require dose calculations to be performed using MRI data. The aim of this work was to develop an atlas-based method to map realistic electron densities to MRI scans for dose calculations and digitally reconstructed radiograph (DRR) generation. Methods and Materials: Whole-pelvis MRI and CT scan data were collected from 39 prostate patients. Scans from 2 patients showed significantly different anatomy from that of the remaining patient population, and these patients were excluded. A whole-pelvis MRI atlas was generated based on the manually delineated MRI scans. In addition, a conjugate electron-density atlas was generated from the coregistered computed tomography (CT)-MRI scans. Pseudo-CT scans for each patient were automatically generated by global and nonrigid registration of the MRI atlas to the patient MRI scan, followed by application of the same transformations to the electron-density atlas. Comparisons were made between organ segmentations by using the Dice similarity coefficient (DSC) and point dose calculations for 26 patients on planning CT and pseudo-CT scans. Results: The agreement between pseudo-CT and planning CT was quantified by differences in the point dose at isocenter and distance to agreement in corresponding voxels. Dose differences were found to be less than 2%. Chi-squared values indicated that the planning CT and pseudo-CT dose distributions were equivalent. No significant differences (p > 0.9) were found between CT and pseudo-CT Hounsfield units for organs of interest. Mean {+-} standard deviation DSC scores for the atlas-based segmentation of the pelvic bones were 0.79 {+-} 0.12, 0.70 {+-} 0.14 for the prostate, 0.64 {+-} 0.16 for the bladder, and 0.63 {+-} 0.16 for the rectum

  13. 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,…

  14. Dynamic drag force based on iterative density mapping: A new numerical tool for three-dimensional analysis of particle trajectories in a dielectrophoretic system.

    PubMed

    Knoerzer, Markus; Szydzik, Crispin; Tovar-Lopez, Francisco Javier; Tang, Xinke; Mitchell, Arnan; Khoshmanesh, Khashayar

    2016-02-01

    Dielectrophoresis is a widely used means of manipulating suspended particles within microfluidic systems. In order to efficiently design such systems for a desired application, various numerical methods exist that enable particle trajectory plotting in two or three dimensions based on the interplay of hydrodynamic and dielectrophoretic forces. While various models are described in the literature, few are capable of modeling interactions between particles as well as their surrounding environment as these interactions are complex, multifaceted, and computationally expensive to the point of being prohibitive when considering a large number of particles. In this paper, we present a numerical model designed to enable spatial analysis of the physical effects exerted upon particles within microfluidic systems employing dielectrophoresis. The model presents a means of approximating the effects of the presence of large numbers of particles through dynamically adjusting hydrodynamic drag force based on particle density, thereby introducing a measure of emulated particle-particle and particle-liquid interactions. This model is referred to as "dynamic drag force based on iterative density mapping." The resultant numerical model is used to simulate and predict particle trajectory and velocity profiles within a microfluidic system incorporating curved dielectrophoretic microelectrodes. The simulated data are compared favorably with experimental data gathered using microparticle image velocimetry, and is contrasted against simulated data generated using traditional "effective moment Stokes-drag method," showing more accurate particle velocity profiles for areas of high particle density.

  15. Coronal temperature, density, and magnetic field maps of a solar acitve region using the Owens Valley Solar Array

    NASA Technical Reports Server (NTRS)

    Gary, Dale E.; Hurford, G. J.

    1994-01-01

    We present the first results of solar active region observations with the recently completed five-element Owens Valley Solar Array. On 1991 October 24, maps of Active Region AR 6891 were obtained at 22 frequencies from 1.2-7.0 GHz to provide brightness temperature spectra at each point. This is the first time that both high spatial and frequency-resolution brightness temperature spectra have been available over such a broad radio-frequency range. We find that over most of the region the spectra fall into one of the two well-defined categories: thermal free-free or thermal gyroresonance. In these cases, we use the spectra to deduce the spatial variation of physical parameters-electron temperature, column emission measure (intergral n(sup 2)(sub e) dl), and the coronal magnetic field strength-in and around the active region. Over a limited area of the region, the spectra resemble neither of the simple types, and alternative interpretations are required. The possibilties include the presence of fine structure that is unresolved at low frequencies; the presence of a small number of nonthermal electrons; or the presence of overlying, cooler 10(exp 6) K material which at low frequencies absorbs the hot (3 x 10(exp 6) K) thermal emission generated below.

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

    PubMed

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Grange, Pascal

    2015-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  19. Computer controlled performance mapping of thermionic converters: effect of collector, guard-ring potential imbalances on the observed collector current-density, voltage characteristics and limited range performance map of an etched-rhenium, niobium planar converter

    NASA Technical Reports Server (NTRS)

    Manista, E. J.

    1972-01-01

    The effect of collector, guard-ring potential imbalance on the observed collector-current-density J, collector-to-emitter voltage V characteristic was evaluated in a planar, fixed-space, guard-ringed thermionic converter. The J,V characteristic was swept in a period of 15 msec by a variable load. A computerized data acquisition system recorded test parameters. The results indicate minimal distortion of the J,V curve in the power output quadrant for the nominal guard-ring circuit configuration. Considerable distortion, along with a lowering of the ignited-mode striking voltage, was observed for the configuration with the emitter shorted to the guard ring. A limited-range performance map of an etched-rhenium, niobium, planar converter was obtained by using an improved computer program for the data acquisition system.

  20. Magnetic Field, Density Current, and Lorentz Force Full Vector Maps of the NOAA 10808 Double Sunspot: Evidence of Strong Horizontal Current Flows in the Penumbra

    NASA Astrophysics Data System (ADS)

    Bommier, V.; Landi Degl'Innocenti, E.; Schmieder, B.; Gelly, B.

    2011-04-01

    The context is that of the so-called “fundamental ambiguity” (also azimuth ambiguity, or 180° ambiguity) in magnetic field vector measurements: two field vectors symmetrical with respect to the line-of-sight have the same polarimetric signature, so that they cannot be discriminated. We propose a method to solve this ambiguity by applying the “simulated annealing” algorithm to the minimization of the field divergence, added to the longitudinal current absolute value, the line-of-sight derivative of the magnetic field being inferred by the interpretation of the Zeeman effect observed by spectropolarimetry in two lines formed at different depths. We find that the line pair Fe I λ 6301.5 and Fe I λ 6302.5 is appropriate for this purpose. We treat the example case of the δ-spot of NOAA 10808 observed on 13 September 2005 between 14:25 and 15:25 UT with the THEMIS telescope. Besides the magnetic field resolved map, the electric current density vector map is also obtained. A strong horizontal current density flow is found surrounding each spot inside its penumbra, associated to a non-zero Lorentz force centripetal with respect to the spot center (i.e., oriented towards the spot center). The current wrapping direction is found to depend on the spot polarity: clockwise for the positive polarity, counterclockwise for the negative one. This analysis is made possible thanks to the UNNOFIT2 Milne-Eddington inversion code, where the usual theory is generalized to the case of a line Fe I λ 6301.5) that is not a normal Zeeman triplet line (like Fe I λ 6302.5).

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

    PubMed

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

    2011-04-01

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

  2. A quantitative spatial comparison of high-density diffuse optical tomography and fMRI cortical mapping

    PubMed Central

    Eggebrecht, Adam T.; White, Brian R.; Ferradal, Silvina L.; Chen, Chunxiao; Zhan, Yuxuan; Snyder, Abraham Z.; Dehghani, Hamid; Culver, Joseph P.

    2012-01-01

    Functional neuroimaging commands a dominant role in current neuroscience research. However its use in bedside clinical and certain neuro-scientific studies has been limited because the current tools lack the combination of being non-invasive, non-ionizing and portable while maintaining moderate resolution and localization accuracy. Optical neuroimaging satisfies many of these requirements, but, until recent advances in high-density diffuse optical tomography (HD-DOT), has been hampered by limited resolution. While early results of HD-DOT have been promising, a quantitative voxel-wise comparison and validation of HD-DOT against the gold standard of functional magnetic resonance imaging (fMRI) has been lacking. Herein, we provide such an analysis within the visual cortex using matched visual stimulation protocols in a single group of subjects (n=5) during separate HD-DOT and fMRI scanning sessions. To attain the needed voxel-to-voxel co-registration between HD-DOT and fMRI image spaces, we implemented subject-specific head modeling that incorporated MRI anatomy, detailed segmentation, and alignment of source and detector positions. Comparisons of the visual responses found an average localization error between HD-DOT and fMRI of 4.4 +/− 1 mm, significantly less than the average distance between cortical gyri. This specificity demonstrates that HD-DOT has sufficient image quality to be useful as a surrogate for fMRI. PMID:22330315

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

    PubMed

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

    2011-04-01

    Recent studies suggest that visual object recognition is a proactive process through which perceptual evidence accumulates over time before a decision can be made about the object. However, the exact electrophysiological correlates and time-course of this complex process remain unclear. In addition, the potential influence of emotion on this process has not been investigated yet. We recorded high density EEG in healthy adult participants performing a novel perceptual recognition task. For each trial, an initial blurred visual scene was first shown, before the actual content of the stimulus was gradually revealed by progressively adding diagnostic high spatial frequency information. Participants were asked to stop this stimulus sequence as soon as they could correctly perform an animacy judgment task. Behavioral results showed that participants reliably gathered perceptual evidence before recognition. Furthermore, prolonged exploration times were observed for pleasant, relative to either neutral or unpleasant scenes. ERP results showed distinct effects starting at 280 ms post-stimulus onset in distant brain regions during stimulus processing, mainly characterized by: (i) a monotonic accumulation of evidence, involving regions of the posterior cingulate cortex/parahippocampal gyrus, and (ii) true categorical recognition effects in medial frontal regions, including the dorsal anterior cingulate cortex. These findings provide evidence for the early involvement, following stimulus onset, of non-overlapping brain networks during proactive processes eventually leading to visual object recognition. PMID:21237274

  4. Mapping of cortical activity in the first two decades of life: a high-density sleep electroencephalogram study.

    PubMed

    Kurth, Salomé; Ringli, Maya; Geiger, Anja; LeBourgeois, Monique; Jenni, Oskar G; Huber, Reto

    2010-10-01

    Evidence that electroencephalography (EEG) slow-wave activity (SWA) (EEG spectral power in the 1-4.5 Hz band) during non-rapid eye movement sleep (NREM) reflects plastic changes is increasing (Tononi and Cirelli, 2006). Regional assessment of gray matter development from neuroimaging studies reveals a posteroanterior trajectory of cortical maturation in the first three decades of life (Shaw et al., 2008). Our aim was to test whether this regional cortical maturation is reflected in regional changes of sleep SWA. We evaluated all-night high-density EEG (128 channels) in 55 healthy human subjects (2.4-19.4 years) and assessed age-related changes in NREM sleep topography. As in adults, we observed frequency-specific topographical distributions of sleep EEG power in all subjects. However, from early childhood to late adolescence, the location on the scalp showing maximal SWA underwent a shift from posterior to anterior regions. This shift along the posteroanterior axis was only present in the SWA frequency range and remained stable across the night. Changes in the topography of SWA during sleep parallel neuroimaging study findings indicating cortical maturation starts early in posterior areas and spreads rostrally over the frontal cortex. Thus, SWA might reflect the underlying processes of cortical maturation. In the future, sleep SWA assessments may be used as a clinical tool to detect aberrations in cortical maturation.

  5. A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution

    PubMed Central

    Kawakami, Takeshi; Smeds, Linnéa; Backström, Niclas; Husby, Arild; Qvarnström, Anna; Mugal, Carina F; Olason, Pall; Ellegren, Hans

    2014-01-01

    Detailed linkage and recombination rate maps are necessary to use the full potential of genome sequencing and population genomic analyses. We used a custom collared flycatcher 50 K SNP array to develop a high-density linkage map with 37 262 markers assigned to 34 linkage groups in 33 autosomes and the Z chromosome. The best-order map contained 4215 markers, with a total distance of 3132 cm and a mean genetic distance between markers of 0.12 cm. Facilitated by the array being designed to include markers from most scaffolds, we obtained a second-generation assembly of the flycatcher genome that approaches full chromosome sequences (N50 super-scaffold size 20.2 Mb and with 1.042 Gb (of 1.116 Gb) anchored to and mostly ordered and oriented along chromosomes). We found that flycatcher and zebra finch chromosomes are entirely syntenic but that inversions at mean rates of 1.5–2.0 event (6.6–7.5 Mb) per My have changed the organization within chromosomes, rates high enough for inversions to potentially have been involved with many speciation events during avian evolution. The mean recombination rate was 3.1 cm/Mb and correlated closely with chromosome size, from 2 cm/Mb for chromosomes >100 Mb to >10 cm/Mb for chromosomes <10 Mb. This size dependence seemed entirely due to an obligate recombination event per chromosome; if 50 cm was subtracted from the genetic lengths of chromosomes, the rate per physical unit DNA was constant across chromosomes. Flycatcher recombination rate showed similar variation along chromosomes as chicken but lacked the large interior recombination deserts characteristic of zebra finch chromosomes. PMID:24863701

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

    PubMed

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

    2015-01-01

    Soil deposition density maps of gamma-ray emitting radioactive nuclides from the Fukushima Dai-ichi Nuclear Power Plant (NPP) accident were constructed on the basis of results from large-scale soil sampling. In total 10,915 soil samples were collected at 2168 locations. Gamma rays emitted from the samples were measured by Ge detectors and analyzed using a reliable unified method. The determined radioactivity was corrected to that of June 14, 2011 by considering the intrinsic decay constant of each nuclide. Finally the deposition maps were created for (134)Cs, (137)Cs, (131)I, (129m)Te and (110m)Ag. The radioactivity ratio of (134)Cs-(137)Cs was almost constant at 0.91 regardless of the locations of soil sampling. The radioactivity ratios of (131)I and (129m)Te-(137)Cs were relatively high in the regions south of the Fukushima NPP site. Effective doses for 50 y after the accident were evaluated for external and inhalation exposures due to the observed radioactive nuclides. The radiation doses from radioactive cesium were found to be much higher than those from the other radioactive nuclides. PMID:24703526

  7. A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses.

    PubMed Central

    Bowers, John E; Abbey, Colette; Anderson, Sharon; Chang, Charlene; Draye, Xavier; Hoppe, Alison H; Jessup, Russell; Lemke, Cornelia; Lennington, Jennifer; Li, Zhikang; Lin, Yann-Rong; Liu, Sin-Chieh; Luo, Lijun; Marler, Barry S; Ming, Reiguang; Mitchell, Sharon E; Qiang, Dou; Reischmann, Kim; Schulze, Stefan R; Skinner, D Neil; Wang, Yue-Wen; Kresovich, Stephen; Schertz, Keith F; Paterson, Andrew H

    2003-01-01

    We report a genetic recombination map for Sorghum of 2512 loci spaced at average 0.4 cM ( approximately 300 kb) intervals based on 2050 RFLP probes, including 865 heterologous probes that foster comparative genomics of Saccharum (sugarcane), Zea (maize), Oryza (rice), Pennisetum (millet, buffelgrass), the Triticeae (wheat, barley, oat, rye), and Arabidopsis. Mapped loci identify 61.5% of the recombination events in this progeny set and reveal strong positive crossover interference acting across intervals of density are related to possible centromeric regions and to probable chromosome structural rearrangements between Sorghum bicolor and S. propinquum, but not to variation in levels of intraspecific allelic richness. While cDNA and genomic clones are similarly distributed across the genome, SSR-containing clones show different abundance patterns. Rapidly evolving hypomethylated DNA may contribute to intraspecific genomic differentiation. Nonrandom distribution patterns of multiple loci detected by 357 probes suggest ancient chromosomal duplication followed by extensive rearrangement and gene loss. Exemplifying the value of these data for comparative genomics, we support and extend prior findings regarding maize-sorghum synteny-in particular, 45% of comparative loci fall outside the inferred colinear/syntenic regions, suggesting that many small rearrangements have occurred since maize-sorghum divergence. These genetically anchored sequence-tagged sites will foster many structural, functional and evolutionary genomic studies in major food, feed, and biomass crops. PMID:14504243

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2012-10-31

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

  10. The neural dynamics of somatosensory processing and adaptation across childhood: a high-density electrical mapping study.

