Science.gov

Sample records for density equalizing maps

  1. Density Equalizing Map Projections

    SciTech Connect

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

    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 disease can be readily identified, and their statistical significance determined, on a density equalized map.

  2. Density Equalizing Map Projections

    Energy Science and Technology Software Center (ESTSC)

    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

  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: 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.

  5. 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.

  6. 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

  7. 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

  8. 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

  9. 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. PMID:26208117

  10. 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

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

    PubMed

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

    2015-11-01

    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

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

    PubMed Central

    2013-01-01

    Background A number of scientific papers on yellow fever have been published but no broad scientometric analysis on the published research of yellow fever has been reported. The aim of the article based study was to provide an in-depth evaluation of the yellow fever field using large-scale data analysis and employment of bibliometric indicators of production and quantity. Methods Data were retrieved from the Web of Science database (WoS) and analyzed as part of the NewQis platform. Then data were extracted from each file, transferred to databases and visualized as diagrams. Partially by means of density-equalizing mapping makes the findings clear and emphasizes the output of the analysis. Results In the study period from 1900 to 2012 a total of 5,053 yellow fever-associated items were published by 79 countries. The United States (USA) having the highest publication rate at 42% (n = 751) followed by far from Brazil (n = 203), France (n = 149) and the United Kingdom (n = 113). The most productive journals are the “Public Health Reports”, the “American Journal of Tropical Medicine and Hygiene” and the “Journal of Virology”. The gender analysis showed an overall steady increase of female authorship from 1950 to 2011. Brazil is the only country of the five most productive countries with a higher proportion of female scientists. Conclusions The present data shows an increase in research productivity over the entire study period, in particular an increase of female scientists. Brazil shows a majority of female authors, a fact that is confirmed by other studies. PMID:24245856

  13. 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.

    1995-04-01

    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. The density equalized map portrays both individual cases and rates, and can be understood by untrained observers. Simple statistical techniques can be used to test the uniformity of the transformed map. This report describes application of the DEMP technique to a sizeable `real-world` data set: 401 childhood cancer cases occurring between 1980 and 1988 in four California counties. In an earlier analysis of the same data, the California Department of Health Services (DHS) calculated rates for 101 communities and found no significant geographic variability. The DDS 1980--88 population estimates are no longer available, so in this analysis 1980 Census data were used; geographic units were 262 census tracts. A k`th nearest neighbor analysis, corrected for boundary effects and for within-tract variability, provides strong evidence for geographic nonuniformity in tract rates ({rho} < l0{sup {minus}4}). No such effect is observed for artificial cases generated under the assumption of constant rates. Pending reanalysis with 1980-88 population estimates, no epidemiologic conclusions can be drawn at this time.

  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. Use of Density Equalizing Map Projections (DEMP) in the analysis of childhood cancer in four California counties. Revision 2

    SciTech Connect

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

    1995-10-01

    In studying geographic disease distributions, one normally compares rates among 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. The present report describes the application of the DEMP technique to 401 childhood cancer cases occurring between 1980 and 1988 in four California counties, with the use of map files and population data for the 262 tracts of the 1980 Census. A k`th nearest neighbor analysis provides strong evidence for geographic non-uniformity in tract rates (p < 10{sup {minus}4}). No such effect is observed for artificial cases generated under the assumption of constant rates. Work is in progress to repeat the analysis with improved population estimates derived from both 1980 and 1990 Census data. Final epidemiologic conclusions will be reported when that analysis is complete.

  16. A bibliometric analysis of bipolar affective disorders using density-equalizing mapping and output benchmarking

    PubMed Central

    Vogelzang, B. H.; Scutaru, C.; Mache, S.; Vitzthum, K.; Kusma, B.; Schulte-Herbrüggen, O; Groneberg, D. A.; Quarcoo, D.

    2012-01-01

    Background: Bipolar affective disorder (BaD) has a great impact on health systems worldwide. Although bibliometric studies have been done on this subject, these studies did not do an analysis of the contents of papers, the cooperation between countries, or of the names currently used to describe the condition. Furthermore, the number of publications since the last bibliometric study has doubled. Aim: This study was to examine the recent developments in the field, explore main topics/subject areas of the top 10 authors in this research field, and to compare diagnosis-defined data between International Classification of Diseases, 10th edition (ICD-10) and Diagnostic and Statistical Manual of Mental Disorders, fourth edition (DSM-IV). Materials and Methods: Using distinct search terms, the Web of Science database developed by the Thompson Reuters Institute of Scientific Information was scanned for relevant items published between 1900 and 2008. Results were analyzed using scientometric methods and density-equalizing calculations. Results: We found an important increase of publications on the subject over the last decade. Most published studies came from North America and Europe, while the countries cooperating with each other were comparable to other areas of medical research. Although there has been an increase in publications on BaD (m=3.3 publications per year in the last decade), the number of works using the term bipolar disorder (BD) was considerably higher (m=141.8 publications per year in the last decade). We found that the subject areas, genetics and pharmacology were focuses of research for the 10 most prolific authors, all of whom where psychiatrists. Conclusion: Research interest in BaD is rising. Reflecting the two main disease classification systems, DSM and ICD, both terms BD and BaD are used in research, with a preponderance of the former. The research of the most prolific authors engages genetic and pharmacological questions. PMID:23372233

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed Central

    2011-01-01

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

  19. 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.

  20. 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.

  1. 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.

  2. Biometric recognition via fixation density maps

    NASA Astrophysics Data System (ADS)

    Rigas, Ioannis; Komogortsev, Oleg V.

    2014-05-01

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

  3. Nonlinear Algorithms for Channel Equalization and Map Symbol Detection.

    NASA Astrophysics Data System (ADS)

    Giridhar, K.

    The transfer of information through a communication medium invariably results in various kinds of distortion to the transmitted signal. In this dissertation, a feed -forward neural network-based equalizer, and a family of maximum a posteriori (MAP) symbol detectors are proposed for signal recovery in the presence of intersymbol interference (ISI) and additive white Gaussian noise. The proposed neural network-based equalizer employs a novel bit-mapping strategy to handle multilevel data signals in an equivalent bipolar representation. It uses a training procedure to learn the channel characteristics, and at the end of training, the multilevel symbols are recovered from the corresponding inverse bit-mapping. When the channel characteristics are unknown and no training sequences are available, blind estimation of the channel (or its inverse) and simultaneous data recovery is required. Convergence properties of several existing Bussgang-type blind equalization algorithms are studied through computer simulations, and a unique gain independent approach is used to obtain a fair comparison of their rates of convergence. Although simple to implement, the slow convergence of these Bussgang-type blind equalizers make them unsuitable for many high data-rate applications. Rapidly converging blind algorithms based on the principle of MAP symbol-by -symbol detection are proposed, which adaptively estimate the channel impulse response (CIR) and simultaneously decode the received data sequence. Assuming a linear and Gaussian measurement model, the near-optimal blind MAP symbol detector (MAPSD) consists of a parallel bank of conditional Kalman channel estimators, where the conditioning is done on each possible data subsequence that can convolve with the CIR. This algorithm is also extended to the recovery of convolutionally encoded waveforms in the presence of ISI. Since the complexity of the MAPSD algorithm increases exponentially with the length of the assumed CIR, a suboptimal

  4. 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…

  5. 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.

  6. 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

  7. Wavelet analysis of electron-density maps.

    PubMed

    Main, P; Wilson, J

    2000-05-01

    The wavelet transform is a powerful technique in signal processing and image analysis and it is shown here that wavelet analysis of low-resolution electron-density maps has the potential to increase their resolution. Like Fourier analysis, wavelet analysis expresses the image (electron density) in terms of a set of orthogonal functions. In the case of the Fourier transform, these functions are sines and cosines and each one contributes to the whole of the image. In contrast, the wavelet functions (simply called wavelets) can be quite localized and may only contribute to a small part of the image. This gives control over the amount of detail added to the map as the resolution increases. The mathematical details are outlined and an algorithm which achieves a resolution increase from 10 to 7 A using a knowledge of the wavelet-coefficient histograms, electron-density histogram and the observed structure amplitudes is described. These histograms are calculated from the electron density of known structures, but it seems likely that the histograms can be predicted, just as electron-density histograms are at high resolution. The results show that the wavelet coefficients contain the information necessary to increase the resolution of electron-density maps. PMID:10771431

  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. 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.

  10. 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.

  11. High density transcriptional mapping of chromosome 21 by hybridization selection

    SciTech Connect

    Tassone, F.; Wade, H.; Gardiner, K.

    1994-09-01

    A transcriptional map of human chromosome 21 is important for the study of Down syndrome, development processes and genome organization. To construct a high density transcriptional map, the technique of cDNA hybrid selection is being applied to a minimal tiling path of YAC clones that span 21q. The cDNA used for selection represents a complex pool of sequences obtained from a variety of fetal and adult tissues and cell lines. Approximately 70-80 YAC clones are sufficient to span 21q; each is individually processed through the selection procedure to obtain a YAC-specific {open_quotes}selected cDNA library{close_quotes}. Survey analysis of each library includes determination of levels of ribosomal contamination, verification of enrichment of control genes, identification of a preliminary number of novel unique sequences, and verification that novel sequences map to the correct YAC and chromosomal regions. This analysis has been completed for 19 YACs that together comprise approximately 10 Mb of non-overlapping DNA, 25% of the long arm. Ribosomal cDNA contamination is low (<10%) and all known genes of appropriate tissue specificity of expression have been recovered, as well as new genes from each YAC. Libraries of expression have been recovered, as well as new genes from each YAC. Libraries from 8 of these YACs are now being subjected to exhaustive analysis to identify all novel genes contained within them and to obtain complete cDNAs and expression analysis for each. Not all regions of the chromosome, however, are equally amenable to these analyses. Selected cDNA libraries from the centromeric YACs are yielding apparently novel genes, but confirmation of map position is problematic. Also of interest is a region of several megabases within the Giemsa dark band, 21q21. Selected cDNA libraries from these YACs so far have yielded no novel genes and support the idea of a genuinely very gene-poor region.

  12. The Geometry of Density States, Positive Maps and Tomograms

    NASA Astrophysics Data System (ADS)

    Man'ko, V. I.; Marmo, G.; Sudarshan, E. C. G.; Zaccaria, F.

    The positive and not completely positive maps of density matrices, which are contractive maps, are discussed as elements of a semigroup. A new kind of positive map (the purification map), which is nonlinear map, is introduced. The density matrices are considered as vectors, linear maps among matrices are represented by superoperators given in the form of higher dimensional matrices. Probability representation of spin states (spin tomography) is reviewed and U(N)-tomogram of spin states is presented. Properties of the tomograms as probability distribution functions are studied. Notion of tomographic purity of spin states is introduced. Entanglement and separability of density matrices are expressed in terms of properties of the tomographic joint probability distributions of random spin projections which depend also on unitary group parameters. A new positivity criterion for hermitian matrices is formulated. An entanglement criterion is given in terms of a function depending on unitary group paramete rs and semigroup of positive map parameters. The function is constructed as sum of moduli of U(N)- tomographic symbols of the hermitian matrix obtained after action on the density matrix of composite system by a positive but not completely positive map of the subsystem density matrix. Some two-qubit and two-qutritt states are considered as examples of entangled states. The connection with the star-product quantisation is discussed. The structure of the set of density matrices and their relation to unitary group and Lie algebra of the unitary group are studied. Nonlinear quantum evolution of state vector obtained by means of applying purification rule of density matrices evolving via dynamical maps is considered. Some connection of positive maps and entanglement with random matrices is discussed and used.

  13. 2007 TY430: An Ultra-Red, High Albedo, Low Density, Wide, Equal Sized Plutino Binary

    NASA Astrophysics Data System (ADS)

    Sheppard, S. S.; Ragozzine, D.; Trujillo, C.

    2011-10-01

    Kuiper Belt object 2007 TY430 is the first equal sized binary known in the 3:2 mean motion resonance with Neptune. The two components can have a separation of over 1 arcsecond and are on average less than 0.1 magnitudes different in apparent magnitude with identical ultra-red colors (g - i =1.49 ± 0.01) . Using nearly monthly observations of 2007 TY430 from 2007-2011 with the Gemini telescope, the orbit of the mutual components were found to have a period of 961.2 ± 4.6 days with a semimajor axis of 21000 ±160 km and eccentricity of 0.1529 ± 0.0028 . The inclination with respect to the ecliptic is 15.68 ± 0.22 degrees, where the extensive observations have allowed the mirror orbit to be eliminated as a possibility. A total mass for the binary system was found to be 7.90 ± 0.21×1017 kg. Equal sized, wide binaries and ultra-red colors are common in the low inclination ``cold'' classical part of the Kuiper Belt and likely formed through some sort of three body interactions within a much denser Kuiper Belt. The physical and binary orbital properties of 2007 TY430 indicate it had a formation history similar to the cold classical population. Numerical simulations suggest 2007 TY430 is moderately unstable in the outer part of the 3:2 resonance and thus 2007 TY430 is likely an escaped ``cold'' classical object that got ``stuck'' into the 3:2 resonance. Similar to the equal sized, wide binaries in the cold classical population, the binary 2007 TY430 requires a high albedo and very low density structure to obtain the total mass found for the pair. For a realistic minimum density of 0.5 g/cm3 the albedo of 2007 TY430 would be greater than 0.17. For reasonable densities, the radii of either component should be less than 60 km, and thus the relatively low eccentricity of the binary is interesting since no tides should be operating on the bodies at their large distances from each other. The low prograde inclination of the binary also makes it unlikely the Kozai mechanism

  14. 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.

  15. 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.

  16. Mapping neutral, ion, and electron number densities within laser-ablated plasma plumes

    NASA Astrophysics Data System (ADS)

    Weaver, I.; Doyle, Liam A.; Martin, G. W.; Riley, Dave; Lamb, M. J.; Graham, William G.; Morrow, Tom; Lewis, Ciaran L. S.

    1998-05-01

    Spatially and temporally varying neutral, ion and electron number densities have been mapped out within laser ablated plasma plumes expanding into vacuum. Ablation of a magnesium target was performed using a KrF laser, 30 ns pulse duration and 248 nm wavelength. During the initial stage of plasma expansion (t densities, for laser power densities on target in the range 1.3 - 3.0 X 108 W/cm2. Later in the plasma expansion (t equals 1 microsecond(s) ) simultaneous absorption and laser induced fluorescence spectroscopy has been used to determine 3D neutral and ion number densities, for a power density equal to 6.7 X 107 W/cm2. Two distinct regions within the plume were identified. One is a fast component (approximately 106 cm-1) consisting of ions and neutrals with maximum number densities observed to be approximately 30 and 4 X 1012 cm-3 respectively, and the second consists of slow moving neutral material at a number density of up to 1015 cm-3. Additionally a Langmuir probe has been used to obtain ion and electron number densities at very late times in the plasma expansion (1 microsecond(s) density on target equal to 6 X 108 W/cm2. Two regions within the plume with different velocities were observed. Within a fast component (approximately 3 X 106 cms-1) electron and ion number densities of the order 5 X 1012 cm-3 were observed and within the second slower component (approximately 106 cms-1) electron and ion number densities of the order 1 - 2 X 1013 cm-3 were determined.

  17. 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

  18. 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

  19. Relative surface charge density mapping with the atomic force microscope.

    PubMed Central

    Heinz, W F; Hoh, J H

    1999-01-01

    An experimental approach for producing relative charge density maps of biological surfaces using the atomic force microscope is presented. This approach, called D minus D (D-D) mapping, uses isoforce surfaces collected at different salt concentrations to remove topography and isolate electrostatic contributions to the tip-sample interaction force. This approach is quantitative for surface potentials below 25 mV, and does not require prior knowledge of the cantilever spring constant, tip radius, or tip charge. In addition, D-D mapping does not require tip-sample contact. The performance of D-D mapping is demonstrated on surfaces of constant charge and varying topography (mechanically roughened mica and stacked bilayers of dipalmitolphosphatidylserine), a surface of varying charge and varying topography (patches of dipalmitolphosphatidylcholine on mica), and bacteriorhopsin membranes adsorbed to mica. PMID:9876166

  20. Characterizing uncertainty in high-density maps from multiparental populations.

    PubMed

    Ahfock, Daniel; Wood, Ian; Stephen, Stuart; Cavanagh, Colin R; Huang, B Emma

    2014-09-01

    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

  1. 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

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Statistical quality indicators for electron-density maps

    PubMed Central

    Tickle, Ian J.

    2012-01-01

    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 χ2 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. PMID:22505266

  9. 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.

  10. 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.

  11. 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

  12. Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map.

    PubMed

    Wicks, S R; Yeh, R T; Gish, W R; Waterston, R H; Plasterk, R H

    2001-06-01

    Single nucleotide polymorphisms (SNPs) are valuable genetic markers of human disease. They also comprise the highest potential density marker set available for mapping experimentally derived mutations in model organisms such as Caenorhabditis elegans. To facilitate the positional cloning of mutations we have identified polymorphisms in CB4856, an isolate from a Hawaiian island that shows a uniformly high density of polymorphisms compared with the reference Bristol N2 strain. Based on 5.4 Mbp of aligned sequences, we predicted 6,222 polymorphisms. Furthermore, 3,457 of these markers modify restriction enzyme recognition sites ('snip-SNPs') and are therefore easily detected as RFLPs. Of these, 493 were experimentally confirmed by restriction digest to produce a snip-SNP map of the worm genome. A mapping strategy using snip-SNPs and bulked segregant analysis (BSA) is outlined. CB4856 is crossed into a mutant strain, and exclusion of CB4856 alleles of a subset of snip-SNPs in mutant progeny is assessed with BSA. The proximity of a linked marker to the mutation is estimated by the relative proportion of each form of the biallelic marker in populations of wildtype and mutant genomes. The usefulness of this approach is illustrated by the rapid mapping of the dyf-5 gene. PMID:11381264

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

    SciTech Connect

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

    1995-07-01

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

  14. Ionospheric mapping functions based on electron density fields

    NASA Astrophysics Data System (ADS)

    Zus, Florian; Deng, Zhiguo; Heise, Stefan; Wickert, Jens

    2016-04-01

    We developed an ionospheric Mapping Function (MF) for the Global Navigation Satellite System (GNSS) which is based on the electron density field of the International Reference Ionosphere (IRI). The station specific MF utilizes a look-up table which contains a set of ray-traced ionospheric delays. Hence, unlike the simple MFs that are currently in use, the developed MF depends on the time, location, elevation and azimuth angle. Ray-bending is taken into account, which implies that the MF depends on the carrier frequency as well. This frequency dependency of the MF can be readily used to examine higher-order ionospheric effects due to ray-bending. We compare the proposed MF with the so-called single layer model MF and find significant differences in particular around the equatorial anomaly. In so-far as the proposed MF is based on a realistic electron density field (IRI) our comparison shows the potential error of the single-layer model MF in practice. We conclude that the developed MF concept might be valuable in the GNSS Total Electron Content estimation. The frequency dependency of the MF can be used to mitigate higher-order ionospheric effects.

  15. 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.

  16. 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

  17. 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

  18. 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.

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

    PubMed

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

    2016-04-01

    Most agricultural traits are controlled by quantitative trait loci (QTLs); however, there are few studies on QTL mapping of horticultural traits in pepper (Capsicumspp.) 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 betweenC. annuum'Perennial' andC. 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

  20. A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An ultra-dense consensus (UDC) genetic map of tetraploid cotton was constructed using six high-density component 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 cut...

  1. Galaxy bias from the DES 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.

    2016-04-01

    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 data. This method was first developed in Amara et al. (2012) and later re-examined in a companion paper (Pujol et al. 2016) 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 4 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 dataset using galaxy clustering and cross-correlation of galaxies with CMB 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 catalogs by including shape noise, photo-z errors and masking effects. We show that our bias measurement from the data is consistent with that expected from simulations. With the forthcoming full DES data set, we expect this method to provide additional constraints on the galaxy bias measurement from more traditional methods. Furthermore, in the process of our measurement, we build up a 3D mass map that allows further exploration of the dark matter distribution and its relation to galaxy evolution.

  2. 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.

  3. Can the current density map topology be extracted from the nucleus independent chemical shifts?

    PubMed

    Van Damme, Sofie; Acke, Guillaume; Havenith, Remco W A; Bultinck, Patrick

    2016-04-28

    Aromatic compounds are characterised by the presence of a ring current when in a magnetic field. As a consequence, current density maps are used to assess (the degree of) aromaticity of a compound. However, often a more discrete set of so-called Nucleus Independent Chemical Shift (NICS) values is used that is derived from the current density. It is shown here that there is no simple one-to-one relationship that allows reconstructing current density maps from only NICS-values. NICS values should therefore not be used as aromaticity indices without analysis of the ab initio computed current density map. PMID:26762574

  4. 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

  5. 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

    2015-01-01

    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. PMID:26439740

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

    PubMed Central

    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

    2015-01-01

    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. PMID:26439740

  7. Construction of a high-density linkage map and fine mapping of QTL for growth in Asian seabass

    PubMed Central

    Wang, Le; Wan, Zi Yi; Bai, Bin; Huang, Shu Qing; Chua, Elaine; Lee, May; Pang, Hong Yan; Wen, Yan Fei; Liu, Peng; Liu, Feng; Sun, Fei; Lin, Grace; Ye, Bao Qing; Yue, Gen Hua

    2015-01-01

    A high-density genetic map is essential for comparative genomic studies and fine mapping of QTL, and can also facilitate genome sequence assembly. Here, a high density genetic map of Asian seabass was constructed with 3321 SNPs generated by sequencing 144 individuals in a F2 family. The length of the map was 1577.67 cM with an average marker interval of 0.52 cM. A high level of genomic synteny among Asian seabass, European seabass, Nile tilapia and stickleback was detected. Using this map, one genome-wide significant and five suggestive QTL for growth traits were detected in six linkage groups (i.e. LG4, LG5, LG11, LG13, LG14 and LG15). These QTL explained 10.5–16.0% of phenotypic variance. A candidate gene, ACOX1 within the significant QTL on LG5 was identified. The gene was differentially expressed between fast- and slow-growing Asian seabass. The high-density SNP-based map provides an important tool for fine mapping QTL in molecular breeding and comparative genome analysis. PMID:26553309

  8. Direct Mapping Of Density Response in Recombinant Inbred Lines of Maize (Zea mays L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Breeding for adaptation to higher densities in maize has greatly increased maize yield potential per unit area but the genetic basis for this plant response to density is unknown as is its stability over environments. To elucidate the genetic basis of plant response to density in Maize, we mapped QT...

