Acquisition and Processing of High Resolution Hyperspectral Imageries for the 3d Mapping of Urban Heat Islands and Microparticles of Montreal

NASA Astrophysics Data System (ADS)

Mongeau, R.; Baudouin, Y.; Cavayas, F.

2017-10-01

Ville de Montreal wanted to develop a system to identify heat islands and microparticles at the urban scale and to study their formation. UQAM and UdeM universities have joined their expertise under the framework "Observatoire Spatial Urbain" to create a representative geospatial database of thermal and atmospheric parameters collected during the summer months. They innovated in the development of a methodology for processing high resolution hyperspectral images (1-2 m). In partnership with Ville de Montreal, they integrated 3D geospatial data (topography, transportation and meteorology) in the process. The 3D mapping of intraurban heat islands as well as air micro-particles makes it possible, initially, to identify the problematic situations for future civil protection interventions during extreme heat. Moreover, it will be used as a reference for the Ville de Montreal to establish a strategy for public domain tree planting and in the analysis of urban development projects.

Comparative Transcriptomic Approaches Exploring Contamination Stress Tolerance in Salix sp. Reveal the Importance for a Metaorganismal de Novo Assembly Approach for Nonmodel Plants1[OPEN

PubMed Central

Brereton, Nicholas J. B.; Marleau, Julie; Nissim, Werther Guidi; Labrecque, Michel; Joly, Simon; Pitre, Frederic E.

2016-01-01

Metatranscriptomic study of nonmodel organisms requires strategies that retain the highly resolved genetic information generated from model organisms while allowing for identification of the unexpected. A real-world biological application of phytoremediation, the field growth of 10 Salix cultivars on polluted soils, was used as an exemplar nonmodel and multifaceted crop response well-disposed to the study of gene expression. Sequence reads were assembled de novo to create 10 independent transcriptomes, a global transcriptome, and were mapped against the Salix purpurea 94006 reference genome. Annotation of assembled contigs was performed without a priori assumption of the originating organism. Global transcriptome construction from 3.03 billion paired-end reads revealed 606,880 unique contigs annotated from 1588 species, often common in all 10 cultivars. Comparisons between transcriptomic and metatranscriptomic methodologies provide clear evidence that nonnative RNA can mistakenly map to reference genomes, especially to conserved regions of common housekeeping genes, such as actin, α/β-tubulin, and elongation factor 1-α. In Salix, Rubisco activase transcripts were down-regulated in contaminated trees across all 10 cultivars, whereas thiamine thizole synthase and CP12, a Calvin Cycle master regulator, were uniformly up-regulated. De novo assembly approaches, with unconstrained annotation, can improve data quality; care should be taken when exploring such plant genetics to reduce de facto data exclusion by mapping to a single reference genome alone. Salix gene expression patterns strongly suggest cultivar-wide alteration of specific photosynthetic apparatus and protection of the antenna complexes from oxidation damage in contaminated trees, providing an insight into common stress tolerance strategies in a real-world phytoremediation system. PMID:27002060

Construction of a dictionary of laboratory tests mapped to LOINC at AP-HP.

PubMed

Cormont, Sylvie; Buemi, Antoine; Horeau, Thierry; Zweigenbaum, Pierre; Lepage, Eric

2008-11-06

We report on the ongoing process implemented at Assistance Publique-Hôpitaux de Paris (AP-HP), the largest hospital system in Europe, to build a common reference for laboratory tests in French with LOINC mappings. At the time of writing, it contained 24,000 tests, covering all fields of biology, in use in 19 AP-HP hospitals, 30% of which had a mapping to LOINC with a peak of over 60% in biochemistry.

Reference-guided de novo assembly approach improves genome reconstruction for related species.

PubMed

Lischer, Heidi E L; Shimizu, Kentaro K

2017-11-10

The development of next-generation sequencing has made it possible to sequence whole genomes at a relatively low cost. However, de novo genome assemblies remain challenging due to short read length, missing data, repetitive regions, polymorphisms and sequencing errors. As more and more genomes are sequenced, reference-guided assembly approaches can be used to assist the assembly process. However, previous methods mostly focused on the assembly of other genotypes within the same species. We adapted and extended a reference-guided de novo assembly approach, which enables the usage of a related reference sequence to guide the genome assembly. In order to compare and evaluate de novo and our reference-guided de novo assembly approaches, we used a simulated data set of a repetitive and heterozygotic plant genome. The extended reference-guided de novo assembly approach almost always outperforms the corresponding de novo assembly program even when a reference of a different species is used. Similar improvements can be observed in high and low coverage situations. In addition, we show that a single evaluation metric, like the widely used N50 length, is not enough to properly rate assemblies as it not always points to the best assembly evaluated with other criteria. Therefore, we used the summed z-scores of 36 different statistics to evaluate the assemblies. The combination of reference mapping and de novo assembly provides a powerful tool to improve genome reconstruction by integrating information of a related genome. Our extension of the reference-guided de novo assembly approach enables the application of this strategy not only within but also between related species. Finally, the evaluation of genome assemblies is often not straight forward, as the truth is not known. Thus one should always use a combination of evaluation metrics, which not only try to assess the continuity but also the accuracy of an assembly.

Genetics Home Reference: cone-rod dystrophy

MedlinePlus

... Citation on PubMed Sergouniotis PI, McKibbin M, Robson AG, Bolz HJ, De Baere E, Müller PL, Heller ... qualified healthcare professional . About Selection Criteria for Links Data Files & API Site Map Subscribe Customer Support USA. ...

South American regional ionospheric maps computed by GESA: A pilot service in the framework of SIRGAS

NASA Astrophysics Data System (ADS)

Brunini, C.; Meza, A.; Gende, M.; Azpilicueta, F.

2008-08-01

SIRGAS (Geocentric Reference Frame for the Americas) is an international enterprise of the geodetic community that aims to realize the Terrestrial Reference Frame in the America's countries. In order to fulfill this commitment, SIRGAS manages a network of continuously operational GNSS receivers totalling around one hundred sites in the Caribbean, Central, and South American region. Although the network was not planed for ionospheric studies, its potential to be used for such a purpose was recently recognized and SIRGAS started a pilot experiment devoted to establish a regular service for computing and releasing regional vertical TEC (vTEC) maps based on GNSS data. Since July, 2005, the GESA (Geodesia Espacial y Aeronomía) laboratory belonging to the Facultad de Ciencias Astronómicas y Geofísicas of the Universidad Nacional de La Plata computes hourly maps of vertical Total Electron Content (vTEC) in the framework of the SIRGAS pilot experiment. These maps exploit all the GNSS data available in the South American region and are computed with the LPIM (La Plata Ionospheric Model). LPIM implements a de-biasing procedure that improves data calibration in relation to other procedures commonly used for such purposes. After calibration, slant TEC measurements are converted to vertical and mapped using local-time and modip latitude. The use of modip latitude smoothed the spatial variability of vTEC, especially in the South American low latitude region and hence allows for a better vTEC interpolation. This contribution summarizes the results obtained by GESA in the framework of the SIRGAS pilot experiment.

Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis.

PubMed

Davidson, Nadia M; Oshlack, Alicia

2018-05-01

RNA sequencing (RNA-seq) analyses can benefit from performing a genome-guided and de novo assembly, in particular for species where the reference genome or the annotation is incomplete. However, tools for integrating an assembled transcriptome with reference annotation are lacking. Necklace is a software pipeline that runs genome-guided and de novo assembly and combines the resulting transcriptomes with reference genome annotations. Necklace constructs a compact but comprehensive superTranscriptome out of the assembled and reference data. Reads are subsequently aligned and counted in preparation for differential expression testing. Necklace allows a comprehensive transcriptome to be built from a combination of assembled and annotated transcripts, which results in a more comprehensive transcriptome for the majority of organisms. In addition RNA-seq data are mapped back to this newly created superTranscript reference to enable differential expression testing with standard methods.

Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows.

PubMed

Siebert, Stefan; Robinson, Mark D; Tintori, Sophia C; Goetz, Freya; Helm, Rebecca R; Smith, Stephen A; Shaner, Nathan; Haddock, Steven H D; Dunn, Casey W

2011-01-01

We investigated differential gene expression between functionally specialized feeding polyps and swimming medusae in the siphonophore Nanomia bijuga (Cnidaria) with a hybrid long-read/short-read sequencing strategy. We assembled a set of partial gene reference sequences from long-read data (Roche 454), and generated short-read sequences from replicated tissue samples that were mapped to the references to quantify expression. We collected and compared expression data with three short-read expression workflows that differ in sample preparation, sequencing technology, and mapping tools. These workflows were Illumina mRNA-Seq, which generates sequence reads from random locations along each transcript, and two tag-based approaches, SOLiD SAGE and Helicos DGE, which generate reads from particular tag sites. Differences in expression results across workflows were mostly due to the differential impact of missing data in the partial reference sequences. When all 454-derived gene reference sequences were considered, Illumina mRNA-Seq detected more than twice as many differentially expressed (DE) reference sequences as the tag-based workflows. This discrepancy was largely due to missing tag sites in the partial reference that led to false negatives in the tag-based workflows. When only the subset of reference sequences that unambiguously have tag sites was considered, we found broad congruence across workflows, and they all identified a similar set of DE sequences. Our results are promising in several regards for gene expression studies in non-model organisms. First, we demonstrate that a hybrid long-read/short-read sequencing strategy is an effective way to collect gene expression data when an annotated genome sequence is not available. Second, our replicated sampling indicates that expression profiles are highly consistent across field-collected animals in this case. Third, the impacts of partial reference sequences on the ability to detect DE can be mitigated through workflow choice and deeper reference sequencing.

Differential Gene Expression in the Siphonophore Nanomia bijuga (Cnidaria) Assessed with Multiple Next-Generation Sequencing Workflows

PubMed Central

Siebert, Stefan; Robinson, Mark D.; Tintori, Sophia C.; Goetz, Freya; Helm, Rebecca R.; Smith, Stephen A.; Shaner, Nathan; Haddock, Steven H. D.; Dunn, Casey W.

2011-01-01

We investigated differential gene expression between functionally specialized feeding polyps and swimming medusae in the siphonophore Nanomia bijuga (Cnidaria) with a hybrid long-read/short-read sequencing strategy. We assembled a set of partial gene reference sequences from long-read data (Roche 454), and generated short-read sequences from replicated tissue samples that were mapped to the references to quantify expression. We collected and compared expression data with three short-read expression workflows that differ in sample preparation, sequencing technology, and mapping tools. These workflows were Illumina mRNA-Seq, which generates sequence reads from random locations along each transcript, and two tag-based approaches, SOLiD SAGE and Helicos DGE, which generate reads from particular tag sites. Differences in expression results across workflows were mostly due to the differential impact of missing data in the partial reference sequences. When all 454-derived gene reference sequences were considered, Illumina mRNA-Seq detected more than twice as many differentially expressed (DE) reference sequences as the tag-based workflows. This discrepancy was largely due to missing tag sites in the partial reference that led to false negatives in the tag-based workflows. When only the subset of reference sequences that unambiguously have tag sites was considered, we found broad congruence across workflows, and they all identified a similar set of DE sequences. Our results are promising in several regards for gene expression studies in non-model organisms. First, we demonstrate that a hybrid long-read/short-read sequencing strategy is an effective way to collect gene expression data when an annotated genome sequence is not available. Second, our replicated sampling indicates that expression profiles are highly consistent across field-collected animals in this case. Third, the impacts of partial reference sequences on the ability to detect DE can be mitigated through workflow choice and deeper reference sequencing. PMID:21829563

Evaluation de la qualité de modèles numériques de terrain dérivés par interférométrieEvaluación de la calidad de modelos digitales de elevación derivados por interferometría

NASA Astrophysics Data System (ADS)

Gens, Rüdiger

One of the most important uses of SAR interferometry is in the generation of digital elevation models (DEMs). However, a standard procedure for quality estimation of DEMs does not exist. This paper proposes a method of quality estimation using an adapted Monte Carlo simulation, which has the advantage that it could be used in areas where appropriate reference DEMs are not available. This paper also addresses interferometric processing, with special emphasis on the influence of the input parameters. Practical implementation of the proposed technique is shown on a data set from Lower Saxony in Germany. The error map generated, which is a measure of the quality of the DEM, is also presented. For further analysis of the critical aspects of quality, a reference DEM has also been used.

A comprehensive map of the porcine genome.

PubMed

Rohrer, G A; Alexander, L J; Hu, Z; Smith, T P; Keele, J W; Beattie, C W

1996-05-01

We report the highest density genetic linkage map for a livestock species produced to date. Three published maps for Sus scrofa were merged by genotyping virtually every publicly available microsatellite across a single reference population to yield 1042 linked loci, 536 of which are novel assignments, spanning 2286.2 cM (average interval 2.23 cM) in 19 linkage groups (18 autosomal and X chromosomes, n = 19). Linkage groups were constructed de novo and mapped by locus content to avoid propagation of errors in older genotypes. The physical and genetic maps were integrated with 123 informative loci assigned previously by fluorescence in situ hybridization (FISH). Fourteen linkage groups span the entire length of each chromosome. Coverage of chromosomes 11, 12, 15, and 18 will be evaluated as more markers are physically assigned. Marker-deficient regions were identified only on 11q1.7-qter and 14 cen-q1.2. Recombination rates (cM/Mbp) varied between and within chromosomes. Short chromosomal arms recombined at higher rates than long arms, and recombination was more frequent in telomeric regions than in pericentric regions. The high-resolution comprehensive map has the marker density needed to identify quantitative trait loci (QTL), implement marker-assisted selection or introgression and YAC contig construction or chromosomal microdissection.

Site of the 2016 Summer Olympic Games viewed by NASA MISR

NASA Image and Video Library

2016-08-10

The Multi-angle Imaging SpectroRadiometer (MISR) instrument aboard NASA's Terra satellite passed directly over Rio de Janeiro, Brazil, on Aug. 2, 2016, just prior to the opening of the Summer Olympic Games. On the left is an image from MISR's nadir (downward-looking) camera; the width of the image is 235 miles (378 kilometers), and Rio de Janeiro is visible as the large gray area on the coast in the center. The black asterisk marks the location of the Maracanã Stadium in downtown, where the opening ceremonies were held. In the weeks leading up to the Aug. 5 opening ceremonies in Rio de Janeiro, there have been reports of elevated levels of particulate matter in the region. Particulate matter refers to tiny airborne droplets or pieces of soot and dust that can end up in the lungs, comprising an all-too-common problem for many cities around the world. MISR data are routinely used to estimate the amount of air pollution via measurements of aerosol optical depth, which is a measure of how much incoming light from the sun is blocked by particles in the atmosphere. On the right, a map of aerosol optical depth is superimposed on the image. Individual squares making up this map measure 2.7 miles (4.4 kilometers) on a side, and holes in the map occur where an aerosol amount could not be determined, such as where clouds are present. Optical depth over Rio is slightly elevated compared to its surroundings, most likely due to the presence of air pollution, with values from 0.15-0.25. For reference, an optical depth of 0.2 corresponds to light haze. The product shown here is a prototype of a new version of the MISR aerosol product to be publicly released in the near future, and increases the spatial resolution of the aerosol information by a factor of 16 compared to the currently available product, making it possible to observe the fine details of optical depth over urban areas. These data were captured during Terra orbit 88426. http://photojournal.jpl.nasa.gov/catalog/PIA20885

High-Resolution Maps of Mouse Reference Populations

PubMed Central

Simecek, Petr; Forejt, Jiri; Williams, Robert W.; Shiroishi, Toshihiko; Takada, Toyoyuki; Lu, Lu; Johnson, Thomas E.; Bennett, Beth; Deschepper, Christian F.; Scott-Boyer, Marie-Pier; Pardo-Manuel de Villena, Fernando; Churchill, Gary A.

2017-01-01

Genetic reference panels are widely used to map complex, quantitative traits in model organisms. We have generated new high-resolution genetic maps of 259 mouse inbred strains from recombinant inbred strain panels (C57BL/6J × DBA/2J, ILS/IbgTejJ × ISS/IbgTejJ, and C57BL/6J × A/J) and chromosome substitution strain panels (C57BL/6J-Chr#, C57BL/6J-Chr#, and C57BL/6J-Chr#). We genotyped all samples using the Affymetrix Mouse Diversity Array with an average intermarker spacing of 4.3 kb. The new genetic maps provide increased precision in the localization of recombination breakpoints compared to the previous maps. Although the strains were presumed to be fully inbred, we found residual heterozygosity in 40% of individual mice from five of the six panels. We also identified de novo deletions and duplications, in homozygous or heterozygous state, ranging in size from 21 kb to 8.4 Mb. Almost two-thirds (46 out of 76) of these deletions overlap exons of protein coding genes and may have phenotypic consequences. Twenty-nine putative gene conversions were identified in the chromosome substitution strains. We find that gene conversions are more likely to occur in regions where the homologous chromosomes are more similar. The raw genotyping data and genetic maps of these strain panels are available at http://churchill-lab.jax.org/website/MDA. PMID:28839117

High-Resolution Maps of Mouse Reference Populations.

PubMed

Simecek, Petr; Forejt, Jiri; Williams, Robert W; Shiroishi, Toshihiko; Takada, Toyoyuki; Lu, Lu; Johnson, Thomas E; Bennett, Beth; Deschepper, Christian F; Scott-Boyer, Marie-Pier; Pardo-Manuel de Villena, Fernando; Churchill, Gary A

2017-10-05

Genetic reference panels are widely used to map complex, quantitative traits in model organisms. We have generated new high-resolution genetic maps of 259 mouse inbred strains from recombinant inbred strain panels (C57BL/6J × DBA/2J, ILS/IbgTejJ × ISS/IbgTejJ, and C57BL/6J × A/J) and chromosome substitution strain panels (C57BL/6J-Chr#, C57BL/6J-Chr#, and C57BL/6J-Chr#). We genotyped all samples using the Affymetrix Mouse Diversity Array with an average intermarker spacing of 4.3 kb. The new genetic maps provide increased precision in the localization of recombination breakpoints compared to the previous maps. Although the strains were presumed to be fully inbred, we found residual heterozygosity in 40% of individual mice from five of the six panels. We also identified de novo deletions and duplications, in homozygous or heterozygous state, ranging in size from 21 kb to 8.4 Mb. Almost two-thirds (46 out of 76) of these deletions overlap exons of protein coding genes and may have phenotypic consequences. Twenty-nine putative gene conversions were identified in the chromosome substitution strains. We find that gene conversions are more likely to occur in regions where the homologous chromosomes are more similar. The raw genotyping data and genetic maps of these strain panels are available at http://churchill-lab.jax.org/website/MDA. Copyright © 2017 Simecek et al.

Whole Genome Sequencing of Greater Amberjack (Seriola dumerili) for SNP Identification on Aligned Scaffolds and Genome Structural Variation Analysis Using Parallel Resequencing

PubMed Central

Aokic, Jun-ya; Kawase, Junya; Hamada, Kazuhisa; Fujimoto, Hiroshi; Yamamoto, Ikki; Usuki, Hironori

2018-01-01

Greater amberjack (Seriola dumerili) is distributed in tropical and temperate waters worldwide and is an important aquaculture fish. We carried out de novo sequencing of the greater amberjack genome to construct a reference genome sequence to identify single nucleotide polymorphisms (SNPs) for breeding amberjack by marker-assisted or gene-assisted selection as well as to identify functional genes for biological traits. We obtained 200 times coverage and constructed a high-quality genome assembly using next generation sequencing technology. The assembled sequences were aligned onto a yellowtail (Seriola quinqueradiata) radiation hybrid (RH) physical map by sequence homology. A total of 215 of the longest amberjack sequences, with a total length of 622.8 Mbp (92% of the total length of the genome scaffolds), were lined up on the yellowtail RH map. We resequenced the whole genomes of 20 greater amberjacks and mapped the resulting sequences onto the reference genome sequence. About 186,000 nonredundant SNPs were successfully ordered on the reference genome. Further, we found differences in the genome structural variations between two greater amberjack populations using BreakDancer. We also analyzed the greater amberjack transcriptome and mapped the annotated sequences onto the reference genome sequence. PMID:29785397

The Lyman alpha reference sample. VII. Spatially resolved Hα kinematics

NASA Astrophysics Data System (ADS)

Herenz, Edmund Christian; Gruyters, Pieter; Orlitova, Ivana; Hayes, Matthew; Östlin, Göran; Cannon, John M.; Roth, Martin M.; Bik, Arjan; Pardy, Stephen; Otí-Floranes, Héctor; Mas-Hesse, J. Miguel; Adamo, Angela; Atek, Hakim; Duval, Florent; Guaita, Lucia; Kunth, Daniel; Laursen, Peter; Melinder, Jens; Puschnig, Johannes; Rivera-Thorsen, Thøger E.; Schaerer, Daniel; Verhamme, Anne

2016-03-01

We present integral field spectroscopic observations with the Potsdam Multi-Aperture Spectrophotometer of all 14 galaxies in the z ~ 0.1 Lyman Alpha Reference Sample (LARS). We produce 2D line-of-sight velocity maps and velocity dispersion maps from the Balmer α (Hα) emission in our data cubes. These maps trace the spectral and spatial properties of the LARS galaxies' intrinsic Lyα radiation field. We show our kinematic maps that are spatially registered onto the Hubble Space Telescope Hα and Lyman α (Lyα) images. We can conjecture a causal connection between spatially resolved Hα kinematics and Lyα photometry for individual galaxies, however, no general trend can be established for the whole sample. Furthermore, we compute the intrinsic velocity dispersion σ0, the shearing velocity vshear, and the vshear/σ0 ratio from our kinematic maps. In general LARS galaxies are characterised by high intrinsic velocity dispersions (54 km s-1 median) and low shearing velocities (65 km s-1 median). The vshear/σ0 values range from 0.5 to 3.2 with an average of 1.5. It is noteworthy that five galaxies of the sample are dispersion-dominated systems with vshear/σ0< 1, and are thus kinematically similar to turbulent star-forming galaxies seen at high redshift. When linking our kinematical statistics to the global LARS Lyα properties, we find that dispersion-dominated systems show higher Lyα equivalent widths and higher Lyα escape fractions than systems with vshear/σ0> 1. Our result indicates that turbulence in actively star-forming systems is causally connected to interstellar medium conditions that favour an escape of Lyα radiation. Based on observations collected at the Centro Astronómico Hispano Alemán (CAHA) at Calar Alto, operated jointly by the Max-Planck Institut für Astronomie and the Instituto de Astrofísica de Andalucía (CSIC).The reduced data cubes (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/A78

PoMaMo--a comprehensive database for potato genome data.

PubMed

Meyer, Svenja; Nagel, Axel; Gebhardt, Christiane

2005-01-01

A database for potato genome data (PoMaMo, Potato Maps and More) was established. The database contains molecular maps of all twelve potato chromosomes with about 1000 mapped elements, sequence data, putative gene functions, results from BLAST analysis, SNP and InDel information from different diploid and tetraploid potato genotypes, publication references, links to other public databases like GenBank (http://www.ncbi.nlm.nih.gov/) or SGN (Solanaceae Genomics Network, http://www.sgn.cornell.edu/), etc. Flexible search and data visualization interfaces enable easy access to the data via internet (https://gabi.rzpd.de/PoMaMo.html). The Java servlet tool YAMB (Yet Another Map Browser) was designed to interactively display chromosomal maps. Maps can be zoomed in and out, and detailed information about mapped elements can be obtained by clicking on an element of interest. The GreenCards interface allows a text-based data search by marker-, sequence- or genotype name, by sequence accession number, gene function, BLAST Hit or publication reference. The PoMaMo database is a comprehensive database for different potato genome data, and to date the only database containing SNP and InDel data from diploid and tetraploid potato genotypes.

PoMaMo—a comprehensive database for potato genome data

PubMed Central

Meyer, Svenja; Nagel, Axel; Gebhardt, Christiane

2005-01-01

A database for potato genome data (PoMaMo, Potato Maps and More) was established. The database contains molecular maps of all twelve potato chromosomes with about 1000 mapped elements, sequence data, putative gene functions, results from BLAST analysis, SNP and InDel information from different diploid and tetraploid potato genotypes, publication references, links to other public databases like GenBank (http://www.ncbi.nlm.nih.gov/) or SGN (Solanaceae Genomics Network, http://www.sgn.cornell.edu/), etc. Flexible search and data visualization interfaces enable easy access to the data via internet (https://gabi.rzpd.de/PoMaMo.html). The Java servlet tool YAMB (Yet Another Map Browser) was designed to interactively display chromosomal maps. Maps can be zoomed in and out, and detailed information about mapped elements can be obtained by clicking on an element of interest. The GreenCards interface allows a text-based data search by marker-, sequence- or genotype name, by sequence accession number, gene function, BLAST Hit or publication reference. The PoMaMo database is a comprehensive database for different potato genome data, and to date the only database containing SNP and InDel data from diploid and tetraploid potato genotypes. PMID:15608284

Constructing a 'Chromonome' of Yellowtail (Seriola quinqueradiata) for Comparative Analysis of Chromosomal Rearrangements

PubMed Central

Kawase, Junya; Aoki, Jun-ya; Araki, Kazuo

2018-01-01

To investigate chromosome evolution in fish species, we newly mapped 181 markers that allowed us to construct a yellowtail (Seriola quinqueradiata) radiation hybrid (RH) physical map with 1,713 DNA markers, which was far denser than a previous map, and we anchored the de novo assembled sequences onto the RH physical map. Finally, we mapped a total of 13,977 expressed sequence tags (ESTs) on a genome sequence assembly aligned with the physical map. Using the high-density physical map and anchored genome sequences, we accurately compared the yellowtail genome structure with the genome structures of five model fishes to identify characteristics of the yellowtail genome. Between yellowtail and Japanese medaka (Oryzias latipes), almost all regions of the chromosomes were conserved and some blocks comprising several markers were translocated. Using the genome information of the spotted gar (Lepisosteus oculatus) as a reference, we further documented syntenic relationships and chromosomal rearrangements that occurred during evolution in four other acanthopterygian species (Japanese medaka, zebrafish, spotted green pufferfish and three-spined stickleback). The evolutionary chromosome translocation frequency was 1.5-2-times higher in yellowtail than in medaka, pufferfish, and stickleback. PMID:29290830

Solubilization methods and reference 2-DE map of cow milk fat globules.

PubMed

Bianchi, Laura; Puglia, Michele; Landi, Claudia; Matteoni, Silvia; Perini, Daniele; Armini, Alessandro; Verani, Margherita; Trombetta, Claudia; Soldani, Patrizia; Roncada, Paola; Greppi, Gianfranco; Pallini, Vitaliano; Bini, Luca

2009-07-21

Milk fat globules (MFGs) are secretory vesicles assembled and secreted by mammary epithelial cells during lactation. They consist of fat globules surrounded by a lipid bilayer membrane which is derived from the apical membrane of the lactating cells. MFGs contain, besides lipids, proteins from the apical plasma membrane and from the cytoplasmatic material. Their peculiar vesicle nature makes them a suitable and easily available source of biological material in monitoring the physiopathological state of the mammary gland. Unfortunately, the conspicuous lipidic component of MFGs consistently limits protein extraction and purification for MFG proteomic investigations. This work deals with the development of a suitable procedure for protein extraction from the cow MFGs in order to qualitatively and quantitatively improve 2-D electropherograms of the MFG. MFGs were purified from raw milk by centrifugation and then delipidated/precipitated. The resulting protein pellets were solubilised using four different 2-D SDS PAGE compatible lysis buffers. Applied methodological procedures for protein extraction and evaluation of the resulting 2-D protein-pattern are presented and discussed. Using these procedures a reference 2-D map of cow milk fat globules is also reported. The majority of the obtained identifications was represented by proteins involved in lipid synthesis or in fat globule secretion.

A clone-free, single molecule map of the domestic cow (Bos taurus) genome.

PubMed

Zhou, Shiguo; Goldstein, Steve; Place, Michael; Bechner, Michael; Patino, Diego; Potamousis, Konstantinos; Ravindran, Prabu; Pape, Louise; Rincon, Gonzalo; Hernandez-Ortiz, Juan; Medrano, Juan F; Schwartz, David C

2015-08-28

The cattle (Bos taurus) genome was originally selected for sequencing due to its economic importance and unique biology as a model organism for understanding other ruminants, or mammals. Currently, there are two cattle genome sequence assemblies (UMD3.1 and Btau4.6) from groups using dissimilar assembly algorithms, which were complemented by genetic and physical map resources. However, past comparisons between these assemblies revealed substantial differences. Consequently, such discordances have engendered ambiguities when using reference sequence data, impacting genomic studies in cattle and motivating construction of a new optical map resource--BtOM1.0--to guide comparisons and improvements to the current sequence builds. Accordingly, our comprehensive comparisons of BtOM1.0 against the UMD3.1 and Btau4.6 sequence builds tabulate large-to-immediate scale discordances requiring mediation. The optical map, BtOM1.0, spanning the B. taurus genome (Hereford breed, L1 Dominette 01449) was assembled from an optical map dataset consisting of 2,973,315 (439 X; raw dataset size before assembly) single molecule optical maps (Rmaps; 1 Rmap = 1 restriction mapped DNA molecule) generated by the Optical Mapping System. The BamHI map spans 2,575.30 Mb and comprises 78 optical contigs assembled by a combination of iterative (using the reference sequence: UMD3.1) and de novo assembly techniques. BtOM1.0 is a high-resolution physical map featuring an average restriction fragment size of 8.91 Kb. Comparisons of BtOM1.0 vs. UMD3.1, or Btau4.6, revealed that Btau4.6 presented far more discordances (7,463) vs. UMD3.1 (4,754). Overall, we found that Btau4.6 presented almost double the number of discordances than UMD3.1 across most of the 6 categories of sequence vs. map discrepancies, which are: COMPLEX (misassembly), DELs (extraneous sequences), INSs (missing sequences), ITs (Inverted/Translocated sequences), ECs (extra restriction cuts) and MCs (missing restriction cuts). Alignments of UMD3.1 and Btau4.6 to BtOM1.0 reveal discordances commensurate with previous reports, and affirm the NCBI's current designation of UMD3.1 sequence assembly as the "reference assembly" and the Btau4.6 as the "alternate assembly." The cattle genome optical map, BtOM1.0, when used as a comprehensive and largely independent guide, will greatly assist improvements to existing sequence builds, and later serve as an accurate physical scaffold for studies concerning the comparative genomics of cattle breeds.

Archive of post-Hurricane Charley coastal oblique aerial photographs collected during U.S. Geological Survey field activity 04CCH01 from Marco Island to Fort DeSoto, Florida, August 15, 2004

USGS Publications Warehouse

Subino, Janice A.; Morgan, Karen L.M.; Krohn, M. Dennis; Miller, Gregory K.; Dadisman, Shawn V.; Forde, Arnell S.

2012-01-01

To view the survey maps and navigation files, and for more information about these items, see the Navigation page. Figure 1 displays the acquisition geometry. The tables provide detailed information about the assigned location, name, data, and time the photograph was taken along with links to the photo and corresponding 5-min contact sheet. Refer to table 1 and table 2 for details of the northern and southern county photographs, respectively.

[Neuropsychomotor developmental delay: conceptual map, term definitions, uses and limitations].

PubMed

Dornelas, Lílian de Fátima; Duarte, Neuza Maria de Castro; Magalhães, Lívia de Castro

2015-01-01

To retrieve the origin of the term neuropsychomotor developmental delay" (NPMD), its conceptual evolution over time, and to build a conceptual map based on literature review. A literature search was performed in the SciELO Brazil, Web of Science, Science Direct, OneFile (GALE), Pubmed (Medline), Whiley Online, and Springer databases, from January of 1940 to January of 2013, using the following keywords NPMD delay, NPMD retardation, developmental delay, and global developmental delay. A total of 71 articles were selected, which were used to build the conceptual map of the term. Of the 71 references, 55 were international and 16 national. The terms developmental delay and global developmental delay were the most frequently used in the international literature and, in Brazil, delayed NPMD was the most often used. The term developmental delay emerged in the mid 1940s, gaining momentum in the 1990 s. In Brazil, the term delayed NPMD started to be used in the 1980s, and has been frequently cited and published in the literature. Delayed development was a characteristic of 13 morbidities described in 23 references. Regarding the type of use, 19 references were found, with seven forms of use. Among the references, 34 had definitions of the term, and 16 different concepts were identified. Developmental delay is addressed in the international and national literature under different names, various applications, and heterogeneous concepts. Internationally, ways to improve communication between professionals have been indicated, with standardized definition of the term and use in very specific situations up to the fifth year of life, which was not found in Brazilian publications. Copyright © 2014 Associação de Pediatria de São Paulo. Publicado por Elsevier Editora Ltda. All rights reserved.

Development of a Genetic Map for Onion (Allium cepa L.) Using Reference-Free Genotyping-by-Sequencing and SNP Assays

PubMed Central

Jo, Jinkwan; Purushotham, Preethi M.; Han, Koeun; Lee, Heung-Ryul; Nah, Gyoungju; Kang, Byoung-Cheorl

2017-01-01

Single nucleotide polymorphisms (SNPs) play important roles as molecular markers in plant genomics and breeding studies. Although onion (Allium cepa L.) is an important crop globally, relatively few molecular marker resources have been reported due to its large genome and high heterozygosity. Genotyping-by-sequencing (GBS) offers a greater degree of complexity reduction followed by concurrent SNP discovery and genotyping for species with complex genomes. In this study, GBS was employed for SNP mining in onion, which currently lacks a reference genome. A segregating F2 population, derived from a cross between ‘NW-001’ and ‘NW-002,’ as well as multiple parental lines were used for GBS analysis. A total of 56.15 Gbp of raw sequence data were generated and 1,851,428 SNPs were identified from the de novo assembled contigs. Stringent filtering resulted in 10,091 high-fidelity SNP markers. Robust SNPs that satisfied the segregation ratio criteria and with even distribution in the mapping population were used to construct an onion genetic map. The final map contained eight linkage groups and spanned a genetic length of 1,383 centiMorgans (cM), with an average marker interval of 8.08 cM. These robust SNPs were further analyzed using the high-throughput Fluidigm platform for marker validation. This is the first study in onion to develop genome-wide SNPs using GBS. The resulting SNP markers and developed linkage map will be valuable tools for genetic mapping of important agronomic traits and marker-assisted selection in onion breeding programs. PMID:28959273

Combination of Landsat and Sentinel-2 MSI data for initial assessing of burn severity

NASA Astrophysics Data System (ADS)

Quintano, C.; Fernández-Manso, A.; Fernández-Manso, O.

2018-02-01

Nowadays Earth observation satellites, in particular Landsat, provide a valuable help to forest managers in post-fire operations; being the base of post-fire damage maps that enable to analyze fire impacts and to develop vegetation recovery plans. Sentinel-2A MultiSpectral Instrument (MSI) records data in similar spectral wavelengths that Landsat 8 Operational Land Imager (OLI), and has higher spatial and temporal resolutions. This work compares two types of satellite-based maps for evaluating fire damage in a large wildfire (around 8000 ha) located in Sierra de Gata (central-western Spain) on 6-11 August 2015. 1) burn severity maps based exclusively on Landsat data; specifically, on differenced Normalized Burn Ratio (dNBR) and on its relative versions (Relative dNBR, RdNBR, and Relativized Burn Ratio, RBR) and 2) burn severity maps based on the same indexes but combining pre-fire data from Landsat 8 OLI with post-fire data from Sentinel-2A MSI data. Combination of both Landsat and Sentinel-2 data might reduce the time elapsed since forest fire to the availability of an initial fire damage map. Interpretation of ortho-photograph Pléiades 1 B data (1:10,000) provided us the ground reference data to measure the accuracy of both burn severity maps. Results showed that Landsat based burn severity maps presented an adequate assessment of the damage grade (κ statistic = 0.80) and its spatial distribution in wildfire emergency response. Further using both Landsat and Sentinel-2 MSI data the accuracy of burn severity maps, though slightly lower (κ statistic = 0.70) showed an adequate level for be used by forest managers.

Survey of gene splicing algorithms based on reads.

PubMed

Si, Xiuhua; Wang, Qian; Zhang, Lei; Wu, Ruo; Ma, Jiquan

2017-11-02

Gene splicing is the process of assembling a large number of unordered short sequence fragments to the original genome sequence as accurately as possible. Several popular splicing algorithms based on reads are reviewed in this article, including reference genome algorithms and de novo splicing algorithms (Greedy-extension, Overlap-Layout-Consensus graph, De Bruijn graph). We also discuss a new splicing method based on the MapReduce strategy and Hadoop. By comparing these algorithms, some conclusions are drawn and some suggestions on gene splicing research are made.

Gold occurrences in the Greenville 1 degree by 2 degrees Quadrangle, South Carolina, Georgia, and North Carolina

USGS Publications Warehouse

D'Agostino, John P.; Mason, George T.; Zupan, Alan J.W.; Maybin, Arthur H.; German, Jerry M.; Abrams, Charlotte E.

1994-01-01

All of the gold mines, prospects, placers, and occurrences known in the Greenville 1° x 2° quadrangle are tabulated in this report. The table lists, in consecutive order by county (fig. 1), the map number of each feature, which is located either on the accompanying Greenville 1° x 2° quadrangle map or figure 2. The known name of the feature; the 7.5' topographic map on the which the gold site is located (if known, within 25 ft or 7.6 m), the Universal Transverse Mercator (UTM) northing and easting grid coordinates from the appropriate 7.5' topographic map; the commodity; remarks; and references are also listed. Some locations are known, but many sites are not verified and their locations are only approximate. References are listed in References Cited and referred to by number to save space.

Genome-wide nucleotide diversity of hatchery-reared Atlantic and Mediterranean strains of brown trout Salmo trutta compared to wild Mediterranean populations.

PubMed

Leitwein, M; Gagnaire, P-A; Desmarais, E; Guendouz, S; Rohmer, M; Berrebi, P; Guinand, B

2016-12-01

A genome-wide assessment of diversity is provided for wild Mediterranean brown trout Salmo trutta populations from headwater tributaries of the Orb River and from Atlantic and Mediterranean hatchery-reared strains that have been used for stocking. Double-digest restriction-site-associated DNA sequencing (dd-RADseq) was performed and the efficiency of de novo and reference-mapping approaches to obtain individual genotypes was compared. Large numbers of single nucleotide polymorphism (SNP) markers with similar genome-wide distributions were discovered using both approaches (196 639 v. 121 016 SNPs, respectively), with c. 80% of the loci detected de novo being also found with reference mapping, using the Atlantic salmon Salmo salar genome as a reference. Lower mapping density but larger nucleotide diversity (π) was generally observed near extremities of linkage groups, consistent with regions of residual tetrasomic inheritance observed in salmonids. Genome-wide diversity estimates revealed reduced polymorphism in hatchery strains (π = 0·0040 and π = 0·0029 in Atlantic and Mediterranean strains, respectively) compared to wild populations (π = 0·0049), a pattern that was congruent with allelic richness estimated from microsatellite markers. Finally, pronounced heterozygote deficiency was found in hatchery strains (Atlantic F IS = 0·18; Mediterranean F IS = 0·42), indicating that stocking practices may affect the genetic diversity in wild populations. These new genomic resources will provide important tools to define better conservation strategies in S. trutta. © 2016 The Fisheries Society of the British Isles.

Enhancing Collaborative and Meaningful Language Learning Through Concept Mapping

NASA Astrophysics Data System (ADS)

Marriott, Rita De Cássia Veiga; Torres, Patrícia Lupion

This chapter aims to investigate new ways of foreign-language teaching/learning via a study of how concept mapping can help develop a student's reading, writing and oral skills as part of a blended methodology for language teaching known as LAPLI (Laboratorio de Aprendizagem de LInguas: The Language Learning Lab). LAPLI is a student-centred and collaborative methodology which encourages students to challenge their limitations and expand their current knowledge whilst developing their linguistic and interpersonal skills. We explore the theories that underpin LAPLI and detail the 12 activities comprising its programme with specify reference to the use of "concept mapping". An innovative table enabling a formative and summative assessment of the concept maps is formulated. Also presented are some of the qualitative and quantitative results achieved when this methodology was first implemented with a group of pre-service students studying for a degree in English and Portuguese languages at the Catholic University of Parana (PUCPR) in Brazil. The contribution of concept mapping and LAPLI to an under standing of language learning along with a consideration of the difficulties encountered in its implementation with student groups is discussed and suggestions made for future research.

By any other name: when will preschoolers produce several labels for a referent?

PubMed

Deák, G O; Yen, L; Pettit, J

2001-10-01

Two experiments investigated why preschool children sometimes produce multiple words for a referent (i.e. polynomy), but other times seem to allow only one word. In Experiment 1, 40 three- and four-year-olds completed a modification of Deák & Maratsos' (1998) naming task. Although social demands to produce multiple words were reduced, children produced, on average, more than two words per object. Number of words produced was predicted by receptive vocabulary. Lexical insight (i.e. knowing that a word refers to function or appearance) and metalexical beliefs (i.e. that a hypothetical referent has one label, or more than one) were not preconditions of polynomy. Polynomy was independent of bias to map novel words to unfamiliar referents. In Experiment 2, 40 three- and four-year-olds learned new words for nameable objects. Children showed a correction effect, yet produced more than two words per object. Children do not have a generalized one-word-per-object bias, even during word learning. Other explanations (e.g. contextual restriction of lexical access) are discussed.

De novo transcriptome assembly and identification of genes associated with feed conversion ratio and breast muscle yield in domestic ducks.

PubMed

Zhu, Feng; Yuan, Jian-Ming; Zhang, Zhen-He; Hao, Jin-Ping; Yang, Yu-Ze; Hu, Shen-Qiang; Yang, Fang-Xi; Qu, Lu-Jiang; Hou, Zhuo-Cheng

2015-12-01

Breast muscle yield and feed conversion efficiency are the major breeding aims in duck breeding. Understanding the role of specific transcripts in the muscle and small intestine might lead to the elucidation of interrelated biological processes. In this study, we obtained jejunum and breast muscle samples from two strains of Peking ducks that were sorted by feed conversion ratio (FCR) and breast muscle percentage into two-tailed populations. Ten RNA-Seq libraries were developed from the pooled samples and sequenced using the Hiseq2000 platform. We created a reference duck transcript database using de novo assembly methods, which included 16 663 irredundant contigs with an N50 length of 1530 bp. This new duck reference cDNA dataset significantly improved the mapping rate for RNA-Seq data, from 50% to 70%. Mapping and annotation were followed by Gene Ontology analysis, which showed that numerous genes were differentially expressed between the low and high FCR groups. The differentially expressed genes in the jejunum were enriched in biological processes related to immune response and immune response activation, whereas those in the breast muscle were significantly enriched in biological processes related to muscle cell differentiation and organ development. We identified new candidate genes, that is, PCK1, for improving the FCR and breast muscle yield of ducks and obtained much better reference duck transcripts. This study suggested that de novo assembly is essential when applying transcriptome analysis to a species with an incomplete genome. © 2015 Stichting International Foundation for Animal Genetics.

Dynamics Explorer measurements of particles, fields, and plasma drifts over a horse-collar auroral pattern

NASA Technical Reports Server (NTRS)

Sharber, J. R.; Hones, E. W., Jr.; Heelis, R. A.; Craven, J. D.; Frank, L. A.; Maynard, N. C.; Slavin, J. A.; Birn, J.

1992-01-01

As shown from ground-based measurements and satellite-borne imagers, one type of global auroral pattern characteristic of quiet (usually northward IMF) intervals is that of a contracted but thickened emission region in which the dawn and dusk portions can spread poleward to very high latitudes, (the type of a pattern referred to as a 'horse-collar' aurora by Hones et al., 1989). In this report we use a DE data set to examine a case in which this horse-collar pattern was observed by the DE-1 auroral imager while at the same time the DE-2, at lower altitude, measured precipitating particles, electric and magnetic fields, and plasma drifts. There is close agreement between the optical signatures and the particle precipitation patterns. The particle, plasma, and field measurements made along the satellite track and the 2-D perspective of the imager provide a means of determining the configuration of convective flows in the high-latitude ionosphere during this interval of northward IMF. Recent mapping studies are used to relate the low-altitude observations to possible magnetospheric source regions.

Safety analysis of a Russian phage cocktail: from metagenomic analysis to oral application in healthy human subjects.

PubMed

McCallin, Shawna; Alam Sarker, Shafiqul; Barretto, Caroline; Sultana, Shamima; Berger, Bernard; Huq, Sayeda; Krause, Lutz; Bibiloni, Rodrigo; Schmitt, Bertrand; Reuteler, Gloria; Brüssow, Harald

2013-09-01

Phage therapy has a long tradition in Eastern Europe, where preparations are comprised of complex phage cocktails whose compositions have not been described. We investigated the composition of a phage cocktail from the Russian pharmaceutical company Microgen targeting Escherichia coli/Proteus infections. Electron microscopy identified six phage types, with numerically T7-like phages dominating over T4-like phages. A metagenomic approach using taxonomical classification, reference mapping and de novo assembly identified 18 distinct phage types, including 7 genera of Podoviridae, 2 established and 2 proposed genera of Myoviridae, and 2 genera of Siphoviridae. De novo assembly yielded 7 contigs greater than 30 kb, including a 147-kb Myovirus genome and a 42-kb genome of a potentially new phage. Bioinformatic analysis did not reveal undesired genes and a small human volunteer trial did not associate adverse effects with oral phage exposure. Copyright © 2013 Elsevier Inc. All rights reserved.

Proteomic analysis of Pinus radiata needles: 2-DE map and protein identification by LC/MS/MS and substitution-tolerant database searching.

PubMed

Valledor, Luis; Castillejo, Maria A; Lenz, Christof; Rodríguez, Roberto; Cañal, Maria J; Jorrín, Jesús

2008-07-01

Pinus radiata is one of the most economically important forest tree species, with a worldwide production of around 370 million m (3) of wood per year. Current selection of elite trees to be used in conservation and breeding programes requires the physiological and molecular characterization of available populations. To identify key proteins related to tree growth, productivity and responses to environmental factors, a proteomic approach is being utilized. In this paper, we present the first report of the 2-DE protein reference map of physiologically mature P. radiata needles, as a basis for subsequent differential expression proteomic studies related to growth, development, biomass production and responses to stresses. After TCA/acetone protein extraction of needle tissue, 549 +/- 21 well-resolved spots were detected in Coommassie-stained gels within the 5-8 pH and 10-100 kDa M(r) ranges. The analytical and biological variance determined for 450 spots were of 31 and 42%, respectively. After LC/MS/MS analysis of in-gel tryptic digested spots, proteins were identified by using the novel Paragon algorithm that tolerates amino acid substitution in the first-pass search. It allowed the confident identification of 115 out of the 150 protein spots subjected to MS, quite unusual high percentage for a poor sequence database, as is the case of P. radiata. Proteins were classified into 12 or 18 groups based on their corresponding cell component or biological process/pathway categories, respectively. Carbohydrate metabolism and photosynthetic enzymes predominate in the 2-DE protein profile of P. radiata needles.

Calculation of stochastic broadening due to noise and field errors in the simple map in action-angle coordinates

NASA Astrophysics Data System (ADS)

Hinton, Courtney; Punjabi, Alkesh; Ali, Halima

2008-11-01

The simple map is the simplest map that has topology of divertor tokamaks [1]. Recently, the action-angle coordinates for simple map are analytically calculated, and simple map is constructed in action-angle coordinates [2]. Action-angle coordinates for simple map can not be inverted to real space coordinates (R,Z). Because there is logarithmic singularity on the ideal separatrix, trajectories can not cross separatrix [2]. Simple map in action-angle coordinates is applied to calculate stochastic broadening due to magnetic noise and field errors. Mode numbers for noise + field errors from the DIII-D tokamak are used. Mode numbers are (m,n)=(3,1), (4,1), (6,2), (7,2), (8,2), (9,3), (10,3), (11,3), (12,3) [3]. The common amplitude δ is varied from 0.8X10-5 to 2.0X10-5. For this noise and field errors, the width of stochastic layer in simple map is calculated. This work is supported by US Department of Energy grants DE-FG02-07ER54937, DE-FG02-01ER54624 and DE-FG02-04ER54793 1. A. Punjabi, H. Ali, T. Evans, and A. Boozer, Phys. Let. A 364, 140--145 (2007). 2. O. Kerwin, A. Punjabi, and H. Ali, to appear in Physics of Plasmas. 3. A. Punjabi and H. Ali, P1.012, 35^th EPS Conference on Plasma Physics, June 9-13, 2008, Hersonissos, Crete, Greece.

RATT: Rapid Annotation Transfer Tool

PubMed Central

Otto, Thomas D.; Dillon, Gary P.; Degrave, Wim S.; Berriman, Matthew

2011-01-01

Second-generation sequencing technologies have made large-scale sequencing projects commonplace. However, making use of these datasets often requires gene function to be ascribed genome wide. Although tool development has kept pace with the changes in sequence production, for tasks such as mapping, de novo assembly or visualization, genome annotation remains a challenge. We have developed a method to rapidly provide accurate annotation for new genomes using previously annotated genomes as a reference. The method, implemented in a tool called RATT (Rapid Annotation Transfer Tool), transfers annotations from a high-quality reference to a new genome on the basis of conserved synteny. We demonstrate that a Mycobacterium tuberculosis genome or a single 2.5 Mb chromosome from a malaria parasite can be annotated in less than five minutes with only modest computational resources. RATT is available at http://ratt.sourceforge.net. PMID:21306991

Mines, prospects, and occurrences of metallic (excluding gold), pegmatite, and rare-earth mineral commodities in the Greenville 1 degree by 2 degrees Quadrangle, South Carolina, Georgia, and North Carolina

USGS Publications Warehouse

D'Agostino, John P.; Zupan, Alan Jon; Maybin, Arthur H.; Abrams, Charlotte E.; German, Jerry M.

1994-01-01

All of the known mines, prospects, and occurrences of metallic (excluding gold, pegmatite, and rare-earth mineral commodities for the Greenville 1° x 2° quadrangle are tabulated in this report. The table lists, in consecutive order for each county (fig. 1), the map number of each item, which correlates and locates the item on the accompanying Greenville 1° x 2° quadrangle map. The known name of the feature; the 7.5' topographic map on the which the commodity site is located; the Universal Transverse Mercator (UTM) northing and easting grid coordinates from the appropriate 7.5' topographic map; the commodity; remarks; and references are also listed. Some locations are known, but many sites are not verified and their locations are only approximate. References are listed in References Cited and referred to by number to save space.

Enhancing Collaborative and Meaningful Language Learning through Concept Mapping

NASA Astrophysics Data System (ADS)

de Cássia Veiga Marriott, Rita; Torres, Patrícia Lupion

This chapter aims to investigate new ways of foreign-language teaching/learning via a study of how concept mapping can help develop a student's reading, writing and oral skills as part of a blended methodology for language teaching known as LAPLI (Laboratorio de Aprendizagem de LInguas: The Language Learning Lab). LAPLI is a student-centred and collaborative methodology which encourages students to challenge their limitations and expand their current knowledge whilst developing their linguistic and interpersonal skills. We explore the theories that underpin LAPLI and detail the 12 activities comprising its programme with specify reference to the use of “concept mapping”. An innovative table enabling a formative and summative assessment of the concept maps is formulated. Also presented are some of the qualitative and quantitative results achieved when this methodology was first implemented with a group of pre-service students studying for a degree in English and Portuguese languages at the Catholic University of Parana (PUCPR) in Brazil. The contribution of concept mapping and LAPLI to an understanding of language learning along with a consideration of the difficulties encountered in its implementation with student groups is discussed and suggestions made for future research.

Comparison of the Equine Reference Sequence with Its Sanger Source Data and New Illumina Reads

PubMed Central

Rebolledo-Mendez, Jovan; Hestand, Matthew S.; Coleman, Stephen J.; Zeng, Zheng; Orlando, Ludovic; MacLeod, James N.; Kalbfleisch, Ted

2015-01-01

The reference assembly for the domestic horse, EquCab2, published in 2009, was built using approximately 30 million Sanger reads from a Thoroughbred mare named Twilight. Contiguity in the assembly was facilitated using nearly 315 thousand BAC end sequences from Twilight’s half brother Bravo. Since then, it has served as the foundation for many genome-wide analyses that include not only the modern horse, but ancient horses and other equid species as well. As data mapped to this reference has accumulated, consistent variation between mapped datasets and the reference, in terms of regions with no read coverage, single nucleotide variants, and small insertions/deletions have become apparent. In many cases, it is not clear whether these differences are the result of true sequence variation between the research subjects’ and Twilight’s genome or due to errors in the reference. EquCab2 is regarded as “The Twilight Assembly.” The objective of this study was to identify inconsistencies between the EquCab2 assembly and the source Twilight Sanger data used to build it. To that end, the original Sanger and BAC end reads have been mapped back to this equine reference and assessed with the addition of approximately 40X coverage of new Illumina Paired-End sequence data. The resulting mapped datasets identify those regions with low Sanger read coverage, as well as variation in genomic content that is not consistent with either the original Twilight Sanger data or the new genomic sequence data generated from Twilight on the Illumina platform. As the haploid EquCab2 reference assembly was created using Sanger reads derived largely from a single individual, the vast majority of variation detected in a mapped dataset comprised of those same Sanger reads should be heterozygous. In contrast, homozygous variations would represent either errors in the reference or contributions from Bravo's BAC end sequences. Our analysis identifies 720,843 homozygous discrepancies between new, high throughput genomic sequence data generated for Twilight and the EquCab2 reference assembly. Most of these represent errors in the assembly, while approximately 10,000 are demonstrated to be contributions from another horse. Other results are presented that include the binary alignment map file of the mapped Sanger reads, a list of variants identified as discrepancies between the source data and resulting reference, and a BED annotation file that lists the regions of the genome whose consensus was likely derived from low coverage alignments. PMID:26107638

Rapid Fast-Mapping Abilities in 2-Year-Olds

ERIC Educational Resources Information Center

Spiegel, Chad; Halberda, Justin

2011-01-01

Learning a new word consists of two primary tasks that have often been conflated into a single process: "referent selection", in which a child must determine the correct referent of a novel label, and "referent retention", which is the ability to store this newly formed label-object mapping in memory for later use. In addition, children must be…

Evaluation and Intercomparison of MODIS and GEOV1 Global Leaf Area Index Products over Four Sites in North China

PubMed Central

Li, Zhenwang; Tang, Huan; Zhang, Baohui; Yang, Guixia; Xin, Xiaoping

2015-01-01

This study investigated the performances of the Moderate Resolution Imaging Spectroradiometer (MODIS) and GEOLAND2 Version 1 (GEOV1) Leaf Area Index (LAI) products using ground measurements and LAI reference maps over four sites in North China for 2011–2013. The Terra + Aqua MODIS and Terra MODIS LAI retrieved by the main algorithm and GEOV1 LAI within the valid range were evaluated and intercompared using LAI reference maps to assess their uncertainty and seasonal variability The results showed that GEOV1 LAI is the most similar product with the LAI reference maps (R2 = 0.78 and RMSE = 0.59). The MODIS products performed well for biomes with low LAI values, but considerable uncertainty arose when the LAI was larger than 3. Terra + Aqua MODIS (R2 = 0.72 and RMSE = 0.68) was slightly more accurate than Terra MODIS (R2 = 0.57 and RMSE = 0.90) for producing slightly more successful observations. Both MODIS and GEOV1 products effectively followed the seasonal trajectory of the reference maps, and GEOV1 exhibited a smoother seasonal trajectory than MODIS. MODIS anomalies mainly occurred during summer and likely occurred because of surface reflectance uncertainty, shorter temporal resolutions and inconsistency between simulated and MODIS surface reflectances. This study suggests that further improvements of the MODIS LAI products should focus on finer algorithm inputs and improved seasonal variation modeling of MODIS observations. Future field work considering finer biome maps and better generation of LAI reference maps is still needed. PMID:25781509

De novo assembly and phasing of a Korean human genome.

PubMed

Seo, Jeong-Sun; Rhie, Arang; Kim, Junsoo; Lee, Sangjin; Sohn, Min-Hwan; Kim, Chang-Uk; Hastie, Alex; Cao, Han; Yun, Ji-Young; Kim, Jihye; Kuk, Junho; Park, Gun Hwa; Kim, Juhyeok; Ryu, Hanna; Kim, Jongbum; Roh, Mira; Baek, Jeonghun; Hunkapiller, Michael W; Korlach, Jonas; Shin, Jong-Yeon; Kim, Changhoon

2016-10-13

Advances in genome assembly and phasing provide an opportunity to investigate the diploid architecture of the human genome and reveal the full range of structural variation across population groups. Here we report the de novo assembly and haplotype phasing of the Korean individual AK1 (ref. 1) using single-molecule real-time sequencing, next-generation mapping, microfluidics-based linked reads, and bacterial artificial chromosome (BAC) sequencing approaches. Single-molecule sequencing coupled with next-generation mapping generated a highly contiguous assembly, with a contig N50 size of 17.9 Mb and a scaffold N50 size of 44.8 Mb, resolving 8 chromosomal arms into single scaffolds. The de novo assembly, along with local assemblies and spanning long reads, closes 105 and extends into 72 out of 190 euchromatic gaps in the reference genome, adding 1.03 Mb of previously intractable sequence. High concordance between the assembly and paired-end sequences from 62,758 BAC clones provides strong support for the robustness of the assembly. We identify 18,210 structural variants by direct comparison of the assembly with the human reference, identifying thousands of breakpoints that, to our knowledge, have not been reported before. Many of the insertions are reflected in the transcriptome and are shared across the Asian population. We performed haplotype phasing of the assembly with short reads, long reads and linked reads from whole-genome sequencing and with short reads from 31,719 BAC clones, thereby achieving phased blocks with an N50 size of 11.6 Mb. Haplotigs assembled from single-molecule real-time reads assigned to haplotypes on phased blocks covered 89% of genes. The haplotigs accurately characterized the hypervariable major histocompatability complex region as well as demonstrating allele configuration in clinically relevant genes such as CYP2D6. This work presents the most contiguous diploid human genome assembly so far, with extensive investigation of unreported and Asian-specific structural variants, and high-quality haplotyping of clinically relevant alleles for precision medicine.

Quantitative evaluation of ischemic myocardial scar tissue by unenhanced T1 mapping using 3.0 Tesla MR scanner

PubMed Central

Okur, Aylin; Kantarcı, Mecit; Kızrak, Yeşim; Yıldız, Sema; Pirimoğlu, Berhan; Karaca, Leyla; Oğul, Hayri; Sevimli, Serdar

2014-01-01

PURPOSE We aimed to use a noninvasive method for quantifying T1 values of chronic myocardial infarction scar by cardiac magnetic resonance imaging (MRI), and determine its diagnostic performance. MATERIALS AND METHODS We performed cardiac MRI on 29 consecutive patients with known coronary artery disease (CAD) on 3.0 Tesla MRI scanner. An unenhanced T1 mapping technique was used to calculate T1 relaxation time of myocardial scar tissue, and its diagnostic performance was evaluated. Chronic scar tissue was identified by delayed contrast-enhancement (DE) MRI and T2-weighted images. Sensitivity, specificity, and accuracy values were calculated for T1 mapping using DE images as the gold standard. RESULTS Four hundred and forty-two segments were analyzed in 26 patients. While myocardial chronic scar was demonstrated in 45 segments on DE images, T1 mapping MRI showed a chronic scar area in 54 segments. T1 relaxation time was higher in chronic scar tissue, compared with remote areas (1314±98 ms vs. 1099±90 ms, P < 0.001). Therefore, increased T1 values were shown in areas of myocardium colocalized with areas of DE and normal signal on T2-weighted images. There was a significant correlation between T1 mapping and DE images in evaluation of myocardial wall injury extent (P < 0.05). We calculated sensitivity, specificity, and accuracy as 95.5%, 97%, and 96%, respectively. CONCLUSION The results of the present study reveal that T1 mapping MRI combined with T2-weighted images might be a feasible imaging modality for detecting chronic myocardial infarction scar tissue. PMID:25010366

Two-dimensional proteome reference maps for the human pathogenic filamentous fungus Aspergillus fumigatus.

PubMed

Vödisch, Martin; Albrecht, Daniela; Lessing, Franziska; Schmidt, André D; Winkler, Robert; Guthke, Reinhard; Brakhage, Axel A; Kniemeyer, Olaf

2009-03-01

The filamentous fungus Aspergillus fumigatus has become the most important airborne fungal pathogen causing life-threatening infections in immunosuppressed patients. We established a 2-D reference map for A. fumigatus. Using MALDI-TOF-MS/MS, we identified 381 spots representing 334 proteins. Proteins involved in cellular metabolism, protein synthesis, transport processes and cell cycle were most abundant. Furthermore, we established a protocol for the isolation of mitochondria of A. fumigatus and developed a mitochondrial proteome reference map. 147 proteins represented by 234 spots were identified.

Mines, prospects, and occurrences of nonmetallic mineral commodities in the Greenville 1 degree by 2 degrees Quadrangle, South Carolina, Georgia, and North Carolina

USGS Publications Warehouse

D'Agostino, John P.; O'Connor, Bruce J.; Zupan, Alan J.W.; Maybin, Arthur H.

1994-01-01

Mines, prospects, and occurrences of nonmetal mineral commodities in the Greenville 1° x 2° quadrangle are tabulated in this report. There are 488 symbols representing 579 mines, prospects, and occurrences located in the quadrangle. There are 379 symbols used for 466 features in Georgia, 106 symbols for 110 features in South Carolina, and 3 symbols for 3 features in North Carolina. The table lists, in consecutive orders for each county (fig. 1), the map number of each feature, which correlates and locates the item on the accompanying Greenville 1° x 2° quadrangle map. Also listed are the known name of the feature; the 7.5 topographic map on which the commodity site is located; the Transverse Mercator (UTM) northing and easting grid coordinates from the appropriate 7.5’ topographic map; the commodity; remarks; and references. Some locations are known, but many sites are not verified and their locations are only approximate. Reference are listed in References Cited and referred to by number to save space. The generalized tectonic framework for the quadrangle is shown in figure 2.

Rapid fast-mapping abilities in 2-year-olds.

PubMed

Spiegel, Chad; Halberda, Justin

2011-05-01

Learning a new word consists of two primary tasks that have often been conflated into a single process: referent selection, in which a child must determine the correct referent of a novel label, and referent retention, which is the ability to store this newly formed label-object mapping in memory for later use. In addition, children must be capable of performing these tasks rapidly and repeatedly as they are frequently exposed to novel words during the course of natural conversation. Here we used a preferential pointing task to investigate 2-year-olds' (N=72) ability to infer the referent of a novel noun from a single ambiguous exposure and their ability to retain this mapping over time. Children were asked to identify the referent of a novel label on six critical trials distributed throughout the course of a 10-min study involving many familiar and novel objects. On these critical trials, images of a known object and a novel object (e.g., a ball and a nameless artifact constructed in the laboratory) appeared on two computer screens and a voice asked children to "point at the _____ [e.g., glark]." Following label onset, children were allowed only 3s during which to infer the correct referent, point at it, and potentially store this new word-object mapping. In a final posttest trial, all previously labeled novel objects appeared and children were asked to point to one of them (e.g., "Can you find the glark?"). To succeed, children needed to have initially mapped the novel labels correctly and retained these mappings over the course of the study. Despite the difficult demands of the current task, children successfully identified the target object on the retention trial. We conclude that 2-year-olds are able to fast map novel nouns during a brief single exposure under ambiguous labeling conditions. Copyright © 2010 Elsevier Inc. All rights reserved.

VizieR Online Data Catalog: Warm ISM in the Sagittarius A Complex (Garcia+, 2016)

NASA Astrophysics Data System (ADS)

Garcia, P.; Simon, R.; Stutzki, J.; Gusten, R.; Requena-Torres, M. A.; Higgins, R.

2016-03-01

Files contain the observations of CI 1-0 and CI 2-1, NII 1-0, and CII 3/2-1/2 observed with Herschel-HIFI and 12CO 4-3 observed with NANTEN2/SMART telescope of the SgrA Complex in the GC. The data analysis was done via GILDAS-CLASS, where raw data are processed to obtain regularly sampled data. ************************* IMPORTANT NOTE ************************ These data sets will be blocked until 31.12.16 as agreed on with the A&A Editor. Access to channel maps of all observed transitions is immediately available in electronic format in the link provided in the paper, https://www.astro.uni-koeln.de/online-data/GarciaPSgrA_AA588/. For contact information refer to Dr. Pablo Garcia e-mail: pgarcia@iram.es ******************************************************************* (1 data file).