    PubMed

    Uppal, Neha; Foxe, John J; Butler, John S; Acluche, Frantzy; Molholm, Sophie

    2016-03-01

    Young children are often hyperreactive to somatosensory inputs hardly noticed by adults, as exemplified by irritation to seams or labels in clothing. The neurodevelopmental mechanisms underlying changes in sensory reactivity are not well understood. Based on the idea that neurodevelopmental changes in somatosensory processing and/or changes in sensory adaptation might underlie developmental differences in somatosensory reactivity, high-density electroencephalography was used to examine how the nervous system responds and adapts to repeated vibrotactile stimulation over childhood. Participants aged 6-18 yr old were presented with 50-ms vibrotactile stimuli to the right wrist over the median nerve at 5 blocked interstimulus intervals (ranging from ∼7 to ∼1 stimulus per second). Somatosensory evoked potentials (SEPs) revealed three major phases of activation within the first 200 ms, with scalp topographies suggestive of neural generators in contralateral somatosensory cortex. Although overall SEPs were highly similar for younger, middle, and older age groups (6.1-9.8, 10.0-12.9, and 13.0-17.8 yr old), there were significant age-related amplitude differences in initial and later phases of the SEP. In contrast, robust adaptation effects for fast vs. slow presentation rates were observed that did not differ as a function of age. A greater amplitude response in the later portion of the SEP was observed for the youngest group and may be related to developmental changes in responsivity to somatosensory stimuli. These data suggest the protracted development of the somatosensory system over childhood, whereas adaptation, as assayed in this study, is largely in place by ∼7 yr of age. PMID:26763781

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

    PubMed

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

    2012-10-31

    The frequency of environmental vibrations is sampled by two of the major sensory systems, audition and touch, notwithstanding that these signals are transduced through very different physical media and entirely separate sensory epithelia. Psychophysical studies have shown that manipulating frequency in audition or touch can have a significant cross-sensory impact on perceived frequency in the other sensory system, pointing to intimate links between these senses during computation of frequency. In this regard, the frequency of a vibratory event can be thought of as a multisensory perceptual construct. In turn, electrophysiological studies point to temporally early multisensory interactions that occur in hierarchically early sensory regions where convergent inputs from the auditory and somatosensory systems are to be found. A key question pertains to the level of processing at which the multisensory integration of featural information, such as frequency, occurs. Do the sensory systems calculate frequency independently before this information is combined, or is this feature calculated in an integrated fashion during preattentive sensory processing? The well characterized mismatch negativity, an electrophysiological response that indexes preattentive detection of a change within the context of a regular pattern of stimulation, served as our dependent measure. High-density electrophysiological recordings were made in humans while they were presented with separate blocks of somatosensory, auditory, and audio-somatosensory "standards" and "deviants," where the deviant differed in frequency. Multisensory effects were identified beginning at ∼200 ms, with the multisensory mismatch negativity (MMN) significantly different from the sum of the unisensory MMNs. This provides compelling evidence for preattentive coupling between the somatosensory and auditory channels in the cortical representation of frequency. PMID:23115172

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

    PubMed

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

    2014-07-25

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

  13. Reward Contingencies and the Recalibration of Task Monitoring and Reward Systems: A high-density electrical mapping study

    PubMed Central

    Morie, Kristen P.; De Sanctis, Pierfilippo; Foxe, John J.

    2014-01-01

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

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

    PubMed

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

    2014-07-25

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

  15. Comprehensive process maps for synthesizing high density aluminum oxide-carbon nanotube coatings by plasma spraying for improved mechanical and wear properties

    NASA Astrophysics Data System (ADS)

    Keshri, Anup Kumar

    Plasma sprayed aluminum oxide ceramic coating is widely used due to its outstanding wear, corrosion, and thermal shock resistance. But porosity is the integral feature in the plasma sprayed coating which exponentially degrades its properties. In this study, process maps were developed to obtain Al2O3-CNT composite coatings with the highest density (i.e. lowest porosity) and improved mechanical and wear properties. Process map is defined as a set of relationships that correlates large number of plasma processing parameters to the coating properties. Carbon nanotubes (CNTs) were added as reinforcement to Al2O 3 coating to improve the fracture toughness and wear resistance. Two novel powder processing approaches viz spray drying and chemical vapor growth were adopted to disperse CNTs in Al2O3 powder. The degree of CNT dispersion via chemical vapor deposition (CVD) was superior to spray drying but CVD could not synthesize powder in large amount. Hence optimization of plasma processing parameters and process map development was limited to spray dried Al2O3 powder containing 0, 4 and 8 wt. % CNTs. An empirical model using Pareto diagram was developed to link plasma processing parameters with the porosity of coating. Splat morphology as a function of plasma processing parameter was also studied to understand its effect on mechanical properties. Addition of a mere 1.5 wt. % CNTs via CVD technique showed ˜27% and ˜24% increase in the elastic modulus and fracture toughness respectively. Improved toughness was attributed to combined effect of lower porosity and uniform dispersion of CNTs which promoted the toughening by CNT bridging, crack deflection and strong CNT/Al2O3 interface. Al2O 3-8 wt. % CNT coating synthesized using spray dried powder showed 73% improvement in the fracture toughness when porosity reduced from 4.7% to 3.0%. Wear resistance of all coatings at room and elevated temperatures (573 K, 873 K) showed improvement with CNT addition and decreased porosity

  16. Medical Need, Equality, and Uncertainty.

    PubMed

    Horne, L Chad

    2016-10-01

    Many hold that distributing healthcare according to medical need is a requirement of equality. Most egalitarians believe, however, that people ought to be equal on the whole, by some overall measure of well-being or life-prospects; it would be a massive coincidence if distributing healthcare according to medical need turned out to be an effective way of promoting equality overall. I argue that distributing healthcare according to medical need is important for reducing individuals' uncertainty surrounding their future medical needs. In other words, distributing healthcare according to medical need is a natural feature of healthcare insurance; it is about indemnity, not equality. PMID:27196999

  17. Medical Need, Equality, and Uncertainty.

    PubMed

    Horne, L Chad

    2016-10-01

    Many hold that distributing healthcare according to medical need is a requirement of equality. Most egalitarians believe, however, that people ought to be equal on the whole, by some overall measure of well-being or life-prospects; it would be a massive coincidence if distributing healthcare according to medical need turned out to be an effective way of promoting equality overall. I argue that distributing healthcare according to medical need is important for reducing individuals' uncertainty surrounding their future medical needs. In other words, distributing healthcare according to medical need is a natural feature of healthcare insurance; it is about indemnity, not equality.

  18. Luck, Choice, and Educational Equality

    ERIC Educational Resources Information Center

    Calvert, John

    2015-01-01

    Harry Brighouse discusses two conceptions of educational equality. The first is a type of equality of opportunity, heavily influenced by the work of John Rawls, which he calls the meritocratic conception. According to this conception, an individual's educational prospects should not be influenced by factors such as their social class background.…

  19. Democracy, Equal Citizenship, and Education

    ERIC Educational Resources Information Center

    Callan, Eamonn

    2016-01-01

    Two appealing principles of educational distribution--equality and sufficiency--are comparatively assessed. The initial point of comparison is the distribution of civic educational goods. One reason to favor equality in educational distribution rather than sufficiency is the elimination of undeserved positional advantage in access to labor…

  20. Governing Equality: Mathematics for All?

    ERIC Educational Resources Information Center

    Diaz, Jennifer D.

    2013-01-01

    With the notion of governmentality, this article considers how the equal sign (=) in the U.S. math curriculum organizes knowledge of equality and inscribes cultural rules for thinking, acting, and seeing in the world. Situating the discussion within contemporary math reforms aimed at teaching mathematics for all, I draw attention to how the…

  1. CXCL13/CXCR5 enhances sodium channel Nav1.8 current density via p38 MAP kinase in primary sensory neurons following inflammatory pain

    PubMed Central

    Wu, Xiao-Bo; Cao, De-Li; Zhang, Xin; Jiang, Bao-Chun; Zhao, Lin-Xia; Qian, Bin; Gao, Yong-Jing

    2016-01-01

    CXCL13 is a B lymphocyte chemoattractant and activates CXCR5 receptor in the immune system. Here we investigated whether CXCL13/CXCR5 mediates inflammatory pain in dorsal root ganglia (DRG) and the underlying mechanisms. Peripheral injection of complete Freund’s Adjuvant (CFA) increased the expression of CXCL13 and CXCR5 in DRG neurons. In Cxcr5−/− mice, CFA-induced pain hypersensitivity were attenuated. Whole-cell patch-clamp recording showed that the excitability of dissociated DRG neurons was increased after CFA injection or CXCL13 incubation from wild-type (WT) mice, but not from Cxcr5−/− mice. Additionally, sodium channel Nav1.8 was co-expressed with CXCR5 in dissociated DRG neurons, and the increased neuronal excitability induced by CFA or CXCL13 was reduced by Nav1.8 blocker. Intrathecal injection of Nav1.8 blocker also attenuated intrathecal injection of CXCL13-induced pain hypersensitivity. Furthermore, CXCL13 increased Nav1.8 current density in DRG neurons, which was inhibited by p38 MAP kinase inhibitor. CFA and CXCL13 increased p38 phosphorylation in the DRG of WT mice but not Cxcr5−/− mice. Finally, intrathecal p38 inhibitor alleviated CXCL13-induced pain hypersensitivity. Taken together, these results demonstrated that CXCL13, upregulated by peripheral inflammation, acts on CXCR5 on DRG neurons and activates p38, which increases Nav1.8 current density and further contributes to the maintenance of inflammatory pain. PMID:27708397

  2. Loudspeaker equalization for auditory research.

    PubMed

    MacDonald, Justin A; Tran, Phuong K

    2007-02-01

    The equalization of loudspeaker frequency response is necessary to conduct many types of well-controlled auditory experiments. This article introduces a program that includes functions to measure a loudspeaker's frequency response, design equalization filters, and apply the filters to a set of stimuli to be used in an auditory experiment. The filters can compensate for both magnitude and phase distortions introduced by the loudspeaker. A MATLAB script is included in the Appendix to illustrate the details of the equalization algorithm used in the program.

  3. Analyzing the spatio-temporal relationship between dengue vector larval density and land-use using factor analysis and spatial ring mapping

    PubMed Central

    2012-01-01

    Background Dengue, a mosquito-borne febrile viral disease, is found in tropical and sub-tropical regions and is now extending its range to temperate regions. The spread of the dengue viruses mainly depends on vector population (Aedes aegypti and Aedes albopictus), which is influenced by changing climatic conditions and various land-use/land-cover types. Spatial display of the relationship between dengue vector density and land-cover types is required to describe a near-future viral outbreak scenario. This study is aimed at exploring how land-cover types are linked to the behavior of dengue-transmitting mosquitoes. Methods Surveys were conducted in 92 villages of Phitsanulok Province Thailand. The sampling was conducted on three separate occasions in the months of March, May and July. Dengue indices, i.e. container index (C.I.), house index (H.I.) and Breteau index (B.I.) were used to map habitats conducible to dengue vector growth. Spatial epidemiological analysis using Bivariate Pearson’s correlation was conducted to evaluate the level of interdependence between larval density and land-use types. Factor analysis using principal component analysis (PCA) with varimax rotation was performed to ascertain the variance among land-use types. Furthermore, spatial ring method was used as to visualize spatially referenced, multivariate and temporal data in single information graphic. Results Results of dengue indices showed that the settlements around gasoline stations/workshops, in the vicinity of marsh/swamp and rice paddy appeared to be favorable habitat for dengue vector propagation at highly significant and positive correlation (p = 0.001) in the month of May. Settlements around the institutional areas were highly significant and positively correlated (p = 0.01) with H.I. in the month of March. Moreover, dengue indices in the month of March showed a significant and positive correlation (p <= 0.05) with deciduous forest. The H.I. of people living around horticulture

  4. Equal Education and the Law

    ERIC Educational Resources Information Center

    Shanks, Hershel

    1970-01-01

    A number of court cases are cited which trace the development of various definitions and interpretations of the equal protection clause of the Fourteenth Amendment to the Constitution as would be applicable to inadequate" schools. (DM)

  5. Electronegativity Equalization with Pauling Units.

    ERIC Educational Resources Information Center

    Bratsch, Steven G.

    1984-01-01

    Discusses electronegativity equalization using Pauling units. Although Pauling has qualitatively defined electronegativity as the power of an atom in a molecule to attract electrons to itself, Pauling electronegativities are treated in this paper as prebonded, isolated-atom quantities. (JN)

  6. Electronegativity Equalization and Partial Charge

    ERIC Educational Resources Information Center

    Sanderson, R. T.

    1974-01-01

    This article elaborates the relationship between covalent radius, homonuclear bond energy, and electronegativity, and sets the background for bond energy calculation by discussing the nature of heteronuclear covalent bonding on the basis of electronegativity equalization and particle charge. (DT)

  7. Equal Pay for Comparable Work.

    ERIC Educational Resources Information Center

    Rothman, Nancy Lloyd; Rothman, Daniel A.

    1980-01-01

    Examines the legal battleground upon which one struggle for the equality of women is being fought. Updates a civil rights decision of crucial importance to nursing--Lemons v City and County of Denver. (JOW)

  8. Large-Scale SNP Discovery and Genotyping for Constructing a High-Density Genetic Map of Tea Plant Using Specific-Locus Amplified Fragment Sequencing (SLAF-seq).

    PubMed

    Ma, Jian-Qiang; Huang, Long; Ma, Chun-Lei; Jin, Ji-Qiang; Li, Chun-Fang; Wang, Rong-Kai; Zheng, Hong-Kun; Yao, Ming-Zhe; Chen, Liang

    2015-01-01

    Genetic maps are important tools in plant genomics and breeding. The present study reports the large-scale discovery of single nucleotide polymorphisms (SNPs) for genetic map construction in tea plant. We developed a total of 6,042 valid SNP markers using specific-locus amplified fragment sequencing (SLAF-seq), and subsequently mapped them into the previous framework map. The final map contained 6,448 molecular markers, distributing on fifteen linkage groups corresponding to the number of tea plant chromosomes. The total map length was 3,965 cM, with an average inter-locus distance of 1.0 cM. This map is the first SNP-based reference map of tea plant, as well as the most saturated one developed to date. The SNP markers and map resources generated in this study provide a wealth of genetic information that can serve as a foundation for downstream genetic analyses, such as the fine mapping of quantitative trait loci (QTL), map-based cloning, marker-assisted selection, and anchoring of scaffolds to facilitate the process of whole genome sequencing projects for tea plant.

  9. Equal Employment + Equal Pay = Multiple Problems for Colleges and Universities

    ERIC Educational Resources Information Center

    Steinbach, Sheldon Elliot; Reback, Joyce E.