  9. Nhs: Network-based Hierarchical Segmentation for Cryo-EM Density Maps

    PubMed Central

    Burger, Virginia; Chennubhotla, Chakra

    2012-01-01

    Electron cryo-microscopy (cryo-EM) experiments yield low-resolution (3–30Å) 3D-density maps of macromolecules. These density maps are segmented to identify structurally distinct proteins, protein domains, and sub-units. Such partitioning aids the inference of protein motions and guides fitting of high-resolution atomistic structures. Cryo-EM density map segmentation has traditionally required tedious and subjective manual partitioning or semi-supervised computational methods, while validation of resulting segmentations has remained an open problem in this field. Our network-based bias-free segmentation method for cryo-EM density map segmentation, Nhs (Network-based hierarchical segmentation), provides the user with a multi-scale partitioning, reflecting local and global clustering, while requiring no user input. This approach models each map as a graph, where map voxels constitute nodes and edges connect neighboring voxels. Nhs initiates Markov diffusion (or random walk) on the weighted graph. As Markov probabilities homogenize through diffusion, an intrinsic segmentation emerges. We validate the segmentations with ground-truth maps based on atomistic models. When implemented on density maps in the 2010 Cryo-EM Modeling Challenge, Nhs efficiently and objectively partitions macromolecules into structurally and functionally relevant sub-regions at multiple scales. PMID:22696408

  10. 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

  11. VizieR Online Data Catalog: Column density maps in 4 IRDCs (Schneider+, 2015)

    NASA Astrophysics Data System (ADS)

    Schneider, N.; Csengeri, T.; Klessen, R. S.; Tremblin, P.; Ossenkopf, V.; Peretto, N.; Simon, R.; Bontemps, S.; Fedrrath, C.

    2015-04-01

    Dust column density maps obtained from Herschel observations at 160, 250, 350, and 500 micron by a pixel-to-pixel SED fit. The unit is cm^-2 (regardless what is written in the header). (2 data files).

  12. Strategies to build high-density linkage maps of the porcine 60k SNP chip

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We present here two different strategies to compute high-density linkage maps based on the porcine 60k SNP chip that was genotyped on 4 different pedigrees with a total of 5600 animals. The first strategy uses the draft sequence as a reference order, the SNP being first mapped to it. The second stra...

  13. 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...

  14. Spherical-Harmonic Decomposition for Molecular Recognition in Electron-Density Maps

    PubMed Central

    DiMaio, Frank P.; Soni, Ameet B.; Phillips, George N.; Shavlik, Jude W.

    2008-01-01

    An important problem in high-throughput protein crystallography is constructing a protein model from an electron-density map. DiMaio et al. (2006) describe an automated approach to this otherwise time-consuming process. One important step involves searching the density map for many small protein fragments, or templates. The previous approach uses Fourier convolution to quickly compare some rotation of the template to the entire density map. We propose to instead use the spherical-harmonic decomposition of the template and of some region in the density map. In this new framework, we are able to eliminate areas of the map from the search process if they are unlikely to match to any templates. We design several “first-pass filters” for this elimination task, including one filter which uses a set of rotation-invariant descriptors (derived from the spherical-harmonic decomposition) of a sphere of density to train an accurate classifier. We show our new template-matching method improves accuracy and reduces running time, compared to our previous approach. Protein models constructed using this matching also show significant accuracy improvement. We extend our method to produce a structural-homology detection algorithm that, due to its use of electron-density maps, is more sensitive than sequence-only methods. PMID:19517990

  15. A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: The availability of a high-density SNP chip and a reference genome sequence of the pig have enabled the construction of a high-density linkage map. A high density linkage map is an essential tool for the further fine-mapping of QTL for a variety of traits in the pig and for a better und...

  16. 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

  17. Electron densities in momentum and position spaces. II. Application of density mapping to the helium ground state

    SciTech Connect

    Koga, T.; Yamamoto, Y. ); Kryachko, E.S.

    1989-10-15

    The recently proposed method of density mapping between momentum and position spaces is applied to the ground state of the helium atom. The Kellner densities and wave functions are used as reference, and the Eckart densities {gamma}({bold p}) and {rho}({bold r}) are employed as test densities keeping their parent wave functions in blind. From the momentum density {gamma}({bold p}), the corresponding position density {rho}{sub {gamma}}({bold r}) and the position moments {l angle}{ital r}{sup {ital n}}{r angle}{sub {gamma}} ({minus}2{le}{ital n}{le}4) are generated within a few percent error. The inverse procedure generates the momentum density {gamma}{sub {rho}}({bold p}) and the momentum moments {l angle}{ital p}{sup {ital n}}{r angle}{sub {rho}} ({minus}2{le}{ital n}{le}4) from the position density {rho}({bold r}) with a better accuracy. Density-functional calculations are performed in a simplified manner and the energies close to the Hartree--Fock limit value are obtained.

  18. 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.

  19. 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.

  20. YUP.SCX: Coaxing Atomic Models into Medium Resolution Electron Density Maps

    PubMed Central

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

    2008-01-01

    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 33 Å, they divide themselves into nearly rigid fragments along natural boundaries with smooth transitions between the fragments. PMID:18572416

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. Mapping of the O+/H+ density ratio in the magnetospheric equatorial plane using Cluster data

    NASA Astrophysics Data System (ADS)

    Maggiolo, R.; Kistler, L. M.

    2010-12-01

    We use data from the Cluster/CODIF instrument to analyze the O+/H+ density ratio in the magnetosphere. We present a new method that consists in mapping the observed density ratio along the magnetospheric magnetic field lines to produce statistical maps of nO+/nH+ at the magnetospheric equatorial plane. Using Cluster 3 and 4 data from 2001 to 2008 we construct maps for several energy intervals and for various geomagnetic conditions and solar wind activity levels. After a description of the technique and its limitations, we present preliminary results about the statistical spatial distribution of nO+/nH+ in the magnetosphere and its dependency on geomagnetic and solar wind activity. We compare them to previous results based on in-situ measurements inside the plasma sheet in order to assess the reliability of this mapping technique.

  9. Finding non-crystallographic symmetry in density maps of macromolecular structures.

    PubMed

    Terwilliger, Thomas C

    2013-09-01

    The internal symmetry of a macromolecule is both an important aspect of its function and a useful feature in obtaining a structure by X-ray crystallography and other techniques. A method is presented for finding internal symmetry and other non-crystallographic symmetry in a structure based on patterns of density in a density map for that structure. Regions in map that are similar are identified by cutting out a sphere of density from a region that has high local variation and using an FFT-based correlation search to find other regions that match. The relationships among correlated regions are then refined to maximize their correlations and are found to accurately represent non-crystallographic symmetry in the map. PMID:23881095

  10. 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.

  11. 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

  12. 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.

  13. Equal-Channel Angular Extrusion of a Low-Density High-Entropy Alloy Produced by High-Energy Cryogenic Mechanical Alloying

    NASA Astrophysics Data System (ADS)

    Hammond, Vincent H.; Atwater, Mark A.; Darling, Kristopher A.; Nguyen, Hoang Q.; Kecskes, Laszlo J.

    2014-10-01

    In this study, we demonstrate the feasibility of forming a bulk consolidated, low-density high-entropy alloy, namely AlFeMgTiZn, which shows reasonable mechanical properties and high hardness. The fabrication of the high-entropy alloy from powdered precursors via high-energy mechanical alloying as a function of milling time is presented. In turn, the evolution of the alloy microstructure with postmilling anneal treatment is elucidated. Last, the severe plastic deformation processing methodology, i.e., equal-channel angular extrusion, chosen for consolidation, is described and shown to result in a bulk product with good results.

  14. 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.

  15. A High-Density SNP and SSR Consensus Map Reveals Segregation Distortion Regions in Wheat

    PubMed Central

    Li, Chunlian; Bai, Guihua; Chao, Shiaoman; Wang, Zhonghua

    2015-01-01

    Segregation distortion is a widespread phenomenon in plant and animal genomes and significantly affects linkage map construction and identification of quantitative trait loci (QTLs). To study segregation distortion in wheat, a high-density consensus map was constructed using single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers by merging two genetic maps developed from two recombinant-inbred line (RIL) populations, Ning7840 × Clark and Heyne × Lakin. Chromosome regions with obvious segregation distortion were identified in the map. A total of 3541 SNPs and 145 SSRs were mapped, and the map covered 3258.7 cM in genetic distance with an average interval of 0.88 cM. The number of markers that showed distorted segregation was 490 (18.5%) in the Ning7840 × Clark population and 225 (10.4%) in the Heyne × Lakin population. Most of the distorted markers (630) were mapped in the consensus map, which accounted for 17.1% of mapped markers. The majority of the distorted markers clustered in the segregation distortion regions (SDRs) on chromosomes 1B, 2A, 2B, 3A, 3B, 4B, 5A, 5B, 5D, 6B, 7A, and 7D. All of the markers in a given SDR skewed toward one of the parents, suggesting that gametophytic competition during zygote formation was most likely one of the causes for segregation distortion in the populations. PMID:26601111

  16. 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.

  17. Maps of the little bangs through energy density and temperature fluctuations

    NASA Astrophysics Data System (ADS)

    Basu, Sumit; Chatterjee, Rupa; Nandi, Basanta K.; Nayak, Tapan K.

    2016-01-01

    Heavy-ion collisions at ultra-relativistic energies are often referred to as little bangs. We propose for the first time to map the heavy-ion collisions at ultra-relativistic energies, similar to the maps of the cosmic microwave background radiation, using fluctuations of energy density and temperature in small phase space bins. We study the evolution of fluctuations at each stage of the collision using an event-by-event hydrodynamic framework. We demonstrate the feasibility of making fluctuation maps from experimental data and its usefulness in extracting considerable information regarding the early stages of the collision and its evolution.

  18. 1.0 Mm Maps and Radial Density Distributions of Southern Hii/molecular Cloud Complexes

    NASA Technical Reports Server (NTRS)

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

    1980-01-01

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

  19. CHARACTERIZATION AND PHYSICAL MAPPING OF MAIZE BAC LIBRARIES USING HIGH DENSITY BAC FILTER HYBRIDIZATION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A HindIII and an EcoRI maize BAC library have been constructed from maize inbred line B73. Use of both libraries to make a physical map should minimize the under representation of certain genomic regions caused by the use of a particular restriction enzyme. High-density filter sets from the two libr...

  20. High Density Brassica Oleracea Linkage Map: Identification of Useful New Linkages

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We constructed a 1257-marker, high-density genetic map of Brassica oleracea spanning 703cM in nine linkage groups, named LG1-LG9. It was developed in a F2 segregating population of 143 individuals obtained by crossing two double-haploid plants of broccoli Early-Big and cauliflower An-Nan Early. The...

  1. 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

  2. A guide to the porcine anatomy for the interventional electrophysiologist. Fluoroscopy and high density electroanatomical mapping.

    PubMed

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

    2015-02-01

    Invasive electrophysiology is a rapidly developing field of cardiovascular science with a constant need for inventions and testing of new technologies and concepts. Despite the swine model being an established tool in biomedical research no comprehensive guide for interventional electrophysiologists exists. The aim of the current article is to provide a practical overview of the pig anatomy, fluoroscopic views, and corresponding high density electroanatomic maps using a novel mapping system and a practical guide for interventions and techniques. In 17 pigs, fluoroscopic images of the right atrium, coronary sinus (CS), left atrium, and pulmonary veins as well as the right and left ventricles were obtained and correlated with ultra-high density electroanatomic maps and gross anatomy. Pitfalls of the porcine anatomy are precisely addressed, and alternative access techniques to overcome those issues are suggested. Important differences to human electrophysiological studies are highlighted. Complementary models such as cardiac ischemia induction or renal and pulmonary artery denervation are discussed in detail. PMID:25630688

  3. Interpretation of very low resolution X-ray electron-density maps using core objects

    SciTech Connect

    Heuser, Philipp Langer, Gerrit G.; Lamzin, Victor S.

    2009-07-01

    The interpretation of a 20 Å resolution electron-density map using segmentation and pattern-recognition-based identification of domain shapes is described. A novel approach to obtaining structural information from macromolecular X-ray data extending to resolutions as low as 20 Å is presented. Following a simple map-segmentation procedure, the approximate shapes of the domains forming the structure are identified. A pattern-recognition comparative analysis of these shapes and those derived from the structures of domains from the PDB results in candidate structural models that can be used for a fit into the density map. It is shown that the placed candidate models can be employed for subsequent phase extension to higher resolution.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. Osteoarthritis classification using self organizing map based on gabor kernel and contrast-limited adaptive histogram equalization.

    PubMed

    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

  10. 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

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

    PubMed Central

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

    2004-01-01

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

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

    PubMed Central

    2012-01-01

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

  13. Not all declarative memories are created equal: Fast Mapping as a direct route to cortical declarative representations.

    PubMed

    Merhav, Maayan; Karni, Avi; Gilboa, Asaf

    2015-08-15

    Memory formation for newly acquired associations typically depends on hippocampal-neocortical interactions. Through the process of system-consolidation, the mnemonic binding role of the hippocampus is subsequently replaced by cortical hubs, such as the ventromedial prefrontal cortex (vmPFC) or the anterior temporal lobe (ATL). Here, using BOLD-fMRI, we compared retrieval of semantic associations acquired through Fast Mapping (FM), an incidental, exclusion-based learning procedure, to retrieval of similar associations that were intentionally acquired through Explicit Encoding (EE). Despite an identical retrieval task, the encoding histories of the retrieved semantic associations (FM vs. EE) induced distinct neural substrates and disparate related neural dynamics in time. Retrieval of associations acquired through EE engaged the expected hippocampal and vmPFC related networks. Furthermore, retrieval intentionally encoded associations gave rise to a typical overnight increase in engagement of the vmPFC and increased vmPFC-hippocampal-neocortical functional connectivity. On the other hand, retrieval of associations acquired through FM immediately engaged an ATL related network that typically supports well-established semantic knowledge, a network that did not engage the hippocampus and the vmPFC. Moreover, FM learning was associated with minimal overnight changes in the BOLD responses and in the functional connectivity. Our findings indicate that FM may induce a direct, ATL-mediated acquisition and retention of novel arbitrary associations, bypassing the initial hippocampal-cortical representation phase. A direct, ATL-mediated vocabulary acquisition through FM could support the learning and retention of new associations in young children with presumably an immature hippocampal system, and possibly even in amnesic adults with hippocampal lesions. PMID:25988227

  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 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

  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

    2016-01-01

    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

  18. High-Density Genotypes of Inbred Mouse Strains: Improved Power and Precision of Association Mapping

    PubMed Central

    Rau, Christoph D.; Parks, Brian; Wang, Yibin; Eskin, Eleazar; Simecek, Petr; Churchill, Gary A.; Lusis, Aldons J.

    2015-01-01

    Human genome-wide association studies have identified thousands of loci associated with disease phenotypes. Genome-wide association studies also have become feasible using rodent models and these have some important advantages over human studies, including controlled environment, access to tissues for molecular profiling, reproducible genotypes, and a wide array of techniques for experimental validation. Association mapping with common mouse inbred strains generally requires 100 or more strains to achieve sufficient power and mapping resolution; in contrast, sample sizes for human studies typically are one or more orders of magnitude greater than this. To enable well-powered studies in mice, we have generated high-density genotypes for ∼175 inbred strains of mice using the Mouse Diversity Array. These new data increase marker density by 1.9-fold, have reduced missing data rates, and provide more accurate identification of heterozygous regions compared with previous genotype data. We report the discovery of new loci from previously reported association mapping studies using the new genotype data. The data are freely available for download, and Web-based tools provide easy access for association mapping and viewing of the underlying intensity data for individual loci. PMID:26224782

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-02-01

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

  1. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed

    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 (15)N relaxation rates, introduce significant systematic errors when applied to (13)C 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 (13)C frequencies can be obtained from data acquired at three magnetic fields for uniformly (13)C-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. PMID:27003380

  6. 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.

  7. 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.

  8. 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

  9. A high-density single nucleotide polymorphism map for Neurospora crassa.

    PubMed

    Lambreghts, Randy; Shi, Mi; Belden, William J; Decaprio, David; Park, Danny; Henn, Matthew R; Galagan, James E; Bastürkmen, Meray; Birren, Bruce W; Sachs, Matthew S; Dunlap, Jay C; Loros, Jennifer J

    2009-02-01

    We report the discovery and validation of a set of single nucleotide polymorphisms (SNPs) between the reference Neurospora crassa strain Oak Ridge and the Mauriceville strain (FGSC 2555), of sufficient density to allow fine mapping of most loci. Sequencing of Mauriceville cDNAs and alignment to the completed genomic sequence of the Oak Ridge strain identified 19,087 putative SNPs. Of these, a subset was validated by cleaved amplified polymorphic sequence (CAPS), a simple and robust PCR-based assay that reliably distinguishes between SNP alleles. Experimental confirmation resulted in the development of 250 CAPS markers distributed evenly over the genome. To demonstrate the applicability of this map, we used bulked segregant analysis followed by interval mapping to locate the csp-1 mutation to a narrow region on LGI. Subsequently, we refined mapping resolution to 74 kbp by developing additional markers, resequenced the candidate gene, NCU02713.3, in the mutant background, and phenocopied the mutation by gene replacement in the WT strain. Together, these techniques demonstrate a generally applicable and straightforward approach for the isolation of novel genes from existing mutants. Data on both putative and validated SNPs are deposited in a customized public database at the Broad Institute, which encourages augmentation by community users. PMID:19015548

  10. B1 mapping with a pure phase encode approach: Quantitative density profiling

    NASA Astrophysics Data System (ADS)

    Vashaee, S.; Newling, B.; MacMillan, B.; Balcom, B. J.

    2013-07-01

    In MRI, it is frequently observed that naturally uniform samples do not have uniform image intensities. In many cases this non-uniform image intensity is due to an inhomogeneous B1 field. The ‘principle of reciprocity' states that the received signal is proportional to the local magnitude of the applied B1 field per unit current. Inhomogeneity in the B1 field results in signal intensity variations that limit the ability of MRI to yield quantitative information. In this paper a novel method is described for mapping B1 inhomogeneities based on measurement of the B1 field employing centric-scan pure phase encode MRI measurements. The resultant B1 map may be employed to correct related non-uniformities in MR images. The new method is based on acquiring successive images with systematically incremented low flip angle excitation pulses. The local image intensity variation is proportional to B12, which ensures high sensitivity to B1 field variations. Pure phase encoding ensures the resultant B1 field maps are free from distortions caused by susceptibility variation, chemical shift and paramagnetic impurities. Hence, the method works well in regions of space that are not accessible to other methods such as in the vicinity of conductive metallic structures, such as the RF probe itself. Quantitative density images result when the centric scan pure phase encode measurement is corrected with a relative or absolute B1 field map. The new technique is simple, reliable and robust.

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

    PubMed Central

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

    2015-01-01

    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

  12. Equality Handbook

    ERIC Educational Resources Information Center

    Malzer, Maris; Popovic, Milica; Striedinger, Angelika; Bjorklund, Karin; Olsson, Anna-Clara; Elstad, Linda; Brus, Sanja; Stark, Kat; Stojanovic, Marko; Scholz, Christine

    2009-01-01

    "Tolerance is not enough, discrimination must be fought" is what ESU staff stated in their Seminar on Equality in London, last May. Following their seminar, they decided to provide members with more practical tools to fight discrimination in higher education. This handbook aims at as part of that strategy. Focusing on several issues that are high…

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

    PubMed Central

    2012-01-01

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

  14. 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

  15. 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.

  16. Modeling Current Density Maps Using Aliev-Panfilov Electrophysiological Heart Model.

    PubMed

    Beheshti, M; Foomany, F H; Magtibay, K; Masse, S; Lai, P; Asta, J; Jaffray, D A; Nanthakumar, K; Krishnan, S; Umapathy, K

    2016-09-01

    Most existing studies of cardiac arrhythmia rely on surface measurements through optical or electrical mapping techniques. Current density imaging (CDI) is a method which enables us to study current pathways inside the tissue. However, this method entails implementation complexities for beating ex vivo hearts. Hence, this work presents an approach to simulate and study the current distributions in different cardiac electrophysiological states. The results are corroborated by experimental data, and they indicate that different states were distinguishable. The CDI simulations can be used for studying cardiac arrhythmias under simulation conditions which are otherwise impossible or difficult to be implemented experimentally. PMID:27357301

  17. 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

  18. Zeeman mapping of probability densities in square quantum wells using magnetic probes

    NASA Astrophysics Data System (ADS)

    Prechtl, G.; Heiss, W.; Bonanni, A.; Jantsch, W.; Mackowski, S.; Janik, E.; Karczewski, G.

    2000-06-01

    We use a method to probe experimentally the probability density of carriers confined in semiconductor quantum structures. The exciton Zeeman splitting in quantum wells containing a single, ultranarrow magnetic layer is studied depending on the layer position. In particular, a system consisting of a 1/4 monolayer MnTe embedded at varying positions in nonmagnetic CdTe/CdMgTe quantum wells is investigated. The sp-d exchange interaction results in a drastic increase of the Zeeman splitting, which, because of the strongly localized nature of this interaction, sensitively depends on the position of the MnTe submonolayer in the quantum well. For various interband transitions we show that the dependence of the exciton Zeeman splitting on the position of the magnetic layer directly maps the probability density of free holesin the growth direction.