EnviroAtlas -- Memphis, TN (2012) -- One Meter Resolution Urban Land Cover Data Web Service

EPA Pesticide Factsheets

This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas ). The Memphis, TN EnviroAtlas One Meter-scale Urban Land Cover (MULC) dataset comprises 2,733 km2 around the city of Memphis, surrounding towns, and rural areas. These leaf-on LC data and maps were derived from 1-m pixel, four-band (red, green, blue, and near-infrared) aerial photography acquired from the United States Department of Agriculture (USDA) National Agriculture Imagery Program (NAIP) on four dates in 2012: June 15, June 18, June 21 and June 23, and one date in 2013: July 12. Three separate LiDAR (Light Detection and Ranging) data sets collected on February 19, 2009 00e2?? August 2, 2010, December 1-2, 2011 and January 23-24, 2012 were integrated for Shelby Co., TN, Crittenden Co., AR, and DeSoto Co, MS. Five MULC classes were mapped directly from the NAIP and LiDAR data: Water, Impervious, Soil, Trees, and Grass/Herbaceous. Agriculture was derived from USDA Common Land Unit (CLU) data. Woody and emergent wetlands were copied from existing National Wetlands Inventory (NWI) data. Analysis of a random sampling of 612 photo-interpreted land cover reference points yielded an overall users accuracy of 86.9%. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-u

EnviroAtlas -- Memphis, TN (2012) -- One Meter Resolution Urban Land Cover Data

EPA Pesticide Factsheets

The Memphis, TN EnviroAtlas One Meter-scale Urban Land Cover (MULC) dataset comprises 2,733 km2 around the city of Memphis, surrounding towns, and rural areas. These leaf-on LC data and maps were derived from 1-m pixel, four-band (red, green, blue, and near-infrared) aerial photography acquired from the United States Department of Agriculture (USDA) National Agriculture Imagery Program (NAIP) on four dates in 2012: June 15, June 18, June 21 and June 23, and one date in 2013: July 12. Three separate LiDAR (Light Detection and Ranging) data sets collected on February 19, 2009 00e2?? August 2, 2010, December 1-2, 2011 and January 23-24, 2012 were integrated for Shelby Co., TN, Crittenden Co., AR, and DeSoto Co, MS. Five MULC classes were mapped directly from the NAIP and LiDAR data: Water, Impervious, Soil, Trees, and Grass/Herbaceous. Agriculture was derived from USDA Common Land Unit (CLU) data. Woody and emergent wetlands were copied from existing National Wetlands Inventory (NWI) data. Analysis of a random sampling of 612 photo-interpreted land cover reference points yielded an overall users accuracy of 86.9%. This dataset was produced by the US EPA to support research and online mapping activities related to EnviroAtlas. EnviroAtlas (https://www.epa.gov/enviroatlas) allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the contiguous United States. The dataset is available as do

Radiometric age map of Aleutian Islands

USGS Publications Warehouse

Wilson, Frederic H.; Turner, D.L.

1975-01-01

This map includes published, thesis, and open-file radiometric data available to us as of June, 1975. Some dates are not plotted because of inadequate location data in the original references.The map is divided into five sections, based on 1:1,000,000 scale enlargements of the National Atlas maps of Alaska. Within each section (e.g., southeastern Alaska), radiometric dates are plotted and keyed to 1:250,000 scale quadrangles. Accompanying each map section is table 1, listing map numbers and the sample identification numbers used in DGGS Special Report 10: Radiometric Dates from Alaska-A 1975 Compilation”. The reader is referred to Special Report 10 for more complete information on location, rock type, dating method, and literature references for each age entry. A listing of dates in Special Report lo which require correction or deletion is included S table 2. Corrected and additional entries are listed in table 3. The listings in tables 2 and 3 follow the format of Special Report 10. Table 4 is a glossary of abbreviations used for quadrangle name, rock type, mineral dated, and type of dating method used.

Radiometric age map of southcentral Alaska

USGS Publications Warehouse

Wilson, Frederic H.; Turner, D.L.

1975-01-01

This map includes published, thesis, and open-file radiometric data available to us as of June, 1975. Some dates are not plotted because of inadequate location data in the original references.The map is divided into five sections, based on 1:1,000,000 scale enlargements of the National Atlas maps of Alaska. Within each section (e.g., southeastern Alaska), radiometric dates are plotted and keyed to 1:250,000 scale quadrangles. Accompanying each map section is table 1, listing map numbers and the sample identification numbers used in DGGS Special Report 10: Radiometric Dates from Alaska-A 1975 Compilation”. The reader is referred to Special Report 10 for more complete information on location, rock type, dating method, and literature references for each age entry. A listing of dates in Special Report lo which require correction or deletion is included S table 2. Corrected and additional entries are listed in table 3. The listings in tables 2 and 3 follow the format of Special Report 10. Table 4 is a glossary of abbreviations used for quadrangle name, rock type, mineral dated, and type of dating method used.

Radiometric age map of southwest Alaska

USGS Publications Warehouse

Wilson, Frederic H.; Turner, D.L.

1975-01-01

This map includes published, thesis, and open-file radiometric data available to us as of June, 1975. Some dates are not plotted because of inadequate location data in the original references.The map is divided into five sections, based on 1:1,000,000 scale enlargements of the National Atlas maps of Alaska. Within each section (e.g., southeastern Alaska), radiometric dates are plotted and keyed to 1:250,000 scale quadrangles. Accompanying each map section is table 1, listing map numbers and the sample identification numbers used in DGGS Special Report 10: Radiometric Dates from Alaska-A 1975 Compilation”. The reader is referred to Special Report 10 for more complete information on location, rock type, dating method, and literature references for each age entry. A listing of dates in Special Report lo which require correction or deletion is included S table 2. Corrected and additional entries are listed in table 3. The listings in tables 2 and 3 follow the format of Special Report 10. Table 4 is a glossary of abbreviations used for quadrangle name, rock type, mineral dated, and type of dating method used.

Radiometric age map of southeast Alaska

USGS Publications Warehouse

Wilson, Frederic H.; Turner, D.L.

1975-01-01

This map includes published, thesis, and open-file radiometric data available to us as of June, 1975. Some dates are not plotted because of inadequate location data in the original references.The map is divided into five sections, based on 1:1,000,000 scale enlargements of the National Atlas maps of Alaska. Within each section (e.g., southeastern Alaska), radiometric dates are plotted and keyed to 1:250,000 scale quadrangles. Accompanying each map section is table 1, listing map numbers and the sample identification numbers used in DGGS Special Report 10: Radiometric Dates from Alaska-A 1975 Compilation”. The reader is referred to Special Report 10 for more complete information on location, rock type, dating method, and literature references for each age entry. A listing of dates in Special Report lo which require correction or deletion is included S table 2. Corrected and additional entries are listed in table 3. The listings in tables 2 and 3 follow the format of Special Report 10. Table 4 is a glossary of abbreviations used for quadrangle name, rock type, mineral dated, and type of dating method used.

Radiometric age map of northern Alaska

USGS Publications Warehouse

Wilson, Frederic H.; Turner, D.L.

1975-01-01

This map includes published, thesis, and open-file radiometric data available to us as of June, 1975. Some dates are not plotted because of inadequate location data in the original references.The map is divided into five sections, based on 1:1,000,000 scale enlargements of the National Atlas maps of Alaska. Within each section (e.g., southeastern Alaska), radiometric dates are plotted and keyed to 1:250,000 scale quadrangles. Accompanying each map section is table 1, listing map numbers and the sample identification numbers used in DGGS Special Report 10: Radiometric Dates from Alaska-A 1975 Compilation”. The reader is referred to Special Report 10 for more complete information on location, rock type, dating method, and literature references for each age entry. A listing of dates in Special Report lo which require correction or deletion is included S table 2. Corrected and additional entries are listed in table 3. The listings in tables 2 and 3 follow the format of Special Report 10. Table 4 is a glossary of abbreviations used for quadrangle name, rock type, mineral dated, and type of dating method used.

Proteomic analysis of papaya (Carica papaya L.) displaying typical sticky disease symptoms.

PubMed

Rodrigues, Silas P; Ventura, José A; Aguilar, Clemente; Nakayasu, Ernesto S; Almeida, Igor C; Fernandes, Patricia M B; Zingali, Russolina B

2011-07-01

Papaya (Carica papaya L.) hosts the only described laticifer-infecting virus (Papaya meleira virus, PMeV), which is the causal agent of papaya sticky disease. To understand the systemic effects of PMeV in papaya, we conducted a comprehensive proteomic analysis of leaf samples from healthy and diseased plants grown under field conditions. First, a reference 2-DE map was established for proteins from healthy samples. A total of 486 reproducible spots were identified, and MALDI-TOF-MS/MS data identified 275 proteins accounting for 159 distinct proteins from 231 spots that were annotated. Second, the differential expression of proteins from healthy and diseased leaves was determined through parallel experiments, using 2-DE and DIGE followed by MALDI-TOF-MS/MS and LC-IonTrap-MS/MS, respectively. Conventional 2-DE analysis revealed 75 differentially expressed proteins. Of those, 48 proteins were identified, with 26 being upregulated (U) and 22 downregulated (D). In general, metabolism-related proteins were downregulated, and stress-responsive proteins were upregulated. This expression pattern was corroborated by the results of the DIGE analysis, which identified 79 differentially expressed proteins, with 23 identified (17 U and 6 D). Calreticulin and the proteasome subunits 20S and RPT5a were shown to be upregulated during infection by both 2-DE and DIGE analyses. These data may help shed light on plant responses against stresses and viral infections. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An associative model of adaptive inference for learning word-referent mappings.

PubMed

Kachergis, George; Yu, Chen; Shiffrin, Richard M

2012-04-01

People can learn word-referent pairs over a short series of individually ambiguous situations containing multiple words and referents (Yu & Smith, 2007, Cognition 106: 1558-1568). Cross-situational statistical learning relies on the repeated co-occurrence of words with their intended referents, but simple co-occurrence counts cannot explain the findings. Mutual exclusivity (ME: an assumption of one-to-one mappings) can reduce ambiguity by leveraging prior experience to restrict the number of word-referent pairings considered but can also block learning of non-one-to-one mappings. The present study first trained learners on one-to-one mappings with varying numbers of repetitions. In late training, a new set of word-referent pairs were introduced alongside pretrained pairs; each pretrained pair consistently appeared with a new pair. Results indicate that (1) learners quickly infer new pairs in late training on the basis of their knowledge of pretrained pairs, exhibiting ME; and (2) learners also adaptively relax the ME bias and learn two-to-two mappings involving both pretrained and new words and objects. We present an associative model that accounts for both results using competing familiarity and uncertainty biases.

Geologic map of the La Mesita Negra SE Quadrangle, Bernalillo County, New Mexico

USGS Publications Warehouse

Shroba, Ralph R.; Thompson, Ren A.; Schmidt, Dwight L.; Personius, Stephen F.; Maldonado, Florian; Brandt, Theodore R.

2003-01-01

Geologic mapping, in support of the USGS Middle Rio Grande Basin Geologic Mapping Project, shows the spatial distribution of artificial-fill, alluvial, colluvial, and eolian deposits, lava flows and related sediments of the Albuquerque volcanoes, and upper Santa Fe Group sediments. These deposits are on, beneath, and along the West Mesa (Llano de Albuquerque) just west of Albuquerque, New Mexico. Artificial fill deposits are mapped chiefly beneath and near segments of Interstate 40, in an inactive landfill (or dump) north of Interstate 40 near the eastern boundary of the map area, and in the active Cerro Colorado landfill near the southwestern corner of the map area. Alluvial deposits are mapped in stream channels, beneath treads of terraces, and on hill slopes. They include alluvium in stream channels and beneath treads of low terraces, terrace alluvium, sheetwash deposits, gravelly alluvium, and old alluvium and calcic soils of the Llano de Albuquerque. Alluvial and colluvial deposits are mapped on hill slopes. They include young alluvial-slope deposits, alluvium and colluvium, undivided, and old alluvial-slope deposits. Colluvial deposits are also mapped on hill slopes. They include colluvial deposits, undivided, as well as alluvial deposits, eolian sand, and calcic soils associated with fault scarps. Eolian deposits as well as eolian and alluvial deposits mantle gently slopping surfaces on the Llano de Albuquerque. They include active eolian sand, active and inactive eolian sand and sheetwash deposits, undivided, and inactive eolian sand and sheetwash deposits, undivided. Lava flows and related sediments of the Albuquerque volcanoes were mapped near the southeast corner of the map area. They include five young lava flows, two young cinder deposits, and old lava flows. Upper Santa Fe Group sediments are well exposed and mapped in the western part of the map area. They include a gravel unit, a pebbly sand unit, and a mud and sand unit. Undivided upper Santa Fe Group sediments were mapped in the eastern part of the map area. Sediments and lava flows in the map area record alluvial, eolian, colluvial, and volcanic processes of the past several million years. The surficial deposits (post-Santa Fe Group sediments) on the map are known or estimated to be at least 1 m thick; most deposits are poorly exposed. Thin (< 50 cm), discontinuous deposits of eolian sand and sheetwash (Qea, Qes, and Qsw) locally are present on gently sloping map units older than the alluvium in stream channels and low terraces (Qa). These thin eolian and sheetwash deposits are not mapped, but they are widespread on the gravel unit of the upper Santa Fe Group sediments (Tg) on the eastern flank of the Llano de Albuquerque, near the eastern boundary of the map area (quadrangle). Small deposits of artificial fill (af) less than about 25 m wide are not mapped. Fractional map symbols (for example, Qsw/Qby1) are used where sheetwash deposits mantle lava flows. These fractional units are not described here; instead refer to descriptions of individual units.

Time-efficient high-resolution whole-brain three-dimensional macromolecular proton fraction mapping

PubMed Central

Yarnykh, Vasily L.

2015-01-01

Purpose Macromolecular proton fraction (MPF) mapping is a quantitative MRI method that reconstructs parametric maps of a relative amount of macromolecular protons causing the magnetization transfer (MT) effect and provides a biomarker of myelination in neural tissues. This study aimed to develop a high-resolution whole-brain MPF mapping technique utilizing a minimal possible number of source images for scan time reduction. Methods The described technique is based on replacement of an actually acquired reference image without MT saturation by a synthetic one reconstructed from R1 and proton density maps, thus requiring only three source images. This approach enabled whole-brain three-dimensional MPF mapping with isotropic 1.25×1.25×1.25 mm3 voxel size and scan time of 20 minutes. The synthetic reference method was validated against standard MPF mapping with acquired reference images based on data from 8 healthy subjects. Results Mean MPF values in segmented white and gray matter appeared in close agreement with no significant bias and small within-subject coefficients of variation (<2%). High-resolution MPF maps demonstrated sharp white-gray matter contrast and clear visualization of anatomical details including gray matter structures with high iron content. Conclusions Synthetic reference method improves resolution of MPF mapping and combines accurate MPF measurements with unique neuroanatomical contrast features. PMID:26102097

Conodont and Radiolarian Data from the De Long Mountains Quadrangle and Adjacent Areas, Northern Alaska

USGS Publications Warehouse

Dumoulin, Julie A.; Harris, Anita G.; Blome, Charles D.; Young, Lorne E.

2006-01-01

INTRODUCTION This report presents biostratigraphic data from 289 collections at 189 localities in the De Long Mountains, Misheguk Mountain, and Noatak quadrangles (fig. 1); most of these data have never been previously published. The collections were made during studies of the Red Dog massive sulfide deposit in 1998?2004 and in support of regional mapping projects in 1979, 1981, 1983, and 1997?98. The collections?mostly conodonts and some radiolarians?tightly constrain the age of many stratigraphic units of Devonian through Triassic age exposed within the study area, and provide additional data on the depositional environments and thermal history of these rocks. The data are presented in a series of tables, organized by fossil type, stratigraphic unit, and location. Tables 1?12 contain conodont data, mostly from the De Long Mountains quadrangle. All of these collections were initially examined, or were reevaluated, from 1997 through 2004, and complete faunal lists are given for all samples. Table 13 lists ages and conodont color alteration indices (CAIs) of 27 collections from 24 localities in the Noatak quadrangle; updated faunal lists were not prepared for these samples. Radiolarian data?all from the De Long Mountains quadrangle?are given in table 14; these collections were analyzed between 1998 and 2003. Collection localities are shown in four maps (sheets 1, 2). Map 1 (sheet 1) shows all outcrop samples from the De Long Mountains and western Misheguk Mountain quadrangle (locs. 1-121). Maps 2?4 (sheets 1, 2) show all drill hole sample localities; samples come from the Su-Lik deposit and in and around the Anarraaq deposit (map 2, locs. 122?135), in and adjacent to the Red Dog deposits (Paalaaq, Aqqaluk, Main, and Qanaiyaq) (map 3, locs. 136?158), and from drill holes along the Port Road in the Noatak quadrangle (map 4, locs. 159?160). Map 4 (sheet 2) also shows all outcrop samples from the Noatak quadrangle (locs. 161?189). The text summarizes the lithofacies, age, and biofacies of the Paleozoic and Mesozoic stratigraphic units that produced the fossil collections presented in the tables. Many of the data for the Lisburne Group are taken from Dumoulin and others (2004). Plates 1?4 illustrate important conodonts from the collections listed herein, as well as from coeval collections in the Howard Pass quadrangle; information about the Howard Pass conodonts is given in Table 15.

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.

PubMed

Wymant, Chris; Blanquart, François; Golubchik, Tanya; Gall, Astrid; Bakker, Margreet; Bezemer, Daniela; Croucher, Nicholas J; Hall, Matthew; Hillebregt, Mariska; Ong, Swee Hoe; Ratmann, Oliver; Albert, Jan; Bannert, Norbert; Fellay, Jacques; Fransen, Katrien; Gourlay, Annabelle; Grabowski, M Kate; Gunsenheimer-Bartmeyer, Barbara; Günthard, Huldrych F; Kivelä, Pia; Kouyos, Roger; Laeyendecker, Oliver; Liitsola, Kirsi; Meyer, Laurence; Porter, Kholoud; Ristola, Matti; van Sighem, Ard; Berkhout, Ben; Cornelissen, Marion; Kellam, Paul; Reiss, Peter; Fraser, Christophe

2018-01-01

Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between- and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to pre-process reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with the user's choice of existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We used shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read whole-genome data produced with the Illumina platform, for sixty-five existing publicly available samples and fifty new samples. We show the systematic superiority of mapping to shiver's constructed reference compared with mapping the same reads to the closest of 3,249 real references: median values of 13 bases called differently and more accurately, 0 bases called differently and less accurately, and 205 bases of missing sequence recovered. We also successfully applied shiver to whole-genome samples of Hepatitis C Virus and Respiratory Syncytial Virus. shiver is publicly available from https://github.com/ChrisHIV/shiver.

High resolution Ceres HAMO atlas derived from Dawn FC images

NASA Astrophysics Data System (ADS)

Roatsch, Thomas; Kersten, Elke; Matz, Klaus-Dieter; Preusker, Frank; Scholten, Frank; Jaumann, Ralf; Raymond, Carol A.; Russell, Chris T.

2016-04-01

Introduction: NASA's Dawn spacecraft entered the orbit of dwarf planet Ceres in March 2015, and will characterize the geology, elemental and mineralogical composition, topography, shape, and internal structure of Ceres. One of the major goals of the mission is a global mapping of Ceres. Data: The Dawn mission was mapping Ceres in HAMO (High Altitude Mapping Orbit, 1475 km altitude) between August and October 2015. The framing camera took about 2,600 clear filter images with a resolution of about 140 m/pixel during these cycles. The images were taken with different viewing angles and different illumination conditions. We selected images from one cycle (cycle #1) for the mosaicking process to have similar viewing and illumination conditions. Very minor gaps in the coverage were filled with a few images from cycle #2. Data Processing: The first step of the processing chain towards the cartographic products is to ortho-rectify the images to the proper scale and map projec-tion type. This process requires detailed information of the Dawn orbit and attitude data and of the topography of the targets. Both, improved orientation and a high-resolution shape model, are provided by stereo processing (bundle block adjustment) of the HAMO stereo image dataset [3]. Ceres's HAMO shape model was used for the calculation of the ray intersection points while the map projection itself was done onto the reference sphere of Ceres with a radius of 470 km. The final step is the controlled mosaicking) of all images to a global mosaic of Ceres, the so-called basemap. Ceres map tiles: The Ceres atlas was produced in a scale of 1:750,000 and consists of 15 tiles that conform to the quadrangle scheme proposed by Greeley and Batson [4]. A map scale of 1:750,000 guarantees a mapping at the highest available Dawn resolution in HAMO. The individual tiles were extracted from the global mosaic and reprojected. Nomenclature: The Dawn team proposed 81 names for geological features. By international agreement, craters must be named after gods and goddesses of agriculture and vegetation from world mythology, whereas other geological features must be named after agricultural festivals of the world. The nomenclature proposed by the Dawn team was approved by the IAU [http://planetarynames.wr.usgs.gov/] and is shown in Fig. 1. The entire Ceres HAMO atlas will be available to the public through the Dawn GIS web page [http://dawngis.dlr.de/atlas]. References: [1] Russell, C.T. and Raymond, C.A., Space Sci. Rev., 163, DOI 10.1007/s11214-011-9836-2; [2] Sierks, et al., 2011, Space Sci. Rev., 163, DOI 10.1007/s11214-011-9745-4; [3] Preusker, F. et al., this session; [4] Greeley, R. and Batson, G., 1990, Planetary Mapping, Cambridge University Press.

An integrated pan-tropical biomass map using multiple reference datasets.

PubMed

Avitabile, Valerio; Herold, Martin; Heuvelink, Gerard B M; Lewis, Simon L; Phillips, Oliver L; Asner, Gregory P; Armston, John; Ashton, Peter S; Banin, Lindsay; Bayol, Nicolas; Berry, Nicholas J; Boeckx, Pascal; de Jong, Bernardus H J; DeVries, Ben; Girardin, Cecile A J; Kearsley, Elizabeth; Lindsell, Jeremy A; Lopez-Gonzalez, Gabriela; Lucas, Richard; Malhi, Yadvinder; Morel, Alexandra; Mitchard, Edward T A; Nagy, Laszlo; Qie, Lan; Quinones, Marcela J; Ryan, Casey M; Ferry, Slik J W; Sunderland, Terry; Laurin, Gaia Vaglio; Gatti, Roberto Cazzolla; Valentini, Riccardo; Verbeeck, Hans; Wijaya, Arief; Willcock, Simon

2016-04-01

We combined two existing datasets of vegetation aboveground biomass (AGB) (Proceedings of the National Academy of Sciences of the United States of America, 108, 2011, 9899; Nature Climate Change, 2, 2012, 182) into a pan-tropical AGB map at 1-km resolution using an independent reference dataset of field observations and locally calibrated high-resolution biomass maps, harmonized and upscaled to 14 477 1-km AGB estimates. Our data fusion approach uses bias removal and weighted linear averaging that incorporates and spatializes the biomass patterns indicated by the reference data. The method was applied independently in areas (strata) with homogeneous error patterns of the input (Saatchi and Baccini) maps, which were estimated from the reference data and additional covariates. Based on the fused map, we estimated AGB stock for the tropics (23.4 N-23.4 S) of 375 Pg dry mass, 9-18% lower than the Saatchi and Baccini estimates. The fused map also showed differing spatial patterns of AGB over large areas, with higher AGB density in the dense forest areas in the Congo basin, Eastern Amazon and South-East Asia, and lower values in Central America and in most dry vegetation areas of Africa than either of the input maps. The validation exercise, based on 2118 estimates from the reference dataset not used in the fusion process, showed that the fused map had a RMSE 15-21% lower than that of the input maps and, most importantly, nearly unbiased estimates (mean bias 5 Mg dry mass ha(-1) vs. 21 and 28 Mg ha(-1) for the input maps). The fusion method can be applied at any scale including the policy-relevant national level, where it can provide improved biomass estimates by integrating existing regional biomass maps as input maps and additional, country-specific reference datasets. © 2015 John Wiley & Sons Ltd.

The Genetics of Chemoreception in the Labella and Tarsi of Aedes aegypti

DTIC Science & Technology

2014-01-01

molecular pathway also involved in DEET perception in the dipteran relative Drosophila melanogaster (Ditzen et al., 2008; DeGennaro et al., 2013). Transgenic...Downloads/). Output Fastq Illumina files were map- ped to the reference genome with TopHat (Trapnell et al., 2009). The unambiguous sequence alignment...Q., Pikielny, C.W., 2002. Novel genes expressing in subsets of chemosensory sensilla on the front legs of male Drosophila melanogaster . Cell. Tissue

Accuracy assessment of NOAA gridded daily reference evapotranspiration for the Texas High Plains

USGS Publications Warehouse

Moorhead, Jerry; Gowda, Prasanna H.; Hobbins, Michael; Senay, Gabriel; Paul, George; Marek, Thomas; Porter, Dana

2015-01-01

The National Oceanic and Atmospheric Administration (NOAA) provides daily reference evapotranspiration (ETref) maps for the contiguous United States using climatic data from North American Land Data Assimilation System (NLDAS). This data provides large-scale spatial representation of ETref, which is essential for regional scale water resources management. Data used in the development of NOAA daily ETref maps are derived from observations over surfaces that are different from short (grass — ETos) or tall (alfalfa — ETrs) reference crops, often in nonagricultural settings, which carries an unknown discrepancy between assumed and actual conditions. In this study, NOAA daily ETos and ETrs maps were evaluated for accuracy, using observed data from the Texas High Plains Evapotranspiration (TXHPET) network. Daily ETos, ETrs and the climatic data (air temperature, wind speed, and solar radiation) used for calculating ETref were extracted from the NOAA maps for TXHPET locations and compared against ground measurements on reference grass surfaces. NOAA ETrefmaps generally overestimated the TXHPET observations (1.4 and 2.2 mm/day ETos and ETrs, respectively), which may be attributed to errors in the NLDAS modeled air temperature and wind speed, to which reference ETref is most sensitive. Therefore, a bias correction to NLDAS modeled air temperature and wind speed data, or adjustment to the resulting NOAA ETref, may be needed to improve the accuracy of NOAA ETref maps.

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

PubMed Central

Schneider, Valerie A.; Graves-Lindsay, Tina; Howe, Kerstin; Bouk, Nathan; Chen, Hsiu-Chuan; Kitts, Paul A.; Murphy, Terence D.; Pruitt, Kim D.; Thibaud-Nissen, Françoise; Albracht, Derek; Fulton, Robert S.; Kremitzki, Milinn; Magrini, Vincent; Markovic, Chris; McGrath, Sean; Steinberg, Karyn Meltz; Auger, Kate; Chow, William; Collins, Joanna; Harden, Glenn; Hubbard, Timothy; Pelan, Sarah; Simpson, Jared T.; Threadgold, Glen; Torrance, James; Wood, Jonathan M.; Clarke, Laura; Koren, Sergey; Boitano, Matthew; Peluso, Paul; Li, Heng; Chin, Chen-Shan; Phillippy, Adam M.; Durbin, Richard; Wilson, Richard K.; Flicek, Paul; Eichler, Evan E.; Church, Deanna M.

2017-01-01

The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures, and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues. For the first time, the reference assembly contains sequence-based representations for the centromeres. We also expanded the number of alternate loci to create a reference that provides a more robust representation of human population variation. We demonstrate that the updates render the reference an improved annotation substrate, alter read alignments in unchanged regions, and impact variant interpretation at clinically relevant loci. We additionally evaluated a collection of new de novo long-read haploid assemblies and conclude that although the new assemblies compare favorably to the reference with respect to continuity, error rate, and gene completeness, the reference still provides the best representation for complex genomic regions and coding sequences. We assert that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote our understanding of human biology and advance our efforts to improve health. PMID:28396521

Spatial cognition and navigation

NASA Technical Reports Server (NTRS)

Aretz, Anthony J.

1989-01-01

An experiment that provides data for the development of a cognitive model of pilot flight navigation is described. The experiment characterizes navigational awareness as the mental alignment of two frames of reference: (1) the ego centered reference frame that is established by the forward view out of the cockpit and (2) the world centered reference frame that is established by the aircraft's location on a map. The data support a model involving at least two components: (1) the perceptual encoding of the navigational landmarks and (2) the mental rotation of the map's world reference frame into alignment with the ego centered reference frame. The quantitative relationships of these two factors are provided as possible inputs for a computational model of spatial cognition during flight navigation.

Semantic Image Based Geolocation Given a Map (Author’s Initial Manuscript)

DTIC Science & Technology

2016-09-01

novel technique for detection and identification of building facades from geo-tagged reference view using the map and geometry of the building facades. We...2D map of the environment, and geometry of building facades. We evaluate our approach for building identification and geo-localization on a new...location recognition and building identification is done by matching the query view to a reference set, followed by estimation of 3D building facades

ReadXplorer—visualization and analysis of mapped sequences

PubMed Central

Hilker, Rolf; Stadermann, Kai Bernd; Doppmeier, Daniel; Kalinowski, Jörn; Stoye, Jens; Straube, Jasmin; Winnebald, Jörn; Goesmann, Alexander

2014-01-01

Motivation: Fast algorithms and well-arranged visualizations are required for the comprehensive analysis of the ever-growing size of genomic and transcriptomic next-generation sequencing data. Results: ReadXplorer is a software offering straightforward visualization and extensive analysis functions for genomic and transcriptomic DNA sequences mapped on a reference. A unique specialty of ReadXplorer is the quality classification of the read mappings. It is incorporated in all analysis functions and displayed in ReadXplorer's various synchronized data viewers for (i) the reference sequence, its base coverage as (ii) normalizable plot and (iii) histogram, (iv) read alignments and (v) read pairs. ReadXplorer's analysis capability covers RNA secondary structure prediction, single nucleotide polymorphism and deletion–insertion polymorphism detection, genomic feature and general coverage analysis. Especially for RNA-Seq data, it offers differential gene expression analysis, transcription start site and operon detection as well as RPKM value and read count calculations. Furthermore, ReadXplorer can combine or superimpose coverage of different datasets. Availability and implementation: ReadXplorer is available as open-source software at http://www.readxplorer.org along with a detailed manual. Contact: rhilker@mikrobio.med.uni-giessen.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24790157

2D strain mapping using scanning transmission electron microscopy Moiré interferometry and geometrical phase analysis.

PubMed

Pofelski, A; Woo, S Y; Le, B H; Liu, X; Zhao, S; Mi, Z; Löffler, S; Botton, G A

2018-04-01

A strain characterization technique based on Moiré interferometry in a scanning transmission electron microscope (STEM) and geometrical phase analysis (GPA) method is demonstrated. The deformation field is first captured in a single STEM Moiré hologram composed of multiple sets of periodic fringes (Moiré patterns) generated from the interference between the periodic scanning grating, fixing the positions of the electron probe on the sample, and the crystal structure. Applying basic principles from sampling theory, the Moiré patterns arrangement is then simulated using a STEM electron micrograph reference to convert the experimental STEM Moiré hologram into information related to the crystal lattice periodicities. The GPA method is finally applied to extract the 2D relative strain and rotation fields. The STEM Moiré interferometry enables the local information to be de-magnified to a large length scale, comparable to what can be achieved in dark-field electron holography. The STEM Moiré GPA method thus extends the conventional high-resolution STEM GPA capabilities by providing comparable quantitative 2D strain mapping with a larger field of view (up to a few microns). Copyright © 2017 Elsevier B.V. All rights reserved.

Design and tolerance analysis of a transmission sphere by interferometer model

NASA Astrophysics Data System (ADS)

Peng, Wei-Jei; Ho, Cheng-Fong; Lin, Wen-Lung; Yu, Zong-Ru; Huang, Chien-Yao; Hsu, Wei-Yao

2015-09-01

The design of a 6-in, f/2.2 transmission sphere for Fizeau interferometry is presented in this paper. To predict the actual performance during design phase, we build an interferometer model combined with tolerance analysis in Zemax. Evaluating focus imaging is not enough for a double pass optical system. Thus, we study the interferometer model that includes system error, wavefronts reflected from reference surface and tested surface. Firstly, we generate a deformation map of the tested surface. Because of multiple configurations in Zemax, we can get the test wavefront and the reference wavefront reflected from the tested surface and the reference surface of transmission sphere respectively. According to the theory of interferometry, we subtract both wavefronts to acquire the phase of tested surface. Zernike polynomial is applied to transfer the map from phase to sag and to remove piston, tilt and power. The restored map is the same as original map; because of no system error exists. Secondly, perturbed tolerances including fabrication of lenses and assembly are considered. The system error occurs because the test and reference beam are no longer common path perfectly. The restored map is inaccurate while the system error is added. Although the system error can be subtracted by calibration, it should be still controlled within a small range to avoid calibration error. Generally the reference wavefront error including the system error and the irregularity of the reference surface of 6-in transmission sphere is measured within peak-to-valley (PV) 0.1 λ (λ=0.6328 um), which is not easy to approach. Consequently, it is necessary to predict the value of system error before manufacture. Finally, a prototype is developed and tested by a reference surface with PV 0.1 λ irregularity.

Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library.

PubMed

Hulse-Kemp, Amanda M; Maheshwari, Shamoni; Stoffel, Kevin; Hill, Theresa A; Jaffe, David; Williams, Stephen R; Weisenfeld, Neil; Ramakrishnan, Srividya; Kumar, Vijay; Shah, Preyas; Schatz, Michael C; Church, Deanna M; Van Deynze, Allen

2018-01-01

Linked-Read sequencing technology has recently been employed successfully for de novo assembly of human genomes, however, the utility of this technology for complex plant genomes is unproven. We evaluated the technology for this purpose by sequencing the 3.5-gigabase (Gb) diploid pepper ( Capsicum annuum ) genome with a single Linked-Read library. Plant genomes, including pepper, are characterized by long, highly similar repetitive sequences. Accordingly, significant effort is used to ensure that the sequenced plant is highly homozygous and the resulting assembly is a haploid consensus. With a phased assembly approach, we targeted a heterozygous F 1 derived from a wide cross to assess the ability to derive both haplotypes and characterize a pungency gene with a large insertion/deletion. The Supernova software generated a highly ordered, more contiguous sequence assembly than all currently available C. annuum reference genomes. Over 83% of the final assembly was anchored and oriented using four publicly available  de novo linkage maps. A comparison of the annotation of conserved eukaryotic genes indicated the completeness of assembly. The validity of the phased assembly is further demonstrated with the complete recovery of both 2.5-Kb insertion/deletion haplotypes of the PUN1 locus in the F 1 sample that represents pungent and nonpungent peppers, as well as nearly full recovery of the BUSCO2 gene set within each of the two haplotypes. The most contiguous pepper genome assembly to date has been generated which demonstrates that Linked-Read library technology provides a tool to de novo assemble complex highly repetitive heterozygous plant genomes. This technology can provide an opportunity to cost-effectively develop high-quality genome assemblies for other complex plants and compare structural and gene differences through accurate haplotype reconstruction.

The Trial Software version for DEMETER power spectrum files visualization and mapping

NASA Astrophysics Data System (ADS)

Lozbin, Anatoliy; Inchin, Alexander; Shpadi, Maxim

2010-05-01

In the frame of Kazakhstan's Scientific Space System creation for earthquakes precursors research, the hardware and software of DEMETER satellite was investigated. The data processing Software of DEMETER is based on package SWAN under IDL Virtual machine and realizes many features, but we can't find an important tool for the spectrograms analysis - space-time visualization of power spectrum files from electromagnetic devices as ICE and IMSC. For elimination of this problem we have developed Software which is offered to use. The DeSS (DEMETER Spectrogram Software) - it is Software for visualization, analysis and a mapping of power spectrum data from electromagnetic devices ICE and IMSC. The Software primary goal is to give the researcher friendly tool for the analysis of electromagnetic data from DEMETER Satellite for earthquake precursors and other ionosphere events researches. The Input data for DeSS Software is a power spectrum files: - Power spectrum of 1 component of the electric field in the VLF range (APID 1132); - Power spectrum of 1 component of the electric field in the HF range (APID 1134); - Power spectrum of 1 component of the magnetic field in the VLF range (APID 1137). The main features and operations of the software is possible: - various time and frequency filtration; - visualization of time dependence of signal intensity on fixed frequency; - spectral density visualization for fixed frequency range; - spectrogram autosize and smooth spectrogram; - the information in each point of the spectrogram: time, frequency and intensity; - the spectrum information in the separate window, consisting of 4 blocks; - data mapping with 6 range scale. On the map we can browse next information: - satellite orbit; - conjugate point at the satellite altitude; - north conjugate point at the altitude 110 km; - south conjugate point at the altitude 110 km. This is only trial software version to help the researchers and we always ready collaborate with scientists for software improvement. References: 1. D.Lagoutte, J.Y. Brochot, D. de Carvalho, L.Madrias and M. Parrot. DEMETER Microsatellite. Scientific Mission Center. Data product description. DMT-SP-9-CM-6054-LPC. 2. D.Lagoutte, J.Y. Brochot, P.Latremoliere. SWAN - Software for Waveform Analysis. LPCE/NI/003.E - Part 1 (User's guide), Part 2 (Analysis tools), Part 3 (User's project interface).

Mapping language to visual referents: Does the degree of image realism matter?

PubMed

Saryazdi, Raheleh; Chambers, Craig G

2018-01-01

Studies of real-time spoken language comprehension have shown that listeners rapidly map unfolding speech to available referents in the immediate visual environment. This has been explored using various kinds of 2-dimensional (2D) stimuli, with convenience or availability typically motivating the choice of a particular image type. However, work in other areas has suggested that certain cognitive processes are sensitive to the level of realism in 2D representations. The present study examined the process of mapping language to depictions of objects that are more or less realistic, namely photographs versus clipart images. A custom stimulus set was first created by generating clipart images directly from photographs of real objects. Two visual world experiments were then conducted, varying whether referent identification was driven by noun or verb information. A modest benefit for clipart stimuli was observed during real-time processing, but only for noun-driving mappings. The results are discussed in terms of their implications for studies of visually situated language processing. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Evaluation of the 34S/32S ratio of Soufre de Lacq elemental sulfur isotopic reference material by continuous flow isotope-ratio mass spectrometry

USGS Publications Warehouse

Qi, H.P.; Coplen, T.B.

2003-01-01

Soufre de Lacq elemental sulfur reference material (IAEA-S-4) isotopically is homogeneous in amounts as small as 41 ??g as determined by continuous flow isotope-ratio mass spectrometry. The ??34S value for this reference material is +16.90 ?? 0.12??? (1??) on a scale (Vienna Can??on Diablo troilite, VCDT) where IAEA-S-1 Ag2S is -0.3??? and IAEA-S-2 Ag2S is +22.67???. Published by Elsevier Science B.V.

Additional Value from Road Mapping in Defense Policy Making (meerwaarde van roadmapping bij beleidsontwikkeling van de koninklijke landmacht)

DTIC Science & Technology

2006-05-01

van zogonaamde strategische reserves tot bijvaarbeeld lakaal boschikbare gevechtscapacitoit. 9 11 Joint. Do Nederlandse krijgsmacht ontwikkelt zich tot...8 2 W erkwijze van de KL tot nu toe ............................................................................... 9 2.1 O...ntwikkeling visiedocurnent ....................................................................................... 9 2.2 Opzet beleid- en deelstudies

Safety analysis of a Russian phage cocktail: From MetaGenomic analysis to oral application in healthy human subjects

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

McCallin, Shawna, E-mail: semccallin@yahoo.com; Alam Sarker, Shafiqul, E-mail: sasarker@icddrb.org; Barretto, Caroline, E-mail: Caroline.Barretto@rdls.nestle.com

Phage therapy has a long tradition in Eastern Europe, where preparations are comprised of complex phage cocktails whose compositions have not been described. We investigated the composition of a phage cocktail from the Russian pharmaceutical company Microgen targeting Escherichia coli/Proteus infections. Electron microscopy identified six phage types, with numerically T7-like phages dominating over T4-like phages. A metagenomic approach using taxonomical classification, reference mapping and de novo assembly identified 18 distinct phage types, including 7 genera of Podoviridae, 2 established and 2 proposed genera of Myoviridae, and 2 genera of Siphoviridae. De novo assembly yielded 7 contigs greater than 30 kb,more » including a 147-kb Myovirus genome and a 42-kb genome of a potentially new phage. Bioinformatic analysis did not reveal undesired genes and a small human volunteer trial did not associate adverse effects with oral phage exposure. - Highlights: • We analyzed the composition of a commercial Russian phage cocktail. • The cocktail consists of at least 10 different phage genera. • No undesired genes were detected. • No adverse effects were seen upon oral application in a small human clinical trial.« less

The DIII-D Map -- An Area-Preserving Map for Trajectories of Magnetic Field Lines in the DIII-D Tokamak

NASA Astrophysics Data System (ADS)

Punjabi, Alkesh; Ali, Halima; Boozer, Allen; Evans, Todd

2007-11-01

The EFIT data for the DIII-D shot 115467 3000 ms is used to calculate the generating function for an area-preserving map for trajectories of magnetic field lines in the DIII-D. We call this map the DIII-D map. The generating function is a bivariate polynomial in base vectors &1/2circ;cos(θ) and &1/2circ;sin(θ). ψ is toroidal flux and θ is poloidal angle. The generating function is calculated using a canonical transformation from (ψ,θ) to physical coordinates (R,Z) in the DIII-D [1] and nonlinear regression. The equilibrium generating function gives an excellent representation of the equilibrium flux surfaces in the DIII-D. The DIII-D map is then used to calculate effects of the magnetic perturbations in the DIII-D. Preliminary results of the DIII-D map will be presented. This work is supported by US DOE OFES DE-FG02-01ER54624 and DE-FG02-04ER54793. [1] A. Punjabi, H. Ali, T. Evans, and A. Boozer, Phys Lett A 364 140--145 (2007).

Distributed Interactive Simulation Protocol Extensions

DTIC Science & Technology

1993-05-28

company HQ. The OrgName and Type Code for a unit will be reported in the Notion or Perception I PDU( s ) for that unit. Any unit in a player’s Task Org...this order. The U.I. can have a mapping of that unique ID to some user entered ID if desired. Reference - No map reference is needed, the map( s ...Common (232):I Si. 0) 0xre~t 4 f ne0 W .bti ISM07 GUITI Unw.evwd (131 5u.on e4 ffifldedl) C L~cu S .an e p e a m (1 ) 1 A ~ w 2 O GS iI U~WW 2 - P S 54

Linking flood peak, flood volume and inundation extent: a DEM-based approach

NASA Astrophysics Data System (ADS)

Rebolho, Cédric; Furusho-Percot, Carina; Blaquière, Simon; Brettschneider, Marco; Andréassian, Vazken

2017-04-01

Traditionally, flood inundation maps are computed based on the Shallow Water Equations (SWE) in one or two dimensions, with various simplifications that have proved to give good results. However, the complexity of the SWEs often requires a numerical resolution which can need long computing time, as well as detailed cross section data: this often results in restricting these models to rather small areas abundant with high quality data. This, along with the necessity for fast inundation mapping, are the reason why rapid inundation models are being designed, working for (almost) any river with a minimum amount of data and, above all, easily available data. Our model tries to follow this path by using a 100m DEM over France from which are extracted a drainage network and the associated drainage areas. It is based on two pre-existing methods: (1) SHYREG (Arnaud et al.,2013), a regionalized approach used to calculate the 2-year and 10-year flood quantiles (used as approximated bankfull flow and maximum discharge, respectively) for each river pixel of the DEM (below a 10 000 km2 drainage area) and (2) SOCOSE (Mailhol,1980), which gives, amongst other things, an empirical formula of a characteristic flood duration (for each pixel) based on catchment area, average precipitation and temperature. An overflow volume for each river pixel is extracted from a triangular shaped synthetic hydrograph designed with SHYREG quantiles and SOCOSE flood duration. The volume is then spread from downstream to upstream one river pixel at a time. When the entire hydrographic network is processed, the model stops and generates a map of potential inundation area associated with the 10-year flood quantile. Our model can also be calibrated using past-events inundation maps by adjusting two parameters, one which modifies the overflow duration, and the other, equivalent to a minimum drainage area for river pixels to be flooded. Thus, in calibration on a sample of 42 basins, the first draft of the model showed a 0.51 median Fit (intersection of simulated and observed areas divided by the union of the two, Bates and De Roo, 2000) and a 0.74 maximum. Obviously, this approach is quite rough, and would require testing on events of homogeneous return periods (which is not the case for now). The next steps in the test and the development of our method include the use of the AIGA distributed model to simulate past-events hydrographs, the search for a new way to automatically approach bankfull flow and the integration of the results in our model to build dynamic maps of the flood. References Arnaud, P., Eglin, Y., Janet, B., and Payrastre, O. (2013). Notice utilisateur : bases de données SHYREG-Débit. Méthode - Performances - Limites. Bates, P. D. and De Roo, A. P. J. (2000). A simple raster-based model for flood inundation simulation. Journal of Hydrology, 236(1-2):54-77. Mailhol, J. (1980). Pour une approche plus réaliste du temps caractéristique de crues des bassins versants. In Actes du Colloque d'Oxford, volume 129, pages 229-237, Oxford. IAHS-AISH.

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

PubMed

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

2014-07-01

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

Seafloor mapping of the southeast Iberian margin (from Cabo de Palos to Cabo de Gata)

NASA Astrophysics Data System (ADS)

Lastras, Galderic; Leon, César; Elvira, Elena; Pascual, Laura; Muñoz, Araceli; de Cárdenas, Enrique; Acosta, Juan; Canals, Miquel

2014-05-01

We present the multibeam bathymetry and derived maps of the southeast Iberian margin from Cabo de Palos to Cabo de Gata, 37º35'N to 35º45'N and 2º10'W to 0º20'E, from the coastline down to the Algero-Balearic abyssal plain at depths exceeding 2600 m. The edition of of the maps is carried out within the Complementary Action VALORPLAT ("Scientific valorisation of multibeam bathymetry data from the Spanish continental shelf and slope"), funded by the Spanish Ministry of Economy and Competitivity. The multibeam bathymetry data of the slope and abyssal plain were obtained during different surveys in 2004, 2006 and 2007 on board R/V Vizconde de Eza with a Simrad EM300 multibeam echo-sounder as part of the CAPESME Project, a collaboration between the Spanish Institute of Oceanography (IEO) and General Secretariat of Fisheries (SGP), primarily aiming at creating maps of the fishing grounds of the Mediterranean continental margins of Spain. Multibeam bathymetry data from the continental shelf were obtained within the ESPACE project, also in a cooperative frame between IEO and SGP. The map series is constituted by a general map at 1:400,000 scale and 14 detailed maps at 1:75,000 scale, which include inset maps on slope gradients and seafloor nature (rock or sediment type), the later obtained with rock dredges and Shipeck sediment dredges. Both the detailed maps and the general map are available in paper print, and the whole collection is also distributed in an edited USB. The geological features displayed in the different maps include the continental shelf, with abundant geomorphic features indicative of past sea-level changes, the continental slope carved by the Palos, Tiñoso, Cartagena Este, Cartagena Oeste, Águilas, Almanzora, Alias, Garrucha and Gata submarine canyons, the Mazarrón, Palomares and Al-Mansour escarpments, the Abubácer, Maimonides and Yusuf ridges, the Águilas and Al-Mansour seamounts, and the Algero-Balearic abyssal plain where prominent halokinetic deformation structures have been observed. The edited maps are available from the MAGRAMA (Ministerio de Agricultura, Alimentación y Medio Ambiente) publication store (https://aplicaciones.magrama.es/tienda/index.jsp).

An interoperable standard system for the automatic generation and publication of the fire risk maps based on Fire Weather Index (FWI)

NASA Astrophysics Data System (ADS)

Julià Selvas, Núria; Ninyerola Casals, Miquel

2015-04-01

It has been implemented an automatic system to predict the fire risk in the Principality of Andorra, a small country located in the eastern Pyrenees mountain range, bordered by Catalonia and France, due to its location, his landscape is a set of a rugged mountains with an average elevation around 2000 meters. The system is based on the Fire Weather Index (FWI) that consists on different components, each one, measuring a different aspect of the fire danger calculated by the values of the weather variables at midday. CENMA (Centre d'Estudis de la Neu i de la Muntanya d'Andorra) has a network around 10 automatic meteorological stations, located in different places, peeks and valleys, that measure weather data like relative humidity, wind direction and speed, surface temperature, rainfall and snow cover every ten minutes; this data is sent daily and automatically to the system implemented that will be processed in the way to filter incorrect measurements and to homogenizer measurement units. Then this data is used to calculate all components of the FWI at midday and for the level of each station, creating a database with the values of the homogeneous measurements and the FWI components for each weather station. In order to extend and model this data to all Andorran territory and to obtain a continuous map, an interpolation method based on a multiple regression with spline residual interpolation has been implemented. This interpolation considerer the FWI data as well as other relevant predictors such as latitude, altitude, global solar radiation and sea distance. The obtained values (maps) are validated using a cross-validation leave-one-out method. The discrete and continuous maps are rendered in tiled raster maps and published in a web portal conform to Web Map Service (WMS) Open Geospatial Consortium (OGC) standard. Metadata and other reference maps (fuel maps, topographic maps, etc) are also available from this geoportal.

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.

PubMed

Schneider, Valerie A; Graves-Lindsay, Tina; Howe, Kerstin; Bouk, Nathan; Chen, Hsiu-Chuan; Kitts, Paul A; Murphy, Terence D; Pruitt, Kim D; Thibaud-Nissen, Françoise; Albracht, Derek; Fulton, Robert S; Kremitzki, Milinn; Magrini, Vincent; Markovic, Chris; McGrath, Sean; Steinberg, Karyn Meltz; Auger, Kate; Chow, William; Collins, Joanna; Harden, Glenn; Hubbard, Timothy; Pelan, Sarah; Simpson, Jared T; Threadgold, Glen; Torrance, James; Wood, Jonathan M; Clarke, Laura; Koren, Sergey; Boitano, Matthew; Peluso, Paul; Li, Heng; Chin, Chen-Shan; Phillippy, Adam M; Durbin, Richard; Wilson, Richard K; Flicek, Paul; Eichler, Evan E; Church, Deanna M

2017-05-01

The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures, and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues. For the first time, the reference assembly contains sequence-based representations for the centromeres. We also expanded the number of alternate loci to create a reference that provides a more robust representation of human population variation. We demonstrate that the updates render the reference an improved annotation substrate, alter read alignments in unchanged regions, and impact variant interpretation at clinically relevant loci. We additionally evaluated a collection of new de novo long-read haploid assemblies and conclude that although the new assemblies compare favorably to the reference with respect to continuity, error rate, and gene completeness, the reference still provides the best representation for complex genomic regions and coding sequences. We assert that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote our understanding of human biology and advance our efforts to improve health. © 2017 Schneider et al.; Published by Cold Spring Harbor Laboratory Press.

Proteomic evaluation of sheep serum proteins

PubMed Central

2012-01-01

Background The applications of proteomic strategies to ovine medicine remain limited. The definition of serum proteome may be a good tool to identify useful protein biomarkers for recognising sub-clinical conditions and overt disease in sheep. Findings from bovine species are often directly translated for use in ovine medicine. In order to characterize normal protein patterns and improve knowledge of molecular species-specific characteristics, we generated a two-dimensional reference map of sheep serum. The possible application of this approach was tested by analysing serum protein patterns in ewes with mild broncho-pulmonary disease, which is very common in sheep and in the peripartum period which is a stressful time, with a high incidence of infectious and parasitic diseases. Results This study generated the first reference 2-DE maps of sheep serum. Overall, 250 protein spots were analyzed, and 138 identified. Compared with healthy sheep, serum protein profiles of animals with rhino-tracheo-bronchitis showed a significant decrease in protein spots identified as transthyretin, apolipoprotein A1 and a significant increase in spots identified as haptoglobin, endopin 1b and alpha1B glycoprotein. In the peripartum period, haptoglobin, alpha-1-acid glycoprotein, apolipoprotein A1 levels rose, while transthyretin content dropped. Conclusions This study describes applications of proteomics in putative biomarker discovery for early diagnosis as well as for monitoring the physiological and metabolic situations critical for ovine welfare. PMID:22630135

Evaluation of Reference Centers for Special Immunobiologicals implementation.

PubMed

Nóbrega, Laura Andrade Lagôa; Novaes, Hillegonda Maria Dutilh; Sartori, Ana Marli Christovam

2016-09-01

To describe the Reference Centers for Special Immunobiologicals and evaluate their implementation considering formal regulations. We conducted a program evaluation, of evaluative research type. From August 2011 to January 2012, a questionnaire was applied to the 42 Reference Centers for Special Immunobiologicals existing in the Country, approaching the structure, human resources, and developed activities dimensions. We conducted a descriptive analysis of data and used a clustering for binary data with the squared Euclidean distance, by the farthest neighbor method, to aggregate services with similar features. We observed great diversity among the services in the three dimensions. The clustering resulted in five service profiles, named according to their characteristics. 1) Best structure: 12 Reference Centers for Special Immunobiologicals with the highest proportion of services with the minimum of rooms recommended, purpose-built vaccine refrigerators, preventive maintenance of the cold chain, and oxygen source. 2) Immunobiologicals distributor: six Reference Centers for Special Immunobiologicals that distributed more than applied immunogens; no doctor present for more than half of the working hours and no purpose-built vaccine refrigerators . 3) Incipient implementation: five Reference Centers for Special Immunobiologicals with inadequate structure, such as absence of purpose-built vaccine refrigerators, preventive maintenance of the cold chain and oxygen source; none had computer. 4) Vaccination rooms: 13 Reference Centers for Special Immunobiologicals, everyone did routine immunization, most participated in vaccination campaigns. 5) Teaching and research: six services, all inserted into teaching hospitals, developed researches and received trainees; most had doctors in more than half of the working hours. The evaluation of the Reference Centers for Special Immunobiologicals implementation was based on the profiles found and considered the official regulations: services categorized as "better structure" and "teaching and research" were considered implemented; "immunobiologicals distributor" and "vaccination room" services, partially implemented, and the ones with the "incipient implementation" profile, not implemented. The results of this evaluation can contribute to the reformulation of the services, considering the current context. Descrever os Centros de Referência para Imunobiológicos Especiais e avaliar sua implantação considerando as regulamentações formais. Foi realizada uma avaliação de programa, tipo pesquisa avaliativa. De agosto de 2011 a janeiro de 2012, foi aplicado questionário aos responsáveis pelos 42 Centros de Referência para Imunobiológicos Especiais existentes no País, abordando as dimensões estrutura, recursos humanos e atividades desenvolvidas. Foi feita análise descritiva dos dados e utilizado agrupamento para dados binários com uso da distância euclidiana quadrática, pelo método do vizinho mais distante, para agregar serviços com características semelhantes. Observou-se grande diversidade entre os serviços nas três dimensões. O agrupamento resultou em cinco perfis de serviços, denominados de acordo com suas características. 1) Melhor estrutura: 12 Centros de Referência para Imunobiológicos Especiais com a maior proporção de serviços com o mínimo de salas preconizado, câmaras de vacinas, manutenção preventiva da rede de frio e fonte de oxigênio. 2) Dispensador de imunobiológicos: seis Centros de Referência para Imunobiológicos Especiais que mais dispensavam do que aplicavam imunógenos; sem médico presente por mais da metade do expediente do serviço e sem câmara de vacinas. 3) Implantação incipiente: cinco Centros de Referência para Imunobiológicos Especiais com estrutura inadequada, como ausência de câmaras de vacinas, de manutenção preventiva da rede de frio e de fonte de oxigênio; nenhum possuía computador. 4) Sala de vacinas: 13 Centros de Referência para Imunobiológicos Especiais, todos faziam imunização de rotina, a maioria participava de campanhas de vacinação. 5) Ensino e pesquisa: seis serviços, todos inseridos em hospitais de ensino, desenvolviam pesquisas e recebiam estagiários; a maioria possuía médicos em mais da metade do expediente. A avaliação de implantação dos Centros de Referência para Imunobiológicos Especiais baseou-se nos perfis encontrados e considerou as regulamentações oficiais: os serviços categorizados como "melhor estrutura" e "ensino e pesquisa" foram considerados implantados; os serviços "dispensador de imunobiológicos" e "sala de vacinas", parcialmente implantados e os do perfil "implantação incipiente", não implantados. Os resultados dessa avaliação podem contribuir para a reformulação dos serviços, considerando o contexto atual.

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver

PubMed Central

Blanquart, François; Golubchik, Tanya; Gall, Astrid; Bakker, Margreet; Bezemer, Daniela; Croucher, Nicholas J; Hall, Matthew; Hillebregt, Mariska; Ratmann, Oliver; Albert, Jan; Bannert, Norbert; Fellay, Jacques; Fransen, Katrien; Gourlay, Annabelle; Grabowski, M Kate; Gunsenheimer-Bartmeyer, Barbara; Günthard, Huldrych F; Kivelä, Pia; Kouyos, Roger; Laeyendecker, Oliver; Liitsola, Kirsi; Meyer, Laurence; Porter, Kholoud; Ristola, Matti; van Sighem, Ard; Cornelissen, Marion; Kellam, Paul; Reiss, Peter

2018-01-01

Abstract Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between- and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to pre-process reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with the user’s choice of existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We used shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read whole-genome data produced with the Illumina platform, for sixty-five existing publicly available samples and fifty new samples. We show the systematic superiority of mapping to shiver’s constructed reference compared with mapping the same reads to the closest of 3,249 real references: median values of 13 bases called differently and more accurately, 0 bases called differently and less accurately, and 205 bases of missing sequence recovered. We also successfully applied shiver to whole-genome samples of Hepatitis C Virus and Respiratory Syncytial Virus. shiver is publicly available from https://github.com/ChrisHIV/shiver. PMID:29876136

GIM-TEC adaptive ionospheric weather assessment and forecast system

NASA Astrophysics Data System (ADS)

Gulyaeva, T. L.; Arikan, F.; Hernandez-Pajares, M.; Stanislawska, I.

2013-09-01

The Ionospheric Weather Assessment and Forecast (IWAF) system is a computer software package designed to assess and predict the world-wide representation of 3-D electron density profiles from the Global Ionospheric Maps of Total Electron Content (GIM-TEC). The unique system products include daily-hourly numerical global maps of the F2 layer critical frequency (foF2) and the peak height (hmF2) generated with the International Reference Ionosphere extended to the plasmasphere, IRI-Plas, upgraded by importing the daily-hourly GIM-TEC as a new model driving parameter. Since GIM-TEC maps are provided with 1- or 2-days latency, the global maps forecast for 1 day and 2 days ahead are derived using an harmonic analysis applied to the temporal changes of TEC, foF2 and hmF2 at 5112 grid points of a map encapsulated in IONEX format (-87.5°:2.5°:87.5°N in latitude, -180°:5°:180°E in longitude). The system provides online the ionospheric disturbance warnings in the global W-index map establishing categories of the ionospheric weather from the quiet state (W=±1) to intense storm (W=±4) according to the thresholds set for instant TEC perturbations regarding quiet reference median for the preceding 7 days. The accuracy of IWAF system predictions of TEC, foF2 and hmF2 maps is superior to the standard persistence model with prediction equal to the most recent ‘true’ map. The paper presents outcomes of the new service expressed by the global ionospheric foF2, hmF2 and W-index maps demonstrating the process of origin and propagation of positive and negative ionosphere disturbances in space and time and their forecast under different scenarios.

Digital files for northeast Asia geodynamics, mineral deposit location, and metallogenic belt maps, stratigraphic columns, descriptions of map units, and descriptions of metallogenic belts

USGS Publications Warehouse

Nokleberg, Warren J.; Badarch, Gombosuren; Berzin, Nikolai A.; Diggles, Michael F.; Hwang, Duk-Hwan; Khanchuk, Alexander I.; Miller, Robert J.; Naumova, Vera V.; Obolensky, Alexander A.; Ogasawara, Masatsugu; Parfenov, Leonid M.; Prokopiev, Andrei V.; Rodionov, Sergey M.; Yan, Hongquan

2004-01-01

This is the online version of a CD-ROM publication. It contains all of the data that are on the disc but extra files have been removed: index files, software installers, and Windows autolaunch files. This publication contains a a series of files for Northeast Asia geodynamics, mineral deposit location, and metallogenic belt maps descriptions of map units and metallogenic belts, and stratigraphic columns. This region includes Eastern Siberia, Russian Far East, Mongolia, Northeast China, South Korea, and Japan. The files include: (1) a geodynamics map at a scale of 1:5,000,000; (2) page-size stratigraphic columns for major terranes; (3) a generalized geodynamics map at a scale of 1:15,000,000; (4) a mineral deposit location map at a scale of 1:7,500,000; (5) metallogenic belt maps at a scale of 1:15,000,000; (6) detailed descriptions of geologic units with references; (7) detailed descriptions of metallogenic belts with references; and (8) summary mineral deposit and metallogenic belt tables. The purpose of this publication is to provide high-quality, digital graphic files for maps and figures, and Word files for explanations, descriptions, and references to customers and users.

Sen2-Agri country level demonstration for Ukraine

NASA Astrophysics Data System (ADS)

Kussul, N.; Kolotii, A.; Shelestov, A.; Lavreniuk, M. S.

2016-12-01

Due to launch of Sentinel-2 mission European Space Agency (ESA) started Sentinel-2 for Agriculture (Sen2-Agri) project coordinated by Universite catholique de Louvain (UCL). Ukraine is selected as one of 3 country level demonstration sites for benchmarking Sentinel-2 data due to wide range of main crops (both winter and summer), big fields and high enough climate variability over the territory [1-2]. Within this county level demonstration main objectives are following: i) Sentinel's products quality assessment and their suitability estimation for the territory of Ukraine [2]; ii) demonstration in order to convince decision makers and state authorities; iii) assessment of the personnel and facilities required to run the Sen2-Agri system and creation of Sen-2 Agri products (crop type maps and such essential climatic variable as Leaf Area Index - LAI [3]). During this project ground data were collected for crop land mapping and crop type classification along the roads within main agro-climatic zones of Ukraine. For LAI estimation we used indirect non-destructive method which is based on DHP-images and VALERI protocol. Products created with use of Sen2-Agri system deployed during project execution and results of neural-network approach utilization will be compared. References Kussul, N., Lemoine, G., Gallego, F. J., Skakun, S. V., Lavreniuk, M., & Shelestov, A. Y. Parcel-Based Crop Classification in Ukraine Using Landsat-8 Data and Sentinel-1A Data. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing , 9 (6), 2500-2508. Kussul, N., Skakun, S., Shelestov, A., Lavreniuk, M., Yailymov, B., & Kussul, O. (2015). Regional scale crop mapping using multi-temporal satellite imagery. The International Archives of Photogrammetry, Remote Sensing and Spatial Information Sciences, 40(7), 45-52. Shelestov, A., Kolotii, A., Camacho, F., Skakun, S., Kussul, O., Lavreniuk, M., & Kostetsky, O. (2015, July). Mapping of biophysical parameters based on high resolution EO imagery for JECAM test site in Ukraine. In 2015 IEEE International Geoscience and Remote Sensing Symposium (IGARSS), 1733-1736

Geographic information systems (GIS) spatial data compilation of geodynamic, tectonic, metallogenic, mineral deposit, and geophysical maps and associated descriptive data for northeast Asia

USGS Publications Warehouse

Naumova, Vera V.; Patuk, Mikhail I.; Kapitanchuk, Marina Yu.; Nokleberg, Warren J.; Khanchuk, Alexander I.; Parfenov, Leonid M.; Rodionov, Sergey M.; Miller, Robert J.; Diggles, Michael F.

2006-01-01

This is the online version of a CD-ROM publication. It contains all of the data that are on the disc but extra files have been removed: index files, software installers, and Windows autolaunch files. The purpose of this publication is to provide a high-quality spatial data compilation (Geographical Information System or GIS) of geodynamic, mineral deposit, and metallogenic belt maps, and descriptive data for Northeast Asia for customers and users. This area consists of Eastern Siberia, Russian Far East, Mongolia, northern China, South Korea, and Japan. The GIS compilation contains integrated spatial data for: (1) a geodynamics map at a scale of 1:5,000,000; (2) a mineral deposit location map; (3) metallogenic belt maps; (4) detailed descriptions of geologic units, including tectonostratigraphic terranes, cratons, major melange zones, and overlap assemblages, with references; (5) detailed descriptions of metallogenic belts with references; (6) detailed mineral deposit descriptions with references; and (7) page-size stratigraphic columns for major terranes.

Comprehensive geo-spatial data creation for Qassim region in the KSA

NASA Astrophysics Data System (ADS)

Alrajhi, M.; Hawarey, M.