    1974-01-01

    Issues involved in government regulation of university employment practices are discussed: confidentiality of records, pregnancy as a disability, alleged discrimination in benefits, tests and other employment criteria, seniority and layoff, reverse discrimination, use of statistics for determination of discrimination, and the Equal Pay Act. (JT)

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

    PubMed Central

    Ishida, Hisashi; Matsumoto, Atsushi

    2014-01-01

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

  11. 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.

  12. ON THE ORIGIN OF THE HIGH COLUMN DENSITY TURNOVER IN THE H I COLUMN DENSITY DISTRIBUTION

    SciTech Connect

    Erkal, Denis; Gnedin, Nickolay Y.; Kravtsov, Andrey V.

    2012-12-10

    We study the high column density regime of the H I column density distribution function and argue that there are two distinct features: a turnover at N{sub H{sub I}} Almost-Equal-To 10{sup 21} cm{sup -2}, which is present at both z = 0 and z Almost-Equal-To 3, and a lack of systems above N{sub H{sub I}} Almost-Equal-To 10{sup 22} cm{sup -2} at z = 0. Using observations of the column density distribution, we argue that the H I-H{sub 2} transition does not cause the turnover at N{sub H{sub I}} Almost-Equal-To 10{sup 21} cm{sup -2} but can plausibly explain the turnover at N{sub H{sub I}} {approx}> 10{sup 22} cm{sup -2}. We compute the H I column density distribution of individual galaxies in the THINGS sample and show that the turnover column density depends only weakly on metallicity. Furthermore, we show that the column density distribution of galaxies, corrected for inclination, is insensitive to the resolution of the H I map or to averaging in radial shells. Our results indicate that the similarity of H I column density distributions at z = 3 and 0 is due to the similarity of the maximum H I surface densities of high-z and low-z disks, set presumably by universal processes that shape properties of the gaseous disks of galaxies. Using fully cosmological simulations, we explore other candidate physical mechanisms that could produce a turnover in the column density distribution. We show that while turbulence within giant molecular clouds cannot affect the damped Ly{alpha} column density distribution, stellar feedback can affect it significantly if the feedback is sufficiently effective in removing gas from the central 2-3 kpc of high-redshift galaxies. Finally, we argue that it is meaningful to compare column densities averaged over {approx} kpc scales with those estimated from quasar spectra that probe sub-pc scales due to the steep power spectrum of H I column density fluctuations observed in nearby galaxies.

  13. Equal Time for Creationism? No.

    ERIC Educational Resources Information Center

    Skoog, Gerald

    1983-01-01

    Legal decisions and other arguments support the argument that the exclusion of creationism from school curricula is not the result of censorship or bias. Equal-time legislation for creationism has the potential to entangle the state and religion and to make the task of teachers, textbook authors, and publishers nearly impossible. (PP)

  14. Higher Education and Equal Protection.

    ERIC Educational Resources Information Center

    Finnigan, John J.

    1979-01-01

    The effect of the Bakke case, in which the courts first encountered the question of legality of reverse discrimination, is explored; its constitutional significance is examined. It is concluded that the virtue of the decision is in its support of affirmative action and its equal protection implications. (MSE)

  15. STEM Equality and Diversity Toolkit

    ERIC Educational Resources Information Center

    Collins, Jill

    2011-01-01

    In 2008, the Centre for Science Education at Sheffield Hallam University teamed up with VT Enterprise (now Babcock International) in their submission of a successful bid to deliver the national STEM (Science, Technology, Engineering and Maths) Subject Choice and Careers Project. An integral part of the bid was the promotion of equality and…

  16. The Road to Racial Equality

    ERIC Educational Resources Information Center

    Tatum, Beverly Daniel

    2004-01-01

    In this article, the author describes how he was born in 1954, just four months after the Brown v. Board of Education Supreme Court decision outlawed the "separate but equal" doctrine of school segregation. He discusses how that fact has shaped his life immeasurably. Beginning with entering the world in Tallahassee, Fla., where his father taught…

  17. Primer of Equal Employment Opportunity.

    ERIC Educational Resources Information Center

    Anderson, Howard J.

    This booklet presents laws and court cases concerning discrimination in hiring. It begins with a presentation of the laws and orders regulating equal employment opportunity and the remedies available. It lists those employees and employers to whom the laws apply and exemptions. Sections deal with discrimination on the basis of race, sex, sexual…

  18. Extending Understanding of Equal Protection.

    ERIC Educational Resources Information Center

    Dreyfuss, Elisabeth T.

    1988-01-01

    Presents four strategies for teaching secondary students about equal protection clause of the U.S. Constitution's Fourteenth Amendment. To be taught by the classroom teacher or a visiting lawyer, these strategies use such methods as a panel discussion and examination of Fourteenth Amendment court cases to accomplish their goals. (GEA)

  19. Promote Equality in the Classroom.

    ERIC Educational Resources Information Center

    Brown, Sharon; And Others

    1996-01-01

    Presents suggestions to help physical educators treat all students equally and avoid unconsciously making inequitable gender-based statements and practicing other gender discrimination. Suggestions include encouraging girls to talk more, praising girls' performance and boys' appearance, using gender-neutral language, not stereotyping either sex,…

  20. Equalization among Florida School Districts.

    ERIC Educational Resources Information Center

    Alexander, Kern; Shiver, Lee

    1983-01-01

    This statistical analysis of funding equalization from 1970 to 1981 evaluates the distributional equity achieved by Florida's school finance plan and examines the relationship between selected per pupil revenue measures and variables thought to influence school district spending, concluding that greater equity has not been attained. (MJL)

  1. Development of two major resources for pea genomics: the GenoPea 13.2K SNP Array and a high-density, high-resolution consensus genetic map.

    PubMed

    Tayeh, Nadim; Aluome, Christelle; Falque, Matthieu; Jacquin, Françoise; Klein, Anthony; Chauveau, Aurélie; Bérard, Aurélie; Houtin, Hervé; Rond, Céline; Kreplak, Jonathan; Boucherot, Karen; Martin, Chantal; Baranger, Alain; Pilet-Nayel, Marie-Laure; Warkentin, Thomas D; Brunel, Dominique; Marget, Pascal; Le Paslier, Marie-Christine; Aubert, Grégoire; Burstin, Judith

    2015-12-01

    Single nucleotide polymorphism (SNP) arrays represent important genotyping tools for innovative strategies in both basic research and applied breeding. Pea is an important food, feed and sustainable crop with a large (about 4.45 Gbp) but not yet available genome sequence. In the present study, 12 pea recombinant inbred line populations were genotyped using the newly developed GenoPea 13.2K SNP Array. Individual and consensus genetic maps were built providing insights into the structure and organization of the pea genome. Largely collinear genetic maps of 3918-8503 SNPs were obtained from all mapping populations, and only two of these exhibited putative chromosomal rearrangement signatures. Similar distortion patterns in different populations were noted. A total of 12 802 transcript-derived SNP markers placed on a 15 079-marker high-density, high-resolution consensus map allowed the identification of ohnologue-rich regions within the pea genome and the localization of local duplicates. Dense syntenic networks with sequenced legume genomes were further established, paving the way for the identification of the molecular bases of important agronomic traits segregating in the mapping populations. The information gained on the structure and organization of the genome from this research will undoubtedly contribute to the understanding of the evolution of the pea genome and to its assembly. The GenoPea 13.2K SNP Array and individual and consensus genetic maps are valuable genomic tools for plant scientists to strengthen pea as a model for genetics and physiology and enhance breeding.

  2. 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.

  3. Characterization of 10 new polymorphic dinucleotide repeats and generation of a high-density microsatellite-based physical map of the BRCA1 region of chromosome 17q21

    SciTech Connect

    Couch, F.J.; Xu, J.; Weber, B.L.

    1994-12-01

    A familial early onset breast cancer gene (BRCA1) has been localized to chromosome 17q21. To aid in the identification of this gene a number of new microsatellite markers from the D17S857 to D17S78 region were isolated and characterized. These markers, along with previously published markers from the region, were localized on a physical map by STS content mapping of cosmids from the BRCA1 interval. This high-density STS map of the BRCA1 region will be useful for linkage studies of families with apparent inherited breast cancer and for loss of heterozygosity analysis of breast tumor DNAs. 19 refs., 2 figs., 2 tabs.

  4. Racial equity or racial equality.

    PubMed

    Daymont, T N

    1980-11-01

    This study examines the relationship between racial equity in labor market processes and racial equality in future labor market rewards. In particular, a regression standardization procedure is used to project the degree of racial inequality in earnings that would exist among men at various future points in time based on three different sets of assumptions about attainment processes in labor market and educational institutions. The most important results suggest that even if racial discrimination were eliminated immediately in labor market and educational institutions, it would take almost 50 years for the black-white earnings ratio to reach .95. This incompatibility between equity and equality needs to be considered more explicitly both by those who advocate a color-blind labor market and those who advocate preferential treatment for blacks.

  5. Equal opportunity in the workplace.

    PubMed

    Allen, A

    1992-04-01

    The Equal Employment Opportunity Commission (EEOC) was created by the Civil Rights Act of 1964. The commission encourages voluntary compliance with equal employment opportunity practices, and has authority to investigate complaints alleging discrimination in hiring, firing, wage rates, testing, training, apprenticeship, and other conditions of employment. In October 1991, during the Senate Judiciary Committee hearings, the confirmation of Judge Clarence Thomas for a seat on the United States Supreme Court was placed in jeopardy by a charge of sexual harassment while Thomas was head of the EEOC. This article focuses on aspects of sexual harassment in the workplace, the role of the EEOC, and offers some suggestions for keeping the work environment free of abusive behavior.

  6. Office of Equal Opportunity Programs

    NASA Technical Reports Server (NTRS)

    Chin, Jennifer L.

    2004-01-01

    The NASA Glenn Office of Equal Opportunity Programs works to provide quality service for all programs and/or to assist the Center in becoming a model workplace. During the summer of 2004, I worked with Deborah Cotleur along with other staff members to create and modify customer satisfaction surveys. This office aims to assist in developing a model workplace by providing functions as a change agent to the center by serving as an advisor to management to ensure equity throughout the Center. In addition, the office serves as a mediator for the Center in addressing issues and concerns. Lastly, the office provides assistance to employees to enable attainment of personal and organizational goals. The Office of Equal Opportunities is a staff office which reports and provides advice to the Center Director and Executive Leadership, implements laws, regulations, and presidential executive orders, and provides center wide leadership and assistance to NASA GRC employees. Some of the major responsibilities of the office include working with the discrimination complaints program, special emphasis programs (advisory groups), management support, monitoring and evaluation, contract compliance, and community outreach. During my internship in this office, my main objective was to create four customer satisfaction surveys based on EO retreats, EO observances, EO advisory boards, and EO mediation/counseling. I created these surveys after conducting research on past events and surveys as well as similar survey research created and conducted by other NASA centers, program for EO Advisory group members, leadership training sessions for supervisors, preventing sexual harassment training sessions, and observance events. I also conducted research on the style and format from feedback surveys from the Marshall Equal Opportunity website, the Goddard website, and the main NASA website. Using the material from the Office of Equal Opportunity Programs at Glenn Research Center along with my

  7. The equal right to drink.

    PubMed

    Schmidt, Laura A

    2014-11-01

    The starting place for this essay is Knupfer and Room's insight that more restrictive norms around drinking and intoxication tend to be selectively applied to the economically dependent segments of society, such as women. However, since these authors wrote in 1964, women in the US and many other societies around the globe have experienced rising economic independence. The essay considers how the moral categories of acceptable drinking and drunkenness may have shifted alongside women's rising economic independence, and looks at evidence on the potential consequences for women's health and wellbeing. I argue that, as women have gained economic independence, changes in drinking norms have produced two different kinds of negative unintended consequences for women at high and low extremes of economic spectrum. As liberated women of the middle and upper classes have become more economically equal to men, they have enjoyed the right to drink with less restraint. For them, alongside the equal right to drink has come greater equality in exposure to alcohol-attributable harms, abuse and dependence. I further suggest that, as societies become more liberated, the economic dependency of low-income women is brought into greater question. Under such conditions, women in poverty-particularly those economically dependent on the state, such as welfare mothers-have become subject to more restrictive norms around drinking and intoxication, and more punitive social controls.

  8. The equal right to drink.

    PubMed

    Schmidt, Laura A

    2014-11-01

    The starting place for this essay is Knupfer and Room's insight that more restrictive norms around drinking and intoxication tend to be selectively applied to the economically dependent segments of society, such as women. However, since these authors wrote in 1964, women in the US and many other societies around the globe have experienced rising economic independence. The essay considers how the moral categories of acceptable drinking and drunkenness may have shifted alongside women's rising economic independence, and looks at evidence on the potential consequences for women's health and wellbeing. I argue that, as women have gained economic independence, changes in drinking norms have produced two different kinds of negative unintended consequences for women at high and low extremes of economic spectrum. As liberated women of the middle and upper classes have become more economically equal to men, they have enjoyed the right to drink with less restraint. For them, alongside the equal right to drink has come greater equality in exposure to alcohol-attributable harms, abuse and dependence. I further suggest that, as societies become more liberated, the economic dependency of low-income women is brought into greater question. Under such conditions, women in poverty-particularly those economically dependent on the state, such as welfare mothers-have become subject to more restrictive norms around drinking and intoxication, and more punitive social controls. PMID:25303360

  9. Equal is as equal does: challenging Vatican views on women.

    PubMed

    1995-01-01

    The authors of this piece are women from the Roman Catholic tradition who are critical of the Vatican position on women's rights. The Report of the Holy See in Preparation for the Fourth World Conference on Women reveals a religious fundamentalism that misuses tradition and anthropology to limit women's roles and rights. The Vatican is itself a self-proclaimed state that offers women neither opportunities nor protections within its own organization, and there is no evidence of women's participation in the preparation of its report. The Vatican document constructs a vision of women and men in which men are normative persons, whose dignity is conferred by their humanity, and women are the variant other, defined by and granted dignity by their reproductive and mothering functions. The Vatican document is anti-feminist. It criticizes the "radical feminists" of the 1960s for trying to deny sexual differences, and accuses today's Western feminists of ignoring the needs of women in developing countries while pursuing selfish and hedonistic goals. It makes no recognition of the work of feminists to improve the lives of women worldwide. The Vatican document claims to support women's equality, but it qualifies each statement of equality with a presumption of difference. The document defines women as vulnerable without naming men as responsible for the oppression and violence to which women are vulnerable. It ridicules as feminist cant the well-documented fact that the home is the setting of most violence against women. The Vatican decries the suffering families undergo as a result of cumpulsory birth control and abortion policies, while it would deny families sex education, contraceptives, and safe abortion, thereby making pregnancy cumpulsory. A new vision of social justice is needed, one that: 1) rests on a radical equality, in which both women and men are expected to contribute to work, education, culture, morality, and reproduction; 2) accepts a "discipleship of equals

  10. Equal is as equal does: challenging Vatican views on women.

    PubMed

    1995-01-01

    The authors of this piece are women from the Roman Catholic tradition who are critical of the Vatican position on women's rights. The Report of the Holy See in Preparation for the Fourth World Conference on Women reveals a religious fundamentalism that misuses tradition and anthropology to limit women's roles and rights. The Vatican is itself a self-proclaimed state that offers women neither opportunities nor protections within its own organization, and there is no evidence of women's participation in the preparation of its report. The Vatican document constructs a vision of women and men in which men are normative persons, whose dignity is conferred by their humanity, and women are the variant other, defined by and granted dignity by their reproductive and mothering functions. The Vatican document is anti-feminist. It criticizes the "radical feminists" of the 1960s for trying to deny sexual differences, and accuses today's Western feminists of ignoring the needs of women in developing countries while pursuing selfish and hedonistic goals. It makes no recognition of the work of feminists to improve the lives of women worldwide. The Vatican document claims to support women's equality, but it qualifies each statement of equality with a presumption of difference. The document defines women as vulnerable without naming men as responsible for the oppression and violence to which women are vulnerable. It ridicules as feminist cant the well-documented fact that the home is the setting of most violence against women. The Vatican decries the suffering families undergo as a result of cumpulsory birth control and abortion policies, while it would deny families sex education, contraceptives, and safe abortion, thereby making pregnancy cumpulsory. A new vision of social justice is needed, one that: 1) rests on a radical equality, in which both women and men are expected to contribute to work, education, culture, morality, and reproduction; 2) accepts a "discipleship of equals

  11. Average density in cosmology

    SciTech Connect

    Bonnor, W.B.