  19. 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

  20. 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

  1. Functional Nature of Electrogram Fractionation Demonstrated by Left Atrial High Density Mapping

    PubMed Central

    Jadidi, Amir S.; Duncan, Edward; Miyazaki, Shinsuke; Lellouche, Nicolas; Shah, Ashok J.; Forclaz, Andrei; Nault, Isabelle; Wright, Matthew; Rivard, Lena; Liu, Xingpeng; Scherr, Daniel; Wilton, Stephen; Sacher, Frédéric; Derval, Nicolas; Knecht, Sebastien; Kim, Steven J.; Hocini, Mélèze; Narayan, Sanjiv; Haïssaguerre, Michel; Jaïs, Pierre

    2012-01-01

    Background Complex fractionated electrograms (CFAE) are targets of atrial fibrillation (AF) ablation. Serial high density maps were evaluated to understand the impact of activation direction and rate on electrogram (EGM) fractionation. Methods and Results 18 patients (9 persistent) underwent high density, 3D, left atrial mapping (>400 points/map) during AF, Sinus (SR) and CS-paced (CSp) rhythms. In SR and CSp, fractionation was defined as EGM with ≥4 deflections, while in AF CFEmean <80ms was considered as continuous CFAE. The anatomic distribution of CFAE sites was assessed, quantified and correlated between rhythms. Mechanisms underlying fractionation were investigated by analysis of voltage, activation and propagation maps. A minority of continuous CFAE sites displayed EGM fractionation in SR (15+/−4%) and CSp (12+/(12+/−8%). EGM fractionation did not match between SR and CSp at 70+/−10% sites. Activation maps in SR and CSp showed that wave collision (71%) and regional slow conduction (24%) caused EGM fractionation. EGM voltage during AF (0.59+/−0.58mV) was lower than during SR and CSp (>1.0mV) at all sites. During AF, the EGM voltage was higher at continuous CFAE sites than at non-CFAE sites (0.53mV (Q1, Q3: 0.33–0.83) vs. 0.30 mV (Q1, Q3: 0.18–0.515), p<0.00001). Global LA voltage in AF was lower in persistent vs. paroxysmal AF patients (0.6+/−0.59mV vs. 1.12+/−1.32mV, p<0.01). Conclusions The distribution of fractionated EGMs is highly variable, depending on direction and rate of activation (SR vs. CSp vs. AF). Fractionation in sinus and CSp rhythms mostly resulted from wave collision. All sites with continuous fractionation in AF displayed normal voltage in SR suggesting absence of structural scar. Thus, many fractionated EGMs are functional in nature and their sites dynamic. PMID:22215849

  2. 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

  3. 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

  4. 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.

  5. Visualization of cardiac dipole using a current density map: detection of cardiac current undetectable by electrocardiography using magnetocardiography.

    PubMed

    Ikefuji, Hiroyuki; Nomura, Masahiro; Nakaya, Yutaka; Mori, Toshifumi; Kondo, Noriyasu; Ieishi, Kiyoshi; Fujimoto, Sayuri; Ito, Susumu

    2007-02-01

    A close relationship exists between electric current and the magnetic field. However, electricity and magnetism have different physical characteristics, and magnetocardiography (MCG) may provide information on cardiac current that is difficult to obtain by electrocardiography (ECG). In the present study, we investigated the issue of whether the current density map method, in which cardiac current is estimated from the magnetic gradient, facilitates the visualization of cardiac current undetectable by ECG. The subjects were 50 healthy adults (N group), 40 patients with left ventricular overloading (LVO group), 15 patients with right ventricular overloading (RVO group), 10 patients with an old inferior myocardial infarction (OMI group), and 30 patients with diabetes mellitus (DM group). MCGs were recorded with a second derivative superconducting quantum interference device (SQUID) gradiometer using liquid helium. Isopotential maps and current density maps from unipolar precordial ECG leads and MCGs, respectively, were prepared, and the cardiac electric current was examined. The current density map at the ventricular depolarization phase showed one peak of current density in the N group. However, in the OMI group, the current density map showed multiple peaks of current density areas. In the RVO group, two peaks of current densities were detected at the right superior region and left thoracic region and these two diploles appeared to be from the right and left ventricular derived cardiac currents, respectively. Moreover, there was a significant correlation between the magnitude of the current density from the right ventricle and the systolic pulmonary arterial pressure. The current density map at the ventricular repolarization phase in the N group showed only a single current source. However, abnormal current sources in the current density maps were frequently detected even in patients showing no abnormalities on isopotential maps in the LVO, DM, and OMI groups. The

  6. 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. PMID:25775256

  7. High-Density Genetic Linkage Mapping in Turbot (Scophthalmus maximus L.) Based on SNP Markers and Major Sex- and Growth-Related Regions Detection

    PubMed Central

    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. PMID:25775256

  8. R-Z Density Mapping and CFD Simulation of Gas Puff Nozzle Flow

    NASA Astrophysics Data System (ADS)

    McKee, Erik; Valenzuela, Julio; Krasheninnikov, Igor; Frazier, Alister; Covington, Aaron; Beg, Farhat; Darling, Tim; Nevada Terawatt Facility Team; University of San Diego Team

    2015-11-01

    Laser induced fluorescence (LIF) is a technique in which a tracer is added to the gas flow for measurement of its spatial and temporal density profile. The Nd:YAG EKSPLA laser 20mJ/150ps at the fourth harmonic 266nm wavelength is focused down to a <1mm pencil beam to excite the acetone tracer. The use of anr ICCD gating camera is necessary because the 4ns short-lived fluorescence state is an order-of-magnitude dimmer than the 200us long-lived phosphorescence state. Mapping the density profile in time and space requires multiple shots. Once the temporal and spatial density profile is obtained, it can be used and benchmarked for two independent CFD software programs using transient solvers: OpenFOAM and FLUENT. The measurements and simulations serve as the initial conditions for (i) Gas Puff experiments that utilize special nozzle contours to inject the gas load between the electrode gap on pulsed-power machines and (ii) use with future MHD modeling efforts. Support for this work is provided by DOE/NNSA grant DE-NA0002075 and funded by the US Department of Energy, ARPA-E, Control Number 1184-1527.

  9. 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

  10. 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

    2016-01-01

    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. SNP Discovery by GBS in Olive and the Construction of a High-Density Genetic Linkage Map.

    PubMed

    İpek, Ahmet; Yılmaz, Kübra; Sıkıcı, Pelin; Tangu, Nesrin Aktepe; Öz, Ayşe Tülin; Bayraktar, Murat; İpek, Meryem; Gülen, Hatice

    2016-06-01

    Genetic linkage maps are valuable tools for genetic, genomic, and crop breeding studies. Several genetic linkage maps were constructed for the olive (Olea europaea L.) genome, mainly using amplified fragment length polymorphisms (AFLPs) and simple sequence repeat (SSR) markers. However, AFLPs and SSR markers were not enough to develop a high-density olive linkage map. Genotyping-by-sequencing (GBS), a recently developed single-nucleotide polymorphism (SNP) identification methodology based on next-generation sequencing (NGS) technologies, has been demonstrated to be useful for the identification of a high number of SNP markers and the construction of high-density genetic linkage maps. In the present study, we identified a total of 10,941 SNPs from a cross between the olive cultivars 'Gemlik' and 'Edincik Su' using GBS and de novo SNP discovery implemented in the computer program "Stacks." A high-density genetic linkage map for the olive genome was constructed using 121 cross-pollinated full-sib F1 progeny and 5643 markers (21 SSRs, 203 AFLPs, and 5736 SNPs). This linkage map was composed of 25 linkage groups, covering 3049 cM of the olive genome, and the mean distance between the flanking markers was 0.53 cM. To the best of our knowledge, this map is the most saturated genetic linkage map in olive to date. We demonstrated that GBS is a valuable tool for the identification of thousands of SNPs for the construction of a saturated genetic linkage map in olive. The high-density genetic map developed in this study is a useful tool for locating quantitative trait loci and other economically important traits in the olive genome. PMID:26902470

  12. 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. PMID:25914583

  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. Column Density Maps of the I-GALFA HI Survey: Evidence for Dark Gas?

    NASA Astrophysics Data System (ADS)

    Gibson, Steven J.; Koo, B.; Douglas, K. A.; Newton, J. H.; Peek, J. E.; Hughes, J. M.; Spraggs, M.; Park, G.; Kang, J.; Heiles, C. E.; Korpela, E. J.

    2014-01-01

    The gas in galactic disks, including our own, occurs in a wide range of temperatures and densities, most of which are unsuitable for star formation. Somehow, diffuse atomic clouds are collected into colder, denser molecular clouds that can collapse under their own gravity. The molecular condensation process is not directly observable, and the gas itself is often ``dark'' to standard probes like optically thin HI 21cm emission or the CO 2.6mm line. However, the presence of this dark gas can often be inferred from infrared dust emission in excess of what is expected for the observed HI and CO content. We have mapped apparent HI column densities in the Inner-Galaxy Arecibo L-band Feed Array (I-GALFA) survey, which covers a 1600 square degree region at 4-arcminute resolution in the first Galactic quadrant. We compare these ``naive'' HI columns to others derived from Planck first-release CO and dust maps and NE2001 model dispersion measures to identify a number of areas with potentially significant dark gas. We discuss whether optically thick HI or CO-free H2 is more likely to dominate the dark column, and we consider the effects of possible biases on our results. We acknowledge support from the National Science Foundation, the NASA Kentucky Space Grant Consortium, Western Kentucky University, and the Gatton Academy. I-GALFA (www.naic.edu igalfa) is a GALFA-HI survey observed with the 7-beam ALFA receiver on the 305-meter William E. Gordon Telescope. The Arecibo Observatory is a U.S. National Science Foundation facility operated under sequential cooperative agreements with Cornell University and SRI International, the latter in alliance with the Ana G. Mendez-Universidad Metropolitana and the Universities Space Research Association.

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

    PubMed

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

    2002-11-01

    We describe a method for the statistical parametric mapping of low resolution electromagnetic tomography (LORETA) using high-density electroencephalography (EEG) and individual magnetic resonance images (MRI) to investigate the characteristics of the mismatch negativity (MMN) generators in schizophrenia. LORETA, using a realistic head model of the boundary element method derived from the individual anatomy, estimated the current density maps from the scalp topography of the 128-channel EEG. From the current density maps that covered the whole cortical gray matter (up to 20,000 points), volumetric current density images were reconstructed. Intensity normalization of the smoothed current density images was used to reduce the confounding effect of subject specific global activity. After transforming each image into a standard stereotaxic space, we carried out statistical parametric mapping of the normalized current density images. We applied this method to the source localization of MMN in schizophrenia. The MMN generators, produced by a deviant tone of 1,200 Hz (5% of 1,600 trials) under the standard tone of 1,000 Hz, 80 dB binaural stimuli with 300 msec of inter-stimulus interval, were measured in 14 right-handed schizophrenic subjects and 14 age-, gender-, and handedness-matched controls. We found that the schizophrenic group exhibited significant current density reductions of MMN in the left superior temporal gyrus and the left inferior parietal gyrus (P < 0. 0005). This study is the first voxel-by-voxel statistical mapping of current density using individual MRI and high-density EEG. PMID:12391570

  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. PMID:26398139

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

    PubMed Central

    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. PMID:26398139

  20. 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.

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

    PubMed Central

    2011-01-01

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

  2. Measurements of corrosion at defects in painted zinc and zinc alloy coated steels using current density mapping

    SciTech Connect

    Isaacs, H.S.; Aldykiewicz, A.J. Jr.; Thierry, D.; Simpson, T.C.

    1996-03-01

    Current density mapping was used to locate and monitor the early stages of corrosion at defects on painted surfaces in solution. Principles of the technique and methods of analysis were reviewed, and the effects of different scribing techniques were investigated. Results for painted zinc and aluminum-zinc alloy coated steel surfaces showed corrosion occurred initially at localized sites on the exposed zinc in both dilute chloride and sulfate solutions and when zinc was galvanically coupled to or isolated from steel. Current density mapping was shown to locate corrosion-susceptible defects on painted roll-formed materials that were not readily discernible optically.

  3. Identification and high-density mapping of gene-rich regions in chromosome group 1 of wheat.

    PubMed

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

    1996-12-01

    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

  4. 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.

  5. Transient electron density maps of ionic materials from femtosecond x-ray powder diffraction

    NASA Astrophysics Data System (ADS)

    Elsaesser, Thomas

    2014-05-01

    X-ray diffraction represents a key method for spatially resolving electron distributions in crystalline materials. So far, electron density maps have been derived from stationary diffraction patterns, providing detailed insight into the equilibrium charge distribution and crystal geometry. Functional processes in condensed matter are frequently connected with nonequilibrium excitations resulting in atomic motions and charge relocations on ultrashort time scales. Transient structures are resolved in space and time by novel x-ray diffraction methods with a femtosecond time resolution, giving access to the driving mechanisms and underlying interactions. In this talk, new results are presented on transient electron distributions of ionic materials mapped with the help of femtosecond x-ray powder diffraction. Experiments are based on a pump-probe approach in which an optical pulse initiates structural dynamics and a hard x-ray pulse from a synchronized laser-driven plasma source is diffracted from the excited powder sample. Such measurements reveal the interplay of lattice and charge motions in the photoexcited prototype material KDP (KH2PO4) which occur on distinctly different length scales. As a second topic, electron relocations induced by strong external optical fields will be discussed. This interaction mechanism allows for generating coherent superpositions of valence and conduction band quantum states and inducing fully reversible charge dynamics. While the materials LiBH4 and NaBH4 display electron relocations from the (BH4)- ions to the neighboring Li+ and Na+ ions, LiH exhibits an electron transfer from Li to H. The latter is a manifestation of electron correlations and in agreement with theoretical calculations.

  6. Mapping cortical responses to speech using high-density diffuse optical tomography.

    PubMed

    Hassanpour, Mahlega S; Eggebrecht, Adam T; Culver, Joseph P; Peelle, Jonathan E

    2015-08-15

    The functional neuroanatomy of speech processing has been investigated using positron emission tomography (PET) and functional magnetic resonance imaging (fMRI) for more than 20years. However, these approaches have relatively poor temporal resolution and/or challenges of acoustic contamination due to the constraints of echoplanar fMRI. Furthermore, these methods are contraindicated because of safety concerns in longitudinal studies and research with children (PET) or in studies of patients with metal implants (fMRI). High-density diffuse optical tomography (HD-DOT) permits presenting speech in a quiet acoustic environment, has excellent temporal resolution relative to the hemodynamic response, and provides noninvasive and metal-compatible imaging. However, the performance of HD-DOT in imaging the brain regions involved in speech processing is not fully established. In the current study, we use an auditory sentence comprehension task to evaluate the ability of HD-DOT to map the cortical networks supporting speech processing. Using sentences with two levels of linguistic complexity, along with a control condition consisting of unintelligible noise-vocoded speech, we recovered a hierarchically organized speech network that matches the results of previous fMRI studies. Specifically, hearing intelligible speech resulted in increased activity in bilateral temporal cortex and left frontal cortex, with syntactically complex speech leading to additional activity in left posterior temporal cortex and left inferior frontal gyrus. These results demonstrate the feasibility of using HD-DOT to map spatially distributed brain networks supporting higher-order cognitive faculties such as spoken language. PMID:26026816

  7. 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

  8. Quantification of voxel-wise total fibre density: Investigating the problems associated with track-count mapping.

    PubMed

    Calamante, Fernando; Smith, Robert E; Tournier, Jacques-Donald; Raffelt, David; Connelly, Alan

    2015-08-15

    A biological parameter that would be valuable to be able to extract from diffusion MRI data is the local white matter axonal density. Track-density imaging (TDI) has been used as if it could provide such a measure; however, this has been the subject of controversy, primarily due to the fact that track-count quantitation is highly sensitive to tracking biases and errors. The spherical-deconvolution informed filtering of tractograms (SIFT) post-processing method was recently introduced to minimise tractography biases, and thus provides a more biologically meaningful measure that could be used in track-count mapping (i.e. TDI following SIFT). The TDI intensity following SIFT ideally corresponds to the orientational average of the fibre orientation distribution (FOD), which corresponds to the total Apparent Fibre Density (AFDtotal) within the AFD framework; in fact, AFDtotal provides a direct measure of local fibre density at native resolution that does not rely on fibre-tracking. In this study, we demonstrate problems associated with quantitative TDI investigations, which can be avoided by using SIFT processing or directly by using AFDtotal maps. We also characterise the intra- and inter-subject reproducibility of TDI maps (with and without SIFT pre-processing) and AFDtotal maps. It is shown that SIFT improves the quantitative characteristics of TDI, but is still vastly inferior to the properties of the AFDtotal parameter itself, because the latter does not require tracking. While standard TDI might be preferable in applications when high anatomical contrast is required, particularly when combined with super-resolution, for voxel-wise quantitation of total tract density (i.e. without tract orientation information) at native resolution, the total AFD maps are preferable to TDI or other related track-count maps. Regardless of the track-count measure, it should be noted that all of these voxel-averaged approaches discard important information that is retained in fibre

  9. Integration of Self-Organizing Map (SOM) and Kernel Density Estimation (KDE) for network intrusion detection

    NASA Astrophysics Data System (ADS)

    Cao, Yuan; He, Haibo; Man, Hong; Shen, Xiaoping

    2009-09-01

    This paper proposes an approach to integrate the self-organizing map (SOM) and kernel density estimation (KDE) techniques for the anomaly-based network intrusion detection (ABNID) system to monitor the network traffic and capture potential abnormal behaviors. With the continuous development of network technology, information security has become a major concern for the cyber system research. In the modern net-centric and tactical warfare networks, the situation is more critical to provide real-time protection for the availability, confidentiality, and integrity of the networked information. To this end, in this work we propose to explore the learning capabilities of SOM, and integrate it with KDE for the network intrusion detection. KDE is used to estimate the distributions of the observed random variables that describe the network system and determine whether the network traffic is normal or abnormal. Meanwhile, the learning and clustering capabilities of SOM are employed to obtain well-defined data clusters to reduce the computational cost of the KDE. The principle of learning in SOM is to self-organize the network of neurons to seek similar properties for certain input patterns. Therefore, SOM can form an approximation of the distribution of input space in a compact fashion, reduce the number of terms in a kernel density estimator, and thus improve the efficiency for the intrusion detection. We test the proposed algorithm over the real-world data sets obtained from the Integrated Network Based Ohio University's Network Detective Service (INBOUNDS) system to show the effectiveness and efficiency of this method.

  10. High-density single-nucleotide polymorphism maps of the human genome

    PubMed Central

    Miller, Raymond D.; Phillips, Michael S.; Jo, Inho; Donaldson, Miriam A.; Studebaker, Joel F.; Addleman, Nicholas; Alfisi, Steven V.; Ankener, Wendy M.; Bhatti, Hamid A.; Callahan, Chad E.; Carey, Benjamin J.; Conley, Cheryl L.; Cyr, Justin M.; Derohannessian, Vram; Donaldson, Rachel A.; Elosua, Carolina; Ford, Stacey E.; Forman, Angela M.; Gelfand, Craig A.; Grecco, Nicole M.; Gutendorf, Susan M.; Hock, Cricket R.; Hozza, Mark J.; Hur, Soyoung; In, Sun Mi; Jackson, Diana L.; Jo, Sangmee Ahn; Jung, Sung-Chul; Kim, Sook; Kimm, Kuchan; Kloss, Ellen F.; Koboldt, Daniel C.; Kuebler, Jennifer M.; Kuo, Feng-Shen; Lathrop, Jessica A.; Lee, Jong-Keuk; Leis, Kathy L.; Livingston, Stephanie A.; Lovins, Elizabeth G.; Lundy, Maria L.; Maggan, Sima; Minton, Matthew; Mockler, Michael A.; Morris, David W.; Nachtman, Eric P.; Oh, Bermseok; Park, Chan; Park, Chang-Wook; Pavelka, Nicholas; Perkins, Adrienne B.; Restine, Stephanie L.; Sachidanandam, Ravi; Reinhart, Andrew J.; Scott, Kathryn E.; Shah, Gira J.; Tate, Jatana M.; Varde, Shobha A.; Walters, Amy; White, J. Rebecca; Yoo, Yeon-Kyeong; Lee, Jong-Eun; Boyce-Jacino, Michael T.; Kwok, Pui-Yan

    2007-01-01

    Here we report a large, extensively characterized set of single-nucleotide polymorphisms (SNPs) covering the human genome. We determined the allele frequencies of 55,018 SNPs in African Americans, Asians (Japanese–Chinese), and European Americans as part of The SNP Consortium’s Allele Frequency Project. A subset of 8333 SNPs was also characterized in Koreans. Because these SNPs were ascertained in the same way, the data set is particularly useful for modeling. Our results document that much genetic variation is shared among populations. For autosomes, some 44% of these SNPs have a minor allele frequency ≥10% in each population, and the average allele frequency differences between populations with different continental origins are less than 19%. However, the several percentage point allele frequency differences among the closely related Korean, Japanese, and Chinese populations suggest caution in using mixtures of well-established populations for case–control genetic studies of complex traits. We estimate that ~7% of these SNPs are private SNPs with minor allele frequencies <1%. A useful set of characterized SNPs with large allele frequency differences between populations (>60%) can be used for admixture studies. High-density maps of high-quality, characterized SNPs produced by this project are freely available. PMID:15961272

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

    PubMed

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

    2015-10-21

    A high-density amperometric electrode array containing 8192 individually addressable platinum working electrodes with an integrated potentiostat fabricated using Complementary Metal Oxide Semiconductor (CMOS) processes is reported. The array was designed to enable electrochemical imaging of chemical gradients with high spatiotemporal resolution. Electrodes are arranged over a 2 mm × 2 mm surface area into 64 subarrays consisting of 128 individual Pt working electrodes as well as Pt pseudo-reference and auxiliary electrodes. Amperometric measurements of norepinephrine in tissue culture media were used to demonstrate the ability of the array to measure concentration gradients in complex media. Poly(dimethylsiloxane) microfluidics were incorporated to control the chemical concentrations in time and space, and the electrochemical response at each electrode was monitored to generate electrochemical heat maps, demonstrating the array's imaging capabilities. A temporal resolution of 10 ms can be achieved by simultaneously monitoring a single subarray of 128 electrodes. The entire 2 mm × 2 mm area can be electrochemically imaged in 64 seconds by cycling through all subarrays at a rate of 1 Hz per subarray. Monitoring diffusional transport of norepinephrine is used to demonstrate the spatiotemporal resolution capabilities of the system. PMID:26333296

  12. 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

  13. 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

  14. Chromosome rearrangements during domestication of cucumber as revealed from high-density genetic mapping and draft genome assembly

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cucumber is an economically important vegetable crop, but available genetic and genomics resources for cucumber are limited that hinders progress in cucumber breeding. In this study, we made significant contributions to the cucumber research community by developing a high-density genetic map for cul...

  15. A comparison of two algorithms for electron-density map improvement by introduction of atomicity: skeletonization, and map sorting followed by refinement.