2009-04-01

The General Directorate for Surveying and Mapping (GDSM) of the Deputy Ministry for Land and Surveying (DMLS) of the Ministry of Municipal and Rural Affairs (MOMRA) in the Kingdom of Saudi Arabia (KSA) has the exclusive mandate to carry out aerial photography and produce large-scale detailed maps for about 220 cities and villages in the KSA. This presentation is about the comprehensive geo-spatial data creation for the Qassim region, North KSA, that was founded on country-wide horizontal geodetic ground control using Global Navigation Satellite Systems (GNSS) within the MOMRA's Terrestrial Reference Frame 2000 (MTRF2000) that is tied to International Terrestrial Reference Frame 2000 (ITRF2000) Epoch 2004.0, and vertical geodetic ground control using precise digital leveling in reference to Jeddah 1969 mean sea level, and included aerial photography of 1,505 km2 at 1:5,500 scale, 4,081 km2 at scale 22,500 and 22,224 km2 at 1:45,000 scale, full aerial triangulation, production of orthophoto maps at scale of 1:10,000 (463 sheets) for 22,224 km2, and production of GIS-oriented highly-detailed digital line maps in various formats at scales of 1:1,000 (1,534 sheets) and 1:2,500 (383 sheets) for 1,150 km2, 1:10,000 (161 sheets) for 7,700 km2, and 1:20,000 (130 sheets) for 22,000 km2. While aerial photography lasted from Feb 2003 thru May 2003, the line mapping continued May 2005 until December 2008.

Geology and resource assessment of Costa Rica at 1:500,000 scale; a digital representation of maps of the U.S. Geological Survey's 1987 folio I-1865

USGS Publications Warehouse

Schruben, Paul G.

1997-01-01

This CD-ROM contains digital versions of the geology and resource assessment maps of Costa Rica originally published in USGS Folio I-1865 (U.S. Geological Survey, the Direccion General de Geologia, Minas e Hidrocarburos, and the Universidad de Costa Rica, 1987) at a scale of 1:500,000. The following layers are available on the CD-ROM: geology and faults; favorable domains for selected deposit types; Bouguer gravity data; isostatic gravity contours; mineral deposits, prospects, and occurrences; and rock geochemistry sample points. For DOS users, the CD-ROM contains MAPPER, a user-friendly map display program. Some of the maps are also provided in the following additional formats on the CD-ROM: (1) ArcView 1 and 3, (2) ARC/INFO 6.1.2 Export, (3) Digital Line Graph (DLG) Optional, and (4) Drawing Exchange File (DXF.)

The automated reference toolset: A soil-geomorphic ecological potential matching algorithm

USGS Publications Warehouse

Nauman, Travis; Duniway, Michael C.

2016-01-01

Ecological inventory and monitoring data need referential context for interpretation. Identification of appropriate reference areas of similar ecological potential for site comparison is demonstrated using a newly developed automated reference toolset (ART). Foundational to identification of reference areas was a soil map of particle size in the control section (PSCS), a theme in US Soil Taxonomy. A 30-m resolution PSCS map of the Colorado Plateau (366,000 km2) was created by interpolating ∼5000 field soil observations using a random forest model and a suite of raster environmental spatial layers representing topography, climate, general ecological community, and satellite imagery ratios. The PSCS map had overall out of bag accuracy of 61.8% (Kappa of 0.54, p < 0.0001), and an independent validation accuracy of 93.2% at a set of 356 field plots along the southern edge of Canyonlands National Park, Utah. The ART process was also tested at these plots, and matched plots with the same ecological sites (ESs) 67% of the time where sites fell within 2-km buffers of each other. These results show that the PSCS and ART have strong application for ecological monitoring and sampling design, as well as assessing impacts of disturbance and land management action using an ecological potential framework. Results also demonstrate that PSCS could be a key mapping layer for the USDA-NRCS provisional ES development initiative.

Systems and methods that generate height map models for efficient three dimensional reconstruction from depth information

DOEpatents

Frahm, Jan-Michael; Pollefeys, Marc Andre Leon; Gallup, David Robert

2015-12-08

Methods of generating a three dimensional representation of an object in a reference plane from a depth map including distances from a reference point to pixels in an image of the object taken from a reference point. Weights are assigned to respective voxels in a three dimensional grid along rays extending from the reference point through the pixels in the image based on the distances in the depth map from the reference point to the respective pixels, and a height map including an array of height values in the reference plane is formed based on the assigned weights. An n-layer height map may be constructed by generating a probabilistic occupancy grid for the voxels and forming an n-dimensional height map comprising an array of layer height values in the reference plane based on the probabilistic occupancy grid.

Localization in Self-Healing Autonomous Sensor Networks (SASNet): Studies on Cooperative Localization of Sensor Nodes using Distributed Maps

DTIC Science & Technology

2008-01-01

CCA-MAP algorithm are analyzed. Further, we discuss the design considerations of the discussed cooperative localization algorithms to compare and...MAP and CCA-MAP to compare and evaluate their performance. Then a preliminary design analysis is given to address the implementation requirements and...plus précis, avec un nombre inférieur de nœuds ancres, comparativement aux autres types de schémas de localisation. En réalité, les algorithmes de

Integrating genome assemblies with MAIA

PubMed Central

Nijkamp, Jurgen; Winterbach, Wynand; van den Broek, Marcel; Daran, Jean-Marc; Reinders, Marcel; de Ridder, Dick

2010-01-01

Motivation: De novo assembly of a eukaryotic genome with next-generation sequencing data is still a challenging task. Over the past few years several assemblers have been developed, often suitable for one specific type of sequencing data. The number of known genomes is expanding rapidly, therefore it becomes possible to use multiple reference genomes for assembly projects. We introduce an assembly integrator that makes use of all available data, i.e. multiple de novo assemblies and mappings against multiple related genomes, by optimizing a weighted combination of criteria. Results: The developed algorithm was applied on the de novo sequencing of the Saccharomyces cerevisiae CEN.PK 113-7D strain. Using Solexa and 454 read data, two de novo and three comparative assemblies were constructed and subsequently integrated, yielding 29 contigs, covering more than 12 Mbp; a drastic improvement compared with the single assemblies. Availability: MAIA is available as a Matlab package and can be downloaded from http://bioinformatics.tudelft.nl Contact: j.f.nijkamp@tudelft.nl PMID:20823304

Genome-wide identification of the subcellular localization of the Escherichia coli B proteome using experimental and computational methods.

PubMed

Han, Mee-Jung; Yun, Hongseok; Lee, Jeong Wook; Lee, Yu Hyun; Lee, Sang Yup; Yoo, Jong-Shin; Kim, Jin Young; Kim, Jihyun F; Hur, Cheol-Goo

2011-04-01

Escherichia coli K-12 and B strains have most widely been employed for scientific studies as well as industrial applications. Recently, the complete genome sequences of two representative descendants of E. coli B strains, REL606 and BL21(DE3), have been determined. Here, we report the subproteome reference maps of E. coli B REL606 by analyzing cytoplasmic, periplasmic, inner and outer membrane, and extracellular proteomes based on the genome information using experimental and computational approaches. Among the total of 3487 spots, 651 proteins including 410 non-redundant proteins were identified and characterized by 2-DE and LC-MS/MS; they include 440 cytoplasmic, 45 periplasmic, 50 inner membrane, 61 outer membrane, and 55 extracellular proteins. In addition, subcellular localizations of all 4205 ORFs of E. coli B were predicted by combined computational prediction methods. The subcellular localizations of 1812 (43.09%) proteins of currently unknown function were newly assigned. The results of computational prediction were also compared with the experimental results, showing that overall precision and recall were 92.16 and 92.16%, respectively. This work represents the most comprehensive analyses of the subproteomes of E. coli B, and will be useful as a reference for proteome profiling studies under various conditions. The complete proteome data are available online (http://ecolib.kaist.ac.kr). Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

California State Waters Map Series—Offshore of Gaviota, California

USGS Publications Warehouse

Johnson, Samuel Y.; Dartnell, Peter; Cochrane, Guy R.; Hartwell, Stephen R.; Golden, Nadine E.; Kvitek, Rikk G.; Davenport, Clifton W.; Johnson, Samuel Y.; Cochran, Susan A.

2018-04-20

IntroductionIn 2007, the California Ocean Protection Council initiated the California Seafloor Mapping Program (CSMP), designed to create a comprehensive seafloor map of high-resolution bathymetry, marine benthic habitats, and geology within the 3-nautical-mile limit of California’s State Waters. The CSMP approach is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath sonar data, acoustic backscatter, seafloor video, seafloor photography, high-resolution seismic-reflection profiles, and bottom-sediment sampling data. The map products display seafloor morphology and character, identify potential marine benthic habitats, and illustrate both the surficial seafloor geology and shallow subsurface geology.The map area is in the southern part of the Western Transverse Ranges geologic province, which is north of the California Continental Borderland. Significant clockwise rotation—at least 90°—since the early Miocene has been proposed for the Western Transverse Ranges province, and the region is presently undergoing north-south shortening. The offshore part of the map area lies south of the steep south flank of the Santa Ynez Mountains. The crest of the range, which has a maximum elevation of about 760 m in the map area, lies about 4 km north of the shoreline.Gaviota is an unincorporated community that has a sparse population (less than 100), and the coastal zone is largely open space that is locally used for cattle grazing. The Union Pacific railroad tracks extend westward along the coast through the entire map area, within a few hundred meters of the shoreline. Highway 101 crosses the eastern part of the map area, also along the coast, then turns north (inland) and travels through Cañada de la Gaviota and Gaviota Pass en route to Buellton. Gaviota State Park lies at the mouth of Cañada de la Gaviota. West of Gaviota, the onland coastal zone is occupied by the Hollister Ranch, a privately owned, gated community that has no public access.The map area has a long history of petroleum exploration and development. Several offshore gas fields were discovered and were developed by onshore directional drilling in the 1950s and 1960s. Three offshore petroleum platforms were installed in adjacent federal waters in 1976 (platform “Honda”) and 1989 (platforms “Heritage” and “Harmony”). Local offshore and onshore operations were serviced for more than a century by the Gaviota marine terminal, which is currently being decommissioned and will be abandoned in an intended transition to public open space. The Offshore of Gaviota map area lies within the western Santa Barbara Channel region of the Southern California Bight, and it is somewhat protected from large Pacific swells from the north and northwest by Point Conception and from south and southwest swells by offshore islands and banks. Much of the shoreline in the map area is characterized by narrow beaches that have thin sediment cover, backed by low (10- to 20-m-high) cliffs that are capped by a narrow coastal terrace. Beaches are subject to wave erosion during winter storms, followed by gradual sediment recovery or accretion in the late spring, summer, and fall months during the gentler wave climate.The map area lies in the western-central part of the Santa Barbara littoral cell, which is characterized by west-to-east transport of sediment from Point Arguello on the northwest to Hueneme and Mugu Canyons on the southeast. Sediment supply to the western and central part of the littoral cell is mainly from relatively small coastal watersheds. In the map area, sediment sources include Cañada de la Gaviota (52 km2), as well as Cañada de la Llegua, Arroyo el Bulito, Cañada de Santa Anita, Cañada de Alegria, Cañada del Agua Caliente, Cañada del Barro, Cañada del Leon, Cañada San Onofre, and many others. Coastal-watershed discharge and sediment load are highly variable, characterized by brief large events during major winter storms and long periods of low (or no) flow and minimal sediment load between storms. In recent (recorded) history, the majority of high-discharge, high-sediment-flux events have been associated with El Niño phases of the El Niño–Southern Oscillation climatic pattern.Shelf width in the Offshore of Gaviota map area ranges from about 4.3 to 4.7 km, and shelf slopes average about 1.0° to 1.2° but are highly variable because of the presence of the large Gaviota sediment bar. This bar extends southwestward for about 9 km from the mouth of Cañada de la Gaviota to the shelf break, is as wide as 2 km, and is by far the largest shore-attached sediment bar in the Santa Barbara Channel. The shelf is underlain by bedrock and variable amounts (0 to as much as 36 m in the Gaviota bar) of upper Quaternary sediments deposited as sea level fluctuated in the late Pleistocene. The trend of the shelf break changes from about 276° to 236° azimuth over a distance of about 12 km, and it ranges in depth from about 91 m to as shallow as 62 to 73 m where significant shelf-break and upper-slope failure and landsliding has apparently occurred. The shelf break in the western part of the map area is notably embayed by the heads of three large (150- to 300-m-wide) channels that have been referred to as “the Gaviota Canyons” or as “Drake Canyon,” “Sacate Canyon,” and “Alegria Canyon.”Seafloor habitats in the broad Santa Barbara Channel region consist of significant amounts of soft, unconsolidated sediment interspersed with isolated areas of rocky habitat that support kelp-forest communities in the nearshore and rocky-reef communities in deeper water. The potential marine benthic habitat types mapped in the Offshore of Gaviota map area are directly related to its Quaternary geologic history, geomorphology, and active sedimentary processes. These potential habitats lie primarily within the Shelf (continental shelf) but also partly within the Flank (basin flank or continental slope) megahabitats. The fairly homogeneous seafloor of sediment and low-relief bedrock provides characteristic habitat for rockfish, groundfish, crabs, shrimp, and other marine benthic organisms. Several areas of smooth sediment form nearshore terraces that have relatively steep, smooth fronts, which may be attractive to groundfish. Below the steep shelf break, soft, unconsolidated sediment is interrupted by the heads of several submarine canyons and rills, some bedrock exposures, and small carbonate mounds associated with asphalt mounds and pockmarks, also good potential habitat for rockfish. The map area includes the relatively small (5.2 km2) Kashtayit State Marine Conservation Area, which largely occupies the inner part of the Gaviota sediment bar.

Transposon fingerprinting using low coverage whole genome shotgun sequencing in cacao (Theobroma cacao L.) and related species.

PubMed

Sveinsson, Saemundur; Gill, Navdeep; Kane, Nolan C; Cronk, Quentin

2013-07-24

Transposable elements (TEs) and other repetitive elements are a large and dynamically evolving part of eukaryotic genomes, especially in plants where they can account for a significant proportion of genome size. Their dynamic nature gives them the potential for use in identifying and characterizing crop germplasm. However, their repetitive nature makes them challenging to study using conventional methods of molecular biology. Next generation sequencing and new computational tools have greatly facilitated the investigation of TE variation within species and among closely related species. (i) We generated low-coverage Illumina whole genome shotgun sequencing reads for multiple individuals of cacao (Theobroma cacao) and related species. These reads were analysed using both an alignment/mapping approach and a de novo (graph based clustering) approach. (ii) A standard set of ultra-conserved orthologous sequences (UCOS) standardized TE data between samples and provided phylogenetic information on the relatedness of samples. (iii) The mapping approach proved highly effective within the reference species but underestimated TE abundance in interspecific comparisons relative to the de novo methods. (iv) Individual T. cacao accessions have unique patterns of TE abundance indicating that the TE composition of the genome is evolving actively within this species. (v) LTR/Gypsy elements are the most abundant, comprising c.10% of the genome. (vi) Within T. cacao the retroelement families show an order of magnitude greater sequence variability than the DNA transposon families. (vii) Theobroma grandiflorum has a similar TE composition to T. cacao, but the related genus Herrania is rather different, with LTRs making up a lower proportion of the genome, perhaps because of a massive presence (c. 20%) of distinctive low complexity satellite-like repeats in this genome. (i) Short read alignment/mapping to reference TE contigs provides a simple and effective method of investigating intraspecific differences in TE composition. It is not appropriate for comparing repetitive elements across the species boundaries, for which de novo methods are more appropriate. (ii) Individual T. cacao accessions have unique spectra of TE composition indicating active evolution of TE abundance within this species. TE patterns could potentially be used as a "fingerprint" to identify and characterize cacao accessions.

Broadband set-top box using MAP-CA processor

NASA Astrophysics Data System (ADS)

Bush, John E.; Lee, Woobin; Basoglu, Chris

2001-12-01

Advances in broadband access are expected to exert a profound impact in our everyday life. It will be the key to the digital convergence of communication, computer and consumer equipment. A common thread that facilitates this convergence comprises digital media and Internet. To address this market, Equator Technologies, Inc., is developing the Dolphin broadband set-top box reference platform using its MAP-CA Broadband Signal ProcessorT chip. The Dolphin reference platform is a universal media platform for display and presentation of digital contents on end-user entertainment systems. The objective of the Dolphin reference platform is to provide a complete set-top box system based on the MAP-CA processor. It includes all the necessary hardware and software components for the emerging broadcast and the broadband digital media market based on IP protocols. Such reference design requires a broadband Internet access and high-performance digital signal processing. By using the MAP-CA processor, the Dolphin reference platform is completely programmable, allowing various codecs to be implemented in software, such as MPEG-2, MPEG-4, H.263 and proprietary codecs. The software implementation also enables field upgrades to keep pace with evolving technology and industry demands.

75 FR 48235 - Rural Health Care Universal Service Support Mechanism

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-09

... references to recognized broadband mapping studies, such as NTIA's national broadband map, State or local... network area. In addition to referencing such NTIA or State broadband mapping studies, the applicant would... network design studies (but not in excess of the cap identified below); (2) engineering, materials and...

Proteomic analysis of cellular soluble proteins from human bronchial smooth muscle cells by combining nondenaturing micro 2DE and quantitative LC-MS/MS. 2. Similarity search between protein maps for the analysis of protein complexes.

PubMed

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

2015-09-01

Human bronchial smooth muscle cell soluble proteins were analyzed by a combined method of nondenaturing micro 2DE, grid gel-cutting, and quantitative LC-MS/MS and a native protein map was prepared for each of the identified 4323 proteins [1]. A method to evaluate the degree of similarity between the protein maps was developed since we expected the proteins comprising a protein complex would be separated together under nondenaturing conditions. The following procedure was employed using Excel macros; (i) maps that have three or more squares with protein quantity data were selected (2328 maps), (ii) within each map, the quantity values of the squares were normalized setting the highest value to be 1.0, (iii) in comparing a map with another map, the smaller normalized quantity in two corresponding squares was taken and summed throughout the map to give an "overlap score," (iv) each map was compared against all the 2328 maps and the largest overlap score, obtained when a map was compared with itself, was set to be 1.0 thus providing 2328 "overlap factors," (v) step (iv) was repeated for all maps providing 2328 × 2328 matrix of overlap factors. From the matrix, protein pairs that showed overlap factors above 0.65 from both protein sides were selected (431 protein pairs). Each protein pair was searched in a database (UniProtKB) on complex formation and 301 protein pairs, which comprise 35 protein complexes, were found to be documented. These results demonstrated that native protein maps and their similarity search would enable simultaneous analysis of multiple protein complexes in cells. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Map showing locations of mines, prospects, and patented mining claims, and classification of mineral deposits in the Silver City 7 1/2-minute Quadrangle, Black Hills, South Dakota

USGS Publications Warehouse

DeWitt, Ed; Buscher, David; Wilson, A.B.; Johnson, Thomas

1988-01-01

This map is one in a set of 26 maps (see index map) at 1:24,000 scale of the Black Hills region of South Dakota and Wyoming om which are shown a geologic classification of mines, a bibliography of mineral deposits, and locations of active and inactive mines, prospects, and patented mining claims. Some of these maps are published as U. S. Geological Survey Miscellaneous Field Studies Maps (MF series) and some as U.S. Geological Survey Open-File Reports (QF series); see index map. An earlier unpublished version of this set of maps was the data base from which plate 4 (scale 1:250,000) of DeWitt and others (1986) was compiled. Subsequent to that publication, the set has been revised and updated, and prospects and patented claims have been added. These revised and more detailed 1:24,000-scale maps should be used for the equivalent areas of plate 4 of DeWitt and others (1986).

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

NASA Astrophysics Data System (ADS)

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

2003-04-01

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

Parametric methods for characterizing myocardial tissue by magnetic resonance imaging (part 2): T2 mapping.

PubMed

Perea Palazón, R J; Solé Arqués, M; Prat González, S; de Caralt Robira, T M; Cibeira López, M T; Ortiz Pérez, J T

2015-01-01

Cardiac magnetic resonance imaging is considered the reference technique for characterizing myocardial tissue; for example, T2-weighted sequences make it possible to evaluate areas of edema or myocardial inflammation. However, traditional sequences have many limitations and provide only qualitative information. Moreover, traditional sequences depend on the reference to remote myocardium or skeletal muscle, which limits their ability to detect and quantify diffuse myocardial damage. Recently developed magnetic resonance myocardial mapping techniques enable quantitative assessment of parameters indicative of edema. These techniques have proven better than traditional sequences both in acute cardiomyopathy and in acute ischemic heart disease. This article synthesizes current developments in T2 mapping as well as their clinical applications and limitations. Copyright © 2014 SERAM. Published by Elsevier España, S.L.U. All rights reserved.

Comprehensive geo-spatial data creation for Asir region in the KSA

NASA Astrophysics Data System (ADS)

Alrajhi, M.; Hawarey, M.

2009-04-01

The General Directorate for Surveying and Mapping (GDSM) of the Deputy Ministry for Land and Surveying (DMLS) of the Ministry of Municipal and Rural Affairs (MOMRA) in the Kingdom of Saudi Arabia (KSA) has the exclusive mandate to carry out aerial photography and produce large-scale detailed maps for about 220 cities and villages in the KSA. This presentation is about the comprehensive geo-spatial data creation for the Asir region, South West KSA, that was founded on country-wide horizontal geodetic ground control using Global Navigation Satellite Systems (GNSS) within the MOMRA's Terrestrial Reference Frame 2000 (MTRF2000) that is tied to International Terrestrial Reference Frame 2000 (ITRF2000) Epoch 2004.0, and vertical geodetic ground control using precise digital leveling in reference to Jeddah 1969 mean sea level, and included aerial photography of area 2,188 km2 at 1:5,500 scale and 32,640 km2 at 1:45,000 scale, full aerial triangulation, and production of orthophoto maps at scale of 1:10,000 (680 sheets) for 32,640 km2, with aerial photography lasting from July 2007 thru October 2007.

Effect of Spatial Locality Prefetching on Structural Locality

DTIC Science & Technology

1991-12-01

Pollution module calculates the SLC and CAM cache pollution percentages. And finally, the Generate Reference Frequency List module produces the output...3.2.5 Generate Reference Frequency List 3.2.6 Each program module in the structure chart is mapped into an Ada package. By performing this encapsulation...call routine to generate reference -- frequency list -- end if -- end loop -- close input, output, and reference files end Cache Simulator Figure 3.5

Hydroacoustic mapping to define sedimentation rates and characterize lentic habitats in DeSoto Lake, DeSoto National Wildlife Refuge

USGS Publications Warehouse

Elliott, Caroline M.; Jacobson, Robert B.; Chojnacki, Kimberly A.

2006-01-01

Hydroacoustic tools were used to map depth, elevation, and substrate on DeSoto Lake in March 2006. DeSoto Lake, located on the DeSoto National Wildlife Refuge in Iowa and Nebraska, is one of the largest oxbow lakes of the Missouri River system. It is used by over 500,000 migratory birds each fall and spring and is also an important aquatic resource for anglers. Management concerns at the lake include the effects of erosion and sedimentation, aquatic vegetation establishment, shorebird habitat availability at different lake levels, and fish habitat structure. DeSoto Lake was cut off from the Missouri River in 1960, and the current mapping updates previous lower-resolution bathymetric maps created from lake surveys in 1967 and 1979. The new maps provide managers tools to assess aquatic habitats and provide a baseline for future monitoring of lake sedimentation and erosion.

Next-Generation NATO Reference Mobility Model (NRMM) Development (Developpement de la nouvella generation du modele de mobilite de reference de l’OTAN (NRMM))

DTIC Science & Technology

2018-01-01

Profile Database E-17 Attachment 2: NRMM Data Input Requirements E-25 Attachment 3: General Physics -Based Model Data Input Requirements E-28...E-15 Figure E-11 Examples of Unique Surface Types E-20 Figure E-12 Correlating Physical Testing with Simulation E-21 Figure E-13 Simplified Tire...Table 10-8 Scoring Values 10-19 Table 10-9 Accuracy – Physics -Based 10-20 Table 10-10 Accuracy – Validation Through Measurement 10-22 Table 10-11

Maritime Claims Reference Manual

DTIC Science & Technology

1990-07-12

line connecting the following points: Cap de la Morsetta--Pointe des Scoglietti-llot de Gargalo--Cap Rosso --Pointe d’Omignis--Cap de Feno (Golfe de...Tg. Rua. 127. 09 - 45.5 S 119 - 11.6 T Tg. Mambo. 128. 09 - 40.5 S 119 - 02.0 T 129. 08 - 53.6 S 118 - 29.9 T Toro Doro. 2-229 REFERENCE CO-ORDINATES...8217 - 12013.40’) to Capo Linaro (42001.70’ - 11050.20’); From Civitavecchia beacon (42005.75’ - 11046.65’) to Isola Giannutri Punta del Capel Rosso

The RHYTMME system: an operational real-time warning and mapping system for flash floods, debris flows, landslide and rock falls in Southeastern France.

NASA Astrophysics Data System (ADS)

Fouchier, Catherine; Mériaux, Patrice; Atger, Frédéric; Ecrepont, Stéphane; Liébault, Frédéric; Bertrand, Mélanie; Bel, Coraline; Batista, Dominique; Azemard, Pierre; Saint-Martin, Clotilde; Javelle, Pierre

2016-04-01

Almost all municipalities of Southeastern France are concerned by natural hazards triggered by heavy rainfalls such as floods, debris flows, landslides and rock falls. Although some tools exist to forecast and monitor heavy rains and floods in France, their spatial resolution sometimes does not meet the needs of local risk managers who have to monitor events at a small spatial scale. In order to improve the risk management in the mountainous and Mediterranean areas of Southeastern France, Irstea and Météo-France have led the RHYTMME project. The goal of this project is to improve the ability to forecast and localize high-risk rainfall-induced hazards in the Provence-Alpes-Côte d'Azur administrative area. This goal is currently under achievement thanks to the implementation of a real-time warning and mapping system for rainfall induced natural hazards, fed by radar data and whose outputs are made available via the Internet to operators in charge of risk management (local and regional authorities, emergency and rescue services, road and rail networks managers, ...). This system provides maps which display in real-time: - the radar estimations of rainfall for different rain durations and at the spatial resolution of 1 km² (Westrelin et al., 2013), - the estimation of the scarcity of these rainfall estimations, also at the spatial resolution of 1 km², thanks to a comparison with threshold values provided by a regionalized stochastic hourly point rainfall generator (Arnaud et al., 2007), - an anticipation of the rivers discharges, computed at the outlet of 1700 watersheds of Southeastern France thanks to the AIGA warning system which combines a rainfall runoff model and an estimation of the scarcity of the discharges thanks to a comparison with threshold values (Javelle et al., 2014). Maps of susceptibility to debris flow, landslide and rock falls can also be displayed in the RHYTMME warning system along with the real time maps of rainfall hazard (Batista, 2013a, 2013b; Bertrand, 2014). It enables to identify, during intense events, the reaches the more likely to generate and/or to spread debris flow and the areas the more likely to generate landslide and/or rock falls. The RHYTMME warning and mapping system is now fully operational. It is currently being provided to local authorities (City councils, River boards, …) as well as State authorities in charge of risk managements in the Provence-Alpes-Côte d'Azur administrative area. Training sessions are organized in order to help these end-users to handle the system. References Arnaud P., Fine J.-A. and Lavabre J. (2007). An hourly rainfall generation model applicable to all types of climate. Atmospheric Research 85(2): 230-242. Batista D., Azémard P., Boutry M. (2013). Prévision de l'aléa glissement de terrain et analyse statistique des facteurs de prédisposition par l'outil SIG, sur la région Provence-Alpes-Côte d'Azur. Journées Aléas Gravitaires, 17 et 18/9/2013 - Grenoble, 11 p. Batista D., Azémard P., Rougé A.C., Dumalin M., Rault C. (2013). Prévision de l'aléa chute de blocs, analyse statistique des facteurs de prédisposition et des critères de déclenchement sur la région Provence-Alpes-Côte d'Azur. Journées Aléas Gravitaires, 17 et 18/9/2013 - Grenoble, 11 p. Bertrand M. (2014). Approches régionales de la susceptibilité torrentielle dans les Alpes du Sud. Thèse de Doctorat, École Normale Supérieure de Lyon, 162 pp. Javelle P., Demargne J., Defrance D., Pansu J., Arnaud P. (2014). Evaluating flash-flood warnings at ungauged locations using post-event surveys: A case study with the AIGA warning system. Hydrological Sciences Journal 59 (7): 1390-1402. Westrelin S., Mériaux P., Dalle S., Fradon B., Jamet G. (2013). Déploiement d'un réseau de radars pour anticiper les risques hydro-météorologiques, La Météorologie 8 (83): 69-79.

Marketing Tools for Increasing Proactivity in Technical Information Centers. (Les Outils de Marketing dans la Stimulation de la Proactivite au Sein des Infocentres)

DTIC Science & Technology

1994-02-01

others in the cluster . Think about this map when you develop your research survey. The positioning map technique can help you discover customer percep...AD-A277 574 ________________!___ Il~llrlrIJill 11 II ’I IlI !Ill ,,______,.____.,,___A.RD AR 32 AGARD-A-2 SADVISORY GROUP FOR AEROSPACE RESEARCH ...Published February 1994 Dlstrihhutlon and Avwilahillv nn RA.k rnytr AGARD-AR-326 ADVISORY GROUP FOR AEROSPACE RESEARCH & DEVELOPMENT 7 RUE ANCELLE

Effects of Elongation on Stochastic Layer and Magnetic Footprint in Divertor Tokamaks

NASA Astrophysics Data System (ADS)

Wadi, Hasina; Jones, Morgin; Ali, Halima; Punjabi, Alkesh

2007-11-01

An area-preserving map is constructed to calculate effects of elongation on the stochastic layer and magnetic footprint in divertor tokamaks. The generating function for the map is S(x,y) = -(1/2)α^2y^2 (1-y^2/2a^2)+(1/2)β^2x^2. Method of maps developed by Punjabi and Boozer [1,2] is used to construct the map and to calculate the stochastic layer and the magnetic footprints. The poloidal magnetic flux inside the ideal separatrix and the safety factor profile are held constant, and elongation is varied by (1) varying the width of separatrix surface in the midplane keeping the height fixed, and (2) varying the height keeping the width of separatrix surface fixed. As the width is increased, the stochastic layer and the footprint become narrower. As the height is increased, the width of stochastic layer and the footprint become narrower. Detailed results of this study will be presented. This work is supported by US DOE OFES DE-FG02-01ER54624 and DE-FG02-04ER54793. [1] A. Punjabi, A. Verma, and A. Boozer, Phys Rev Lett, 69, 3322-3325 (1992). [2] A. Punjabi, H. Ali, T. Evans, and A. Boozer, Phys Lett A 364 140--145 (2007).

AADL Fault Modeling and Analysis Within an ARP4761 Safety Assessment

DTIC Science & Technology

2014-10-01

Analysis Generator 27 3.2.3 Mapping to OpenFTA Format File 27 3.2.4 Mapping to Generic XML Format 28 3.2.5 AADL and FTA Mapping Rules 28 3.2.6 Issues...PSSA), System Safety Assessment (SSA), Common Cause Analysis (CCA), Fault Tree Analysis ( FTA ), Failure Modes and Effects Analysis (FMEA), Failure...Modes and Effects Summary, Mar - kov Analysis (MA), and Dependence Diagrams (DDs), also referred to as Reliability Block Dia- grams (RBDs). The

Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study.

PubMed

de Vries, Paul S; Sabater-Lleal, Maria; Chasman, Daniel I; Trompet, Stella; Ahluwalia, Tarunveer S; Teumer, Alexander; Kleber, Marcus E; Chen, Ming-Huei; Wang, Jie Jin; Attia, John R; Marioni, Riccardo E; Steri, Maristella; Weng, Lu-Chen; Pool, Rene; Grossmann, Vera; Brody, Jennifer A; Venturini, Cristina; Tanaka, Toshiko; Rose, Lynda M; Oldmeadow, Christopher; Mazur, Johanna; Basu, Saonli; Frånberg, Mattias; Yang, Qiong; Ligthart, Symen; Hottenga, Jouke J; Rumley, Ann; Mulas, Antonella; de Craen, Anton J M; Grotevendt, Anne; Taylor, Kent D; Delgado, Graciela E; Kifley, Annette; Lopez, Lorna M; Berentzen, Tina L; Mangino, Massimo; Bandinelli, Stefania; Morrison, Alanna C; Hamsten, Anders; Tofler, Geoffrey; de Maat, Moniek P M; Draisma, Harmen H M; Lowe, Gordon D; Zoledziewska, Magdalena; Sattar, Naveed; Lackner, Karl J; Völker, Uwe; McKnight, Barbara; Huang, Jie; Holliday, Elizabeth G; McEvoy, Mark A; Starr, John M; Hysi, Pirro G; Hernandez, Dena G; Guan, Weihua; Rivadeneira, Fernando; McArdle, Wendy L; Slagboom, P Eline; Zeller, Tanja; Psaty, Bruce M; Uitterlinden, André G; de Geus, Eco J C; Stott, David J; Binder, Harald; Hofman, Albert; Franco, Oscar H; Rotter, Jerome I; Ferrucci, Luigi; Spector, Tim D; Deary, Ian J; März, Winfried; Greinacher, Andreas; Wild, Philipp S; Cucca, Francesco; Boomsma, Dorret I; Watkins, Hugh; Tang, Weihong; Ridker, Paul M; Jukema, Jan W; Scott, Rodney J; Mitchell, Paul; Hansen, Torben; O'Donnell, Christopher J; Smith, Nicholas L; Strachan, David P; Dehghan, Abbas

2017-01-01

An increasing number of genome-wide association (GWA) studies are now using the higher resolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap imputation. In order to assess the improvement of 1000G over HapMap imputation in identifying associated loci, we compared the results of GWA studies of circulating fibrinogen based on the two reference panels. Using both HapMap and 1000G imputation we performed a meta-analysis of 22 studies comprising the same 91,953 individuals. We identified six additional signals using 1000G imputation, while 29 loci were associated using both HapMap and 1000G imputation. One locus identified using HapMap imputation was not significant using 1000G imputation. The genome-wide significance threshold of 5×10-8 is based on the number of independent statistical tests using HapMap imputation, and 1000G imputation may lead to further independent tests that should be corrected for. When using a stricter Bonferroni correction for the 1000G GWA study (P-value < 2.5×10-8), the number of loci significant only using HapMap imputation increased to 4 while the number of loci significant only using 1000G decreased to 5. In conclusion, 1000G imputation enabled the identification of 20% more loci than HapMap imputation, although the advantage of 1000G imputation became less clear when a stricter Bonferroni correction was used. More generally, our results provide insights that are applicable to the implementation of other dense reference panels that are under development.

Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study

PubMed Central

de Vries, Paul S.; Sabater-Lleal, Maria; Chasman, Daniel I.; Trompet, Stella; Kleber, Marcus E.; Chen, Ming-Huei; Wang, Jie Jin; Attia, John R.; Marioni, Riccardo E.; Weng, Lu-Chen; Grossmann, Vera; Brody, Jennifer A.; Venturini, Cristina; Tanaka, Toshiko; Rose, Lynda M.; Oldmeadow, Christopher; Mazur, Johanna; Basu, Saonli; Yang, Qiong; Ligthart, Symen; Hottenga, Jouke J.; Rumley, Ann; Mulas, Antonella; de Craen, Anton J. M.; Grotevendt, Anne; Taylor, Kent D.; Delgado, Graciela E.; Kifley, Annette; Lopez, Lorna M.; Berentzen, Tina L.; Mangino, Massimo; Bandinelli, Stefania; Morrison, Alanna C.; Hamsten, Anders; Tofler, Geoffrey; de Maat, Moniek P. M.; Draisma, Harmen H. M.; Lowe, Gordon D.; Zoledziewska, Magdalena; Sattar, Naveed; Lackner, Karl J.; Völker, Uwe; McKnight, Barbara; Huang, Jie; Holliday, Elizabeth G.; McEvoy, Mark A.; Starr, John M.; Hysi, Pirro G.; Hernandez, Dena G.; Guan, Weihua; Rivadeneira, Fernando; McArdle, Wendy L.; Slagboom, P. Eline; Zeller, Tanja; Psaty, Bruce M.; Uitterlinden, André G.; de Geus, Eco J. C.; Stott, David J.; Binder, Harald; Hofman, Albert; Franco, Oscar H.; Rotter, Jerome I.; Ferrucci, Luigi; Spector, Tim D.; Deary, Ian J.; März, Winfried; Greinacher, Andreas; Wild, Philipp S.; Cucca, Francesco; Boomsma, Dorret I.; Watkins, Hugh; Tang, Weihong; Ridker, Paul M.; Jukema, Jan W.; Scott, Rodney J.; Mitchell, Paul; Hansen, Torben; O'Donnell, Christopher J.; Smith, Nicholas L.; Strachan, David P.

2017-01-01

An increasing number of genome-wide association (GWA) studies are now using the higher resolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap imputation. In order to assess the improvement of 1000G over HapMap imputation in identifying associated loci, we compared the results of GWA studies of circulating fibrinogen based on the two reference panels. Using both HapMap and 1000G imputation we performed a meta-analysis of 22 studies comprising the same 91,953 individuals. We identified six additional signals using 1000G imputation, while 29 loci were associated using both HapMap and 1000G imputation. One locus identified using HapMap imputation was not significant using 1000G imputation. The genome-wide significance threshold of 5×10−8 is based on the number of independent statistical tests using HapMap imputation, and 1000G imputation may lead to further independent tests that should be corrected for. When using a stricter Bonferroni correction for the 1000G GWA study (P-value < 2.5×10−8), the number of loci significant only using HapMap imputation increased to 4 while the number of loci significant only using 1000G decreased to 5. In conclusion, 1000G imputation enabled the identification of 20% more loci than HapMap imputation, although the advantage of 1000G imputation became less clear when a stricter Bonferroni correction was used. More generally, our results provide insights that are applicable to the implementation of other dense reference panels that are under development. PMID:28107422

Simple Map in Action-Angle Coordinates.

NASA Astrophysics Data System (ADS)

Kerwin, Olivia; Punjabi, Alkesh; Ali, Halima

2008-04-01

The simple map is the simplest map that has the topology of a divertor tokamak. The simple map has three canonical representations: (i) the natural coordinates - toroidal magnetic flux and poloidal angle (ψ,θ), (ii) the physical coordinates - the physical variables (R,Z) or (X,Y), and (iii) the action-angle coordinates - (J,θ) or magnetic coordinates (ψ, θ). All three are canonical coordinates for field lines. The simple map in the (X,Y) representation has been studied extensively ^1, 2. Here we analytically calculate the action-angle coordinates and safety factor q for the simple map. We construct the equilibrium generating function for the simple map in action-angle coordinates. We derive the simple map in action-angle representation, and calculate the stochastic broadening of the ideal separatrix due to topological noise in action-angle representation. We also show how the geometric effects such as elongation, the height, and width of the ideal separatrix surface can be investigated using a slight modification of the simple map in action-angle representation. This work is supported by the following grants US Department of Energy - OFES DE-FG02-01ER54624 and DE-FG02-04ER54793 and National Science Foundation - HRD-0630372 and 0411394. [1] A. Punjabi, H. Ali, T. Evans, and A. Boozer, Phys Lett A, 364 140-145 (2007). [2] A. Punjabi, A. Verma, and A. Boozer, Phys.Rev. Lett. 69, 3322 (1992).

Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing.

PubMed

Misra, Sanchit; Agrawal, Ankit; Liao, Wei-keng; Choudhary, Alok

2011-01-15

Recently, a number of programs have been proposed for mapping short reads to a reference genome. Many of them are heavily optimized for short-read mapping and hence are very efficient for shorter queries, but that makes them inefficient or not applicable for reads longer than 200 bp. However, many sequencers are already generating longer reads and more are expected to follow. For long read sequence mapping, there are limited options; BLAT, SSAHA2, FANGS and BWA-SW are among the popular ones. However, resequencing and personalized medicine need much faster software to map these long sequencing reads to a reference genome to identify SNPs or rare transcripts. We present AGILE (AliGnIng Long rEads), a hash table based high-throughput sequence mapping algorithm for longer 454 reads that uses diagonal multiple seed-match criteria, customized q-gram filtering and a dynamic incremental search approach among other heuristics to optimize every step of the mapping process. In our experiments, we observe that AGILE is more accurate than BLAT, and comparable to BWA-SW and SSAHA2. For practical error rates (< 5%) and read lengths (200-1000 bp), AGILE is significantly faster than BLAT, SSAHA2 and BWA-SW. Even for the other cases, AGILE is comparable to BWA-SW and several times faster than BLAT and SSAHA2. http://www.ece.northwestern.edu/~smi539/agile.html.

Proceedings of a Hydrology and Hydraulics Workshop (23rd) on Hydrologic Studies in Support of Project Functions Held in Angel Fire, New Mexico on 7-9 August 1990

DTIC Science & Technology

1990-01-01

Pecos River Watershed. Refer to the vicinity map on Plate 1. The source of the Pecos River basin is in the Sangre de Cristo Mountains about 395 miles...resulted in a favorable court decision for the Corps and never actually impacted hydropower or the quantity of water supply storage reallocated...sensing gage. The stage warning gage consists of a telephone alarm dialer mounted in a shelter atop a stilling well which contains float switches

Genetics Home Reference: 16p11.2 duplication

MedlinePlus

... Marshall CR, Scherer SW. Phenotypic spectrum associated with de novo and inherited deletions and duplications at 16p11. ... ND, Thorleifsson G, Belfiore M, Bouquillon S, Campion D, de Leeuw N, de Vries BB, Esko T, Fernandez ...

Qualitative and quantitative evaluation of rigid and deformable motion correction algorithms using dual-energy CT images in view of application to CT perfusion measurements in abdominal organs affected by breathing motion

PubMed Central

Skornitzke, S; Fritz, F; Klauss, M; Pahn, G; Hansen, J; Hirsch, J; Grenacher, L; Kauczor, H-U

2015-01-01

Objective: To compare six different scenarios for correcting for breathing motion in abdominal dual-energy CT (DECT) perfusion measurements. Methods: Rigid [RRComm(80 kVp)] and non-rigid [NRComm(80 kVp)] registration of commercially available CT perfusion software, custom non-rigid registration [NRCustom(80 kVp], demons algorithm) and a control group [CG(80 kVp)] without motion correction were evaluated using 80 kVp images. Additionally, NRCustom was applied to dual-energy (DE)-blended [NRCustom(DE)] and virtual non-contrast [NRCustom(VNC)] images, yielding six evaluated scenarios. After motion correction, perfusion maps were calculated using a combined maximum slope/Patlak model. For qualitative evaluation, three blinded radiologists independently rated motion correction quality and resulting perfusion maps on a four-point scale (4 = best, 1 = worst). For quantitative evaluation, relative changes in metric values, R2 and residuals of perfusion model fits were calculated. Results: For motion-corrected images, mean ratings differed significantly [NRCustom(80 kVp) and NRCustom(DE), 3.3; NRComm(80 kVp), 3.1; NRCustom(VNC), 2.9; RRComm(80 kVp), 2.7; CG(80 kVp), 2.7; all p < 0.05], except when comparing NRCustom(80 kVp) with NRCustom(DE) and RRComm(80 kVp) with CG(80 kVp). NRCustom(80 kVp) and NRCustom(DE) achieved the highest reduction in metric values [NRCustom(80 kVp), 48.5%; NRCustom(DE), 45.6%; NRComm(80 kVp), 29.2%; NRCustom(VNC), 22.8%; RRComm(80 kVp), 0.6%; CG(80 kVp), 0%]. Regarding perfusion maps, NRCustom(80 kVp) and NRCustom(DE) were rated highest [NRCustom(80 kVp), 3.1; NRCustom(DE), 3.0; NRComm(80 kVp), 2.8; NRCustom(VNC), 2.6; CG(80 kVp), 2.5; RRComm(80 kVp), 2.4] and had significantly higher R2 and lower residuals. Correlation between qualitative and quantitative evaluation was low to moderate. Conclusion: Non-rigid motion correction improves spatial alignment of the target region and fit of CT perfusion models. Using DE-blended and DE-VNC images for deformable registration offers no significant improvement. Advances in knowledge: Non-rigid algorithms improve the quality of abdominal CT perfusion measurements but do not benefit from DECT post processing. PMID:25465353

Reference frames in virtual spatial navigation are viewpoint dependent

PubMed Central

Török, Ágoston; Nguyen, T. Peter; Kolozsvári, Orsolya; Buchanan, Robert J.; Nadasdy, Zoltan

2014-01-01

Spatial navigation in the mammalian brain relies on a cognitive map of the environment. Such cognitive maps enable us, for example, to take the optimal route from a given location to a known target. The formation of these maps is naturally influenced by our perception of the environment, meaning it is dependent on factors such as our viewpoint and choice of reference frame. Yet, it is unknown how these factors influence the construction of cognitive maps. Here, we evaluated how various combinations of viewpoints and reference frames affect subjects' performance when they navigated in a bounded virtual environment without landmarks. We measured both their path length and time efficiency and found that (1) ground perspective was associated with egocentric frame of reference, (2) aerial perspective was associated with allocentric frame of reference, (3) there was no appreciable performance difference between first and third person egocentric viewing positions and (4) while none of these effects were dependent on gender, males tended to perform better in general. Our study provides evidence that there are inherent associations between visual perspectives and cognitive reference frames. This result has implications about the mechanisms of path integration in the human brain and may also inspire designs of virtual reality applications. Lastly, we demonstrated the effective use of a tablet PC and spatial navigation tasks for studying spatial and cognitive aspects of human memory. PMID:25249956

Reference frames in virtual spatial navigation are viewpoint dependent.

PubMed

Török, Agoston; Nguyen, T Peter; Kolozsvári, Orsolya; Buchanan, Robert J; Nadasdy, Zoltan

2014-01-01

Spatial navigation in the mammalian brain relies on a cognitive map of the environment. Such cognitive maps enable us, for example, to take the optimal route from a given location to a known target. The formation of these maps is naturally influenced by our perception of the environment, meaning it is dependent on factors such as our viewpoint and choice of reference frame. Yet, it is unknown how these factors influence the construction of cognitive maps. Here, we evaluated how various combinations of viewpoints and reference frames affect subjects' performance when they navigated in a bounded virtual environment without landmarks. We measured both their path length and time efficiency and found that (1) ground perspective was associated with egocentric frame of reference, (2) aerial perspective was associated with allocentric frame of reference, (3) there was no appreciable performance difference between first and third person egocentric viewing positions and (4) while none of these effects were dependent on gender, males tended to perform better in general. Our study provides evidence that there are inherent associations between visual perspectives and cognitive reference frames. This result has implications about the mechanisms of path integration in the human brain and may also inspire designs of virtual reality applications. Lastly, we demonstrated the effective use of a tablet PC and spatial navigation tasks for studying spatial and cognitive aspects of human memory.

A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation.

PubMed

Howe, Glenn T; Yu, Jianbin; Knaus, Brian; Cronn, Richard; Kolpak, Scott; Dolan, Peter; Lorenz, W Walter; Dean, Jeffrey F D

2013-02-28

Douglas-fir (Pseudotsuga menziesii), one of the most economically and ecologically important tree species in the world, also has one of the largest tree breeding programs. Although the coastal and interior varieties of Douglas-fir (vars. menziesii and glauca) are native to North America, the coastal variety is also widely planted for timber production in Europe, New Zealand, Australia, and Chile. Our main goal was to develop a SNP resource large enough to facilitate genomic selection in Douglas-fir breeding programs. To accomplish this, we developed a 454-based reference transcriptome for coastal Douglas-fir, annotated and evaluated the quality of the reference, identified putative SNPs, and then validated a sample of those SNPs using the Illumina Infinium genotyping platform. We assembled a reference transcriptome consisting of 25,002 isogroups (unique gene models) and 102,623 singletons from 2.76 million 454 and Sanger cDNA sequences from coastal Douglas-fir. We identified 278,979 unique SNPs by mapping the 454 and Sanger sequences to the reference, and by mapping four datasets of Illumina cDNA sequences from multiple seed sources, genotypes, and tissues. The Illumina datasets represented coastal Douglas-fir (64.00 and 13.41 million reads), interior Douglas-fir (80.45 million reads), and a Yakima population similar to interior Douglas-fir (8.99 million reads). We assayed 8067 SNPs on 260 trees using an Illumina Infinium SNP genotyping array. Of these SNPs, 5847 (72.5%) were called successfully and were polymorphic. Based on our validation efficiency, our SNP database may contain as many as ~200,000 true SNPs, and as many as ~69,000 SNPs that could be genotyped at ~20,000 gene loci using an Infinium II array-more SNPs than are needed to use genomic selection in tree breeding programs. Ultimately, these genomic resources will enhance Douglas-fir breeding and allow us to better understand landscape-scale patterns of genetic variation and potential responses to climate change.

A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation

PubMed Central

2013-01-01

Background Douglas-fir (Pseudotsuga menziesii), one of the most economically and ecologically important tree species in the world, also has one of the largest tree breeding programs. Although the coastal and interior varieties of Douglas-fir (vars. menziesii and glauca) are native to North America, the coastal variety is also widely planted for timber production in Europe, New Zealand, Australia, and Chile. Our main goal was to develop a SNP resource large enough to facilitate genomic selection in Douglas-fir breeding programs. To accomplish this, we developed a 454-based reference transcriptome for coastal Douglas-fir, annotated and evaluated the quality of the reference, identified putative SNPs, and then validated a sample of those SNPs using the Illumina Infinium genotyping platform. Results We assembled a reference transcriptome consisting of 25,002 isogroups (unique gene models) and 102,623 singletons from 2.76 million 454 and Sanger cDNA sequences from coastal Douglas-fir. We identified 278,979 unique SNPs by mapping the 454 and Sanger sequences to the reference, and by mapping four datasets of Illumina cDNA sequences from multiple seed sources, genotypes, and tissues. The Illumina datasets represented coastal Douglas-fir (64.00 and 13.41 million reads), interior Douglas-fir (80.45 million reads), and a Yakima population similar to interior Douglas-fir (8.99 million reads). We assayed 8067 SNPs on 260 trees using an Illumina Infinium SNP genotyping array. Of these SNPs, 5847 (72.5%) were called successfully and were polymorphic. Conclusions Based on our validation efficiency, our SNP database may contain as many as ~200,000 true SNPs, and as many as ~69,000 SNPs that could be genotyped at ~20,000 gene loci using an Infinium II array—more SNPs than are needed to use genomic selection in tree breeding programs. Ultimately, these genomic resources will enhance Douglas-fir breeding and allow us to better understand landscape-scale patterns of genetic variation and potential responses to climate change. PMID:23445355

Comprehensive geo-spatial data creation for Najran region in the KSA

NASA Astrophysics Data System (ADS)

Alrajhi, M.; Hawarey, M.

2009-04-01

The General Directorate for Surveying and Mapping (GDSM) of the Deputy Ministry for Land and Surveying (DMLS) of the Ministry of Municipal and Rural Affairs (MOMRA) in the Kingdom of Saudi Arabia (KSA) has the exclusive mandate to carry out aerial photography and produce large-scale detailed maps for about 220 cities and villages in the KSA. This presentation is about the comprehensive geo-spatial data creation for the Najran region, South KSA, that was founded on country-wide horizontal geodetic ground control using Global Navigation Satellite Systems (GNSS) within the MOMRA's Terrestrial Reference Frame 2000 (MTRF2000) that is tied to International Terrestrial Reference Frame 2000 (ITRF2000) Epoch 2004.0, and vertical geodetic ground control using precise digital leveling in reference to Jeddah 1969 mean sea level, and included aerial photography of area 917 km2 at 1:5,500 scale and 14,304 km2 at 1:45,000 scale, full aerial triangulation, and production of orthophoto maps at scale of 1:10,000 (298 sheets) for 14,304 km2, with aerial photography lasting from May 2006 until July 2006.

Comprehensive geo-spatial data creation for Ar-Riyadh region in the KSA

NASA Astrophysics Data System (ADS)

Alrajhi, M.; Hawarey, M.

2009-04-01

The General Directorate for Surveying and Mapping (GDSM) of the Deputy Ministry for Land and Surveying (DMLS) of the Ministry of Municipal and Rural Affairs (MOMRA) in the Kingdom of Saudi Arabia (KSA) has the exclusive mandate to carry out aerial photography and produce large-scale detailed maps for about 220 cities and villages in the KSA. This presentation is about the comprehensive geo-spatial data creation for the Ar-Riyadh region, Central KSA, that was founded on country-wide horizontal geodetic ground control using Global Navigation Satellite Systems (GNSS) within the MOMRA's Terrestrial Reference Frame 2000 (MTRF2000) that is tied to International Terrestrial Reference Frame 2000 (ITRF2000) Epoch 2004.0, and vertical geodetic ground control using precise digital leveling in reference to Jeddah 1969 mean sea level, and included aerial photography of area 3,000 km2 at 1:5,500 scale and 10,000 km2 at 1:45,000 scale, full aerial triangulation, and production of orthophoto maps at scale of 1:10,000 (480 sheets) for 10,000 km2, with aerial photography lasting from July 2007 thru August 2007.

Dissection of the Octoploid Strawberry Genome by Deep Sequencing of the Genomes of Fragaria Species

PubMed Central

Hirakawa, Hideki; Shirasawa, Kenta; Kosugi, Shunichi; Tashiro, Kosuke; Nakayama, Shinobu; Yamada, Manabu; Kohara, Mistuyo; Watanabe, Akiko; Kishida, Yoshie; Fujishiro, Tsunakazu; Tsuruoka, Hisano; Minami, Chiharu; Sasamoto, Shigemi; Kato, Midori; Nanri, Keiko; Komaki, Akiko; Yanagi, Tomohiro; Guoxin, Qin; Maeda, Fumi; Ishikawa, Masami; Kuhara, Satoru; Sato, Shusei; Tabata, Satoshi; Isobe, Sachiko N.

2014-01-01

Cultivated strawberry (Fragaria x ananassa) is octoploid and shows allogamous behaviour. The present study aims at dissecting this octoploid genome through comparison with its wild relatives, F. iinumae, F. nipponica, F. nubicola, and F. orientalis by de novo whole-genome sequencing on an Illumina and Roche 454 platforms. The total length of the assembled Illumina genome sequences obtained was 698 Mb for F. x ananassa, and ∼200 Mb each for the four wild species. Subsequently, a virtual reference genome termed FANhybrid_r1.2 was constructed by integrating the sequences of the four homoeologous subgenomes of F. x ananassa, from which heterozygous regions in the Roche 454 and Illumina genome sequences were eliminated. The total length of FANhybrid_r1.2 thus created was 173.2 Mb with the N50 length of 5137 bp. The Illumina-assembled genome sequences of F. x ananassa and the four wild species were then mapped onto the reference genome, along with the previously published F. vesca genome sequence to establish the subgenomic structure of F. x ananassa. The strategy adopted in this study has turned out to be successful in dissecting the genome of octoploid F. x ananassa and appears promising when applied to the analysis of other polyploid plant species. PMID:24282021

LIDAR mapping of ozone-episode dynamics in Paris and intercomparison with spot analyzers Supplementary material available at http://link.springer.de/journals/apb

NASA Astrophysics Data System (ADS)

Thomasson, A.; Geffroy, S.; Frejafon, E.; Weidauer, D.; Fabian, R.; Godet, Y.; Nominé, M.; Ménard, T.; Rairoux, P.; Moeller, D.; Wolf, J. P.

Continuous mapping of an ozone episode in Paris in June 1999 has been performed using a differential absorption lidar system. The 2D ozone concentration vertical maps recorded over 33 h at the Champ de Mars are compiled in a video clip that gives access to local photochemical dynamics with unprecedented precision. The lidar data are compared over the whole period with point monitors located at 0-, 50-, and 300-m altitudes on the Eiffel Tower. Very good agreement is found when spatial resolution, acquisition time, and required concentration accuracy are optimized. Sensitivity to these parameters for successful intercomparison in urban areas is discussed.

A Topographic Image Map of The Mc-18 Quadrangle "coprates" At 1: 2,000,000 Using Data Obtained From The Mars Orbiter Camera and The Mars Orbiter Laser Altimeter of Mars Global Surveyor

NASA Astrophysics Data System (ADS)

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

We present a new topographic image map of Mars using 8 bit data obtained from the Mars Orbiter Camera (MOC) of the Mars Global Surveyor (MGS) [1]. The new map covers the Mars surface from 270 E (90 W) to 315 E (45 W) and from 0 North to 30 South with a resolution of 231.529 m/pixel (256 pixel/degree). For map creation, digital image processing methods have been applied. Furthermore, we managed to de- velop a general processing method for creating image mosaics based on MOC data. From a total amount of 66,081 images, 4,835 images (4,339 Context and 496 Geodesy images [3]) were finally used for the creation of the mosaic. After radiometric and brightness corrections, the images were Mars referenced [5], geometrically [6] cor- rected and sinusoidal map projected [4] using a global Martian Digital Terrain Model (DTM), developed by the DLR and based on MGS Mars Orbiter Laser Altimeter (MOLA) topographic datasets [2]. Three layers of MOC mosaics were created, which were stacked afterwards. The upper layer contains the context images with a resolution < 250 m/pixel. The middle layer contains the images of the Geodesy Campaign with a resolution < 250 m/pixel. The bottom layer consists of the Geodesy Campaign im- ages with a resolution > 250 m/pixel and < 435 m/pixel. The contour lines have been extracted from the global Martian DTM, developed at DLR. The contour data were imported as vector data into Macromedia Freehand as separate layer and corrected interactively. The map format of 1,15 m × 1,39 m represents the western part of the MDIM2 j quadrangle. The map is used for geological and morphological interpreta- tions in order to review and improve our current Viking-based knowledge about the Martian surface. References: [1] www.msss.com [2] wufs.wustl.edu [3] Caplinger, M. and M. Malin, The Mars Orbiter Camera Geodesy Campaign, JGR, in press. [4] Scholten, F., Vol XXXI, Part B2, Wien, 1996, p.351-356 [5] naif.jpl.nasa.gov [6] Kirk, R.L. et al., Geometric Calibration of the Mars Orbiter Cameras and Coalignment with Mars Orbiter Laser Altimeter, (abstract #1863), LPSC XXXII, 2001

Next Generation Genetic Mapping of the Ligon-lintless-2 (Li2) Locus in Upland Cotton (Gossypium hirsutum L.)

USDA-ARS?s Scientific Manuscript database

Next generation sequencing offers new ways to identify the genetic mechanisms that underlie mutant phenotypes. The release of a reference diploid Gossypium raimondii (D5) genome and bioinformatics tools to sort tetraploid reads into subgenomes has brought cotton genetic mapping into the genomics er...

An editor for pathway drawing and data visualization in the Biopathways Workbench.

PubMed

Byrnes, Robert W; Cotter, Dawn; Maer, Andreia; Li, Joshua; Nadeau, David; Subramaniam, Shankar

2009-10-02

Pathway models serve as the basis for much of systems biology. They are often built using programs designed for the purpose. Constructing new models generally requires simultaneous access to experimental data of diverse types, to databases of well-characterized biological compounds and molecular intermediates, and to reference model pathways. However, few if any software applications provide all such capabilities within a single user interface. The Pathway Editor is a program written in the Java programming language that allows de-novo pathway creation and downloading of LIPID MAPS (Lipid Metabolites and Pathways Strategy) and KEGG lipid metabolic pathways, and of measured time-dependent changes to lipid components of metabolism. Accessed through Java Web Start, the program downloads pathways from the LIPID MAPS Pathway database (Pathway) as well as from the LIPID MAPS web server http://www.lipidmaps.org. Data arises from metabolomic (lipidomic), microarray, and protein array experiments performed by the LIPID MAPS consortium of laboratories and is arranged by experiment. Facility is provided to create, connect, and annotate nodes and processes on a drawing panel with reference to database objects and time course data. Node and interaction layout as well as data display may be configured in pathway diagrams as desired. Users may extend diagrams, and may also read and write data and non-lipidomic KEGG pathways to and from files. Pathway diagrams in XML format, containing database identifiers referencing specific compounds and experiments, can be saved to a local file for subsequent use. The program is built upon a library of classes, referred to as the Biopathways Workbench, that convert between different file formats and database objects. An example of this feature is provided in the form of read/construct/write access to models in SBML (Systems Biology Markup Language) contained in the local file system. Inclusion of access to multiple experimental data types and of pathway diagrams within a single interface, automatic updating through connectivity to an online database, and a focus on annotation, including reference to standardized lipid nomenclature as well as common lipid names, supports the view that the Pathway Editor represents a significant, practicable contribution to current pathway modeling tools.

Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification.

PubMed

Ramos, Miguel Jesus Nunes; Coito, João Lucas; Fino, Joana; Cunha, Jorge; Silva, Helena; de Almeida, Patrícia Gomes; Costa, Maria Manuela Ribeiro; Amâncio, Sara; Paulo, Octávio S; Rocheta, Margarida

2017-01-01

RNA-seq of Vitis during early stages of bud development, in male, female and hermaphrodite flowers, identified new loci outside of annotated gene models, suggesting their involvement in sex establishment. The molecular mechanisms responsible for flower sex specification remain unclear for most plant species. In the case of V. vinifera ssp. vinifera, it is not fully understood what determines hermaphroditism in the domesticated subspecies and male or female flowers in wild dioecious relatives (Vitis vinifera ssp. sylvestris). Here, we describe a de novo assembly of the transcriptome of three flower developmental stages from the three Vitis vinifera flower types. The validation of de novo assembly showed a correlation of 0.825. The main goals of this work were the identification of V. v. sylvestris exclusive transcripts and the characterization of differential gene expression during flower development. RNA from several flower developmental stages was used previously to generate Illumina sequence reads. Through a sequential de novo assembly strategy one comprehensive transcriptome comprising 95,516 non-redundant transcripts was assembled. From this dataset 81,064 transcripts were annotated to V. v. vinifera reference transcriptome and 11,084 were annotated against V. v. vinifera reference genome. Moreover, we found 3368 transcripts that could not be mapped to Vitis reference genome. From all the non-redundant transcripts that were assembled, bioinformatics analysis identified 133 specific of V. v. sylvestris and 516 transcripts differentially expressed among the three flower types. The detection of transcription from areas of the genome not currently annotated suggests active transcription of previously unannotated genomic loci during early stages of bud development.

Genetics Home Reference: 16p11.2 deletion syndrome

MedlinePlus

... Schuurs-Hoeijmakers JH, van Haeringen A, Fransen van de Putte DE, Anderlid BM, Lundin J, Lapunzina P, Pérez Jurado ... Marshall CR, Scherer SW. Phenotypic spectrum associated with de novo and inherited deletions and duplications at 16p11. ...