    1987-05-01

    The Einstein-Straus (1945) vacuole is here used to represent a bound cluster of galaxies embedded in a standard pressure-free cosmological model, and the average density of the cluster is compared with the density of the surrounding cosmic fluid. The two are nearly but not quite equal, and the more condensed the cluster, the greater the difference. A theoretical consequence of the discrepancy between the two densities is discussed. 25 references.

  12. Midwives, gender equality and feminism.

    PubMed

    Walsh, Denis

    2016-03-01

    Gender inequality and the harmful effects of patriarchy are sustaining the wide spread oppression of women across the world and this is also having an impact on maternity services with unacceptable rates of maternal mortality, the continued under investment in the midwifery profession and the limiting of women's place of birth options. However alongside these effects, the current zeitgeist is affirming an alignment of feminism and gender equality such that both have a high profile in public discourse. This presents a once in a generation opportunity for midwives to self-declare as feminists and commit to righting the wrongs of this most pernicious form of discrimination. PMID:27044191

  13. Midwives, gender equality and feminism.

    PubMed

    Walsh, Denis

    2016-03-01

    Gender inequality and the harmful effects of patriarchy are sustaining the wide spread oppression of women across the world and this is also having an impact on maternity services with unacceptable rates of maternal mortality, the continued under investment in the midwifery profession and the limiting of women's place of birth options. However alongside these effects, the current zeitgeist is affirming an alignment of feminism and gender equality such that both have a high profile in public discourse. This presents a once in a generation opportunity for midwives to self-declare as feminists and commit to righting the wrongs of this most pernicious form of discrimination.

  14. Educational Equality: Luck Egalitarian, Pluralist and Complex

    ERIC Educational Resources Information Center

    Calvert, John

    2014-01-01

    The basic principle of educational equality is that each child should receive an equally good education. This sounds appealing, but is rather vague and needs substantial working out. Also, educational equality faces all the objections to equality per se, plus others specific to its subject matter. Together these have eroded confidence in the…

  15. Gender equality and human rights.

    PubMed

    1998-01-01

    This editorial introduces an issue of INSTRAW News that commemorates the 50th anniversary of the UN's Universal Declaration of Human Rights. This introduction notes that the lead article in the journal expresses optimism about potential progress towards achieving gender equity and human rights because 1) industrialized countries are undergoing a "powershift" to an information society that will offer more and better jobs for women and give women greater access to the power of information, 2) women's earnings have increased worldwide, 3) more and more women are organizing on their own behalf, and 4) a public discourse is being created that promotes the mainstreaming of women's rights and their equality. In addition, several of the UN's international treaties promote gender equality and women's human rights. Foremost among these are 1) the Convention on the Elimination of All Forms of Discrimination Against Women; 2) the Vienna Declaration and Programme of Action, adopted by the 1993 World Conference on Human Rights; 3) the Declaration on the Elimination of Violence Against Women; and 4) the Platform for Action of the Fourth World Conference on women. Counteracting these positive steps is a trend towards defining identity and rights on the basis of community membership only, which ignores the fact that cultures, traditions, and religions are not gender neutral. Given the challenges ahead, the partnership model of society created by women when they have political power is more likely to result in sustainable solutions than the dominator model that men have forwarded for the past 6000 years.

  16. 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.

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

    PubMed

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

    2003-12-01

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

  18. Brightness-equalized quantum dots

    PubMed Central

    Lim, Sung Jun; Zahid, Mohammad U.; Le, Phuong; Ma, Liang; Entenberg, David; Harney, Allison S.; Condeelis, John; Smith, Andrew M.

    2015-01-01

    As molecular labels for cells and tissues, fluorescent probes have shaped our understanding of biological structures and processes. However, their capacity for quantitative analysis is limited because photon emission rates from multicolour fluorophores are dissimilar, unstable and often unpredictable, which obscures correlations between measured fluorescence and molecular concentration. Here we introduce a new class of light-emitting quantum dots with tunable and equalized fluorescence brightness across a broad range of colours. The key feature is independent tunability of emission wavelength, extinction coefficient and quantum yield through distinct structural domains in the nanocrystal. Precise tuning eliminates a 100-fold red-to-green brightness mismatch of size-tuned quantum dots at the ensemble and single-particle levels, which substantially improves quantitative imaging accuracy in biological tissue. We anticipate that these materials engineering principles will vastly expand the optical engineering landscape of fluorescent probes, facilitate quantitative multicolour imaging in living tissue and improve colour tuning in light-emitting devices. PMID:26437175

  19. Risk Mapping of Anopheles gambiae s.l. Densities Using Remotely-Sensed Environmental and Meteorological Data in an Urban Area: Dakar, Senegal

    PubMed Central

    Machault, Vanessa; Vignolles, Cécile; Pagès, Frédéric; Gadiaga, Libasse; Tourre, Yves M.; Gaye, Abdoulaye; Sokhna, Cheikh; Trape, Jean-François; Lacaux, Jean-Pierre; Rogier, Christophe

    2012-01-01

    Introduction High malaria transmission heterogeneity in an urban environment is basically due to the complex distribution of Anopheles larval habitats, sources of vectors. Understanding 1) the meteorological and ecological factors associated with differential larvae spatio-temporal distribution and 2) the vectors dynamic, both may lead to improving malaria control measures with remote sensing and high resolution data as key components. In this study a robust operational methodology for entomological malaria predictive risk maps in urban settings is developed. Methods The Tele-epidemiology approach, i.e., 1) intensive ground measurements (Anopheles larval habitats and Human Biting Rate, or HBR), 2) selection of the most appropriate satellite data (for mapping and extracting environmental and meteorological information), and 3) use of statistical models taking into account the spatio-temporal data variability has been applied in Dakar, Senegal. Results First step was to detect all water bodies in Dakar. Secondly, environmental and meteorological conditions in the vicinity of water bodies favoring the presence of Anopheles gambiae s.l. larvae were added. Then relationship between the predicted larval production and the field measured HBR was identified, in order to generate An. gambiae s.l. HBR high resolution maps (daily, 10-m pixel in space). Discussion and Conclusion A robust operational methodology for dynamic entomological malaria predictive risk maps in an urban setting includes spatio-temporal variability of An. gambiae s.l. larval habitats and An. gambiae s.l. HBR. The resulting risk maps are first examples of high resolution products which can be included in an operational warning and targeting system for the implementation of vector control measures. PMID:23226351

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

    SciTech Connect

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

    2015-06-15

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

  1. High-density physical mapping of a 3-Mb region in Xp22.3 and refined localization of the gene for X-linked recessive chondrodysplasia punctata (CDPX1)

    SciTech Connect

    Wang, I.; Levilliers, J.; Petit, C.

    1995-03-20

    The study of patients with chromosomal rearrangements has led to the mapping of the gene responsible for X-linked recessive chondrodysplasia punctata (CDPX1; MIM 302950) to the distal part of the Xp22.3 region, between the loci PABX and DXS31. To refine this mapping, a yeast artificial chromosome (YAC) contig map spanning this region has been constructed. Together with the YAC contig of the pseudo-autosomal region that we previously established, this map covers the terminal 6 Mb of Xp, with an average density of 1 probe every 100 kb. Newly isolated probes that detect segmental X-Y homologies on Yp and Yq suggest multiple complex rearrangements of the ancestral pseudoautosomal region during evolution. Compilation of the data obtained from the study of individuals carrying various Xp22.3 deletions led us to conclude that the CDPX disease displays incomplete penetrance and, consequently, to refine the localization of CDPX1 to a 600-kb interval immediately adjacent to the pseudoautosomal boundary. This interval, in which 12 probes are ordered, provides the starting point for the isolation of CDPX1. 67 refs., 3 figs., 2 tabs.

  2. Density - Velocity Relationships in Explosive Volcanic Plumes

    NASA Astrophysics Data System (ADS)

    Fisher, M. A.; Kobs-Nawotniak, S. E.

    2015-12-01

    Positively buoyant volcanic plumes rise until the bulk density of the plume is equal to the density of the ambient atmosphere. As ambient air mixes with the plume, it lowers the plume bulk density; thus, the plume is diluted enough to reach neutral density in a naturally stratified atmospheric environment. We produced scaled plumes in analogue laboratory experiments by injecting a saline solution with a tracer dye into distilled water, using a high-pressure injection system. We recorded each eruption with a CASIO HD digital camera and used ImageJ's FeatureJ Edge toolbox to identify individual eddies. We used an optical flow software based off the ImageJ toolbox FlowJ to determine the velocities along the edge of each eddy. Eddy densities were calculated by mapping the dye concentration to the RGB digital color value. We overlaid the eddy velocities over the densities in order to track the behavioral relationship between the two variables with regard to plume motion. As an eddy's bulk density decreases, the vertical velocity decreases; this is a result of decreased mass, and therefore momentum, in the eddy. Furthermore as the density rate of change increases, the eddy deceleration increases. Eddies are most dense at their top and least dense at their bottom. The less dense sections of the eddies have lower vertical velocities than the sections of the eddies with the higher densities, relating to the expanding radial size of an eddy as it rises and the preferential ingestion of ambient air at the base of eddies. Thus the mixing rate in volcanic plumes fluctuates not only as a function of height as described by the classic 1D entrainment hypothesis, but also as a function of position in an eddy itself.

  3. Promoting Racial Equality in the Nursing Curriculum.

    ERIC Educational Resources Information Center

    Foolchand, M. K.

    1995-01-01

    Equality in nursing education and the profession can be promoted in the following ways: a working policy on racism and equal opportunities; curriculum content that explores stereotypes, values, attitudes, and prejudices; and multicultural health research, education, and promotion. (SK)

  4. CONMAP - USGS MARINE MAPPING PROGRAM.

    USGS Publications Warehouse

    Escowitz, Edward C.

    1985-01-01

    The U. S. Geological Survey has commenced a marine mapping program, CONMAP (the Continental Margin Maps), which is supported by, and dependent on, a foundation of digital data-bases. The goal of the program's first phase is to prepare a series of maps that completely cover the Exclusive Economic Zone. The maps will be prepared using an Albers' Conic Equal-Area Projection at a scale of 1:1,000,000. An initial product of CONMAP will be a series of base map panels portraying the topographic and bathymetric relief, political boundaries and key geographic locations. Additional maps will be prepared which portray other data types and analytical themes.

  5. Gandhigram: fostering equality through development.

    PubMed

    Devi, R K

    1991-12-01

    A noticeable trend towards 1-child families reveals the success of Gandhigram, an integrated rural development program in Tamil Nadu, India. Founded in 1947 by T.S. Soundram, Gandhigram has adhered to Gandhian principles of truth, nonviolence, castlessness, and equality between the sexes. The program has combined health and family planning with social welfare, education, and economic development. From the outset, Gandhigram has sought community participation, including the involvement of women. Girls have been encouraged to attend school up to at least the 10th level, and employment opportunities for women have been increased. Women's increased economic independence and level of education have influenced their decision to delay marriage by about 2 1/2 years, to choose their own partners, and to decide on the number of children they want. And increasingly, women are opting to limit family size to 2 -- and sometimes 1 -- child. Women are choosing to undergo tubectomies at a younger age, partly because of the availability of recanalization surgery, which has allowed mothers who have lost a child to conceive again. Unlike typical government family planning programs, which usually provide only contraception to meet the objective of a small family norm, Gandhigram also offers infertility services. Not all of Gandhigram's efforts have resulted in success. For example, a plan to develop a health insurance program did not succeed. However, Gandhigram's 44 years of experience have revealed the necessary elements for success. These elements include community participation, the participation of women through educational and employment programs, and easy access to services. PMID:12317116

  6. 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…

  7. Construction of a high-density linkage map of Italian ryegrass (Lolium multiflorum Lam) using restriction fragment length polymorphism, amplified fragment length polymorphism, and telomeric repeat associated sequence markers.

    PubMed

    Inoue, Maiko; Gao, Zhensheng; Hirata, Mariko; Fujimori, Masahiro; Cai, Hongwei

    2004-02-01

    To construct a high-density molecular linkage map of Italian ryegrass (Lolium multiflorum Lam), we used a two-way pseudo-testcross F1 population consisting of 82 individuals to analyze three types of markers: restriction fragment length polymorphism markers, which we detected by using genomic probes from Italian ryegrass as well as heterologous anchor probes from other species belonging to the Poaceae family, amplified fragment length polymorphism markers, which we detected by using PstI/MseI primer combinations, and telomeric repeat associated sequence markers. Of the restriction fragment length polymorphism probes that we generated from a PstI genomic library, 74% (239 of 323) of randomly selected probes detected hybridization patterns consistent with single-copy or low-copy genetic locus status in the screening. The 385 (mostly restriction fragment length polymorphism) markers that we selected from the 1226 original markers were grouped into seven linkage groups. The maps cover 1244.4 cM, with an average of 3.7 cM between markers. This information will prove useful for gene targeting, quantitative trait loci mapping, and marker-assisted selection in Italian ryegrass.

  8. High-density linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and provides clues to the extent and distribution of meiotic recombination

    PubMed Central

    2013-01-01

    Background The availability of a large expressed sequence tags (EST) resource and recent advances in high-throughput genotyping technology have made it possible to develop highly multiplexed SNP arrays for multi-objective genetic applications, including the construction of meiotic maps. Such approaches are particularly useful in species with a large genome size, precluding the use of whole-genome shotgun assembly with current technologies. Results In this study, a 12 k-SNP genotyping array was developed for maritime pine from an extensive EST resource assembled into a unigene set. The offspring of three-generation outbred and inbred mapping pedigrees were then genotyped. The inbred pedigree consisted of a classical F2 population resulting from the selfing of a single inter-provenance (Landes x Corsica) hybrid tree, whereas the outbred pedigree (G2) resulted from a controlled cross of two intra-provenance (Landes x Landes) hybrid trees. This resulted in the generation of three linkage maps based on SNP markers: one from the parental genotype of the F2 population (1,131 markers in 1,708 centimorgan (cM)), and one for each parent of the G2 population (1,015 and 1,110 markers in 1,447 and 1,425 cM for the female and male parents, respectively). A comparison of segregation patterns in the progeny obtained from the two types of mating (inbreeding and outbreeding) led to the identification of a chromosomal region carrying an embryo viability locus with a semi-lethal allele. Following selfing and segregation, zygote mortality resulted in a deficit of Corsican homozygous genotypes in the F2 population. This dataset was also used to study the extent and distribution of meiotic recombination along the length of the chromosomes and the effect of sex and/or genetic background on recombination. The genetic background of trees in which meiotic recombination occurred was found to have a significant effect on the frequency of recombination. Furthermore, only a small proportion of

  9. Fine mapping of chromosome 5p15.33 based on a targeted deep sequencing and high density genotyping identifies novel lung cancer susceptibility loci.