    PubMed

    Vellieux, F M

    1998-01-01

    A comparison has been made of two methods for electron-density map improvement by the introduction of atomicity, namely the iterative skeletonization procedure of the CCP4 program DM [Cowtan & Main (1993). Acta Cryst. D49, 148-157] and the pseudo-atom introduction followed by the refinement protocol in the program suite DEMON/ANGEL [Vellieux, Hunt, Roy & Read (1995). J. Appl. Cryst. 28, 347-351]. Tests carried out using the 3.0 A resolution electron density resulting from iterative 12-fold non-crystallographic symmetry averaging and solvent flattening for the Pseudomonas aeruginosa ornithine transcarbamoylase [Villeret, Tricot, Stalon & Dideberg (1995). Proc. Natl Acad. Sci. USA, 92, 10762-10766] indicate that pseudo-atom introduction followed by refinement performs much better than iterative skeletonization: with the former method, a phase improvement of 15.3 degrees is obtained with respect to the initial density modification phases. With iterative skeletonization a phase degradation of 0.4 degrees is obtained. Consequently, the electron-density maps obtained using pseudo-atom phases or pseudo-atom phases combined with density-modification phases are much easier to interpret. These tests also show that for ornithine transcarbamoylase, where 12-fold non-crystallographic symmetry is present in the P1 crystals, G-function coupling leads to the simultaneous decrease of the conventional R factor and of the free R factor, a phenomenon which is not observed when non-crystallographic symmetry is absent from the crystal. The method is far less effective in such a case, and the results obtained suggest that the map sorting followed by refinement stage should be by-passed to obtain interpretable electron-density distributions. PMID:9761819

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

    PubMed

    Sekiguchi, Yuki; Oroguchi, Tomotaka; Nakasako, Masayoshi

    2016-01-01

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

  17. 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

  18. 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

  19. 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

  20. 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

  1. Functional Connectivity Density Mapping of Depressive Symptoms and Loneliness in Non-Demented Elderly Male

    PubMed Central

    Lan, Chen-Chia; Tsai, Shih-Jen; Huang, Chu-Chung; Wang, Ying-Hsiu; Chen, Tong-Ru; Yeh, Heng-Liang; Liu, Mu-En; Lin, Ching-Po; Yang, Albert C.

    2016-01-01

    Background: Depression and loneliness are prevalent and highly correlated phenomena among the elderly and influence both physical and mental health. Brain functional connectivity changes associated with depressive symptoms and loneliness are not fully understood. Methods: A cross-sectional functional MRI study was conducted among 85 non-demented male elders. Geriatric depression scale-short form (GDS) and loneliness scale were used to evaluate the severity of depressive symptoms and loneliness, respectively. Whole brain voxel-wise resting-state functional connectivity density (FCD) mapping was performed to delineate short-range FCD (SFCD) and long-range FCD (LFCD). Regional correlations between depressive symptoms or loneliness and SFCD or LFCD were examined using general linear model (GLM), with age incorporated as a covariate and depressive symptoms and loneliness as predictors. Results: Positive correlations between depressive symptoms and LFCD were observed in left rectal gyrus, left superior frontal gyrus, right supraorbital gyrus, and left inferior temporal gyrus. Positive correlations between depressive symptoms and SFCD were observed in left middle frontal gyrus, left superior frontal gyrus, bilateral superior medial frontal gyrus, left inferior temporal gyrus, and left middle occipital region. Positive correlations between SFCD and loneliness were centered over bilateral lingual gyrus. Conclusion: Depressive symptoms are associated with FCD changes over frontal and temporal regions, which may involve the cognitive control, affective regulation, and default mode networks. Loneliness is associated with FCD changes in bilateral lingual gyri that are known to be important in social cognition. Depressive symptoms and loneliness may be associated with different brain regions in non-demented elderly male. PMID:26793101

  2. 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

  3. 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

  4. A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat.

    PubMed

    Steen, R G; Kwitek-Black, A E; Glenn, C; Gullings-Handley, J; Van Etten, W; Atkinson, O S; Appel, D; Twigger, S; Muir, M; Mull, T; Granados, M; Kissebah, M; Russo, K; Crane, R; Popp, M; Peden, M; Matise, T; Brown, D M; Lu, J; Kingsmore, S; Tonellato, P J; Rozen, S; Slonim, D; Young, P; Jacob, H J

    1999-06-01

    The laboratory rat (Rattus norvegicus) is a key animal model for biomedical research. However, the genetic infrastructure required for connecting phenotype and genotype in the rat is currently incomplete. Here, we report the construction and integration of two genomic maps: a dense genetic linkage map of the rat and the first radiation hybrid (RH) map of the rat. The genetic map was constructed in two F2 intercrosses (SHRSP x BN and FHH x ACI), containing a total of 4736 simple sequence length polymorphism (SSLP) markers. Allele sizes for 4328 of the genetic markers were characterized in 48 of the most commonly used inbred strains. The RH map is a lod >/= 3 framework map, including 983 SSLPs, thereby allowing integration with markers on various genetic maps and with markers mapped on the RH panel. Together, the maps provide an integrated reference to >3000 genes and ESTs and >8500 genetic markers (5211 of our SSLPs and >3500 SSLPs developed by other groups). [Bihoreau et al. (1997); James and Tanigami, RHdb (http:www.ebi.ac.uk/RHdb/index.html); Wilder (http://www.nih.gov/niams/scientific/ratgbase); Serikawa et al. (1992); RATMAP server (http://ratmap.gen.gu.se)] RH maps (v. 2.0) have been posted on our web sites at http://goliath.ifrc.mcw.edu/LGR/index.html or http://curatools.curagen.com/ratmap. Both web sites provide an RH mapping server where investigators can localize their own RH vectors relative to this map. The raw data have been deposited in the RHdb database. Taken together, these maps provide the basic tools for rat genomics. The RH map provides the means to rapidly localize genetic markers, genes, and ESTs within the rat genome. These maps provide the basic tools for rat genomics. They will facilitate studies of multifactorial disease and functional genomics, allow construction of physical maps, and provide a scaffold for both directed and large-scale sequencing efforts and comparative genomics in this important experimental organism. PMID:10400928

  5. 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. PMID:25874931

  6. A high-density gene map of loblolly pine (Pinus taeda L.) based on exome sequence capture genotyping.

    PubMed

    Neves, Leandro Gomide; Davis, John M; Barbazuk, William B; Kirst, Matias

    2014-01-01

    Loblolly pine (Pinus taeda L.) is an economically and ecologically important conifer for which a suite of genomic resources is being generated. Despite recent attempts to sequence the large genome of conifers, their assembly and the positioning of genes remains largely incomplete. The interspecific synteny in pines suggests that a gene-based map would be useful to support genome assemblies and analysis of conifers. To establish a reference gene-based genetic map, we performed exome sequencing of 14729 genes on a mapping population of 72 haploid samples, generating a resource of 7434 sequence variants segregating for 3787 genes. Most markers are single-nucleotide polymorphisms, although short insertions/deletions and multiple nucleotide polymorphisms also were used. Marker segregation in the population was used to generate a high-density, gene-based genetic map. A total of 2841 genes were mapped to pine's 12 linkage groups with an average of one marker every 0.58 cM. Capture data were used to detect gene presence/absence variations and position 65 genes on the map. We compared the marker order of genes previously mapped in loblolly pine and found high agreement. We estimated that 4123 genes had enough sequencing depth for reliable detection of markers, suggesting a high marker conversation rate of 92% (3787/4123). This is possible because a significant portion of the gene is captured and sequenced, increasing the chances of identifying a polymorphic site for characterization and mapping. This sub-centiMorgan genetic map provides a valuable resource for gene positioning on chromosomes and guide for the assembly of a reference pine genome. PMID:24192835

  7. 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

  8. 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...

  9. 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

  10. 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

  11. Molecular scene analysis: application of a topological approach to the automated interpretation of protein electron-density maps.

    PubMed

    Leherte, L; Fortier, S; Glasgow, J; Allen, F H

    1994-03-01

    Methods to assist in the spatial and visual analysis of electron-density maps have been investigated as part of a project in molecular scene analysis [Fortier, Castleden, Glasgow, Conklin, Walmsley, Leherte & Allen (1993). Acta Cryst. D49, 168-178]. In particular, the usefulness of the topological approach for the segmentation of medium-resolution (3 A) maps of proteins and their interpretation in terms of structural motifs has been assessed. The approach followed is that proposed by Johnson [Johnson (1977). ORCRIT. The Oak Ridge Critical Point Network Program. Chemistry Division, Oak Ridge National Laboratory, USA] which provides a global representation of the electron-density distribution through the location, identification and linkage of its critical points. In the first part of the study, the topological approach was applied to calculated maps of three proteins of small to medium size so as to develop a methodology that could then be used for analyzing maps of medium resolution. The methodology was then applied to both calculated and experimental maps of penicillopepsin at 3 A resolution. The study shows that the networks of critical points can provide a useful segmentation of the maps, tracing the protein main chains and capturing their conformation. In addition, these networks can be parsed in terms of secondary-structure motifs, through a geometrical analysis of the critical points. The procedure adopted for secondary-structure recognition, which was phrased in terms of geometry-based rules, provides a basis for a further automated implementation of a more complete set of recognition operations through the use of artificial-intelligence techniques. PMID:15299453

  12. 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

  13. 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

  14. 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)

  15. Border collision bifurcations and power spectral density of chaotic signals generated by one-dimensional discontinuous piecewise linear maps

    NASA Astrophysics Data System (ADS)

    Feltekh, Kais; Jemaa, Zouhair Ben; Fournier-Prunaret, Danièle; Belghith, Safya

    2014-08-01

    Recently, many papers have appeared which study the power spectral density (PSD) of signals issued from some specific maps. This interest in the PSD is due to the importance of frequency in the telecommunications and transmission security. With the large number of wireless systems, the availability of frequencies for transmission and reception is increasingly uncommon for wireless communications. Also, guided media have limitations related to the bandwidth of a signal. In this paper, we investigate some properties associated to the border-collision bifurcations in a one-dimensional piecewise-linear map with three slopes and two parameters. We derive analytical expressions for the autocorrelation sequence, power spectral density (PSD) of chaotic signals generated by our piecewise-linear map. We prove the existence of strong relation between different types of the power spectral density (low-pass, high-pass or band-stop) and the parameters. We also find a relation between the type of spectrum and the order of attractive cycles which are located after the border collision bifurcation between chaos and cycles.

  16. View-independent Contour Culling of 3D Density Maps for Far-field Viewing of Iso-surfaces

    PubMed Central

    Feng, Powei; Ju, Tao; Warren, Joe

    2011-01-01

    In many applications, iso-surface is the primary method for visualizing the structure of 3D density maps. We consider a common scenario where the user views the iso-surfaces from a distance and varies the level associated with the iso-surface as well as the view direction to gain a sense of the general 3D structure of the density map. For many types of density data, the iso-surfaces associated with a particular threshold may be nested and never visible during this type of viewing. In this paper, we discuss a simple, conservative culling method that avoids the generation of interior portions of iso-surfaces at the contouring stage. Unlike existing methods that perform culling based on the current view direction, our culling is performed once for all views and requires no additional computation as the view changes. By pre-computing a single visibility map, culling is done at any iso-value with little overhead in contouring. We demonstrate the effectiveness of the algorithm on a range of bio-medical data and discuss a practical application in online visualization. PMID:21673830

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

    PubMed Central

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

    2014-01-01

    Transcriptome sequencing using Illumina RNA-seq was performed on populations of black tiger shrimp from India. Samples were collected from (i) four landing centres around the east coastline (EC) of India, (ii) survivors of a severe WSSV infection during pond culture (SUR) and (iii) the Andaman Islands (AI) in the Bay of Bengal. Equal quantities of purified total RNA from homogenates of hepatopancreas, muscle, nervous tissue, intestinal tract, heart, gonad, gills, pleopod and lymphoid organs were combined to create AI, EC and SUR pools for RNA sequencing. De novo transcriptome assembly resulted in 136,223 contigs (minimum size 100 base pairs, bp) with a total length 61 Mb, an average length of 446 bp and an average coverage of 163× across all pools. Approximately 16% of contigs were annotated with BLAST hit information and gene ontology annotations. A total of 473,620 putative SNPs/indels were identified. An Illumina iSelect genotyping array containing 6,000 SNPs was developed and used to genotype 1024 offspring belonging to seven full-sibling families. A total of 3959 SNPs were mapped to 44 linkage groups. The linkage groups consisted of between 16–129 and 13–130 markers, of length between 139–10.8 and 109.1–10.5 cM and with intervals averaging between 1.2 and 0.9 cM for the female and male maps respectively. The female map was 28% longer than the male map (4060 and 2917 cM respectively) with a 1.6 higher recombination rate observed for female compared to male meioses. This approach has substantially increased expressed sequence and DNA marker resources for tiger shrimp and is a useful resource for QTL mapping and association studies for evolutionarily and commercially important traits. PMID:24465553

  18. 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

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

    PubMed Central

    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

  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. Calculation of the Potential and Electric Flux Lines for Parallel Plate Capacitors with Symmetrically Placed Equal Lengths by Using the Method of Conformal Mapping

    NASA Astrophysics Data System (ADS)

    Albayrak, Erhan

    2001-05-01

    The classical problem of the parallel-plate capacitors has been investigated by a number of authors, including Love [1], Langton [2] and Lin [3]. In this paper, the exact equipotentials and electric flux lines of symmetrically placed two thin conducting plates are obtained using the Schwarz- Cristoffel transformation and the method of conformal mapping. The coordinates x , y in the z-plane corresponding to the constant electric flux lines and equipotential lines are obtained after very detailed and cumbersome calculations. The complete field distribution is given by constructing the family of lines of electric flux and equipotential.

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

    PubMed

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

    2016-04-01

    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

  5. 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.

  6. A high-density physical map of Sinorhizobium meliloti 1021 chromosome derived from bacterial artificial chromosome library

    PubMed Central

    Capela, Delphine; Barloy-Hubler, Frédérique; Gatius, Marie-Thérèse; Gouzy, Jérôme; Galibert, Francis

    1999-01-01

    As part of the European Sinorhizobium meliloti (strain 1021) chromosome sequencing project, four genomic bacterial artificial chromosome (BAC) libraries have been constructed, one of which was mainly used for chromosome mapping. This library consists of 1,824 clones with an average insert size of 80 kilobases and represents approximately 20-fold total genome coverage [6.8 megabases (Mbs)]. PCR screening of 384 BAC clones with 447 chromosomal markers (PCR primer pairs), consisting of 73 markers representing 118 genes (40 individual genes and 78 genes clustered in 23 operons), two markers from the rrn operon (three loci), four markers from insertion sequences (≈16 loci) and 368 sequence-tagged sites allowed the identification of 252 chromosomal BAC clones and the construction of a high-density physical map of the whole 3.7-Mb chromosome of S. meliloti. An average of 5.5 overlapping and colinear BAC clones per marker, correlated with a low rate of deleted or rearranged clones (0.8%) indicate a solid BAC contigation and a correct mapping. Systematic blastx analysis of sequence-tagged site marker sequences allowed prediction of a biological function for a number of putative ORFs. Results are available at http://www-recomgen.univ-rennes1.fr/meliloti. This map, whose resolution averages one marker every 9 kilobases, should provide a valuable tool for further sequencing, functional analysis, and positional cloning. PMID:10430947

  7. Mapping somatosensory connectivity in adult mice using diffusion MRI tractography and super-resolution track density imaging.

    PubMed

    Richards, Kay; Calamante, Fernando; Tournier, Jacques-Donald; Kurniawan, Nyoman D; Sadeghian, Farnoosh; Retchford, Alexander R; Jones, Gabriel Davis; Reid, Christopher A; Reutens, David C; Ordidge, Roger; Connelly, Alan; Petrou, Steven

    2014-11-15

    In this study we combined ultra-high field diffusion MRI fiber tracking and super-resolution track density imaging (TDI) to map the relay locations and connectivity of the somatosensory pathway in paraformaldehyde fixed, C57Bl/6J mouse brains. Super-resolution TDI was used to achieve 20 μm isotropic resolution to inform the 3D topography of the relay locations including thalamic barreloids and brainstem barrelettes, not described previously using MRI methodology. TDI-guided mapping results for thalamo-cortical connectivity were consistent with thalamo-cortical projections labeled using virus mediated fluorescent protein expression. Trigemino-thalamic TDI connectivity maps were concordant with results obtained using anterograde dye tracing from brainstem to thalamus. Importantly, TDI mapping overcame the constraint of tissue distortion observed in mechanically sectioned tissue, enabling 3D reconstruction and long-range connectivity data. In conclusion, our results showed that diffusion micro-imaging at ultra-high field MRI revealed the stereotypical pattern of somatosensory connectivity and is a valuable tool to complement histologic methods, achieving 3D spatial preservation of whole brain networks for characterization in mouse models of human disease. PMID:25087481

  8. The properties of (2Fo - Fc) and (Fo - Fc) electron-density maps at medium-to-high resolutions.

    PubMed

    Minichino, A; Habash, J; Raftery, J; Helliwell, J R

    2003-05-01

    This paper reports on the efficacy of (F(o) - F(c)) versus (2F(o) - F(c)) electron-density maps at 3.2 A resolution. Firstly, a study is reported of a simple truncation at 2.3 and 3.2 A of the 1.6 A resolution crystal structure of concanavalin A at room temperature [Emmerich et al. (1994), Acta Cryst. D50, 749-756] with 149 known bound water molecules. Secondly, the concanavalin A 1.6 A resolution model was re-refined but with the data truncated to 3.2 A. In a similar evaluation, these procedures were repeated for the apocrustacyanin A1 cryotemperature 1.4 A resolution model [Cianci et al. (2001), Acta Cryst. D57, 1219-1229]. Maps at 1.4, 2.3 and 3.2 A resolutions were first generated and the structure was then re-refined at 3.2 A and additionally at 2.3 A resolution. The results on concanavalin A show that the number of bound water molecules that are resolved decreases by two thirds from 1.6 to 3.2 A, but that key structural waters, for example at the transition metal and the calcium ion, are still resolved in the (F(o) - F(c)) map but not in the (2F(o) - F(c)) map. For apocrustacyanin A1, the results with these two difference maps were less clear-cut. Two key structural bound waters (w93 and w105) were selected that had been previously identified in beta-crustacyanin [Cianci et al. (2002), Proc. Natl Acad. Sci. USA, 99, 9795-9800] in protein-carotenoid interactions. The behaviour of w93 is similar to that of concanavalin A key waters, but that of w105 is not. These behaviours were therefore explored in finer resolution increments, namely 2.9, 2.7 and 2.5 A. Finally, further tests on "real" data sets for peanut lectin and concanavalin A at medium resolution confirm these map properties, namely that an (F(o) - F(c)) difference electron-density map is more effective than a (2F(o) - F(c)) map in showing bound water structure at lower resolutions ( approximately 3.2 A). This result is important since a growing number of protein crystal structure studies are concerned

  9. 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. PMID:26011256

  10. 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

  11. 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

  12. 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

  13. High density physical mapping of chromosome 3p by hybridization of somatic cell hybrid derived Alu-PCR products

    SciTech Connect

    Shearman, A.M.; Andresen, J.M.; Aburatani, H.

    1994-09-01

    We have produced high density physical maps covering most of chromosome 3 using a hybridization-based approach to YAC isolation and contig assembly. The strategy has been to use a well characterized panel of somatic cell hybrids to generate probe sets distributed across the chromosome. From each of 50 somatic cell hybrids, a library of {approximately}100-600 cloned Alu-PCR products was isolated and Alu-PCR inserts from the full set of clones was spotted at high density on nylon membranes. Representative sets of unique clones from most of the hybrids were used to screen {approximately}16 genome equivalents of CEPH YACs by hybridization. These results, combined with our previous results and data from CEPH, produced contigs covering most of the chromosomes. The use of somatic cell hybrid-derived probe sets allowed easy integration of contigs with physical mapping boundaries defined by the somatic cell hybrids. We will describe various Alu-PCR strategies subsequently used to achieve closure, including successful identification of Alu-PCR products from the spotted set which lie in regions not previously covered by YAC contigs and use of Alu-PCR walking strategies to fill gaps and confirm tentative linkages. Our basic YAC screening methodology allows one individual to screen {approximately}16 genome equivalents of CEPH YACs with 96 probes/week at a material cost of less than $1 per locus. We have now mapped >2,200 loci on chromosome 3, with average interlocus distances of {approximately}50-100 kb over large regions. Alu-PCR-defined loci spaced along the chromosome at regular intervals are being converted to STSs. Our results indicate that use of a hybridization-based approach to physical mapping constitutes an efficient, accurate, high throughput method for isolating YACs and assembling YAC contigs.

  14. 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.

  15. 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).

  16. Recombination mapping using Boolean logic and high-density SNP genotyping for exome sequence filtering

    PubMed Central

    Markello, Thomas C.; Han, Ted; Carlson-Donohoe, Hannah; Ahaghotu, Chidi; Harper, Ursula; Jones, MaryPat; Chandrasekharappa, Settara; Anikster, Yair; Adams, David R.; Gahl, William A.; Boerkoel, Cornelius F.

    2012-01-01

    Whole genome sequence data for small pedigrees has been shown to provide sufficient information to resolve detailed haplotypes in small pedigrees. Using such information, recombinations can be mapped onto chromosomes, compared with the segregation of a disease of interest and used to filter genome sequence variants. We now show that relatively inexpensive SNP array data from small pedigrees can be used in a similar manner to provide a means of identifying regions of interest in exome sequencing projects. We demonstrate that in those situations where one can assume complete penetrance and parental DNA is available, SNP recombination mapping using Boolean logic identifies chromosomal regions identical to those detected by multipoint linkage using microsatellites but with much less computation. We further show that this approach is successful because the probability of a double crossover between informative SNP loci is negligible. Our observations provide a rationale for using SNP arrays and recombination mapping as a rapid and cost-effective means of incorporating chromosome segregation information into exome sequencing projects intended for disease-gene identification. PMID:22264778

  17. 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

  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. CHARACTERIZATION AND PHYSICAL MAPPING OF MAIZE BAC LIBRARIES USING HIGH DENSITY BAC FILTER HYBRIDIZATION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High-density filter sets from two maize B73 libraries containing 6X (HindIII) and 7X (EcoRI) haploid genome equivalents, respectively, were evaluated with a set of complex probes. The complex probes will provide information on chromosome architecture and organellar DNA content. A second set of pro...