Transcriptome Assembly, Gene Annotation and Tissue Gene Expression Atlas of the Rainbow Trout

PubMed Central

Salem, Mohamed; Paneru, Bam; Al-Tobasei, Rafet; Abdouni, Fatima; Thorgaard, Gary H.; Rexroad, Caird E.; Yao, Jianbo

2015-01-01

Efforts to obtain a comprehensive genome sequence for rainbow trout are ongoing and will be complemented by transcriptome information that will enhance genome assembly and annotation. Previously, transcriptome reference sequences were reported using data from different sources. Although the previous work added a great wealth of sequences, a complete and well-annotated transcriptome is still needed. In addition, gene expression in different tissues was not completely addressed in the previous studies. In this study, non-normalized cDNA libraries were sequenced from 13 different tissues of a single doubled haploid rainbow trout from the same source used for the rainbow trout genome sequence. A total of ~1.167 billion paired-end reads were de novo assembled using the Trinity RNA-Seq assembler yielding 474,524 contigs > 500 base-pairs. Of them, 287,593 had homologies to the NCBI non-redundant protein database. The longest contig of each cluster was selected as a reference, yielding 44,990 representative contigs. A total of 4,146 contigs (9.2%), including 710 full-length sequences, did not match any mRNA sequences in the current rainbow trout genome reference. Mapping reads to the reference genome identified an additional 11,843 transcripts not annotated in the genome. A digital gene expression atlas revealed 7,678 housekeeping and 4,021 tissue-specific genes. Expression of about 16,000–32,000 genes (35–71% of the identified genes) accounted for basic and specialized functions of each tissue. White muscle and stomach had the least complex transcriptomes, with high percentages of their total mRNA contributed by a small number of genes. Brain, testis and intestine, in contrast, had complex transcriptomes, with a large numbers of genes involved in their expression patterns. This study provides comprehensive de novo transcriptome information that is suitable for functional and comparative genomics studies in rainbow trout, including annotation of the genome. PMID:25793877

Efficient high-throughput sequencing of a laser microdissected chromosome arm

PubMed Central

2013-01-01

Background Genomic sequence assemblies are key tools for a broad range of gene function and evolutionary studies. The diploid amphibian Xenopus tropicalis plays a pivotal role in these fields due to its combination of experimental flexibility, diploid genome, and early-branching tetrapod taxonomic position, having diverged from the amniote lineage ~360 million years ago. A genome assembly and a genetic linkage map have recently been made available. Unfortunately, large gaps in the linkage map attenuate long-range integrity of the genome assembly. Results We laser dissected the short arm of X. tropicalis chromosome 7 for next generation sequencing and computational mapping to the reference genome. This arm is of particular interest as it encodes the sex determination locus, but its genetic map contains large gaps which undermine available genome assemblies. Whole genome amplification of 15 laser-microdissected 7p arms followed by next generation sequencing yielded ~35 million reads, over four million of which uniquely mapped to the X. tropicalis genome. Our analysis placed more than 200 previously unmapped scaffolds on the analyzed chromosome arm, providing valuable low-resolution physical map information for de novo genome assembly. Conclusion We present a new approach for improving and validating genetic maps and sequence assemblies. Whole genome amplification of 15 microdissected chromosome arms provided sufficient high-quality material for localizing previously unmapped scaffolds and genes as well as recognizing mislocalized scaffolds. PMID:23714049

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

NASA Astrophysics Data System (ADS)

Ardalan, A. A.; Safari, A.

2004-09-01

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

A two-dimensional proteome reference map of Herbaspirillum seropedicae proteins.

PubMed

Chaves, Daniela Fojo Seixas; Ferrer, Pércio Pereira; de Souza, Emanuel Maltempi; Gruz, Leonardo Magalhães; Monteiro, Rose Adele; de Oliveira Pedrosa, Fábio

2007-10-01

Herbaspirillum seropedicae is an endophytic diazotroph associated with economically important crops such as rice, sugarcane, and wheat. Here, we present a 2-D reference map for H. seropedicae. Using MALDI-TOF-MS we identified 205 spots representing 173 different proteins with a calculated average of 1.18 proteins/gene. Seventeen hypothetical or conserved hypothetical ORFs were shown to code for true gene products. These data will support the genome annotation process and provide a basis on which to undertake comparative proteomic studies.

The Hygiene Hypothesis and Breast Cancer a Novel Application of an Etiologic Theory for Allergies, Asthma, and Other Immune Disorders

DTIC Science & Technology

2007-05-01

REFERENCE YEAR-2] and [REFERENCE YEAR], on average, how many days per month did you eat the following kinds of foods: Q68. Yogurt (not the frozen...kind)? days/month Q69. Kim chee or sauerkraut ( fermented cabbage) days/month Q70. Lactobacillus or probiotic supplements...entre [AÑO DE REFERENCIA-2] y [AÑO DE REFERENCIA]: Q68. Yogurt (no del tipo congelado)? días / mes Q69. Kim chee o chukrut (repollo

Dual-energy imaging method to improve the image quality and the accuracy of dose calculation for cone-beam computed tomography.

PubMed

Men, Kuo; Dai, Jianrong; Chen, Xinyuan; Li, Minghui; Zhang, Ke; Huang, Peng

2017-04-01

To improve the image quality and accuracy of dose calculation for cone-beam computed tomography (CT) images through implementation of a dual-energy cone-beam computed tomography method (DE-CBCT), and evaluate the improvement quantitatively. Two sets of CBCT projections were acquired using the X-ray volumetric imaging (XVI) system on a Synergy (Elekta, Stockholm, Sweden) system with 120kV (high) and 70kV (low) X-rays, respectively. Then, the electron density relative to water (relative electron density (RED)) of each voxel was calculated using a projection-based dual-energy decomposition method. As a comparison, single-energy cone-beam computed tomography (SE-CBCT) was used to calculate RED with the Hounsfield unit-RED calibration curve generated by a CIRS phantom scan with identical imaging parameters. The imaging dose was measured with a dosimetry phantom. The image quality was evaluated quantitatively using a Catphan 503 phantom with the evaluation indices of the reproducibility of the RED values, high-contrast resolution (MTF 50% ), uniformity, and signal-to-noise ratio (SNR). Dose calculation of two simulated volumetric-modulated arc therapy plans using an Eclipse treatment-planning system (Varian Medical Systems, Palo Alto, CA, USA) was performed on an Alderson Rando Head and Neck (H&N) phantom and a Pelvis phantom. Fan-beam planning CT images for the H&N and Pelvis phantom were set as the reference. A global three-dimensional gamma analysis was used to compare dose distributions with the reference. The average gamma values for targets and OAR were analyzed with paired t-tests between DE-CBCT and SE-CBCT. In two scans (H&N scan and body scan), the imaging dose of DE-CBCT increased by 1.0% and decreased by 1.3%. It had a better reproducibility of the RED values (mean bias: 0.03 and 0.07) compared with SE-CBCT (mean bias: 0.13 and 0.16). It also improved the image uniformity (57.5% and 30.1%) and SNR (9.7% and 2.3%), but did not affect the MTF 50% . Gamma analyses of the 3D dose distribution with criteria of 1%/1mm showed a pass rate of 99.0-100% and 85.3-97.6% for DE-CBCT and 73.5-99.1% and 80.4-92.7% for SE-CBCT. The average gamma values were reduced significantly by DE-CBCT (p< 0.05). Gamma index maps showed that matching of the dose distribution between CBCT-based and reference was improved by DE-CBCT. DE-CBCT can achieve both better image quality and higher accuracy of dose calculation, and could be applied to adaptive radiotherapy. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

A Task-Based Analysis of Information Requirements of Tactical Maps

DTIC Science & Technology

1979-08-01

work began with the precept that military maps are primarily intended to serve users in the performance of functional tasks. By capitalizing on the task...Recherche Des Facteurs, Humaine de la Defense Natimla Onissels 2 Canadian ,losir Stall Washtington 1 C/Air Staff. Royal Canadian AF, ATTN: Pars Slid

Publications - SR 32 | Alaska Division of Geological & Geophysical Surveys

Science.gov Websites

DGGS SR 32 Publication Details Title: Oil and gas basins map of Alaska Authors: Ehm, Arlen Publication ): Alaska Statewide Bibliographic Reference Ehm, Arlen, 1983, Oil and gas basins map of Alaska: Alaska Sheets Sheet 1 Oil and gas basins map of Alaska, scale 1:2,500,000 (21.0 M) Keywords Alaska Statewide

A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping

PubMed Central

2012-01-01

Background Most modern citrus cultivars have an interspecific origin. As a foundational step towards deciphering the interspecific genome structures, a reference whole genome sequence was produced by the International Citrus Genome Consortium from a haploid derived from Clementine mandarin. The availability of a saturated genetic map of Clementine was identified as an essential prerequisite to assist the whole genome sequence assembly. Clementine is believed to be a ‘Mediterranean’ mandarin × sweet orange hybrid, and sweet orange likely arose from interspecific hybridizations between mandarin and pummelo gene pools. The primary goals of the present study were to establish a Clementine reference map using codominant markers, and to perform comparative mapping of pummelo, sweet orange, and Clementine. Results Five parental genetic maps were established from three segregating populations, which were genotyped with Single Nucleotide Polymorphism (SNP), Simple Sequence Repeats (SSR) and Insertion-Deletion (Indel) markers. An initial medium density reference map (961 markers for 1084.1 cM) of the Clementine was established by combining male and female Clementine segregation data. This Clementine map was compared with two pummelo maps and a sweet orange map. The linear order of markers was highly conserved in the different species. However, significant differences in map size were observed, which suggests a variation in the recombination rates. Skewed segregations were much higher in the male than female Clementine mapping data. The mapping data confirmed that Clementine arose from hybridization between ‘Mediterranean’ mandarin and sweet orange. The results identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome. Conclusions A reference genetic map of citrus, used to facilitate the chromosome assembly of the first citrus reference genome sequence, was established. The high conservation of marker order observed at the interspecific level should allow reasonable inferences of most citrus genome sequences by mapping next-generation sequencing (NGS) data in the reference genome sequence. The genome of the haploid Clementine used to establish the citrus reference genome sequence appears to have been inherited primarily from the ‘Mediterranean’ mandarin. The high frequency of skewed allelic segregations in the male Clementine data underline the probable extent of deviation from Mendelian segregation for characters controlled by heterozygous loci in male parents. PMID:23126659

Mapping and proteomic analysis of albumin and globulin proteins in hexaploid wheat kernels (Triticum aestivum L.).

PubMed

Merlino, Marielle; Leroy, Philippe; Chambon, Christophe; Branlard, Gérard

2009-05-01

Albumins and globulins of wheat endosperm represent 20% of total kernel protein. They are soluble proteins, mainly enzymes and proteins involved in cell functions. Two-dimensional gel immobiline electrophoresis (2DE) (pH 4-7) x SDS-Page revealed around 2,250 spots. Ninety percent of the spots were common between the very distantly related cultivars 'Opata 85' and 'Synthetic W7984', the two parents of the International Triticeae Mapping Initiative (ITMI) progeny. 'Opata' had 130 specific spots while 'Synthetic' had 96. 2DE and image analysis of the soluble proteins present in 112 recombinant inbred lines of the F9-mapped ITMI progeny enabled 120 unbiased segregating spots to be mapped on 21 wheat (Triticum aestivum L. em. Thell) chromosomes. After trypsic digestion, mapped spots were subjected to MALDI-Tof or tandem mass spectrometry for protein identification by database mining. Among the 'Opata' and 'Synthetic' spots identified, many enzymes have already been mapped in the barley and rice genomes. Multigene families of Heat Shock Proteins, beta-amylases, UDP-glucose pyrophosphorylases, peroxydases and thioredoxins were successfully identified. Although other proteins remain to be identified, some differences were found in the number of segregating proteins involved in response to stress: 11 proteins found in the modern selected cultivar 'Opata 85' as compared to 4 in the new hexaploid ;Synthetic W7984'. In addition, 'Opata' and 'Synthetic' differed in the number of proteins involved in protein folding (2 and 10, respectively). The usefulness of the mapped enzymes for future research on seed composition and characteristics is discussed.

Publications - PIR 2001-3C | Alaska Division of Geological & Geophysical

Science.gov Websites

content DGGS PIR 2001-3C Publication Details Title: Surficial-geologic map of the Eagle A-2 Quadrangle publication sales page for more information. Quadrangle(s): Eagle Bibliographic Reference Pinney, D.S., 2001 , Surficial-geologic map of the Eagle A-2 Quadrangle, Fortymile mining district, Alaska: Alaska Division of

Publications - PIR 2001-3A | Alaska Division of Geological & Geophysical

Science.gov Websites

content DGGS PIR 2001-3A Publication Details Title: Geologic map of the Eagle A-2 Quadrangle, Fortymile ): Eagle Bibliographic Reference Werdon, M.B., Newberry, R.J., Szumigala, D.J., and Pinney, D.S., 2001 , Geologic map of the Eagle A-2 Quadrangle, Fortymile mining district, Alaska: Alaska Division of Geological

Publications - PIR 2001-3B | Alaska Division of Geological & Geophysical

Science.gov Websites

content DGGS PIR 2001-3B Publication Details Title: Bedrock geologic map of the Eagle A-2 Quadrangle more information. Quadrangle(s): Eagle Bibliographic Reference Werdon, M.B., Newberry, R.J., and Szumigala, D.J., 2001, Bedrock geologic map of the Eagle A-2 Quadrangle, Fortymile mining district, Alaska

A symplectic map for trajectories of magnetic field lines in double-null divertor tokamaks

NASA Astrophysics Data System (ADS)

Crank, Willie; Ali, Halima; Punjabi, Alkesh

2009-11-01

The coordinates of the area-preserving map equations for integration of magnetic field line trajectories in tokamaks can be any coordinates for which a transformation to (ψ,θ,φ) coordinates exists [A. Punjabi, H. Ali, T. Evans, and A. Boozer, Phys. Lett. A 364, 140 (2007)]. ψ is toroidal magnetic flux, θ is poloidal angle, and φ is toroidal angle. This freedom is exploited to construct a map that represents the magnetic topology of double-null divertor tokamaks. For this purpose, the generating function of the simple map [A. Punjabi, A. Verma, and A. Boozer, Phys. Rev. Lett. 69, 3322 (1992)] is slightly modified. The resulting map equations for the double-null divertor tokamaks are: x1=x0-ky0(1-y0^2 ), y1=y0+kx1. k is the map parameter. It represents the generic topological effects of toroidal asymmetries. The O-point is at (0.0). The X-points are at (0,±1). The equilibrium magnetic surfaces are calculated. These surfaces are symmetric about the x- and y- axes. The widths of stochastic layer near the X-points in the principal plane, and the fractal dimensions of the magnetic footprints on the inboard and outboard side of upper and lower X-points are calculated from the map. This work is supported by US Department of Energy grants DE-FG02-07ER54937, DE-FG02-01ER54624 and DE-FG02-04ER54793.

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome.

PubMed

Bickhart, Derek M; Rosen, Benjamin D; Koren, Sergey; Sayre, Brian L; Hastie, Alex R; Chan, Saki; Lee, Joyce; Lam, Ernest T; Liachko, Ivan; Sullivan, Shawn T; Burton, Joshua N; Huson, Heather J; Nystrom, John C; Kelley, Christy M; Hutchison, Jana L; Zhou, Yang; Sun, Jiajie; Crisà, Alessandra; Ponce de León, F Abel; Schwartz, John C; Hammond, John A; Waldbieser, Geoffrey C; Schroeder, Steven G; Liu, George E; Dunham, Maitreya J; Shendure, Jay; Sonstegard, Tad S; Phillippy, Adam M; Van Tassell, Curtis P; Smith, Timothy P L

2017-04-01

The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus) based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced what is, to our knowledge, the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps. Our assembly represents a ∼400-fold improvement in continuity due to properly assembled gaps, compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex yet produced for an individual of a ruminant species.

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

PubMed Central

Bickhart, Derek M.; Rosen, Benjamin D.; Koren, Sergey; Sayre, Brian L.; Hastie, Alex R.; Chan, Saki; Lee, Joyce; Lam, Ernest T.; Liachko, Ivan; Sullivan, Shawn T.; Burton, Joshua N.; Huson, Heather J.; Nystrom, John C.; Kelley, Christy M.; Hutchison, Jana L.; Zhou, Yang; Sun, Jiajie; Crisà, Alessandra; de León, F. Abel Ponce; Schwartz, John C.; Hammond, John A.; Waldbieser, Geoffrey C.; Schroeder, Steven G.; Liu, George E.; Dunham, Maitreya J.; Shendure, Jay; Sonstegard, Tad S.; Phillippy, Adam M.; Van Tassell, Curtis P.; Smith, Timothy P.L.

2018-01-01

The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus), based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps. Our assembly represents a ~400-fold improvement in continuity due to properly assembled gaps compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex ever produced for an individual of a ruminant species. PMID:28263316

Chromosome-scale assembly of the Monopterus genome.

PubMed

Zhao, Xueya; Luo, Majing; Li, Zhigang; Zhong, Pei; Cheng, Yibin; Lai, Fengling; Wang, Xin; Min, Jiumeng; Bai, Mingzhou; Yang, Yulan; Cheng, Hanhua; Zhou, Rongjia

2018-05-01

The teleost fish Monopterus albus is emerging as a new model for biological studies due to its natural sex transition and small genome, in addition to its enormous economic and potential medical value. However, no genomic information for the Monopterus is currently available. Here, we sequenced and de novo assembled the genome of M. albus and report the de novochromosome assembly by FISH walking assisted by conserved synteny (Cafs). Using Cafs, 328 scaffolds were assembled into 12 chromosomes, which covered genomic sequences of 555 Mb, accounting for 81.3% of the sequences assembled in scaffolds (∼689 Mb). A total of 18 ,660 genes were mapped on the chromosomes and showed a nonrandom distribution along chromosomes. We report the first reference genome of the Monopterus and provide an efficient Cafs strategy for a de novo chromosome-level assembly of the Monopterus genome, which provides a valuable resource, not only for further studies in genetics, evolution, and development, particularly sex determination, but also for breed improvement of the species.

Evaluation of Three Protein-Extraction Methods for Proteome Analysis of Maize Leaf Midrib, a Compound Tissue Rich in Sclerenchyma Cells.

PubMed

Wang, Ning; Wu, Xiaolin; Ku, Lixia; Chen, Yanhui; Wang, Wei

2016-01-01

Leaf morphology is closely related to the growth and development of maize (Zea mays L.) plants and final kernel production. As an important part of the maize leaf, the midrib holds leaf blades in the aerial position for maximum sunlight capture. Leaf midribs of adult plants contain substantial sclerenchyma cells with heavily thickened and lignified secondary walls and have a high amount of phenolics, making protein extraction and proteome analysis difficult in leaf midrib tissue. In the present study, three protein-extraction methods that are commonly used in plant proteomics, i.e., phenol extraction, TCA/acetone extraction, and TCA/acetone/phenol extraction, were qualitatively and quantitatively evaluated based on 2DE maps and MS/MS analysis using the midribs of the 10th newly expanded leaves of maize plants. Microscopy revealed the existence of substantial amounts of sclerenchyma underneath maize midrib epidermises (particularly abaxial epidermises). The spot-number order obtained via 2DE mapping was as follows: phenol extraction (655) > TCA/acetone extraction (589) > TCA/acetone/phenol extraction (545). MS/MS analysis identified a total of 17 spots that exhibited 2-fold changes in abundance among the three methods (using phenol extraction as a control). Sixteen of the proteins identified were hydrophilic, with GRAVY values ranging from -0.026 to -0.487. For all three methods, we were able to obtain high-quality protein samples and good 2DE maps for the maize leaf midrib. However, phenol extraction produced a better 2DE map with greater resolution between spots, and TCA/acetone extraction produced higher protein yields. Thus, this paper includes a discussion regarding the possible reasons for differential protein extraction among the three methods. This study provides useful information that can be used to select suitable protein extraction methods for the proteome analysis of recalcitrant plant tissues that are rich in sclerenchyma cells.

Using genic sequence capture in combination with a syntenic pseudo genome to map a deletion mutant in a wheat species.

PubMed

Gardiner, Laura-Jayne; Gawroński, Piotr; Olohan, Lisa; Schnurbusch, Thorsten; Hall, Neil; Hall, Anthony

2014-12-01

Mapping-by-sequencing analyses have largely required a complete reference sequence and employed whole genome re-sequencing. In species such as wheat, no finished genome reference sequence is available. Additionally, because of its large genome size (17 Gb), re-sequencing at sufficient depth of coverage is not practical. Here, we extend the utility of mapping by sequencing, developing a bespoke pipeline and algorithm to map an early-flowering locus in einkorn wheat (Triticum monococcum L.) that is closely related to the bread wheat genome A progenitor. We have developed a genomic enrichment approach using the gene-rich regions of hexaploid bread wheat to design a 110-Mbp NimbleGen SeqCap EZ in solution capture probe set, representing the majority of genes in wheat. Here, we use the capture probe set to enrich and sequence an F2 mapping population of the mutant. The mutant locus was identified in T. monococcum, which lacks a complete genome reference sequence, by mapping the enriched data set onto pseudo-chromosomes derived from the capture probe target sequence, with a long-range order of genes based on synteny of wheat with Brachypodium distachyon. Using this approach we are able to map the region and identify a set of deleted genes within the interval. © 2014 The Authors.The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

Costs of Public Pharmaceutical Services in Rio de Janeiro Compared to Farmácia Popular Program.

PubMed

Silva, Rondineli Mendes da; Caetano, Rosângela

2016-12-22

To analyze the costs of public pharmaceutical services compared to Farmácia Popular Program (Popular Pharmacy Program). Comparison between prices paid by Aqui Tem Farmácia Popular Program (Farmácia Popular is available here) with the full costs of medicine provision by the Municipal Health Department of Rio de Janeiro. The comparison comprised 25 medicines supplied by both the municipal pharmaceutical service and Aqui Tem Farmácia Popular Program. Calculating the cost per pharmaceutical unit of each medicine included expenditure by Municipal Health Department of Rio de Janeiro with procurement (price), logistics, and local dispensation. The reference price of medicines paid by Aqui Tem Farmácia Popular was taken from the Brazilian Ministry of Health standard in force in 2012. Comparisons included full reference price; reference price minus 10.0% copayment by users; and maximum reference paid by the Ministry of Health (minus copayment and taxes). Simulations were carried out of the differences between the costs of Municipal Health Department of Rio de Janeiro with the common medicines and those potentially incurred based on the reference price of Aqui Tem Farmácia Popular. The Municipal Health Department of Rio de Janeiro spent R$28,526,526.57 with 25 medicines of the common list in 2012; 58.7% accounted for direct procurement costs. The estimated costs of the Health Department were generally lower than the reference prices of the Aqui Tem Farmácia Popular Program for 20 medicines, regardless of reference prices. The potential costs incurred by Health Department if expenditure of its consumption pattern were based on the reference prices of Aqui Tem Farmácia Popular would be R$124,170,777.76, considering the best scenario of payment by the Brazilian Ministry of Health (90.0% of the reference price, minus taxes). The difference in costs between public provision by Municipal Health Department of Rio de Janeiro and Farmácia Popular Program indicates that some reference prices could be reviewed aiming at their reduction. Analisar custos da assistência farmacêutica pública frente ao Programa Farmácia Popular. Comparação entre os valores pagos pelo Programa Aqui Tem Farmácia Popular com os custos integrais relativos à provisão de medicamentos pela Secretaria Municipal de Saúde do Rio de Janeiro. A comparação compreendeu 25 medicamentos, comuns tanto à provisão pela assistência farmacêutica pública municipal quanto pelo Programa Aqui Tem Farmácia Popular. O cálculo do custo unitário por unidade farmacotécnica de cada medicamento envolveu os gastos da Secretaria Municipal de Saúde com custos de aquisição (preço), logísticos e com a dispensação em nível local. O valor de referência dos medicamentos pago pelo Aqui Tem Farmácia Popular foi extraído da norma ministerial em vigor em 2012. As comparações envolveram o valor de referência pleno; valor de referência com desconto dos 10,0% pagos de contrapartida pelos usuários; e valor de referência máximo pago pelo Ministério da Saúde (descontados contrapartida e sem impostos).Foram realizadas simulações das diferenças entre os gastos da Secretaria Municipal de Saúde do Rio de Janeiro com os medicamentos do elenco comum e os que seriam incorridos se esses tivessem sido executados com base no valor de referência do Aqui Tem Farmácia Popular. A Secretaria Municipal de Saúde do Rio de Janeiro gastou R$28.526.526,57 com 25 medicamentos do rol comum em 2012; 58,7% corresponderam a custos diretos com a aquisição dos produtos. Os custos estimados da Secretaria Municipal de Saúde do Rio de Janeiro foram, em geral, menores que os valores de referência do Programa Aqui Tem Farmácia Popular em 20 medicamentos, independentemente dos valores de referência. Os custos que seriam incorridos pela Secretaria Municipal de Saúde do Rio de Janeiro, caso seu padrão de consumo tivesse como valor de pagamento os valores de referência do Aqui Tem Farmácia Popular seriam de R$124.170.777,76 considerando a melhor situação de pagamento pelo Ministério da Saúde (90,0% do valor de referência, com impostos descontados). A diferença de custos entre a provisão pública pela Secretaria Municipal de Saúde do Rio de Janeiro e o Programa Aqui Tem Farmácia Popular sinaliza que alguns valores de referência poderiam ser objetos de exame para sua redução.

Automated de novo phasing and model building of coiled-coil proteins.

PubMed

Rämisch, Sebastian; Lizatović, Robert; André, Ingemar

2015-03-01

Models generated by de novo structure prediction can be very useful starting points for molecular replacement for systems where suitable structural homologues cannot be readily identified. Protein-protein complexes and de novo-designed proteins are examples of systems that can be challenging to phase. In this study, the potential of de novo models of protein complexes for use as starting points for molecular replacement is investigated. The approach is demonstrated using homomeric coiled-coil proteins, which are excellent model systems for oligomeric systems. Despite the stereotypical fold of coiled coils, initial phase estimation can be difficult and many structures have to be solved with experimental phasing. A method was developed for automatic structure determination of homomeric coiled coils from X-ray diffraction data. In a benchmark set of 24 coiled coils, ranging from dimers to pentamers with resolutions down to 2.5 Å, 22 systems were automatically solved, 11 of which had previously been solved by experimental phasing. The generated models contained 71-103% of the residues present in the deposited structures, had the correct sequence and had free R values that deviated on average by 0.01 from those of the respective reference structures. The electron-density maps were of sufficient quality that only minor manual editing was necessary to produce final structures. The method, named CCsolve, combines methods for de novo structure prediction, initial phase estimation and automated model building into one pipeline. CCsolve is robust against errors in the initial models and can readily be modified to make use of alternative crystallographic software. The results demonstrate the feasibility of de novo phasing of protein-protein complexes, an approach that could also be employed for other small systems beyond coiled coils.

Mapping Children--Mapping Space.

ERIC Educational Resources Information Center

Pick, Herbert L., Jr.

Research is underway concerning the way the perception, conception, and representation of spatial layout develops. Three concepts are important here--space itself, frame of reference, and cognitive map. Cognitive map refers to a form of representation of the behavioral space, not paired associate or serial response learning. Other criteria…

A synthetic peptide vaccine directed against the 2ß2-2ß3 loop of domain 2 of protective antigen protects rabbits from inhalation anthrax.

PubMed

Oscherwitz, Jon; Yu, Fen; Cease, Kemp B

2010-09-15

The current vaccines for anthrax in the United States and United Kingdom are efficacious in the two most accepted animal models of inhalation anthrax, nonhuman primates and rabbits, but require extensive immunization protocols. We previously demonstrated that a linear determinant in domain 2 of Bacillus anthracis protective Ag (PA) is a potentially important target for an epitope-specific vaccine for anthrax, as Abs specific for this site, referred to as the loop-neutralizing determinant (LND), neutralize lethal toxin in vitro, yet are virtually absent in PA-immunized rabbits. In this study, we evaluated the immunogenicity and protective efficacy in rabbits of multiple antigenic peptides (MAPs) consisting of aa 304-319 from the LND of PA colinearly synthesized at the C terminus (T-B MAP) or N terminus (B-T MAP) with a heterologous T cell epitope from Plasmodium falciparum. Immunogenicity studies demonstrated that both MAPs elicited toxin-neutralizing Ab in rabbits. To evaluate the MAPs as potential anthrax vaccines, we immunized groups of rabbits (n = 7) with each MAP in Freund's adjuvant and then exposed all rabbits to a 200-LD(50) challenge with aerosolized spores of B. anthracis Ames strain. All seven rabbits immunized with the B-T MAP and 89% (six of seven) of rabbits immunized with the T-B MAP survived the spore challenge. Corollary studies with reference sera from human vaccinees immunized with rPA or anthrax vaccine absorbed and nonhuman primates immunized with PA revealed no detectable Ab with specificity for the LND. We conclude that a synthetic peptide vaccine targeting the LND would be a potentially efficacious vaccine for anthrax.

Dynamics Explorer measurements of particles, fields, and plasma drifts over a horse-collar auroral pattern

NASA Technical Reports Server (NTRS)

Sharber, J. R.; Hones, E. W., Jr.; Heelis, R. A.; Craven, J. D.; Frank, L. A.; Maynard, N. C.; Slavin, J. A.; Birn, J.

1992-01-01

As shown from ground-based measurements and satellite-borne imagers, one type of global auroral pattern characteristic of quiet (usually northward IMF) intervals is that of a contracted but thickened emission region of a pattern referred to as 'horse-collar' aurora (Hones et al., 1989). In this report we use the Dynamics Explorer data set to examine a case in which this horse-collar pattern was observed by the DE-1 auroral imager, while at the same time DE-2, at lower altitude, measured precipitating particles, electric and magnetic fields, and plasma drifts. Our analysis shows that, in general, there is close agreement between the optical signatures and the particle precipitation patterns. In many instances, over scales ranging from tens to a few hundred kilometers, electron precipitation features and upward field-aligned currents are observed at locations where the plasma flow gradients indicate negative V-average x E. The particle, plasma, and field measurements made along the satellite track and the 2D perspective of the imager provide a means of determining the configuration of convective flows in the high-latitude ionosphere during this interval of northward IMF. Recent mapping studies are used to relate the low-altitude observations to possible magnetospheric source regions.

Transposon fingerprinting using low coverage whole genome shotgun sequencing in Cacao (Theobroma cacao L.) and related species

PubMed Central

2013-01-01

Background Transposable elements (TEs) and other repetitive elements are a large and dynamically evolving part of eukaryotic genomes, especially in plants where they can account for a significant proportion of genome size. Their dynamic nature gives them the potential for use in identifying and characterizing crop germplasm. However, their repetitive nature makes them challenging to study using conventional methods of molecular biology. Next generation sequencing and new computational tools have greatly facilitated the investigation of TE variation within species and among closely related species. Results (i) We generated low-coverage Illumina whole genome shotgun sequencing reads for multiple individuals of cacao (Theobroma cacao) and related species. These reads were analysed using both an alignment/mapping approach and a de novo (graph based clustering) approach. (ii) A standard set of ultra-conserved orthologous sequences (UCOS) standardized TE data between samples and provided phylogenetic information on the relatedness of samples. (iii) The mapping approach proved highly effective within the reference species but underestimated TE abundance in interspecific comparisons relative to the de novo methods. (iv) Individual T. cacao accessions have unique patterns of TE abundance indicating that the TE composition of the genome is evolving actively within this species. (v) LTR/Gypsy elements are the most abundant, comprising c.10% of the genome. (vi) Within T. cacao the retroelement families show an order of magnitude greater sequence variability than the DNA transposon families. (vii) Theobroma grandiflorum has a similar TE composition to T. cacao, but the related genus Herrania is rather different, with LTRs making up a lower proportion of the genome, perhaps because of a massive presence (c. 20%) of distinctive low complexity satellite-like repeats in this genome. Conclusions (i) Short read alignment/mapping to reference TE contigs provides a simple and effective method of investigating intraspecific differences in TE composition. It is not appropriate for comparing repetitive elements across the species boundaries, for which de novo methods are more appropriate. (ii) Individual T. cacao accessions have unique spectra of TE composition indicating active evolution of TE abundance within this species. TE patterns could potentially be used as a “fingerprint” to identify and characterize cacao accessions. PMID:23883295

The limits of boundaries: unpacking localization and cognitive mapping relative to a boundary.

PubMed

Zhou, Ruojing; Mou, Weimin

2018-05-01

Previous research (Zhou, Mou, Journal of Experimental Psychology: Learning, Memory and Cognition 42(8):1316-1323, 2016) showed that learning individual locations relative to a single landmark, compared to learning relative to a boundary, led to more accurate inferences of inter-object spatial relations (cognitive mapping of multiple locations). Following our past findings, the current study investigated whether the larger number of reference points provided by a homogeneous circular boundary, as well as less accessible knowledge of direct spatial relations among the multiple reference points, would lead to less effective cognitive mapping relative to the boundary. Accordingly, we manipulated (a) the number of primary reference points (one segment drawn from a circular boundary, four such segments, vs. the complete boundary) available when participants were localizing four objects sequentially (Experiment 1) and (b) the extendedness of each of the four segments (Experiment 2). The results showed that cognitive mapping was the least accurate in the whole boundary condition. However, expanding each of the four segments did not affect the accuracy of cognitive mapping until the four were connected to form a continuous boundary. These findings indicate that when encoding locations relative to a homogeneous boundary, participants segmented the boundary into differentiated pieces and subsequently chose the most informative local part (i.e., the segment closest in distance to one location) as the primary reference point for a particular location. During this process, direct spatial relations among the reference points were likely not attended to. These findings suggest that people might encode and represent bounded space in a fragmented fashion when localizing within a homogeneous boundary.

Geologic map of the Venezuela part of the Puerto Ayacucho 2 degrees x 3 degrees Quadrangle, Amazonas Federal Territory, Venezuela

USGS Publications Warehouse

Wynn, Jeffrey C.; Olmore, Steven D.; Mendoza, Vicente; García, Andrés; Rendon, Ines; Estanga, Yasmin; Rincon, Haydee; Martinez, Felix; Lugo, Elis; Rivero, Nelson; Schruben, Paul G.

1994-01-01

This map is one of a series of 1:500,000-scale maps that, along with several other products, stems from a cooperative agreement between the U.S. Geological Survey (USGS) and the Corporacion Venezolana de Guayana, Tecnica Minera, C.A. (TECMIN), a Venezuelan Government-owned mining and mineral exploration company. The agreement covered cooperative work carried out in the Precambrian Shield of southern Venezuela during 1987-1991 and included a geologic and mineral resource inventory, technology transfer, and scientific training (Wynn and others, in press). The Precambrian Guayana Shield (Escudo de Guyana, not to be confused with the neighboring country of Guyana) includes some of the oldest known rocks in the world (Mendoza, 1977) and also covers parts of neighboring Guyana, Surinam, French Guiana, Columbia, and Brazil. In Venezuela, it underlies most of Bolivar state and all of the Amazonas Federal Territory (see index map).

The Reference Elevation Model of Antarctica (REMA): A High Resolution, Time-Stamped Digital Elevation Model for the Antarctic Ice Sheet

NASA Astrophysics Data System (ADS)

Howat, I.; Noh, M. J.; Porter, C. C.; Smith, B. E.; Morin, P. J.

2017-12-01

We are creating the Reference Elevation Model of Antarctica (REMA), a continuous, high resolution (2-8 m), high precision (accuracy better than 1 m) reference surface for a wide range of glaciological and geodetic applications. REMA will be constructed from stereo-photogrammetric Digital Surface Models (DSM) extracted from pairs of submeter resolution DigitalGlobe satellite imagery and vertically registred to precise elevations from near-coincident airborne LiDAR, ground-based GPS surveys and Cryosat-2 radar altimetry. Both a seamless mosaic and individual, time-stamped DSM strips, collected primarily between 2012 and 2016, will be distributed to enable change measurement. These data will be used for mapping bed topography from ice thickness, measuring ice thickness changes, constraining ice flow and geodynamic models, mapping glacial geomorphology, terrain corrections and filtering of remote sensing observations, and many other science tasks. Is will also be critical for mapping ice traverse routes, landing sites and other field logistics planning. REMA will also provide a critical elevation benchmark for future satellite altimetry missions including ICESat-2. Here we report on REMA production progress, initial accuracy assessment and data availability.

Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains.

PubMed

Zych, Konrad; Li, Yang; van der Velde, Joeri K; Joosen, Ronny V L; Ligterink, Wilco; Jansen, Ritsert C; Arends, Danny

2015-02-19

Genetic markers and maps are instrumental in quantitative trait locus (QTL) mapping in segregating populations. The resolution of QTL localization depends on the number of informative recombinations in the population and how well they are tagged by markers. Larger populations and denser marker maps are better for detecting and locating QTLs. Marker maps that are initially too sparse can be saturated or derived de novo from high-throughput omics data, (e.g. gene expression, protein or metabolite abundance). If these molecular phenotypes are affected by genetic variation due to a major QTL they will show a clear multimodal distribution. Using this information, phenotypes can be converted into genetic markers. The Pheno2Geno tool uses mixture modeling to select phenotypes and transform them into genetic markers suitable for construction and/or saturation of a genetic map. Pheno2Geno excludes candidate genetic markers that show evidence for multiple possibly epistatically interacting QTL and/or interaction with the environment, in order to provide a set of robust markers for follow-up QTL mapping. We demonstrate the use of Pheno2Geno on gene expression data of 370,000 probes in 148 A. thaliana recombinant inbred lines. Pheno2Geno is able to saturate the existing genetic map, decreasing the average distance between markers from 7.1 cM to 0.89 cM, close to the theoretical limit of 0.68 cM (with 148 individuals we expect a recombination every 100/148=0.68 cM); this pinpointed almost all of the informative recombinations in the population. The Pheno2Geno package makes use of genome-wide molecular profiling and provides a tool for high-throughput de novo map construction and saturation of existing genetic maps. Processing of the showcase dataset takes less than 30 minutes on an average desktop PC. Pheno2Geno improves QTL mapping results at no additional laboratory cost and with minimum computational effort. Its results are formatted for direct use in R/qtl, the leading R package for QTL studies. Pheno2Geno is freely available on CRAN under "GNU GPL v3". The Pheno2Geno package as well as the tutorial can also be found at: http://pheno2geno.nl .

Environmental assessment of biofuel chains based on ecosystem modelling, including land-use change effects

NASA Astrophysics Data System (ADS)

Gabrielle, B.; Gagnaire, N.; Massad, R.; Prieur, V.; Python, Y.

2012-04-01

The potential greenhouse gas (GHG) savings resulting from the displacement of fossil energy sources by bioenergy mostly hinges on the uncertainty on the magnitude of nitrous oxide (N2O) emissions from arable soils occuring during feedstock production. These emissions are broadly related to fertilizer nitrogen input rates, but largely controlled by soil and climate factors which makes their estimation highly uncertain. Here, we set out to improve estimates of N2O emissions from bioenergy feedstocks by using ecosystem models and measurements and modeling of atmospheric N2O in the greater Paris (France) area. Ground fluxes were measured in two locations to assess the effect of soil type and management, crop type (including lignocellulosics such as triticale, switchgrass and miscanthus), and climate on N2O emission rates and dynamics. High-resolution maps of N2O emissions were generated over the Ile-de-France region (around Paris) with two ecosystem models using geographical databases on soils, weather data, land-use and crop management. The models were tested against ground flux measurements and the emission maps were fed into the atmospheric chemistry-transport model CHIMERE. The maps were tested by comparing the CHIMERE simulations with time series of N2O concentrations measured at various heights above the ground in two locations in 2007. The emissions of N2O, as integrated over the region, were used in a life-cycle assessment of representative biofuel pathways: bioethanol from wheat and sugar-beet (1st generation), and miscanthus (2nd generation chain); bio-diesel from oilseed rape. Effects related to direct and indirect land-use changes (in particular on soil carbon stocks) were also included in the assessment based on various land-use scenarios and literature references. The potential deployment of miscanthus was simulated by assuming it would be grown on the current sugar-beet growing area in Ile-de-France, or by converting land currently under permanent fallow. Compared to the standard methodology currently used in LCA, based on fixed emissions for N2O, the use of model-derived estimates leads to a 10 to 40% reduction in the overall life-cycle GHG emissions of biofuels. This emphasizes the importance of regional factors in the relationship between agricultural inputs and emissions (altogether with biomass yields) in the outcome of LCAs. When excluding indirect land-use change effects (iLUC), 1st generation pathways enabled GHG savings ranging from 50 to 73% compared to fossile-derived equivalents, while this figure reached 88% for 2nd generation bioethanol from miscanthus. Including iLUC reduced the savings to less than 5% for bio-diesel from rapeseed, 10 to 45% for 1st generation bioethanol and to 60% for miscanthus. These figures apply to the year 2007 and should be extended to a larger number of years, but the magnitude of N2O emissions was similar between 2007, 2008 and 2009 over the Ile de France region.

Construction of Pseudomolecule Sequences of the aus Rice Cultivar Kasalath for Comparative Genomics of Asian Cultivated Rice

PubMed Central

Sakai, Hiroaki; Kanamori, Hiroyuki; Arai-Kichise, Yuko; Shibata-Hatta, Mari; Ebana, Kaworu; Oono, Youko; Kurita, Kanako; Fujisawa, Hiroko; Katagiri, Satoshi; Mukai, Yoshiyuki; Hamada, Masao; Itoh, Takeshi; Matsumoto, Takashi; Katayose, Yuichi; Wakasa, Kyo; Yano, Masahiro; Wu, Jianzhong

2014-01-01

Having a deep genetic structure evolved during its domestication and adaptation, the Asian cultivated rice (Oryza sativa) displays considerable physiological and morphological variations. Here, we describe deep whole-genome sequencing of the aus rice cultivar Kasalath by using the advanced next-generation sequencing (NGS) technologies to gain a better understanding of the sequence and structural changes among highly differentiated cultivars. The de novo assembled Kasalath sequences represented 91.1% (330.55 Mb) of the genome and contained 35 139 expressed loci annotated by RNA-Seq analysis. We detected 2 787 250 single-nucleotide polymorphisms (SNPs) and 7393 large insertion/deletion (indel) sites (>100 bp) between Kasalath and Nipponbare, and 2 216 251 SNPs and 3780 large indels between Kasalath and 93-11. Extensive comparison of the gene contents among these cultivars revealed similar rates of gene gain and loss. We detected at least 7.39 Mb of inserted sequences and 40.75 Mb of unmapped sequences in the Kasalath genome in comparison with the Nipponbare reference genome. Mapping of the publicly available NGS short reads from 50 rice accessions proved the necessity and the value of using the Kasalath whole-genome sequence as an additional reference to capture the sequence polymorphisms that cannot be discovered by using the Nipponbare sequence alone. PMID:24578372

Rapid Parametric Mapping of the Longitudinal Relaxation Time T1 Using Two-Dimensional Variable Flip Angle Magnetic Resonance Imaging at 1.5 Tesla, 3 Tesla, and 7 Tesla

PubMed Central

Dieringer, Matthias A.; Deimling, Michael; Santoro, Davide; Wuerfel, Jens; Madai, Vince I.; Sobesky, Jan; von Knobelsdorff-Brenkenhoff, Florian; Schulz-Menger, Jeanette; Niendorf, Thoralf

2014-01-01

Introduction Visual but subjective reading of longitudinal relaxation time (T1) weighted magnetic resonance images is commonly used for the detection of brain pathologies. For this non-quantitative measure, diagnostic quality depends on hardware configuration, imaging parameters, radio frequency transmission field (B1+) uniformity, as well as observer experience. Parametric quantification of the tissue T1 relaxation parameter offsets the propensity for these effects, but is typically time consuming. For this reason, this study examines the feasibility of rapid 2D T1 quantification using a variable flip angles (VFA) approach at magnetic field strengths of 1.5 Tesla, 3 Tesla, and 7 Tesla. These efforts include validation in phantom experiments and application for brain T1 mapping. Methods T1 quantification included simulations of the Bloch equations to correct for slice profile imperfections, and a correction for B1+. Fast gradient echo acquisitions were conducted using three adjusted flip angles for the proposed T1 quantification approach that was benchmarked against slice profile uncorrected 2D VFA and an inversion-recovery spin-echo based reference method. Brain T1 mapping was performed in six healthy subjects, one multiple sclerosis patient, and one stroke patient. Results Phantom experiments showed a mean T1 estimation error of (-63±1.5)% for slice profile uncorrected 2D VFA and (0.2±1.4)% for the proposed approach compared to the reference method. Scan time for single slice T1 mapping including B1+ mapping could be reduced to 5 seconds using an in-plane resolution of (2×2) mm2, which equals a scan time reduction of more than 99% compared to the reference method. Conclusion Our results demonstrate that rapid 2D T1 quantification using a variable flip angle approach is feasible at 1.5T/3T/7T. It represents a valuable alternative for rapid T1 mapping due to the gain in speed versus conventional approaches. This progress may serve to enhance the capabilities of parametric MR based lesion detection and brain tissue characterization. PMID:24621588

Rapid parametric mapping of the longitudinal relaxation time T1 using two-dimensional variable flip angle magnetic resonance imaging at 1.5 Tesla, 3 Tesla, and 7 Tesla.

PubMed

Dieringer, Matthias A; Deimling, Michael; Santoro, Davide; Wuerfel, Jens; Madai, Vince I; Sobesky, Jan; von Knobelsdorff-Brenkenhoff, Florian; Schulz-Menger, Jeanette; Niendorf, Thoralf

2014-01-01

Visual but subjective reading of longitudinal relaxation time (T1) weighted magnetic resonance images is commonly used for the detection of brain pathologies. For this non-quantitative measure, diagnostic quality depends on hardware configuration, imaging parameters, radio frequency transmission field (B1+) uniformity, as well as observer experience. Parametric quantification of the tissue T1 relaxation parameter offsets the propensity for these effects, but is typically time consuming. For this reason, this study examines the feasibility of rapid 2D T1 quantification using a variable flip angles (VFA) approach at magnetic field strengths of 1.5 Tesla, 3 Tesla, and 7 Tesla. These efforts include validation in phantom experiments and application for brain T1 mapping. T1 quantification included simulations of the Bloch equations to correct for slice profile imperfections, and a correction for B1+. Fast gradient echo acquisitions were conducted using three adjusted flip angles for the proposed T1 quantification approach that was benchmarked against slice profile uncorrected 2D VFA and an inversion-recovery spin-echo based reference method. Brain T1 mapping was performed in six healthy subjects, one multiple sclerosis patient, and one stroke patient. Phantom experiments showed a mean T1 estimation error of (-63±1.5)% for slice profile uncorrected 2D VFA and (0.2±1.4)% for the proposed approach compared to the reference method. Scan time for single slice T1 mapping including B1+ mapping could be reduced to 5 seconds using an in-plane resolution of (2×2) mm2, which equals a scan time reduction of more than 99% compared to the reference method. Our results demonstrate that rapid 2D T1 quantification using a variable flip angle approach is feasible at 1.5T/3T/7T. It represents a valuable alternative for rapid T1 mapping due to the gain in speed versus conventional approaches. This progress may serve to enhance the capabilities of parametric MR based lesion detection and brain tissue characterization.

A mapping closure for turbulent scalar mixing using a time-evolving reference field

NASA Technical Reports Server (NTRS)

Girimaji, Sharath S.

1992-01-01

A general mapping-closure approach for modeling scalar mixing in homogeneous turbulence is developed. This approach is different from the previous methods in that the reference field also evolves according to the same equations as the physical scalar field. The use of a time-evolving Gaussian reference field results in a model that is similar to the mapping closure model of Pope (1991), which is based on the methodology of Chen et al. (1989). Both models yield identical relationships between the scalar variance and higher-order moments, which are in good agreement with heat conduction simulation data and can be consistent with any type of epsilon(phi) evolution. The present methodology can be extended to any reference field whose behavior is known. The possibility of a beta-pdf reference field is explored. The shortcomings of the mapping closure methods are discussed, and the limit at which the mapping becomes invalid is identified.

The Importance of Measurement Errors for Deriving Accurate Reference Leaf Area Index Maps for Validation of Moderate-Resolution Satellite LAI Products

NASA Technical Reports Server (NTRS)

Huang, Dong; Yang, Wenze; Tan, Bin; Rautiainen, Miina; Zhang, Ping; Hu, Jiannan; Shabanov, Nikolay V.; Linder, Sune; Knyazikhin, Yuri; Myneni, Ranga B.

2006-01-01

The validation of moderate-resolution satellite leaf area index (LAI) products such as those operationally generated from the Moderate Resolution Imaging Spectroradiometer (MODIS) sensor data requires reference LAI maps developed from field LAI measurements and fine-resolution satellite data. Errors in field measurements and satellite data determine the accuracy of the reference LAI maps. This paper describes a method by which reference maps of known accuracy can be generated with knowledge of errors in fine-resolution satellite data. The method is demonstrated with data from an international field campaign in a boreal coniferous forest in northern Sweden, and Enhanced Thematic Mapper Plus images. The reference LAI map thus generated is used to assess modifications to the MODIS LAI/fPAR algorithm recently implemented to derive the next generation of the MODIS LAI/fPAR product for this important biome type.

Effect of packaging technology on microbiological and sensory quality of a cooked blood sausage, Morcela de Arroz, from Monchique region of Portugal.

PubMed

Pereira, J A; Dionísio, L; Patarata, L; Matos, T J S

2015-03-01

Morcela de Arroz (MA), a popular Portuguese blood sausage, with high pH and water activity (aw), is traditionally commercialized without preservatives and unpacked. This study evaluated the best packaging solution to extend MA shelf life stored at 4±1°C for 44days: without packaging (WP), vacuum (VP) and modified atmosphere packaging (MAP) (80% CO2; 20% N2). Mesophilic (MTVC), psychrotrophic (PTVC), lactic acid bacteria (LAB), pseudomonads, molds and yeasts, Enterobacteriaceae, Listeria monocytogenes, Salmonella spp., Bacillus cereus, Clostridium perfringens, sensory properties, pH, moisture and aw were studied. Moisture and aw decreased (p<0.05) in WP. pH decreased in WP and MAP during storage. MTVC and PTVC counts increased to values around 7logCFU/g at 44days of storage. LAB and Enterobacteriaceae counts were higher (p<0.05) in VP. Pseudomonads were inhibited (p<0.05) by MAP after 8days of storage. Sensory parameters were affected (p<0.05) by packaging and storage time. Globally, MAP performed better. Copyright © 2014 Elsevier Ltd. All rights reserved.

Use of diversity arrays technology markers for integration into a cotton reference map and anchoring to a recombinant inbred line map

USDA-ARS?s Scientific Manuscript database

A DArT marker platform is developed for the cotton genome to evaluate the use of DArT markers compared to AFLPs in mapping, and transferability across the mapping populations. We used a reference genetic map of tetraploid Gossypium that already contained ~5000 loci which coalesced into 26 chromosom...

Guidelines for Designing User Interface Software

DTIC Science & Technology

1986-08-01

2.4.4 Bar Graphs 150 2.4.5 Pie Charts 154 2.4.6 Pictures and Diagrams 156 2.4.7 Flowcharts 159 2.4.8 Maps and Situation Displays 163 2.5 Format...Pictures and diagrams 156 2.4.7 Flowcharts 159 2.4.8 Maps and situation displays 163 2.5 Format refers to the organization of different types of...computer aids for calculating area, volume, center of gravity, modes of vibration, stresses, heat transfer, etc. 158 DATA DISPLAY Flowcharts

Ionospheric TEC Weather Map Over South America

NASA Astrophysics Data System (ADS)

Takahashi, H.; Wrasse, C. M.; Denardini, C. M.; Pádua, M. B.; de Paula, E. R.; Costa, S. M. A.; Otsuka, Y.; Shiokawa, K.; Monico, J. F. Galera; Ivo, A.; Sant'Anna, N.

2016-11-01

Ionospheric weather maps using the total electron content (TEC) monitored by ground-based Global Navigation Satellite Systems (GNSS) receivers over South American continent, TECMAP, have been operationally produced by Instituto Nacional de Pesquisas Espaciais's Space Weather Study and Monitoring Program (Estudo e Monitoramento Brasileiro de Clima Especial) since 2013. In order to cover the whole continent, four GNSS receiver networks, (Rede Brasileiro de Monitoramento Contínuo) RBMC/Brazilian Institute for Geography and Statistics, Low-latitude Ionospheric Sensor Network, International GNSS Service, and Red Argentina de Monitoreo Satelital Continuo, in total 140 sites, have been used. TECMAPs with a time resolution of 10 min are produced in 12 h time delay. Spatial resolution of the map is rather low, varying between 50 and 500 km depending on the density of the observation points. Large day-to-day variabilities of the equatorial ionization anomaly have been observed. Spatial gradient of TEC from the anomaly trough (total electron content unit, 1 TECU = 1016 el m-2 (TECU) <10) to the crest region (TECU > 80) causes a large ionospheric range delay in the GNSS positioning system. Ionospheric plasma bubbles, their seeding and development, could be monitored. This plasma density (spatial and temporal) variability causes not only the GNSS-based positioning error but also radio wave scintillations. Monitoring of these phenomena by TEC mapping becomes an important issue for space weather concern for high-technology positioning system and telecommunication.

"X-Map 2.0" for Edema Signal Enhancement for Acute Ischemic Stroke Using Non-Contrast-Enhanced Dual-Energy Computed Tomography.

PubMed

Taguchi, Katsuyuki; Itoh, Toshihide; Fuld, Matthew K; Fournie, Eric; Lee, Okkyun; Noguchi, Kyo

2018-03-14

A novel imaging technique ("X-map") has been developed to identify acute ischemic lesions for stroke patients using non-contrast-enhanced dual-energy computed tomography (NE-DE-CT). Using the 3-material decomposition technique, the original X-map ("X-map 1.0") eliminates fat and bone from the images, suppresses the gray matter (GM)-white matter (WM) tissue contrast, and makes signals of edema induced by severe ischemia easier to detect. The aim of this study was to address the following 2 problems with the X-map 1.0: (1) biases in CT numbers (or artifacts) near the skull of NE-DE-CT images and (2) large intrapatient and interpatient variations in X-map 1.0 values. We improved both an iterative beam-hardening correction (iBHC) method and the X-map algorithm. The new iBHC (iBHC2) modeled x-ray physics more accurately. The new X-map ("X-map 2.0") estimated regional GM values-thus, maximizing the ability to suppress the GM-WM contrast, make edema signals quantitative, and enhance the edema signals that denote an increased water density for each pixel. We performed a retrospective study of 11 patients (3 men, 8 women; mean age, 76.3 years; range, 68-90 years) who presented to the emergency department with symptoms of acute stroke. Images were reconstructed with the old iBHC (iBHC1) and the iBHC2, and biases in CT numbers near the skull were measured. Both X-map 2.0 maps and X-map 1.0 maps were computed from iBHC2 images, both with and without a material decomposition-based edema signal enhancement (ESE) process. X-map values were measured at 5 to 9 locations on GM without infarct per patient; the mean value was calculated for each patient (we call it the patient-mean X-map value) and subtracted from the measured X-map values to generate zero-mean X-map values. The standard deviation of the patient-mean X-map values over multiple patients denotes the interpatient variation; the standard deviation over multiple zero-mean X-map values denotes the intrapatient variation. The Levene F test was performed to assess the difference in the standard deviations with different algorithms. Using 5 patient data who had diffusion weighted imaging (DWI) within 2 hours of NE-DE-CT, mean values at and near ischemic lesions were measured at 7 to 14 locations per patient with X-map images, CT images (low kV and high kV), and DWI images. The Pearson correlation coefficient was calculated between a normalized increase in DWI signals and either X-map or CT. The bias in CT numbers was lower with iBHC2 than with iBHC1 in both high- and low-kV images (2.5 ± 2.0 HU [95% confidence interval (CI), 1.3-3.8 HU] for iBHC2 vs 6.9 ± 2.3 HU [95% CI, 5.4-8.3 HU] for iBHC1 with high-kV images, P < 0.01; 1.5 ± 3.6 HU [95% CI, -0.8 to 3.7 HU] vs 12.8 ± 3.3 HU [95% CI, 10.7-14.8 HU] with low-kV images, P < 0.01). The interpatient variation was smaller with X-map 2.0 than with X-map 1.0, both with and without ESE (4.3 [95% CI, 3.0-7.6] for X-map 2.0 vs 19.0 [95% CI, 13.3-22.4] for X-map 1.0, both with ESE, P < 0.01; 3.0 [95% CI, 2.1-5.3] vs 12.0 [95% CI, 8.4-21.0] without ESE, P < 0.01). The intrapatient variation was also smaller with X-map 2.0 than with X-map 1.0 (6.2 [95% CI, 5.3-7.3] vs 8.5 [95% CI, 7.3-10.1] with ESE, P = 0.0122; 4.1 [95% CI, 3.6-4.9] vs 6.3 [95% CI, 5.5-7.6] without ESE, P < 0.01). The best 3 correlation coefficients (R) with DWI signals were -0.733 (95% CI, -0.845 to -0.560, P < 0.001) for X-map 2.0 with ESE, -0.642 (95% CI, -0.787 to -0.429, P < 0.001) for high-kV CT, and -0.609 (95% CI, -0.766 to -0.384, P < 0.001) for X-map 1.0 with ESE. Both of the 2 problems outlined in the objectives have been addressed by improving both iBHC and X-map algorithm. The iBHC2 improved the bias in CT numbers and the visibility of GM-WM contrast throughout the brain space. The combination of iBHC2 and X-map 2.0 with ESE decreased both intrapatient and interpatient variations of edema signals significantly and had a strong correlation with DWI signals in terms of the strength of edema signals.

BAIT: Organizing genomes and mapping rearrangements in single cells.

PubMed

Hills, Mark; O'Neill, Kieran; Falconer, Ester; Brinkman, Ryan; Lansdorp, Peter M

2013-01-01

Strand-seq is a single-cell sequencing technique to finely map sister chromatid exchanges (SCEs) and other rearrangements. To analyze these data, we introduce BAIT, software which assigns templates and identifies and localizes SCEs. We demonstrate BAIT can refine completed reference assemblies, identifying approximately 21 Mb of incorrectly oriented fragments and placing over half (2.6 Mb) of the orphan fragments in mm10/GRCm38. BAIT also stratifies scaffold-stage assemblies, potentially accelerating the assembling and finishing of reference genomes. BAIT is available at http://sourceforge.net/projects/bait/.

Whole-genome mapping reveals a large chromosomal inversion on Iberian Brucella suis biovar 2 strains.

PubMed

Ferreira, Ana Cristina; Dias, Ricardo; de Sá, Maria Inácia Corrêa; Tenreiro, Rogério

2016-08-30

Optical mapping is a technology able to quickly generate high resolution ordered whole-genome restriction maps of bacteria, being a proven approach to search for diversity among bacterial isolates. In this work, optical whole-genome maps were used to compare closely-related Brucella suis biovar 2 strains. This biovar is the unique isolated in domestic pigs and wild boars in Portugal and Spain and most of the strains share specific molecular characteristics establishing an Iberian clonal lineage that can be differentiated from another lineage mainly isolated in several Central European countries. We performed the BamHI whole-genome optical maps of five B. suis biovar 2 field strains, isolated from wild boars in Portugal and Spain (three from the Iberian lineage and two from the Central European one) as well as of the reference strain B. suis biovar 2 ATCC 23445 (Central European lineage, Denmark). Each strain showed a distinct, highly individual configuration of 228-231 BamHI fragments. Nevertheless, a low divergence was globally observed in chromosome II (1.6%) relatively to chromosome I (2.4%). Optical mapping also disclosed genomic events associated with B. suis strains in chromosome I, namely one indel (3.5kb) and one large inversion (944kb). By using targeted-PCR in a set of 176 B. suis strains, including all biovars and haplotypes, the indel was found to be specific of the reference strain ATCC 23445 and the large inversion was shown to be an exclusive genomic marker of the Iberian clonal lineage of biovar 2. Copyright © 2016 Elsevier B.V. All rights reserved.

Estimated costs of advanced lung cancer care in a public reference hospital.

PubMed

Knust, Renata Erthal; Portela, Margareth Crisóstomo; Pereira, Claudia Cristina de Aguiar; Fortes, Guilherme Bastos

2017-08-17

To estimate the direct medical costs of advanced non-small cell lung cancer care. We assessed a cohort of 277 patients treated in the Brazilian National Cancer Institute in 2011. The costs were estimated from the perspective of the hospital as a service provider of reference for the Brazilian Unified Health System. The materials and procedures used were identified and quantified, per patient, and we assigned to them monetary values, consolidated in phases of the assistance defined. The analyses had a descriptive character with costs in Real (R$). Overall, the cohort represented a cost of R$2,473,559.91, being 71.5% related to outpatient care and 28.5% to hospitalizations. In the outpatient care, costs with radiotherapy (34%) and chemotherapy (22%) predominated. The results pointed to lower costs in the initial phase of treatment (7.2%) and very high costs in the maintenance phase (61.6%). Finally, we identified statistically significant differences of average cost by age groups, education levels, physical performance, and histological type. This study provides a current, useful, and relevant picture of the costs of patients with non-small cell lung cancer treated in a public hospital of reference and it provides information on the magnitude of the problem of cancer in the context of public health. The results confirm the importance of radiation treatment and hospitalizations as the main components of the cost of treatment. Despite some losses of follow-up, we assess that, for approximately 80% of the patients included in the study, the estimates presented herein are satisfactory for the care of the disease, from the perspective of a service provider of reference of the Brazilian Unified Health System, as it provides elements for the management of the service, as well as for studies that result in more rational forms of resource allocation. Estimar os custos médicos diretos da assistência ao câncer de pulmão não pequenas células avançado. Foi avaliada uma coorte de 277 pacientes matriculados no Instituto Nacional do Câncer em 2011. Os custos foram estimados sob a perspectiva do hospital como prestador de serviços de referência para o SUS. Insumos e procedimentos utilizados foram identificados e quantificados, por paciente, sendo a eles atribuídos valores monetários, consolidados por fases da assistência definidas. As análises tiveram caráter descritivo com custos em reais (R$). Em termos globais, a coorte representou um custo de R$2.473.559,91, sendo 71,5% relacionados à atenção ambulatorial e 28,5% as internações. Na atenção ambulatorial, predominaram os custos com radioterapia (34%) e quimioterapia (22%). Os resultados apontaram para custos menores na fase inicial de tratamento (7,2%) e custos muito elevados na fase de manutenção (61,6%). Por fim, identificaram-se diferenças estatisticamente significativas das médias dos custos por faixas etárias, níveis de escolaridade, desempenho físico e tipo histológico. Este estudo fornece um retrato atual, útil e relevante sobre os custos de pacientes com câncer de pulmão não pequenas células assistidos em um hospital público de referência e provê elementos sobre a magnitude do problema do câncer no âmbito da saúde pública. Os resultados ratificam a importância do tratamento radioterápico e das internações como principais componentes de custo do tratamento. Apesar de algumas perdas de seguimento avalia-se que, para cerca de 80% dos pacientes incluídos no estudo, as estimativas aqui apresentadas sejam satisfatoriamente fidedignas ao cuidado da doença, sob a perspectiva de um prestador de referência do SUS, fornecendo elementos para a gestão do serviço, bem como para estudos que redundem em formas mais racionais de alocação de recursos.

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes.

PubMed

Staňková, Helena; Hastie, Alex R; Chan, Saki; Vrána, Jan; Tulpová, Zuzana; Kubaláková, Marie; Visendi, Paul; Hayashi, Satomi; Luo, Mingcheng; Batley, Jacqueline; Edwards, David; Doležel, Jaroslav; Šimková, Hana

2016-07-01

The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Connecting Spatial Memories of Two Nested Spaces

ERIC Educational Resources Information Center

Zhang, Hui; Mou, Weimin; McNamara, Timothy P.; Wang, Lin

2014-01-01

Four experiments investigated the manner in which people use spatial reference directions to organize spatial memories of 2 conceptually nested layouts. Participants learned directions of 8 remote cities centered to Beijing or Edmonton, where the experiments occurred, using a map or using direct pointing. The map and the environment were aligned,…

SNP Discovery in the Transcriptome of White Pacific Shrimp Litopenaeus vannamei by Next Generation Sequencing

PubMed Central

Yu, Yang; Wei, Jiankai; Zhang, Xiaojun; Liu, Jingwen; Liu, Chengzhang; Li, Fuhua; Xiang, Jianhai

2014-01-01

The application of next generation sequencing technology has greatly facilitated high throughput single nucleotide polymorphism (SNP) discovery and genotyping in genetic research. In the present study, SNPs were discovered based on two transcriptomes of Litopenaeus vannamei (L. vannamei) generated from Illumina sequencing platform HiSeq 2000. One transcriptome of L. vannamei was obtained through sequencing on the RNA from larvae at mysis stage and its reference sequence was de novo assembled. The data from another transcriptome were downloaded from NCBI and the reads of the two transcriptomes were mapped separately to the assembled reference by BWA. SNP calling was performed using SAMtools. A total of 58,717 and 36,277 SNPs with high quality were predicted from the two transcriptomes, respectively. SNP calling was also performed using the reads of two transcriptomes together, and a total of 96,040 SNPs with high quality were predicted. Among these 96,040 SNPs, 5,242 and 29,129 were predicted as non-synonymous and synonymous SNPs respectively. Characterization analysis of the predicted SNPs in L. vannamei showed that the estimated SNP frequency was 0.21% (one SNP per 476 bp) and the estimated ratio for transition to transversion was 2.0. Fifty SNPs were randomly selected for validation by Sanger sequencing after PCR amplification and 76% of SNPs were confirmed, which indicated that the SNPs predicted in this study were reliable. These SNPs will be very useful for genetic study in L. vannamei, especially for the high density linkage map construction and genome-wide association studies. PMID:24498047

Genetics Home Reference: intestinal pseudo-obstruction

MedlinePlus

... of Pittsburgh GeneReview: ACTG2-Related Disorders Lauro A, De Giorgio R, Pinna AD. Advancement in the clinical ... Lupski JR, Akdemir ZHC, Doukas M, Stoop HJ, de Graaf BM, Brouwer RWW, van Ijcken WFJ, Oury ...