    PubMed

    Kachuri, Linda; Amos, Christopher I; McKay, James D; Johansson, Mattias; Vineis, Paolo; Bueno-de-Mesquita, H Bas; Boutron-Ruault, Marie-Christine; Johansson, Mikael; Quirós, J Ramón; Sieri, Sabina; Travis, Ruth C; Weiderpass, Elisabete; Le Marchand, Loic; Henderson, Brian E; Wilkens, Lynne; Goodman, Gary E; Chen, Chu; Doherty, Jennifer A; Christiani, David C; Wei, Yongyue; Su, Li; Tworoger, Shelley; Zhang, Xuehong; Kraft, Peter; Zaridze, David; Field, John K; Marcus, Michael W; Davies, Michael P A; Hyde, Russell; Caporaso, Neil E; Landi, Maria Teresa; Severi, Gianluca; Giles, Graham G; Liu, Geoffrey; McLaughlin, John R; Li, Yafang; Xiao, Xiangjun; Fehringer, Gord; Zong, Xuchen; Denroche, Robert E; Zuzarte, Philip C; McPherson, John D; Brennan, Paul; Hung, Rayjean J

    2016-01-01

    Chromosome 5p15.33 has been identified as a lung cancer susceptibility locus, however the underlying causal mechanisms were not fully elucidated. Previous fine-mapping studies of this locus have relied on imputation or investigated a small number of known, common variants. This study represents a significant advance over previous research by investigating a large number of novel, rare variants, as well as their underlying mechanisms through telomere length. Variants for this fine-mapping study were identified through a targeted deep sequencing (average depth of coverage greater than 4000×) of 576 individuals. Subsequently, 4652 SNPs, including 1108 novel SNPs, were genotyped in 5164 cases and 5716 controls of European ancestry. After adjusting for known risk loci, rs2736100 and rs401681, we identified a new, independent lung cancer susceptibility variant in LPCAT1: rs139852726 (OR = 0.46, P = 4.73×10(-9)), and three new adenocarcinoma risk variants in TERT: rs61748181 (OR = 0.53, P = 2.64×10(-6)), rs112290073 (OR = 1.85, P = 1.27×10(-5)), rs138895564 (OR = 2.16, P = 2.06×10(-5); among young cases, OR = 3.77, P = 8.41×10(-4)). In addition, we found that rs139852726 (P = 1.44×10(-3)) was associated with telomere length in a sample of 922 healthy individuals. The gene-based SKAT-O analysis implicated TERT as the most relevant gene in the 5p15.33 region for adenocarcinoma (P = 7.84×10(-7)) and lung cancer (P = 2.37×10(-5)) risk. In this largest fine-mapping study to investigate a large number of rare and novel variants within 5p15.33, we identified novel lung and adenocarcinoma susceptibility loci with large effects and provided support for the role of telomere length as the potential underlying mechanism.

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

    PubMed

    Wang, Jinpeng; Li, Li; Zhang, Guofan

    2016-01-01

    Oysters are among the most important species in global aquaculture. Crassostrea gigas, and its subspecies C. angulata, are the major cultured species. To determine the genetic basis of growth-related traits in oysters, we constructed a second-generation linkage map from 3367 single-nucleotide polymorphisms (SNPs) based on genotyping-by-sequencing, genotyped from a C. gigas × C. angulata hybrid family. These 3367 SNPs were distributed on 1695 markers, which were assigned to 10 linkage groups. The genetic linkage map had a total length of 1084.3 cM, with an average of 0.8 cM between markers; it thus represents the densest genetic map constructed for oysters to date. Twenty-seven quantitative trait loci (QTL) for five growth-related traits were detected. These QTL could explain 4.2-7.7% (mean = 5.4%) of the phenotypic variation. In total, 50.8% of phenotypic variance for shell width, 7.7% for mass weight, and 34.1% for soft tissue weight were explained. The detected QTL were distributed among eight linkage groups, and more than half (16) were concentrated within narrow regions in their respective linkage groups. Thirty-eight annotated genes were identified within the QTL regions, two of which are key genes for carbohydrate metabolism. Other genes were found to participate in assembly and regulation of the actin cytoskeleton, signal transduction, and regulation of cell differentiation and development. The newly developed high-density genetic map, and the QTL and candidate genes identified provide a valuable genetic resource and a basis for marker-assisted selection for C. gigas and C. angulata. PMID:26994291

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

    PubMed Central

    Wang, Jinpeng; Li, Li; Zhang, Guofan

    2016-01-01

    Oysters are among the most important species in global aquaculture. Crassostrea gigas, and its subspecies C. angulata, are the major cultured species. To determine the genetic basis of growth-related traits in oysters, we constructed a second-generation linkage map from 3367 single-nucleotide polymorphisms (SNPs) based on genotyping-by-sequencing, genotyped from a C. gigas × C. angulata hybrid family. These 3367 SNPs were distributed on 1695 markers, which were assigned to 10 linkage groups. The genetic linkage map had a total length of 1084.3 cM, with an average of 0.8 cM between markers; it thus represents the densest genetic map constructed for oysters to date. Twenty-seven quantitative trait loci (QTL) for five growth-related traits were detected. These QTL could explain 4.2–7.7% (mean = 5.4%) of the phenotypic variation. In total, 50.8% of phenotypic variance for shell width, 7.7% for mass weight, and 34.1% for soft tissue weight were explained. The detected QTL were distributed among eight linkage groups, and more than half (16) were concentrated within narrow regions in their respective linkage groups. Thirty-eight annotated genes were identified within the QTL regions, two of which are key genes for carbohydrate metabolism. Other genes were found to participate in assembly and regulation of the actin cytoskeleton, signal transduction, and regulation of cell differentiation and development. The newly developed high-density genetic map, and the QTL and candidate genes identified provide a valuable genetic resource and a basis for marker-assisted selection for C. gigas and C. angulata. PMID:26994291

  12. Most diamonds were created equal

    NASA Astrophysics Data System (ADS)

    Jablon, Brooke Matat; Navon, Oded

    2016-06-01

    Diamonds crystallize deep in the mantle (>150 km), leaving their carbon sources and the mechanism of their crystallization debatable. They can form from elemental carbon, by oxidation of reduced species (e.g. methane) or reduction of oxidized ones (e.g. carbonate-bearing minerals or melts), in response to decreasing carbon solubility in melts or fluids or due to changes in pH. The mechanism of formation is clear for fibrous diamonds that grew from the carbonate-bearing fluids trapped in their microinclusions. However, these diamonds look different and, based on their lower level of nitrogen aggregation, are much younger than most monocrystalline (MC) diamonds. In the first systematic search for microinclusions in MC diamonds we examined twinned crystals (macles), assuming that during their growth, microinclusions were trapped along the twinning plane. Visible mineral inclusions (>10 μm) and nitrogen aggregation levels in these clear macles are similar to other MC diamonds. We found 32 microinclusions along the twinning planes in eight out of 30 diamonds. Eight inclusions are orthopyroxene; four contain >50% K2O (probably as K2(Mg, Ca)(CO3)2); but the major element compositions of the remaining 20 are similar to those of carbonate-bearing high-density fluids (HDFs) found in fibrous diamonds. We conclude that the source of carbon for these macles and for most diamonds is carbonate-bearing HDFs similar to those found here and in fibrous diamonds. Combined with the old ages of MC diamonds (up to 3.5 Ga), our new findings suggest that carbonates have been introduced into the reduced lithospheric mantle since the Archaean and that the mechanism of diamond formation is the same for most diamonds.

  13. High affinity DNA-microtubule interactions: evidence for a conserved DNA-MAP interaction involving unusual high CsCl density repetitious DNA families.

    PubMed

    Marx, K A; Denial, T

    1992-12-01

    We have examined high affinity interactions of chick brain microtubule proteins with 35S labelled tracer DNAs from chick, mouse and D. melanogaster under equilibrium conditions by the nitrocellulose filter binding technique. Ternary reaction mixtures of the above two components and a third component, an excess of unlabelled competitor DNA from either E. coli., mouse, D. melanogaster or chick, were used to measure small fractions of DNA in each case (1-4%) bound to microtubule protein under high stringency- large competitor DNA concentration and 0.5 M NaCl. As seen in part previously (Marx, K.A. and Denial, T. (1985) in The Molecular Basis of Cancer, 172B, 65-75 (Rein, ed), A. Liss, N.Y.) the measured order of competitor DNA strengths was identical for all three tracer DNAs. That is: chick > mouse > D. melanogaster > E. coli competitor DNA. Since the homologous interaction, chick competitor DNA with chick brain microtubule protein, is always the strongest interaction measured, we interpret this as evidence for a conserved protein-DNA sequence interaction. 35S chick DNA tracer sequences, isolated from nitrocellulose filters following the stringent binding in the presence of 0.9 mM-1 E. coli. competitor DNA, was used in driven reassociation reactions with total chick driver DNA. This fraction was found to be significantly enriched in repetitive chick DNA sequences. Since we have observed a similar phenomenon in mouse, we then compared the stringent binding mouse sequences and showed that the bulk of these sequences did not cross-hybridize with total chick DNA. Finally, all three 35S tracer DNAs binding to nitrocellulose were isolated and sedimented to equilibrium on CsCl density gradients. The CsCl density distributions from all three DNAs showed significant (100-fold) enrichment in classical satellite DNAs as well as higher enrichment in two very unusual high CsCl density families of DNA (1.720-1.740 g/cm3; 1.750-1.765 g/cm3). These families are never observed as

  14. Benzene on Cu(111): I. Application of van der Waals-Density Functional Formalism to Determine Binding Sites and Energy Contour Map

    NASA Astrophysics Data System (ADS)

    Berland, Kristian; Einstein, T. L.; Hyldgaard, Per

    2010-03-01

    With a recently developed van der Waals density functional (vdW-DF)footnotetextM. Dion et al., Phys. Rev. Lett. 92 (2004) 246401 we study the adsorption of benzene on Cu(111).footnotetextKB, TLE, and PH, Phys. Rev. B 80 (2009) 155431 The vdW-DF inclusion of nonlocal correlations changes the relative stability of 8 high-symmetry binding-position options and increases the adsorption energy by over an order of magnitude, achieving good agreement with experiment. The metallic surface state survives benzene adsorption. From a contour plot of the potential energy, we find that benzene can move almost freely along a honeycomb web of ``corridors" linking fcc and hcp sites via bridge sites, consistent with the low diffusion barrier in experiment.

  15. A Genetic Relationship between Phosphorus Efficiency and Photosynthetic Traits in Soybean As Revealed by QTL Analysis Using a High-Density Genetic Map.

    PubMed

    Li, Hongyan; Yang, Yuming; Zhang, Hengyou; Chu, Shanshan; Zhang, Xingguo; Yin, Dongmei; Yu, Deyue; Zhang, Dan

    2016-01-01

    Plant productivity relies on photosynthesis, and the photosynthetic process relies on phosphorus (P). The genetic basis of photosynthesis and P efficiency (PE) affecting yield has been separately characterized in various crop plants. However, the genetic relationship between PE and photosynthesis remains to be elucidated. In this study, we used a combined analysis of phenotypic correlation, linkage mapping, and expression analysis to dissect the relationship between PE and photosynthesis. We found significant phenotypic correlations between PE and photosynthetic related traits, particularly under low P stress. A total of 172 QTLs for both traits were detected and classified into 29 genomic regions. 12 (41.4%) of 29 regions were detected to be associated with both PE and photosynthetic related traits. Three major QTLs, q14-2, q15-2, and q19-2, were found to be associated with both traits and explained 6.6-58.9% of phenotypic variation. A photosynthetic-specific QTL cluster, q12-1, was detected under both normal and low P conditions, suggesting that genes responsible for this region were less effected by low P stress, and could be used in high photosynthetic efficiency breeding programs. In addition, several candidate genes with significantly differential expression upon low P stress, such as a purple acid phosphatase gene (Glyma.19G193900) within q19-2 region, were considered as promising candidates involved in regulating both soybean PE and photosynthetic capacity. Our results reveal a significant genetic relationship between PE and photosynthetic traits, and uncover several major genomic regions specific or common to these traits. The markers linked closely to these major QTLs may be used for selection of soybean varieties with improved P efficiency and photosynthetic capacity.

  16. A Genetic Relationship between Phosphorus Efficiency and Photosynthetic Traits in Soybean As Revealed by QTL Analysis Using a High-Density Genetic Map

    PubMed Central

    Li, Hongyan; Yang, Yuming; Zhang, Hengyou; Chu, Shanshan; Zhang, Xingguo; Yin, Dongmei; Yu, Deyue; Zhang, Dan

    2016-01-01

    Plant productivity relies on photosynthesis, and the photosynthetic process relies on phosphorus (P). The genetic basis of photosynthesis and P efficiency (PE) affecting yield has been separately characterized in various crop plants. However, the genetic relationship between PE and photosynthesis remains to be elucidated. In this study, we used a combined analysis of phenotypic correlation, linkage mapping, and expression analysis to dissect the relationship between PE and photosynthesis. We found significant phenotypic correlations between PE and photosynthetic related traits, particularly under low P stress. A total of 172 QTLs for both traits were detected and classified into 29 genomic regions. 12 (41.4%) of 29 regions were detected to be associated with both PE and photosynthetic related traits. Three major QTLs, q14-2, q15-2, and q19-2, were found to be associated with both traits and explained 6.6–58.9% of phenotypic variation. A photosynthetic-specific QTL cluster, q12-1, was detected under both normal and low P conditions, suggesting that genes responsible for this region were less effected by low P stress, and could be used in high photosynthetic efficiency breeding programs. In addition, several candidate genes with significantly differential expression upon low P stress, such as a purple acid phosphatase gene (Glyma.19G193900) within q19-2 region, were considered as promising candidates involved in regulating both soybean PE and photosynthetic capacity. Our results reveal a significant genetic relationship between PE and photosynthetic traits, and uncover several major genomic regions specific or common to these traits. The markers linked closely to these major QTLs may be used for selection of soybean varieties with improved P efficiency and photosynthetic capacity. PMID:27446154

  17. Confirmation of quantitative trait loci using a low-density single nucleotide polymorphism map for twinning and ovulation rate on bovine chromosome 5.

    PubMed

    Allan, M F; Kuehn, L A; Cushman, R A; Snelling, W M; Echternkamp, S E; Thallman, R M

    2009-01-01

    Traditional genetic selection in cattle for traits with low heritability, such as reproduction, has had very little success. With the addition of DNA technologies to the genetic selection toolbox for livestock, the opportunity may exist to improve reproductive efficiency more rapidly in cattle. The US Meat Animal Research Center Production Efficiency Population has 9,186 twinning and 29,571 ovulation rate records for multiple generations of animals, but a significant number of these animals do not have tissue samples available for DNA genotyping. The objectives of this study were to confirm QTL for twinning and ovulation rate previously found on BTA5 and to evaluate the ability of GenoProb to predict genotypic information in a pedigree containing 16,035 animals when using genotypes for 24 SNP from 3 data sets containing 48, 724, or 2,900 animals. Marker data for 21 microsatellites on BTA5 with 297 to 3,395 animals per marker were used in conjunction with each data set of genotyped animals. Genotypic probabilities for females were used to calculate independent variables for regressions of additive, dominance, and imprinting effects. Genotypic regressions were fitted as fixed effects in a 2-trait mixed model analysis by using multiple-trait derivative-free REML. Each SNP was analyzed individually, followed by backward selection fitting all individually significant SNP simultaneously and then removing the least significant SNP until only significant SNP were left. Five significant SNP associations were detected for twinning rate and 3 were detected for ovulation rate. Two of these SNP, 1 for each trait, were significant for imprinting. Additional modeling of paternal and maternal allelic effects confirmed the initial results of imprinting done by contrasting heterozygotes. These results are supported by comparative mapping of mouse and human imprinted genes to this region of bovine chromosome 5.