  20. 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.

  1. 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

  2. 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...

  3. FEM: Feature-enhanced map

    DOE PAGESBeta

    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

  4. 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

  5. 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.

  6. 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...

  7. 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...

  8. 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...

  9. Development of high density SNP-based linkage map and tagging leaf spot resistance trait in pearl millet using GBS 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...

  10. Multi-view areal-density maps of compressed shells in OMEGA direct-drive implosions extracted from MMI data

    NASA Astrophysics Data System (ADS)

    Johns, Heather; Joshi, Tirtha; Mayes, Daniel; Durmaz, Tunay; Mancini, Roberto; Tommasini, Riccardo; Delettrez, Jacques; Regan, Sean; Nagayama, Taisuke

    2012-10-01

    In a series of implosion experiments performed at the OMEGA laser facility, spherical plastic shells doped with an embedded titanium tracer-layer and filled with deuterium gas were driven with high- and low-adiabat laser pulse shapes. The titanium emergent intensity distribution was recorded with a streaked spectrometer and three identical gated, multi-monochromatic x-ray imaging instruments (MMI) that observed the implosion along three quasi-orthogonal lines-of-sight. The data shows spectral signatures due to absorption K-shell line transitions in titanium L-shell ions that are backlit by the continuum radiation from the hot core. To interpret these observations, the MMI spectrally-resolved image data were processed to obtain narrow-band images and spatially-resolved spectra based on the titanium spectral features.footnotetextT. Nagayama, R.C. Mancini, R. Florido, et al, J. App. Phys. 109, 093303 (2011) Areal-density maps were extracted using two independent methods based on narrow-band images and spatially-resolved spectra. The areal-density maps reveal the 3D structure and state of the compressed shell through the collapse of the implosion and the performance differences between high- and low-adiabat implosions.

  11. 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

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

    PubMed

    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

  13. Toward Mapping the Detailed Density Structure of Classical Be Circumstellar Disks

    NASA Technical Reports Server (NTRS)

    Wisniewski, J. P.; Kowalski, A. F.; Bjorkman, K. S.; Bjorkman, J. E.

    2005-01-01

    We present the preliminary results of near contemporaneous optical and infrared spectroscopic observations of select classical Be stars. We find strong evidence of oppositely oriented V/R hydrogen line profiles in the optical versus infrared spectra of zeta Tau, and briefly discuss how sustained contemporaneous optical and infrared spectroscopic observations might enable us to trace the detailed density structure of classical Be circumstellar disks.

  14. Mapping track density changes in nigrostriatal and extranigral pathways in Parkinson's disease☆

    PubMed Central

    Ziegler, Erik; Rouillard, Maud; André, Elodie; Coolen, Tim; Stender, Johan; Balteau, Evelyne; Phillips, Christophe; Garraux, Gaëtan

    2014-01-01

    In Parkinson's disease (PD) the demonstration of neuropathological disturbances in nigrostriatal and extranigral brain pathways using magnetic resonance imaging remains a challenge. Here, we applied a novel diffusion-weighted imaging approach—track density imaging (TDI). Twenty-seven non-demented Parkinson's patients (mean disease duration: 5 years, mean score on the Hoehn & Yahr scale = 1.5) were compared with 26 elderly controls matched for age, sex, and education level. Track density images were created by sampling each subject's spatially normalized fiber tracks in 1 mm isotropic intervals and counting the fibers that passed through each voxel. Whole-brain voxel-based analysis was performed and significance was assessed with permutation testing. Statistically significant increases in track density were found in the Parkinson's patients, relative to controls. Clusters were distributed in disease-relevant areas including motor, cognitive, and limbic networks. From the lower medulla to the diencephalon and striatum, clusters encompassed the known location of the locus coeruleus and pedunculopontine nucleus in the pons, and from the substantia nigra up to medial aspects of the posterior putamen, bilaterally. The results identified in brainstem and nigrostriatal pathways show a large overlap with the known distribution of neuropathological changes in non-demented PD patients. Our results also support an early involvement of limbic and cognitive networks in Parkinson's disease. PMID:24956065

  15. 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.

  16. 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

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

    PubMed

    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

  18. 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.

  19. 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

  20. 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

  1. Analysis of low-density lipoprotein-associated proteins using the method of digitized native protein mapping.

    PubMed

    Jin, Ya; Chen, Jin; Wang, Ahui; Zhang, Jun; Chen, Shumin; Manabe, Takashi; Tan, Wen

    2016-07-01

    The method of digitized native protein mapping, combining nondenaturing micro 2DE, grid gel-cutting, and quantitative LC-MS/MS (in data-independent acquisition mode, or MS(E) ), was improved by using a new MS/MS mode, ion mobility separation enhanced-MS(E) (HDMS(E) ), and applied to analyze the area of human plasma low-density lipoprotein (LDL). An 18 mm × 4.8 mm rectangular area which included LDL on a nondenaturing micro 2D gel of human plasma was grid-cut into 72 square gel pieces and subjected to quantitative LC-MS/MS. Compared with MS(E) , HDMS(E) showed significantly higher performance, by assigning 50% more proteins and detecting each protein in more squares. A total of 253 proteins were assigned with LC-HDMS(E) and the quantity distribution of each was reconstructed as a native protein map. The maps showed that Apo B-100 was the most abundant protein in the grid-cut area, concentrated at pI ca. 5.4-6.1 and apparent mass ca. 1000 kDa, which corresponded to four gel pieces, squares 39-42. An Excel macro was prepared to search protein maps which showed protein quantity peaks localized within this concentrated region of Apo B-100. Twenty-two proteins out of the 252 matched this criterion, in which 19 proteins have been reported to be associated with LDL. This method only requires several microliters of a plasma sample and the principle of the protein separation is totally different from the commonly used ultracentrifugation. The results obtained by this method would provide new insights on the structure and function of LDL. PMID:27174546

  2. 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

    2015-01-01

    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

  3. 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

  4. 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

  5. Refining a model electron-density map via the Phantom Derivative method.

    PubMed

    Burla, Maria Cristina; Carrozzini, Benedetta; Cascarano, Giovanni Luca; Giacovazzo, Carmelo; Polidori, Giampiero

    2015-09-01

    The Phantom Derivative (PhD) method [Giacovazzo (2015), Acta Cryst. A71, 483-512] has recently been described for ab initio and non-ab initio phasing. It is based on the random generation of structures with the same unit cell and the same space group as the target structure (called ancil structures), which are used to create derivatives devoid of experimental diffraction amplitudes. In this paper, the non-ab initio variant of the method was checked using phase sets obtained by molecular-replacement techniques as a starting point for phase extension and refinement. It has been shown that application of PhD is able to extend and refine phases in a way that is competitive with other electron-density modification techniques. PMID:26327376

  6. Photoemission and density functional theory study of Ir(111); energy band gap mapping

    NASA Astrophysics Data System (ADS)

    Pletikosić, I.; Kralj, M.; Šokčević, D.; Brako, R.; Lazić, P.; Pervan, P.

    2010-04-01

    We have performed combined angle-resolved photoemission spectroscopy (ARPES) experiments and density functional theory (DFT) calculations of the electronic structure of the Ir(111) surface, with the focus on the existence of energy band gaps. The investigation was motivated by the experimental results suggesting Ir(111) as an ideal support for the growth of weakly bonded graphene. Therefore, our prime interest was electronic structure around the \\bar {\\mathrm {K}} symmetry point. In accordance with DFT calculations, ARPES has shown a wide energy band gap with the shape of a parallelogram centred around the \\bar {\\mathrm {K}} point. Within the gap three surface states were identified; one just below the Fermi level and two spin-orbit split surface states at the bottom of the gap.

  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. PMID:25424506

  8. Mapping the polarity and stimulus density requirements for T-cell activation

    NASA Astrophysics Data System (ADS)

    Wei, Xunbin; Krasieva, Tatiana B.; Zhang, Zhanxiang; Negulescu, Paul A.; Sun, Chung-Ho; Berns, Michael W.; Cahalan, Michael D.; Tromberg, Bruce J.

    1998-08-01

    T-cell contact with antigen-presenting cells (APC) initiates an activation cascade which includes an increase in T-cell intracellular calcium [(Ca2+)i] and leads to T-cell proliferation and differentiation. Although T-cell/APC physical contact is required for an immune response, little is known about the patterns of cellular interaction and their relation to activation. We have combined fluorescence spectroscopy and imaging with optical manipulation to investigate the contact requirements for T-cell activation, using optical tweezers to control the orientation of T- cell/APC pairs and fluorescence microscopy to measure the subsequent (Ca2+)i response, detected as an emission shift from the combination of fura-red and oregon- green, two cytoplasmic (Ca2+) indicators. APCs or beads coated with antibodies to the T-cell receptor (TCR) are trapped with a near-infrared titanium-sapphire laser and placed at different locations along the T-cell, which has a polarized appearance defined by the shape and direction of crawling (2-5 micrometers /min). T cells contacted with antigen- presenting cells or antibody-coated beads entered a dynamic and reproducible program in the first 10 - 20 mins, including (Ca2+)i increase, changes in shape and motility, engulfment, and stable contact. T cells presented with antigen at the leading edge had a higher probability of responding (85%) and a shorter latency of response (50 secs) than those contacting APCs or beads with their trailing end (APCs: 30%, 150 secs; beads: 6%, 300 secs). Alterations in antibody density, quantified by FACS analysis, and bead size were used to determine the spatial requirements for T cell activation and the minimum number of receptors which must be engaged in order to transmit a positive signal. Preliminary data show that T cell responses [response percentage, latency and (Ca2+)i pattern] depend on both antibody density and bead size.

  9. 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…

  10. Magnetic Resonance Q Mapping Reveals a Decrease in Microvessel Density in the arcAβ Mouse Model of Cerebral Amyloidosis

    PubMed Central

    Ielacqua, Giovanna D.; Schlegel, Felix; Füchtemeier, Martina; Xandry, Jael; Rudin, Markus; Klohs, Jan

    2016-01-01

    Alterations in density and morphology of the cerebral microvasculature have been reported to occur in Alzheimer's disease patients and animal models of the disease. In this study we compared magnetic resonance imaging (MRI) techniques for their utility to detect age-dependent changes of the cerebral vasculature in the arcAβ mouse model of cerebral amyloidosis. Dynamic susceptibility contrast (DSC)-MRI was performed by tracking the passage of a superparamagnetic iron oxide nanoparticle in the brain with dynamic gradient echo planar imaging (EPI). From this measurements relative cerebral blood volume [rCBV(DSC)] and relative cerebral blood flow (rCBF) were estimated. For the same animal maps of the relaxation shift index Q were computed from high resolution gradient echo and spin echo data that were acquired before and after superparamagnetic iron oxide (SPIO) nanoparticle injection. Q-values were used to derive estimates of microvessel density. The change in the relaxation rates ΔR2* obtained from pre- and post-contrast gradient echo data was used for the alternative determination of rCBV [rCBV(ΔR2*)]. Linear mixed effects modeling found no significant association between rCBV(DSC), rCBV(ΔR2*), rCBF, and Q with genotype in 13-month old mice [compared to age-matched non-transgenic littermates (NTLs)] for any of the evaluated brain regions. In 24-month old mice there was a significant association for rCBV(DSC) with genotype in the cerebral cortex, and for rCBV(ΔR2*) in the cerebral cortex and cerebellum. For rCBF there was a significant association in the cerebellum but not in other brain regions. Q-values in the olfactory bulb, cerebral cortex, striatum, hippocampus, and cerebellum in 24-month old mice were significantly associated with genotype. In those regions Q-values were reduced between 11 and 26% in arcAβ mice compared to age-matched NTLs. Vessel staining with CD31 immunohistochemistry confirmed a reduction of microvessel density in the old arcAβ mice

  11. 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

  12. 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

  13. 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

  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. 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. PMID:25796191

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

    PubMed Central

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

    2014-01-01

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

  17. 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.

  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. 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. PMID:27085420

  20. 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

  1. A High-Density SNP Map of Sunflower Derived from RAD-Sequencing Facilitating Fine-Mapping of the Rust Resistance Gene R12

    PubMed Central

    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. PMID:25014030

  2. 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

  3. 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

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

    PubMed

    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

    2015-09-01

    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

  5. Equal Justice Under Law.

    ERIC Educational Resources Information Center

    Johnson, Earl, Jr., Ed.

    1994-01-01

    This special theme issue of "Update on Law-Related Education""tells about the past, present, and future of equal legal representation for all in our society." It is dedicated to the history and heroes of legal aid for the poor and the need to further that cause if the United States hopes to achieve equal justice for all. In his foreword, Justice…

  6. 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…

  7. 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…

  8. 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)

  9. 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.

  10. 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. PMID:26801965

  11. Structure, evolution, and comparative genomics of tetraploid cotton based on a high-density genetic linkage map

    PubMed Central

    Li, Ximei; Jin, Xin; Wang, Hantao; Zhang, Xianlong; Lin, Zhongxu

    2016-01-01

    A high-density linkage map was constructed using 1,885 newly obtained loci and 3,747 previously published loci, which included 5,152 loci with 4696.03 cM in total length and 0.91 cM in mean distance. Homology analysis in the cotton genome further confirmed the 13 expected homologous chromosome pairs and revealed an obvious inversion on Chr10 or Chr20 and repeated inversions on Chr07 or Chr16. In addition, two reciprocal translocations between Chr02 and Chr03 and between Chr04 and Chr05 were confirmed. Comparative genomics between the tetraploid cotton and the diploid cottons showed that no major structural changes exist between DT and D chromosomes but rather between AT and A chromosomes. Blast analysis between the tetraploid cotton genome and the mixed genome of two diploid cottons showed that most AD chromosomes, regardless of whether it is from the AT or DT genome, preferentially matched with the corresponding homologous chromosome in the diploid A genome, and then the corresponding homologous chromosome in the diploid D genome, indicating that the diploid D genome underwent converted evolution by the diploid A genome to form the DT genome during polyploidization. In addition, the results reflected that a series of chromosomal translocations occurred among Chr01/Chr15, Chr02/Chr14, Chr03/Chr17, Chr04/Chr22, and Chr05/Chr19. PMID:27084896

  12. 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...

  13. Genetic dissection of yield and its component traits using high-density composite map of wheat chromosome 3A: bridging gaps between QTLs and underlying genes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 compon...

  14. Influence of Within-season Densities of Heliothines and Tarnished Plant Bugs on Variability in End-of-season Cotton Yield Mapping

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nineteen different experiments were compiled to examine temporal trends in fruit accumulation among various insect related treatments based on end-of-season yield mapping of cotton, Gossypium hirsutum L., plants. Fourteen of these data sets were used to examine the effect of varying densities of bo...

  15. First Case of Automatic His Potential Detection With a Novel Ultra High-density Electroanatomical Mapping System for AV Nodal Ablation

    PubMed Central

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

    2016-01-01

    A 74-year old was considered for atrioventricular (AV) nodal ablation in view of atrial fibrillation (AF) with poorly controlled ventricular rate despite being on amiodarone. Targeted AV nodal ablation was successfully performed after identifying the target site for ablation by reviewing an ultra high-density map of the His region produced by automatic electrogram annotation. PMID:25852249

  16. 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.

  17. 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...

  18. 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

  19. Probability densities for the sums of iterates of the sine-circle map in the vicinity of the quasiperiodic edge of chaos

    NASA Astrophysics Data System (ADS)

    Afsar, Ozgur; Tirnakli, Ugur

    2010-10-01

    We investigate the probability density of rescaled sum of iterates of sine-circle map within quasiperiodic route to chaos. When the dynamical system is strongly mixing (i.e., ergodic), standard central limit theorem (CLT) is expected to be valid, but at the edge of chaos where iterates have strong correlations, the standard CLT is not necessarily valid anymore. We discuss here the main characteristics of the probability densities for the sums of iterates of deterministic dynamical systems which exhibit quasiperiodic route to chaos. At the golden-mean onset of chaos for the sine-circle map, we numerically verify that the probability density appears to converge to a q -Gaussian with q<1 as the golden mean value is approached.

  20. 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

  1. 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

  2. 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

  3. 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. PMID:26631981

  4. 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

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

    PubMed

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

    2013-08-01

    High-density genetic maps were constructed for loci involved in nuclear male sterility (NMS1-locus) and sporophytic self-incompatibility (S-locus) in chicory (Cichorium intybus L.). The mapping population consisted of 389 F1' individuals derived from a cross between two plants, K28 (male-sterile) and K59 (pollen-fertile), both heterozygous at the S-locus. This F1' mapping population segregated for both male sterility (MS) and strong self-incompatibility (SI) phenotypes. Phenotyping F1' individuals for MS allowed us to map the NMS1-locus to linkage group (LG) 5, while controlled diallel and factorial crosses to identify compatible/incompatible phenotypes mapped the S-locus to LG2. To increase the density of markers around these loci, bulked segregant analysis was used. Bulks and parental plants K28 and K59 were screened using amplified fragment length polymorphism (AFLP) analysis, with a complete set of 256 primer combinations of EcoRI-ANN and MseI-CNN. A total of 31,000 fragments were generated, of which 2,350 showed polymorphism between K59 and K28. Thirteen AFLP markers were identified close to the NMS1-locus and six in the vicinity of the S-locus. From these AFLP markers, eight were transformed into sequence-characterized amplified region (SCAR) markers and of these five showed co-dominant polymorphism. The chromosomal regions containing the NMS1-locus and the S-locus were each confined to a region of 0.8 cM. In addition, we mapped genes encoding proteins similar to S-receptor kinase, the female determinant of sporophytic SI in the Brasicaceae, and also markers in the vicinity of the putative S-locus of sunflower, but none of these genes or markers mapped close to the chicory S-locus. PMID:23689744

  6. 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

  7. 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. PMID:17845448

  8. 43 CFR 2201.6 - Value equalization; cash equalization waiver.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 43 Public Lands: Interior 2 2011-10-01 2011-10-01 false Value equalization; cash equalization... PROCEDURES Exchanges-Specific Requirements § 2201.6 Value equalization; cash equalization waiver. (a) To equalize the agreed upon values of the Federal and non-Federal lands involved in an exchange, either...

  9. 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

  10. 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

  11. 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:...

  12. 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.

  13. 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.

  14. 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

  15. Fine mapping of QTL for twinning and ovulation rate using low density SNP map in conjunction with microsatellite marker information in the USMARC twinning population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USMARC twinning population originated from 307 females and 53 males representing 12 different breeds of cattle and has been under selection for 25 years. The objective of this study was to initiate fine mapping of QTL for twinning and ovulation rate previously found on BTA5. This population ha...

  16. Equal Opportunity in Housing.

    ERIC Educational Resources Information Center

    Commission on Civil Rights, Washington, DC.

    This overview of developments in housing opportunities for minorities and women includes an historical review of housing discrimination, its nature, and its effects. Federal legislation and Federal actions which were taken to assure equal housing opportunities for women and minorities are described. Other topic areas addressed include minority…

  17. 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…

  18. 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…

  19. Status Equalization Project.

    ERIC Educational Resources Information Center

    Cohen, Elizabeth G.; Deslonde, James

    The introduction of the Multiple Ability Curriculum (MAC) and Expectation Training (ET) into the curriculum of racially integrated elementary schools appears to improve the equal status interaction between students of differing academic and social status. The goals of the MAC and ET are the following: (1) prevent classroom dominance by students of…

  20. 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…

  1. Mapping wildland-urban interfaces at large scales integrating housing density and vegetation aggregation for fire prevention in the South of France.

    PubMed

    Lampin-Maillet, Corinne; Jappiot, Marielle; Long, Marlène; Bouillon, Christophe; Morge, Denis; Ferrier, Jean-Paul

    2010-01-01

    Every year, more than 50,000 wildland fires affect about 500,000ha of vegetation in southern European countries, particularly in wildland-urban interfaces (WUI). This paper presents a method to characterize and map WUIs at large scales and over large areas for wildland fire prevention in the South of France. Based on the combination of four types of building configuration and three classes of vegetation structure, 12 interface types were classified. Through spatial analysis, fire ignition density and burned area ratio were linked with the different types of WUI. Among WUI types, isolated WUIs with the lowest housing density represent the highest level of fire risk. PMID:19879685

  2. 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…

  3. 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.

  4. 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

  5. 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

  6. Construction of an Integrated High Density Simple Sequence Repeat Linkage Map in Cultivated Strawberry (Fragaria × ananassa) and its Applicability

    PubMed Central

    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

    2013-01-01

    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. PMID:23248204

  7. 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

  8. 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

  9. 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.

  10. 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.

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

    PubMed Central

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

    2014-01-01

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

  12. Battery equalization active methods

    NASA Astrophysics Data System (ADS)

    Gallardo-Lozano, Javier; Romero-Cadaval, Enrique; Milanes-Montero, M. Isabel; Guerrero-Martinez, Miguel A.

    2014-01-01

    Many different battery technologies are available for the applications which need energy storage. New researches are being focused on Lithium-based batteries, since they are becoming the most viable option for portable energy storage applications. As most of the applications need series battery strings to meet voltage requirements, battery imbalance is an important matter to be taken into account, since it leads the individual battery voltages to drift apart over time, and premature cells degradation, safety hazards, and capacity reduction will occur. A large number of battery equalization methods can be found, which present different advantages/disadvantages and are suitable for different applications. The present paper presents a summary, comparison and evaluation of the different active battery equalization methods, providing a table that compares them, which is helpful to select the suitable equalization method depending on the application. By applying the same weight to the different parameters of comparison, switch capacitor and double-tiered switching capacitor have the highest ratio. Cell bypass methods are cheap and cell to cell ones are efficient. Cell to pack, pack to cell and cell to pack to cell methods present a higher cost, size, and control complexity, but relatively low voltage and current stress in high-power applications.

  13. CHARACTERIZATION OF THREE MAIZE BAC LIBRARIES AND ANCHORING OF THE PHYSICAL MAP TO THE GENETIC MAP USING HIGH-DENSITY BAC FILTER HYBRIDIZATION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Three maize (Zea mays L.) bacterial artificial chromosome (BAC) libraries, HindIII, EcoRI and MboI, were constructed from inbred line B73 to minimize under-representation of certain genomic regions caused by the use of a single restriction enzyme library. High-density filter sets from all three lib...