Error and Uncertainty in the Accuracy Assessment of Land Cover Maps

NASA Astrophysics Data System (ADS)

Sarmento, Pedro Alexandre Reis

Traditionally the accuracy assessment of land cover maps is performed through the comparison of these maps with a reference database, which is intended to represent the "real" land cover, being this comparison reported with the thematic accuracy measures through confusion matrixes. Although, these reference databases are also a representation of reality, containing errors due to the human uncertainty in the assignment of the land cover class that best characterizes a certain area, causing bias in the thematic accuracy measures that are reported to the end users of these maps. The main goal of this dissertation is to develop a methodology that allows the integration of human uncertainty present in reference databases in the accuracy assessment of land cover maps, and analyse the impacts that uncertainty may have in the thematic accuracy measures reported to the end users of land cover maps. The utility of the inclusion of human uncertainty in the accuracy assessment of land cover maps is investigated. Specifically we studied the utility of fuzzy sets theory, more precisely of fuzzy arithmetic, for a better understanding of human uncertainty associated to the elaboration of reference databases, and their impacts in the thematic accuracy measures that are derived from confusion matrixes. For this purpose linguistic values transformed in fuzzy intervals that address the uncertainty in the elaboration of reference databases were used to compute fuzzy confusion matrixes. The proposed methodology is illustrated using a case study in which the accuracy assessment of a land cover map for Continental Portugal derived from Medium Resolution Imaging Spectrometer (MERIS) is made. The obtained results demonstrate that the inclusion of human uncertainty in reference databases provides much more information about the quality of land cover maps, when compared with the traditional approach of accuracy assessment of land cover maps. None

Yeast proteome map (last update).

PubMed

Perrot, Michel; Moes, Suzette; Massoni, Aurélie; Jenoe, Paul; Boucherie, Hélian

2009-10-01

The identification of proteins separated on 2-D gels is essential to exploit the full potential of 2-D gel electrophoresis for proteomic investigations. For this purpose we have undertaken the systematic identification of Saccharomyces cerevisiae proteins separated on 2-D gels. We report here the identification by mass spectrometry of 100 novel yeast protein spots that have so far not been tackled due to their scarcity on our standard 2-D gels. These identifications extend the number of protein spots identified on our yeast 2-D proteome map to 716. They correspond to 485 unique proteins. Among these, 154 were resolved into several isoforms. The present data set can now be expanded to report for the first time a map of 363 protein isoforms that significantly deepens our knowledge of the yeast proteome. The reference map and a list of all identified proteins can be accessed on the Yeast Protein Map server (www.ibgc.u-bordeaux2.fr/YPM).

Monthly water balance model for climate change analysis in agriculture with R

NASA Astrophysics Data System (ADS)

Kalicz, Péter; Herceg, András; Gribovszki, Zoltán

2015-04-01

For Hungary regional climate models projections suggest a warmer climate and some changes in annual precipitation distribution. These changes force the whole agrarian sector to consider the traditional cropping technologies. This situation is more serious in forestry because some forest populations are on their xeric distributional limits (Gálos et. al, 2014). Additionally, a decision has an impact sometimes longer than one hundred years. To support the stakeholder there is a project which develops a GIS (Geographic Information System) based decision support system. Hydrology plays significant role in this system because water is often one of the most important limiting factor in Hungary. A modified Thorntwaite-type monthly water balance model was choosen to produce hydrological estimations for the GIS modules. This model is calibrated with the available data between 2000 and 2008. Beside other meteorological data we used mainly an actual evapotranspiration map in the calibration phase, which was derived with the Complementary-relationship-based evapotranspiration mapping (CREMAP; Szilágyi and Kovács, 2011) technique. The calibration process is pixel based and it has several stochastic steps. We try to find a flexible solution for the model implementation which easy to automatize and can be integrate in GIS systems. The open source R programming language was selected which well satisfied these demands. The result of this development is summarized as an R package. This publication has been supported by AGRARKLIMA.2 VKSZ_12-1-2013-0034 project. References Gálos B., Antal V., Czimber K., Mátyás Cs. (2014) Forest ecosystems, sewage works and droughts - possibilities for climate change adaptation. In: Santamarta J.C., Hernandez-Gutiérrez L.E., Arraiza M.P. (eds) 2014. Natural Hazards and Climate Change/Riesgos Naturales y Cambio Climático. Madrid: Colegio de Ingenieros de Montes. ISBN 978-84-617-1060-7, D.L. TF 565-2014, 91-104 pp Szilágyi J., Kovács Á. (2011) A calibration-free evapotranspiration mapping technique for spatially-distributed regional-scale hydrologic modeling, J. Hydrol. Hydromech., 59, 2011, 2, 118-130.

Time-REferenced data Kriging (TREK): mapping hydrological statistics given their time of reference

NASA Astrophysics Data System (ADS)

Porcheron, Delphine; Leblois, Etienne; Sauquet, Eric

2016-04-01

A major issue in water sciences is to predict runoff parameters at ungauged sites. Estimates can be obtained by various methods. Among them, geostatistical approaches provide interpolation methods that consequently use explicit assumptions on the variable of interest. Geostatistical techniques have been applied to precipitation and temperature fields and later extended to estimate runoff features considered as basin-support variates along the river network (e.g. Gottschalk, 1993; Sauquet et al., 2000; Skoien et al., 2006; Gottschalk et al., 2011). To obtain robust estimations, the first step is to collect a relevant dataset. Sauquet et al. (2000) and Sauquet (2006) suggest including a large number of catchments with long and common observation periods to ensure both reliability and temporal consistency in runoff estimates. However most observation networks evolve with time. Several choices are thus possible to define an optimal reference period maximizing either spatial or temporal overlap. However, the constraints usually lead to discard a significant number of stations. Time-REferenced data Kriging method (TREK) has been developed to overcome this issue. Here is proposed a method of geostatistical estimation considering the temporal support over which a hydrological statistic has been estimated. This allows attenuating the loss of data previously caused by the application of a strict reference period. The time reference remains for the targeted map itself. The weights depend on the observation period of the data included in the dataset and how near this is to the target period. In this presentation, the concepts of TREK will be introduced and thereafter illustrated to map mean annual runoff in France. References Gottschalk, L., 1993, Correlation and covariance of runoff. Stochastic Hydrology and Hydraulics 7(2), 85-101. Sauquet, E., Gottschalk, L. and Leblois, E., 2000, Mapping average annual runoff: a hierarchical approach applying a stochastic interpolation scheme. Hydrological Sciences Journal 45(6), 799-815. Skoien, J.O., Merz, R. and Bloschl, G., 2006, Top-kriging - geostatistics on stream networks. Hydrology and Earth System Sciences 10(2), 277-287. Gottschalk, L., Leblois, E. and Skoien, J.O., 2011, Correlation and covariance of runoff revisited. Journal of Hydrology 398(1-2), 76-90. Sauquet, E., 2006, Mapping mean annual river discharges: Geostatistical developments for incorporating river network dependencies. Journal of Hydrology 331(1-2), 300-314.

A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs.

PubMed

Muchero, Wellington; Diop, Ndeye N; Bhat, Prasanna R; Fenton, Raymond D; Wanamaker, Steve; Pottorff, Marti; Hearne, Sarah; Cisse, Ndiaga; Fatokun, Christian; Ehlers, Jeffrey D; Roberts, Philip A; Close, Timothy J

2009-10-27

Consensus genetic linkage maps provide a genomic framework for quantitative trait loci identification, map-based cloning, assessment of genetic diversity, association mapping, and applied breeding in marker-assisted selection schemes. Among "orphan crops" with limited genomic resources such as cowpea [Vigna unguiculata (L.) Walp.] (2n = 2x = 22), the use of transcript-derived SNPs in genetic maps provides opportunities for automated genotyping and estimation of genome structure based on synteny analysis. Here, we report the development and validation of a high-throughput EST-derived SNP assay for cowpea, its application in consensus map building, and determination of synteny to reference genomes. SNP mining from 183,118 ESTs sequenced from 17 cDNA libraries yielded approximately 10,000 high-confidence SNPs from which an Illumina 1,536-SNP GoldenGate genotyping array was developed and applied to 741 recombinant inbred lines from six mapping populations. Approximately 90% of the SNPs were technically successful, providing 1,375 dependable markers. Of these, 928 were incorporated into a consensus genetic map spanning 680 cM with 11 linkage groups and an average marker distance of 0.73 cM. Comparison of this cowpea genetic map to reference legumes, soybean (Glycine max) and Medicago truncatula, revealed extensive macrosynteny encompassing 85 and 82%, respectively, of the cowpea map. Regions of soybean genome duplication were evident relative to the simpler diploid cowpea. Comparison with Arabidopsis revealed extensive genomic rearrangement with some conserved microsynteny. These results support evolutionary closeness between cowpea and soybean and identify regions for synteny-based functional genomics studies in legumes.

Geological mapping of the Kuiper quadrangle (H06) of Mercury

NASA Astrophysics Data System (ADS)

Giacomini, Lorenza; Massironi, Matteo; Galluzzi, Valentina

2017-04-01

Kuiper quadrangle (H06) is located at the equatorial zone of Mercury and encompasses the area between longitudes 288°E - 360°E and latitudes 22.5°N - 22.5°S. The quadrangle was previously mapped for its most part by De Hon et al. (1981) that, using Mariner10 data, produced a final 1:5M scale map of the area. In this work we present the preliminary results of a more detailed geological map (1:3M scale) of the Kuiper quadrangle that we compiled using the higher resolution of MESSENGER data. The main basemap used for the mapping is the MDIS (Mercury Dual Imaging System) 166 m/pixel BDR (map-projected Basemap reduced Data Record) mosaic. Additional datasets were also taken into account, such as DLR stereo-DEM of the region (Preusker et al., 2016), global mosaics with high-incidence illumination from the east and west (Chabot et al., 2016) and MDIS global color mosaic (Denevi et al., 2016). The preliminary geological map shows that the western part of the quadrangle is characterized by a prevalence of crater materials (i.e. crater floor, crater ejecta) which were distinguished into three classes on the basis of their degradation degree (Galluzzi et al., 2016). Different plain units were also identified and classified as: (i) intercrater plains, represented by densely cratered terrains, (ii) intermediate plains, which are terrains with a moderate density of superposed craters, and (iii) smooth plains, which are poorly cratered volcanic deposits emplaced mainly on the larger crater floors. Finally, several structures were mapped all over the quadrangle. Most of these features are represented by thrusts, some of which appear to form systematic alignments. In particular, two main thrust systems have been identified: i) the "Thakur" system, a 1500 km-long system including several scarps with a NNE-SSW orientation, located at the edge between the Kuiper and Beethoven (H07) quadrangles; ii) the "Santa Maria" system, located at the centre of the quadrangle. It is a 1700 km-long system encompassing faults with a prevalent NNW-SSE orientation. Once the mapping activity is accomplished, the geological map of Kuiper quadrangle will be integrated into the global 1:3M geological map of Mercury (Galluzzi et al., 2017). References Chabot et al., 2016, LPS XLVII, #1256. De Hon et al., 1981, IMAP #1233. Denevi et al., 2016 LPS XLVII, #1264. Galluzzi et al., 2016, Geology, J. Maps, 12, 226-238. Galluzzi et al., 2017, EGU General Assembly 2017, #13822. Preusker et al., 2016, Earth and Planet. Astrophys., arXiv:1608.08487.

Teledetection passive et processus decisionnel a reference spatiale: Application a l'aquaculture en milieu marin

NASA Astrophysics Data System (ADS)

Habbane, Mohamed

L'objectif de cette etude est d'elaborer un processus decisionnel a reference spatiale (PDRS) pour la mariculture. Le PDRS est applique aux eaux cotieres de la baie des Chaleurs, dans le golfe du Saint-Laurent (Canada). Une carte preliminaire regionale d'indices du potentiel maricole, d'une limite de resolution spatiale de 1 kmsp2, est produite avec des parametres du niveau 1. Ces parametres englobent la temperature de l'eau de surface, extraite des images AVHRR, la salinite, les courants ainsi que les pigments chlorophylliens, quantifies a l'aide de mesures in situ. Les images AVHRR, prises en 1994, ont ete utiliees comme reference primaire pour selectionner des aires pouvant supporter une activite maricole sur la cote nord de la baie des Chaleurs. La temperature de surface extraite de ces images permet une analyse mesoechelle a la fois qualitative et quantitative des processus cotiers observes pendant la periode d'acquisition des donnees. Les autres donnees, soit la salinite, les courants et les concentrations en pigments chlorophylliens, sont analysees de facon a identifier la variabilite spatio-temporelle des caracteristiques des eaux de surface. L'ensemble des informations permet de produire une carte preliminaire regionale d'indices du potentiel maricole de la partie centrale de la baie des Chaleurs. Selon cet indice (defini entre 0 et 1), le secteur de potentiel aquicole de 0,5 a 0,75 s'etend sur une superficie d'environ 300 kmsp2. La localisation de cette aire potentielle est en accord avec les fortes concentrations en pigments chlrophylliens, presentant des conditions environnementales ideales a une haute productivite biologique. Par la suite la carte preliminaire est modifiee en tenant compte des parametres du niveau 2. Ces parametres sont la geomorphologie littorale, la bathymetrie, les sediments en suspension, les vents, les vagues, le debit d'eau douce, la glace marine, le carbone organique dissous, les aires de peche et les sources de pollution. Ces parametres sont compares deux a deux par rapport a la carte preliminaire regionale d'indices du potentiel maricole pour determiner leur poids relatif. La carte finale produite avec ces parametres du niveau 2 presente un secteur ou les indices du potentiel maricole sont de 0,5 a 0,75. Ce secteur longe la cote et epouse les isobathes de 10 a 30 m de profondeur. L'effet de la profondeur d'eau semble avoir jouer un role important. Le secteur de potentiel maricole de 0,25 a 0,5 est toujours present et couvre une superficie d'environ 426 kmsp2. L'etude necessitera toujours un suivi des conditions environnementales prevalant dans la region. Ce suivi peut etre effectue a l'aide d'un outil de vision aerospatiale (capteurs de teledetection) et d'analyse spatio-temporelle (SIG-PDRS). (Abstract shortened by UMI.)

Superior cognitive mapping through single landmark-related learning than through boundary-related learning.

PubMed

Zhou, Ruojing; Mou, Weimin

2016-08-01

Cognitive mapping is assumed to be through hippocampus-dependent place learning rather than striatum-dependent response learning. However, we proposed that either type of spatial learning, as long as it involves encoding metric relations between locations and reference points, could lead to a cognitive map. Furthermore, the fewer reference points to specify individual locations, the more accurate a cognitive map of these locations will be. We demonstrated that participants have more accurate representations of vectors between 2 locations and of configurations among 3 locations when locations are individually encoded in terms of a single landmark than when locations are encoded in terms of a boundary. Previous findings have shown that learning locations relative to a boundary involve stronger place learning and higher hippocampal activation whereas learning relative to a single landmark involves stronger response learning and higher striatal activation. Recognizing this, we have provided evidence challenging the cognitive map theory but favoring our proposal. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Coalition Information Interoperability (Interoperabilite d’informations de coalition)

DTIC Science & Technology

2008-12-01

rddc.gc.ca FRANCE Dr. Michel Bares DGA/SPDTI/ST/INFO/DSI 18, rue du Docteur Zamenhoff 92131 Issy- Les -Moulineaux e-mail: michel.bares...references reports. ES - 2 RTO-TR-IST-028 Interopérabilité d’informations de coalition (RTO-TR-IST-028) Synthèse Le Groupe Opérationnel (TG...de vue de l’ontologie ; et • La représentation de l’information sous la forme d’importants modèles de données. Les réseaux de communication

Development of Ground Reference GIS for Assessing Land Cover Maps of Northeast Yellowstone National Park

NASA Technical Reports Server (NTRS)

Spruce, Joe; Warner, Amanda; Terrie, Greg; Davis, Bruce

2001-01-01

GIS technology and ground reference data often play vital roles in assessing land cover maps derived from remotely sensed data. This poster illustrates these roles, using results from a study done in Northeast Yellowstone National Park. This area holds many forest, range, and wetland cover types of interest to park managers. Several recent studies have focused on this locale, including the NASA Earth Observations Commercial Applications Program (EOCAP) hyperspectral project performed by Yellowstone Ecosystems Studies (YES) on riparian and in-stream habitat mapping. This poster regards a spin-off to the EOCAP project in which YES and NASA's Earth Science Applications Directorate explored the potential for synergistic use of hyperspecral, synthetic aperture radar, and multiband thermal imagery in mapping land cover types. The project included development of a ground reference GIS for site-specific data needed to evaluate maps from remotely sensed imagery. Field survey data included reflectance of plant communities, native and exotic plant species, and forest health conditions. Researchers also collected GPS points, annotated aerial photographs, and took hand held photographs of reference sites. The use of ESRI, ERDAS, and ENVI software enabled reference data entry into a GIS for comparision to georeferenced imagery and thematic maps. The GIS-based ground reference data layers supported development and assessment of multiple maps from remotely sensed data sets acquired over the study area.

Centimeter-Level Robust Gnss-Aided Inertial Post-Processing for Mobile Mapping Without Local Reference Stations

NASA Astrophysics Data System (ADS)

Hutton, J. J.; Gopaul, N.; Zhang, X.; Wang, J.; Menon, V.; Rieck, D.; Kipka, A.; Pastor, F.

2016-06-01

For almost two decades mobile mapping systems have done their georeferencing using Global Navigation Satellite Systems (GNSS) to measure position and inertial sensors to measure orientation. In order to achieve cm level position accuracy, a technique referred to as post-processed carrier phase differential GNSS (DGNSS) is used. For this technique to be effective the maximum distance to a single Reference Station should be no more than 20 km, and when using a network of Reference Stations the distance to the nearest station should no more than about 70 km. This need to set up local Reference Stations limits productivity and increases costs, especially when mapping large areas or long linear features such as roads or pipelines. An alternative technique to DGNSS for high-accuracy positioning from GNSS is the so-called Precise Point Positioning or PPP method. In this case instead of differencing the rover observables with the Reference Station observables to cancel out common errors, an advanced model for every aspect of the GNSS error chain is developed and parameterized to within an accuracy of a few cm. The Trimble Centerpoint RTX positioning solution combines the methodology of PPP with advanced ambiguity resolution technology to produce cm level accuracies without the need for local reference stations. It achieves this through a global deployment of highly redundant monitoring stations that are connected through the internet and are used to determine the precise satellite data with maximum accuracy, robustness, continuity and reliability, along with advance algorithms and receiver and antenna calibrations. This paper presents a new post-processed realization of the Trimble Centerpoint RTX technology integrated into the Applanix POSPac MMS GNSS-Aided Inertial software for mobile mapping. Real-world results from over 100 airborne flights evaluated against a DGNSS network reference are presented which show that the post-processed Centerpoint RTX solution agrees with the DGNSS solution to better than 2.9 cm RMSE Horizontal and 5.5 cm RMSE Vertical. Such accuracies are sufficient to meet the requirements for a majority of airborne mapping applications.

The Geography Teacher. Volume 4, Number 2, 2007

ERIC Educational Resources Information Center

Geography Teacher, 2007

2007-01-01

"The Geography Teacher" provides hands-on reference and educative material for K-12 Geography teachers. The journal also pioneers innovative ideas for contemporary teaching methods, including lesson plans. This issue contains the following: (1) Ask Dr. de Blij (Dr. Harm de Blij); (2) Improving Geographic Understanding with a State Atlas…

An automated approach to mapping corn from Landsat imagery

USGS Publications Warehouse

Maxwell, S.K.; Nuckols, J.R.; Ward, M.H.; Hoffer, R.M.

2004-01-01

Most land cover maps generated from Landsat imagery involve classification of a wide variety of land cover types, whereas some studies may only need spatial information on a single cover type. For example, we required a map of corn in order to estimate exposure to agricultural chemicals for an environmental epidemiology study. Traditional classification techniques, which require the collection and processing of costly ground reference data, were not feasible for our application because of the large number of images to be analyzed. We present a new method that has the potential to automate the classification of corn from Landsat satellite imagery, resulting in a more timely product for applications covering large geographical regions. Our approach uses readily available agricultural areal estimates to enable automation of the classification process resulting in a map identifying land cover as ‘highly likely corn,’ ‘likely corn’ or ‘unlikely corn.’ To demonstrate the feasibility of this approach, we produced a map consisting of the three corn likelihood classes using a Landsat image in south central Nebraska. Overall classification accuracy of the map was 92.2% when compared to ground reference data.

Preferred Reporting Items for Studies Mapping onto Preference-Based Outcome Measures: The MAPS Statement.

PubMed

Petrou, Stavros; Rivero-Arias, Oliver; Dakin, Helen; Longworth, Louise; Oppe, Mark; Froud, Robert; Gray, Alastair

2015-10-01

'Mapping' onto generic preference-based outcome measures is increasingly being used as a means of generating health utilities for use within health economic evaluations. Despite publication of technical guides for the conduct of mapping research, guidance for the reporting of mapping studies is currently lacking. The MAPS (MApping onto Preference-based measures reporting Standards) statement is a new checklist, which aims to promote complete and transparent reporting of mapping studies. In the absence of previously published reporting checklists or reporting guidance documents, a de novo list of reporting items was created by a working group comprising six health economists and one Delphi methodologist. A two-round, modified Delphi survey, with representatives from academia, consultancy, health technology assessment agencies and the biomedical journal editorial community, was used to identify a list of essential reporting items from this larger list. From the initial de novo list of 29 candidate items, a set of 23 essential reporting items was developed. The items are presented numerically and categorized within six sections: (1) title and abstract; (2) introduction; (3) methods; (4) results; (5) discussion; and (6) other. The MAPS statement is best applied in conjunction with the accompanying MAPS Explanation and Elaboration paper. It is anticipated that the MAPS statement will improve the clarity, transparency and completeness of the reporting of mapping studies. To facilitate dissemination and uptake, the MAPS statement is being co-published by seven health economics and quality-of-life journals, and broader endorsement is encouraged. The MAPS working group plans to assess the need for an update of the reporting checklist in 5 years' time.

Preferred Reporting Items for Studies Mapping onto Preference-Based Outcome Measures: The MAPS Statement.

PubMed

Petrou, Stavros; Rivero-Arias, Oliver; Dakin, Helen; Longworth, Louise; Oppe, Mark; Froud, Robert; Gray, Alastair

2015-08-01

"Mapping" onto generic preference-based outcome measures is increasingly being used as a means of generating health utilities for use within health economic evaluations. Despite the publication of technical guides for the conduct of mapping research, guidance for the reporting of mapping studies is currently lacking. The MAPS (MApping onto Preference-based measures reporting Standards) statement is a new checklist that aims to promote complete and transparent reporting of mapping studies. In the absence of previously published reporting checklists or reporting guidance documents, a de novo list of reporting items was created by a working group comprised of 6 health economists and 1 Delphi methodologist. A 2-round, modified Delphi survey with representatives from academia, consultancy, health technology assessment agencies, and the biomedical journal editorial community was used to identify a list of essential reporting items from this larger list. From the initial de novo list of 29 candidate items, a set of 23 essential reporting items was developed. The items are presented numerically and categorized within 6 sections, namely: (i) title and abstract; (ii) introduction; (iii) methods; (iv) results; (v) discussion; and (vi) other. The MAPS statement is best applied in conjunction with the accompanying MAPS explanation and elaboration document. It is anticipated that the MAPS statement will improve the clarity, transparency, and completeness of reporting of mapping studies. To facilitate dissemination and uptake, the MAPS statement is being co-published by 7 health economics and quality-of-life journals, and broader endorsement is encouraged. The MAPS working group plans to assess the need for an update of the reporting checklist in 5 years.

Genetics Home Reference: congenital central hypoventilation syndrome

MedlinePlus

... M, Stevens CA, Berry-Kravis EM, Weese-Mayer DE. PHOX2B mutation-confirmed congenital central hypoventilation syndrome: presentation ... on PubMed Axelrod FB, Chelimsky GG, Weese-Mayer DE. Pediatric autonomic disorders. Pediatrics. 2006 Jul;118(1): ...

Remote sensing as a mineral prospecting technique

NASA Technical Reports Server (NTRS)

Meneses, P. R. (Principal Investigator)

1984-01-01

Remote sensing and its application as an alternative technique to mineral resource exploration are reviewed. Emphasis is given here to the analysis of the three basic attributes of remote sensing, i.e., spatial attributes related to regional structural mapping, spectral attributes related to rock discrimination and seasonal attributes related to geobotanic anomalies mapping, all of which are employed in mineral exploration. Special emphasis is given to new developments of the Thematic Mapper of the LANDSAT-5, principally with reference to the application of the bands 1.6 and 2.2 microns to map hydrothermally altered rocks and the band of red and blue shift to geobotanical anomalies mapping.

Teamwork in a coronary care unit: facilitating and hindering aspects.

PubMed

Goulart, Bethania Ferreira; Camelo, Silvia Helena Henriques; Simões, Ana Lúcia de Assis; Chaves, Lucieli Dias Pedreschi

2016-01-01

To identify, within a multidisciplinary team, the facilitating and hindering aspects for teamwork in a coronary care unit. A descriptive study, with qualitative and quantitative data, was carried out in the coronary care unit of a public hospital. The study population consisted of professionals working in the unit for at least one year. Those who were on leave or who were not located were excluded. The critical incident technique was used for data collection, by means of semi-structured interviews. For data analysis, content analysis and the critical incident technique were applied. Participants were 45 professionals: 29 nursing professionals; 11 physicians; 4 physical therapists; and 1 psychologist. A total of 49 situations (77.6% with negative references); 385 behaviors (54.2% with positive references); and 182 consequences emerged (71.9% with negative references). Positive references facilitate teamwork, whereas negative references hinder it. A collaborative/communicative interprofessional relationship was evidenced as a facilitator; whereas poor collaboration among agents/inadequate management was a hindering aspect. Despite the prevalence of negative situations and consequences, the emphasis on positive behaviors reveals the efforts the agents make in order to overcome obstacles and carry out teamwork. Identificar, junto à equipe multiprofissional, aspectos facilitadores e dificultadores do trabalho em equipe em Unidade Coronariana. Estudo descritivo, com dados qualitativos e quantitativos, realizado em Unidade Coronariana/Hospital público. População constituída de profissionais atuantes na Unidade há, pelo menos, um ano. Excluídos os afastados do trabalho e os que não foram não localizados. Para a coleta de informações, utilizou-se da Técnica do Incidente Crítico por meio de entrevista semiestruturada. Para a análise dos dados, utilizaram-se da Análise de Conteúdo e Técnica do Incidente Crítico. Participaram 45 profissionais: 29 profissionais de enfermagem; 11 médicos; quatro fisioterapeutas e um psicólogo. Emergiram 49 situações (77,6% com referências negativas); 385 comportamentos (54,2% com referências positivas); e 182 consequências (71,9% com referências negativas). Referências positivas facilitam o trabalho em equipe, e as negativas o dificultam. Relacionamento interprofissional colaborativo/comunicativo foi evidenciado como facilitador; baixa colaboração entre agentes/gerenciamento inadequado como dificultador. Apesar de predominarem situações e consequências negativas, ênfase em comportamentos positivos revela esforço dos agentes para vencer obstáculos e realizar trabalho em equipe.

Importance of Baseline Specification in Evaluating Conservation Interventions and Achieving No Net Loss of Biodiversity

PubMed Central

Bull, J W; Gordon, A; Law, E A; Suttle, K B; Milner-Gulland, E J

2014-01-01

There is an urgent need to improve the evaluation of conservation interventions. This requires specifying an objective and a frame of reference from which to measure performance. Reference frames can be baselines (i.e., known biodiversity at a fixed point in history) or counterfactuals (i.e., a scenario that would have occurred without the intervention). Biodiversity offsets are interventions with the objective of no net loss of biodiversity (NNL). We used biodiversity offsets to analyze the effects of the choice of reference frame on whether interventions met stated objectives. We developed 2 models to investigate the implications of setting different frames of reference in regions subject to various biodiversity trends and anthropogenic impacts. First, a general analytic model evaluated offsets against a range of baseline and counterfactual specifications. Second, a simulation model then replicated these results with a complex real world case study: native grassland offsets in Melbourne, Australia. Both models showed that achieving NNL depended upon the interaction between reference frame and background biodiversity trends. With a baseline, offsets were less likely to achieve NNL where biodiversity was decreasing than where biodiversity was stable or increasing. With a no-development counterfactual, however, NNL was achievable only where biodiversity was declining. Otherwise, preventing development was better for biodiversity. Uncertainty about compliance was a stronger determinant of success than uncertainty in underlying biodiversity trends. When only development and offset locations were considered, offsets sometimes resulted in NNL, but not across an entire region. Choice of reference frame determined feasibility and effort required to attain objectives when designing and evaluating biodiversity offset schemes. We argue the choice is thus of fundamental importance for conservation policy. Our results shed light on situations in which biodiversity offsets may be an inappropriate policy instrument Importancia de la Especificación de Línea de Base en la Evaluación de Intervenciones de Conservación y la Obtención de Ninguna Pérdida Neta de la Biodiversidad PMID:24945031

The IST-05 Reference Model in Evaluation and Design

DTIC Science & Technology

2004-04-01

bits and bytes in a computer memory. To avoid the need for telepathy in manipulating and understanding the data, the IST-05 Reference Model... synthetic views from digital elevation maps and from photographic imagery, but today’s technology makes this possible. Example 2: Instructions for the arrival

Frames of reference for helicopter electronic maps - The relevance of spatial cognition and componential analysis

NASA Technical Reports Server (NTRS)

Harwood, Kelly; Wickens, Christopher D.

1991-01-01

Computer-generated map displays for NOE and low-level helicopter flight were formed according to prior research on maps, navigational problem solving, and spatial cognition in large-scale environments. The north-up map emphasized consistency of object location, wheareas, the track-up map emphasized map-terrain congruency. A component analysis indicates that different cognitive components, e.g., orienting and absolute object location, are supported to varying degrees by properties of different frames of reference.

Do Doppler color flow algorithms for mapping disturbed flow make sense?

PubMed

Gardin, J M; Lobodzinski, S M

1990-01-01

It has been suggested that a major advantage of Doppler color flow mapping is its ability to visualize areas of disturbed ("turbulent") flow, for example, in valvular stenosis or regurgitation and in shunts. To investigate how various color flow mapping instruments display disturbed flow information, color image processing was used to evaluate the most common velocity-variance color encoding algorithms of seven commercially available ultrasound machines. In six of seven machines, green was reportedly added by the variance display algorithms to map areas of disturbed flow. The amount of green intensity added to each pixel along the red and blue portions of the velocity reference color bar was calculated for each machine. In this study, velocities displayed on the reference color bar ranged from +/- 46 to +/- 64 cm/sec, depending on the Nyquist limit. Of note, changing the Nyquist limits depicted on the color reference bars did not change the distribution of the intensities of red, blue, or green within the contour of the reference map, but merely assigned different velocities to the pixels. Most color flow mapping algorithms in our study added increasing intensities of green to increasing positive (red) or negative (blue) velocities along their color reference bars. Most of these machines also added increasing green to red and blue color intensities horizontally across their reference bars as a marker of increased variance (spectral broadening). However, at any given velocity, marked variations were noted between different color flow mapping instruments in the amount of green added to their color velocity reference bars.(ABSTRACT TRUNCATED AT 250 WORDS)

Stratus 12 Twelfth Setting of the Stratus Ocean Reference Station

DTIC Science & Technology

2012-10-01

22 - June 4, 2012 Valparaiso, Chile - Galapagos Islands, Ecuador by Sebastien Bigorre,1 Robert A. Weller,1 Jeff Lord,1 Nancy Galbraith,1 Sean Whelan,1...Institution, Woods Hole, MA 2 Universidad de Concepción, Chile 3 FICOLAB, Universidad de Concepción, Chile 4 National observer, Ecuador 5...Ocean Reference Station at 20°S, 85°W under the stratus clouds west of northern Chile is being maintained to provide ongoing climate-quality records

Increasing the availability of national mapping products.

USGS Publications Warehouse

Roney, J.I.; Ogilvie, B.C.

1981-01-01

A discussion of the means employed by the US Geological Survey to facilitate map usage, covering aspects of project Map Accessibility Program including special rolled and folded map packaging, new market testing, parks and campgrounds program, expanded map dealer program, new booklet-type State sales index and catalog and new USGS map reference code. The USGS is seen as the producer of a tremendous nation-wide inventory of topographic and related map products available in unprecedented types, formats and scales, and as endeavouring to increase access to its products. The new USGS map reference code is appended. -J.C.Stone

Seismic ground motion scenarios in Lower Tagus Valley Basin

NASA Astrophysics Data System (ADS)

Borges, José; Torres, Ricardo; Furtado, José; Silva, Hugo; Caldeira, Bento; Pinto, Carlos; Bezzeghoud, Mourad; Carvalho, João

2013-04-01

Throughout its history the Lower Tagus Valley (LTV) has been struck by several earthquakes which produced important material damage and loss of lives: The 1st of November 1755 Lisbon earthquake and the 1969 earthquake (Mw=7.3), located in the SW Iberia Margin and the 1344, 1531 and 1909 (M= 6 to 7) with epicenter located inside the LTV basin. Since this region is the most highly populated region in Portugal, it is expected that an earthquake of similar magnitude of those that have occurred in the past will cause an enormous destruction and casualties. This fact makes LTV a high priority area for earthquake research in Portugal. In order to overcome the problems related to the absence of geological outcrops, low slip-rates (<0,4 mm/year) and the processes of sedimentation and erosion, we use in this work seismic reflection profiles, potential field data, soundings, wells and geological cartography to obtain a map of the main seismogenic structures and to characterize their seismic potential [1]. Moreover, a 3D structural model has been developed for de LTV based on Seismic reflection, Seismic Noise and potential field data [2,3]. In order to improve assessment of the seismic hazard in the LTV basin, we simulate long-period (0-1 Hz) ground motion time histories for a suite of scenarios earthquakes (Mw =5.5 to 7) within the basin, using fault geometries and the 3D seismic velocity structure based on the previous mentioned works. References [1] Pinto, Carlos C. (2011). Identification of Seismogenic Structures in the Lower Tagus Basin. Master Thesis, Universidade de Évora, 128 pp. [2] Torres, R.J.G., (2012). Modelo de velocidade da Bacia do Vale do Tejo: uma abordagem baseada no estudo do ruído sísmico ambiental, Master Thesis, Universidade de Évora, 83pp. [3] Furtado, J.A (2010). Confirmação do modelo da estrutura 3D do Vale Inverior do Tejo a partir de dados de ruído sísmico ambiente, Master Thesis, Universidade de Évora, 136pp.

ABACAS: algorithm-based automatic contiguation of assembled sequences

PubMed Central

Assefa, Samuel; Keane, Thomas M.; Otto, Thomas D.; Newbold, Chris; Berriman, Matthew

2009-01-01

Summary: Due to the availability of new sequencing technologies, we are now increasingly interested in sequencing closely related strains of existing finished genomes. Recently a number of de novo and mapping-based assemblers have been developed to produce high quality draft genomes from new sequencing technology reads. New tools are necessary to take contigs from a draft assembly through to a fully contiguated genome sequence. ABACAS is intended as a tool to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. The input to ABACAS is a set of contigs which will be aligned to the reference genome, ordered and orientated, visualized in the ACT comparative browser, and optimal primer sequences are automatically generated. Availability and Implementation: ABACAS is implemented in Perl and is freely available for download from http://abacas.sourceforge.net Contact: sa4@sanger.ac.uk PMID:19497936

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

PubMed

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

2016-07-07

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

Protecting the privacy of individual general practice patient electronic records for geospatial epidemiology research.

PubMed

Mazumdar, Soumya; Konings, Paul; Hewett, Michael; Bagheri, Nasser; McRae, Ian; Del Fante, Peter

2014-12-01

General practitioner (GP) practices in Australia are increasingly storing patient information in electronic databases. These practice databases can be accessed by clinical audit software to generate reports that inform clinical or population health decision making and public health surveillance. Many audit software applications also have the capacity to generate de-identified patient unit record data. However, the de-identified nature of the extracted data means that these records often lack geographic information. Without spatial references, it is impossible to build maps reflecting the spatial distribution of patients with particular conditions and needs. Links to socioeconomic, demographic, environmental or other geographically based information are also not possible. In some cases, relatively coarse geographies such as postcode are available, but these are of limited use and researchers cannot undertake precision spatial analyses such as calculating travel times. We describe a method that allows researchers to implement meaningful mapping and spatial epidemiological analyses of practice level patient data while preserving privacy. This solution has been piloted in a diabetes risk research project in the patient population of a practice in Adelaide. The method offers researchers a powerful means of analysing geographic clinic data in a privacy-protected manner. © 2014 Public Health Association of Australia.

Improved Digitization of Lunar Mare Ridges with LROC Derived Products

NASA Astrophysics Data System (ADS)

Crowell, J. M.; Robinson, M. S.; Watters, T. R.; Bowman-Cisneros, E.; Enns, A. C.; Lawrence, S.

2011-12-01

Lunar wrinkle ridges (mare ridges) are positive-relief structures formed from compressional stress in basin-filling flood basalt deposits [1]. Previous workers have measured wrinkle ridge orientations and lengths to investigate their spatial distribution and infer basin-localized stress fields [2,3]. Although these plots include the most prominent mare ridges and their general trends, they may not have fully captured all of the ridges, particularly the smaller-scale ridges. Using Lunar Reconnaissance Orbiter Wide Angle Camera (WAC) global mosaics and derived topography (100m pixel scale) [4], we systematically remapped wrinkle ridges in Mare Serenitatis. By comparing two WAC mosaics with different lighting geometry, and shaded relief maps made from a WAC digital elevation model (DEM) [5], we observed that some ridge segments and some smaller ridges are not visible in previous structure maps [2,3]. In the past, mapping efforts were limited by a fixed Sun direction [6,7]. For systematic mapping we created three shaded relief maps from the WAC DEM with solar azimuth angles of 0°, 45°, and 90°, and a fourth map was created by combining the three shaded reliefs into one, using a simple averaging scheme. Along with the original WAC mosaic and the WAC DEM, these four datasets were imported into ArcGIS, and the mare ridges of Imbrium, Serenitatis, and Tranquillitatis were digitized from each of the six maps. Since the mare ridges are often divided into many ridge segments [8], each major component was digitized separately, as opposed to the ridge as a whole. This strategy enhanced our ability to analyze the lengths, orientations, and abundances of these ridges. After the initial mapping was completed, the six products were viewed together to identify and resolve discrepancies in order to produce a final wrinkle ridge map. Comparing this new mare ridge map with past lunar tectonic maps, we found that many mare ridges were not recorded in the previous works. It was noted in some cases, the lengths and orientations of previously digitized ridges were different than those of the ridges digitized in this study. This method of multi-map digitizing allows for a greater accuracy in spatial characterization of mare ridges than previous methods. We intend to map mare ridges on a global scale, creating a more comprehensive ridge map due to higher resolution. References Cited: [1] Schultz P.H. (1976) Moon Morphology, 308. [2] Wilhelms D.E. (1987) USGS Prof. Paper 1348, 5A-B. [3] Carr, M.H. (1966) USGS Geologic Atlas of the Moon, I-498. [4] Robinson M.S. (2010) Space Sci. Rev., 150:82. [5] Scholten F. et al. (2011) LPSC XLII, 2046. [6] Fielder G. and Kiang T. (1962) The Observatory: No. 926, 8. [7] Watters T.R. and Konopliv A.S. (2001) Planetary and Space Sci. 49. 743-748. [8] Aubele J.C. (1988) LPSC XIX, 19.

Development of the first consensus genetic map of intermediate wheatgrass (Thinopyrum intermedium) using genotyping-by-sequencing.

PubMed

Kantarski, Traci; Larson, Steve; Zhang, Xiaofei; DeHaan, Lee; Borevitz, Justin; Anderson, James; Poland, Jesse

2017-01-01

Development of the first consensus genetic map of intermediate wheatgrass gives insight into the genome and tools for molecular breeding. Intermediate wheatgrass (Thinopyrum intermedium) has been identified as a candidate for domestication and improvement as a perennial grain, forage, and biofuel crop and is actively being improved by several breeding programs. To accelerate this process using genomics-assisted breeding, efficient genotyping methods and genetic marker reference maps are needed. We present here the first consensus genetic map for intermediate wheatgrass (IWG), which confirms the species' allohexaploid nature (2n = 6x = 42) and homology to Triticeae genomes. Genotyping-by-sequencing was used to identify markers that fit expected segregation ratios and construct genetic maps for 13 heterogeneous parents of seven full-sib families. These maps were then integrated using a linear programming method to produce a consensus map with 21 linkage groups containing 10,029 markers, 3601 of which were present in at least two populations. Each of the 21 linkage groups contained between 237 and 683 markers, cumulatively covering 5061 cM (2891 cM--Kosambi) with an average distance of 0.5 cM between each pair of markers. Through mapping the sequence tags to the diploid (2n = 2x = 14) barley reference genome, we observed high colinearity and synteny between these genomes, with three homoeologous IWG chromosomes corresponding to each of the seven barley chromosomes, and mapped translocations that are known in the Triticeae. The consensus map is a valuable tool for wheat breeders to map important disease-resistance genes within intermediate wheatgrass. These genomic tools can help lead to rapid improvement of IWG and development of high-yielding cultivars of this perennial grain that would facilitate the sustainable intensification of agricultural systems.

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

PubMed Central

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

2016-01-01

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

Young Children's Intonational Marking of New, Given and Contrastive Referents

ERIC Educational Resources Information Center

Grünloh, Thomas; Lieven, Elena; Tomasello, Michael

2015-01-01

In the current study we investigate whether 2- and 3-year-old German children use intonation productively to mark the informational status of referents. Using a story-telling task, we compared children's and adults' intonational realization via pitch accent (H*, L* and de-accentuation) of New, Given, and Contrastive referents. Both children and…

Method and system for a network mapping service

DOEpatents

Bynum, Leo

2017-10-17

A method and system of publishing a map includes providing access to a plurality of map data files or mapping services between at least one publisher and at least one subscriber; defining a map in a map context comprising parameters and descriptors to substantially duplicate a map by reference to mutually accessible data or mapping services, publishing a map to a channel in a table file on server; accessing the channel by at least one subscriber, transmitting the mapping context from the server to the at least one subscriber, executing the map context by the at least one subscriber, and generating the map on a display software associated with the at least one subscriber by reconstituting the map from the references and other data in the mapping context.

The Geography Teacher. Volume 6, Number 2, 2009

ERIC Educational Resources Information Center

Geography Teacher, 2009

2009-01-01

"The Geography Teacher" provides hands-on reference and educative material for K-12 Geography teachers. The journal also pioneers innovative ideas for contemporary teaching methods, including lesson plans. This issue contains the following: (1) Census in Schools Program (census.gov); (2) Ask Dr. de Blij (Dr. Harm de Blij); (3) Eritrea:…

The Geography Teacher. Volume 5, Number 2, 2008

ERIC Educational Resources Information Center

Geography Teacher, 2008

2008-01-01

"The Geography Teacher" provides hands-on reference and educative material for K-12 Geography teachers. The journal also pioneers innovative ideas for contemporary teaching methods, including lesson plans. This issue contains the following: (1) Ask Dr. de Blij (Harm de Blij); (2) Geography: Is it a Boy's Subject? (Lisa Smitreski); (3) A…

Mapping the mineralogy and lithology of Canyonlands, Utah with imaging spectrometer data and the multiple spectral feature mapping algorithm

NASA Technical Reports Server (NTRS)

Clark, Roger N.; Swayze, Gregg A.; Gallagher, Andrea

1992-01-01

The sedimentary sections exposed in the Canyonlands and Arches National Parks region of Utah (generally referred to as 'Canyonlands') consist of sandstones, shales, limestones, and conglomerates. Reflectance spectra of weathered surfaces of rocks from these areas show two components: (1) variations in spectrally detectable mineralogy, and (2) variations in the relative ratios of the absorption bands between minerals. Both types of information can be used together to map each major lithology and the Clark spectral features mapping algorithm is applied to do the job.

A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea

PubMed Central

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

2015-01-01

We identified 44844 high-quality SNPs by sequencing 92 diverse chickpea accessions belonging to a seed and pod trait-specific association panel using reference genome- and de novo-based GBS (genotyping-by-sequencing) assays. A GWAS (genome-wide association study) in an association panel of 211, including the 92 sequenced accessions, identified 22 major genomic loci showing significant association (explaining 23–47% phenotypic variation) with pod and seed number/plant and 100-seed weight. Eighteen trait-regulatory major genomic loci underlying 13 robust QTLs were validated and mapped on an intra-specific genetic linkage map by QTL mapping. A combinatorial approach of GWAS, QTL mapping and gene haplotype-specific LD mapping and transcript profiling uncovered one superior haplotype and favourable natural allelic variants in the upstream regulatory region of a CesA-type cellulose synthase (Ca_Kabuli_CesA3) gene regulating high pod and seed number/plant (explaining 47% phenotypic variation) in chickpea. The up-regulation of this superior gene haplotype correlated with increased transcript expression of Ca_Kabuli_CesA3 gene in the pollen and pod of high pod/seed number accession, resulting in higher cellulose accumulation for normal pollen and pollen tube growth. A rapid combinatorial genome-wide SNP genotyping-based approach has potential to dissect complex quantitative agronomic traits and delineate trait-regulatory genomic loci (candidate genes) for genetic enhancement in crop plants, including chickpea. PMID:26058368

Karstic Phenomena Susceptibility Map of MÉXICO

NASA Astrophysics Data System (ADS)

Espinasa-Pereña, R.

2013-05-01

Approximately 20% of the territory of México is underlain by karstifiable rocks, mostly limestones and in lesser proportions gypsum. The majority of these rocks are distributed along the eastern and southern Sierra Madre, the state of Chiapas and the Yucatán peninsula. Differences in geological structure, climate and geomorphic history have resulted in a great variety of karstic landscapes and types of forms. Several important population centers, including large cities with several million inhabitants and numerous smaller towns are built on karstic terrains and obtain their water supplies from karstic aquifers and/or dispose of their waste products on this type of terrain. Severe problems of waste disposal and aquifer contamination have occurred. Additionally, numerous instances of catastrophic collapse and formation of karstic sinkholes have been registered in the Mexican territory, which have affected many communities, roads and other infrastructure, and have even cost several lives. Lack of knowledge of the special characteristics of karstic terrains and their distribution has compounded these problems. As a first approach to these issues, the existing map of Mexican karst (Espinasa-Pereña, 2007) was modified according to the geotechnical classification proposed by Waltham & Fookes (2003). An important consideration taken into account is the difference in speed of development of karstic features depending on lithology, which makes karst developed in gypsum much more hazardous than limestone karst, and also the degree of soil coverage and the types of sinkholes developed on the cover. Also taken in consideration are the differences between karst developed in the Sierra Madre, with rocks highly deformed and fractured, and karst developed on the Yucatán peninsula with almost negligible deformation of the rocks. The resulting map will be useful to Civil Protection authorities as a tool in prognosticating possible affectations due to karstic phenomena. References: ESPINASA-PEREÑA, R., 2007, "El Karst de México", Mapa NA III 3, in Coll-Hurtado, A., Coord., "Nuevo Atlas Nacional de México", Instituto de Geografía, Universidad Nacional Autónoma de México. WALTHAM, A.C. and FOOKES, P.G., 2003, Engineering classification of karst ground conditions, Quarterly Journal of Engineering Geology and Hydrology, Vol. 36, pp. 101-118.

A reference linkage map for Eucalyptus

PubMed Central

2012-01-01

Background Genetic linkage maps are invaluable resources in plant research. They provide a key tool for many genetic applications including: mapping quantitative trait loci (QTL); comparative mapping; identifying unlinked (i.e. independent) DNA markers for fingerprinting, population genetics and phylogenetics; assisting genome sequence assembly; relating physical and recombination distances along the genome and map-based cloning of genes. Eucalypts are the dominant tree species in most Australian ecosystems and of economic importance globally as plantation trees. The genome sequence of E. grandis has recently been released providing unprecedented opportunities for genetic and genomic research in the genus. A robust reference linkage map containing sequence-based molecular markers is needed to capitalise on this resource. Several high density linkage maps have recently been constructed for the main commercial forestry species in the genus (E. grandis, E. urophylla and E. globulus) using sequenced Diversity Arrays Technology (DArT) and microsatellite markers. To provide a single reference linkage map for eucalypts a composite map was produced through the integration of data from seven independent mapping experiments (1950 individuals) using a marker-merging method. Results The composite map totalled 1107 cM and contained 4101 markers; comprising 3880 DArT, 213 microsatellite and eight candidate genes. Eighty-one DArT markers were mapped to two or more linkage groups, resulting in the 4101 markers being mapped to 4191 map positions. Approximately 13% of DArT markers mapped to identical map positions, thus the composite map contained 3634 unique loci at an average interval of 0.31 cM. Conclusion The composite map represents the most saturated linkage map yet produced in Eucalyptus. As the majority of DArT markers contained on the map have been sequenced, the map provides a direct link to the E. grandis genome sequence and will serve as an important reference for progressing eucalypt research. PMID:22702473

De novo transcriptome assembly analysis of weed Apera spica-venti from seven tissues and growth stages.

PubMed

Babineau, Marielle; Mahmood, Khalid; Mathiassen, Solvejg K; Kudsk, Per; Kristensen, Michael

2017-02-06

Loose silky bentgrass (Apera spica-venti) is an important weed in Europe with a recent increase in herbicide resistance cases. The lack of genetic information about this noxious weed limits its biological understanding such as growth, reproduction, genetic variation, molecular ecology and metabolic herbicide resistance. This study produced a reference transcriptome for A. spica-venti from different tissues (leaf, root, stem) and various growth stages (seed at phenological stages 05, 07, 08, 09). The de novo assembly was performed on individual and combined dataset followed by functional annotations. Individual transcripts and gene families involved in metabolic based herbicide resistance were identified. Eight separate transcriptome assemblies were performed and compared. The combined transcriptome assembly consists of 83,349 contigs with an N50 and average contig length of 762 and 658 bp, respectively. This dataset contains 74,724 transcripts consisting of total 54,846,111 bp. Among them 94% had a homologue to UniProtKB, 73% retrieved a GO mapping, and 50% were functionally annotated. Compared with other grass species, A. spica-venti has 26% proteins in common to Brachypodium distachyon, and 41% to Lolium spp. Glycosyltransferases had the highest number of transcripts in each tissue followed by the cytochrome P450s. The GSTF1 and CYP89A2 transcripts were recovered from the majority of tissues and aligned at a maximum of 66 and 30% to proven herbicide resistant allele from Alopecurus myosuroides and Lolium rigidum, respectively. De novo transcriptome assembly enabled the generation of the first reference transcriptome of A. spica-venti. This can serve as stepping stone for understanding the metabolic herbicide resistance as well as the general biology of this problematic weed. Furthermore, this large-scale sequence data is a valuable scientific resource for comparative transcriptome analysis for Poaceae grasses.

Linkage Map of Escherichia coli K-12, Edition 10: The Traditional Map

PubMed Central

Berlyn, Mary K. B.

1998-01-01

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715–1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included. PMID:9729611

Motion-induced error reduction by combining Fourier transform profilometry with phase-shifting profilometry.

PubMed

Li, Beiwen; Liu, Ziping; Zhang, Song

2016-10-03

We propose a hybrid computational framework to reduce motion-induced measurement error by combining the Fourier transform profilometry (FTP) and phase-shifting profilometry (PSP). The proposed method is composed of three major steps: Step 1 is to extract continuous relative phase maps for each isolated object with single-shot FTP method and spatial phase unwrapping; Step 2 is to obtain an absolute phase map of the entire scene using PSP method, albeit motion-induced errors exist on the extracted absolute phase map; and Step 3 is to shift the continuous relative phase maps from Step 1 to generate final absolute phase maps for each isolated object by referring to the absolute phase map with error from Step 2. Experiments demonstrate the success of the proposed computational framework for measuring multiple isolated rapidly moving objects.

RNA-Seq analysis and transcriptome assembly for blackberry (Rubus sp. Var. Lochness) fruit.

PubMed

Garcia-Seco, Daniel; Zhang, Yang; Gutierrez-Mañero, Francisco J; Martin, Cathie; Ramos-Solano, Beatriz

2015-01-22

There is an increasing interest in berries, especially blackberries in the diet, because of recent reports of their health benefits due to their high content of flavonoids. A broad range of genomic tools are available for other Rosaceae species but these tools are still lacking in the Rubus genus, thus limiting gene discovery and the breeding of improved varieties. De novo RNA-seq of ripe blackberries grown under field conditions was performed using Illumina Hiseq 2000. Almost 9 billion nucleotide bases were sequenced in total. Following assembly, 42,062 consensus sequences were detected. For functional annotation, 33,040 (NR), 32,762 (NT), 21,932 (Swiss-Prot), 20,134 (KEGG), 13,676 (COG), 24,168 (GO) consensus sequences were annotated using different databases; in total 34,552 annotated sequences were identified. For protein prediction analysis, the number of coding DNA sequences (CDS) that mapped to the protein database was 32,540. Non redundant (NR), annotation showed that 25,418 genes (73.5%) has the highest similarity with Fragaria vesca subspecies vesca. Reanalysis was undertaken by aligning the reads with this reference genome for a deeper analysis of the transcriptome. We demonstrated that de novo assembly, using Trinity and later annotation with Blast using different databases, were complementary to alignment to the reference sequence using SOAPaligner/SOAP2. The Fragaria reference genome belongs to a species in the same family as blackberry (Rosaceae) but to a different genus. Since blackberries are tetraploids, the possibility of artefactual gene chimeras resulting from mis-assembly was tested with one of the genes sequenced by RNAseq, Chalcone Synthase (CHS). cDNAs encoding this protein were cloned and sequenced. Primers designed to the assembled sequences accurately distinguished different contigs, at least for chalcone synthase genes. We prepared and analysed transcriptome data from ripe blackberries, for which prior genomic information was limited. This new sequence information will improve the knowledge of this important and healthy fruit, providing an invaluable new tool for biological research.

Preferred reporting items for studies mapping onto preference-based outcome measures: the MAPS statement.

PubMed

Petrou, Stavros; Rivero-Arias, Oliver; Dakin, Helen; Longworth, Louise; Oppe, Mark; Froud, Robert; Gray, Alastair

2016-02-01

'Mapping' onto generic preference-based outcome measures is increasingly being used as a means of generating health utilities for use within health economic evaluations. Despite publication of technical guides for the conduct of mapping research, guidance for the reporting of mapping studies is currently lacking. The MApping onto Preference-based measures reporting Standards (MAPS) statement is a new checklist, which aims to promote complete and transparent reporting of mapping studies. In the absence of previously published reporting checklists or reporting guidance documents, a de novo list of reporting items was created by a working group comprised of six health economists and one Delphi methodologist. A two-round, modified Delphi survey with representatives from academia, consultancy, health technology assessment agencies and the biomedical journal editorial community was used to identify a list of essential reporting items from this larger list. From the initial de novo list of 29 candidate items, a set of 23 essential reporting items was developed. The items are presented numerically and categorised within six sections, namely (1) title and abstract; (2) introduction; (3) methods; (4) results; (5) discussion; and (6) other. The MAPS statement is best applied in conjunction with the accompanying MAPS explanation and elaboration document. It is anticipated that the MAPS statement will improve the clarity, transparency and completeness of reporting of mapping studies. To facilitate dissemination and uptake, the MAPS statement is being co-published by seven health economics and quality of life journals, and broader endorsement is encouraged. The MAPS working group plans to assess the need for an update of the reporting checklist in 5 years' time.

GPU-Accelerated Optical Coherence Tomography Signal Processing and Visualization

NASA Astrophysics Data System (ADS)

Darbrazi, Seyed Hamid Hosseiny

As piroxenas sao um vasto grupo de silicatos minerais encontrados em muitas rochas igneas e metamorficas. Na sua forma mais simples, estes silicatos sao constituidas por cadeias de SiO3 ligando grupos tetrahedricos de SiO4. A formula quimica geral das piroxenas e M2M1T2O6, onde M2 se refere a catioes geralmente em uma coordenacao octaedrica distorcida (Mg2+, Fe2+, Mn2+, Li+, Ca2+, Na+), M1 refere-se a catioes numa coordenacao octaedrica regular (Al3+, Fe3+, Ti4+, Cr3+, V3+, Ti3+, Zr4+, Sc3+, Zn2+, Mg2+, Fe2+, Mn2+), e T a catioes em coordenacao tetrahedrica (Si4+, Al3+, Fe3+). As piroxenas com estrutura monoclinica sao designadas de clinopiroxenes. A estabilidade das clinopyroxenes num espectro de composicoes quimicas amplo, em conjugacao com a possibilidade de ajustar as suas propriedades fisicas e quimicas e a durabilidade quimica, tem gerado um interesse mundial devido a suas aplicacoes em ciencia e tecnologia de materiais. Este trabalho trata do desenvolvimento de vidros e de vitro-cerâmicos baseadas de clinopiroxenas para aplicacoes funcionais. O estudo teve objectivos cientificos e tecnologicos; nomeadamente, adquirir conhecimentos fundamentais sobre a formacao de fases cristalinas e solucoes solidas em determinados sistemas vitro-cerâmicos, e avaliar a viabilidade de aplicacao dos novos materiais em diferentes areas tecnologicas, com especial enfase sobre a selagem em celulas de combustivel de oxido solido (SOFC). Com este intuito, prepararam-se varios vidros e materiais vitro-cerâmicos ao longo das juntas Enstatite (MgSiO3) - diopsidio (CaMgSi2O6) e diopsidio (CaMgSi2O6) - Ca - Tschermak (CaAlSi2O6), os quais foram caracterizados atraves de um vasto leque de tecnicas. Todos os vidros foram preparados por fusao-arrefecimento enquanto os vitro-cerâmicos foram obtidos quer por sinterizacao e cristalizacao de fritas, quer por nucleacao e cristalizacao de vidros monoliticos. Estudaram-se ainda os efeitos de varias substituicoes ionicas em composicoes de diopsidio contendo Al na estrutura, sinterizacao e no comportamento durante a cristalizacao de vidros e nas propriedades dos materiais vitro-cerâmicos, com relevância para a sua aplicacao como selantes em SOFC. Verificou-se que Foi observado que os vidros/vitro-cerâmicos a base de enstatite nao apresentavam as caracteristicas necessarias para serem usados como materiais selantes em SOFC, enquanto as melhores propriedades apresentadas pelos vitro-cerâmicos a base de diopsidio qualificaram-nos para futuros estudos neste tipo de aplicacoes. Para alem de investigar a adequacao dos vitro-cerâmicos a base de clinopyroxene como selantes, esta tese tem tambem como objetivo estudar a influencia dos agentes de nucleacao na nucleacao em volume dos vitro-cerâmicos resultantes a base de diopsidio, de modo a qualifica-los como potenciais materiais hopedeiros de residuos nucleares radioactivos.

Albumin and fibronectin adsorption and osteoblast adhesion on titanium oxides

NASA Astrophysics Data System (ADS)

Freitas, Susana Maria Ribeiro e. Sousa Mendes de

As piroxenas sao um vasto grupo de silicatos minerais encontrados em muitas rochas igneas e metamorficas. Na sua forma mais simples, estes silicatos sao constituidas por cadeias de SiO3 ligando grupos tetrahedricos de SiO4. A formula quimica geral das piroxenas e M2M1T2O6, onde M2 se refere a catioes geralmente em uma coordenacao octaedrica distorcida (Mg2+, Fe2+, Mn2+, Li+, Ca2+, Na+), M1 refere-se a catioes numa coordenacao octaedrica regular (Al3+, Fe3+, Ti4+, Cr3+, V3+, Ti3+, Zr4+, Sc3+, Zn2+, Mg2+, Fe2+, Mn2+), e T a catioes em coordenacao tetrahedrica (Si4+, Al3+, Fe3+). As piroxenas com estrutura monoclinica sao designadas de clinopiroxenes. A estabilidade das clinopyroxenes num espectro de composicoes quimicas amplo, em conjugacao com a possibilidade de ajustar as suas propriedades fisicas e quimicas e a durabilidade quimica, tem gerado um interesse mundial devido a suas aplicacoes em ciencia e tecnologia de materiais. Este trabalho trata do desenvolvimento de vidros e de vitro-cerâmicos baseadas de clinopiroxenas para aplicacoes funcionais. O estudo teve objectivos cientificos e tecnologicos; nomeadamente, adquirir conhecimentos fundamentais sobre a formacao de fases cristalinas e solucoes solidas em determinados sistemas vitro-cerâmicos, e avaliar a viabilidade de aplicacao dos novos materiais em diferentes areas tecnologicas, com especial enfase sobre a selagem em celulas de combustivel de oxido solido (SOFC). Com este intuito, prepararam-se varios vidros e materiais vitro-cerâmicos ao longo das juntas Enstatite (MgSiO3) - diopsidio (CaMgSi2O6) e diopsidio (CaMgSi2O6) - Ca - Tschermak (CaAlSi2O6), os quais foram caracterizados atraves de um vasto leque de tecnicas. Todos os vidros foram preparados por fusao-arrefecimento enquanto os vitro-cerâmicos foram obtidos quer por sinterizacao e cristalizacao de fritas, quer por nucleacao e cristalizacao de vidros monoliticos. Estudaram-se ainda os efeitos de varias substituicoes ionicas em composicoes de diopsidio contendo Al na estrutura, sinterizacao e no comportamento durante a cristalizacao de vidros e nas propriedades dos materiais vitro-cerâmicos, com relevância para a sua aplicacao como selantes em SOFC. Verificou-se que Foi observado que os vidros/vitro-cerâmicos a base de enstatite nao apresentavam as caracteristicas necessarias para serem usados como materiais selantes em SOFC, enquanto as melhores propriedades apresentadas pelos vitro-cerâmicos a base de diopsidio qualificaram-nos para futuros estudos neste tipo de aplicacoes. Para alem de investigar a adequacao dos vitro-cerâmicos a base de clinopyroxene como selantes, esta tese tem tambem como objetivo estudar a influencia dos agentes de nucleacao na nucleacao em volume dos vitro-cerâmicos resultantes a base de diopsidio, de modo a qualifica-los como potenciais materiais hopedeiros de residuos nucleares radioactivos.

Birefringence and Bragg grating control in femtosecond laser written optical circuits

NASA Astrophysics Data System (ADS)

Fernandes, Luis A.

As piroxenas sao um vasto grupo de silicatos minerais encontrados em muitas rochas igneas e metamorficas. Na sua forma mais simples, estes silicatos sao constituidas por cadeias de SiO3 ligando grupos tetrahedricos de SiO4. A formula quimica geral das piroxenas e M2M1T2O6, onde M2 se refere a catioes geralmente em uma coordenacao octaedrica distorcida (Mg2+, Fe2+, Mn2+, Li+, Ca2+, Na+), M1 refere-se a catioes numa coordenacao octaedrica regular (Al3+, Fe3+, Ti4+, Cr3+, V3+, Ti3+, Zr4+, Sc3+, Zn2+, Mg2+, Fe2+, Mn2+), e T a catioes em coordenacao tetrahedrica (Si4+, Al3+, Fe3+). As piroxenas com estrutura monoclinica sao designadas de clinopiroxenes. A estabilidade das clinopyroxenes num espectro de composicoes quimicas amplo, em conjugacao com a possibilidade de ajustar as suas propriedades fisicas e quimicas e a durabilidade quimica, tem gerado um interesse mundial devido a suas aplicacoes em ciencia e tecnologia de materiais. Este trabalho trata do desenvolvimento de vidros e de vitro-cerâmicos baseadas de clinopiroxenas para aplicacoes funcionais. O estudo teve objectivos cientificos e tecnologicos; nomeadamente, adquirir conhecimentos fundamentais sobre a formacao de fases cristalinas e solucoes solidas em determinados sistemas vitro-cerâmicos, e avaliar a viabilidade de aplicacao dos novos materiais em diferentes areas tecnologicas, com especial enfase sobre a selagem em celulas de combustivel de oxido solido (SOFC). Com este intuito, prepararam-se varios vidros e materiais vitro-cerâmicos ao longo das juntas Enstatite (MgSiO3) - diopsidio (CaMgSi2O6) e diopsidio (CaMgSi2O6) - Ca - Tschermak (CaAlSi2O6), os quais foram caracterizados atraves de um vasto leque de tecnicas. Todos os vidros foram preparados por fusao-arrefecimento enquanto os vitro-cerâmicos foram obtidos quer por sinterizacao e cristalizacao de fritas, quer por nucleacao e cristalizacao de vidros monoliticos. Estudaram-se ainda os efeitos de varias substituicoes ionicas em composicoes de diopsidio contendo Al na estrutura, sinterizacao e no comportamento durante a cristalizacao de vidros e nas propriedades dos materiais vitro-cerâmicos, com relevância para a sua aplicacao como selantes em SOFC. Verificou-se que Foi observado que os vidros/vitro-cerâmicos a base de enstatite nao apresentavam as caracteristicas necessarias para serem usados como materiais selantes em SOFC, enquanto as melhores propriedades apresentadas pelos vitro-cerâmicos a base de diopsidio qualificaram-nos para futuros estudos neste tipo de aplicacoes. Para alem de investigar a adequacao dos vitro-cerâmicos a base de clinopyroxene como selantes, esta tese tem tambem como objetivo estudar a influencia dos agentes de nucleacao na nucleacao em volume dos vitro-cerâmicos resultantes a base de diopsidio, de modo a qualifica-los como potenciais materiais hopedeiros de residuos nucleares radioactivos.