  18. A High Density SNP Array for the Domestic Horse and Extant Perissodactyla: Utility for Association Mapping, Genetic Diversity, and Phylogeny Studies

    PubMed Central

    McCue, Molly E.; Bannasch, Danika L.; Petersen, Jessica L.; Gurr, Jessica; Bailey, Ernie; Binns, Matthew M.; Distl, Ottmar; Guérin, Gérard; Hasegawa, Telhisa; Hill, Emmeline W.; Leeb, Tosso; Lindgren, Gabriella; Penedo, M. Cecilia T.; Røed, Knut H.; Ryder, Oliver A.; Swinburne, June E.; Tozaki, Teruaki; Valberg, Stephanie J.; Vaudin, Mark; Lindblad-Toh, Kerstin

    2012-01-01

    An equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species. More than 54,000 polymorphic SNPs provided an average inter-SNP spacing of ∼43 kb. The mean minor allele frequency across domestic horse breeds was 0.23, and the number of polymorphic SNPs within breeds ranged from 43,287 to 52,085. Genome-wide linkage disequilibrium (LD) in most breeds declined rapidly over the first 50–100 kb and reached background levels within 1–2 Mb. The extent of LD and the level of inbreeding were highest in the Thoroughbred and lowest in the Mongolian and Quarter Horse. Multidimensional scaling (MDS) analyses demonstrated the tight grouping of individuals within most breeds, close proximity of related breeds, and less tight grouping in admixed breeds. The close relationship between the Przewalski's Horse and the domestic horse was demonstrated by pair-wise genetic distance and MDS. Genotyping of other Perissodactyla (zebras, asses, tapirs, and rhinoceros) was variably successful, with call rates and the number of polymorphic loci varying across taxa. Parsimony analysis placed the modern horse as sister taxa to Equus przewalski. The utility of the SNP array in genome-wide association was confirmed by mapping the known recessive chestnut coat color locus (MC1R) and defining a conserved haplotype of ∼750 kb across all breeds. These results demonstrate the high quality of this SNP genotyping resource, its usefulness in diverse genome analyses of the horse, and potential use in related species. PMID:22253606

  19. A Genetic Relationship between Phosphorus Efficiency and Photosynthetic Traits in Soybean As Revealed by QTL Analysis Using a High-Density Genetic Map.

    PubMed

    Li, Hongyan; Yang, Yuming; Zhang, Hengyou; Chu, Shanshan; Zhang, Xingguo; Yin, Dongmei; Yu, Deyue; Zhang, Dan

    2016-01-01

    Plant productivity relies on photosynthesis, and the photosynthetic process relies on phosphorus (P). The genetic basis of photosynthesis and P efficiency (PE) affecting yield has been separately characterized in various crop plants. However, the genetic relationship between PE and photosynthesis remains to be elucidated. In this study, we used a combined analysis of phenotypic correlation, linkage mapping, and expression analysis to dissect the relationship between PE and photosynthesis. We found significant phenotypic correlations between PE and photosynthetic related traits, particularly under low P stress. A total of 172 QTLs for both traits were detected and classified into 29 genomic regions. 12 (41.4%) of 29 regions were detected to be associated with both PE and photosynthetic related traits. Three major QTLs, q14-2, q15-2, and q19-2, were found to be associated with both traits and explained 6.6-58.9% of phenotypic variation. A photosynthetic-specific QTL cluster, q12-1, was detected under both normal and low P conditions, suggesting that genes responsible for this region were less effected by low P stress, and could be used in high photosynthetic efficiency breeding programs. In addition, several candidate genes with significantly differential expression upon low P stress, such as a purple acid phosphatase gene (Glyma.19G193900) within q19-2 region, were considered as promising candidates involved in regulating both soybean PE and photosynthetic capacity. Our results reveal a significant genetic relationship between PE and photosynthetic traits, and uncover several major genomic regions specific or common to these traits. The markers linked closely to these major QTLs may be used for selection of soybean varieties with improved P efficiency and photosynthetic capacity. PMID:27446154

  20. Achievement of a short term three dimensional electron density mapping of the ionosphere in the European sector: Comparisons with the IRI model for quiet-moderate geomagnetic-ionospheric conditions

    NASA Astrophysics Data System (ADS)

    Pietrella, M.

    2016-10-01

    In this paper will be described the procedure followed for the achievement of a short term three dimensional (3-D) electron density mapping of the ionosphere in the European area. It consists of three main steps: (1) foF2 and M(3000)F2 short-term forecasts, (foF2STF) and (M3000F2STF), are calculated at 12 ionospheric observatories scattered in the European area; (2) the values of foF2STF and M3000F2STF on a grid of equi-spaced points, (foF2STF,GP) and (M3000F2STF,GP), are calculated by means of an appropriate interpolation algorithm by using the foF2STF and M3000F2STF data; (3) foF2STF,GP and M3000F2STF,GP data ingestion into the IRI model is employed to produce a short term 3-D electron density mapping (ST-3D-M) of the ionosphere. The electron density profiles provided by the ST-3D-M and IRI models, were compared with the electron density profiles autoscaled by the Automatic Real-Time Ionogram Scaler with True-height (ARTIST) system, which are here considered as the truth profiles. The results of these comparisons, shown for a certain number of epochs during quiet-moderate geomagnetic-ionospheric conditions, in the truth-sites of Athens (38○.0‧N, 23○.5‧E), Chilton (51○.5‧N, -0○.6‧W), Dourbes (50○.1‧ N, 4○.6‧E), Pruhonice (50○.0‧N, 14○.6‧E), Rome (41○.9‧N, 12○.5‧E), and Tortosa (40○.8‧N, 0○.5‧E), indicate that the ST-3D-M as forecasting tool can be considered generally reliable.

  1. High density mapping of the MHC identifies a shared role for HLA-DRB1*01:03 in inflammatory bowel diseases and heterozygous advantage in ulcerative colitis

    PubMed Central

    Goyette, Philippe; Boucher, Gabrielle; Mallon, Dermot; Ellinghaus, Eva; Jostins, Luke; Huang, Hailiang; Ripke, Stephan; Gusareva, Elena S; Annese, Vito; Hauser, Stephen L; Oksenberg, Jorge R; Thomsen, Ingo; Leslie, Stephen; Daly, Mark J; Van Steen, Kristel; Duerr, Richard H; Barrett, Jeffrey C; McGovern, Dermot PB; Schumm, L Philip; Traherne, James A; Carrington, Mary N; Kosmoliaptsis, Vasilis; Karlsen, Tom H; Franke, Andre; Rioux, John D

    2014-01-01

    Genome-wide association studies of the related chronic inflammatory bowel diseases (IBD) known as Crohn’s disease and ulcerative colitis have shown strong evidence of association to the major histocompatibility complex (MHC). This region encodes a large number of immunological candidates, including the antigen-presenting classical HLA molecules1. Studies in IBD have indicated that multiple independent associations exist at HLA and non-HLA genes, but lacked the statistical power to define the architecture of association and causal alleles2,3. To address this, we performed high-density SNP typing of the MHC in >32,000 patients with IBD, implicating multiple HLA alleles, with a primary role for HLA-DRB1*01:03 in both Crohn’s disease and ulcerative colitis. Significant differences were observed between these diseases, including a predominant role of class II HLA variants and heterozygous advantage observed in ulcerative colitis, suggesting an important role of the adaptive immune response to the colonic environment in the pathogenesis of IBD. PMID:25559196

  2. Visual object processing as a function of stimulus energy, retinal eccentricity and Gestalt configuration: a high-density electrical mapping study.

    PubMed

    Snyder, A C; Shpaner, M; Molholm, S; Foxe, J J

    2012-09-27

    To reveal the fundamental processes underlying the different stages of visual object perception, most studies have manipulated relatively complex images, such as photographs, line drawings of natural objects, or perceptual illusions. Here, rather than starting from complex images and working backward to infer simpler processes, we investigated how the visual system parses and integrates information contained in stimuli of the most basic variety. Simple scatterings of a few points of light were manipulated in terms of their numerosity, spatial extent, and organization, and high-density electrophysiological recordings were made from healthy adults engaged in an unrelated task. We reasoned that this approach permitted an uncontaminated view of the spatio-temporal dynamics of the related neural processes. We were guided in our predictions by the "frame-and-fill" model for object perception, whereby fast inputs to the dorsal stream of the visual "where" system first frame the spatial extent of visual objects, which are subsequently "filled-in" by the slower activation of the ventral stream of the visual "what" system. Our findings were consistent with this view, showing a rapidly-onsetting effect of spatial extent in dorsal stream sources, and later-onsetting effects due to dot number and symmetry, which were deemed to be more closely tied to the details of object identity, from ventral stream sources. This collection of observations provides an important baseline from which to understand the spatio-temporal properties of basic visual object perception, and from which to test dysfunction of this system in clinical populations.

  3. Intact inhibitory control processes in abstinent drug abusers (II): a high-density electrical mapping study in former cocaine and heroin addicts.

    PubMed

    Morie, Kristen P; Garavan, Hugh; Bell, Ryan P; De Sanctis, Pierfilippo; Krakowski, Menachem I; Foxe, John J

    2014-07-01

    Response inhibition deficits are well-documented in drug users, and are related to the impulsive tendencies characteristic of the addictive phenotype. Addicts also show significant motivational issues that may accentuate these inhibitory deficits. We investigated the extent to which these inhibitory deficits are present in abstinence. Salience of the task stimuli was also manipulated on the premise that emotionally-valenced inputs might impact inhibitory efficacy by overcoming the blunted responses to everyday environmental inputs characteristic of this population. Participants performed response inhibition tasks consisting of both neutral and emotionally valenced stimuli while high-density event-related potentials (ERPs) were recorded. Electrophysiological responses (N2/P3 components) to successful inhibitions in abstinent abusers (N = 20) and non-using participants (N = 21) were compared. In contrast to previous work in current users, our abstinent cohort showed no detectable behavioral or electrophysiological differences in their inhibitory responses, and no differences on self-reports of impulsivity, despite their long histories of chronic use (mean = 10.3 years). The current findings are consistent with a recovery of inhibitory control processes as a function of abstinence. Abstinent former users, however, did show a reduced modulation, relative to controls, of their ERPs to valenced input while performing successful inhibitions, although contrary to our hypothesis, the use of valenced inputs had no impact on inhibitory performance. Reduced ERP modulation to emotionally valenced inputs may have implications for relapse in emotional contexts outside the treatment center. PMID:23507565

  4. The development of multisensory integration in high-functioning autism: high-density electrical mapping and psychophysical measures reveal impairments in the processing of audiovisual inputs.

    PubMed

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

    2013-06-01

    Successful integration of auditory and visual inputs is crucial for both basic perceptual functions and for higher-order processes related to social cognition. Autism spectrum disorders (ASD) are characterized by impairments in social cognition and are associated with abnormalities in sensory and perceptual processes. Several groups have reported that individuals with ASD are impaired in their ability to integrate socially relevant audiovisual (AV) information, and it has been suggested that this contributes to the higher-order social and cognitive deficits observed in ASD. However, successful integration of auditory and visual inputs also influences detection and perception of nonsocial stimuli, and integration deficits may impair earlier stages of information processing, with cascading downstream effects. To assess the integrity of basic AV integration, we recorded high-density electrophysiology from a cohort of high-functioning children with ASD (7-16 years) while they performed a simple AV reaction time task. Children with ASD showed considerably less behavioral facilitation to multisensory inputs, deficits that were paralleled by less effective neural integration. Evidence for processing differences relative to typically developing children was seen as early as 100 ms poststimulation, and topographic analysis suggested that children with ASD relied on different cortical networks during this early multisensory processing stage. PMID:22628458

  5. Equal Cell Size and Nonorthogonality in ANCOVA.

    ERIC Educational Resources Information Center

    Llabre, Maria M.; Ware, William B.

    1980-01-01

    Computer programs for analysis of covariance use classical experimental, regression, or hierarchical methods of least squares. In a 3 X 3 factorial experiment with equal cell frequencies, three solutions yielded different sums of squares for main effects although correlation between variables was negligible and cell frequencies were equal.…

  6. Continuing Controversy in Equal Employment Law.

    ERIC Educational Resources Information Center

    Vogt, Carl W.; Robles, Martin J.

    1980-01-01

    Some current controversies in the growing body of equal employment law are examined: wage comparability in the context of sex discrimination; procedural sections of the laws and related litigation; class actions by the Equal Employment Opportunities Commission; the scope of litigation; and the criteria for conferring standing on the plaintiff.…

  7. Equal Opportunity in the Air Force

    ERIC Educational Resources Information Center

    Gatling, Wade S.

    1976-01-01

    Notes that the Affirmative Action Plan of the Air Force is built on the premise that equal opportunity and treatment is everyone's responsibility. Unit Commanders, on-the-job training monitors, recreation centers directors, and others are involved in specific facets of the Plan to insure equality. (Author/AM)

  8. Equal Plate Charges on Series Capacitors?

    ERIC Educational Resources Information Center

    Illman, B. L.; Carlson, G. T.

    1994-01-01

    Provides a line of reasoning in support of the contention that the equal charge proposition is at best an approximation. Shows how the assumption of equal plate charge on capacitors in series contradicts the conservative nature of the electric field. (ZWH)

  9. Vocational Education and Equality of Opportunity.

    ERIC Educational Resources Information Center

    Horowitz, Benjamin; Feinberg, Walter

    1990-01-01

    Examines the concepts of equality of opportunity and equality of educational opportunity and their relationship to vocational education. Traces the history of vocational education. Delineates the distinction between training and education as enumerated in Aristotelian philosophy. Discusses the role vocational education can play in the educative…

  10. 49 CFR 236.792 - Reservoir, equalizing.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 4 2011-10-01 2011-10-01 false Reservoir, equalizing. 236.792 Section 236.792 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION... Reservoir, equalizing. An air reservoir connected with and adding volume to the top portion of...

  11. 49 CFR 236.792 - Reservoir, equalizing.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 4 2012-10-01 2012-10-01 false Reservoir, equalizing. 236.792 Section 236.792 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION... Reservoir, equalizing. An air reservoir connected with and adding volume to the top portion of...

  12. 49 CFR 236.792 - Reservoir, equalizing.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 4 2014-10-01 2014-10-01 false Reservoir, equalizing. 236.792 Section 236.792 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION... Reservoir, equalizing. An air reservoir connected with and adding volume to the top portion of...

  13. 49 CFR 236.792 - Reservoir, equalizing.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 4 2013-10-01 2013-10-01 false Reservoir, equalizing. 236.792 Section 236.792 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION... Reservoir, equalizing. An air reservoir connected with and adding volume to the top portion of...

  14. Mapping the energy and diffusion landscapes of membrane proteins at the cell surface using high-density single-molecule imaging and Bayesian inference: application to the multiscale dynamics of glycine receptors in the neuronal membrane.