  14. 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;…

  15. 43 CFR 2201.6 - Value equalization; cash equalization waiver.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 43 Public Lands: Interior 2 2012-10-01 2012-10-01 false Value equalization; cash equalization... PROCEDURES Exchanges-Specific Requirements § 2201.6 Value equalization; cash equalization waiver. (a) To... as compensation for costs under § 2201.1-3 of this part may not exceed 25 percent of the value of...

  16. 43 CFR 2201.6 - Value equalization; cash equalization waiver.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 43 Public Lands: Interior 2 2013-10-01 2013-10-01 false Value equalization; cash equalization... PROCEDURES Exchanges-Specific Requirements § 2201.6 Value equalization; cash equalization waiver. (a) To... as compensation for costs under § 2201.1-3 of this part may not exceed 25 percent of the value of...

  17. 36 CFR 254.12 - Value equalization; cash equalization waiver.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 36 Parks, Forests, and Public Property 2 2011-07-01 2011-07-01 false Value equalization; cash... AGRICULTURE LANDOWNERSHIP ADJUSTMENTS Land Exchanges § 254.12 Value equalization; cash equalization waiver. (a) To equalize the agreed upon values of the Federal and non-Federal lands involved in an...

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

    SciTech Connect

    Leroy, Adam K.; Lee, Cheoljong; Schruba, Andreas; Bolatto, Alberto; Hughes, Annie; Sandstrom, Karin; Schinnerer, Eva; Walter, Fabian; Pety, Jerome

    2013-05-20

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

  19. 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

  20. 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.

  1. 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

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

    PubMed

    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

  3. 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. PMID:26010095

  4. 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

  5. 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 ...

  6. Genes and equality.

    PubMed

    Farrelly, C

    2004-12-01

    The way people think about equality as a value will influence how they think genetic interventions should be regulated. In this paper the author uses the taxonomy of equality put forth by Derek Parfit and applies this to the issue of genetic interventions. It is argued that telic egalitarianism is untenable and that deontic egalitarianism collapses into prioritarianism. The priority view maintains that it is morally more important to benefit the people who are worse off. Once this precision has been given to the concerns egalitarians have, a number of diverse issues must be considered before determining what the just regulation of genetic interventions would be. Consideration must be given to the current situation of the least advantaged, the fiscal realities behind genetic interventions, the budget constraints on other social programmes egalitarians believe should receive scarce public funds, and the interconnected nature of genetic information. These considerations might lead egalitarians to abandon what they take to be the obvious policy recommendations for them to endorse regarding the regulation of gene therapies and enhancements. PMID:15574450

  7. 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.

  8. 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 PAGESBeta

    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

  9. 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.

  10. 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.

  11. 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)

  12. Webster and women's equality.

    PubMed

    Johnsen, D; Wilder, M J

    1989-01-01

    The National Abortion Rights Action League (NARAL) and the Women's Legal Defense Fund (WLDF) co-authored an "amicus curiae" brief in "Webster." The brief was written for 77 organizations who believe in equality of women. The brief said that constitutional protection of a woman's right to choose is guaranteed by the right to privacy. The brief said that if abortions were illegal, women would not be able to take place in society equally with men. Liberty would be taken away from women. If the state interferes with abortion, the principle of bodily integrity is violated. In "Winston v. Lee," the Supreme Court found that the state could not compel a criminal to undergo an invasive surgical procedure to retrieve a bullet necessary for the state to prosecute with. 1 in 4 women have a cesarean section, which requires a larger incision in the abdomen, and has many risks. Bearing and raising children often puts a damper on women's employment opportunities. Therefore, if the Supreme Court denied women the right to bear children when and where they wanted, women would not have the right to plan their futures. If the Supreme Court were to agree that "interest in potential life outweighs" a woman's tight to procreate autonomously, states could declare all abortions illegal, investigate them to see if they were induced on purpose, and murder women who induced them. Contraceptive devices could be declared illegal. Laws could be used to force women to submit to cesarean sections and other fetal surgery. Pre-viability abortion restrictions should be rejected because they have old-fashioned notions of women's role in society. They reinforce stereotypes. Missouri's law stresses aiding "potential," rather than actual life. PMID:2603859

  13. 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. PMID:26132169

  14. 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

  15. 36 CFR 254.12 - Value equalization; cash equalization waiver.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 36 Parks, Forests, and Public Property 2 2012-07-01 2012-07-01 false Value equalization; cash... AGRICULTURE LANDOWNERSHIP ADJUSTMENTS Land Exchanges § 254.12 Value equalization; cash equalization waiver. (a... to as compensation for costs under § 254.7 of this subpart may not exceed 25 percent of the value...

  16. 36 CFR 254.12 - Value equalization; cash equalization waiver.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 36 Parks, Forests, and Public Property 2 2013-07-01 2013-07-01 false Value equalization; cash... AGRICULTURE LANDOWNERSHIP ADJUSTMENTS Land Exchanges § 254.12 Value equalization; cash equalization waiver. (a... to as compensation for costs under § 254.7 of this subpart may not exceed 25 percent of the value...

  17. 36 CFR 254.12 - Value equalization; cash equalization waiver.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 36 Parks, Forests, and Public Property 2 2010-07-01 2010-07-01 false Value equalization; cash... AGRICULTURE LANDOWNERSHIP ADJUSTMENTS Land Exchanges § 254.12 Value equalization; cash equalization waiver. (a... to as compensation for costs under § 254.7 of this subpart may not exceed 25 percent of the value...

  18. 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.

  19. 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.

  20. HermiteFit: fast-fitting atomic structures into a low-resolution density map using three-dimensional orthogonal Hermite functions.

    PubMed

    Derevyanko, Georgy; Grudinin, Sergei

    2014-08-01

    HermiteFit, a novel algorithm for fitting a protein structure into a low-resolution electron-density map, is presented. The algorithm accelerates the rotation of the Fourier image of the electron density by using three-dimensional orthogonal Hermite functions. As part of the new method, an algorithm for the rotation of the density in the Hermite basis and an algorithm for the conversion of the expansion coefficients into the Fourier basis are presented. HermiteFit was implemented using the cross-correlation or the Laplacian-filtered cross-correlation as the fitting criterion. It is demonstrated that in the Hermite basis the Laplacian filter has a particularly simple form. To assess the quality of density encoding in the Hermite basis, an analytical way of computing the crystallographic R factor is presented. Finally, the algorithm is validated using two examples and its efficiency is compared with two widely used fitting methods, ADP_EM and colores from the Situs package. HermiteFit will be made available at http://nano-d.inrialpes.fr/software/HermiteFit or upon request from the authors. PMID:25084327

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

    PubMed Central

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

    2012-01-01

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

  2. Genetic control of juvenile growth and botanical architecture in an ornamental woody plant, Prunus mume Sieb. et Zucc. as revealed by a high-density linkage map

    PubMed Central

    2014-01-01

    Mei, Prunus mume Sieb. et Zucc., is an ornamental plant popular in East Asia and, as an important member of genus Prunus, has played a pivotal role in systematic studies of the Rosaceae. However, the genetic architecture of botanical traits in this species remains elusive. This paper represents the first genome-wide mapping study of quantitative trait loci (QTLs) that affect stem growth and form, leaf morphology and leaf anatomy in an intraspecific cross derived from two different mei cultivars. Genetic mapping based on a high-density linkage map constricted from 120 SSRs and 1,484 SNPs led to the detection of multiple QTLs for each trait, some of which exert pleiotropic effects on correlative traits. Each QTL explains 3-12% of the phenotypic variance. Several leaf size traits were found to share common QTLs, whereas growth-related traits and plant form traits might be controlled by a different set of QTLs. Our findings provide unique insights into the genetic control of tree growth and architecture in mei and help to develop an efficient breeding program for selecting superior mei cultivars. PMID:25078672

  3. High-Density Nucleosome Occupancy Map of Human Chromosome 9p21–22 Reveals Chromatin Organization of the Type I Interferon Gene Cluster

    PubMed Central

    Freaney, Jonathan E.; Zhang, Quanwei; Yigit, Erbay; Kim, Rebecca; Widom, Jonathan; Wang, Ji-Ping

    2014-01-01

    Genome-wide investigations have dramatically increased our understanding of nucleosome positioning and the role of chromatin in gene regulation, yet some genomic regions have been poorly represented in human nucleosome maps. One such region is represented by human chromosome 9p21–22, which contains the type I interferon gene cluster that includes 16 interferon alpha genes and the single interferon beta, interferon epsilon, and interferon omega genes. A high-density nucleosome mapping strategy was used to generate locus-wide maps of the nucleosome organization of this biomedically important locus at a steady state and during a time course of infection with Sendai virus, an inducer of interferon gene expression. Detailed statistical and computational analysis illustrates that nucleosomes in this locus exhibit preferences for particular dinucleotide and oligomer DNA sequence motifs in vivo, which are similar to those reported for lower eukaryotic nucleosome–DNA interactions. These data were used to visualize the region's chromatin architecture and reveal features that are common to the organization of all the type I interferon genes, indicating a common nucleosome-mediated gene regulatory paradigm. Additionally, this study clarifies aspects of the dynamic changes that occur with the nucleosome occupying the transcriptional start site of the interferon beta gene after virus infection. PMID:24673249

  4. Genetic Control of the Leaf Angle and Leaf Orientation Value as Revealed by Ultra-High Density Maps in Three Connected Maize Populations

    PubMed Central

    Li, Chunhui; Li, Yongxiang; Shi, Yunsu; Song, Yanchun; Zhang, Dengfeng; Buckler, Edward S.; Zhang, Zhiwu; Wang, Tianyu; Li, Yu

    2015-01-01

    Plant architecture is a key factor for high productivity maize because ideal plant architecture with an erect leaf angle and optimum leaf orientation value allow for more efficient light capture during photosynthesis and better wind circulation under dense planting conditions. To extend our understanding of the genetic mechanisms involved in leaf-related traits, three connected recombination inbred line (RIL) populations including 538 RILs were genotyped by genotyping-by-sequencing (GBS) method and phenotyped for the leaf angle and related traits in six environments. We conducted single population quantitative trait locus (QTL) mapping and joint linkage analysis based on high-density recombination bin maps constructed from GBS genotype data. A total of 45 QTLs with phenotypic effects ranging from 1.2% to 29.2% were detected for four leaf architecture traits by using joint linkage mapping across the three populations. All the QTLs identified for each trait could explain approximately 60% of the phenotypic variance. Four QTLs were located on small genomic regions where candidate genes were found. Genomic predictions from a genomic best linear unbiased prediction (GBLUP) model explained 45±9% to 68±8% of the variation in the remaining RILs for the four traits. These results extend our understanding of the genetics of leaf traits and can be used in genomic prediction to accelerate plant architecture improvement. PMID:25807369

  5. 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,…

  6. 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

  7. 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.

  8. 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.

  9. GENOME-WIDE MAPPING OF COPY NUMBER VARIATIONS IN COMMERCIAL HYBRID PIGS USING A HIGH-DENSITY SNP GENOTYPING ARRAY.

    PubMed

    Zhou, L S; Li, J; Yang, J; Liu, C L; Xie, X H; He, Y N; Liu, X X; Xin, W S; Zhang, W C; Ren, J; Ma, J W; Huang, L S

    2016-01-01

    Copy number variations (CNVs) are important forms of structural variation in human and animals and can be considered as a major genetic component of phenotypic diversity. Here we used the Illumina PorcineSNP60 BeadChip V2 and a DLY [Duroc x (Large White x Landrace)] commercial hybrid population to identify 272 CNVs belonging to 165 CNV regions (CNVRs), of which 66 are new. As CNVRs are specific to origin of population, our DLY-specific data is an important complementary to the existing CNV map in the pig genome. Eight CNVRs were selected. for validation by quantitative real-time PCR (qRT-PCR) and the accurate rate was high (87.25%). Gene function analysis suggested that a common CNVR may play an important role in multiple traits, including growth rate and carcass quality. PMID:27183798

  10. 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

  11. 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. PMID:26643028

  12. Effect of equal daily doses achieved by different power densities of low-level laser therapy at 635 nm on open skin wound healing in normal and corticosteroid-treated rats.

    PubMed

    Gál, Peter; Mokrý, Michal; Vidinský, Boris; Kilík, Róbert; Depta, Filip; Harakalová, Magdaléna; Longauer, Frantisek; Mozes, Stefan; Sabo, Ján

    2009-07-01

    Optimal parameters of low-level laser therapy (LLLT) for wound healing are still discussed. Hence, our study was aimed to compare effects of different power densities of LLLT at 635 nm in rats. Four, round, full-thickness, skin wounds were made on the backs of 48 rats that were divided into two groups (non-steroid laser-treated and steroid laser-treated). Three wounds were stimulated daily with a diode laser (daily dose 5 J/cm(2)) each with different power density (1 mW/cm(2), 5 mW/cm(2), and 15 mW/cm(2)), whereas the fourth wound served as a control. Two days, 6 days, and 14 days after surgery, eight animals from each group were killed and samples were removed for histological evaluation. In the non-steroid laser-treated rats, significant acceleration of epithelization and collagen synthesis 2 days and 6 days after surgery was observed in stimulated wounds. In steroid laser-treated rats, 2 days and 14 days after surgery, a decreased leucocyte/macrophage ratio and a reduction in the area of granulation tissue were recorded, respectively. In conclusion, LLLT, by the method we used, improved wound healing in the non-steroid laser-treated rats, but it was useless after corticosteroid treatment. PMID:18716824

  13. 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.

  14. 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.

  15. 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. PMID:23894373

  16. 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.

  17. 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.

  18. Vertical density contrast and mapping of basement, Conrad and Moho morphologies through 2D spectral analysis of gravity data in and around Odisha, India

    NASA Astrophysics Data System (ADS)

    Kumar, Arbind; S. Roy, P. N.; Das, L. K.

    2016-07-01

    Power spectrum analysis of Complete Bouguer Anomaly (CBA) map of Eastern Ghat Mobile Belt (EGMB) and its surroundings in India through Two Dimensional (2D) spectral analysis has provided estimates of the ensemble average depths for the density discontinuities which represent crustal inhomogeneities. The spectral analysis method has helped to estimate the depths of a perturbing body sources which are obtained from the negative slopes of the linear relationship between the logarithmic power spectrum and the wave-numbers of the gravity field. The detailed analysis reveals three horizontal discontinuities (i) Phanerozoic sediment thickness (ii) Basement depth and (iii) Conrad discontinuity. The average thickness of Phanerozoic sediments is estimated to be 3 km whereas depth of basement and Conrad discontinuity are at 7 km and 14.5 km respectively. Additionally Mohorovicic discontinuity also estimated at a depth of 32.8 km in the study region.

  19. Reframing Inclusive Education: Educational Equality as Capability Equality

    ERIC Educational Resources Information Center

    Terzi, Lorella

    2014-01-01

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

  20. 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

  1. 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).

  2. 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

  3. 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

  4. 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

  5. Effect of Equal Daily Doses Achieved by Different Power Densities of Low-Level Laser Therapy at 635 nm on Open Skin Wound Healing in Normal and Diabetic Rats

    PubMed Central

    Kilík, Róbert; Lakyová, Lucia; Sabo, Ján; Lacjaková, Kamila; Vasilenko, Tomáš; Vidová, Martina; Longauer, František; Radoňak, Jozef

    2014-01-01

    Background and Objective. Despite the fact that the molecular mechanism of low-level laser therapy (LLLT) is not yet known, the exploitation of phototherapy in clinical medicine and surgery is of great interest. The present study investigates the effects of LLLT on open skin wound healing in normal and diabetic rats. Materials and Methods. Four round full-thickness skin wounds on dorsum were performed in male adult nondiabetic (n = 24) and diabetic (n = 24) Sprague–Dawley rats. AlGaInP (635 nm, wavelength; 5 J/cm2, daily dose) was used to deliver power densities of 1, 5, and 15 mW/cm2 three times daily until euthanasia. Results. PMNL infiltration was lower in the irradiated groups (15 mW/cm2). The synthesis and organisation of collagen fibres were consecutively enhanced in the 5 mW/cm2 and 15 mW/cm2 groups compared to the others in nondiabetic rats. In the diabetic group the only significant difference was recorded in the ratio PMNL/Ma at 15 mW/cm2. A significant difference in the number of newly formed capillaries in the irradiated group (5, 15 mW/cm2) was recorded on day six after injury compared to the control group. Conclusion. LLLT confers a protective effect against excessive inflammatory tissue response; it stimulates neovascularization and the early formation of collagen fibres. PMID:24551842

  6. 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

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

    PubMed Central

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

    2013-01-01

    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 pre-attentive sensory processing? The well-characterized mismatch negativity, an electrophysiological response that indexes pre-attentive 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 ~200ms, with the multisensory 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

  8. 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

  9. Spatio-temporal dynamics of adaptation in the human visual system: A high-density electrical mapping study

    PubMed Central

    Andrade, Gizely N.; Butler, John S.; Mercier, Manuel R.; Molholm, Sophie; Foxe, John J.

    2015-01-01

    When sensory inputs are presented serially, response amplitudes to stimulus repetitions generally decrease as a function of presentation rate, diminishing rapidly as inter-stimulus-intervals (ISIs) fall below a second. This “adaptation” is believed to represent mechanisms by which sensory systems reduce responsivity to consistent environmental inputs, freeing resources to respond to potentially more relevant inputs. While auditory adaptation functions have been relatively well-characterized, considerably less is known about visual adaptation in humans. Here, high-density visual evoked potentials (VEPs) were recorded while two paradigms were used to interrogate visual adaptation. The first presented stimulus pairs with varying ISIs, comparing VEP amplitude to the second stimulus to that of the first (paired-presentation). The second involved blocks of stimulation (N=100) at various ISIs and comparison of VEP amplitude between blocks of differing ISIs (block-presentation). Robust VEP modulations were evident as a function of presentation rate in the block-paradigm with strongest modulations in the 130–150ms and 160–180ms visual processing phases. In paired-presentations, with ISIs of just 200–300 ms, an enhancement of VEP was evident when comparing S2 to S1, with no significant effect of presentation rate. Importantly, in block-presentations, adaptation effects were statistically robust at the individual participant level. These data suggest that a more taxing block-presentation paradigm is better suited to engage visual adaptation mechanisms than a paired-presentation design. The increased sensitivity of the visual processing metric obtained in the block-paradigm has implications for the examination of visual processing deficits in clinical populations. PMID:25688539

  10. Fine Mapping of Five Loci Associated with Low-Density Lipoprotein Cholesterol Detects Variants That Double the Explained Heritability

    PubMed Central

    Sidore, Carlo; Kang, Hyun M.; Jackson, Anne U.; Piras, Maria Grazia; Usala, Gianluca; Maninchedda, Giuseppe; Sassu, Alessandro; Serra, Fabrizio; Palmas, Maria Antonietta; Wood, William H.; Njølstad, Inger; Laakso, Markku; Hveem, Kristian; Tuomilehto, Jaakko; Lakka, Timo A.; Rauramaa, Rainer; Boehnke, Michael; Cucca, Francesco; Uda, Manuela; Schlessinger, David; Nagaraja, Ramaiah; Abecasis, Gonçalo R.

    2011-01-01

    Complex trait genome-wide association studies (GWAS) provide an efficient strategy for evaluating large numbers of common variants in large numbers of individuals and for identifying trait-associated variants. Nevertheless, GWAS often leave much of the trait heritability unexplained. We hypothesized that some of this unexplained heritability might be due to common and rare variants that reside in GWAS identified loci but lack appropriate proxies in modern genotyping arrays. To assess this hypothesis, we re-examined 7 genes (APOE, APOC1, APOC2, SORT1, LDLR, APOB, and PCSK9) in 5 loci associated with low-density lipoprotein cholesterol (LDL-C) in multiple GWAS. For each gene, we first catalogued genetic variation by re-sequencing 256 Sardinian individuals with extreme LDL-C values. Next, we genotyped variants identified by us and by the 1000 Genomes Project (totaling 3,277 SNPs) in 5,524 volunteers. We found that in one locus (PCSK9) the GWAS signal could be explained by a previously described low-frequency variant and that in three loci (PCSK9, APOE, and LDLR) there were additional variants independently associated with LDL-C, including a novel and rare LDLR variant that seems specific to Sardinians. Overall, this more detailed assessment of SNP variation in these loci increased estimates of the heritability of LDL-C accounted for by these genes from 3.1% to 6.5%. All association signals and the heritability estimates were successfully confirmed in a sample of ∼10,000 Finnish and Norwegian individuals. Our results thus suggest that focusing on variants accessible via GWAS can lead to clear underestimates of the trait heritability explained by a set of loci. Further, our results suggest that, as prelude to large-scale sequencing efforts, targeted re-sequencing efforts paired with large-scale genotyping will increase estimates of complex trait heritability explained by known loci. PMID:21829380

  11. Equality and Education -- Part 1

    ERIC Educational Resources Information Center

    Porter, John

    1975-01-01

    Discusses equality in education within the framework of the ideas of John Rawls, asserting that even though in the real world it is not easy to implement his version of equality and justice without endangering his prior principle of liberty, he provides a philosophical foundation for the reconsideration of the meritocratic principle. (Author/JM)

  12. Ensuring equal opportunity sprinkler irrigation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Equal opportunity for plants to sprinkler irrigation water must be carefully considered by crop producers, irrigation consultants, and the industry that supplies the irrigation equipment. Equal opportunity can be negated by improper marketing, design, and installation, as well as through improper f...

  13. Equal Educational Opportunity Resource Handbook.

    ERIC Educational Resources Information Center

    Oregon State Dept. of Education, Salem.

    Since theory and practice of equal educational opportunity is an issue which is currently confronting decisionmakers at all levels of American education, this handbook presents key federal regulations and Oregon statutes, and administrative rules which provide for equality in employment and in the delivery of educational services. Sources of…

  14. Gender Equality in Teacher Organisations.

    ERIC Educational Resources Information Center

    Lund, Torill Scharning

    1995-01-01

    Most senior trade union posts are held by men, even in organizations where most members are women. The paper examines how the Norwegian Union of Teachers has advanced in this area, noting the status of gender equality in Norway, Norway's work toward gender equality, and the country's focus on educational change. (SM)

  15. 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…

  16. 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…

  17. 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.…

  18. Equalization of data transmission cable

    NASA Technical Reports Server (NTRS)

    Zobrist, G. W.