Single Point Incremental Forming and Multi-Stage Incremental Forming on Aluminium Alloy 1050

NASA Astrophysics Data System (ADS)

Suriyaprakan, Premika

As piroxenas sao um vasto grupo de silicatos minerais encontrados em muitas rochas igneas e metamorficas. Na sua forma mais simples, estes silicatos sao constituidas por cadeias de SiO3 ligando grupos tetrahedricos de SiO4. A formula quimica geral das piroxenas e M2M1T2O6, onde M2 se refere a catioes geralmente em uma coordenacao octaedrica distorcida (Mg2+, Fe2+, Mn2+, Li+, Ca2+, Na+), M1 refere-se a catioes numa coordenacao octaedrica regular (Al3+, Fe3+, Ti4+, Cr3+, V3+, Ti3+, Zr4+, Sc3+, Zn2+, Mg2+, Fe2+, Mn2+), e T a catioes em coordenacao tetrahedrica (Si4+, Al3+, Fe3+). As piroxenas com estrutura monoclinica sao designadas de clinopiroxenes. A estabilidade das clinopyroxenes num espectro de composicoes quimicas amplo, em conjugacao com a possibilidade de ajustar as suas propriedades fisicas e quimicas e a durabilidade quimica, tem gerado um interesse mundial devido a suas aplicacoes em ciencia e tecnologia de materiais. Este trabalho trata do desenvolvimento de vidros e de vitro-cerâmicos baseadas de clinopiroxenas para aplicacoes funcionais. O estudo teve objectivos cientificos e tecnologicos; nomeadamente, adquirir conhecimentos fundamentais sobre a formacao de fases cristalinas e solucoes solidas em determinados sistemas vitro-cerâmicos, e avaliar a viabilidade de aplicacao dos novos materiais em diferentes areas tecnologicas, com especial enfase sobre a selagem em celulas de combustivel de oxido solido (SOFC). Com este intuito, prepararam-se varios vidros e materiais vitro-cerâmicos ao longo das juntas Enstatite (MgSiO3) - diopsidio (CaMgSi2O6) e diopsidio (CaMgSi2O6) - Ca - Tschermak (CaAlSi2O6), os quais foram caracterizados atraves de um vasto leque de tecnicas. Todos os vidros foram preparados por fusao-arrefecimento enquanto os vitro-cerâmicos foram obtidos quer por sinterizacao e cristalizacao de fritas, quer por nucleacao e cristalizacao de vidros monoliticos. Estudaram-se ainda os efeitos de varias substituicoes ionicas em composicoes de diopsidio contendo Al na estrutura, sinterizacao e no comportamento durante a cristalizacao de vidros e nas propriedades dos materiais vitro-cerâmicos, com relevância para a sua aplicacao como selantes em SOFC. Verificou-se que Foi observado que os vidros/vitro-cerâmicos a base de enstatite nao apresentavam as caracteristicas necessarias para serem usados como materiais selantes em SOFC, enquanto as melhores propriedades apresentadas pelos vitro-cerâmicos a base de diopsidio qualificaram-nos para futuros estudos neste tipo de aplicacoes. Para alem de investigar a adequacao dos vitro-cerâmicos a base de clinopyroxene como selantes, esta tese tem tambem como objetivo estudar a influencia dos agentes de nucleacao na nucleacao em volume dos vitro-cerâmicos resultantes a base de diopsidio, de modo a qualifica-los como potenciais materiais hopedeiros de residuos nucleares radioactivos.

Magnetism at the nanoscale: Nanoparticles, nanowires, nanotubes and their ordered arrays

NASA Astrophysics Data System (ADS)

Proenca, Mariana Jesus Paiva

As piroxenas sao um vasto grupo de silicatos minerais encontrados em muitas rochas igneas e metamorficas. Na sua forma mais simples, estes silicatos sao constituidas por cadeias de SiO3 ligando grupos tetrahedricos de SiO4. A formula quimica geral das piroxenas e M2M1T2O6, onde M2 se refere a catioes geralmente em uma coordenacao octaedrica distorcida (Mg2+, Fe2+, Mn2+, Li+, Ca2+, Na+), M1 refere-se a catioes numa coordenacao octaedrica regular (Al3+, Fe3+, Ti4+, Cr3+, V3+, Ti3+, Zr4+, Sc3+, Zn2+, Mg2+, Fe2+, Mn2+), e T a catioes em coordenacao tetrahedrica (Si4+, Al3+, Fe3+). As piroxenas com estrutura monoclinica sao designadas de clinopiroxenes. A estabilidade das clinopyroxenes num espectro de composicoes quimicas amplo, em conjugacao com a possibilidade de ajustar as suas propriedades fisicas e quimicas e a durabilidade quimica, tem gerado um interesse mundial devido a suas aplicacoes em ciencia e tecnologia de materiais. Este trabalho trata do desenvolvimento de vidros e de vitro-cerâmicos baseadas de clinopiroxenas para aplicacoes funcionais. O estudo teve objectivos cientificos e tecnologicos; nomeadamente, adquirir conhecimentos fundamentais sobre a formacao de fases cristalinas e solucoes solidas em determinados sistemas vitro-cerâmicos, e avaliar a viabilidade de aplicacao dos novos materiais em diferentes areas tecnologicas, com especial enfase sobre a selagem em celulas de combustivel de oxido solido (SOFC). Com este intuito, prepararam-se varios vidros e materiais vitro-cerâmicos ao longo das juntas Enstatite (MgSiO3) - diopsidio (CaMgSi2O6) e diopsidio (CaMgSi2O6) - Ca - Tschermak (CaAlSi2O6), os quais foram caracterizados atraves de um vasto leque de tecnicas. Todos os vidros foram preparados por fusao-arrefecimento enquanto os vitro-cerâmicos foram obtidos quer por sinterizacao e cristalizacao de fritas, quer por nucleacao e cristalizacao de vidros monoliticos. Estudaram-se ainda os efeitos de varias substituicoes ionicas em composicoes de diopsidio contendo Al na estrutura, sinterizacao e no comportamento durante a cristalizacao de vidros e nas propriedades dos materiais vitro-cerâmicos, com relevância para a sua aplicacao como selantes em SOFC. Verificou-se que Foi observado que os vidros/vitro-cerâmicos a base de enstatite nao apresentavam as caracteristicas necessarias para serem usados como materiais selantes em SOFC, enquanto as melhores propriedades apresentadas pelos vitro-cerâmicos a base de diopsidio qualificaram-nos para futuros estudos neste tipo de aplicacoes. Para alem de investigar a adequacao dos vitro-cerâmicos a base de clinopyroxene como selantes, esta tese tem tambem como objetivo estudar a influencia dos agentes de nucleacao na nucleacao em volume dos vitro-cerâmicos resultantes a base de diopsidio, de modo a qualifica-los como potenciais materiais hopedeiros de residuos nucleares radioactivos.

Improving the characteristics of foundry alloys AlSiCuMg during manufacturing

NASA Astrophysics Data System (ADS)

Fragoso, Bruno Filipe Marques

As piroxenas sao um vasto grupo de silicatos minerais encontrados em muitas rochas igneas e metamorficas. Na sua forma mais simples, estes silicatos sao constituidas por cadeias de SiO3 ligando grupos tetrahedricos de SiO4. A formula quimica geral das piroxenas e M2M1T2O6, onde M2 se refere a catioes geralmente em uma coordenacao octaedrica distorcida (Mg2+, Fe2+, Mn2+, Li+, Ca2+, Na+), M1 refere-se a catioes numa coordenacao octaedrica regular (Al3+, Fe3+, Ti4+, Cr3+, V3+, Ti3+, Zr4+, Sc3+, Zn2+, Mg2+, Fe2+, Mn2+), e T a catioes em coordenacao tetrahedrica (Si4+, Al3+, Fe3+). As piroxenas com estrutura monoclinica sao designadas de clinopiroxenes. A estabilidade das clinopyroxenes num espectro de composicoes quimicas amplo, em conjugacao com a possibilidade de ajustar as suas propriedades fisicas e quimicas e a durabilidade quimica, tem gerado um interesse mundial devido a suas aplicacoes em ciencia e tecnologia de materiais. Este trabalho trata do desenvolvimento de vidros e de vitro-cerâmicos baseadas de clinopiroxenas para aplicacoes funcionais. O estudo teve objectivos cientificos e tecnologicos; nomeadamente, adquirir conhecimentos fundamentais sobre a formacao de fases cristalinas e solucoes solidas em determinados sistemas vitro-cerâmicos, e avaliar a viabilidade de aplicacao dos novos materiais em diferentes areas tecnologicas, com especial enfase sobre a selagem em celulas de combustivel de oxido solido (SOFC). Com este intuito, prepararam-se varios vidros e materiais vitro-cerâmicos ao longo das juntas Enstatite (MgSiO3) - diopsidio (CaMgSi2O6) e diopsidio (CaMgSi2O6) - Ca - Tschermak (CaAlSi2O6), os quais foram caracterizados atraves de um vasto leque de tecnicas. Todos os vidros foram preparados por fusao-arrefecimento enquanto os vitro-cerâmicos foram obtidos quer por sinterizacao e cristalizacao de fritas, quer por nucleacao e cristalizacao de vidros monoliticos. Estudaram-se ainda os efeitos de varias substituicoes ionicas em composicoes de diopsidio contendo Al na estrutura, sinterizacao e no comportamento durante a cristalizacao de vidros e nas propriedades dos materiais vitro-cerâmicos, com relevância para a sua aplicacao como selantes em SOFC. Verificou-se que Foi observado que os vidros/vitro-cerâmicos a base de enstatite nao apresentavam as caracteristicas necessarias para serem usados como materiais selantes em SOFC, enquanto as melhores propriedades apresentadas pelos vitro-cerâmicos a base de diopsidio qualificaram-nos para futuros estudos neste tipo de aplicacoes. Para alem de investigar a adequacao dos vitro-cerâmicos a base de clinopyroxene como selantes, esta tese tem tambem como objetivo estudar a influencia dos agentes de nucleacao na nucleacao em volume dos vitro-cerâmicos resultantes a base de diopsidio, de modo a qualifica-los como potenciais materiais hopedeiros de residuos nucleares radioactivos.

Seismic assessment of reinforced concrete frame structures with a new flexibility based element

NASA Astrophysics Data System (ADS)

Arede, Antonio Jose Coelho Dias

As piroxenas sao um vasto grupo de silicatos minerais encontrados em muitas rochas igneas e metamorficas. Na sua forma mais simples, estes silicatos sao constituidas por cadeias de SiO3 ligando grupos tetrahedricos de SiO4. A formula quimica geral das piroxenas e M2M1T2O6, onde M2 se refere a catioes geralmente em uma coordenacao octaedrica distorcida (Mg2+, Fe2+, Mn2+, Li+, Ca2+, Na+), M1 refere-se a catioes numa coordenacao octaedrica regular (Al3+, Fe3+, Ti4+, Cr3+, V3+, Ti3+, Zr4+, Sc3+, Zn2+, Mg2+, Fe2+, Mn2+), e T a catioes em coordenacao tetrahedrica (Si4+, Al3+, Fe3+). As piroxenas com estrutura monoclinica sao designadas de clinopiroxenes. A estabilidade das clinopyroxenes num espectro de composicoes quimicas amplo, em conjugacao com a possibilidade de ajustar as suas propriedades fisicas e quimicas e a durabilidade quimica, tem gerado um interesse mundial devido a suas aplicacoes em ciencia e tecnologia de materiais. Este trabalho trata do desenvolvimento de vidros e de vitro-cerâmicos baseadas de clinopiroxenas para aplicacoes funcionais. O estudo teve objectivos cientificos e tecnologicos; nomeadamente, adquirir conhecimentos fundamentais sobre a formacao de fases cristalinas e solucoes solidas em determinados sistemas vitro-cerâmicos, e avaliar a viabilidade de aplicacao dos novos materiais em diferentes areas tecnologicas, com especial enfase sobre a selagem em celulas de combustivel de oxido solido (SOFC). Com este intuito, prepararam-se varios vidros e materiais vitro-cerâmicos ao longo das juntas Enstatite (MgSiO3) - diopsidio (CaMgSi2O6) e diopsidio (CaMgSi2O6) - Ca - Tschermak (CaAlSi2O6), os quais foram caracterizados atraves de um vasto leque de tecnicas. Todos os vidros foram preparados por fusao-arrefecimento enquanto os vitro-cerâmicos foram obtidos quer por sinterizacao e cristalizacao de fritas, quer por nucleacao e cristalizacao de vidros monoliticos. Estudaram-se ainda os efeitos de varias substituicoes ionicas em composicoes de diopsidio contendo Al na estrutura, sinterizacao e no comportamento durante a cristalizacao de vidros e nas propriedades dos materiais vitro-cerâmicos, com relevância para a sua aplicacao como selantes em SOFC. Verificou-se que Foi observado que os vidros/vitro-cerâmicos a base de enstatite nao apresentavam as caracteristicas necessarias para serem usados como materiais selantes em SOFC, enquanto as melhores propriedades apresentadas pelos vitro-cerâmicos a base de diopsidio qualificaram-nos para futuros estudos neste tipo de aplicacoes. Para alem de investigar a adequacao dos vitro-cerâmicos a base de clinopyroxene como selantes, esta tese tem tambem como objetivo estudar a influencia dos agentes de nucleacao na nucleacao em volume dos vitro-cerâmicos resultantes a base de diopsidio, de modo a qualifica-los como potenciais materiais hopedeiros de residuos nucleares radioactivos.

Viscoelastic nanocapsules under flow in microdevices

NASA Astrophysics Data System (ADS)

Cordeiro, Ana Lucinda Teixeira

As piroxenas sao um vasto grupo de silicatos minerais encontrados em muitas rochas igneas e metamorficas. Na sua forma mais simples, estes silicatos sao constituidas por cadeias de SiO3 ligando grupos tetrahedricos de SiO4. A formula quimica geral das piroxenas e M2M1T2O6, onde M2 se refere a catioes geralmente em uma coordenacao octaedrica distorcida (Mg2+, Fe2+, Mn2+, Li+, Ca2+, Na+), M1 refere-se a catioes numa coordenacao octaedrica regular (Al3+, Fe3+, Ti4+, Cr3+, V3+, Ti3+, Zr4+, Sc3+, Zn2+, Mg2+, Fe2+, Mn2+), e T a catioes em coordenacao tetrahedrica (Si4+, Al3+, Fe3+). As piroxenas com estrutura monoclinica sao designadas de clinopiroxenes. A estabilidade das clinopyroxenes num espectro de composicoes quimicas amplo, em conjugacao com a possibilidade de ajustar as suas propriedades fisicas e quimicas e a durabilidade quimica, tem gerado um interesse mundial devido a suas aplicacoes em ciencia e tecnologia de materiais. Este trabalho trata do desenvolvimento de vidros e de vitro-cerâmicos baseadas de clinopiroxenas para aplicacoes funcionais. O estudo teve objectivos cientificos e tecnologicos; nomeadamente, adquirir conhecimentos fundamentais sobre a formacao de fases cristalinas e solucoes solidas em determinados sistemas vitro-cerâmicos, e avaliar a viabilidade de aplicacao dos novos materiais em diferentes areas tecnologicas, com especial enfase sobre a selagem em celulas de combustivel de oxido solido (SOFC). Com este intuito, prepararam-se varios vidros e materiais vitro-cerâmicos ao longo das juntas Enstatite (MgSiO3) - diopsidio (CaMgSi2O6) e diopsidio (CaMgSi2O6) - Ca - Tschermak (CaAlSi2O6), os quais foram caracterizados atraves de um vasto leque de tecnicas. Todos os vidros foram preparados por fusao-arrefecimento enquanto os vitro-cerâmicos foram obtidos quer por sinterizacao e cristalizacao de fritas, quer por nucleacao e cristalizacao de vidros monoliticos. Estudaram-se ainda os efeitos de varias substituicoes ionicas em composicoes de diopsidio contendo Al na estrutura, sinterizacao e no comportamento durante a cristalizacao de vidros e nas propriedades dos materiais vitro-cerâmicos, com relevância para a sua aplicacao como selantes em SOFC. Verificou-se que Foi observado que os vidros/vitro-cerâmicos a base de enstatite nao apresentavam as caracteristicas necessarias para serem usados como materiais selantes em SOFC, enquanto as melhores propriedades apresentadas pelos vitro-cerâmicos a base de diopsidio qualificaram-nos para futuros estudos neste tipo de aplicacoes. Para alem de investigar a adequacao dos vitro-cerâmicos a base de clinopyroxene como selantes, esta tese tem tambem como objetivo estudar a influencia dos agentes de nucleacao na nucleacao em volume dos vitro-cerâmicos resultantes a base de diopsidio, de modo a qualifica-los como potenciais materiais hopedeiros de residuos nucleares radioactivos.

Stellar activity in high-precision photometric and spectroscopic transit observations

NASA Astrophysics Data System (ADS)

Oshagh, Mahmoudreza

As piroxenas sao um vasto grupo de silicatos minerais encontrados em muitas rochas igneas e metamorficas. Na sua forma mais simples, estes silicatos sao constituidas por cadeias de SiO3 ligando grupos tetrahedricos de SiO4. A formula quimica geral das piroxenas e M2M1T2O6, onde M2 se refere a catioes geralmente em uma coordenacao octaedrica distorcida (Mg2+, Fe2+, Mn2+, Li+, Ca2+, Na+), M1 refere-se a catioes numa coordenacao octaedrica regular (Al3+, Fe3+, Ti4+, Cr3+, V3+, Ti3+, Zr4+, Sc3+, Zn2+, Mg2+, Fe2+, Mn2+), e T a catioes em coordenacao tetrahedrica (Si4+, Al3+, Fe3+). As piroxenas com estrutura monoclinica sao designadas de clinopiroxenes. A estabilidade das clinopyroxenes num espectro de composicoes quimicas amplo, em conjugacao com a possibilidade de ajustar as suas propriedades fisicas e quimicas e a durabilidade quimica, tem gerado um interesse mundial devido a suas aplicacoes em ciencia e tecnologia de materiais. Este trabalho trata do desenvolvimento de vidros e de vitro-cerâmicos baseadas de clinopiroxenas para aplicacoes funcionais. O estudo teve objectivos cientificos e tecnologicos; nomeadamente, adquirir conhecimentos fundamentais sobre a formacao de fases cristalinas e solucoes solidas em determinados sistemas vitro-cerâmicos, e avaliar a viabilidade de aplicacao dos novos materiais em diferentes areas tecnologicas, com especial enfase sobre a selagem em celulas de combustivel de oxido solido (SOFC). Com este intuito, prepararam-se varios vidros e materiais vitro-cerâmicos ao longo das juntas Enstatite (MgSiO3) - diopsidio (CaMgSi2O6) e diopsidio (CaMgSi2O6) - Ca - Tschermak (CaAlSi2O6), os quais foram caracterizados atraves de um vasto leque de tecnicas. Todos os vidros foram preparados por fusao-arrefecimento enquanto os vitro-cerâmicos foram obtidos quer por sinterizacao e cristalizacao de fritas, quer por nucleacao e cristalizacao de vidros monoliticos. Estudaram-se ainda os efeitos de varias substituicoes ionicas em composicoes de diopsidio contendo Al na estrutura, sinterizacao e no comportamento durante a cristalizacao de vidros e nas propriedades dos materiais vitro-cerâmicos, com relevância para a sua aplicacao como selantes em SOFC. Verificou-se que Foi observado que os vidros/vitro-cerâmicos a base de enstatite nao apresentavam as caracteristicas necessarias para serem usados como materiais selantes em SOFC, enquanto as melhores propriedades apresentadas pelos vitro-cerâmicos a base de diopsidio qualificaram-nos para futuros estudos neste tipo de aplicacoes. Para alem de investigar a adequacao dos vitro-cerâmicos a base de clinopyroxene como selantes, esta tese tem tambem como objetivo estudar a influencia dos agentes de nucleacao na nucleacao em volume dos vitro-cerâmicos resultantes a base de diopsidio, de modo a qualifica-los como potenciais materiais hopedeiros de residuos nucleares radioactivos.

Starch and polyethylene based bone-analogue composite biomaterials

NASA Astrophysics Data System (ADS)

Reis, Rui Luis Goncalves dos

As piroxenas sao um vasto grupo de silicatos minerais encontrados em muitas rochas igneas e metamorficas. Na sua forma mais simples, estes silicatos sao constituidas por cadeias de SiO3 ligando grupos tetrahedricos de SiO4. A formula quimica geral das piroxenas e M2M1T2O6, onde M2 se refere a catioes geralmente em uma coordenacao octaedrica distorcida (Mg2+, Fe2+, Mn2+, Li+, Ca2+, Na+), M1 refere-se a catioes numa coordenacao octaedrica regular (Al3+, Fe3+, Ti4+, Cr3+, V3+, Ti3+, Zr4+, Sc3+, Zn2+, Mg2+, Fe2+, Mn2+), e T a catioes em coordenacao tetrahedrica (Si4+, Al3+, Fe3+). As piroxenas com estrutura monoclinica sao designadas de clinopiroxenes. A estabilidade das clinopyroxenes num espectro de composicoes quimicas amplo, em conjugacao com a possibilidade de ajustar as suas propriedades fisicas e quimicas e a durabilidade quimica, tem gerado um interesse mundial devido a suas aplicacoes em ciencia e tecnologia de materiais. Este trabalho trata do desenvolvimento de vidros e de vitro-cerâmicos baseadas de clinopiroxenas para aplicacoes funcionais. O estudo teve objectivos cientificos e tecnologicos; nomeadamente, adquirir conhecimentos fundamentais sobre a formacao de fases cristalinas e solucoes solidas em determinados sistemas vitro-cerâmicos, e avaliar a viabilidade de aplicacao dos novos materiais em diferentes areas tecnologicas, com especial enfase sobre a selagem em celulas de combustivel de oxido solido (SOFC). Com este intuito, prepararam-se varios vidros e materiais vitro-cerâmicos ao longo das juntas Enstatite (MgSiO3) - diopsidio (CaMgSi2O6) e diopsidio (CaMgSi2O6) - Ca - Tschermak (CaAlSi2O6), os quais foram caracterizados atraves de um vasto leque de tecnicas. Todos os vidros foram preparados por fusao-arrefecimento enquanto os vitro-cerâmicos foram obtidos quer por sinterizacao e cristalizacao de fritas, quer por nucleacao e cristalizacao de vidros monoliticos. Estudaram-se ainda os efeitos de varias substituicoes ionicas em composicoes de diopsidio contendo Al na estrutura, sinterizacao e no comportamento durante a cristalizacao de vidros e nas propriedades dos materiais vitro-cerâmicos, com relevância para a sua aplicacao como selantes em SOFC. Verificou-se que Foi observado que os vidros/vitro-cerâmicos a base de enstatite nao apresentavam as caracteristicas necessarias para serem usados como materiais selantes em SOFC, enquanto as melhores propriedades apresentadas pelos vitro-cerâmicos a base de diopsidio qualificaram-nos para futuros estudos neste tipo de aplicacoes. Para alem de investigar a adequacao dos vitro-cerâmicos a base de clinopyroxene como selantes, esta tese tem tambem como objetivo estudar a influencia dos agentes de nucleacao na nucleacao em volume dos vitro-cerâmicos resultantes a base de diopsidio, de modo a qualifica-los como potenciais materiais hopedeiros de residuos nucleares radioactivos.

Clinopyroxene based glasses and glass-ceramics for functional applications

NASA Astrophysics Data System (ADS)

Goel, Ashutosh

As piroxenas sao um vasto grupo de silicatos minerais encontrados em muitas rochas igneas e metamorficas. Na sua forma mais simples, estes silicatos sao constituidas por cadeias de SiO3 ligando grupos tetrahedricos de SiO4. A formula quimica geral das piroxenas e M2M1T2O6, onde M2 se refere a catioes geralmente em uma coordenacao octaedrica distorcida (Mg2+, Fe2+, Mn2+, Li+, Ca2+, Na+), M1 refere-se a catioes numa coordenacao octaedrica regular (Al3+, Fe3+, Ti4+, Cr3+, V3+, Ti3+, Zr4+, Sc3+, Zn2+, Mg2+, Fe2+, Mn2+), e T a catioes em coordenacao tetrahedrica (Si4+, Al3+, Fe3+). As piroxenas com estrutura monoclinica sao designadas de clinopiroxenes. A estabilidade das clinopyroxenes num espectro de composicoes quimicas amplo, em conjugacao com a possibilidade de ajustar as suas propriedades fisicas e quimicas e a durabilidade quimica, tem gerado um interesse mundial devido a suas aplicacoes em ciencia e tecnologia de materiais. Este trabalho trata do desenvolvimento de vidros e de vitro-cerâmicos baseadas de clinopiroxenas para aplicacoes funcionais. O estudo teve objectivos cientificos e tecnologicos; nomeadamente, adquirir conhecimentos fundamentais sobre a formacao de fases cristalinas e solucoes solidas em determinados sistemas vitro-cerâmicos, e avaliar a viabilidade de aplicacao dos novos materiais em diferentes areas tecnologicas, com especial enfase sobre a selagem em celulas de combustivel de oxido solido (SOFC). Com este intuito, prepararam-se varios vidros e materiais vitro-cerâmicos ao longo das juntas Enstatite (MgSiO3) - diopsidio (CaMgSi2O6) e diopsidio (CaMgSi2O6) - Ca - Tschermak (CaAlSi2O6), os quais foram caracterizados atraves de um vasto leque de tecnicas. Todos os vidros foram preparados por fusao-arrefecimento enquanto os vitro-cerâmicos foram obtidos quer por sinterizacao e cristalizacao de fritas, quer por nucleacao e cristalizacao de vidros monoliticos. Estudaram-se ainda os efeitos de varias substituicoes ionicas em composicoes de diopsidio contendo Al na estrutura, sinterizacao e no comportamento durante a cristalizacao de vidros e nas propriedades dos materiais vitro-cerâmicos, com relevância para a sua aplicacao como selantes em SOFC. Verificou-se que Foi observado que os vidros/vitro-cerâmicos a base de enstatite nao apresentavam as caracteristicas necessarias para serem usados como materiais selantes em SOFC, enquanto as melhores propriedades apresentadas pelos vitro-cerâmicos a base de diopsidio qualificaram-nos para futuros estudos neste tipo de aplicacoes. Para alem de investigar a adequacao dos vitro-cerâmicos a base de clinopyroxene como selantes, esta tese tem tambem como objetivo estudar a influencia dos agentes de nucleacao na nucleacao em volume dos vitro-cerâmicos resultantes a base de diopsidio, de modo a qualifica-los como potenciais materiais hopedeiros de residuos nucleares radioactivos.

An overview on the history of pedology and soil mapping in Italy

NASA Astrophysics Data System (ADS)

Calzolari, C.

2012-04-01

In Italy, the word pedology (pedologia) was introduced in a text book as synonym of soil science for the first time in 1904 by Vinassa de Regny. In the literature, the term cohabitates with the words agrology (agrologia), agro-geology (agro-geologia), agricultural geognostic (geognostica agraria), geopedology (geo-pedologia) used in different historical moments by differently rooted soil scientists. When early pedologists started with systematic studies of soils, their characteristics and geography, they were strongly influenced by their cultural background, mainly geology and agro-chemistry. Along the time, the soil concept evolved, as did the concept of pedology, and this is somehow witnessed by the use of different Italian words with reference to soil: suolo, terreno, terra. Differently from agro-chemists, early pedologists based the soil study on the field description of soil profile. This was firstly based on the vertical differentiation between humus rich layers and "inactive" layers and later on, as long as the discipline evolved, on the presence of genetic horizons. The first complete soil map of Italy is dated 1928. Its Author, the geologist De Angelis d'Ossat, was the president of the organising committee of the 1924 International Soil Conference of Rome, where the International Society of Soil Science was founded. The map was based on the geological map of Italy, drafted in scale 1:1,000,000 after the creation of the Kingdom of Italy in 1861. The internal disputes within the Geological Society, together with the scarce interest of most of geologists for soil, did not facilitate the birth of a central soil survey. Soil mapping was mainly conducted by universities and research institutes, and we had to wait until 1953 for a new soil map (scale 1:3,125,000) at national level to be realised by Paolo Principi, based on literature data. In 1966 a new 1:1,000,000 soil map of Italy was eventually published by a national committee, led by Fiorenzo Mancini. This was based on literature data and on field surveys, and the mapping units limits, based on geomorphology, are still the basis of the most updated European 1:1,000,000 soil map. At the end of the 80ies of the past century, soil survey and mapping were taken over by the Italian regional administrations, which set up regional soil surveys working in co-ordination among them and with the research institutions.

Surface materials map of Afghanistan: iron-bearing minerals and other materials

USGS Publications Warehouse

King, Trude V.V.; Kokaly, Raymond F.; Hoefen, Todd M.; Dudek, Kathleen B.; Livo, Keith E.

2012-01-01

This map shows the distribution of selected iron-bearing minerals and other materials derived from analysis of HyMap imaging spectrometer data of Afghanistan. Using a NASA (National Aeronautics and Space Administration) WB-57 aircraft flown at an altitude of ~15,240 meters or ~50,000 feet, 218 flight lines of data were collected over Afghanistan between August 22 and October 2, 2007. The HyMap data were converted to apparent surface reflectance, then further empirically adjusted using ground-based reflectance measurements. The reflectance spectrum of each pixel of HyMap data was compared to the spectral features of reference entries in a spectral library of minerals, vegetation, water, ice, and snow. This map shows the spatial distribution of iron-bearing minerals and other materials having diagnostic absorptions at visible and near-infrared wavelengths. These absorptions result from electronic processes in the minerals. Several criteria, including (1) the reliability of detection and discrimination of minerals using the HyMap spectrometer data, (2) the relative abundance of minerals, and (3) the importance of particular minerals to studies of Afghanistan's natural resources, guided the selection of entries in the reference spectral library and, therefore, guided the selection of mineral classes shown on this map. Minerals occurring abundantly at the surface and those having unique spectral features were easily detected and discriminated. Minerals having similar spectral features were less easily discriminated, especially where the minerals were not particularly abundant and (or) where vegetation cover reduced the absorption strength of mineral features. Complications in reflectance calibration also affected the detection and identification of minerals.

Surface materials map of Afghanistan: carbonates, phyllosilicates, sulfates, altered minerals, and other materials

USGS Publications Warehouse

Kokaly, Raymond F.; King, Trude V.V.; Hoefen, Todd M.; Dudek, Kathleen B.; Livo, Keith E.

2012-01-01

This map shows the distribution of selected carbonates, phyllosilicates, sulfates, altered minerals, and other materials derived from analysis of HyMap imaging spectrometer data of Afghanistan. Using a NASA (National Aeronautics and Space Administration) WB-57 aircraft flown at an altitude of ~15,240 meters or ~50,000 feet, 218 flight lines of data were collected over Afghanistan between August 22 and October 2, 2007. The HyMap data were converted to apparent surface reflectance, then further empirically adjusted using ground-based reflectance measurements. The reflectance spectrum of each pixel of HyMap data was compared to the spectral features of reference entries in a spectral library of minerals, vegetation, water, ice, and snow. This map shows the spatial distribution of minerals that have diagnostic absorption features in the shortwave infrared wavelengths. These absorption features result primarily from characteristic chemical bonds and mineralogical vibrations. Several criteria, including (1) the reliability of detection and discrimination of minerals using the HyMap spectrometer data, (2) the relative abundance of minerals, and (3) the importance of particular minerals to studies of Afghanistan's natural resources, guided the selection of entries in the reference spectral library and, therefore, guided the selection of mineral classes shown on this map. Minerals occurring abundantly at the surface and those having unique spectral features were easily detected and discriminated. Minerals having similar spectral features were less easily discriminated, especially where the minerals were not particularly abundant and (or) where vegetation cover reduced the absorption strength of mineral features. Complications in reflectance calibration also affected the detection and identification of minerals.

Sobre os sistemas de referência celeste

NASA Astrophysics Data System (ADS)

Poppe, P. C. R.; Martin, V. A. F.

2003-02-01

Apresentamos neste trabalho, algumas discussões sobre os sistemas de referência utilizados em Astronomia. Claramente, não é possível esgotar todo este assunto num único texto, mas esperamos, contudo, que o presente material possa ser apreciado nos cursos de Introdução à Astronomia, que estão cada vez mais presentes nas atuais propostas curriculares das graduações de Física. As discussões pertinentes às "Bases de Referência Celeste", serão apresentadas em um outro trabalho.

Dissecting Pistil Responses to Incompatible and Compatible Pollen in Self-Incompatibility Brassica oleracea Using Comparative Proteomics.

PubMed

Zeng, Jing; Gao, Qiguo; Shi, Songmei; Lian, Xiaoping; Converse, Richard; Zhang, Hecui; Yang, Xiaohong; Ren, Xuesong; Chen, Song; Zhu, Liquan

2017-04-01

Angiosperms have developed self-incompatibility (SI) systems to reject self-pollen, thereby promoting outcrossing. The Brassicaceae belongs to typical sporophytic system, having a single S-locus controlled SI response, and was chosen as a model system to study SI-related intercellular signal transduction. In this regard, the downstream factor of EXO70A1 was unknown. Here, protein two-dimensional electrophoresis (2-DE) method and coupled with matrix-assisted laser desorption ionization/time of flight of flight mass spectrometry (MALDI-TOF -MS) and peptide mass fingerprinting (PMF) was used to further explore the mechanism of SI responses in Brassica oleracea L. var. capitata L. at protein level. To further confirm the time point of protein profile change, total proteins were collected from B. oleracea pistils at 0 min, 1 h, and 2 h after self-pollination. In total 902, 1088 and 1023 protein spots were separated in 0 min, 1 h and 2 h 2-DE maps, respectively. Our analyses of self-pollination profiles indicated that proteins mainly changed at 1 h post-pollination in B. oleracea. Moreover, 1077 protein spots were separated in cross-pollinated 1 h (CP) pistil 2-DE map. MALDI-TOF-MS and PMF successfully identified 34 differentially-expressed proteins (DEPs) in SP and CP 1 h 2-DE maps. Gene ontology and KEGG analysis revealed an array of proteins grouped in the following categories: stress and defense response (35%), protein metabolism (18%), carbohydrate and energy metabolism (12%), regulation of translation (9%), pollen tube development (12%), transport (9%) and cytoskeletal (6%). Sets of DEPs identified specifically in SP or only up-regulated expressed in CP pistils were chosen for funther investigating in floral organs and during the process of self- and cross-pollination. The function of these DEPs in terms of their potential involvement in SI in B. oleracea is discussed.

Transcript expression profiling for adventitious roots of Panax ginseng Meyer.

PubMed

Subramaniyam, Sathiyamoorthy; Mathiyalagan, Ramya; Natarajan, Sathishkumar; Kim, Yu-Jin; Jang, Moon-Gi; Park, Jun-Hyung; Yang, Deok Chun

2014-08-01

Panax ginseng Meyer is one of the major medicinal plants in oriental countries belonging to the Araliaceae family which are the primary source for ginsenosides. However, very few genes were characterized for ginsenoside pathway, due to the limited genome information. Through this study, we obtained a comprehensive transcriptome from adventitious roots, which were treated with methyl jasmonic acids for different time points (control, 2h, 6h, 12h, and 24h) and sequenced by RNA 454 pyrosequencing technology. Reference transcriptome 39,304,529 (0.04GB) was obtained from 5,724,987,880 bases (5.7GB) of 22 libraries by de novo assembly and 35,266 (58.5%) transcripts were annotated with biological schemas (GO and KEGG). The digital gene expression patterns were obtained from in vitro grown adventitious root sequences which mapped to reference, from that, 3813 (6.3%) unique transcripts were involved in ≥2 fold up and downregulations. Finally, candidates for ginsenoside pathway genes were predicted from observed expression patterns. Among them, 30 transcription factors, 20 cytochromes, and 11 glycosyl transferases were predicted as ginsenoside candidates. These data can remarkably expand the existing transcriptome resources of Panax, especially to predict existence of gene networks in P. ginseng. The entity of the data provides a valuable platform to reveal more on secondary metabolism and abiotic stresses from P. ginseng in vitro grown adventitious roots. Copyright © 2014 Elsevier B.V. All rights reserved.

Deglaciation and post-glacial environmental evolution in the Western Massif of Picos de Europa

NASA Astrophysics Data System (ADS)

Ruiz-Fernández, Jesús; Oliva, Marc; García, Cristina; López-Sáez, José Antonio; Gallinar, David; Geraldes, Miguel

2014-05-01

This study examines the process of deglaciation of the Western Massif of Picos de Europa through field work, geomorphological mapping, sedimentary records and absolute datings of 14C. This massif has several peaks over 2,400 m a.s.l. (Peña Santa de Castilla, 2,596 m; Torre Santa María, 2,486 m; Torre del Mediu, 2,467 m). It is composed mainly by Carboniferous limestones. This area has been intensively affected by karstic dissolution, Quaternary glaciers and fluvio-torrential processes (Miotke, 1968; Moreno et al, 2010; Ruiz-Fernández et al, 2009; Ruiz-Fernández, 2013). At present day, periglacial processes are active at the highest elevations (Ruiz-Fernández, 2013). We have identified four main glacial stages regarding the deglaciation of the massif: (i) maximum advance corresponding to the Last Glaciation, (ii) retreat and stabilization after the maximum advance, (iii) Late Glacial, and (iv) Little Ice Age. Sedimentological studies also contribute data to the understanding of the chronological framework of these environmental changes. The datings of the bottom sediments in two long sequences (8 and 5.4 m) provided a minimum age of 18,075 ± 425 cal BP for the maximum advance stage and 11,150 ± 900 cal BP for retreat and stabilization in the phase following the maximum advance. The ongoing analyses of these sequences at very high resolution will provide new knowledge about the environmental conditions prevailing since the deglaciation of the massif. References Miotke, F.D. (1968). Karstmorphologische studien in der glazial-überformten Höhenstufe der Picos de Europa, Nordspanien. Hannover, Selbtverlag der Geografischen Gessellschaft, 161 pp. Moreno, A., Valero, B.L., Jiménez, M., Domínguez, M.J., Mata, M.P., Navas, A., González, P., Stoll, H., Farias, P., Morellón, M., Corella, J.P. & Rico, M. (2010). The last deglaciation in the Picos de Europa National Park (Cantabrian Mountains, Northern Spain). Journal of Quaternary Science, 25 (7), 1076-1091. Ruiz-Fernández, J. (2013). Las formas de modelado glaciar, periglaciar y fluviotorrencial del Macizo Occidental de los Picos de Europa (Cordillera Cantábrica). Unpublished PhD Thesis, University of Oviedo, 314 pp. Ruiz-Fernández, J., Poblete. M.A., Serrano, P., Martí, C. & García-Ruiz, J.M. (2009). Morphometry of glacial cirques in the Cantabrian Range (Northwest Spain). Zeitschrift für Geomorphologie N. F., 53, 47-68.

Unified View of Backward Backtracking in Short Read Mapping

NASA Astrophysics Data System (ADS)

Mäkinen, Veli; Välimäki, Niko; Laaksonen, Antti; Katainen, Riku

Mapping short DNA reads to the reference genome is the core task in the recent high-throughput technologies to study e.g. protein-DNA interactions (ChIP-seq) and alternative splicing (RNA-seq). Several tools for the task (bowtie, bwa, SOAP2, TopHat) have been developed that exploit Burrows-Wheeler transform and the backward backtracking technique on it, to map the reads to their best approximate occurrences in the genome. These tools use different tailored mechanisms for small error-levels to prune the search phase significantly. We propose a new pruning mechanism that can be seen a generalization of the tailored mechanisms used so far. It uses a novel idea of storing all cyclic rotations of fixed length substrings of the reference sequence with a compressed index that is able to exploit the repetitions created to level out the growth of the input set. For RNA-seq we propose a new method that combines dynamic programming with backtracking to map efficiently and correctly all reads that span two exons. Same mechanism can also be used for mapping mate-pair reads.

Ground mapping resolution accuracy of a scanning radiometer from a geostationary satellite.

PubMed

Stremler, F G; Khalil, M A; Parent, R J

1977-06-01

Measures of the spatial and spatial rate (frequency) mapping of scanned visual imagery from an earth reference system to a spin-scan geostationary satellite are examined. Mapping distortions and coordinate inversions to correct for these distortions are formulated in terms of geometric transformations between earth and satellite frames of reference. Probabilistic methods are used to develop relations for obtainable mapping resolution when coordinate inversions are employed.

An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes

PubMed Central

Cho, Yun Sung; Kim, Hyunho; Kim, Hak-Min; Jho, Sungwoong; Jun, JeHoon; Lee, Yong Joo; Chae, Kyun Shik; Kim, Chang Geun; Kim, Sangsoo; Eriksson, Anders; Edwards, Jeremy S.; Lee, Semin; Kim, Byung Chul; Manica, Andrea; Oh, Tae-Kwang; Church, George M.; Bhak, Jong

2016-01-01

Human genomes are routinely compared against a universal reference. However, this strategy could miss population-specific and personal genomic variations, which may be detected more efficiently using an ethnically relevant or personal reference. Here we report a hybrid assembly of a Korean reference genome (KOREF) for constructing personal and ethnic references by combining sequencing and mapping methods. We also build its consensus variome reference, providing information on millions of variants from 40 additional ethnically homogeneous genomes from the Korean Personal Genome Project. We find that the ethnically relevant consensus reference can be beneficial for efficient variant detection. Systematic comparison of human assemblies shows the importance of assembly quality, suggesting the necessity of new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population genome projects, the leveraging of ethnicity-specific genome assemblies as well as the human reference genome will accelerate mapping all human genome diversity. PMID:27882922

Geology and resource assessment of Costa Rica at 1:500,000 scale; a digital representation of maps of the U.S. Geological Survey's 1987 Folio I-1865

USGS Publications Warehouse

Schruben, Paul G.

1996-01-01

This CD-ROM contains digital versions of the geology and resource assessment maps of Costa Rica originally published by the U.S. Geological Survey (USGS), the Direccion General de Geologia, Minas e Hidrocarburos, and the Universidad de Costa Rica in 1987 at a scale of 1:500,000 in USGS Folio I-1865. The following layers of the map are available on the CD-ROM: geology, favorable domains for selected deposit types, Bouguer gravity, isostatic gravity, mineral deposits, and rock geochemistry sample points. Some of the layers are provided in the following formats: ArcView 1 for Windows and UNIX, ARC/INFO 6.1.2 Export, Digital Line Graph (DLG) Optional, and Drawing Exchange File (DXF). This CD-ROM was produced in accordance with the ISO 9660 and Apple Computer's HFS standards.

Superior Cognitive Mapping through Single Landmark-Related Learning than through Boundary-Related Learning

ERIC Educational Resources Information Center

Zhou, Ruojing; Mou, Weimin

2016-01-01

Cognitive mapping is assumed to be through hippocampus-dependent place learning rather than striatum-dependent response learning. However, we proposed that either type of spatial learning, as long as it involves encoding metric relations between locations and reference points, could lead to a cognitive map. Furthermore, the fewer reference points…

sscMap: an extensible Java application for connecting small-molecule drugs using gene-expression signatures.

PubMed

Zhang, Shu-Dong; Gant, Timothy W

2009-07-31

Connectivity mapping is a process to recognize novel pharmacological and toxicological properties in small molecules by comparing their gene expression signatures with others in a database. A simple and robust method for connectivity mapping with increased specificity and sensitivity was recently developed, and its utility demonstrated using experimentally derived gene signatures. This paper introduces sscMap (statistically significant connections' map), a Java application designed to undertake connectivity mapping tasks using the recently published method. The software is bundled with a default collection of reference gene-expression profiles based on the publicly available dataset from the Broad Institute Connectivity Map 02, which includes data from over 7000 Affymetrix microarrays, for over 1000 small-molecule compounds, and 6100 treatment instances in 5 human cell lines. In addition, the application allows users to add their custom collections of reference profiles and is applicable to a wide range of other 'omics technologies. The utility of sscMap is two fold. First, it serves to make statistically significant connections between a user-supplied gene signature and the 6100 core reference profiles based on the Broad Institute expanded dataset. Second, it allows users to apply the same improved method to custom-built reference profiles which can be added to the database for future referencing. The software can be freely downloaded from http://purl.oclc.org/NET/sscMap.

12 CFR 204.125 - Foreign, international, and supranational entities referred to in §§ 204.2(c)(1)(iv)(E) and 204.8...

Code of Federal Regulations, 2011 CFR

2011-01-01

... Bank. Banque Centrale des Etats de l'Afrique Equatorial et du Cameroun. Banque Centrale des Etats d'Afrique del'Ouest. Conseil de l'Entente. East African Community. Organisation Commune Africaine et Malagache. Organization of African Unity. Union des Etats de l'Afrique Centrale. Union Douaniere et...

Mapping analysis of scaffold/matrix attachment regions (s/MARs) from two different mammalian cell lines

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

Pilus, Nur Shazwani Mohd; Ahmad, Azrin; Yusof, Nurul Yuziana Mohd

Scaffold/matrix attachment regions (S/MARs) are potential element that can be integrated into expression vector to increase expression of recombinant protein. Many studies on S/MAR have been done but none has revealed the distribution of S/MAR in a genome. In this study, we have isolated S/MAR sequences from HEK293 and Chinese hamster ovary cell lines (CHO DG44) using two different methods utilizing 2 M NaCl and lithium-3,5-diiodosalicylate (LIS). The isolated S/MARs were sequenced using Next Generation Sequencing (NGS) platform. Based on reference mapping analysis against human genome database, a total of 8,994,856 and 8,412,672 contigs of S/MAR sequences were retrieved frommore » 2M NaCl and LIS extraction of HEK293 respectively. On the other hand, reference mapping analysis of S/MAR derived from CHO DG44 against our own CHO DG44 database have generated a total of 7,204,348 and 4,672,913 contigs from 2 M NaCl and LIS extraction method respectively.« less

Osculating Relative Orbit Elements Resulting from Chief Eccentricity and J2 Perturbing Forces

DTIC Science & Technology

2011-03-01

significant importance to the analytical investigation in this study and is described in depth in Section 3.1.1. There do exist approaches to mapping the...necessary to introduce the environment which the majority of models describe. 2.2.1 Inertial Reference Frame. A geocentric reference frame will be used for...closest approach , modifying the period and minima locations of the radial and in-track components. This change impacts the periodicity of the radial

Single-breath-hold abdominal [Formula: see text]  mapping using 3D Cartesian Look-Locker with spatiotemporal sparsity constraints.

PubMed

Lugauer, Felix; Wetzl, Jens; Forman, Christoph; Schneider, Manuel; Kiefer, Berthold; Hornegger, Joachim; Nickel, Dominik; Maier, Andreas

2018-06-01

Our aim was to develop and validate a 3D Cartesian Look-Locker [Formula: see text] mapping technique that achieves high accuracy and whole-liver coverage within a single breath-hold. The proposed method combines sparse Cartesian sampling based on a spatiotemporally incoherent Poisson pattern and k-space segmentation, dedicated for high-temporal-resolution imaging. This combination allows capturing tissue with short relaxation times with volumetric coverage. A joint reconstruction of the 3D + inversion time (TI) data via compressed sensing exploits the spatiotemporal sparsity and ensures consistent quality for the subsequent multistep [Formula: see text] mapping. Data from the National Institute of Standards and Technology (NIST) phantom and 11 volunteers, along with reference 2D Look-Locker acquisitions, are used for validation. 2D and 3D methods are compared based on [Formula: see text] values in different abdominal tissues at 1.5 and 3 T. [Formula: see text] maps obtained from the proposed 3D method compare favorably with those from the 2D reference and additionally allow for reformatting or volumetric analysis. Excellent agreement is shown in phantom [bias[Formula: see text] < 2%, bias[Formula: see text] < 5% for (120; 2000) ms] and volunteer data (3D and 2D deviation < 4% for liver, muscle, and spleen) for clinically acceptable scan (20 s) and reconstruction times (< 4 min). Whole-liver [Formula: see text] mapping with high accuracy and precision is feasible in one breath-hold using spatiotemporally incoherent, sparse 3D Cartesian sampling.

G-Anchor: a novel approach for whole-genome comparative mapping utilizing evolutionary conserved DNA sequences.

PubMed

Lenis, Vasileios Panagiotis E; Swain, Martin; Larkin, Denis M

2018-05-01

Cross-species whole-genome sequence alignment is a critical first step for genome comparative analyses, ranging from the detection of sequence variants to studies of chromosome evolution. Animal genomes are large and complex, and whole-genome alignment is a computationally intense process, requiring expensive high-performance computing systems due to the need to explore extensive local alignments. With hundreds of sequenced animal genomes available from multiple projects, there is an increasing demand for genome comparative analyses. Here, we introduce G-Anchor, a new, fast, and efficient pipeline that uses a strictly limited but highly effective set of local sequence alignments to anchor (or map) an animal genome to another species' reference genome. G-Anchor makes novel use of a databank of highly conserved DNA sequence elements. We demonstrate how these elements may be aligned to a pair of genomes, creating anchors. These anchors enable the rapid mapping of scaffolds from a de novo assembled genome to chromosome assemblies of a reference species. Our results demonstrate that G-Anchor can successfully anchor a vertebrate genome onto a phylogenetically related reference species genome using a desktop or laptop computer within a few hours and with comparable accuracy to that achieved by a highly accurate whole-genome alignment tool such as LASTZ. G-Anchor thus makes whole-genome comparisons accessible to researchers with limited computational resources. G-Anchor is a ready-to-use tool for anchoring a pair of vertebrate genomes. It may be used with large genomes that contain a significant fraction of evolutionally conserved DNA sequences and that are not highly repetitive, polypoid, or excessively fragmented. G-Anchor is not a substitute for whole-genome aligning software but can be used for fast and accurate initial genome comparisons. G-Anchor is freely available and a ready-to-use tool for the pairwise comparison of two genomes.

mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.

PubMed

Hach, Faraz; Sarrafi, Iman; Hormozdiari, Farhad; Alkan, Can; Eichler, Evan E; Sahinalp, S Cenk

2014-07-01

High throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for processing and downstream analysis. While tools that report the 'best' mapping location of each read provide a fast way to process HTS data, they are not suitable for many types of downstream analysis such as structural variation detection, where it is important to report multiple mapping loci for each read. For this purpose we introduce mrsFAST-Ultra, a fast, cache oblivious, SNP-aware aligner that can handle the multi-mapping of HTS reads very efficiently. mrsFAST-Ultra improves mrsFAST, our first cache oblivious read aligner capable of handling multi-mapping reads, through new and compact index structures that reduce not only the overall memory usage but also the number of CPU operations per alignment. In fact the size of the index generated by mrsFAST-Ultra is 10 times smaller than that of mrsFAST. As importantly, mrsFAST-Ultra introduces new features such as being able to (i) obtain the best mapping loci for each read, and (ii) return all reads that have at most n mapping loci (within an error threshold), together with these loci, for any user specified n. Furthermore, mrsFAST-Ultra is SNP-aware, i.e. it can map reads to reference genome while discounting the mismatches that occur at common SNP locations provided by db-SNP; this significantly increases the number of reads that can be mapped to the reference genome. Notice that all of the above features are implemented within the index structure and are not simple post-processing steps and thus are performed highly efficiently. Finally, mrsFAST-Ultra utilizes multiple available cores and processors and can be tuned for various memory settings. Our results show that mrsFAST-Ultra is roughly five times faster than its predecessor mrsFAST. In comparison to newly enhanced popular tools such as Bowtie2, it is more sensitive (it can report 10 times or more mappings per read) and much faster (six times or more) in the multi-mapping mode. Furthermore, mrsFAST-Ultra has an index size of 2GB for the entire human reference genome, which is roughly half of that of Bowtie2. mrsFAST-Ultra is open source and it can be accessed at http://mrsfast.sourceforge.net. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Connection Between the ICRF and the Dynamical Reference Frame for the Outer Planets

NASA Astrophysics Data System (ADS)

da Silva Neto, D. N.; Assafin, M.; Andrei, A. H.; Vieira Martins, R.

2005-01-01

This work brings an approach intending to improve the connection between the Dynamical Reference Frame and the Extragalactic Reference Frame. For that, close encounters of outer Solar System objects and quasars are used. With this goal, Uranus, Neptune and two quasars were observed at Laborat´orio Nacional de Astrof´ısica (LNA), Brazil. The optical reference frame is the HCRF, as given by the UCAC2 catalogue. The first results show an accuracy of 45 mas - 50 mas in the optical positions. The optical minus radio offsets give the local orientation between the catalogue and radio frame. From this, it is possible to place the optical planet coordinates on the extragalactic frame. A comparison between the new corrected optical coordinates and the respective DE ephemeris to these planets can give the instant orientations of the Dynamical Reference Frame with regard to the ICRS, for this zone of outer Solar System.

ILP-based maximum likelihood genome scaffolding

PubMed Central

2014-01-01

Background Interest in de novo genome assembly has been renewed in the past decade due to rapid advances in high-throughput sequencing (HTS) technologies which generate relatively short reads resulting in highly fragmented assemblies consisting of contigs. Additional long-range linkage information is typically used to orient, order, and link contigs into larger structures referred to as scaffolds. Due to library preparation artifacts and erroneous mapping of reads originating from repeats, scaffolding remains a challenging problem. In this paper, we provide a scalable scaffolding algorithm (SILP2) employing a maximum likelihood model capturing read mapping uncertainty and/or non-uniformity of contig coverage which is solved using integer linear programming. A Non-Serial Dynamic Programming (NSDP) paradigm is applied to render our algorithm useful in the processing of larger mammalian genomes. To compare scaffolding tools, we employ novel quantitative metrics in addition to the extant metrics in the field. We have also expanded the set of experiments to include scaffolding of low-complexity metagenomic samples. Results SILP2 achieves better scalability throughg a more efficient NSDP algorithm than previous release of SILP. The results show that SILP2 compares favorably to previous methods OPERA and MIP in both scalability and accuracy for scaffolding single genomes of up to human size, and significantly outperforms them on scaffolding low-complexity metagenomic samples. Conclusions Equipped with NSDP, SILP2 is able to scaffold large mammalian genomes, resulting in the longest and most accurate scaffolds. The ILP formulation for the maximum likelihood model is shown to be flexible enough to handle metagenomic samples. PMID:25253180

DROMO Propagator Revisited

NASA Astrophysics Data System (ADS)

Urrutxua, H.; Sanjurjo-Rivo, M.; Peláez, J.

2013-12-01

In year 2000 a house-made orbital propagator was developed by the SDGUPM (former Grupo de Dinámica de Tethers) based in a set of redundant variables including Euler parameters. This propagator was called DROMO. and it was mainly used in numerical simulations of electrodynamic tethers. It was presented for the first time in the international meeting V Jornadas de Trabajo en Mecánica Celeste, held in Albarracín, Spain, in 2002 (see reference 1). The special perturbation method associated with DROMO can be consulted in the paper.2 In year 1975, Andre Deprit in reference 3 proposes a propagation scheme very similar to the one in which DROMO is based, by using the ideal frame concept of Hansen. The different approaches used in references 3 and 2 gave rise to a small controversy. In this paper we carried out a different deduction of the DROMO propagator, underlining its close relation with the Hansen ideal frame concept, and also the similarities and the differences with the theory carried out by Deprit in 3. Simultaneously we introduce some improvements in the formulation that leads to a more synthetic propagator.

A New Determination of Planetary Precession

NASA Astrophysics Data System (ADS)

Harada, Wataru; Fukushima, Toshio

2004-01-01

By using a nonlinear method of harmonic analysis, we have analyzed the motion of two angles, Ω and ɛ, specifying the direction of the Newtonian heliocentric orbital angular momentum of the Earth-Moon barycenter in the latest lunar and planetary ephemeris, DE405, from 1629 to 2169. Here Ω is the longitude of the node of the ecliptic of date with respect to the International Celestial Reference Frame (ICRF) equator, measured from the ICRF x-axis, while ɛ is the obliquity of the ecliptic of date referred to the ICRF equator. After dropping 86 Fourier terms and four mixed secular terms that were detected, we determined their secular variation in the form of quadratic polynomials as ΩDE405=-0.02109+10.54227t+0.48609t2 and ɛDE405=84,381.40578-46.81972t+0.04817t2 , where the units are arcseconds and t is the time since J2000.0 measured in Julian centuries. This is the latest determination of the planetary precession in the inertial sense and referred to the ICRF.

Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms

PubMed Central

Asamizu, Erika; Shirasawa, Kenta; Hirakawa, Hideki; Sato, Shusei; Tabata, Satoshi; Yano, Kentaro; Ariizumi, Tohru; Shibata, Daisuke; Ezura, Hiroshi

2012-01-01

A total of 93,682 BAC-end sequences (BESs) were generated from a dwarf model tomato, cv. Micro-Tom. After removing repetitive sequences, the BESs were similarity searched against the reference tomato genome of a standard cultivar, “Heinz 1706.” By referring to the “Heinz 1706” physical map and by eliminating redundant or nonsignificant hits, 28,804 “unique pair ends” and 8,263 “unique ends” were selected to construct hypothetical BAC contigs. The total physical length of the BAC contigs was 495, 833, 423 bp, covering 65.3% of the entire genome. The average coverage of euchromatin and heterochromatin was 58.9% and 67.3%, respectively. From this analysis, two possible genome rearrangements were identified: one in chromosome 2 (inversion) and the other in chromosome 3 (inversion and translocation). Polymorphisms (SNPs and Indels) between the two cultivars were identified from the BLAST alignments. As a result, 171,792 polymorphisms were mapped on 12 chromosomes. Among these, 30,930 polymorphisms were found in euchromatin (1 per 3,565 bp) and 140,862 were found in heterochromatin (1 per 2,737 bp). The average polymorphism density in the genome was 1 polymorphism per 2,886 bp. To facilitate the use of these data in Micro-Tom research, the BAC contig and polymorphism information are available in the TOMATOMICS database. PMID:23227037

A de Bruijn graph approach to the quantification of closely-related genomes in a microbial community.

PubMed

Wang, Mingjie; Ye, Yuzhen; Tang, Haixu

2012-06-01

The wide applications of next-generation sequencing (NGS) technologies in metagenomics have raised many computational challenges. One of the essential problems in metagenomics is to estimate the taxonomic composition of a microbial community, which can be approached by mapping shotgun reads acquired from the community to previously characterized microbial genomes followed by quantity profiling of these species based on the number of mapped reads. This procedure, however, is not as trivial as it appears at first glance. A shotgun metagenomic dataset often contains DNA sequences from many closely-related microbial species (e.g., within the same genus) or strains (e.g., within the same species), thus it is often difficult to determine which species/strain a specific read is sampled from when it can be mapped to a common region shared by multiple genomes at high similarity. Furthermore, high genomic variations are observed among individual genomes within the same species, which are difficult to be differentiated from the inter-species variations during reads mapping. To address these issues, a commonly used approach is to quantify taxonomic distribution only at the genus level, based on the reads mapped to all species belonging to the same genus; alternatively, reads are mapped to a set of representative genomes, each selected to represent a different genus. Here, we introduce a novel approach to the quantity estimation of closely-related species within the same genus by mapping the reads to their genomes represented by a de Bruijn graph, in which the common genomic regions among them are collapsed. Using simulated and real metagenomic datasets, we show the de Bruijn graph approach has several advantages over existing methods, including (1) it avoids redundant mapping of shotgun reads to multiple copies of the common regions in different genomes, and (2) it leads to more accurate quantification for the closely-related species (and even for strains within the same species).

Mapping rice ecosystem dynamics and greenhouse gas emissions using multiscale imagery and biogeochemical models

NASA Astrophysics Data System (ADS)

Salas, W.; Torbick, N.

2017-12-01

Rice greenhouse gas (GHG) emissions in production hot spots have been mapped using multiscale satellite imagery and a processed-based biogeochemical model. The multiscale Synthetic Aperture Radar (SAR) and optical imagery were co-processed and fed into a machine leanring framework to map paddy attributes that are tuned using field observations and surveys. Geospatial maps of rice extent, crop calendar, hydroperiod, and cropping intensity were then used to parameterize the DeNitrification-DeComposition (DNDC) model to estimate emissions. Results, in the Red River Detla for example, show total methane emissions at 345.4 million kgCH4-C equivalent to 11.5 million tonnes CO2e (carbon dioxide equivalent). We further assessed the role of Alternative Wetting and Drying and the impact on GHG and yield across production hot spots with uncertainty estimates. The approach described in this research provides a framework for using SAR to derive maps of rice and landscape characteristics to drive process models like DNDC. These types of tools and approaches will support the next generation of Monitoring, Reporting, and Verification (MRV) to combat climate change and support ecosystem service markets.

Cytoarchitectonic identification and probabilistic mapping of two distinct areas within the anterior ventral bank of the human intraparietal sulcus

PubMed Central

Choi, Hi-Jae; Zilles, Karl; Mohlberg, Hartmut; Schleicher, Axel; Fink, Gereon R.; Armstrong, Este; Amunts, Katrin

2008-01-01

Anatomical studies in the macaque cortex and functional imaging studies in humans have demonstrated the existence of different cortical areas within the IntraParietal Sulcus (IPS). Such functional segregation, however, does not correlate with presently available architectonic maps of the human brain. This is particularly true for the classical Brodmann map, which is still widely used as an anatomical reference in functional imaging studies. The aim of this cytoarchitectonic mapping study was to use previously defined algorithms to determine whether consistent regions and borders can be found within the cortex of the anterior IPS in a population of ten postmortem human brains. Two areas, the human IntraParietal area 1 (hIP1) and the human IntraParietal area 2 (hIP2), were delineated in serial histological sections of the anterior, lateral bank of the human IPS. The region hIP1 is located posterior and medial to hIP2, and the former is always within the depths of the IPS. The latter, on the other hand, sometimes reaches the free surface of the superior parietal lobule. The delineations were registered to standard reference space, and probabilistic maps were calculated, thereby quantifying the intersubject variability in location and extent of both areas. In the future, they can be a tool in analyzing structure – function relationships and a basis for determining degrees of homology in the IPS among anthropoid primates. We conclude that the human intraparietal sulcus has a finer grained parcellation than shown in Brodmann’s map. PMID:16432904

Leveraging terminological resources for mapping between rare disease information sources.

PubMed

Rance, Bastien; Snyder, Michelle; Lewis, Janine; Bodenreider, Olivier

2013-01-01

Rare disease information sources are incompletely and inconsistently cross-referenced to one another, making it difficult for information seekers to navigate across them. The development of such cross-references established manually by experts is generally labor intensive and costly. To develop an automatic mapping between two of the major rare diseases information sources, GARD and Orphanet, by leveraging terminological resources, especially the UMLS. We map the rare disease terms from Orphanet and ORDR to the UMLS. We use the UMLS as a pivot to bridge between the rare disease terminologies. We compare our results to a mapping obtained through manually established cross-references to OMIM. Our mapping has a precision of 94%, a recall of 63% and an F1-score of 76%. Our automatic mapping should help facilitate the development of more complete and consistent cross-references between GARD and Orphanet, and is applicable to other rare disease information sources as well.

Mapping soil erosion risk in Serra de Grândola (Portugal)

NASA Astrophysics Data System (ADS)

Neto Paixão, H. M.; Granja Martins, F. M.; Zavala, L. M.; Jordán, A.; Bellinfante, N.