    PubMed

    Masson, Jean-Baptiste; Dionne, Patrice; Salvatico, Charlotte; Renner, Marianne; Specht, Christian G; Triller, Antoine; Dahan, Maxime

    2014-01-01

    Protein mobility is conventionally analyzed in terms of an effective diffusion. Yet, this description often fails to properly distinguish and evaluate the physical parameters (such as the membrane friction) and the biochemical interactions governing the motion. Here, we present a method combining high-density single-molecule imaging and statistical inference to separately map the diffusion and energy landscapes of membrane proteins across the cell surface at ~100 nm resolution (with acquisition of a few minutes). Upon applying these analytical tools to glycine neurotransmitter receptors at inhibitory synapses, we find that gephyrin scaffolds act as shallow energy traps (~3 kBT) for glycine neurotransmitter receptors, with a depth modulated by the biochemical properties of the receptor-gephyrin interaction loop. In turn, the inferred maps can be used to simulate the dynamics of proteins in the membrane, from the level of individual receptors to that of the population, and thereby, to model the stochastic fluctuations of physiological parameters (such as the number of receptors at synapses). Overall, our approach provides a powerful and comprehensive framework with which to analyze biochemical interactions in living cells and to decipher the multiscale dynamics of biomolecules in complex cellular environments. PMID:24411239

  15. Chaotic Polynomial Maps

    NASA Astrophysics Data System (ADS)

    Zhang, Xu

    This paper introduces a class of polynomial maps in Euclidean spaces, investigates the conditions under which there exist Smale horseshoes and uniformly hyperbolic invariant sets, studies the chaotic dynamical behavior and strange attractors, and shows that some maps are chaotic in the sense of Li-Yorke or Devaney. This type of maps includes both the Logistic map and the Hénon map. For some diffeomorphisms with the expansion dimension equal to one or two in three-dimensional spaces, the conditions under which there exist Smale horseshoes and uniformly hyperbolic invariant sets on which the systems are topologically conjugate to the two-sided fullshift on finite alphabet are obtained; for some expanding maps, the chaotic region is analyzed by using the coupled-expansion theory and the Brouwer degree theory. For three types of higher-dimensional polynomial maps with degree two, the conditions under which there are Smale horseshoes and uniformly hyperbolic invariant sets are given, and the topological conjugacy between the maps on the invariant sets and the two-sided fullshift on finite alphabet is obtained. Some interesting maps with chaotic attractors and positive Lyapunov exponents in three-dimensional spaces are found by using computer simulations. In the end, two examples are provided to illustrate the theoretical results.

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  17. The response of the inductively coupled argon plasma to solvent plasma load: spatially resolved maps of electron density obtained from the intensity of one argon line

    NASA Astrophysics Data System (ADS)

    Weir, D. G. J.; Blades, M. W.

    1994-12-01

    A survey of spatially resolved electron number density ( ne) in the tail cone of the inductively coupled argon plasma (ICAP) is presented: all of the results of the survey have been radially inverted by numerical, asymmetric Abel inversion. The survey extends over the entire volume of the plasma beyond the exit of the ICAP torch; It extends over distances of z = 5-25 mm downstream from the induction coil, and over radial distances of ± 8 mm from the discharge axis. The survey also explores a range of inner argon flow rates ( QIN), solvent plasma load ( Qspl) and r.f. power: moreover, it explores loading by water, methanol and chloroform. Throughout the survey, ne was determined from the intensity of one, optically thin argon line, by a method which assumes that the atomic state distribution function (ASDF) for argon lies close to local thermal equilibrium (LTE). The validity of this assumption is reviewed. Also examined are the discrepancies between ne from this method and ne from Stark broadening measurements. With the error taken into account, the results of the survey reveal how time averaged values of ne in the ICAP respond over an extensive, previously unexplored range of experimental parameters. Moreover, the spatial information lends insight into how the thermal conditions and the transport of energy respond. Overall, the response may be described in terms of energy consumption along the axial channel and thermal pinch within the induction region. The predominating effect depends on the solvent plasma load, the solvent composition, the robustness of the discharge, and the distribution of solvent material over the argon stream.

  18. Two novel susceptibility loci for non-small cell lung cancer map to low-density lipoprotein receptor-related protein 5

    PubMed Central

    Wang, Ying; Zhang, Yongjun; Fang, Meiyu; Bao, Wenglong; Deng, Dehou

    2016-01-01

    This study investigated the effect of single-nucleotide polymorphisms (SNPs) of low-density lipoprotein receptor-related protein 5 (LRP5) on the risk of developing non-small cell lung cancer (NSCLC). A total of 500 NSCLC patients and 500 healthy controls were recruited for genotyping of 11 SNPs of LRP5. The association between genotype and NSCLC risk was evaluated by computing the odds ratio (OR) and 95% confidence interval (CI) from multivariate unconditional logistic regression analyses. Eleven Tag SNPs were detected. The frequency of the LRP5 rs3736228 T allele (18.9% in male NSCLC cases and 23.9% in male controls) was statistically different between male NSCLCs and male controls (P=0.03), and the T allele was associated with a lower risk of NSCLC (OR=0.74; 95% CI, 0.56–0.67), whereas the C/C homozygous genotype and the LRP5 rs64843 T/T genotype were associated with an increased risk of NSCLC and squamous cell carcinoma (SCC), respectively (OR=1.43 and 1.77, respectively). Using Haploview software, the frequency of the haplotypes of rs312009/rs3120015/rs3120014 CCC was was significantly higher in female SCC cases compared with female controls (0.064 vs. 0.009, P=0.04). LRP5 rs3736228 and rs64843 SNPs were significantly associated with an increased risk of NSCLC and SCC, respectively. Further studies are required to investigate the functional changes in LRP5 expression and activity in NSCLC in vitro.

  19. Two novel susceptibility loci for non-small cell lung cancer map to low-density lipoprotein receptor-related protein 5

    PubMed Central

    Wang, Ying; Zhang, Yongjun; Fang, Meiyu; Bao, Wenglong; Deng, Dehou

    2016-01-01

    This study investigated the effect of single-nucleotide polymorphisms (SNPs) of low-density lipoprotein receptor-related protein 5 (LRP5) on the risk of developing non-small cell lung cancer (NSCLC). A total of 500 NSCLC patients and 500 healthy controls were recruited for genotyping of 11 SNPs of LRP5. The association between genotype and NSCLC risk was evaluated by computing the odds ratio (OR) and 95% confidence interval (CI) from multivariate unconditional logistic regression analyses. Eleven Tag SNPs were detected. The frequency of the LRP5 rs3736228 T allele (18.9% in male NSCLC cases and 23.9% in male controls) was statistically different between male NSCLCs and male controls (P=0.03), and the T allele was associated with a lower risk of NSCLC (OR=0.74; 95% CI, 0.56–0.67), whereas the C/C homozygous genotype and the LRP5 rs64843 T/T genotype were associated with an increased risk of NSCLC and squamous cell carcinoma (SCC), respectively (OR=1.43 and 1.77, respectively). Using Haploview software, the frequency of the haplotypes of rs312009/rs3120015/rs3120014 CCC was was significantly higher in female SCC cases compared with female controls (0.064 vs. 0.009, P=0.04). LRP5 rs3736228 and rs64843 SNPs were significantly associated with an increased risk of NSCLC and SCC, respectively. Further studies are required to investigate the functional changes in LRP5 expression and activity in NSCLC in vitro. PMID:27698794

  20. Unique Microstructural Changes in the Brain Associated with Urological Chronic Pelvic Pain Syndrome (UCPPS) Revealed by Diffusion Tensor MRI, Super-Resolution Track Density Imaging, and Statistical Parameter Mapping: A MAPP Network Neuroimaging Study

    PubMed Central

    Woodworth, Davis; Mayer, Emeran; Leu, Kevin; Ashe-McNalley, Cody; Naliboff, Bruce D.; Labus, Jennifer S.; Tillisch, Kirsten; Kutch, Jason J.; Farmer, Melissa A.; Apkarian, A. Vania; Johnson, Kevin A.; Mackey, Sean C.; Ness, Timothy J.; Landis, J. Richard; Deutsch, Georg; Harris, Richard E.; Clauw, Daniel J.; Mullins, Chris; Ellingson, Benjamin M.

    2015-01-01

    Studies have suggested chronic pain syndromes are associated with neural reorganization in specific regions associated with perception, processing, and integration of pain. Urological chronic pelvic pain syndrome (UCPPS) represents a collection of pain syndromes characterized by pelvic pain, namely Chronic Prostatitis/Chronic Pelvic Pain Syndrome (CP/CPPS) and Interstitial Cystitis/Painful Bladder Syndrome (IC/PBS), that are both poorly understood in their pathophysiology, and treated ineffectively. We hypothesized patients with UCPPS may have microstructural differences in the brain compared with healthy control subjects (HCs), as well as patients with irritable bowel syndrome (IBS), a common gastrointestinal pain disorder. In the current study we performed population-based voxel-wise DTI and super-resolution track density imaging (TDI) in a large, two-center sample of phenotyped patients from the multicenter cohort with UCPPS (N = 45), IBS (N = 39), and HCs (N = 56) as part of the MAPP Research Network. Compared with HCs, UCPPS patients had lower fractional anisotropy (FA), lower generalized anisotropy (GA), lower track density, and higher mean diffusivity (MD) in brain regions commonly associated with perception and integration of pain information. Results also showed significant differences in specific anatomical regions in UCPPS patients when compared with IBS patients, consistent with microstructural alterations specific to UCPPS. While IBS patients showed clear sex related differences in FA, MD, GA, and track density consistent with previous reports, few such differences were observed in UCPPS patients. Heat maps illustrating the correlation between specific regions of interest and various pain and urinary symptom scores showed clustering of significant associations along the cortico-basal ganglia-thalamic-cortical loop associated with pain integration, modulation, and perception. Together, results suggest patients with UCPPS have extensive microstructural

  1. Unique Microstructural Changes in the Brain Associated with Urological Chronic Pelvic Pain Syndrome (UCPPS) Revealed by Diffusion Tensor MRI, Super-Resolution Track Density Imaging, and Statistical Parameter Mapping: A MAPP Network Neuroimaging Study.

    PubMed

    Woodworth, Davis; Mayer, Emeran; Leu, Kevin; Ashe-McNalley, Cody; Naliboff, Bruce D; Labus, Jennifer S; Tillisch, Kirsten; Kutch, Jason J; Farmer, Melissa A; Apkarian, A Vania; Johnson, Kevin A; Mackey, Sean C; Ness, Timothy J; Landis, J Richard; Deutsch, Georg; Harris, Richard E; Clauw, Daniel J; Mullins, Chris; Ellingson, Benjamin M

    2015-01-01

    Studies have suggested chronic pain syndromes are associated with neural reorganization in specific regions associated with perception, processing, and integration of pain. Urological chronic pelvic pain syndrome (UCPPS) represents a collection of pain syndromes characterized by pelvic pain, namely Chronic Prostatitis/Chronic Pelvic Pain Syndrome (CP/CPPS) and Interstitial Cystitis/Painful Bladder Syndrome (IC/PBS), that are both poorly understood in their pathophysiology, and treated ineffectively. We hypothesized patients with UCPPS may have microstructural differences in the brain compared with healthy control subjects (HCs), as well as patients with irritable bowel syndrome (IBS), a common gastrointestinal pain disorder. In the current study we performed population-based voxel-wise DTI and super-resolution track density imaging (TDI) in a large, two-center sample of phenotyped patients from the multicenter cohort with UCPPS (N = 45), IBS (N = 39), and HCs (N = 56) as part of the MAPP Research Network. Compared with HCs, UCPPS patients had lower fractional anisotropy (FA), lower generalized anisotropy (GA), lower track density, and higher mean diffusivity (MD) in brain regions commonly associated with perception and integration of pain information. Results also showed significant differences in specific anatomical regions in UCPPS patients when compared with IBS patients, consistent with microstructural alterations specific to UCPPS. While IBS patients showed clear sex related differences in FA, MD, GA, and track density consistent with previous reports, few such differences were observed in UCPPS patients. Heat maps illustrating the correlation between specific regions of interest and various pain and urinary symptom scores showed clustering of significant associations along the cortico-basal ganglia-thalamic-cortical loop associated with pain integration, modulation, and perception. Together, results suggest patients with UCPPS have extensive microstructural

  2. The L_infinity constrained global optimal histogram equalization technique for real time imaging

    NASA Astrophysics Data System (ADS)

    Ren, Qiongwei; Niu, Yi; Liu, Lin; Jiao, Yang; Shi, Guangming

    2015-08-01

    Although the current imaging sensors can achieve 12 or higher precision, the current display devices and the commonly used digital image formats are still only 8 bits. This mismatch causes significant waste of the sensor precision and loss of information when storing and displaying the images. For better usage of the precision-budget, tone mapping operators have to be used to map the high-precision data into low-precision digital images adaptively. In this paper, the classic histogram equalization tone mapping operator is reexamined in the sense of optimization. We point out that the traditional histogram equalization technique and its variants are fundamentally improper by suffering from local optimum problems. To overcome this drawback, we remodel the histogram equalization tone mapping task based on graphic theory which achieves the global optimal solutions. Another advantage of the graphic-based modeling is that the tone-continuity is also modeled as a vital constraint in our approach which suppress the annoying boundary artifacts of the traditional approaches. In addition, we propose a novel dynamic programming technique to solve the histogram equalization problem in real time. Experimental results shows that the proposed tone-preserved global optimal histogram equalization technique outperforms the traditional approaches by exhibiting more subtle details in the foreground while preserving the smoothness of the background.

  3. Equality Assurance: Self-Assessment for Equal Opportunities in Further Education.

    ERIC Educational Resources Information Center

    Dadzie, Stella, Comp.

    This manual is intended as a tool kit for further education (FE) colleges to use to develop their own approaches to equal opportunities policy development and implementation. The following topics are discussed in the eight sections: the manual's development; the case for equality; things an equal opportunities policy should cover; strategic and…

  4. 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

  5. Equal Remuneration Convention (ILO No. 100).

    PubMed

    1989-01-01

    The government of Uruguay ratified this UN International Labor Organization convention on equal remuneration on November 16, 1989, and the Government of Zimbabwe ratified this Convention on December 14, 1989.

  6. 7 CFR 622.6 - Equal opportunity.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... of Agriculture (7 CFR Part 15), which provide that no person in the United States shall, on the... AGRICULTURE WATER RESOURCES WATERSHED PROJECTS General § 622.6 Equal opportunity. The Pub. L. 83-566 and...

  7. 7 CFR 622.6 - Equal opportunity.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... of Agriculture (7 CFR Part 15), which provide that no person in the United States shall, on the... AGRICULTURE WATER RESOURCES WATERSHED PROJECTS General § 622.6 Equal opportunity. The Pub. L. 83-566 and...

  8. 7 CFR 622.6 - Equal opportunity.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... of Agriculture (7 CFR Part 15), which provide that no person in the United States shall, on the... AGRICULTURE WATER RESOURCES WATERSHED PROJECTS General § 622.6 Equal opportunity. The Pub. L. 83-566 and...

  9. 7 CFR 622.6 - Equal opportunity.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... of Agriculture (7 CFR Part 15), which provide that no person in the United States shall, on the... AGRICULTURE WATER RESOURCES WATERSHED PROJECTS General § 622.6 Equal opportunity. The Pub. L. 83-566 and...

  10. Publicly Supported, Universally Available Education and Equality

    ERIC Educational Resources Information Center

    Boulding, Kenneth E.

    1976-01-01

    It was once thought that publicly supported, universally available education would produce socioeconomic equality. Family inheritance--financial, cultural, social--explains much of its failure to do so. (Author)

  11. 49 CFR 236.792 - Reservoir, equalizing.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... equalizing piston chamber of the automatic brake valve, to provide uniform service reductions in brake pipe pressure regardless of the length of the train. Cross Reference: Rocker, see § 236.755....