    1975-01-01

    The paper describes an equalization approach utilizing a simple RLC network which can obtain a maximum slope of -12dB/octave for reshaping the frequency characteristics of a data transmission cable, so that data may be generated and detected at the receiver. An experimental procedure for determining equalizer design specifications using distortion analysis is presented. It was found that for lengths of 16 PEV-L cable of up to 5 miles and data transmission rates of up to 1 Mbs, the equalization scheme proposed here is sufficient for generation of the data with acceptable error rates.

  19. 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)

  20. 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)

  1. 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)

  2. 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)

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

    PubMed Central

    2012-01-01

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

  4. Flood detection/monitoring using adjustable histogram equalization technique.

    PubMed

    Nazir, Fakhera; Riaz, Muhammad Mohsin; Ghafoor, Abdul; Arif, Fahim

    2014-01-01

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

  5. Flood Detection/Monitoring Using Adjustable Histogram Equalization Technique

    PubMed Central

    Riaz, Muhammad Mohsin; Ghafoor, Abdul

    2014-01-01

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

  6. 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

  7. Definitive support by transmission electron microscopy, electron diffraction, and electron density maps for the formation of a BCC lattice from poly[N-[3,4,5-tris(n-dodecan-1-yloxy)benzoyl]ethyleneimine].

    PubMed

    Duan, H; Hudson, S D; Ungar, G; Holerca, M N; Percec, V

    2001-10-01

    Transmission electron microscopy (TEM), electron diffraction (ED), and electron density maps (EDM) experiments were carried out on a poly[N-[3,4,5-tris(n-dodecan-1-yloxy)benzoyl]ethyleneimine] [poly[(3,4,5)12G1-Oxz

  8. 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)

  9. Genomics and equal opportunity ethics.

    PubMed

    Cappelen, A W; Norheim, O F; Tungodden, B

    2008-05-01

    Genomics provides information on genetic susceptibility to diseases and new possibilities for interventions which can fundamentally alter the design of fair health policies. The aim of this paper is to explore implications of genomics from the perspective of equal opportunity ethics. The ideal of equal opportunity requires that individuals are held responsible for some, but not all, factors that affect their health. Informational problems, however, often make it difficult to implement the ideal of equal opportunity in the context of healthcare. In this paper, examples are considered of how new genetic information may affect the way individual responsibility for choice is assigned. It is also argued that genomics may result in relocation of the responsibility cut by providing both new information and new technology. Finally, how genomics may affect healthcare policies and the market for health insurance is discussed. PMID:18448717

  10. 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. PMID:26035838

  11. 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)

  12. 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…

  13. 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)

  14. 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…

  15. Equalizing Educational Opportunity Through Funding.

    ERIC Educational Resources Information Center

    McGary, Carroll R.

    This speech incorporates a major policy statement regarding school subsidies in Maine. The author discusses equality of educational opportunity; and he comments on the property tax, wealth-connected inequities, and class action suits. The speech focuses on a discussion of the Maine subsidy law and its effects; as well as the Maine property, sales,…

  16. The Forces of Information Equality.

    ERIC Educational Resources Information Center

    Davidow, William H.

    1996-01-01

    It is argued that college trustees and campus executives must understand the tools of information technology and be open to the changes created by equalized access to information, even if they threaten traditions and symbols. This means addressing new issues of organizational functions, changes in the order of teaching/learning and life events,…

  17. Religious Freedom vs. Sex Equality

    ERIC Educational Resources Information Center

    Song, Sarah

    2006-01-01

    This essay examines Susan Moller Okin's writing on conflicts between religious freedom and sex equality, and her criticism of "political liberal" approaches to these conflicts, which I take to be a part of her lifelong critique of the public-private distinction. I argue that, while Okin ultimately accepted a version of the distinction, she was…

  18. 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)

  19. Mapping key regions of the RXFP2 low-density lipoprotein class-A module that are involved in signal activation.

    PubMed

    Kong, Roy C K; Bathgate, Ross A D; Bruell, Shoni; Wade, John D; Gooley, Paul R; Petrie, Emma J

    2014-07-22

    The peptide hormone INSL3 and its receptor, RXFP2, have co-evolved alongside relaxin and its receptor, RXFP1. Both RXFP1 and RXFP2 are G protein-coupled receptors (GPCRs) containing the hallmark seven transmembrane helices in addition to a distinct ectodomain of leucine-rich repeats (LRRs) and a single low-density lipoprotein class-A (LDLa) module at the N-terminus. RXFP1 and RXFP2 are the only mammalian GPCRs known to contain an LDLa, and its removal does not perturb primary ligand binding to the LRRs; however, signaling is abolished. This presents a general mechanism whereby ligand binding induces a conformational change in the receptor to position the LDLa to elicit a signal response. Although the LDLa interaction site has not been identified, the residues important to the action have been mapped within the RXFP1 LDLa module. In this study, we comprehensively study the RXFP2 LDLa module. We determine its structure using nuclear magnetic resonance (NMR) and concurrently investigate the signaling of an RXFP2 with the LDLa removed (RXFP2-short), confirming that the LDLa is essential to signaling. We then replaced the LDLa with the second ligand binding module from the LDL receptor, LB2, creating the RXFP2-LB2 chimera. Unlike that in the equivalent RXFP1-LB2 chimera, signaling is rescued albeit modestly. Guided by the NMR structure, we dissected regions of the RXFP2 LDLa to identify specific residues that are important to signal activation. We determine that although the module is important to the activation of RXFP2, unlike the RXFP1 receptor, specific residues in the N-terminus of the domain are not involved in signal activation. PMID:24983702

  20. 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

  1. Resting-state functional connectivity density mapping of etiology confirmed unilateral pulsatile tinnitus patients: Altered functional hubs in the early stage of disease.

    PubMed

    Han, L; Pengfei, Z; Zhaohui, L; Fei, Y; Ting, L; Cheng, D; Zhenchang, W

    2015-12-01

    Functional magnetic resonance imaging (fMRI) has been widely used to identify altered intrinsic local neural activities and global networks of tinnitus patients. In this study, functional connectivity density (FCD) mapping, a newly developed voxelwise data-driven method based on fMRI, was applied for the first time to measure the functional reorganization pattern in thirty-two unilateral pulsatile tinnitus (PT) patients in the early stage of disease (less than 48 months). FCD analysis was employed to compute short-range and long-range FCD values. A correlation analysis with clinical variables was also performed. Compared with normal controls, PT patients showed significantly increased short-range FCD, mainly in the precuneus (PCu), bilateral inferior frontal gyrus (IFG) and middle occipital gyrus (MOG), and increased long-range FCD in the PCu, posterior cingulate cortex (PCC), and bilateral middle frontal gyrus (MFG). In addition, correlation analysis showed positive correlations between PT duration and short-range FCD values in the right MOG. Positive correlations were also found between the disease duration and the long-range FCD value in the PCC. The increased short-/long-range FCD in bilateral dorsal visual areas indicated that the enhanced pathway between the auditory cortex and bilateral dorsal visual areas may have activated the "auditory occipital activations" (AOAs) pathway. The bilaterally altered FCD values in the dorsal visual areas reflected the cooperation of different brain areas. This study is a foundation of the connectivity research in PT patients. Our work may advance the understanding of the disrupted neural network of patients with PT. PMID:26384961

  2. Bias or equality? Unconscious thought equally integrates temporally scattered information.

    PubMed

    Li, Jiansheng; Gao, Qiyang; Zhou, Jifan; Li, Xinyu; Zhang, Meng; Shen, Mowei

    2014-04-01

    In previous experiments on unconscious thought, information was presented to participants in one continuous session; however, in daily life, information is delivered in a temporally partitioned way. We examined whether unconscious thought could equally integrate temporally scattered information when making overall evaluations. When presenting participants with information in two temporally partitioned sessions, participants' overall evaluation was based on neither the information in the first session (Experiment 1) nor that in the second session (Experiment 2); instead, information in both sessions were equally integrated to reach a final judgment. Conscious thought, however, overemphasized information in the second session. Experiments 3 and 4 further ruled out possible influencing factors including differences in the distributions of positive/negative attributes in the first and second sessions and on-line judgment. These findings suggested that unconscious thought can integrate information from a wider range of periods during an evaluation, while conscious thought cannot. PMID:24583456

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

    PubMed

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

    2014-07-01

    A human plasma sample was subjected to nondenaturing micro 2DE and a gel area (5 mm × 18 mm) that includes high-density lipoprotein (HDL) was cut into 1 mm × 1 mm squares, then the proteins in the 90 gel pieces were analyzed by quantitative LC-MS/MS. Grid-cutting of the gel was employed to; (i) ensure the total analysis of the proteins in the area, (ii) standardize the conditions of analysis by LC-MS/MS, (iii) reconstruct the protein distribution patterns from the quantity data. Totally 154 proteins were assigned in the 90 gel pieces and the quantity distribution of each was reconstructed as a color density pattern (a native protein map). The map of apolipoprotein (Apo) A-I showed a wide apparent mass distribution characteristic to HDL and was compared with the maps of the other 153 proteins. Eleven proteins showed maps of wide distribution that overlapped with the map of Apo A-I, and all have been reported to be the components of HDL. Further, seven minor proteins associated with HDL were detected at the gel positions of high Apo A-I quantity. These results for the first time visualized the localization of HDL apolipoproteins on a nondenaturing 2DE gel and strongly suggested their interactions. PMID:24668886

  4. 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.

  5. 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.

  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. PMID:25303360

  8. 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

  9. 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. PMID:10578045

  10. 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

  11. Shape from equal thickness contours

    SciTech Connect

    Cong, G.; Parvin, B.

    1998-05-10

    A unique imaging modality based on Equal Thickness Contours (ETC) has introduced a new opportunity for 3D shape reconstruction from multiple views. We present a computational framework for representing each view of an object in terms of its object thickness, and then integrating these representations into a 3D surface by algebraic reconstruction. The object thickness is inferred by grouping curve segments that correspond to points of second derivative maxima. At each step of the process, we use some form of regularization to ensure closeness to the original features, as well as neighborhood continuity. We apply our approach to images of a sub-micron crystal structure obtained through a holographic process.

  12. 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…

  13. 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.

  14. Time resolved interferometric study of the plasma plume induced shock wave in confined geometry: Two-dimensional mapping of the ambient and plasma density

    NASA Astrophysics Data System (ADS)

    Choudhury, Kaushik; Singh, R. K.; Narayan, Surya; Srivastava, Atul; Kumar, Ajai

    2016-04-01

    An experimental investigation of the laser produced plasma induced shock wave in the presence of confining walls placed along the axial as well as the lateral direction has been performed. A time resolved Mach Zehnder interferometer is set up to track the primary as well as the reflected shock waves and its effect on the evolving plasma plume has been studied. An attempt has been made to discriminate the electronic and medium density contributions towards the changes in the refractive index of the medium. Two dimensional spatial distributions for both ambient medium density and plasma density (electron density) have been obtained by employing customised inversion technique and algorithm on the recorded interferograms. The observed density pattern of the surrounding medium in the presence of confining walls is correlated with the reflected shock wave propagation in the medium. Further, the shock wave plasma interaction and the subsequent changes in the shape and density of the plasma plume in confined geometry are briefly described.

  15. Gender equality and women empowerment.

    PubMed

    Dargan, R

    1996-01-01

    This article lists 11 suggestions for empowering women that the government of India should take, if it has a sincere commitment to gender equality and women's empowerment grounded in social change and not just rhetoric: 1) education should be made compulsory for all female children and places held on a 50/50 basis in all technical institutions; 2) a uniform civil code should be adopted for all citizens regardless of cast, creed, and religion; 3) women should have an equal right to own property and receive inheritance; 4) the National Women's Commission should be enlarged, representative of diversity, and effective in making policy decisions related to welfare, education, recruitment, and promotion; 5) a State Women's Commission should be established with affiliates at the block, district, and division levels; 6) the National and State Women's Commission should be established as a Statutory Body with binding decisions mandating government action; 7) the National and State Women's Commissions should have transparent functions, be regulatory, and offer workshops and seminars for women; 8) state governments should not interfere in the functions of National and State Women's Commissions; 9) women should fill 50% of all Center and State government service posts and concessions should be made on minimum academic qualifications and completed years of service, until all positions are filled; 10) 50% of the seats of Parliament should be reserved for women in both the State Legislature, Council of Ministry Boards, Corporations, Committees, and Commissions; and 11) the Constitution should provide for women judges in courts of law. PMID:12179426

  16. A 1. 8-Mb YAC contig in Xp11. 23: Identification of Cpg islands and physical mapping of CA repeats in a region of high gene density

    SciTech Connect

    Coleman, M.P.; Nemeth, A.H.; Campbell, L.; Raut, C.P.; Davies, K.E. ); Weissenbach, J. )

    1994-05-15

    The genes ARAF1, SYN1, TIMP, and PFC are clustered within 70 kb of one another, and, as reported in the accompanying paper, at least four more genes map within 400 kb: a cluster of Krueppel-type zinc finger genes (including ZNF21, ZNF41, and ZNF81) and ELK-1, a member of the ets oncogene superfamily. This gene-rich region is of particular interest because of the large number of disease genes mapping to Xp11.23: At least three eye diseases (retinitis pigmentosa type 2, congenital stationary night blindness CSNB1, and Aland Island eye disease), Wiskott-Aldrich syndrome, X-linked nephrolithiasis, and a translocation breakpoint associated with synovial sarcoma. The authors have constructed a 1.8-Mb YAC contig in this region, confirming the link between TIMP and OATL1 reported by Knight et al. (1994) and extending the map in the distal direction. To investigate the likelihood that more genes are located within this region, they have carried out detailed mapping of rare-cutter restriction sites in these YACs and identified seven CpG islands. At least six of these islands are located over 50 kb from any known gene locations, suggesting that the region contains at least this many as yet unidentified genes. They have also mapped the physical locations of six highly polymorphic CA repeats within the contig, thus integrating the physical, genetic, and transcriptional maps of the region and facilitating the mapping and identification of disease genes. Together with the report by Knight et al., these data indicate the following order of loci: Xpter-DXS1264-DXS1055-DXS1003-DXS1146-DXS1266-(ZNF41, ARAF1)-SYN1 CA repeat-SYN1 (3[prime] end)-TIMP-SYN1 (5[prime] end)-PFC CA repeat-PFC-(DXS426, ELK1)-(DXS1265, ZNF81)-ZNF21-DXS1267-OATL1-Xcen. 40 refs., 4 figs., 3 tabs.

  17. Klystron equalization for RF feedback

    SciTech Connect

    Corredoura, P.

    1993-01-01

    The next generation of colliding beam storage rings support higher luminosities by significantly increasing the number of bunches and decreasing the spacing between respective bunches. The heavy beam loading requires large RF cavity detuning which drives several lower coupled bunch modes very strongly. One technique which has proven to be very successful in reducing the coupled bunch mode driving impedance is RF feedback around the klystron-cavity combination. The gain and bandwidth of the feedback loop is limited by the group delay around the feedback loop. Existing klystrons on the world market have not been optimized for this application and contribute a large portion of the total loop group delay. This paper describes a technique to reduce klystron group delay by adding an equalizing filter to the klystron RF drive. Such a filter was built and tested on a 500 kill klystron as part of the on going PEP-II R D effort here at SLAC.

  18. Klystron equalization for RF feedback

    SciTech Connect

    Corredoura, P.

    1993-01-01

    The next generation of colliding beam storage rings support higher luminosities by significantly increasing the number of bunches and decreasing the spacing between respective bunches. The heavy beam loading requires large RF cavity detuning which drives several lower coupled bunch modes very strongly. One technique which has proven to be very successful in reducing the coupled bunch mode driving impedance is RF feedback around the klystron-cavity combination. The gain and bandwidth of the feedback loop is limited by the group delay around the feedback loop. Existing klystrons on the world market have not been optimized for this application and contribute a large portion of the total loop group delay. This paper describes a technique to reduce klystron group delay by adding an equalizing filter to the klystron RF drive. Such a filter was built and tested on a 500 kill klystron as part of the on going PEP-II R&D effort here at SLAC.

  19. Brightness-equalized quantum dots

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

    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.

  20. 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

  1. Extended equal area criterion revisited

    SciTech Connect

    Xue, X.; Wehenkel, L.; Belhomme, R.; Rousseaux, P.; Pavella, M. ); Euxibie, E.; Heilbronn, B.; Lesigne, J.F. )

    1992-08-01

    This paper reports on a case study conducted on the EHV French power system in order to revisit the extended equal area criterion and test its suitability as a fast transient stability indicator. The assumptions underlying the method are reexamined, causes liable to invalidate them are identified, and indices are devised to automatically circumvent them. The selection of candidate critical machines is also reconsidered and an augmented criterion is proposed. The various improvements are developed and tested on about 1000 stability scenarios, covering the entire 400-kV system; the severity of the scenarios, resulting from the combination of weakened both pre- and post-fault configurations, subjects the method to particularly stringent conditions. The obtained results show that the devised tools contribute to significantly reinforce its robustness and reliability.

  2. 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.

  3. Development and characterization of BAC-end sequence derived SSRs, and their incorporation into a new higher density genetic map for cultivated peanut (Arachis hypogaea L.)

    PubMed Central

    2012-01-01

    Background Cultivated peanut (Arachis hypogaea L.) is an important crop worldwide, valued for its edible oil and digestible protein. It has a very narrow genetic base that may well derive from a relatively recent single polyploidization event. Accordingly molecular markers have low levels of polymorphism and the number of polymorphic molecular markers available for cultivated peanut is still limiting. Results Here, we report a large set of BAC-end sequences (BES), use them for developing SSR (BES-SSR) markers, and apply them in genetic linkage mapping. The majority of BESs had no detectable homology to known genes (49.5%) followed by sequences with similarity to known genes (44.3%), and miscellaneous sequences (6.2%) such as transposable element, retroelement, and organelle sequences. A total of 1,424 SSRs were identified from 36,435 BESs. Among these identified SSRs, dinucleotide (47.4%) and trinucleotide (37.1%) SSRs were predominant. The new set of 1,152 SSRs as well as about 4,000 published or unpublished SSRs were screened against two parents of a mapping population, generating 385 polymorphic loci. A genetic linkage map was constructed, consisting of 318 loci onto 21 linkage groups and covering a total of 1,674.4 cM, with an average distance of 5.3 cM between adjacent loci. Two markers related to resistance gene homologs (RGH) were mapped to two different groups, thus anchoring 1 RGH-BAC contig and 1 singleton. Conclusions The SSRs mined from BESs will be of use in further molecular analysis of the peanut genome, providing a novel set of markers, genetically anchoring BAC clones, and incorporating gene sequences into a linkage map. This will aid in the identification of markers linked to genes of interest and map-based cloning. PMID:22260238

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

    PubMed

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

    2015-08-01

    Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is an economically important vegetable crop grown extensively worldwide. To facilitate the identification of agronomically important traits and provide new information for genetic and genomic research on this species, a high-density genetic linkage map of watermelon was constructed using an F2 population derived from a cross between elite watermelon cultivar K3 and wild watermelon germplasm PI 189225. Based on a sliding window approach, a total of 1,161 bin markers representing 3,465 SNP markers were mapped onto 11 linkage groups corresponding to the chromosome pair number of watermelon. The total length of the genetic map is 1,099.2 cM, with an average distance between bins of 1.0 cM. The number of markers in each chromosome varies from 62 in chromosome 07 to 160 in chromosome 05. The length of individual chromosomes ranged between 61.8 cM for chromosome 07 and 140.2 cM for chromosome 05. A total of 616 SNP bin markers showed significant (P < 0.05) segregation distortion across all 11 chromosomes, and 513 (83.3 %) of these distorted loci showed distortion in favor of the elite watermelon cultivar K3 allele and 103 were skewed toward PI 189225. The number of SNPs and InDels per Mb varied considerably across the segregation distorted regions (SDRs) on each chromosome, and a mixture of dense and sparse SNPs and InDel SDRs coexisted on some chromosomes suggesting that SDRs were randomly distributed throughout the genome. Recombination rates varied greatly among each chromosome, from 2.0 to 4.2 centimorgans per megabase (cM/Mb). An inconsistency was found between the genetic and physical positions on the map for a segment on chromosome 11. The high-density genetic map described in the present study will facilitate fine mapping of quantitative trait loci, the identification of candidate genes, map-based cloning, as well as marker-assisted selection (MAS) in watermelon breeding programs. PMID:25702268

  5. 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

  6. 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.

  7. 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.

  8. 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)

  9. The neural bases for valuing social equality.

    PubMed

    Aoki, Ryuta; Yomogida, Yukihito; Matsumoto, Kenji

    2015-01-01

    The neural basis of how humans value and pursue social equality has become a major topic in social neuroscience research. Although recent studies have identified a set of brain regions and possible mechanisms that are involved in the neural processing of equality of outcome between individuals, how the human brain processes equality of opportunity remains unknown. In this review article, first we describe the importance of the distinction between equality of outcome and equality of opportunity, which has been emphasized in philosophy and economics. Next, we discuss possible approaches for empirical characterization of human valuation of equality of opportunity vs. equality of outcome. Understanding how these two concepts are distinct and interact with each other may provide a better explanation of complex human behaviors concerning fairness and social equality. PMID:25452125

  10. 34 CFR 108.6 - Equal access.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 1 2010-07-01 2010-07-01 false Equal access. 108.6 Section 108.6 Education Regulations of the Offices of the Department of Education OFFICE FOR CIVIL RIGHTS, DEPARTMENT OF EDUCATION EQUAL ACCESS TO PUBLIC SCHOOL FACILITIES FOR THE BOY SCOUTS OF AMERICA AND OTHER DESIGNATED YOUTH GROUPS § 108.6 Equal access. (a) General....

  11. 76 FR 59237 - Equal Credit Opportunity

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-26

    ... 7100 AD 78 Equal Credit Opportunity AGENCY: Board of Governors of the Federal Reserve System. ACTION: Final rule. SUMMARY: The Board is publishing a final rule amending Regulation B (Equal Credit Opportunity). Section 704B of the Equal Credit Opportunity Act (ECOA), as added by Section 1071 of the...

  12. 45 CFR 98.43 - Equal access.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 1 2010-10-01 2010-10-01 false Equal access. 98.43 Section 98.43 Public Welfare... Operations (Child Care Services)-Lead Agency and Provider Requirements § 98.43 Equal access. (a) The Lead... sufficient to ensure equal access, for eligible families in the area served by the Lead Agency, to child...