2012-04-01

Geomorphological processes can pose environmental risks to people and economical activities. Information and a better knowledge of the genesis of these processes is important for environmental planning, since it allows to model, quantify and classify risks, what can mitigate the threats. The objective of this research is to assess the soil erosion risk in Serra de Grândola, which is a north-south oriented mountain ridge with an altitude of 383 m, located in southwest of Alentejo (southern Portugal). The study area is 675 km2, including the councils of Grândola, Santiago do Cacém and Sines. The process for mapping of erosive status was based on the guidelines for measuring and mapping the processes of erosion of coastal areas of the Mediterranean proposed by PAP/RAC (1997), developed and later modified by other authors in different areas. This method is based on the application of a geographic information system that integrates different types of spatial information inserted into a digital terrain model and in their derivative models. Erosive status are classified using information from soil erodibility, slope, land use and vegetation cover. The rainfall erosivity map was obtained using the modified Fournier index, calculated from the mean monthly rainfall, as recorded in 30 meteorological stations with influence in the study area. Finally, the soil erosion risk map was designed by ovelaying the erosive status map and the rainfall erosivity map.

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

PubMed Central

Howie, Bryan N.; Donnelly, Peter; Marchini, Jonathan

2009-01-01

Genotype imputation methods are now being widely used in the analysis of genome-wide association studies. Most imputation analyses to date have used the HapMap as a reference dataset, but new reference panels (such as controls genotyped on multiple SNP chips and densely typed samples from the 1,000 Genomes Project) will soon allow a broader range of SNPs to be imputed with higher accuracy, thereby increasing power. We describe a genotype imputation method (IMPUTE version 2) that is designed to address the challenges presented by these new datasets. The main innovation of our approach is a flexible modelling framework that increases accuracy and combines information across multiple reference panels while remaining computationally feasible. We find that IMPUTE v2 attains higher accuracy than other methods when the HapMap provides the sole reference panel, but that the size of the panel constrains the improvements that can be made. We also find that imputation accuracy can be greatly enhanced by expanding the reference panel to contain thousands of chromosomes and that IMPUTE v2 outperforms other methods in this setting at both rare and common SNPs, with overall error rates that are 15%–20% lower than those of the closest competing method. One particularly challenging aspect of next-generation association studies is to integrate information across multiple reference panels genotyped on different sets of SNPs; we show that our approach to this problem has practical advantages over other suggested solutions. PMID:19543373

[Bibliographic errors in Revista Española de Enfermedades Digestivas. A retrospective study of the year 1995].

PubMed

Acea Nebril, B; Gómez Freijoso, C

1997-03-01

To determine the accuracy of bibliographic citation in Revista Española de Enfermedades Digestivas (REED) and compare it with other Spanish and international journals. We reviewed all 1995 volumes of the REED and randomly selected 100 references from these volumes. Nine citations of non-journal articles were excluded and the remaining 91 citations were carefully scrutinized. Each original article was compared for author's name, title of article, name of journal, volume number, year of publication and pages. Some type of error was detected in 61.6% of the references and on 3 occasions (3.3%) impeded finding to the original article. Errors were found in authors (37.3%); article title (16.4%), pages (6.6%), journal title (4.4%), volume (2.2%) and year (1%). A single error was found in 42 citations, 2 were found in 13 and 3 were found in 1. REED's rate of error in references is comparable to the rates of other spanish and international journals. Authors should exercise more care in preparing bibliographies and should invest more effort in verification of quoted references.

Aligner optimization increases accuracy and decreases compute times in multi-species sequence data.

PubMed

Robinson, Kelly M; Hawkins, Aziah S; Santana-Cruz, Ivette; Adkins, Ricky S; Shetty, Amol C; Nagaraj, Sushma; Sadzewicz, Lisa; Tallon, Luke J; Rasko, David A; Fraser, Claire M; Mahurkar, Anup; Silva, Joana C; Dunning Hotopp, Julie C

2017-09-01

As sequencing technologies have evolved, the tools to analyze these sequences have made similar advances. However, for multi-species samples, we observed important and adverse differences in alignment specificity and computation time for bwa- mem (Burrows-Wheeler aligner-maximum exact matches) relative to bwa-aln. Therefore, we sought to optimize bwa-mem for alignment of data from multi-species samples in order to reduce alignment time and increase the specificity of alignments. In the multi-species cases examined, there was one majority member (i.e. Plasmodium falciparum or Brugia malayi ) and one minority member (i.e. human or the Wolbachia endosymbiont w Bm) of the sequence data. Increasing bwa-mem seed length from the default value reduced the number of read pairs from the majority sequence member that incorrectly aligned to the reference genome of the minority sequence member. Combining both source genomes into a single reference genome increased the specificity of mapping, while also reducing the central processing unit (CPU) time. In Plasmodium , at a seed length of 18 nt, 24.1 % of reads mapped to the human genome using 1.7±0.1 CPU hours, while 83.6 % of reads mapped to the Plasmodium genome using 0.2±0.0 CPU hours (total: 107.7 % reads mapping; in 1.9±0.1 CPU hours). In contrast, 97.1 % of the reads mapped to a combined Plasmodium- human reference in only 0.7±0.0 CPU hours. Overall, the results suggest that combining all references into a single reference database and using a 23 nt seed length reduces the computational time, while maximizing specificity. Similar results were found for simulated sequence reads from a mock metagenomic data set. We found similar improvements to computation time in a publicly available human-only data set.

LANDSAT and radar mapping of intrusive rocks in SE-Brazil

NASA Technical Reports Server (NTRS)

Parada, N. D. J. (Principal Investigator); Dossantos, A. R.; Dosanjos, C. E.; Moreira, J. C.; Barbosa, M. P.; Veneziani, P.

1982-01-01

The feasibility of intrusive rock mapping was investigated and criteria for regional geological mapping established at the scale of 1:500,00 in polycyclic and polymetamorphic areas using the logic method of photointerpretation of LANDSAT imagery and radar from the RADAMBRASIL project. The spectral behavior of intrusive rocks, was evaluated using the interactive multispectral image analysis system (Image-100). The region of Campos (city) in northern Rio de Janeiro State was selected as the study area and digital imagery processing and pattern recognition techniques were applied. Various maps at the 2:250,000 scale were obtained to evaluate the results of automatic data processing.

A systematic evaluation of three different cardiac T2-mapping sequences at 1.5 and 3T in healthy volunteers.

PubMed

Baeßler, Bettina; Schaarschmidt, Frank; Stehning, Christian; Schnackenburg, Bernhard; Maintz, David; Bunck, Alexander C

2015-11-01

Previous studies showed that myocardial T2 relaxation times measured by cardiac T2-mapping vary significantly depending on sequence and field strength. Therefore, a systematic comparison of different T2-mapping sequences and the establishment of dedicated T2 reference values is mandatory for diagnostic decision-making. Phantom experiments using gel probes with a range of different T1 and T2 times were performed on a clinical 1.5T and 3T scanner. In addition, 30 healthy volunteers were examined at 1.5 and 3T in immediate succession. In each examination, three different T2-mapping sequences were performed at three short-axis slices: Multi Echo Spin Echo (MESE), T2-prepared balanced SSFP (T2prep), and Gradient Spin Echo with and without fat saturation (GraSEFS/GraSE). Segmented T2-Maps were generated according to the AHA 16-segment model and statistical analysis was performed. Significant intra-individual differences between mean T2 times were observed for all sequences. In general, T2prep resulted in lowest and GraSE in highest T2 times. A significant variation with field strength was observed for mean T2 in phantom as well as in vivo, with higher T2 values at 1.5T compared to 3T, regardless of the sequence used. Segmental T2 values for each sequence at 1.5 and 3T are presented. Despite a careful selection of sequence parameters and volunteers, significant variations of the measured T2 values were observed between field strengths, MR sequences and myocardial segments. Therefore, we present segmental T2 values for each sequence at 1.5 and 3T with the inherent potential to serve as reference values for future studies. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Database for the geologic map of upper Eocene to Holocene volcanic and related rocks in the Cascade Range, Washington

USGS Publications Warehouse

Barron, Andrew D.; Ramsey, David W.; Smith, James G.

2014-01-01

This digital database contains information used to produce the geologic map published as Sheet 1 in U.S. Geological Survey Miscellaneous Investigations Series Map I-2005. (Sheet 2 of Map I-2005 shows sources of geologic data used in the compilation and is available separately). Sheet 1 of Map I-2005 shows the distribution and relations of volcanic and related rock units in the Cascade Range of Washington at a scale of 1:500,000. This digital release is produced from stable materials originally compiled at 1:250,000 scale that were used to publish Sheet 1. The database therefore contains more detailed geologic information than is portrayed on Sheet 1. This is most noticeable in the database as expanded polygons of surficial units and the presence of additional strands of concealed faults. No stable compilation materials exist for Sheet 1 at 1:500,000 scale. The main component of this digital release is a spatial database prepared using geographic information systems (GIS) applications. This release also contains links to files to view or print the map sheet, main report text, and accompanying mapping reference sheet from Map I-2005. For more information on volcanoes in the Cascade Range in Washington, Oregon, or California, please refer to the U.S. Geological Survey Volcano Hazards Program website.

Large-Scale Development of Cost-Effective Single-Nucleotide Polymorphism Marker Assays for Genetic Mapping in Pigeonpea and Comparative Mapping in Legumes

PubMed Central

Saxena, Rachit K.; Varma Penmetsa, R.; Upadhyaya, Hari D.; Kumar, Ashish; Carrasquilla-Garcia, Noelia; Schlueter, Jessica A.; Farmer, Andrew; Whaley, Adam M.; Sarma, Birinchi K.; May, Gregory D.; Cook, Douglas R.; Varshney, Rajeev K.

2012-01-01

Single-nucleotide polymorphisms (SNPs, >2000) were discovered by using RNA-seq and allele-specific sequencing approaches in pigeonpea (Cajanus cajan). For making the SNP genotyping cost-effective, successful competitive allele-specific polymerase chain reaction (KASPar) assays were developed for 1616 SNPs and referred to as PKAMs (pigeonpea KASPar assay markers). Screening of PKAMs on 24 genotypes [23 from cultivated species and 1 wild species (Cajanus scarabaeoides)] defined a set of 1154 polymorphic markers (77.4%) with a polymorphism information content (PIC) value from 0.04 to 0.38. One thousand and ninety-four PKAMs showed polymorphisms between parental lines of the reference mapping population (C. cajan ICP 28 × C. scarabaeoides ICPW 94). By using high-quality marker genotyping data on 167 F2 lines from the population, a comprehensive genetic map comprising 875 PKAMs with an average inter-marker distance of 1.11 cM was developed. Previously mapped 35 simple sequence repeat markers were integrated into the PKAM map and an integrated genetic map of 996.21 cM was constructed. Mapped PKAMs showed a higher degree of synteny with the genome of Glycine max followed by Medicago truncatula and Lotus japonicus and least with Vigna unguiculata. These PKAMs will be useful for genetics research and breeding applications in pigeonpea and for utilizing genome information from other legume species. PMID:23103470

Assessing ecological departure from reference conditions with the Fire Regime Condition Class (FRCC) Mapping Tool

Treesearch

Stephen W. Barrett; Thomas DeMeo; Jeffrey L. Jones; J.D. Zeiler; Lee C. Hutter

2006-01-01

Knowledge of ecological departure from a range of reference conditions provides a critical context for managing sustainable ecosystems. Fire Regime Condition Class (FRCC) is a qualitative measure characterizing possible departure from historical fire regimes. The FRCC Mapping Tool was developed as an ArcMap extension utilizing the protocol identified by the Interagency...

Two Dimensional Positioning and Heading Solution for Flying Vehicles using a Line-Scanning Laser Radar (LADAR)

DTIC Science & Technology

2011-03-24

6 2.4.1 Reference Frames . . . . . . . . . . . . . . . . . 6 2.4.2 Line and Feature Extraction . . . . . . . . . . . 7 2.4.3 SLAM ...Positioning System . . . . . . . . . . . . . . . . . . 1 LADAR Laser Radar . . . . . . . . . . . . . . . . . . . . . . . . . . 1 LiDAR Light Detection and...Ranging . . . . . . . . . . . . . . . . 2 SLAM Simultaneous Localization and Mapping . . . . . . . . . . 2 ANT Advanced Navigation Technology

Thematic accuracy of the National Land Cover Database (NLCD) 2001 land cover for Alaska

USGS Publications Warehouse

Selkowitz, D.J.; Stehman, S.V.

2011-01-01

The National Land Cover Database (NLCD) 2001 Alaska land cover classification is the first 30-m resolution land cover product available covering the entire state of Alaska. The accuracy assessment of the NLCD 2001 Alaska land cover classification employed a geographically stratified three-stage sampling design to select the reference sample of pixels. Reference land cover class labels were determined via fixed wing aircraft, as the high resolution imagery used for determining the reference land cover classification in the conterminous U.S. was not available for most of Alaska. Overall thematic accuracy for the Alaska NLCD was 76.2% (s.e. 2.8%) at Level II (12 classes evaluated) and 83.9% (s.e. 2.1%) at Level I (6 classes evaluated) when agreement was defined as a match between the map class and either the primary or alternate reference class label. When agreement was defined as a match between the map class and primary reference label only, overall accuracy was 59.4% at Level II and 69.3% at Level I. The majority of classification errors occurred at Level I of the classification hierarchy (i.e., misclassifications were generally to a different Level I class, not to a Level II class within the same Level I class). Classification accuracy was higher for more abundant land cover classes and for pixels located in the interior of homogeneous land cover patches. ?? 2011.

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

PubMed Central

Li, Junhua; Chen, Weineng; Chen, Hua; Mende, Daniel R.; Arumugam, Manimozhiyan; Pan, Qi; Liu, Binghang; Qin, Junjie; Wang, Jun; Bork, Peer

2012-01-01

MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/. PMID:23082188

MOCAT: a metagenomics assembly and gene prediction toolkit.

PubMed

Kultima, Jens Roat; Sunagawa, Shinichi; Li, Junhua; Chen, Weineng; Chen, Hua; Mende, Daniel R; Arumugam, Manimozhiyan; Pan, Qi; Liu, Binghang; Qin, Junjie; Wang, Jun; Bork, Peer

2012-01-01

MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/.

Particulate matter and polycyclic aromatic hydrocarbons from forest fires: impacts on air quality and occupational risks assessment

NASA Astrophysics Data System (ADS)

Oliveira, Marta Madalena Marques de

As piroxenas sao um vasto grupo de silicatos minerais encontrados em muitas rochas igneas e metamorficas. Na sua forma mais simples, estes silicatos sao constituidas por cadeias de SiO3 ligando grupos tetrahedricos de SiO4. A formula quimica geral das piroxenas e M2M1T2O6, onde M2 se refere a catioes geralmente em uma coordenacao octaedrica distorcida (Mg2+, Fe2+, Mn2+, Li+, Ca2+, Na+), M1 refere-se a catioes numa coordenacao octaedrica regular (Al3+, Fe3+, Ti4+, Cr3+, V3+, Ti3+, Zr4+, Sc3+, Zn2+, Mg2+, Fe2+, Mn2+), e T a catioes em coordenacao tetrahedrica (Si4+, Al3+, Fe3+). As piroxenas com estrutura monoclinica sao designadas de clinopiroxenes. A estabilidade das clinopyroxenes num espectro de composicoes quimicas amplo, em conjugacao com a possibilidade de ajustar as suas propriedades fisicas e quimicas e a durabilidade quimica, tem gerado um interesse mundial devido a suas aplicacoes em ciencia e tecnologia de materiais. Este trabalho trata do desenvolvimento de vidros e de vitro-cerâmicos baseadas de clinopiroxenas para aplicacoes funcionais. O estudo teve objectivos cientificos e tecnologicos; nomeadamente, adquirir conhecimentos fundamentais sobre a formacao de fases cristalinas e solucoes solidas em determinados sistemas vitro-cerâmicos, e avaliar a viabilidade de aplicacao dos novos materiais em diferentes areas tecnologicas, com especial enfase sobre a selagem em celulas de combustivel de oxido solido (SOFC). Com este intuito, prepararam-se varios vidros e materiais vitro-cerâmicos ao longo das juntas Enstatite (MgSiO3) - diopsidio (CaMgSi2O6) e diopsidio (CaMgSi2O6) - Ca - Tschermak (CaAlSi2O6), os quais foram caracterizados atraves de um vasto leque de tecnicas. Todos os vidros foram preparados por fusao-arrefecimento enquanto os vitro-cerâmicos foram obtidos quer por sinterizacao e cristalizacao de fritas, quer por nucleacao e cristalizacao de vidros monoliticos. Estudaram-se ainda os efeitos de varias substituicoes ionicas em composicoes de diopsidio contendo Al na estrutura, sinterizacao e no comportamento durante a cristalizacao de vidros e nas propriedades dos materiais vitro-cerâmicos, com relevância para a sua aplicacao como selantes em SOFC. Verificou-se que Foi observado que os vidros/vitro-cerâmicos a base de enstatite nao apresentavam as caracteristicas necessarias para serem usados como materiais selantes em SOFC, enquanto as melhores propriedades apresentadas pelos vitro-cerâmicos a base de diopsidio qualificaram-nos para futuros estudos neste tipo de aplicacoes. Para alem de investigar a adequacao dos vitro-cerâmicos a base de clinopyroxene como selantes, esta tese tem tambem como objetivo estudar a influencia dos agentes de nucleacao na nucleacao em volume dos vitro-cerâmicos resultantes a base de diopsidio, de modo a qualifica-los como potenciais materiais hopedeiros de residuos nucleares radioactivos.

Reciprocal interaction between human microvascular endothelial cells and mesenchymal stem cells on macroporous granules of nanostructured-hydroxyapatite agglomerates

NASA Astrophysics Data System (ADS)

Laranjeira, Marta de Sousa

As piroxenas sao um vasto grupo de silicatos minerais encontrados em muitas rochas igneas e metamorficas. Na sua forma mais simples, estes silicatos sao constituidas por cadeias de SiO3 ligando grupos tetrahedricos de SiO4. A formula quimica geral das piroxenas e M2M1T2O6, onde M2 se refere a catioes geralmente em uma coordenacao octaedrica distorcida (Mg2+, Fe2+, Mn2+, Li+, Ca2+, Na+), M1 refere-se a catioes numa coordenacao octaedrica regular (Al3+, Fe3+, Ti4+, Cr3+, V3+, Ti3+, Zr4+, Sc3+, Zn2+, Mg2+, Fe2+, Mn2+), e T a catioes em coordenacao tetrahedrica (Si4+, Al3+, Fe3+). As piroxenas com estrutura monoclinica sao designadas de clinopiroxenes. A estabilidade das clinopyroxenes num espectro de composicoes quimicas amplo, em conjugacao com a possibilidade de ajustar as suas propriedades fisicas e quimicas e a durabilidade quimica, tem gerado um interesse mundial devido a suas aplicacoes em ciencia e tecnologia de materiais. Este trabalho trata do desenvolvimento de vidros e de vitro-cerâmicos baseadas de clinopiroxenas para aplicacoes funcionais. O estudo teve objectivos cientificos e tecnologicos; nomeadamente, adquirir conhecimentos fundamentais sobre a formacao de fases cristalinas e solucoes solidas em determinados sistemas vitro-cerâmicos, e avaliar a viabilidade de aplicacao dos novos materiais em diferentes areas tecnologicas, com especial enfase sobre a selagem em celulas de combustivel de oxido solido (SOFC). Com este intuito, prepararam-se varios vidros e materiais vitro-cerâmicos ao longo das juntas Enstatite (MgSiO3) - diopsidio (CaMgSi2O6) e diopsidio (CaMgSi2O6) - Ca - Tschermak (CaAlSi2O6), os quais foram caracterizados atraves de um vasto leque de tecnicas. Todos os vidros foram preparados por fusao-arrefecimento enquanto os vitro-cerâmicos foram obtidos quer por sinterizacao e cristalizacao de fritas, quer por nucleacao e cristalizacao de vidros monoliticos. Estudaram-se ainda os efeitos de varias substituicoes ionicas em composicoes de diopsidio contendo Al na estrutura, sinterizacao e no comportamento durante a cristalizacao de vidros e nas propriedades dos materiais vitro-cerâmicos, com relevância para a sua aplicacao como selantes em SOFC. Verificou-se que Foi observado que os vidros/vitro-cerâmicos a base de enstatite nao apresentavam as caracteristicas necessarias para serem usados como materiais selantes em SOFC, enquanto as melhores propriedades apresentadas pelos vitro-cerâmicos a base de diopsidio qualificaram-nos para futuros estudos neste tipo de aplicacoes. Para alem de investigar a adequacao dos vitro-cerâmicos a base de clinopyroxene como selantes, esta tese tem tambem como objetivo estudar a influencia dos agentes de nucleacao na nucleacao em volume dos vitro-cerâmicos resultantes a base de diopsidio, de modo a qualifica-los como potenciais materiais hopedeiros de residuos nucleares radioactivos.

Analysis of vegetation dynamics using time-series vegetation index data from Earth observation satellites

NASA Astrophysics Data System (ADS)

Rodrigues, Arlete da Silva

As piroxenas sao um vasto grupo de silicatos minerais encontrados em muitas rochas igneas e metamorficas. Na sua forma mais simples, estes silicatos sao constituidas por cadeias de SiO3 ligando grupos tetrahedricos de SiO4. A formula quimica geral das piroxenas e M2M1T2O6, onde M2 se refere a catioes geralmente em uma coordenacao octaedrica distorcida (Mg2+, Fe2+, Mn2+, Li+, Ca2+, Na+), M1 refere-se a catioes numa coordenacao octaedrica regular (Al3+, Fe3+, Ti4+, Cr3+, V3+, Ti3+, Zr4+, Sc3+, Zn2+, Mg2+, Fe2+, Mn2+), e T a catioes em coordenacao tetrahedrica (Si4+, Al3+, Fe3+). As piroxenas com estrutura monoclinica sao designadas de clinopiroxenes. A estabilidade das clinopyroxenes num espectro de composicoes quimicas amplo, em conjugacao com a possibilidade de ajustar as suas propriedades fisicas e quimicas e a durabilidade quimica, tem gerado um interesse mundial devido a suas aplicacoes em ciencia e tecnologia de materiais. Este trabalho trata do desenvolvimento de vidros e de vitro-cerâmicos baseadas de clinopiroxenas para aplicacoes funcionais. O estudo teve objectivos cientificos e tecnologicos; nomeadamente, adquirir conhecimentos fundamentais sobre a formacao de fases cristalinas e solucoes solidas em determinados sistemas vitro-cerâmicos, e avaliar a viabilidade de aplicacao dos novos materiais em diferentes areas tecnologicas, com especial enfase sobre a selagem em celulas de combustivel de oxido solido (SOFC). Com este intuito, prepararam-se varios vidros e materiais vitro-cerâmicos ao longo das juntas Enstatite (MgSiO3) - diopsidio (CaMgSi2O6) e diopsidio (CaMgSi2O6) - Ca - Tschermak (CaAlSi2O6), os quais foram caracterizados atraves de um vasto leque de tecnicas. Todos os vidros foram preparados por fusao-arrefecimento enquanto os vitro-cerâmicos foram obtidos quer por sinterizacao e cristalizacao de fritas, quer por nucleacao e cristalizacao de vidros monoliticos. Estudaram-se ainda os efeitos de varias substituicoes ionicas em composicoes de diopsidio contendo Al na estrutura, sinterizacao e no comportamento durante a cristalizacao de vidros e nas propriedades dos materiais vitro-cerâmicos, com relevância para a sua aplicacao como selantes em SOFC. Verificou-se que Foi observado que os vidros/vitro-cerâmicos a base de enstatite nao apresentavam as caracteristicas necessarias para serem usados como materiais selantes em SOFC, enquanto as melhores propriedades apresentadas pelos vitro-cerâmicos a base de diopsidio qualificaram-nos para futuros estudos neste tipo de aplicacoes. Para alem de investigar a adequacao dos vitro-cerâmicos a base de clinopyroxene como selantes, esta tese tem tambem como objetivo estudar a influencia dos agentes de nucleacao na nucleacao em volume dos vitro-cerâmicos resultantes a base de diopsidio, de modo a qualifica-los como potenciais materiais hopedeiros de residuos nucleares radioactivos.

Biological effects of polyacrylic acid-coated and non-coated superparamagnetic iron oxide nanoparticles in in vitro and in vivo experimental models

NASA Astrophysics Data System (ADS)

Couto, Diana Manuel Mocho de Bastos

As piroxenas sao um vasto grupo de silicatos minerais encontrados em muitas rochas igneas e metamorficas. Na sua forma mais simples, estes silicatos sao constituidas por cadeias de SiO3 ligando grupos tetrahedricos de SiO4. A formula quimica geral das piroxenas e M2M1T2O6, onde M2 se refere a catioes geralmente em uma coordenacao octaedrica distorcida (Mg2+, Fe2+, Mn2+, Li+, Ca2+, Na+), M1 refere-se a catioes numa coordenacao octaedrica regular (Al3+, Fe3+, Ti4+, Cr3+, V3+, Ti3+, Zr4+, Sc3+, Zn2+, Mg2+, Fe2+, Mn2+), e T a catioes em coordenacao tetrahedrica (Si4+, Al3+, Fe3+). As piroxenas com estrutura monoclinica sao designadas de clinopiroxenes. A estabilidade das clinopyroxenes num espectro de composicoes quimicas amplo, em conjugacao com a possibilidade de ajustar as suas propriedades fisicas e quimicas e a durabilidade quimica, tem gerado um interesse mundial devido a suas aplicacoes em ciencia e tecnologia de materiais. Este trabalho trata do desenvolvimento de vidros e de vitro-cerâmicos baseadas de clinopiroxenas para aplicacoes funcionais. O estudo teve objectivos cientificos e tecnologicos; nomeadamente, adquirir conhecimentos fundamentais sobre a formacao de fases cristalinas e solucoes solidas em determinados sistemas vitro-cerâmicos, e avaliar a viabilidade de aplicacao dos novos materiais em diferentes areas tecnologicas, com especial enfase sobre a selagem em celulas de combustivel de oxido solido (SOFC). Com este intuito, prepararam-se varios vidros e materiais vitro-cerâmicos ao longo das juntas Enstatite (MgSiO3) - diopsidio (CaMgSi2O6) e diopsidio (CaMgSi2O6) - Ca - Tschermak (CaAlSi2O6), os quais foram caracterizados atraves de um vasto leque de tecnicas. Todos os vidros foram preparados por fusao-arrefecimento enquanto os vitro-cerâmicos foram obtidos quer por sinterizacao e cristalizacao de fritas, quer por nucleacao e cristalizacao de vidros monoliticos. Estudaram-se ainda os efeitos de varias substituicoes ionicas em composicoes de diopsidio contendo Al na estrutura, sinterizacao e no comportamento durante a cristalizacao de vidros e nas propriedades dos materiais vitro-cerâmicos, com relevância para a sua aplicacao como selantes em SOFC. Verificou-se que Foi observado que os vidros/vitro-cerâmicos a base de enstatite nao apresentavam as caracteristicas necessarias para serem usados como materiais selantes em SOFC, enquanto as melhores propriedades apresentadas pelos vitro-cerâmicos a base de diopsidio qualificaram-nos para futuros estudos neste tipo de aplicacoes. Para alem de investigar a adequacao dos vitro-cerâmicos a base de clinopyroxene como selantes, esta tese tem tambem como objetivo estudar a influencia dos agentes de nucleacao na nucleacao em volume dos vitro-cerâmicos resultantes a base de diopsidio, de modo a qualifica-los como potenciais materiais hopedeiros de residuos nucleares radioactivos.

Impact evaluation of the large scale integration of electric vehicles in the security of supply

NASA Astrophysics Data System (ADS)

Bremermann, Leonardo Elizeire

As piroxenas sao um vasto grupo de silicatos minerais encontrados em muitas rochas igneas e metamorficas. Na sua forma mais simples, estes silicatos sao constituidas por cadeias de SiO3 ligando grupos tetrahedricos de SiO4. A formula quimica geral das piroxenas e M2M1T2O6, onde M2 se refere a catioes geralmente em uma coordenacao octaedrica distorcida (Mg2+, Fe2+, Mn2+, Li+, Ca2+, Na+), M1 refere-se a catioes numa coordenacao octaedrica regular (Al3+, Fe3+, Ti4+, Cr3+, V3+, Ti3+, Zr4+, Sc3+, Zn2+, Mg2+, Fe2+, Mn2+), e T a catioes em coordenacao tetrahedrica (Si4+, Al3+, Fe3+). As piroxenas com estrutura monoclinica sao designadas de clinopiroxenes. A estabilidade das clinopyroxenes num espectro de composicoes quimicas amplo, em conjugacao com a possibilidade de ajustar as suas propriedades fisicas e quimicas e a durabilidade quimica, tem gerado um interesse mundial devido a suas aplicacoes em ciencia e tecnologia de materiais. Este trabalho trata do desenvolvimento de vidros e de vitro-cerâmicos baseadas de clinopiroxenas para aplicacoes funcionais. O estudo teve objectivos cientificos e tecnologicos; nomeadamente, adquirir conhecimentos fundamentais sobre a formacao de fases cristalinas e solucoes solidas em determinados sistemas vitro-cerâmicos, e avaliar a viabilidade de aplicacao dos novos materiais em diferentes areas tecnologicas, com especial enfase sobre a selagem em celulas de combustivel de oxido solido (SOFC). Com este intuito, prepararam-se varios vidros e materiais vitro-cerâmicos ao longo das juntas Enstatite (MgSiO3) - diopsidio (CaMgSi2O6) e diopsidio (CaMgSi2O6) - Ca - Tschermak (CaAlSi2O6), os quais foram caracterizados atraves de um vasto leque de tecnicas. Todos os vidros foram preparados por fusao-arrefecimento enquanto os vitro-cerâmicos foram obtidos quer por sinterizacao e cristalizacao de fritas, quer por nucleacao e cristalizacao de vidros monoliticos. Estudaram-se ainda os efeitos de varias substituicoes ionicas em composicoes de diopsidio contendo Al na estrutura, sinterizacao e no comportamento durante a cristalizacao de vidros e nas propriedades dos materiais vitro-cerâmicos, com relevância para a sua aplicacao como selantes em SOFC. Verificou-se que Foi observado que os vidros/vitro-cerâmicos a base de enstatite nao apresentavam as caracteristicas necessarias para serem usados como materiais selantes em SOFC, enquanto as melhores propriedades apresentadas pelos vitro-cerâmicos a base de diopsidio qualificaram-nos para futuros estudos neste tipo de aplicacoes. Para alem de investigar a adequacao dos vitro-cerâmicos a base de clinopyroxene como selantes, esta tese tem tambem como objetivo estudar a influencia dos agentes de nucleacao na nucleacao em volume dos vitro-cerâmicos resultantes a base de diopsidio, de modo a qualifica-los como potenciais materiais hopedeiros de residuos nucleares radioactivos.

Reuse of de-inking sludge from wastepaper recycling in cement mortar products.

PubMed

Yan, Shiqin; Sagoe-Crentsil, Kwesi; Shapiro, Gretta

2011-08-01

This paper presents results of an investigation into the use of de-inking sludge from a paper recycling mill as feedstock material in the manufacture of cement mortar products, including masonry blocks and mortar renders. Both physical and mechanical properties of mortar specimens containing various amounts of de-inking sludge were investigated. It was observed that the addition of de-inking sludge to cement mortar at a fixed water-to-cement ratio significantly reduced flow properties and increased setting time. Water absorption and volume of permeable voids of cement mortar increased with increased dosage of de-inking sludge, with a corresponding reduction of bulk density. The 91-day compressive strength of mortar samples with 2.5 wt% and 20 wt% de-inking sludge loadings retained 83% and 62% respectively of the reference mortar strength. The corresponding drying shrinkage increased by up to 160% compared to reference samples. However, a de-inking sludge loading of up to 2.5 wt% did not significantly alter measured physical and mechanical properties. The results demonstrate that despite the high moisture absorbance of de-inking sludge due to its organic matter and residual cellulose fibre content, it serves as a potential supplementary additive and its cellulosic content proving to be an active set retardant to cementitious masonry products. Copyright © 2011 Elsevier Ltd. All rights reserved.

Temps d'Educacio. Revista de la Divisio de Ciencies de l'Educacio (Educational Times. Journal of the Education Sciences Department. Numbers 13 & 14).

ERIC Educational Resources Information Center

Temps d'Educacio, 1995

1995-01-01

Each of the two issues of this Catalan-language journal offers book reviews and articles on general topics in education. Issues contain Spanish-, English- and French-language abstracts of included articles with keyword references. Number 13 (1st. semester 1995) examines environmental and multicultural education; number 14 (2nd. semester 1995)…

Contour maps of lunar remanent magnetic fields

NASA Technical Reports Server (NTRS)

Hood, L. L.; Russell, C. T.; Coleman, P. J., Jr.

1981-01-01

The 2605 usable orbits of Apollo 15 and 16 subsatellite magnetometer data have been reexamined for intervals suitable for analysis of crustal magnetic anomalies. To minimize plasma-related disturbances, segments from 274 of these orbits were selected from times when the moon was either in a lobe of the geomagnetic tail or in the solar wind with the subsatellites in the lunar wake. External field contributions which remained in the selected intervals were minimized by (1) quadratic detrending of individual orbit segments with lengths much greater than anomaly wavelengths and (2) two-dimensional filtering with minimum passed wavelengths less than or equal to anomaly wavelengths. Improvements in coverage, accuracy, and resolution of previously published anomaly maps produced from these data are obtained. In addition to improved maps of the Reiner Gamma and Van de Graaff-Aitken anomalies studied previously, a third region of relatively high-amplitude anomalies centered near the crater Gerasimovich on the southeastern far side has been mapped. Both the Van de Graaff-Aitken region and the Gerasimovich region are marked by the general occurrence of extensive groups of Reiner Gamma-type swirls.

Myocardial Mapping With Cardiac Magnetic Resonance: The Diagnostic Value of Novel Sequences.

PubMed

Sanz, Javier; LaRocca, Gina; Mirelis, Jesús G

2016-09-01

Cardiac magnetic resonance has evolved into a crucial modality for the evaluation of cardiomyopathy due to its ability to characterize myocardial structure and function. In the last few years, interest has increased in the potential of "mapping" techniques that provide direct and objective quantification of myocardial properties such as T1, T2, and T2* times. These approaches enable the detection of abnormalities that affect the myocardium in a diffuse fashion and/or may be too subtle for visual recognition. This article reviews the current state of myocardial T1 and T2-mapping in both health and disease. Copyright © 2016 Sociedad Española de Cardiología. Published by Elsevier España, S.L.U. All rights reserved.

78 FR 58334 - Proposed Flood Hazard Determinations

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-23

.... Upper Great Miami, Indiana, Ohio Watershed Shelby County, Ohio, and Incorporated Areas Maps Available... De Tour Village Hall, 260 South Superior Street, De Tour Village, MI 49725. Erie County, Ohio, and... Watershed Lawrence County, Ohio, and Incorporated Areas Maps Available for Inspection Online at: www.fema...

Minimum Map of Social Institutional Network: a multidimensional strategy for research in Nursing.

PubMed

Carlos, Diene Monique; Pádua, Elisabete Matallo Marchesini de; Nakano, Ana Márcia Spanó; Ferriani, Maria das Graças Carvalho

2016-06-01

To analyze the use of methodological strategies in qualitative research - Minimum Maps of Social Institutional Network, as proposed to understand the phenomena in the multidimensional perspective. Methodological theoretical essay in which we aimed to reflect on the use of innovative methodological strategies in nursing research, supported in Complex Paradigm fundamentals. The minimum map of Social Institutional External Network aims to identify institutional linkages and gaps for the intervention work of the surveyed institutions. The use of these maps provided important advances in know-how qualitative research in Health and Nursing. In this perspective, the use of minimum Social Intitutional Network maps can be stimulated and enhanced to meet the current demands of the contemporary world, particularly for its flexibility in adapting to various research subjects; breadth and depth of discussion; and possibilities with health services. Analisar o uso de estratégias metodológicas em pesquisas qualitativas - Mapa mínimo da Rede Social Institucional, como proposta para compreender os fenômenos na perspectiva multidimensional. Ensaio teórico metodológico em que buscou-se refletir sobre o uso de estratégias metodológicas inovadoras de pesquisa na enfermagem, sustentada nos fundamentos do Pensamento Complexo. O mapa mínimo da Rede Social Institucional Externa tem o objetivo de identificar os vínculos institucionais e lacunas para o trabalho de intervenção das instituições pesquisadas. O uso destes mapas proporcionou avanços importantes no saber-fazer pesquisa qualitativa em Saúde e Enfermagem. Nessa perspectiva, o uso de mapas mínimos da Rede Social Institucional pode ser estimulado e potencializado para responder às atuais demandas da contemporaneidade, em especial pela sua flexibilidade na adequação a diversos objetos de pesquisa; amplitude e profundidade de discussão; e possibilidades de articulação com a prática dos serviços.

JPRS Report, Reference Aid: Glossary of Acronyms and Abbreviations of Spain

DTIC Science & Technology

1988-12-01

Emigraciön INSS Instituto Nacional de la Seguridad Social INTA Instituto Nacional de Tecnica Aeroespacial INTUSA Industrias Turisticas, S. A. INUR...Marconi Espafiola, S. A. META (plan de) Modernizaciön del Ejercito de Tierra MFCS Medidas destinadas a Fomentar la Confianza y Seguridad MIL...Favored-Nations System S/R (S/Ref.) su referenda your reference SS Seguridad Social SSUPC Sistema de Seguimiento de Uso de la Celula Social

Assembly and diploid architecture of an individual human genome via single-molecule technologies

PubMed Central

Pendleton, Matthew; Sebra, Robert; Pang, Andy Wing Chun; Ummat, Ajay; Franzen, Oscar; Rausch, Tobias; Stütz, Adrian M; Stedman, William; Anantharaman, Thomas; Hastie, Alex; Dai, Heng; Fritz, Markus Hsi-Yang; Cao, Han; Cohain, Ariella; Deikus, Gintaras; Durrett, Russell E; Blanchard, Scott C; Altman, Roger; Chin, Chen-Shan; Guo, Yan; Paxinos, Ellen E; Korbel, Jan O; Darnell, Robert B; McCombie, W Richard; Kwok, Pui-Yan; Mason, Christopher E; Schadt, Eric E; Bashir, Ali

2015-01-01

We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality. PMID:26121404

Assembly and diploid architecture of an individual human genome via single-molecule technologies.

PubMed

Pendleton, Matthew; Sebra, Robert; Pang, Andy Wing Chun; Ummat, Ajay; Franzen, Oscar; Rausch, Tobias; Stütz, Adrian M; Stedman, William; Anantharaman, Thomas; Hastie, Alex; Dai, Heng; Fritz, Markus Hsi-Yang; Cao, Han; Cohain, Ariella; Deikus, Gintaras; Durrett, Russell E; Blanchard, Scott C; Altman, Roger; Chin, Chen-Shan; Guo, Yan; Paxinos, Ellen E; Korbel, Jan O; Darnell, Robert B; McCombie, W Richard; Kwok, Pui-Yan; Mason, Christopher E; Schadt, Eric E; Bashir, Ali

2015-08-01

We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality.

Geologic map of the western Haji-Gak iron deposit, Bamyan Province, Afghanistan, modified from the 1965 original map compilation of V.V. Reshetniak and I.K. Kusov

USGS Publications Warehouse

Renaud, Karine M.; Tucker, Robert D.; Peters, Stephen G.; Stettner, Will R.; Masonic, Linda M.; Moran, Thomas W.

2011-01-01

This map is a modified version of Geologic-prospecting plan of western area of Hajigak iron-ore deposit, scale 1:2,000, which was compiled by V.V. Reshetniak and I.K. Kusov in 1965. (Refer to the References Cited section in the Map PDF for complete citations of the original map and related reports.) USGS scientists, in cooperation with the Afghan Geological Survey and the Task Force for Business and Stability Operations of the U.S. Department of Defense, studied the original documents and also visited the field area in November 2009. This modified map illustrates the geological structure of the western Haji-Gak iron deposit and includes cross sections of the same area. The map reproduces the topology (contacts, faults, and so forth) of the original Soviet map and includes modifications based on our examination of that document. We constructed the cross sections from data derived from the original map. Elevations on the cross sections are derived from the original Soviet topography and may not match the newer topography used on the current map. We have attempted to translate the original Russian terminology and rock classification into modern English geologic usage as literally as possible without changing any genetic or process-oriented implications in the original descriptions. We also use the age designations from the original map. The unit colors on the map and cross sections differ from the colors shown on the original version. The units are colored according to the color and pattern scheme of the Commission for the Geological Map of the World (CGMW) (http://www.ccgm.org).

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

PubMed

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

2018-06-25

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

Site characterization and site response in Port-au-Prince, Haiti

USGS Publications Warehouse

Hough, Susan E.; Yong, Alan K.; Altidor, Jean Robert; Anglade, Dieuseul; Given, Douglas D.; Mildor, Saint-Louis

2011-01-01

Waveform analysis of aftershocks of the Mw7.0 Haiti earthquake of 12 January 2010 reveals amplification of ground motions at sites within the Cul de Sac valley in which Port-au-Prince is situated. Relative to ground motions recorded at a hard-rock reference site, peak acceleration values are amplified by a factor of approximately 1.8 at sites on low-lying Mio-Pliocene deposits in central Port-au-Prince and by a factor of approximately 2.5–3 on a steep foothill ridge in the southern Port-au-Prince metropolitan region. The observed amplitude, predominant periods, variability, and polarization of amplification are consistent with predicted topographic amplification by a steep, narrow ridge. A swath of unusually high damage in this region corresponds with the extent of the ridge where high weak-motion amplifications are observed. We use ASTER (Advanced Spaceborne Thermal Emission and Reflection Radiometer) imagery to map local geomorphology, including characterization of both near-surface and of small-scale topographic structures that correspond to zones of inferred amplification.

Embodied Interaction Priority: Other's Body Part Affects Numeral-Space Mappings.

PubMed

You, Xuqun; Zhang, Yu; Zhu, Rongjuan; Guo, Yu

2018-01-01

Traditionally, the spatial-numerical association of response codes (SNARC) effect was presented in two-choice condition, in which only one individual reacted to both even (small) and odd (large) numbers. Few studies explored SNARC effect in a social situation. Moreover, there are many reference frames involved in SNARC effect, and it has not yet been investigated which reference frame is dominated when two participants perform the go-nogo task together. In the present study, we investigated which reference frame plays a primary role in SNARC effect when allocentric and egocentric reference frames were consistent or inconsistent in social settings. Furthermore, we explored how two actors corepresent number-space mapping interactively. Results of the two experiments demonstrated that egocentric reference frame was at work primarily when two reference frames were consistent and inconsistent. This shows that body-centered coordinate frames influence number-space mapping in social settings, and one actor may represent another actor's action and tasks.

Adaptive optimization of reference intensity for optical coherence imaging using galvanometric mirror tilting method

NASA Astrophysics Data System (ADS)

Kim, Ji-hyun; Han, Jae-Ho; Jeong, Jichai

2015-09-01

Integration time and reference intensity are important factors for achieving high signal-to-noise ratio (SNR) and sensitivity in optical coherence tomography (OCT). In this context, we present an adaptive optimization method of reference intensity for OCT setup. The reference intensity is automatically controlled by tilting a beam position using a Galvanometric scanning mirror system. Before sample scanning, the OCT system acquires two dimensional intensity map with normalized intensity and variables in color spaces using false-color mapping. Then, the system increases or decreases reference intensity following the map data for optimization with a given algorithm. In our experiments, the proposed method successfully corrected the reference intensity with maintaining spectral shape, enabled to change integration time without manual calibration of the reference intensity, and prevented image degradation due to over-saturation and insufficient reference intensity. Also, SNR and sensitivity could be improved by increasing integration time with automatic adjustment of the reference intensity. We believe that our findings can significantly aid in the optimization of SNR and sensitivity for optical coherence tomography systems.

Advanced concentration analysis of atom probe tomography data: Local proximity histograms and pseudo-2D concentration maps.

PubMed

Felfer, Peter; Cairney, Julie

2018-06-01

Analysing the distribution of selected chemical elements with respect to interfaces is one of the most common tasks in data mining in atom probe tomography. This can be represented by 1D concentration profiles, 2D concentration maps or proximity histograms, which represent concentration, density etc. of selected species as a function of the distance from a reference surface/interface. These are some of the most useful tools for the analysis of solute distributions in atom probe data. In this paper, we present extensions to the proximity histogram in the form of 'local' proximity histograms, calculated for selected parts of a surface, and pseudo-2D concentration maps, which are 2D concentration maps calculated on non-flat surfaces. This way, local concentration changes at interfaces or and other structures can be assessed more effectively. Copyright © 2018 Elsevier B.V. All rights reserved.

Reference-guided assembly of four diverse Arabidopsis thaliana genomes

PubMed Central

Schneeberger, Korbinian; Ossowski, Stephan; Ott, Felix; Klein, Juliane D.; Wang, Xi; Lanz, Christa; Smith, Lisa M.; Cao, Jun; Fitz, Joffrey; Warthmann, Norman; Henz, Stefan R.; Huson, Daniel H.; Weigel, Detlef

2011-01-01

We present whole-genome assemblies of four divergent Arabidopsis thaliana strains that complement the 125-Mb reference genome sequence released a decade ago. Using a newly developed reference-guided approach, we assembled large contigs from 9 to 42 Gb of Illumina short-read data from the Landsberg erecta (Ler-1), C24, Bur-0, and Kro-0 strains, which have been sequenced as part of the 1,001 Genomes Project for this species. Using alignments against the reference sequence, we first reduced the complexity of the de novo assembly and later integrated reads without similarity to the reference sequence. As an example, half of the noncentromeric C24 genome was covered by scaffolds that are longer than 260 kb, with a maximum of 2.2 Mb. Moreover, over 96% of the reference genome was covered by the reference-guided assembly, compared with only 87% with a complete de novo assembly. Comparisons with 2 Mb of dideoxy sequence reveal that the per-base error rate of the reference-guided assemblies was below 1 in 10,000. Our assemblies provide a detailed, genomewide picture of large-scale differences between A. thaliana individuals, most of which are difficult to access with alignment-consensus methods only. We demonstrate their practical relevance in studying the expression differences of polymorphic genes and show how the analysis of sRNA sequencing data can lead to erroneous conclusions if aligned against the reference genome alone. Genome assemblies, raw reads, and further information are accessible through http://1001genomes.org/projects/assemblies.html. PMID:21646520

Mapping wildland fuels for fire management across multiple scales: integrating remote sensing, GIS, and biophysical modeling

USGS Publications Warehouse

Keane, Robert E.; Burgan, Robert E.; Van Wagtendonk, Jan W.

2001-01-01

Fuel maps are essential for computing spatial fire hazard and risk and simulating fire growth and intensity across a landscape. However, fuel mapping is an extremely difficult and complex process requiring expertise in remotely sensed image classification, fire behavior, fuels modeling, ecology, and geographical information systems (GIS). This paper first presents the challenges of mapping fuels: canopy concealment, fuelbed complexity, fuel type diversity, fuel variability, and fuel model generalization. Then, four approaches to mapping fuels are discussed with examples provided from the literature: (1) field reconnaissance; (2) direct mapping methods; (3) indirect mapping methods; and (4) gradient modeling. A fuel mapping method is proposed that uses current remote sensing and image processing technology. Future fuel mapping needs are also discussed which include better field data and fuel models, accurate GIS reference layers, improved satellite imagery, and comprehensive ecosystem models.

Deriving Daily Time Series Evapotranspiration, Evaporation and Transpiration Maps With Landsat Data

NASA Astrophysics Data System (ADS)

Paul, G.; Gowda, P. H.; Marek, T.; Xiao, X.; Basara, J. B.

2014-12-01

Mapping high resolution evapotranspiration (ET) over large region at daily time step is complex and computationally intensive. Utility of high resolution daily ET maps are large ranging from crop water management to watershed management. The aim of this work is to generate daily time series (10 years) ET and its components vegetation transpiration (T) and soil water evaporation (E) maps using Landsat 5 satellite data for Southern Great Plains forage-rangeland-winter wheat production system in Oklahoma (OK). Framework for generating these products included the two source energy balance (TSEB) algorithm and other important features were: (a) atmospheric correction algorithm; (b) spatially interpolated weather inputs; (c) functions for varying Priestley-Taylor coefficient; and (d) ET, E and T extrapolating algorithm utilizing reference ET. An extensive network of 140 weather stations managed by Oklahoma Mesonet was utilized to generate spatially interpolated inputs of air temperature, relative humidity, wind speed, solar radiation, pressure, and reference ET. Validation of the ET maps were done against eddy covariance data from two grassland sites at El Reno, OK suggested good performance (Table 1). Figure 1 illustrates a daily ET map for a very small subset of 18thJuly 2006 ET map, where difference in ET among different land uses such as the irrigated cropland, vegetation along drainage, and grassland is very distinct. Results indicated that the proposed ET mapping framework is suitable for deriving high resolution time series daily ET maps at regional scale with Landsat Thematic Mapper data. . Table 1: Daily actual ET performance statistics for two grassland locations at El Reno OK for year 2005 . Management Type Mean (obs) (mm d-1) Mean (est) (mm d-1) MBE (mm d-1) % MBE (%) RMSE (mm d-1) RMSE (%) MAE (mm d-1) MAPD (%) NSE R2 Control 2.2 1.8 -0.43 -19.4 0.87 38.9 0.65 29.5 0.71 0.79 Burnt 2.0 1.8 -0.15 -7.7 0.80 39.8 0.62 30.7 0.73 0.77

Preliminary metallogenic belt and mineral deposit maps for northeast Asia

USGS Publications Warehouse

Obolenskiy, Alexander A.; Rodionov, Sergey M.; Dejidmaa, Gunchin; Gerel, Ochir; Hwang, Duk-Hwan; Distanov, Elimir G.; Badarch, Gombosuren; Khanchuk, Alexander I.; Ogasawara, Masatsugu; Nokleberg, Warren J.; Parfenov, Leonid M.; Prokopiev, Andrei V.; Seminskiy, Zhan V.; Smelov, Alexander P.; Yan, Hongquan; Birul'kin, Gennandiy V.; Davydov, Yuriy V.V.; Fridovskiy, Valeriy Yu.; Gamyanin, Gennandiy N.; Kostin, Alexei V.; Letunov, Sergey A.; Li, Xujun; Nikitin, Valeriy M.; Sotnikov, Sadahisa; Sudo, Vitaly I.; Spiridonov, Alexander V.; Stepanov, Vitaly A.; Sun, Fengyue; Sun, Jiapeng; Sun, Weizhi; Supletsov, Valeriy M.; Timofeev, Vladimir F.; Tyan, Oleg A.; Vetluzhskikh, Valeriy G.; Wakita, Koji; Yakovlev, Yakov V.; Zorina, Lydia M.

2003-01-01

The metallogenic belts and locations of major mineral deposits of Northeast Asia are portrayed on Sheets 1-4. Sheet 1 portrays the location of significant lode deposits and placer districts at a scale of 1:7,500,000. Sheets 2-4 portray the metallogenic belts of the region in a series of 12 time-slices from the Archean through the Quaternary at a scale of 1:15,000,000. For all four map sheets, a generalized geodynamics base map, derived from a more detailed map by Parfenov and others (2003), is used as an underlay for the metallogenic belt maps. This geodynamics map underlay permits depicts the major host geologic units and structures that host metallogenic belts. Four tables are included in this report. A hierarchial ranking of mineral deposit models is listed in Table 1. And summary features of lode deposits, placer districts, and metallogenic belts are described in Tables 2, 3, and 4, respectively. The metallogenic belts for Northeast Asia are synthesized, compiled, described, and interpreted with the use of modern concepts of plate tectonics, analysis of terranes and overlap assemblages, and synthesis of mineral deposit models. The data supporting the compilation are: (1) comprehensive descriptions of mineral deposits; (2) compilation and synthesis of a regional geodynamics map the region at 5 million scale with detailed explanations and cited references; and (3) compilation and synthesis of metallogenic belt maps at 15 million scale with detailed explanations and cited references. These studies are part of a major international collaborative study of the Mineral Resources, Metallogenesis, and Tectonics of Northeast Asia that is being conducted from 1997 through 2002 by geologists from earth science agencies and universities in Russia, Mongolia, Northeastern China, South Korea, Japan, and the USA. Companion studies and previous publications are: (1) a detailed geodynamics map of Northeast Asia (Parfenov and 2003); (2) a compilation of major mineral deposit models (Rodionov and Nokleberg, 2000; Rodionov and others, 2000; Obolenskiy and others, 2003); and (3) a database on significant metalliferous and selected nonmetalliferous lode deposits, and selected placer districts (Ariunbileg and others, 2003).

Stream channel reference sites: An illustrated guide to field technique

Treesearch

Cheryl C Harrelson; C. L. Rawlins; John P. Potyondy

1994-01-01

This document is a guide to establishing permanent reference sites for gathering data about the physical characteristics of streams and rivers. The minimum procedure consists of the following: (1) select a site, (2) map the site and location, (3) measure the channel cross-section, (4) survey a longitudinal profile of the channel, (5) measure stream flow, (6) measure...

Linkage maps of the Atlantic salmon (Salmo salar) genome derived from RAD sequencing

PubMed Central

2014-01-01

Background Genetic linkage maps are useful tools for mapping quantitative trait loci (QTL) influencing variation in traits of interest in a population. Genotyping-by-sequencing approaches such as Restriction-site Associated DNA sequencing (RAD-Seq) now enable the rapid discovery and genotyping of genome-wide SNP markers suitable for the development of dense SNP linkage maps, including in non-model organisms such as Atlantic salmon (Salmo salar). This paper describes the development and characterisation of a high density SNP linkage map based on SbfI RAD-Seq SNP markers from two Atlantic salmon reference families. Results Approximately 6,000 SNPs were assigned to 29 linkage groups, utilising markers from known genomic locations as anchors. Linkage maps were then constructed for the four mapping parents separately. Overall map lengths were comparable between male and female parents, but the distribution of the SNPs showed sex-specific patterns with a greater degree of clustering of sire-segregating SNPs to single chromosome regions. The maps were integrated with the Atlantic salmon draft reference genome contigs, allowing the unique assignment of ~4,000 contigs to a linkage group. 112 genome contigs mapped to two or more linkage groups, highlighting regions of putative homeology within the salmon genome. A comparative genomics analysis with the stickleback reference genome identified putative genes closely linked to approximately half of the ordered SNPs and demonstrated blocks of orthology between the Atlantic salmon and stickleback genomes. A subset of 47 RAD-Seq SNPs were successfully validated using a high-throughput genotyping assay, with a correspondence of 97% between the two assays. Conclusions This Atlantic salmon RAD-Seq linkage map is a resource for salmonid genomics research as genotyping-by-sequencing becomes increasingly common. This is aided by the integration of the SbfI RAD-Seq SNPs with existing reference maps and the draft reference genome, as well as the identification of putative genes proximal to the SNPs. Differences in the distribution of recombination events between the sexes is evident, and regions of homeology have been identified which are reflective of the recent salmonid whole genome duplication. PMID:24571138

Precise detection of de novo single nucleotide variants in human genomes.

PubMed

Gómez-Romero, Laura; Palacios-Flores, Kim; Reyes, José; García, Delfino; Boege, Margareta; Dávila, Guillermo; Flores, Margarita; Schatz, Michael C; Palacios, Rafael

2018-05-22

The precise determination of de novo genetic variants has enormous implications across different fields of biology and medicine, particularly personalized medicine. Currently, de novo variations are identified by mapping sample reads from a parent-offspring trio to a reference genome, allowing for a certain degree of differences. While widely used, this approach often introduces false-positive (FP) results due to misaligned reads and mischaracterized sequencing errors. In a previous study, we developed an alternative approach to accurately identify single nucleotide variants (SNVs) using only perfect matches. However, this approach could be applied only to haploid regions of the genome and was computationally intensive. In this study, we present a unique approach, coverage-based single nucleotide variant identification (COBASI), which allows the exploration of the entire genome using second-generation short sequence reads without extensive computing requirements. COBASI identifies SNVs using changes in coverage of exactly matching unique substrings, and is particularly suited for pinpointing de novo SNVs. Unlike other approaches that require population frequencies across hundreds of samples to filter out any methodological biases, COBASI can be applied to detect de novo SNVs within isolated families. We demonstrate this capability through extensive simulation studies and by studying a parent-offspring trio we sequenced using short reads. Experimental validation of all 58 candidate de novo SNVs and a selection of non-de novo SNVs found in the trio confirmed zero FP calls. COBASI is available as open source at https://github.com/Laura-Gomez/COBASI for any researcher to use. Copyright © 2018 the Author(s). Published by PNAS.

Ganymede’s stratigraphy and crater distributions in Voyager and Galileo SSI images: results from the anti-jovian hemisphere

NASA Astrophysics Data System (ADS)

Wagner, Roland Josef; Schmedemann, Nico; Stephan, Katrin; Werner, Stephanie; Ivanov, Boris A.; Roatsch, Thomas; Jaumann, Ralf; Palumbo, Pasquale

2017-10-01

Crater size distributions are a valuable tool in planetary stratigraphy to derive the sequence of geologic events. In this study, we extend our previous work [1] in Ganymede’s sub-jovian hemisphere to the anti-jovian hemisphere. For geologic mapping, the map by [2] is used as a reference. Our study provides groundwork for the upcoming imaging by the JANUS camera aboard ESA’s JUICE mission [3]. Voyager-2 images are reprocessed using a map scale of 700 m/pxl achieved for parts of the anti-jovian hemisphere. To obtain relative ages from crater frequencies, we apply an updated crater scaling law for cratering into icy targets in order to derive a crater production function for Ganymede [1]. Also, we adopt the Poisson timing analysis method discussed and implemented recently [4] to obtain relative (and absolute model) ages. Results are compared to those from the sub-jovian hemisphere [1] as well as to support and/or refine the global stratigraphic system by [2]. Further emphasis is placed on local target areas in the anti-jovian hemisphere imaged by Galileo SSI at regional map scales of 100 to 300 m/pxl in order to study local geologic effects and processes. These areas incorporate (1) dark and (2) light tectonized materials, and (3) impact crater materials including an area with numerous secondaries from ray crater Osiris. References: [1] Wagner R. et al. (2014), DPS meeting #46, abstract 418.09. [2] Collins G. et al. (2013), U.S.G.S. Sci. Inv. Map 3237. [3] Della Corte V. et al. (2014), Proc. SPIE 9143, doi:10.1117/12.2056353. [4] Michael G. et al. (2016), Icarus 277, 279-285.

Long Period Seismic Waves

DTIC Science & Technology

1976-08-01

Geoffsica, TPHM. No. 5 , p. 161. Vargas, Freddy (To he published in 1976) 1 .-DTSCRP1TNACTON DE EVENTO«; NATHDALE«; Y ARTTFTCT ALES. 2.- CALCULO DEL...seismic risk, bv de - fininn relative weiqht of maximum MM intensity at a pivon distance ponulation density, area feolupy and attenuation of intensity wit...Population densitv, area peolopv and attenuation of intensitv with distance, is presented topether with a map anplvinp theorv to Bo- livia. ^«^a

Temps d'Educacio. Revista de la Divisio de Ciencies de l'Educacio (Educational Times. Journal of the Education Sciences Department. Volumes 1 & 2).

ERIC Educational Resources Information Center

Temps d'Educacio, 1989

1989-01-01

Each of the 12 issues of this Catalan-language journal offers book reviews and articles on general issues in education. Some issues contain a Spanish-language translation of the Catalan articles; issues 3 and later contain only Spanish-, English- and French-language abstracts of included articles with keyword references. Number 1 (1st. semester…

ARTS: a web-based tool for the set-up of high-throughput genome-wide mapping panels for the SNP genotyping of mouse mutants.

PubMed

Klaften, Matthias; Hrabé de Angelis, Martin

2005-07-01

Genome-wide mapping in the identification of novel candidate genes has always been the standard method in genetics and genomics to correlate a clinically interesting phenotypic trait with a genotype. However, the performance of a mapping experiment using classical microsatellite approaches can be very time consuming. The high-throughput analysis of single-nucleotide polymorphisms (SNPs) has the potential of being the successor of microsatellite analysis routinely used for these mapping approaches, where one of the major obstacles is the design of the appropriate SNP marker set itself. Here we report on ARTS, an advanced retrieval tool for SNPs, which allows researchers to comb freely the public mouse dbSNP database for multiple reference and test strains. Several filters can be applied in order to improve the sensitivity and the specificity of the search results. By employing the panel generator function of this program, it is possible to abbreviate the extraction of reliable sequence data for a large marker panel including several different mouse strains from days to minutes. The concept of ARTS is easily adaptable to other species for which SNP databases are available, making it a versatile tool for the use of SNPs as markers for genotyping. The web interface is accessible at http://andromeda.gsf.de/arts.

Isotopic reconstruction of ancient human migrations: A comprehensive Sr isotope reference database for France and the first case study at Tumulus de Sables, south-western France

NASA Astrophysics Data System (ADS)

Willmes, M.; Boel, C.; Grün, R.; Armstrong, R.; Chancerel, A.; Maureille, B.; Courtaud, P.

2012-04-01

Strontium isotope ratios (87Sr/86Sr) can be used for the reconstruction of human and animal migrations across geologically different terrains. Sr isotope ratios in rocks are a product of age and composition and thus vary between geologic units. From the eroding environment Sr is transported into the soils, plants and rivers of a region. Humans and animals incorporate Sr from their diet into their bones and teeth, where it substitutes for calcium. Tooth enamel contains Sr isotope signatures acquired during childhood and is most resistant to weathering and overprinting, while the dentine is often diagenetically altered towards the local Sr signature. For the reconstruction of human and animal migrations the tooth enamel 87Sr/86Sr ratio is compared to the Sr isotope signature in the vicinity of the burial site and the surrounding area. This study focuses on the establishment of a comprehensive reference map of bioavailable 87Sr/86Sr ratios for France. In a next step we will compare human and animal teeth from key archaeological sites to this reference map to investigate mobility. So far, we have analysed plant and soil samples from ~200 locations across France including the Aquitaine basin, the western and northern parts of the Paris basin, as well as three transects through the Pyrenees Mountains. The isotope data, geologic background information (BRGM 1:1M), field images, and detailed method descriptions are available through our online database iRhum (http://rses.anu.edu.au/research/ee). This database can also be used in forensic studies and food sciences. As an archaeological case study teeth from 16 adult and 8 juvenile individuals were investigated from an early Bell Beaker (2500-2000 BC) site at Le Tumulus des Sables, south-west France (Gironde). The teeth were analysed for Sr isotope ratios using laser ablation ICP-MS. Four teeth were also analysed using solution ICP-MS, which showed a significant offset to the laser ablation results. This requires further detailed investigation. Nevertheless, the teeth showed clear differences between enamel and diagenetically overprinted dentine, which suggests mobility. Unfortunately, the sandy sediment units in the close vicinity of Le Tumulus des Sables show large variations in their 87Sr/86Sr ratios so it is currently not possible to distinguish between migration from outside of the Médoc region from mobility within the region based solely on Sr isotope ratios. The case study illustrates the importance of detailed reference maps, which are required for any isotope studies used for the reconstruction of migrations. Other isotope data, such as O and Pb, will complement the investigation at Tumulus de Sables and may enable us to tie down the range of mobility of the humans that were buried at Le Tumulus des Sables.