  12. The Bakke Opinions and Equal Protection Doctrine.

    ERIC Educational Resources Information Center

    Karst, Kenneth L.; Horowitz, Harold W.

    1979-01-01

    Constitutional issues addressed in the Supreme Court's decision are reviewed. The opinions rendered by Justice Powell are viewed as reflections of the weakness of recent equal protection theory, and as signs of future doctrine. (GC)

  13. The Equality Act 2010 and mental health.

    PubMed

    Lockwood, Graeme; Henderson, Claire; Thornicroft, Graham

    2012-03-01

    One aim of the Equality Act 2010 is to protect people with disabilities and prevent disability discrimination. We review the key provisions of the Act relevant to disability discrimination with respect to mental illness.

  14. Summary of the second equal opportunity conference

    SciTech Connect

    Not Available

    1984-02-01

    Reports and recommendations are included for: Hispanic Employment Program; Federal Women's Program; Equal Employment Opportunity Program; complaint processing workshop; Affirmative Actions Program Workshop; EEO programs in the Office of Personnel Management; and an overall evaluation of the program. (PSB)

  15. Turbo Equalization Using Partial Gaussian Approximation

    NASA Astrophysics Data System (ADS)

    Zhang, Chuanzong; Wang, Zhongyong; Manchon, Carles Navarro; Sun, Peng; Guo, Qinghua; Fleury, Bernard Henri

    2016-09-01

    This paper deals with turbo-equalization for coded data transmission over intersymbol interference (ISI) channels. We propose a message-passing algorithm that uses the expectation-propagation rule to convert messages passed from the demodulator-decoder to the equalizer and computes messages returned by the equalizer by using a partial Gaussian approximation (PGA). Results from Monte Carlo simulations show that this approach leads to a significant performance improvement compared to state-of-the-art turbo-equalizers and allows for trading performance with complexity. We exploit the specific structure of the ISI channel model to significantly reduce the complexity of the PGA compared to that considered in the initial paper proposing the method.

  16. Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints.

    PubMed Central

    Künzel, G; Korzun, L; Meister, A

    2000-01-01

    We have developed a new technique for the physical mapping of barley chromosomes using microdissected translocation chromosomes for PCR with sequence-tagged site primers derived from >300 genetically mapped RFLP probes. The positions of 240 translocation breakpoints were integrated as physical landmarks into linkage maps of the seven barley chromosomes. This strategy proved to be highly efficient in relating physical to genetic distances. A very heterogeneous distribution of recombination rates was found along individual chromosomes. Recombination is mainly confined to a few relatively small areas spaced by large segments in which recombination is severely suppressed. The regions of highest recombination frequency (map. The results for barley correspond well with those obtained by deletion mapping in wheat. This indicates that chromosomal regions characterized by similar recombination frequencies and marker densities are highly conserved between the genomes of barley and wheat. The findings for barley support the conclusions drawn from deletion mapping in wheat that for all plant genomes, notwithstanding their size, the marker-rich regions are all of similar gene density and recombination activity and, therefore, should be equally accessible to map-based cloning. PMID:10628998

  17. 29 CFR 1620.14 - Testing equality of jobs.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 29 Labor 4 2010-07-01 2010-07-01 false Testing equality of jobs. 1620.14 Section 1620.14 Labor... Testing equality of jobs. (a) In general. What constitutes equal skill, equal effort, or equal..., or responsibility required for the performance of jobs will not render the equal pay...

  18. 29 CFR 1620.14 - Testing equality of jobs.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 29 Labor 4 2011-07-01 2011-07-01 false Testing equality of jobs. 1620.14 Section 1620.14 Labor... Testing equality of jobs. (a) In general. What constitutes equal skill, equal effort, or equal..., or responsibility required for the performance of jobs will not render the equal pay...

  19. 29 CFR 1620.14 - Testing equality of jobs.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 29 Labor 4 2012-07-01 2012-07-01 false Testing equality of jobs. 1620.14 Section 1620.14 Labor... Testing equality of jobs. (a) In general. What constitutes equal skill, equal effort, or equal..., or responsibility required for the performance of jobs will not render the equal pay...

  20. 29 CFR 1620.14 - Testing equality of jobs.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 29 Labor 4 2014-07-01 2014-07-01 false Testing equality of jobs. 1620.14 Section 1620.14 Labor... Testing equality of jobs. (a) In general. What constitutes equal skill, equal effort, or equal..., or responsibility required for the performance of jobs will not render the equal pay...

  1. 29 CFR 1620.14 - Testing equality of jobs.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 29 Labor 4 2013-07-01 2013-07-01 false Testing equality of jobs. 1620.14 Section 1620.14 Labor... Testing equality of jobs. (a) In general. What constitutes equal skill, equal effort, or equal..., or responsibility required for the performance of jobs will not render the equal pay...

  2. Planetary maps

    USGS Publications Warehouse

    ,

    1992-01-01

    An important goal of the USGS planetary mapping program is to systematically map the geology of the Moon, Mars, Venus, and Mercury, and the satellites of the outer planets. These geologic maps are published in the USGS Miscellaneous Investigations (I) Series. Planetary maps on sale at the USGS include shaded-relief maps, topographic maps, geologic maps, and controlled photomosaics. Controlled photomosaics are assembled from two or more photographs or images using a network of points of known latitude and longitude. The images used for most of these planetary maps are electronic images, obtained from orbiting television cameras, various optical-mechanical systems. Photographic film was only used to map Earth's Moon.

  3. The MAPK cascade in equally cleaving spiralian embryos.

    PubMed

    Lambert, J David; Nagy, Lisa M

    2003-11-15

    Spiralian development is shared by several protostome phyla and characterized by regularities in early cleavage, fate map, and larva. Experimental evidence from multiple spiralian species implicates cells in the D quadrant lineage as the organizer of future axial development of the embryo. However, the mechanisms by which the D quadrant is specified differ between species with equal and unequal spiral cleavage. Equally cleaving mollusc embryos establish the D quadrant via cell-cell interactions between the micromeres and macromeres at the 24- to 36-cell stage. In unequally cleaving embryos, the D quadrant is established at the 4-cell stage via asymmetries in the first 2 cell divisions. We have begun to explore the molecular mechanisms of D quadrant patterning in spiralians. Previously, we showed that, in the unequally cleaving embryo of the mollusc Ilyanassa obsoleta, the MAPK pathway is activated and functionally required in 3D and also in the micromeres known to require a signal from 3D. Here, we examine the role of MAPK signaling in 4 spiralians with equal cleavage. In 3 equally cleaving molluscs, the chiton Chaetopleura, the limpet Tectura, and the snail Lymnaea, the MAPK pathway is activated in the 3D cell but not in the overlying micromeres. In the equally cleaving embryo of the polychaete annelid Hydroides, MAPK activation was not detected in the 3D macromere but was observed in one of its daughter cells, 4d. In addition, inhibiting Tectura MAPK activation disrupts differentiation of 3D and cells induced by it, supporting a functional role for MAPK in axis specification in equally cleaving spiralians. Thus, MAPK signaling may have a conserved role in the D quadrant organizer cell 3D in molluscs. However, there have been at least 2 evolutionary changes in the activation of the MAPK pathway during spiralian evolution. MAPK function in the Ilyanassa micromeres is a recent cooption and, since the divergence of annelids and molluscs, there has been a shift in

  4. Early science from the Pan-STARRS1 Optical Galaxy Survey (POGS): Maps of stellar mass and star formation rate surface density obtained from distributed-computing pixel-SED fitting

    NASA Astrophysics Data System (ADS)

    Thilker, David A.; Vinsen, K.; Galaxy Properties Key Project, PS1

    2014-01-01

    To measure resolved galactic physical properties unbiased by the mask of recent star formation and dust features, we are conducting a citizen-scientist enabled nearby galaxy survey based on the unprecedented optical (g,r,i,z,y) imaging from Pan-STARRS1 (PS1). The PS1 Optical Galaxy Survey (POGS) covers 3π steradians (75% of the sky), about twice the footprint of SDSS. Whenever possible we also incorporate ancillary multi-wavelength image data from the ultraviolet (GALEX) and infrared (WISE, Spitzer) spectral regimes. For each cataloged nearby galaxy with a reliable redshift estimate of z < 0.05 - 0.1 (dependent on donated CPU power), publicly-distributed computing is being harnessed to enable pixel-by-pixel spectral energy distribution (SED) fitting, which in turn provides maps of key physical parameters such as the local stellar mass surface density, crude star formation history, and dust attenuation. With pixel SED fitting output we will then constrain parametric models of galaxy structure in a more meaningful way than ordinarily achieved. In particular, we will fit multi-component (e.g. bulge, bar, disk) galaxy models directly to the distribution of stellar mass rather than surface brightness in a single band, which is often locally biased. We will also compute non-parametric measures of morphology such as concentration, asymmetry using the POGS stellar mass and SFR surface density images. We anticipate studying how galactic substructures evolve by comparing our results with simulations and against more distant imaging surveys, some of which which will also be processed in the POGS pipeline. The reliance of our survey on citizen-scientist volunteers provides a world-wide opportunity for education. We developed an interactive interface which highlights the science being produced by each volunteer’s own CPU cycles. The POGS project has already proven popular amongst the public, attracting about 5000 volunteers with nearly 12,000 participating computers, and is

  5. Map accuracy

    USGS Publications Warehouse

    ,

    1981-01-01

    An inaccurate map is not a reliable map. "X" may mark the spot where the treasure is buried, but unless the seeker can locate "X" in relation to known landmarks or positions, the map is not very useful.

  6. Martian drainage densities

    USGS Publications Warehouse

    Carr, M.H.; Chuang, F.C.

    1997-01-01

    Drainage densities on Mars range from zero over large areas of volcanic plains to 0.3-0.5 km-1 locally on some volcanoes. These values refer to geologic units, not to drainage basins, as is normal for terrestrial drainage densities. The highest values are close to the lowest terrestrial values derived by similar techniques. Drainage densities were determined for every geologic unit portrayed on the 1:15,000,000 geologic map of Mars. Except for volcanoes the geologic unit with the highest drainage density is the dissected Noachian plains with a drainage density of 0.0074 km-1. The average drainage density for Noachian units is 0.0032 km-1, for Hesperian units is 0.00047 km-1, and for Amazonian units is 0.00007 km-1, excluding the volcanoes. These values are 2-3 orders of magnitude lower than typical terrestrial densities as determined by similar techniques from Landsat images. The low drainage densities, despite a cumulative record that spans billions of years, indicate that compared with the Earth, the channel-forming processes have been very inefficient or have operated only rarely or that the surface is extremely permeable. The high drainage density on volcanoes is attributed to a local cause, such as hydrothermal activity, rather than to a global cause such as climate change. Copyright. Published in 1997 by the American Geophysical Union.

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  8. All Are Equal, but Some Are More Equal than Others: Managerialism and Gender Equality in Higher Education in Comparative Perspective

    ERIC Educational Resources Information Center

    Teelken, Christine; Deem, Rosemary

    2013-01-01

    The main purpose of this paper is to investigate what impact new regimes of management and governance, including new managerialism, have had on perceptions of gender equality at universities in three Western European countries. While in accordance with national laws and EU directives, contemporary current management approaches in universities…

  9. Irreversible quantum baker map.

    PubMed

    Łoziński, Artur; Pakoński, Prot; Zyczkowski, Karol

    2002-12-01

    We propose a generalization of the model of classical baker map on the torus, in which the images of two parts of the phase space do overlap. This transformation is irreversible and cannot be quantized by means of a unitary Floquet operator. A corresponding quantum system is constructed as a completely positive map acting in the space of density matrices. We investigate spectral properties of this superoperator and their link with the increase of the entropy of initially pure states.

  10. Equal Opportunity and Racial Differences in IQ.

    ERIC Educational Resources Information Center

    Fagan, Joseph F.; Holland, Cynthia R.

    2002-01-01

    Administered an intelligence test to blacks and whites in 2 studies involving 254 community college students and 2 more studies involving 115 community college students. Results show that differences in knowledge between blacks and whites for items on an intelligence test, the meanings of words, can be eliminated when equal opportunities for…

  11. Gender Equality Policies and Higher Education Careers

    ERIC Educational Resources Information Center

    Berggren, Caroline

    2011-01-01

    Gender equality policies regulate the Swedish labour market, including higher education. This study analyses and discusses the career development of postgraduate students in the light of labour market influences. The principle of gender separation is used to understand these effects. Swedish register data encompassing information on 585…

  12. Gender Equality in Academia: A Critical Reflection

    ERIC Educational Resources Information Center

    Winchester, Hilary P. M.; Browning, Lynette

    2015-01-01

    Gender equality in academia has been monitored in Australia for the past three decades so it is timely to reflect on what progress has been made, what works, and what challenges remain. When data were first published on the gender composition of staff in Australian universities in the mid-1980s women comprised 20 per cent of academic staff and…

  13. 75 FR 53559 - Women's Equality Day, 2010

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-31

    ... ladies'' in the ``new code of laws'' of our fledgling country. It has taken the collective efforts of... Constitution. Standing on the shoulders of these trailblazers, we pay tribute to the brave women who dot the... remains committed to advancing women's equality in all areas of our society and around the world. I...

  14. Racial Equality. To Protect These Rights Series.

    ERIC Educational Resources Information Center

    McDonald, Laughlin

    A historical review of racial discrimination against Negroes is the scope of this volume, part of a series of six volumes which explore the basic American rights. These include due process of law, freedom of speech and religious freedom. This volume traces the development of racial equality in the legal system, explores the controversies and…

  15. 45 CFR 98.43 - Equal access.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION CHILD CARE AND DEVELOPMENT FUND Program Operations (Child Care Services)-Lead Agency and Provider Requirements § 98.43 Equal access. (a) The Lead Agency shall certify that the payment rates for the provision of child care services under this part...

  16. 45 CFR 98.43 - Equal access.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION CHILD CARE AND DEVELOPMENT FUND Program Operations (Child Care Services)-Lead Agency and Provider Requirements § 98.43 Equal access. (a) The Lead Agency shall certify that the payment rates for the provision of child care services under this part...

  17. 45 CFR 98.43 - Equal access.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... Department of Health and Human Services GENERAL ADMINISTRATION CHILD CARE AND DEVELOPMENT FUND Program Operations (Child Care Services)-Lead Agency and Provider Requirements § 98.43 Equal access. (a) The Lead Agency shall certify that the payment rates for the provision of child care services under this part...

  18. 45 CFR 98.43 - Equal access.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION CHILD CARE AND DEVELOPMENT FUND Program Operations (Child Care Services)-Lead Agency and Provider Requirements § 98.43 Equal access. (a) The Lead Agency shall certify that the payment rates for the provision of child care services under this part...

  19. 45 CFR 98.43 - Equal access.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION CHILD CARE AND DEVELOPMENT FUND Program Operations (Child Care Services)-Lead Agency and Provider Requirements § 98.43 Equal access. (a) The Lead Agency shall certify that the payment rates for the provision of child care services under this part...

  20. Equality by Default: Women in Dual Roles

    ERIC Educational Resources Information Center

    Campbell, Ena

    1978-01-01

    The struggle for an Equal Rights Amendment (ERA) to the American Constitution is one of the most controversial issues of this era. Discusses the changing role of women amidst a fast-changing society, the styles of those opposing the women's revolution, the debate over women as persons, women in dual roles, and the implications of ERA for the world…