  13. 45 CFR 98.43 - Equal access.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 1 2011-10-01 2011-10-01 false Equal access. 98.43 Section 98.43 Public Welfare... Operations (Child Care Services)-Lead Agency and Provider Requirements § 98.43 Equal access. (a) The Lead... sufficient to ensure equal access, for eligible families in the area served by the Lead Agency, to child...

  14. Does 0.999... Really Equal 1?

    ERIC Educational Resources Information Center

    Norton, Anderson; Baldwin, Michael

    2012-01-01

    This article confronts the issue of why secondary and post-secondary students resist accepting the equality of 0.999... and 1, even after they have seen and understood logical arguments for the equality. In some sense, we might say that the equality holds by definition of 0.999..., but this definition depends upon accepting properties of the real…

  15. A Genome-wide Analysis of Admixture in Uyghurs and a High-Density Admixture Map for Disease-Gene Discovery

    PubMed Central

    Xu, Shuhua; Jin, Li

    2008-01-01

    Following up on our previous study, we conducted a genome-wide analysis of admixture for two Uyghur population samples (HGDP-UG and PanAsia-UG), collected from the northern and southern regions of Xinjiang in China, respectively. Both HGDP-UG and PanAsia-UG showed a substantial admixture of East-Asian (EAS) and European (EUR) ancestries, with an empirical estimation of ancestry contribution of 53:47 (EAS:EUR) and 48:52 for HGDP-UG and PanAsia-UG, respectively. The effective admixture time under a model with a single pulse of admixture was estimated as 110 generations and 129 generations, or admixture events occurred about 2200 and 2580 years ago for HGDP-UG and PanAsia-UG, respectively, assuming an average of 20 yr per generation. Despite Uyghurs' earlier history compared to other admixture populations, admixture mapping, holds promise for this population, because of its large size and its mixture of ancestry from different continents. We screened multiple databases and identified a genome-wide single-nucleotide polymorphism panel that can distinguish EAS and EUR ancestry of chromosomal segments in Uyghurs. The panel contains 8150 ancestry-informative markers (AIMs) showing large frequency differences between EAS and EUR populations (FST > 0.25, mean FST = 0.43) but small frequency differences (7999 AIMs validated) within both populations (FST < 0.05, mean FST < 0.01). We evaluated the effectiveness of this admixture map for localizing disease genes in two Uyghur populations. To our knowledge, our map constitutes the first practical resource for admixture mapping in Uyghurs, and it will enable studies of diseases showing differences in genetic risk between EUR and EAS populations. PMID:18760393

  16. 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

  17. Map-likelihood phasing

    PubMed Central

    Terwilliger, Thomas C.

    2001-01-01

    The recently developed technique of maximum-likelihood density modification [Terwilliger (2000 ▶), Acta Cryst. D56, 965–972] allows a calculation of phase probabilities based on the likelihood of the electron-density map to be carried out separately from the calculation of any prior phase probabilities. Here, it is shown that phase-probability distributions calculated from the map-likelihood function alone can be highly accurate and that they show minimal bias towards the phases used to initiate the calculation. Map-likelihood phase probabilities depend upon expected characteristics of the electron-density map, such as a defined solvent region and expected electron-density distributions within the solvent region and the region occupied by a macromolecule. In the simplest case, map-likelihood phase-probability distributions are largely based on the flatness of the solvent region. Though map-likelihood phases can be calculated without prior phase information, they are greatly enhanced by high-quality starting phases. This leads to the technique of prime-and-switch phasing for removing model bias. In prime-and-switch phasing, biased phases such as those from a model are used to prime or initiate map-likelihood phasing, then final phases are obtained from map-likelihood phasing alone. Map-likelihood phasing can be applied in cases with solvent content as low as 30%. Potential applications of map-likelihood phasing include unbiased phase calculation from molecular-replacement models, iterative model building, unbiased electron-density maps for cases where 2Fo − Fc or σA-weighted maps would currently be used, structure validation and ab initio phase determination from solvent masks, non-crystallographic symmetry or other knowledge about expected electron density. PMID:11717488

  18. 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.

  19. 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…

  20. High-density molecular characterization and association mapping in Ethiopian durum wheat landraces reveals high diversity and potential for wheat breeding.

    PubMed

    Mengistu, Dejene Kassahun; Kidane, Yosef Gebrehawaryat; Catellani, Marcello; Frascaroli, Elisabetta; Fadda, Carlo; Pè, Mario Enrico; Dell'Acqua, Matteo

    2016-09-01

    Durum wheat (Triticum turgidum subsp. durum) is a key crop worldwide, and yet, its improvement and adaptation to emerging environmental threats is made difficult by the limited amount of allelic variation included in its elite pool. New allelic diversity may provide novel loci to international crop breeding through quantitative trait loci (QTL) mapping in unexplored material. Here, we report the extensive molecular and phenotypic characterization of hundreds of Ethiopian durum wheat landraces and several Ethiopian improved lines. We test 81 587 markers scoring 30 155 single nucleotide polymorphisms and use them to survey the diversity, structure, and genome-specific variation in the panel. We show the uniqueness of Ethiopian germplasm using a siding collection of Mediterranean durum wheat accessions. We phenotype the Ethiopian panel for ten agronomic traits in two highly diversified Ethiopian environments for two consecutive years and use this information to conduct a genome-wide association study. We identify several loci underpinning agronomic traits of interest, both confirming loci already reported and describing new promising genomic regions. These loci may be efficiently targeted with molecular markers already available to conduct marker-assisted selection in Ethiopian and international wheat. We show that Ethiopian durum wheat represents an important and mostly unexplored source of durum wheat diversity. The panel analysed in this study allows the accumulation of QTL mapping experiments, providing the initial step for a quantitative, methodical exploitation of untapped diversity in producing a better wheat. PMID:26853077

  1. 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.

  2. 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

  3. 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

  4. High-density genetic and physical mapping of DNA markers near the X-linked Alport syndrome locus: definition and use of flanking polymorphic markers.

    PubMed

    Barker, D F; Fain, P R; Goldgar, D E; Dietz-Band, J N; Turco, A E; Kashtan, C E; Gregory, M C; Tryggvason, K; Skolnick, M H; Atkin, C L

    1991-12-01

    To refine the genetic and physical mapping of the locus for Alport syndrome (ATS), 22 X-chromosome restriction fragment length polymorphism (RFLP) markers that fall between Xq21.3 and Xq25 were tested for genetic linkage with the disease and also mapped with respect to a series of physical breakpoints in this region. The location of the COL4A5 gene, which has recently been shown to be mutated in at least some families with Alport syndrome, was determined with respect to the same physical breakpoints. Two large Utah kindreds were included in the genetic studies, kindreds P and C, with 125 and 63 potentially informative meioses, respectively. Both kindreds have essentially identical nephritis; however, kindred P has sensorineural hearing loss associated with the nephritis, while kindred C does not. A mutation in COL4A5 has been demonstrated for kindred P, but no change in this gene has yet been detected for kindred C. Twelve informative probes did not recombine with the disease locus in either kindred (theta = 0.0, with combined lod scores for the two kindreds ranging from 7.7 to 30.0). The closest markers that could be demonstrated to flank the disease locus were the same for each kindred and thus the locations of the mutations causing the two disease phenotypes are not distinguishable at the current level of genetic resolution. The flanking markers are also useful for the resolution of questionable diagnoses and allow accurate estimates for these families of the rate of sporadic hematuria in noncarrier females (7%) and the penetrance of hematuria for carrier females (93%). PMID:1684566

  5. A ChIP-seq-defined genome-wide map of MEF2C binding reveals inflammatory pathways associated with its role in bone density determination.

    PubMed

    Johnson, Matthew E; Deliard, Sandra; Zhu, Fengchang; Xia, Qianghua; Wells, Andrew D; Hankenson, Kurt D; Grant, Struan F A

    2014-04-01

    Genome-wide association studies (GWAS) have demonstrated that genetic variation at the MADS box transcription enhancer factor 2, polypeptide C (MEF2C) locus is robustly associated with bone mineral density, primarily at the femoral neck. MEF2C is a transcription factor known to operate via the Wnt signaling pathway. Our hypothesis was that MEF2C regulates the expression of a set of molecular pathways critical to skeletal function. Drawing on our laboratory and bioinformatic experience with ChIP-seq, we analyzed ChIP-seq data for MEF2C available via the ENCODE project to gain insight in to its global genomic binding pattern. We aligned the ChIP-seq data generated for GM12878 (an established lymphoblastoid cell line) and, using the analysis package HOMER, a total of 17,611 binding sites corresponding to 8,118 known genes were observed. We then performed a pathway analysis of the gene list using Ingenuity. At 5 kb, the gene list yielded 'EIF2 Signaling' as the most significant annotation, with a P value of 5.01 × 10(-26). Moving further out, this category remained the top pathway at 50 and 100 kb, then dropped to just second place at 500 kb and beyond by 'Molecular Mechanisms of Cancer'. In addition, at 50 kb and beyond 'RANK Signaling in Osteoclasts' was a consistent feature and resonates with the main general finding from GWAS of bone density. We also observed that MEF2C binding sites were significantly enriched primarily near inflammation associated genes identified from GWAS; indeed, a similar enrichment for inflammation genes has been reported previously using a similar approach for the vitamin D receptor, an established key regulator of bone turnover. Our analyses point to known connective tissue and skeletal processes but also provide novel insights in to networks involved in skeletal regulation. The fact that a specific GWAS category is enriched points to a possible role of inflammation through which it impacts bone mineral density. PMID:24337390

  6. 78 FR 53231 - Women's Equality Day, 2013

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-28

    ... hundred and thirty- eighth. (Presidential Sig.) [FR Doc. 2013-21188 Filed 8-27-13; 11:15 am] Billing code... march toward gender equality. We have fought for equal pay, prohibited gender discrimination in America... strategy to close any gender pay gap within the Federal workforce. To build on this work, I will...

  7. 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...

  8. 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...

  9. 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...

  10. 49 CFR 236.792 - Reservoir, equalizing.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 4 2010-10-01 2010-10-01 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, 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...

  12. School Law: A Question of Equality.

    ERIC Educational Resources Information Center

    Dowling-Sendor, Benjamin

    2003-01-01

    This article discusses the Equal Access Act (EAA) as it pertains to high-school student clubs. It raises basics questions about EAA: What does "equal" mean? What level of access is required? Does the First Amendment's free-speech clause offer broader protection to student clubs than the EAA? (WFA)

  13. Combining Vector Quantization and Histogram Equalization.

    ERIC Educational Resources Information Center

    Cosman, Pamela C.; And Others

    1992-01-01

    Discussion of contrast enhancement techniques focuses on the use of histogram equalization with a data compression technique, i.e., tree-structured vector quantization. The enhancement technique of intensity windowing is described, and the use of enhancement techniques for medical images is explained, including adaptive histogram equalization.…

  14. 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…

  15. 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)

  16. Brown and the Politics of Equality.

    ERIC Educational Resources Information Center

    Brown, Frank

    1994-01-01

    Assesses the progress of equality since Brown v Topeka Board of Education and argues that there still has not been a full implementation of that Supreme Court decree. School integration is shown to be declining. It is recommended that The court could merge the equality standards of Plessy v Ferguson with Brown to provide quality education. (GR)

  17. 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

  18. 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

  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. 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.

  1. 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

  2. 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

  3. Nonequilibrium equalities in absolutely irreversible processes

    NASA Astrophysics Data System (ADS)

    Murashita, Yuto; Funo, Ken; Ueda, Masahito

    2015-03-01

    Nonequilibrium equalities have attracted considerable attention in the context of statistical mechanics and information thermodynamics. Integral nonequilibrium equalities reveal an ensemble property of the entropy production σ as = 1 . Although nonequilibrium equalities apply to rather general nonequilibrium situations, they break down in absolutely irreversible processes, where the forward-path probability vanishes and the entropy production diverges. We identify the mathematical origins of this inapplicability as the singularity of probability measure. As a result, we generalize conventional integral nonequilibrium equalities to absolutely irreversible processes as = 1 -λS , where λS is the probability of the singular part defined based on Lebesgue's decomposition theorem. The acquired equality contains two physical quantities related to irreversibility: σ characterizing ordinary irreversibility and λS describing absolute irreversibility. An inequality derived from the obtained equality demonstrates the absolute irreversibility leads to the fundamental lower bound on the entropy production. We demonstrate the validity of the obtained equality for a simple model.

  4. 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

  5. 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

  6. New spatial diversity equalizer based on PLL

    NASA Astrophysics Data System (ADS)

    Rao, Wei

    2011-10-01

    A new Spatial Diversity Equalizer (SDE) based on phase-locked loop (PLL) is proposed to overcome the inter-symbol interference (ISI) and phase rotations simultaneously in the digital communication system. The proposed SDE consists of equal gain combining technique based on a famous blind equalization algorithm constant modulus algorithm (CMA) and a PLL. Compared with conventional SDE, the proposed SDE has not only faster convergence rate and lower residual error but also the ability to recover carrier phase rotation. The efficiency of the method is proved by computer simulation.

  7. Contributorships Are Not 'Weighable' to be Equal.

    PubMed

    Moustafa, Khaled

    2016-05-01

    A new trend to assign some authors as 'first co-authors' is noticeable in scientific publications as a statement highlighting that two or more authors 'contributed equally' to a reported work. However, the requirements of scientific rigor, honesty, and accuracy in academic standards make such statements invalid and, thus, should be avoided. A potential solution is to specify the role of each co-author, from study conception to communication of results, and let readers judge the importance of each contribution by themselves. Alternatively, authors should demonstrate how they contributed 'equally' when they are defined as 'equal contributors'. PMID:27025412

  8. 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.

  9. 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.

  10. 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)

  11. 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...

  12. 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...

  13. 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.

  14. 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...

  15. 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

  16. 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...

  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, 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...

  20. 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...

  1. The influence of the modulus-density relationship and the material mapping method on the simulated mechanical response of the proximal femur in side-ways fall loading configuration.

    PubMed

    Helgason, B; Gilchrist, S; Ariza, O; Vogt, P; Enns-Bray, W; Widmer, R P; Fitze, T; Pálsson, H; Pauchard, Y; Guy, P; Ferguson, S J; Cripton, P A

    2016-07-01

    Contributing to slow advance of finite element (FE) simulations for hip fracture risk prediction, into clinical practice, could be a lack of consensus in the biomechanics community on how to map properties to the models. Thus, the aim of the present study was first, to systematically quantify the influence of the modulus-density relationship (E-ρ) and the material mapping method (MMM) on the predicted mechanical response of the proximal femur in a side-ways fall (SWF) loading configuration and second, to perform a model-to-model comparison of the predicted mechanical response within the femoral neck for all the specimens tested in the present study, using three different modelling techniques that have yielded good validation outcome in terms of surface strain prediction and whole bone response according to the literature. We found the outcome to be highly dependent on both the E-ρ relationship and the MMM. In addition, we found that the three modelling techniques that have resulted in good validation outcome in the literature yielded different principal strain prediction both on the surface as well as internally in the femoral neck region of the specimens modelled in the present study. We conclude that there exists a need to carry out a more comprehensive validation study for the SWF loading mode to identify which combination of MMMs and E-ρ relationship leads to the best match for whole bone and local mechanical response. The MMMs tested in the present study have been made publicly available at https://simtk.org/home/mitk-gem. PMID:27185044

  2. Overpaying morbidity adjusters in risk equalization models.

    PubMed

    van Kleef, R C; van Vliet, R C J A; van de Ven, W P M M

    2016-09-01

    Most competitive social health insurance markets include risk equalization to compensate insurers for predictable variation in healthcare expenses. Empirical literature shows that even the most sophisticated risk equalization models-with advanced morbidity adjusters-substantially undercompensate insurers for selected groups of high-risk individuals. In the presence of premium regulation, these undercompensations confront consumers and insurers with incentives for risk selection. An important reason for the undercompensations is that not all information with predictive value regarding healthcare expenses is appropriate for use as a morbidity adjuster. To reduce incentives for selection regarding specific groups we propose overpaying morbidity adjusters that are already included in the risk equalization model. This paper illustrates the idea of overpaying by merging data on morbidity adjusters and healthcare expenses with health survey information, and derives three preconditions for meaningful application. Given these preconditions, we think overpaying may be particularly useful for pharmacy-based cost groups. PMID:26420555

  3. 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…

  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. 34 CFR 108.6 - Equal access.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... limited to, school-related means of communication, such as bulletin board notices and literature... ACCESS TO PUBLIC SCHOOL FACILITIES FOR THE BOY SCOUTS OF AMERICA AND OTHER DESIGNATED YOUTH GROUPS § 108... equal access to school premises or facilities to conduct meetings. (2) Benefits and services. Any...

  6. The Equal Access Act: Recent Court Decisions.

    ERIC Educational Resources Information Center

    Bjorklun, Eugene C.

    1989-01-01

    Examines court decisions which led to the passage of the Equal Access Act of 1984. Although the act was designed to clarify the issue over the legality of permitting religious clubs to meet on school property, it may have created more confusion. Concludes that the Supreme Court may have to decide the issue. (SLM)

  7. The Path to Equal Rights in Michigan

    ERIC Educational Resources Information Center

    Gratz, Jennifer

    2007-01-01

    The litigant in a historic reverse-discrimination case against the University of Michigan, and subsequently the leader of a Michigan ballot initiative that carried the day against long odds, recounts how her simple call for equal treatment under the law persuaded the people of her state that color-conscious preferences are wrong.

  8. The Internet and Equality of Educational Opportunity.

    ERIC Educational Resources Information Center

    Schofield, Janet Ward; Davidson, Ann Locke

    One benefit often expected to flow from Internet use in schools is an increase in equality of educational opportunity as all kinds of schools gain access to the same extraordinary set of resources. Yet, prior research suggests that patterns of technology access often mirror existing inequalities rather than mitigate them. This paper discusses the…

  9. An American Perspective on Equal Educational Opportunities

    ERIC Educational Resources Information Center

    Russo, Charles; Perkins, Brian

    2004-01-01

    The United States Supreme Court ushered in a new era in American history on May 17, 1954 in its monumental ruling in "Brown v Board of Education," Topeka, Kansas. "Brown" is not only the Court's most significant decision on race and equal educational opportunities, but also ranks among the most important cases it has ever decided. In "Brown" a…

  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. Power Equalization through Organization Development Training.

    ERIC Educational Resources Information Center

    Bartunek, Jean M.; Keys, Christopher B.

    The effects of a three-year Organization Development (OD) intervention on power equalization were examined in seven experimental and seven control schools. The principals and teachers from experimental schools participated in OD workshops, in a project-coordinating council for planning and policy, and in school goal-setting activities. The power…

  12. 75 FR 53559 - Women's Equality Day, 2010

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-31

    ... hundred and thirty-fifth. (Presidential Sig.) [FR Doc. 2010-21904 Filed 8-30-10; 11:15 am] Billing code... education and economic opportunity, face gender-based violence, and cannot participate fully and equally in... to all Americans, regardless of gender, race, ethnicity, sexual orientation, disability,...

  13. Race Equality Scheme 2005-2008

    ERIC Educational Resources Information Center

    Her Majesty's Inspectorate of Education, 2005

    2005-01-01

    Her Majesty's Inspectorate of Education (HMIE) is strongly committed to promoting race equality in the way that HMIE staff go about performing their role within Scottish education. Scottish society reflects cultural, ethnic, religious and linguistic diversity and Scottish education should be accessible to all. No-one should be disadvantaged or…

  14. When Equal Masses Don't Balance

    ERIC Educational Resources Information Center

    Newburgh, Ronald; Peidle, Joseph; Rueckner, Wolfgang

    2004-01-01

    We treat a modified Atwood's machine in which equal masses do not balance because of being in an accelerated frame of reference. Analysis of the problem illuminates the meaning of inertial forces, d'Alembert's principle, the use of free-body diagrams and the selection of appropriate systems for the diagrams. In spite of the range of these…

  15. Great Constitutional Ideas: Justice, Equality, and Property.

    ERIC Educational Resources Information Center

    Starr, Isidore

    1987-01-01

    Examines the ideas of justice, equality, and property as they are represented in the Declaration of Independence, the U.S. Constitution and the Bill of Rights. Discusses how these ideas affect the way public schools operate and the lessons educators teach or don't teach about our society. Includes ideas for classroom activities. (JDH)

  16. 77 FR 52583 - Women's Equality Day, 2012

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-29

    ... Independence of the United States of America the two hundred and thirty- seventh. (Presidential Sig.) [FR Doc... August 29, 2012 Part IV The President Proclamation 8848--Women's Equality Day, 2012 #0; #0; #0... / Presidential Documents#0;#0; #0; #0;Title 3-- #0;The President ] Proclamation 8848 of August 24, 2012...

  17. 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... 7 Agriculture 6 2010-01-01 2010-01-01 false Equal opportunity. 622.6 Section 622.6 Agriculture Regulations of the Department of Agriculture (Continued) NATURAL RESOURCES CONSERVATION SERVICE, DEPARTMENT...

  18. Three Utilities for the Equal Sign

    ERIC Educational Resources Information Center

    Jones, Ian; Pratt, Dave

    2005-01-01

    We compare the activity of young children using a microworld and a JavaScript relational calculator with the literature on children using traditional calculators. We describe how the children constructed different meanings for the equal sign in each setting. It appears that the nature of the meaning constructed is highly dependent on specificities…

  19. Disability in the UK: Measuring Equality

    ERIC Educational Resources Information Center

    Purdam, Kingsley; Afkhami, Reza; Olsen, Wendy; Thornton, Patricia

    2008-01-01

    In this article we identify the key survey data for examining the issue of equality in the lives of disabled people in the UK. Such data is essential for assessing change in quality of life over time and for the evaluation of the impact of policy initiatives. For each data source we consider definitions, data collection, issue coverage, sample…

  20. Position Paper: NO equals x Measurement

    ERIC Educational Resources Information Center

    Hauser, Thomas R.; Shy, Carl M.

    1972-01-01

    Doubts about the accuracy of measured concentrations of nitrogen dioxide (NO 2) in ambient air have led the Environmental Protection Agency to reassess both the analytical technique and the extent to which nitrogen oxides (NO equals x) control will need to satisfy federal laws. (BL)