PeRL: a circum-Arctic Permafrost Region Pond and Lake database

NASA Astrophysics Data System (ADS)

Muster, Sina; Roth, Kurt; Langer, Moritz; Lange, Stephan; Cresto Aleina, Fabio; Bartsch, Annett; Morgenstern, Anne; Grosse, Guido; Jones, Benjamin; Sannel, A. Britta K.; Sjöberg, Ylva; Günther, Frank; Andresen, Christian; Veremeeva, Alexandra; Lindgren, Prajna R.; Bouchard, Frédéric; Lara, Mark J.; Fortier, Daniel; Charbonneau, Simon; Virtanen, Tarmo A.; Hugelius, Gustaf; Palmtag, Juri; Siewert, Matthias B.; Riley, William J.; Koven, Charles D.; Boike, Julia

2017-06-01

Ponds and lakes are abundant in Arctic permafrost lowlands. They play an important role in Arctic wetland ecosystems by regulating carbon, water, and energy fluxes and providing freshwater habitats. However, ponds, i.e., waterbodies with surface areas smaller than 1. 0 × 104 m2, have not been inventoried on global and regional scales. The Permafrost Region Pond and Lake (PeRL) database presents the results of a circum-Arctic effort to map ponds and lakes from modern (2002-2013) high-resolution aerial and satellite imagery with a resolution of 5 m or better. The database also includes historical imagery from 1948 to 1965 with a resolution of 6 m or better. PeRL includes 69 maps covering a wide range of environmental conditions from tundra to boreal regions and from continuous to discontinuous permafrost zones. Waterbody maps are linked to regional permafrost landscape maps which provide information on permafrost extent, ground ice volume, geology, and lithology. This paper describes waterbody classification and accuracy, and presents statistics of waterbody distribution for each site. Maps of permafrost landscapes in Alaska, Canada, and Russia are used to extrapolate waterbody statistics from the site level to regional landscape units. PeRL presents pond and lake estimates for a total area of 1. 4 × 106 km2 across the Arctic, about 17 % of the Arctic lowland ( < 300 m a.s.l.) land surface area. PeRL waterbodies with sizes of 1. 0 × 106 m2 down to 1. 0 × 102 m2 contributed up to 21 % to the total water fraction. Waterbody density ranged from 1. 0 × 10 to 9. 4 × 101 km-2. Ponds are the dominant waterbody type by number in all landscapes representing 45-99 % of the total waterbody number. The implementation of PeRL size distributions in land surface models will greatly improve the investigation and projection of surface inundation and carbon fluxes in permafrost lowlands. Waterbody maps, study area boundaries, and maps of regional permafrost landscapes including detailed metadata are available at https://doi.pangaea.de/10.1594/PANGAEA.868349.

Leveraging Terminological Resources for Mapping between Rare Disease Information Sources

PubMed Central

Rance, Bastien; Snyder, Michelle; Lewis, Janine; Bodenreider, Olivier

2015-01-01

Background Rare disease information sources are incompletely and inconsistently cross-referenced to one another, making it difficult for information seekers to navigate across them. The development of such cross-references established manually by experts is generally labor intensive and costly. Objectives To develop an automatic mapping between two of the major rare diseases information sources, GARD and Orphanet, by leveraging terminological resources, especially the UMLS. Methods We map the rare disease terms from Orphanet and ORDR to the UMLS. We use the UMLS as a pivot to bridge between the rare disease terminologies. We compare our results to a mapping obtained through manually established cross-references to OMIM. Results Our mapping has a precision of 94%, a recall of 63% and an F1-score of 76%. Our automatic mapping should help facilitate the development of more complete and consistent cross-references between GARD and Orphanet, and is applicable to other rare disease information sources as well. PMID:23920611

Application of thin plate splines for accurate regional ionosphere modeling with multi-GNSS data

NASA Astrophysics Data System (ADS)

Krypiak-Gregorczyk, Anna; Wielgosz, Pawel; Borkowski, Andrzej

2016-04-01

GNSS-derived regional ionosphere models are widely used in both precise positioning, ionosphere and space weather studies. However, their accuracy is often not sufficient to support precise positioning, RTK in particular. In this paper, we presented new approach that uses solely carrier phase multi-GNSS observables and thin plate splines (TPS) for accurate ionospheric TEC modeling. TPS is a closed solution of a variational problem minimizing both the sum of squared second derivatives of a smoothing function and the deviation between data points and this function. This approach is used in UWM-rt1 regional ionosphere model developed at UWM in Olsztyn. The model allows for providing ionospheric TEC maps with high spatial and temporal resolutions - 0.2x0.2 degrees and 2.5 minutes, respectively. For TEC estimation, EPN and EUPOS reference station data is used. The maps are available with delay of 15-60 minutes. In this paper we compare the performance of UWM-rt1 model with IGS global and CODE regional ionosphere maps during ionospheric storm that took place on March 17th, 2015. During this storm, the TEC level over Europe doubled comparing to earlier quiet days. The performance of the UWM-rt1 model was validated by (a) comparison to reference double-differenced ionospheric corrections over selected baselines, and (b) analysis of post-fit residuals to calibrated carrier phase geometry-free observational arcs at selected test stations. The results show a very good performance of UWM-rt1 model. The obtained post-fit residuals in case of UWM maps are lower by one order of magnitude comparing to IGS maps. The accuracy of UWM-rt1 -derived TEC maps is estimated at 0.5 TECU. This may be directly translated to the user positioning domain.

Computational methods for constructing protein structure models from 3D electron microscopy maps.

PubMed

Esquivel-Rodríguez, Juan; Kihara, Daisuke

2013-10-01

Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided. Copyright © 2013 Elsevier Inc. All rights reserved.

Quantitative Skeletal Muscle MRI: Part 1, Derived T2 Fat Map in Differentiation Between Boys With Duchenne Muscular Dystrophy and Healthy Boys.

PubMed

Johnston, Jennifer H; Kim, Hee Kyung; Merrow, Arnold C; Laor, Tal; Serai, Suraj; Horn, Paul S; Kim, Dong Hoon; Wong, Brenda L

2015-08-01

The purpose of this study was to validate derived T2 maps as an objective measure of muscular fat for discrimination between boys with Duchenne muscular dystrophy (DMD) and healthy boys. Forty-two boys with DMD (mean age, 9.9 years) and 31 healthy boys (mean age, 11.4 years) were included in the study. Age, body mass index, and clinical function scale grade were evaluated. T1-weighted MR images and T2 maps with and without fat suppression were obtained. Fatty infiltration was graded 0-4 on T1-weighted images, and derived T2 fat values (difference between mean T2 values from T2 maps with and without fat suppression) of the gluteus maximus and vastus lateralis muscles were calculated. Group comparisons were performed. The upper limit of the 95% reference interval of T2 fat values from the control group was applied. There was no significant difference in age or body mass index between groups. All healthy boys and 19 boys (45.2%) with DMD had a normal clinical function scale grade. Grade 1 fatty infiltration was seen in 90.3% (gluteus maximus) and 71.0% (vastus lateralis) of healthy boys versus 33.3% (gluteus maximus) and 52.4% (vastus lateralis) of boys with DMD. T2 fat values of boys with DMD were significantly longer than in the control group (p < 0.001). Using a 95% reference interval for healthy boys for the gluteus maximus (28.3 milliseconds) allowed complete separation from boys with DMD (100% sensitivity, 100% specificity), whereas the values for the vastus lateralis (7.28 milliseconds) resulted in 83.3% sensitivity and 100% specificity. Measurement of muscular fat with T2 maps is accurate for differentiating boys with DMD from healthy boys.

The Spanish National Reference Database for Ionizing Radiations (BANDRRI)

PubMed

Los Arcos JM; Bailador; Gonzalez; Gonzalez; Gorostiza; Ortiz; Sanchez; Shaw; Williart

2000-03-01

The Spanish National Reference Database for Ionizing Radiations (BANDRRI) is being implemented by a reasearch team in the frame of a joint project between CIEMAT (Unidad de Metrologia de Radiaciones Ionizantes and Direccion de Informatica) and the Universidad Nacional de Educacion a Distancia (UNED, Departamento de Mecanica y Departamento de Fisica de Materiales). This paper presents the main objectives of BANDRRI, its dynamic and relational data base structure, interactive Web accessibility and its main radionuclide-related contents at this moment.

Appalachian Basin Play Fairway Analysis: Thermal Quality Analysis in Low-Temperature Geothermal Play Fairway Analysis (GPFA-AB

DOE Data Explorer

Teresa E. Jordan

2015-11-15

This collection of files are part of a larger dataset uploaded in support of Low Temperature Geothermal Play Fairway Analysis for the Appalachian Basin (GPFA-AB, DOE Project DE-EE0006726). Phase 1 of the GPFA-AB project identified potential Geothermal Play Fairways within the Appalachian basin of Pennsylvania, West Virginia and New York. This was accomplished through analysis of 4 key criteria or ‘risks’: thermal quality, natural reservoir productivity, risk of seismicity, and heat utilization. Each of these analyses represent a distinct project task, with the fifth task encompassing combination of the 4 risks factors. Supporting data for all five tasks has been uploaded into the Geothermal Data Repository node of the National Geothermal Data System (NGDS). This submission comprises the data for Thermal Quality Analysis (project task 1) and includes all of the necessary shapefiles, rasters, datasets, code, and references to code repositories that were used to create the thermal resource and risk factor maps as part of the GPFA-AB project. The identified Geothermal Play Fairways are also provided with the larger dataset. Figures (.png) are provided as examples of the shapefiles and rasters. The regional standardized 1 square km grid used in the project is also provided as points (cell centers), polygons, and as a raster. Two ArcGIS toolboxes are available: 1) RegionalGridModels.tbx for creating resource and risk factor maps on the standardized grid, and 2) ThermalRiskFactorModels.tbx for use in making the thermal resource maps and cross sections. These toolboxes contain “item description” documentation for each model within the toolbox, and for the toolbox itself. This submission also contains three R scripts: 1) AddNewSeisFields.R to add seismic risk data to attribute tables of seismic risk, 2) StratifiedKrigingInterpolation.R for the interpolations used in the thermal resource analysis, and 3) LeaveOneOutCrossValidation.R for the cross validations used in the thermal interpolations. Some file descriptions make reference to various 'memos'. These are contained within the final report submitted October 16, 2015. Each zipped file in the submission contains an 'about' document describing the full Thermal Quality Analysis content available, along with key sources, authors, citation, use guidelines, and assumptions, with the specific file(s) contained within the .zip file highlighted.

Genetics Home Reference: pseudohypoaldosteronism type 2

MedlinePlus

... Thameem F, Al-Shahrouri HZ, Radhakrishnan J, Gharavi AG, Goilav B, Lifton RP. Mutations in kelch-like ... qualified healthcare professional . About Selection Criteria for Links Data Files & API Site Map Subscribe Customer Support USA. ...

Linking in situ LAI and fine resolution remote sensing data to map reference LAI over cropland and grassland using geostatistical regression method

NASA Astrophysics Data System (ADS)

He, Yaqian; Bo, Yanchen; Chai, Leilei; Liu, Xiaolong; Li, Aihua

2016-08-01

Leaf Area Index (LAI) is an important parameter of vegetation structure. A number of moderate resolution LAI products have been produced in urgent need of large scale vegetation monitoring. High resolution LAI reference maps are necessary to validate these LAI products. This study used a geostatistical regression (GR) method to estimate LAI reference maps by linking in situ LAI and Landsat TM/ETM+ and SPOT-HRV data over two cropland and two grassland sites. To explore the discrepancies of employing different vegetation indices (VIs) on estimating LAI reference maps, this study established the GR models for different VIs, including difference vegetation index (DVI), normalized difference vegetation index (NDVI), and ratio vegetation index (RVI). To further assess the performance of the GR model, the results from the GR and Reduced Major Axis (RMA) models were compared. The results show that the performance of the GR model varies between the cropland and grassland sites. At the cropland sites, the GR model based on DVI provides the best estimation, while at the grassland sites, the GR model based on DVI performs poorly. Compared to the RMA model, the GR model improves the accuracy of reference LAI maps in terms of root mean square errors (RMSE) and bias.

Grammatical gender effects on cognition: implications for language learning and language use.

PubMed

Vigliocco, Gabriella; Vinson, David P; Paganelli, Federica; Dworzynski, Katharina

2005-11-01

In 4 experiments, the authors addressed the mechanisms by which grammatical gender (in Italian and German) may come to affect meaning. In Experiments 1 (similarity judgments) and 2 (semantic substitution errors), the authors found Italian gender effects for animals but not for artifacts; Experiment 3 revealed no comparable effects in German. These results suggest that gender effects arise as a generalization from an established association between gender of nouns and sex of human referents, extending to nouns referring to sexuated entities. Across languages, such effects are found when the language allows for easy mapping between gender of nouns and sex of human referents (Italian) but not when the mapping is less transparent (German). A final experiment provided further constraints: These effects during processing arise at a lexical-semantic level rather than at a conceptual level. Copyright (c) 2005 APA, all rights reserved.

A Reference Proteomic Database of Lactobacillus plantarum CMCC-P0002

PubMed Central

Tian, Wanhong; Yu, Gang; Liu, Xiankai; Wang, Jie; Feng, Erling; Zhang, Xuemin; Chen, Bei; Zeng, Ming; Wang, Hengliang

2011-01-01

Lactobacillus plantarum is a widespread probiotic bacteria found in many fermented food products. In this study, the whole-cell proteins and secretory proteins of L. plantarum were separated by two-dimensional electrophoresis method. A total of 434 proteins were identified by tandem mass spectrometry, including a plasmid-encoded hypothetical protein pLP9000_05. The information of first 20 highest abundance proteins was listed for the further genetic manipulation of L. plantarum, such as construction of high-level expressions system. Furthermore, the first interaction map of L. plantarum was established by Blue-Native/SDS-PAGE technique. A heterodimeric complex composed of maltose phosphorylase Map3 and Map2, and two homodimeric complexes composed of Map3 and Map2 respectively, were identified at the same time, indicating the important roles of these proteins. These findings provided valuable information for the further proteomic researches of L. plantarum. PMID:21998671

Topographic mapping of the Moon

USGS Publications Warehouse

Wu, S.S.C.

1985-01-01

Contour maps of the Moon have been compiled by photogrammetric methods that use stereoscopic combinations of all available metric photographs from the Apollo 15, 16, and 17 missions. The maps utilize the same format as the existing NASA shaded-relief Lunar Planning Charts (LOC-1, -2, -3, and -4), which have a scale of 1:2 750 000. The map contour interval is 500m. A control net derived from Apollo photographs by Doyle and others was used for the compilation. Contour lines and elevations are referred to the new topographic datum of the Moon, which is defined in terms of spherical harmonics from the lunar gravity field. Compilation of all four LOC charts was completed on analytical plotters from 566 stereo models of Apollo metric photographs that cover approximately 20% of the Moon. This is the first step toward compiling a global topographic map of the Moon at a scale of 1:5 000 000. ?? 1985 D. Reidel Publishing Company.

A reference proteomic database of Lactobacillus plantarum CMCC-P0002.

PubMed

Zhu, Li; Hu, Wei; Liu, Datao; Tian, Wanhong; Yu, Gang; Liu, Xiankai; Wang, Jie; Feng, Erling; Zhang, Xuemin; Chen, Bei; Zeng, Ming; Wang, Hengliang

2011-01-01

Lactobacillus plantarum is a widespread probiotic bacteria found in many fermented food products. In this study, the whole-cell proteins and secretory proteins of L. plantarum were separated by two-dimensional electrophoresis method. A total of 434 proteins were identified by tandem mass spectrometry, including a plasmid-encoded hypothetical protein pLP9000_05. The information of first 20 highest abundance proteins was listed for the further genetic manipulation of L. plantarum, such as construction of high-level expressions system. Furthermore, the first interaction map of L. plantarum was established by Blue-Native/SDS-PAGE technique. A heterodimeric complex composed of maltose phosphorylase Map3 and Map2, and two homodimeric complexes composed of Map3 and Map2 respectively, were identified at the same time, indicating the important roles of these proteins. These findings provided valuable information for the further proteomic researches of L. plantarum.

National Oceanic and Atmospheric Administration's Cetacean and Sound Mapping Effort: Continuing Forward with an Integrated Ocean Noise Strategy.

PubMed

Harrison, Jolie; Ferguson, Megan; Gedamke, Jason; Hatch, Leila; Southall, Brandon; Van Parijs, Sofie

2016-01-01

To help manage chronic and cumulative impacts of human activities on marine mammals, the National Oceanic and Atmospheric Administration (NOAA) convened two working groups, the Underwater Sound Field Mapping Working Group (SoundMap) and the Cetacean Density and Distribution Mapping Working Group (CetMap), with overarching effort of both groups referred to as CetSound, which (1) mapped the predicted contribution of human sound sources to ocean noise and (2) provided region/time/species-specific cetacean density and distribution maps. Mapping products were presented at a symposium where future priorities were identified, including institutionalization/integration of the CetSound effort within NOAA-wide goals and programs, creation of forums and mechanisms for external input and funding, and expanded outreach/education. NOAA is subsequently developing an ocean noise strategy to articulate noise conservation goals and further identify science and management actions needed to support them.

Dual-pathway multi-echo sequence for simultaneous frequency and T2 mapping

NASA Astrophysics Data System (ADS)

Cheng, Cheng-Chieh; Mei, Chang-Sheng; Duryea, Jeffrey; Chung, Hsiao-Wen; Chao, Tzu-Cheng; Panych, Lawrence P.; Madore, Bruno

2016-04-01

Purpose: To present a dual-pathway multi-echo steady state sequence and reconstruction algorithm to capture T2, T2∗ and field map information. Methods: Typically, pulse sequences based on spin echoes are needed for T2 mapping while gradient echoes are needed for field mapping, making it difficult to jointly acquire both types of information. A dual-pathway multi-echo pulse sequence is employed here to generate T2 and field maps from the same acquired data. The approach might be used, for example, to obtain both thermometry and tissue damage information during thermal therapies, or susceptibility and T2 information from a same head scan, or to generate bonus T2 maps during a knee scan. Results: Quantitative T2, T2∗ and field maps were generated in gel phantoms, ex vivo bovine muscle, and twelve volunteers. T2 results were validated against a spin-echo reference standard: A linear regression based on ROI analysis in phantoms provided close agreement (slope/R2 = 0.99/0.998). A pixel-wise in vivo Bland-Altman analysis of R2 = 1/T2 showed a bias of 0.034 Hz (about 0.3%), as averaged over four volunteers. Ex vivo results, with and without motion, suggested that tissue damage detection based on T2 rather than temperature-dose measurements might prove more robust to motion. Conclusion: T2, T2∗ and field maps were obtained simultaneously, from the same datasets, in thermometry, susceptibility-weighted imaging and knee-imaging contexts.

[Evolution of the bibliometric indicators of production and consumption of Archivos de Bronchopneumología in the last 20 years].

PubMed

García Río, F; Dorgham, A; Serrano, S; Terreros Caro, J G; Alvarez-Sala, R; Prados, C; Alvarez-Sala, J L; Villamor, J

1997-01-01

The aim of this study was to evaluate the evolution of bibliometric indicators for authorship and citation of ARCHIVOS DE BRONCONEUMOLOGIA over the past 20 years. At least 16 articles reporting new research or case reports were analyzed for every other year from 1976 to 1996. The following data were collected for each article: type of document, number of authors and their place of work and specialty, time interval between acceptance and publication, and references (including number, types, language, journal name and year of publication). The number of authors per article (collaboration index) averaged around five and has not varied significantly over the 20 years studied. Pulmonologists predominated among the authors, accounting for about 60% of the total, and most contributions came from a few provinces, mainly Barcelona and Madrid. The interval between reception and publication has gradually increased over the 20 years under review, coming to stand around 9.9 +/- 1.6 months in 1996. Most references (over 80%) cite journals and the proportion of references to books has decreased in recent years (from 12.3% in 1976 to 3.5% in 1996). The journal's index of isolation has increased (from 6.2 to 12.1%), as has the index of self-citation (from 0.4 to 6.2%). Although most cited works are in English (over 80%), the proportion of Spanish-language references increased (from 6.2 to 12.1%). In conclusion, maintenance of the number of collaborating authors, the predominance of journals and English-language sources among references are the main traits that characterize the bibliometric indicators for authorship and citation in ARCHIVOS DE BRONCONEUMOLOGIA.

Erratic boulders in Switzerland, a geological and cultural heritage

NASA Astrophysics Data System (ADS)

Reynard, Emmanuel

2015-04-01

Erratic boulders are stones transported over quite long distances by glaciers and that differ from the type of rock upon which they rely. They range from the size of pebbles to large boulders weighing several thousand tons. Erratic boulders are significant geosites (Reynard, 2004) for several reasons. (1) First, they are indicators of former glacier extensions by marking glaciers' path, size and volume. In Switzerland, they allowed mapping the extension of large Alpine glaciers (the Rhine and Rhone glaciers, in particular) and their retreat stages (e.g. the Monthey erratic boulders that mark an important lateglacial stage of the Rhone glacier). Crystalline erratic boulders along the Jura range (limestone mountains) were used to map the altitude reached by the Rhone glacier during the two last glaciations. Precise mapping of crystalline and limestone boulders distribution also enabled mapping local Jura glaciers' recurrences after the Rhone glacier retreat. (2) During the last decades, several erratic boulders were used for cosmogenic nuclide exposure dating, which allowed impressive advances in palaeoclimatic research. (3) Erratic blocks have also an ecological interest by the fact that they "have transported" specific habitats in areas far away from their origin (e.g. acid crystalline rocks and soils in limestone areas such as in the Jura). For all these reasons, several erratic boulders were classified in the inventory of Swiss geosites. Erratic boulders also have a significant cultural value (Lugon et al., 2006). (1) The Glacier Garden in Lucerne was discovered in 1872. It comprises various surfaces of "roches moutonnées", potholes and large erratic blocks that document the presence of the Reuss glacier. Considered as a natural monument it is now one of the most famous touristic attraction of Lucerne and Central Switzerland. (2) The Pierre Bergère stone, situated in Salvan (Mont-Blanc massif, South-western Switzerland), is the place where future Nobel Prize Guglielmo Marconi made his first wireless experiments in the late 19th century. An interpretive panel explaining the origin of the block was posted near the site along a cultural path created by the Marconi Foundation. (3) The Pierre des Marmettes, in Monthey, is one of the key-sites where the nature conservation movement was initiated in the first decade of the 20th century. The block is the property of the Swiss Academy of Sciences and was chosen as an emblematic site for celebrating the 200 years of the Academy in 2015. Moreover, in several cantons the protection of erratic blocks was the first initiative for nature conservation. (4) Several blocks were dedicated or offered to famous scientists (De Charpentier, Agassiz, Studer, Venetz) involved in the development of glaciology during the 19th century. Their names (e.g. Agassiz Block, Studer Block, Venetz Block) remind this important period in the history of Swiss geosciences. In fact, several of these scientists - in particular Jean de Charpentier - not only demonstrated the glacial origin of these blocks, but also used them as a proof of former glacial extensions. (5) Finally, several blocks have a symbolic (most of them have a name, several refer to legends), mythical, religious or an archaeological value - with the presence of petroglyphs. This communication will focus on the cultural value of erratic boulders - in particular for the nature conservation movement and for the history of glaciology and geosciences - and will propose a strategy for their geotourist promotion. References Lugon R., Pralong J.-P., Reynard E. (2006). Patrimoine culturel et géomorphologie: le cas valaisan de quelques blocs erratiques, d'une marmite glaciaire et d'une moraine. Bull. Murithienne, 124, 73-87. Reynard E. (2004). Protecting Stones: conservation of erratic blocks in Switzerland. In: Prikryl R. (ed.) Dimension Stone 2004. New perspectives for a traditional building material, Leiden, Balkema, 3-7.

Simultaneous comparison and assessment of eight remotely sensed maps of Philippine forests

NASA Astrophysics Data System (ADS)

Estoque, Ronald C.; Pontius, Robert G.; Murayama, Yuji; Hou, Hao; Thapa, Rajesh B.; Lasco, Rodel D.; Villar, Merlito A.

2018-05-01

This article compares and assesses eight remotely sensed maps of Philippine forest cover in the year 2010. We examined eight Forest versus Non-Forest maps reclassified from eight land cover products: the Philippine Land Cover, the Climate Change Initiative (CCI) Land Cover, the Landsat Vegetation Continuous Fields (VCF), the MODIS VCF, the MODIS Land Cover Type product (MCD12Q1), the Global Tree Canopy Cover, the ALOS-PALSAR Forest/Non-Forest Map, and the GlobeLand30. The reference data consisted of 9852 randomly distributed sample points interpreted from Google Earth. We created methods to assess the maps and their combinations. Results show that the percentage of the Philippines covered by forest ranges among the maps from a low of 23% for the Philippine Land Cover to a high of 67% for GlobeLand30. Landsat VCF estimates 36% forest cover, which is closest to the 37% estimate based on the reference data. The eight maps plus the reference data agree unanimously on 30% of the sample points, of which 11% are attributable to forest and 19% to non-forest. The overall disagreement between the reference data and Philippine Land Cover is 21%, which is the least among the eight Forest versus Non-Forest maps. About half of the 9852 points have a nested structure such that the forest in a given dataset is a subset of the forest in the datasets that have more forest than the given dataset. The variation among the maps regarding forest quantity and allocation relates to the combined effects of the various definitions of forest and classification errors. Scientists and policy makers must consider these insights when producing future forest cover maps and when establishing benchmarks for forest cover monitoring.

The Geography Teacher. Volume 5, Number 1, 2008

ERIC Educational Resources Information Center

Geography Teacher, 2008

2008-01-01

"The Geography Teacher" provides hands-on reference and educative material for K-12 Geography teachers. The journal also pioneers innovative ideas for contemporary teaching methods, including lesson plans. This issue contains the following: (1) Ask Dr. de Blij (Dr. Harm de Blij); (2) Around the World in Eighty Days (Donald P. Albert);…

The Geography Teacher. Volume 4, Number 1, 2007

ERIC Educational Resources Information Center

Geography Teacher, 2007

2007-01-01

"The Geography Teacher" provides hands-on reference and educative material for K-12 Geography teachers. The journal also pioneers innovative ideas for contemporary teaching methods, including lesson plans. This issue contains the following: (1) Ask Dr. de Blij (Dr. Harm de Blij); (2) Refugees in America (TGT); (3) Guinness and the Irish…

The Geography Teacher. Volume 6, Number 1, 2009

ERIC Educational Resources Information Center

Geography Teacher, 2009

2009-01-01

"The Geography Teacher" provides hands-on reference and educative material for K-12 Geography teachers. The journal also pioneers innovative ideas for contemporary teaching methods, including lesson plans. This issue contains the following: (1) Ask Dr. de Blij (Dr. Harm de Blij); (2) Meet GADO (TGT); (3) Why French? (David Bulambo Bitingingwa);…

GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies.

PubMed

Kim, Jeremie S; Senol Cali, Damla; Xin, Hongyi; Lee, Donghyuk; Ghose, Saugata; Alser, Mohammed; Hassan, Hasan; Ergin, Oguz; Alkan, Can; Mutlu, Onur

2018-05-09

Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. State-of-the-art read mappers 1) quickly generate possible mapping locations for seeds (i.e., smaller segments) within each read, 2) extract reference sequences at each of the mapping locations, and 3) check similarity between each read and its associated reference sequences with a computationally-expensive algorithm (i.e., sequence alignment) to determine the origin of the read. A seed location filter comes into play before alignment, discarding seed locations that alignment would deem a poor match. The ideal seed location filter would discard all poor match locations prior to alignment such that there is no wasted computation on unnecessary alignments. We propose a novel seed location filtering algorithm, GRIM-Filter, optimized to exploit 3D-stacked memory systems that integrate computation within a logic layer stacked under memory layers, to perform processing-in-memory (PIM). GRIM-Filter quickly filters seed locations by 1) introducing a new representation of coarse-grained segments of the reference genome, and 2) using massively-parallel in-memory operations to identify read presence within each coarse-grained segment. Our evaluations show that for a sequence alignment error tolerance of 0.05, GRIM-Filter 1) reduces the false negative rate of filtering by 5.59x-6.41x, and 2) provides an end-to-end read mapper speedup of 1.81x-3.65x, compared to a state-of-the-art read mapper employing the best previous seed location filtering algorithm. GRIM-Filter exploits 3D-stacked memory, which enables the efficient use of processing-in-memory, to overcome the memory bandwidth bottleneck in seed location filtering. We show that GRIM-Filter significantly improves the performance of a state-of-the-art read mapper. GRIM-Filter is a universal seed location filter that can be applied to any read mapper. We hope that our results provide inspiration for new works to design other bioinformatics algorithms that take advantage of emerging technologies and new processing paradigms, such as processing-in-memory using 3D-stacked memory devices.

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

PubMed

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

2017-01-01

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

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

PubMed

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

2017-01-01

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

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

PubMed Central

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

2017-01-01

Foxtail millet (Setaria italica), a very important grain crop in China, has become a new model plant for cereal crops and biofuel grasses. Although its reference genome sequence was released recently, quantitative trait loci (QTLs) controlling complex agronomic traits remains limited. The development of massively parallel genotyping methods and next-generation sequencing technologies provides an excellent opportunity for developing single-nucleotide polymorphisms (SNPs) for linkage map construction and QTL analysis of complex quantitative traits. In this study, a high-throughput and cost-effective RAD-seq approach was employed to generate a high-density genetic map for foxtail millet. A total of 2,668,587 SNP loci were detected according to the reference genome sequence; meanwhile, 9,968 SNP markers were used to genotype 124 F2 progenies derived from the cross between Hongmiaozhangu and Changnong35; a high-density genetic map spanning 1648.8 cM, with an average distance of 0.17 cM between adjacent markers was constructed; 11 major QTLs for eight agronomic traits were identified; five co-dominant DNA markers were developed. These findings will be of value for the identification of candidate genes and marker-assisted selection in foxtail millet. PMID:28644843

Aligning a New Reference Genetic Map of Lupinus angustifolius with the Genome Sequence of the Model Legume, Lotus japonicus

PubMed Central

Nelson, Matthew N.; Moolhuijzen, Paula M.; Boersma, Jeffrey G.; Chudy, Magdalena; Lesniewska, Karolina; Bellgard, Matthew; Oliver, Richard P.; Święcicki, Wojciech; Wolko, Bogdan; Cowling, Wallace A.; Ellwood, Simon R.

2010-01-01

We have developed a dense reference genetic map of Lupinus angustifolius (2n = 40) based on a set of 106 publicly available recombinant inbred lines derived from a cross between domesticated and wild parental lines. The map comprised 1090 loci in 20 linkage groups and three small clusters, drawing together data from several previous mapping publications plus almost 200 new markers, of which 63 were gene-based markers. A total of 171 mainly gene-based, sequence-tagged site loci served as bridging points for comparing the Lu. angustifolius genome with the genome sequence of the model legume, Lotus japonicus via BLASTn homology searching. Comparative analysis indicated that the genomes of Lu. angustifolius and Lo. japonicus are highly diverged structurally but with significant regions of conserved synteny including the region of the Lu. angustifolius genome containing the pod-shatter resistance gene, lentus. We discuss the potential of synteny analysis for identifying candidate genes for domestication traits in Lu. angustifolius and in improving our understanding of Fabaceae genome evolution. PMID:20133394

P17.04 Radiomics analysis of primary central nervous system lymphoma (PCNSL) - A LOC network study

PubMed Central

Royer-Perron, L.; Bruno, A.; Daniau, M.; Labrèche, K.; Mokhtari, K.; Nguyen Them, L.; Houillier, C.; Soussain, C.; Hoang-Xuan, K.; Alentorn, A.

2016-01-01

Abstract Background: PCNSL are rare extranodal, malignant non-Hodgkin lymphomas of diffuse large B-cell type confined to the CNS. In the last years, several recurrent molecular genetic alterations have been described in PCNSL but whether they are correlated with the tumor anatomical localization has never been investigated. Objectives: We sought to analyze a genotype (molecular alterations) - phenotype (MRI data) in PCNSL. Material and methods: 50 PCNSL MR images of treatment-naïve patients were correlated with molecular alterations (i.e. MYD88 L265P, CD79B and TERT promoter mutations as well as a novel chimeric transcript that our laboratory has recently identified in PCNSL) obtained by Sanger sequencing. MRI data was analyzed as follows: (i) NIfTI data were registered to a 1.0 mm isotropic, high-resolution T1-weighted brain atlas provided by the Montreal Neurological Institute (MNI152) using a mutual information algorithm with a 12-degree of freedom transformation with FSL-FLIRT; (ii) gadolinium-enhancing lesions were manually segmented and saved as voxels-of-interest (VOIs); (iii) A heat-map for the frequency of lesion occurrence was reconstructed and superimposed on the reference MNI152; (iv) Structure probability maps (brain regions) were defined according to Talairach MRI Atlas and (v) genotype - phenotype correlation was performed using voxel-based lesion-symptom mapping (VLSM) using FDR < 0.05 after 4000 permutations. Results: We found mutations of MYD88 in 18 patients, of CD79B in 15 patients and of TERT promoter in 6 patients. The novel chimeric transcript was identified in 11 patients. PCNSL harboring TERT promoter mutations and the chimeric transcript were more frequently found in the corpus callosum (FDR < 0.05). Conversely, we did not find a specific genotype-phenotype correlation with the rest of molecular alterations. Conclusion: We provide a MRI probabilistic atlas linking genotype to phenotype in PCNSL. These results need further investigation. Acknowledgements: Association pour la Recherche sur les Tumeurs Cérébrales (ARTC), Ligue contre le Cancer, Fondation pour la recherche médicale, Institut National du Cancer (INCa), Cancéropôle Île-de-France, Département de la Recherche Clinique de l’APHP, CRC de l’APHP, réseau Lymphomes Oculo-Cérébraux (LOC).

A complete mass spectrometric map for the analysis of the yeast proteome and its application to quantitative trait analysis

PubMed Central

Picotti, Paola; Clement-Ziza, Mathieu; Lam, Henry; Campbell, David S.; Schmidt, Alexander; Deutsch, Eric W.; Röst, Hannes; Sun, Zhi; Rinner, Oliver; Reiter, Lukas; Shen, Qin; Michaelson, Jacob J.; Frei, Andreas; Alberti, Simon; Kusebauch, Ulrike; Wollscheid, Bernd; Moritz, Robert; Beyer, Andreas; Aebersold, Ruedi

2013-01-01

Complete reference maps or datasets, like the genomic map of an organism, are highly beneficial tools for biological and biomedical research. Attempts to generate such reference datasets for a proteome so far failed to reach complete proteome coverage, with saturation apparent at approximately two thirds of the proteomes tested, even for the most thoroughly characterized proteomes. Here, we used a strategy based on high-throughput peptide synthesis and mass spectrometry to generate a close to complete reference map (97% of the genome-predicted proteins) of the S. cerevisiae proteome. We generated two versions of this mass spectrometric map one supporting discovery- (shotgun) and the other hypothesis-driven (targeted) proteomic measurements. The two versions of the map, therefore, constitute a complete set of proteomic assays to support most studies performed with contemporary proteomic technologies. The reference libraries can be browsed via a web-based repository and associated navigation tools. To demonstrate the utility of the reference libraries we applied them to a protein quantitative trait locus (pQTL) analysis, which requires measurement of the same peptides over a large number of samples with high precision. Protein measurements over a set of 78 S. cerevisiae strains revealed a complex relationship between independent genetic loci, impacting on the levels of related proteins. Our results suggest that selective pressure favors the acquisition of sets of polymorphisms that maintain the stoichiometry of protein complexes and pathways. PMID:23334424

HapMap tagSNP transferability in multiple populations: general guidelines

PubMed Central

Xing, Jinchuan; Witherspoon, David J.; Watkins, W. Scott; Zhang, Yuhua; Tolpinrud, Whitney; Jorde, Lynn B.

2008-01-01

This PDF receipt will only be used as the basis for generating PubMed Central (PMC) documents. PMC documents will be made available for review after conversion (approx. 2–3 weeks time). Any corrections that need to be made will be done at that time. No materials will be released to PMC without the approval of an author. Only the PMC documents will appear on PubMed Central -- this PDF Receipt will not appear on PubMed Central. Linkage disequilibrium (LD) has received much recent attention because of its value in localizing disease-causing genes. Due to the extensive LD between neighboring loci in the human genome, it is believed that a subset of the single nucleotide polymorphisms in a region (tagSNPs) can be selected to capture most of the remaining SNP variants. In this study, we examined LD patterns and HapMap tagSNP transferability in more than 300 individuals. A South Indian and an African Mbuti Pygmy population sample were included to evaluate the performance of HapMap tagSNPs in geographically distinct and genetically isolated populations. Our results show that HapMap tagSNPs selected with r2 >= 0.8 can capture more than 85% of the SNPs in populations that are from the same continental group. Combined tagSNPs from HapMap CEU and CHB+JPT serve as the best reference for the Indian sample. The HapMap YRI are a sufficient reference for tagSNP selection in the Pygmy sample. In addition to our findings, we reviewed over 25 recent studies of tagSNP transferability and propose a general guideline for selecting tagSNPs from HapMap populations. PMID:18482828

Map of surficial deposits and materials in the eastern and central United States (east of 102 degrees West longitude)

USGS Publications Warehouse

Fullerton, David S.; Bush, Charles A.; Pennell, Jean N.

2003-01-01

This data set contains surficial geologic units in the Eastern and Central United States, as well as a glacial limit line showing the position of maximum glacial advance during various geologic time periods. The geologic units represent surficial deposits and other surface materials that accumulated or formed during the past 2+ million years, such as soils, alluvium, and glacial deposits. These surface materials are referred to collectively by many geologists as regolith, the mantle of fragmented and generally unconsolidated material that overlies the bedrock foundation of a continent. This data set and the printed map produced from it, U.S. Geological Survey (USGS) Geologic Investigation Series I-2789, were based on 31 published maps in the USGS's Quaternary Geologic Atlas of the United States map series (USGS Miscellaneous Investigations Series I-1420). The data were compiled at 1:1,000,000 scale, to be viewed as a digital map at 1:2,000,000 nominal scale and to be printed as a conventional paper map at 1:2,500,000 scale.

Comparison of two landslide susceptibility assessments in the Champagne-Ardenne region (France)

NASA Astrophysics Data System (ADS)

Den Eeckhaut, M. Van; Marre, A.; Poesen, J.

2010-02-01

The vineyards of the Montagne de Reims are mostly planted on steep south-oriented cuesta fronts receiving a maximum of sun radiation. Due to the location of the vineyards on steep hillslopes, the viticultural activity is threatened by slope failures. This study attempts to better understand the spatial patterns of landslide susceptibility in the Champagne-Ardenne region by comparing a heuristic (qualitative) and a statistical (quantitative) model in a 1120 km² study area. The heuristic landslide susceptibility model was adopted from the Bureau de Recherches Géologiques et Minières, the GEGEAA - Reims University and the Comité Interprofessionnel du Vin de Champagne. In this model, expert knowledge of the region was used to assign weights to all slope classes and lithologies present in the area, but the final susceptibility map was never evaluated with the location of mapped landslides. For the statistical landslide susceptibility assessment, logistic regression was applied to a dataset of 291 'old' (Holocene) landslides. The robustness of the logistic regression model was evaluated and ROC curves were used for model calibration and validation. With regard to the variables assumed to be important environmental factors controlling landslides, the two models are in agreement. They both indicate that present and future landslides are mainly controlled by slope gradient and lithology. However, the comparison of the two landslide susceptibility maps through (1) an evaluation with the location of mapped 'old' landslides and through (2) a temporal validation with spatial data of 'recent' (1960-1999; n = 48) and 'very recent' (2000-2008; n = 46) landslides showed a better prediction capacity for the statistical model produced in this study compared to the heuristic model. In total, the statistically-derived landslide susceptibility map succeeded in correctly classifying 81.0% of the 'old' and 91.6% of the 'recent' and 'very recent' landslides. On the susceptibility map derived from the heuristic model, on the other hand, only 54.6% of the 'old' and 64.0% of the 'recent' and 'very recent' landslides were correctly classified as unstable. Hence, the landslide susceptibility map obtained from logistic regression is a better tool for regional landslide susceptibility analysis in the study area of the Montagne de Reims. The accurate classification of zones with very high and high susceptibility allows delineating zones where viticulturists should be informed and where implementation of precaution measures is needed to secure slope stability.

Poly-gamma-Glutamate Capsule-Degrading Enzyme Treatment Enhances Phagocytosis and Killing of Encapsulated Bacillus Anthracis

DTIC Science & Technology

2006-10-14

including the use of extracts of Bacillus pyo- cyaneus to treat anthrax (see reference 2 and references therein) and of Aspergillus fumigatus to...as overexpression could lead to a high level of de- polymerization and a loss of capsule from the bacterial surface. A preliminary proteomic analysis

Geologic map of Detrital, Hualapai, and Sacramento Valleys and surrounding areas, northwest Arizona

USGS Publications Warehouse

Beard, L. Sue; Kennedy, Jeffrey; Truini, Margot; Felger, Tracey

2011-01-01

A 1:250,000-scale geologic map and report covering the Detrital, Hualapai, and Sacramento valleys in northwest Arizona is presented for the purpose of improving understanding of the geology and geohydrology of the basins beneath those valleys. The map was compiled from existing geologic mapping, augmented by digital photogeologic reconnaissance mapping. The most recent geologic map for the area, and the only digital one, is the 1:1,000,000-scale Geologic Map of Arizona. The larger scale map presented here includes significantly more detailed geology than the Geologic Map of Arizona in terms of accuracy of geologic unit contacts, number of faults, fault type, fault location, and details of Neogene and Quaternary deposits. Many sources were used to compile the geology; the accompanying geodatabase includes a source field in the polygon feature class that lists source references for polygon features. The citations for the source field are included in the reference section.

2D and 3D visualization methods of endoscopic panoramic bladder images

NASA Astrophysics Data System (ADS)

Behrens, Alexander; Heisterklaus, Iris; Müller, Yannick; Stehle, Thomas; Gross, Sebastian; Aach, Til

2011-03-01

While several mosaicking algorithms have been developed to compose endoscopic images of the internal urinary bladder wall into panoramic images, the quantitative evaluation of these output images in terms of geometrical distortions have often not been discussed. However, the visualization of the distortion level is highly desired for an objective image-based medical diagnosis. Thus, we present in this paper a method to create quality maps from the characteristics of transformation parameters, which were applied to the endoscopic images during the registration process of the mosaicking algorithm. For a global first view impression, the quality maps are laid over the panoramic image and highlight image regions in pseudo-colors according to their local distortions. This illustration supports then surgeons to identify geometrically distorted structures easily in the panoramic image, which allow more objective medical interpretations of tumor tissue in shape and size. Aside from introducing quality maps in 2-D, we also discuss a visualization method to map panoramic images onto a 3-D spherical bladder model. Reference points are manually selected by the surgeon in the panoramic image and the 3-D model. Then the panoramic image is mapped by the Hammer-Aitoff equal-area projection onto the 3-D surface using texture mapping. Finally the textured bladder model can be freely moved in a virtual environment for inspection. Using a two-hemisphere bladder representation, references between panoramic image regions and their corresponding space coordinates within the bladder model are reconstructed. This additional spatial 3-D information thus assists the surgeon in navigation, documentation, as well as surgical planning.

Viscoelastic Mapping of the Arterial Ovine System using a Kelvin Model

DTIC Science & Technology

2007-03-19

University Campus Box 8205 Raleigh, NC 27695. 2) Department of Physiology School of Medicine Universidad de la Republica General Flores 2125, PC: 11800...not differ significantly across locations. We also showed that for all locations, the inclusion of viscoelastic behavior, e.g., using the Kelvin model...All protocols were approved by the Research and Development Council of the Universidad de la Republica, and were conducted in accordance with the

SU-F-T-315: Comparative Studies of Planar Dose with Different Spatial Resolution for Head and Neck IMRT QA

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

Hwang, T; Koo, T

Purpose: To quantitatively investigate the planar dose difference and the γ value between the reference fluence map with the 1 mm detector-to-detector distance and the other fluence maps with less spatial resolution for head and neck intensity modulated radiation (IMRT) therapy. Methods: For ten head and neck cancer patients, the IMRT quality assurance (QA) beams were generated using by the commercial radiation treatment planning system, Pinnacle3 (ver. 8.0.d Philips Medical System, Madison, WI). For each beam, ten fluence maps (detector-to-detector distance: 1 mm to 10 mm by 1 mm) were generated. The fluence maps with larger than 1 mm detector-todetectormore » distance were interpolated using MATLAB (R2014a, the Math Works,Natick, MA) by four different interpolation Methods: for the bilinear, the cubic spline, the bicubic, and the nearest neighbor interpolation, respectively. These interpolated fluence maps were compared with the reference one using the γ value (criteria: 3%, 3 mm) and the relative dose difference. Results: As the detector-to-detector distance increases, the dose difference between the two maps increases. For the fluence map with the same resolution, the cubic spline interpolation and the bicubic interpolation are almost equally best interpolation methods while the nearest neighbor interpolation is the worst.For example, for 5 mm distance fluence maps, γ≤1 are 98.12±2.28%, 99.48±0.66%, 99.45±0.65% and 82.23±0.48% for the bilinear, the cubic spline, the bicubic, and the nearest neighbor interpolation, respectively. For 7 mm distance fluence maps, γ≤1 are 90.87±5.91%, 90.22±6.95%, 91.79±5.97% and 71.93±4.92 for the bilinear, the cubic spline, the bicubic, and the nearest neighbor interpolation, respectively. Conclusion: We recommend that the 2-dimensional detector array with high spatial resolution should be used as an IMRT QA tool and that the measured fluence maps should be interpolated using by the cubic spline interpolation or the bicubic interpolation for head and neck IMRT delivery. This work was supported by Radiation Technology R&D program through the National Research Foundation of Korea funded by the Ministry of Science, ICT & Future Planning (No. 2013M2A2A7038291)« less

Linking sounds to meanings: infant statistical learning in a natural language.

PubMed

Hay, Jessica F; Pelucchi, Bruna; Graf Estes, Katharine; Saffran, Jenny R

2011-09-01

The processes of infant word segmentation and infant word learning have largely been studied separately. However, the ease with which potential word forms are segmented from fluent speech seems likely to influence subsequent mappings between words and their referents. To explore this process, we tested the link between the statistical coherence of sequences presented in fluent speech and infants' subsequent use of those sequences as labels for novel objects. Notably, the materials were drawn from a natural language unfamiliar to the infants (Italian). The results of three experiments suggest that there is a close relationship between the statistics of the speech stream and subsequent mapping of labels to referents. Mapping was facilitated when the labels contained high transitional probabilities in the forward and/or backward direction (Experiment 1). When no transitional probability information was available (Experiment 2), or when the internal transitional probabilities of the labels were low in both directions (Experiment 3), infants failed to link the labels to their referents. Word learning appears to be strongly influenced by infants' prior experience with the distribution of sounds that make up words in natural languages. Copyright © 2011 Elsevier Inc. All rights reserved.

Combining Quantitative Susceptibility Mapping with Automatic Zero Reference (QSM0) and Myelin Water Fraction Imaging to Quantify Iron-Related Myelin Damage in Chronic Active MS Lesions.

PubMed

Yao, Y; Nguyen, T D; Pandya, S; Zhang, Y; Hurtado Rúa, S; Kovanlikaya, I; Kuceyeski, A; Liu, Z; Wang, Y; Gauthier, S A

2018-02-01

A hyperintense rim on susceptibility in chronic MS lesions is consistent with iron deposition, and the purpose of this study was to quantify iron-related myelin damage within these lesions as compared with those without rim. Forty-six patients had 2 longitudinal quantitative susceptibility mapping with automatic zero reference scans with a mean interval of 28.9 ± 11.4 months. Myelin water fraction mapping by using fast acquisition with spiral trajectory and T2 prep was obtained at the second time point to measure myelin damage. Mixed-effects models were used to assess lesion quantitative susceptibility mapping and myelin water fraction values. Quantitative susceptibility mapping scans were on average 6.8 parts per billion higher in 116 rim-positive lesions compared with 441 rim-negative lesions ( P < .001). All rim-positive lesions retained a hyperintense rim over time, with increasing quantitative susceptibility mapping values of both the rim and core regions ( P < .001). Quantitative susceptibility mapping scans and myelin water fraction in rim-positive lesions decreased from rim to core, which is consistent with rim iron deposition. Whole lesion myelin water fractions for rim-positive and rim-negative lesions were 0.055 ± 0.07 and 0.066 ± 0.04, respectively. In the mixed-effects model, rim-positive lesions had on average 0.01 lower myelin water fraction compared with rim-negative lesions ( P < .001). The volume of the rim at the initial quantitative susceptibility mapping scan was negatively associated with follow-up myelin water fraction ( P < .01). Quantitative susceptibility mapping rim-positive lesions maintained a hyperintense rim, increased in susceptibility, and had more myelin damage compared with rim-negative lesions. Our results are consistent with the identification of chronic active MS lesions and may provide a target for therapeutic interventions to reduce myelin damage. © 2018 by American Journal of Neuroradiology.

Numerical modeling of debris avalanches at Nevado de Toluca (Mexico): implications for hazard evaluation and mapping

NASA Astrophysics Data System (ADS)

Grieco, F.; Capra, L.; Groppelli, G.; Norini, G.

2007-05-01

The present study concerns the numerical modeling of debris avalanches on the Nevado de Toluca Volcano (Mexico) using TITAN2D simulation software, and its application to create hazard maps. Nevado de Toluca is an andesitic to dacitic stratovolcano of Late Pliocene-Holocene age, located in central México near to the cities of Toluca and México City; its past activity has endangered an area with more than 25 million inhabitants today. The present work is based upon the data collected during extensive field work finalized to the realization of the geological map of Nevado de Toluca at 1:25,000 scale. The activity of the volcano has developed from 2.6 Ma until 10.5 ka with both effusive and explosive events; the Nevado de Toluca has presented long phases of inactivity characterized by erosion and emplacement of debris flow and debris avalanche deposits on its flanks. The largest epiclastic events in the history of the volcano are wide debris flows and debris avalanches, occurred between 1 Ma and 50 ka, during a prolonged hiatus in eruptive activity. Other minor events happened mainly during the most recent volcanic activity (less than 50 ka), characterized by magmatic and tectonic-induced instability of the summit dome complex. According to the most recent tectonic analysis, the active transtensive kinematics of the E-W Tenango Fault System had a strong influence on the preferential directions of the last three documented lateral collapses, which generated the Arroyo Grande and Zaguàn debris avalanche deposits towards E and Nopal debris avalanche deposit towards W. The analysis of the data collected during the field work permitted to create a detailed GIS database of the spatial and temporal distribution of debris avalanche deposits on the volcano. Flow models, that have been performed with the software TITAN2D, developed by GMFG at Buffalo, were entirely based upon the information stored in the geological database. The modeling software is built upon equations solved by a parallel and adaptive mesh, that can concentrate computing power in region of special interest. First of all, simulations of known past events, were compared with the geological data validating the effectiveness of the method. Afterwards, numerous simulations have been executed varying input parameters as friction angles, starting point and initial volume, in order to obtain a global perspective over the possible expected debris avalanche scenarios. The input parameters were selected considering the geological, structural and topographic factors controlling instability of the volcanic cone, especially in case of renewed eruptive activity. The interoperability between TITAN2D and GIS softwares permitted to draw a semi-quantitative hazard map by crossing simulation outputs with the distribution of deposits generated by past episodes of instability, mapped during the field work.

Distortions in memory for visual displays

NASA Technical Reports Server (NTRS)

Tversky, Barbara

1989-01-01

Systematic errors in perception and memory present a challenge to theories of perception and memory and to applied psychologists interested in overcoming them as well. A number of systematic errors in memory for maps and graphs are reviewed, and they are accounted for by an analysis of the perceptual processing presumed to occur in comprehension of maps and graphs. Visual stimuli, like verbal stimuli, are organized in comprehension and memory. For visual stimuli, the organization is a consequence of perceptual processing, which is bottom-up or data-driven in its earlier stages, but top-down and affected by conceptual knowledge later on. Segregation of figure from ground is an early process, and figure recognition later; for both, symmetry is a rapidly detected and ecologically valid cue. Once isolated, figures are organized relative to one another and relative to a frame of reference. Both perceptual (e.g., salience) and conceptual factors (e.g., significance) seem likely to affect selection of a reference frame. Consistent with the analysis, subjects perceived and remembered curves in graphs and rivers in maps as more symmetric than they actually were. Symmetry, useful for detecting and recognizing figures, distorts map and graph figures alike. Top-down processes also seem to operate in that calling attention to the symmetry vs. asymmetry of a slightly asymmetric curve yielded memory errors in the direction of the description. Conceptual frame of reference effects were demonstrated in memory for lines embedded in graphs. In earlier work, the orientation of map figures was distorted in memory toward horizontal or vertical. In recent work, graph lines, but not map lines, were remembered as closer to an imaginary 45 deg line than they had been. Reference frames are determined by both perceptual and conceptual factors, leading to selection of the canonical axes as a reference frame in maps, but selection of the imaginary 45 deg as a reference frame in graphs.

An optimized protocol for generation and analysis of Ion Proton sequencing reads for RNA-Seq.

PubMed

Yuan, Yongxian; Xu, Huaiqian; Leung, Ross Ka-Kit

2016-05-26

Previous studies compared running cost, time and other performance measures of popular sequencing platforms. However, comprehensive assessment of library construction and analysis protocols for Proton sequencing platform remains unexplored. Unlike Illumina sequencing platforms, Proton reads are heterogeneous in length and quality. When sequencing data from different platforms are combined, this can result in reads with various read length. Whether the performance of the commonly used software for handling such kind of data is satisfactory is unknown. By using universal human reference RNA as the initial material, RNaseIII and chemical fragmentation methods in library construction showed similar result in gene and junction discovery number and expression level estimated accuracy. In contrast, sequencing quality, read length and the choice of software affected mapping rate to a much larger extent. Unspliced aligner TMAP attained the highest mapping rate (97.27 % to genome, 86.46 % to transcriptome), though 47.83 % of mapped reads were clipped. Long reads could paradoxically reduce mapping in junctions. With reference annotation guide, the mapping rate of TopHat2 significantly increased from 75.79 to 92.09 %, especially for long (>150 bp) reads. Sailfish, a k-mer based gene expression quantifier attained highly consistent results with that of TaqMan array and highest sensitivity. We provided for the first time, the reference statistics of library preparation methods, gene detection and quantification and junction discovery for RNA-Seq by the Ion Proton platform. Chemical fragmentation performed equally well with the enzyme-based one. The optimal Ion Proton sequencing options and analysis software have been evaluated.

Unexpected effects of different genetic backgrounds on identification of genomic rearrangements via whole-genome next generation sequencing.

PubMed

Chen, Zhangguo; Gowan, Katherine; Leach, Sonia M; Viboolsittiseri, Sawanee S; Mishra, Ameet K; Kadoishi, Tanya; Diener, Katrina; Gao, Bifeng; Jones, Kenneth; Wang, Jing H

2016-10-21

Whole genome next generation sequencing (NGS) is increasingly employed to detect genomic rearrangements in cancer genomes, especially in lymphoid malignancies. We recently established a unique mouse model by specifically deleting a key non-homologous end-joining DNA repair gene, Xrcc4, and a cell cycle checkpoint gene, Trp53, in germinal center B cells. This mouse model spontaneously develops mature B cell lymphomas (termed G1XP lymphomas). Here, we attempt to employ whole genome NGS to identify novel structural rearrangements, in particular inter-chromosomal translocations (CTXs), in these G1XP lymphomas. We sequenced six lymphoma samples, aligned our NGS data with mouse reference genome (in C57BL/6J (B6) background) and identified CTXs using CREST algorithm. Surprisingly, we detected widespread CTXs in both lymphomas and wildtype control samples, majority of which were false positive and attributable to different genetic backgrounds. In addition, we validated our NGS pipeline by sequencing multiple control samples from distinct tissues of different genetic backgrounds of mouse (B6 vs non-B6). Lastly, our studies showed that widespread false positive CTXs can be generated by simply aligning sequences from different genetic backgrounds of mouse. We conclude that mapping and alignment with reference genome might not be a preferred method for analyzing whole-genome NGS data obtained from a genetic background different from reference genome. Given the complex genetic background of different mouse strains or the heterogeneity of cancer genomes in human patients, in order to minimize such systematic artifacts and uncover novel CTXs, a preferred method might be de novo assembly of personalized normal control genome and cancer cell genome, instead of mapping and aligning NGS data to mouse or human reference genome. Thus, our studies have critical impact on the manner of data analysis for cancer genomics.

Hematocrit Measurement with R2* and Quantitative Susceptibility Mapping in Postmortem Brain.

PubMed

Walsh, A J; Sun, H; Emery, D J; Wilman, A H

2018-05-24

Noninvasive venous oxygenation quantification with MR imaging will improve the neurophysiologic investigation and the understanding of the pathophysiology in neurologic diseases. Available MR imaging methods are limited by sensitivity to flow and often require assumptions of the hematocrit level. In situ postmortem imaging enables evaluation of methods in a fully deoxygenated environment without flow artifacts, allowing direct calculation of hematocrit. This study compares 2 venous oxygenation quantification methods in in situ postmortem subjects. Transverse relaxation (R2*) mapping and quantitative susceptibility mapping were performed on a whole-body 4.7T MR imaging system. Intravenous measurements in major draining intracranial veins were compared between the 2 methods in 3 postmortem subjects. The quantitative susceptibility mapping technique was also applied in 10 healthy control subjects and compared with reference venous oxygenation values. In 2 early postmortem subjects, R2* mapping and quantitative susceptibility mapping measurements within intracranial veins had a significant and strong correlation ( R 2 = 0.805, P = .004 and R 2 = 0.836, P = .02). Higher R2* and susceptibility values were consistently demonstrated within gravitationally dependent venous segments during the early postmortem period. Hematocrit ranged from 0.102 to 0.580 in postmortem subjects, with R2* and susceptibility as large as 291 seconds -1 and 1.75 ppm, respectively. Measurements of R2* and quantitative susceptibility mapping within large intracranial draining veins have a high correlation in early postmortem subjects. This study supports the use of quantitative susceptibility mapping for evaluation of in vivo venous oxygenation and postmortem hematocrit concentrations. © 2018 by American Journal of Neuroradiology.

Calculation of stochastic broadening due to low mn magnetic perturbation in the simple map in action-angle coordinates

NASA Astrophysics Data System (ADS)

Hinton, Courtney; Punjabi, Alkesh; Ali, Halima

2009-11-01

The simple map is the simplest map that has topology of divertor tokamaks [A. Punjabi, H. Ali, T. Evans, and A. Boozer, Phys. Let. A 364, 140--145 (2007)]. Recently, the action-angle coordinates for simple map are analytically calculated, and simple map is constructed in action-angle coordinates [O. Kerwin, A. Punjabi, and H. Ali, Phys. Plasmas 15, 072504 (2008)]. Action-angle coordinates for simple map cannot be inverted to real space coordinates (R,Z). Because there is logarithmic singularity on the ideal separatrix, trajectories cannot cross separatrix [op cit]. Simple map in action-angle coordinates is applied to calculate stochastic broadening due to the low mn magnetic perturbation with mode numbers m=1, and n=±1. The width of stochastic layer near the X-point scales as 0.63 power of the amplitude δ of low mn perturbation, toroidal flux loss scales as 1.16 power of δ, and poloidal flux loss scales as 1.26 power of δ. Scaling of width deviates from Boozer-Rechester scaling by 26% [A. Boozer, and A. Rechester, Phys. Fluids 21, 682 (1978)]. This work is supported by US Department of Energy grants DE-FG02-07ER54937, DE-FG02-01ER54624 and DE-FG02-04ER54793.

Mapping From an Instrumented Glove to a Robot Hand

NASA Technical Reports Server (NTRS)

Goza, Michael

2005-01-01

An algorithm has been developed to solve the problem of mapping from (1) a glove instrumented with joint-angle sensors to (2) an anthropomorphic robot hand. Such a mapping is needed to generate control signals to make the robot hand mimic the configuration of the hand of a human attempting to control the robot. The mapping problem is complicated by uncertainties in sensor locations caused by variations in sizes and shapes of hands and variations in the fit of the glove. The present mapping algorithm is robust in the face of these uncertainties, largely because it includes a calibration sub-algorithm that inherently adapts the mapping to the specific hand and glove, without need for measuring the hand and without regard for goodness of fit. The algorithm utilizes a forward-kinematics model of the glove derived from documentation provided by the manufacturer of the glove. In this case, forward-kinematics model signifies a mathematical model of the glove fingertip positions as functions of the sensor readings. More specifically, given the sensor readings, the forward-kinematics model calculates the glove fingertip positions in a Cartesian reference frame nominally attached to the palm. The algorithm also utilizes an inverse-kinematics model of the robot hand. In this case, inverse-kinematics model signifies a mathematical model of the robot finger-joint angles as functions of the robot fingertip positions. Again, more specifically, the inverse-kinematics model calculates the finger-joint commands needed to place the fingertips at specified positions in a Cartesian reference frame that is attached to the palm of the robot hand and that nominally corresponds to the Cartesian reference frame attached to the palm of the glove. Initially, because of the aforementioned uncertainties, the glove fingertip positions calculated by the forwardkinematics model in the glove Cartesian reference frame cannot be expected to match the robot fingertip positions in the robot-hand Cartesian reference frame. A calibration must be performed to make the glove and robot-hand fingertip positions correspond more precisely. The calibration procedure involves a few simple hand poses designed to provide well-defined fingertip positions. One of the poses is a fist. In each of the other poses, a finger touches the thumb. The calibration subalgorithm uses the sensor readings from these poses to modify the kinematical models to make the two sets of fingertip positions agree more closely.

Training with Simulated Team Members (Trainen met Gesimuleerde Teamieden).

DTIC Science & Technology

1997-11-13

TEAMTAKEN 9 2.1 Teams 9 2.2 Teamtaken 10 2.3 De individuele deeltaken 11 2.4 De teamcomponent 11 2.5 Motivatie en attitudes 14 3 HET TRAINEN VAN TEAMS 15... 11 Fax 0346 35 39 77 datum 13 november 1997 Alle rechten voorbehouden. A oe a jb Miets uit deze uitgave mag worden vermenigvuldigd en/of openbaar...13 November 1997 7. NUMBER OF PAGES 8. NUMBER OF REFERENCES 9 . TYPE OF REPORT AND DATES COVERED 35 64 Interim 10. TITLE AND SUBTITLE Trainen met

Advances in Navigation Sensors and Integration Technology (Les avancees en matiere de capteurs de navigation et de technologies d’integration)

DTIC Science & Technology

2004-02-01

also referred to as a Foucault pendulum gyroscope. Rate about the z-axis (i.e., about the vertical post) is detected by the Coriolis acceleration...paper, DGA/STTC/DTGN: Eric PLESKA MBDA F: Jacky GROSSET SAGEM SA: Jean Michel CARON THALES Avionics; Charles DUSSURGEY CEA-LETI...Gilles DELAPIERRE CEM2/Montpellier: André BOYER IEF: Alain BOSSEBOEUF LPMO: Michel de la BACHELERIE ONERA: Pierre TOUBOUL ²²²²²²²²²²²² RTO

Ceres composition as inferred by the VIR-Dawn imaging spectrometer

NASA Astrophysics Data System (ADS)

Longobardo, Andrea

2016-07-01

The NASA's Dawn spacecraft [1] is orbiting around Ceres since early 2015. The Dawn mission to Ceres is divided in five stages, characterized by different altitudes above the Ceres mean surface. These five stages correspond with the different phases of the mission,, i.e. Approach, Rotational Characterization, Survey, High Altitude Mapping Orbit (HAMO) and Low Altitude Mapping Orbit (LAMO). Each phase is characterized by an increasing spatial resolution linked with the spacecraft altitude. The VIR imaging spectrometer [2] on board the Dawn spacecraft is providing a huge amount of data and giving an essential contribution to understand the Ceres composition and to give constraint about its evolution. VIR observations revealed that Ceres is a dark body, with an average albedo of 0.08 measured at 1.2 mm [3]. However, specific features seen at the local scale may show substantially higher albedo (i.e. greater than 0.2), especially in Occator, Haulani and Oxo craters [4]. VIR data reveal that the Ceres visible and near-infrared spectra (wavelength range from 0.25 to 5 mm) are mainly characterized by the following absorptions: - 2.7 mm band, ascribed to OH-bearing materials [5] and distributed across the Ceres surface; - 3.05 mm band, ascribed to NH4-bearing materials [5] and also ubiquitous on the Ceres surface; - 3.3-3.5 mm complex and 3.9 mm band, ascribed to carbonates [4] and observed only at some locations [6]. The presence of these features, in particular the 3.05 mm band, indicate widespread occurrence of ammoniated phyllosilicates [5], which could be mixed with carbonates in specific regions. The phyllosilicates composition is basically homogeneous across the Ceres surface, as suggested by the low variation of 2.7 mm and 3.05 mm band centers [7]. The presence of ammonia suggests the presence of outer Solar System materials, which could have been brought in the Main Asteroid Belt and accreted during the Ceres formation [8]. Alternatively, Ceres itself could have been formed in the outer Solar System before to migrate in its actual location [9]. References [1] Russell, C.T. et al., Science, 336, 684, 2012 [2] De Sanctis M.C. et al., Space Sci. Rev., 163, 329-336, 2011 [3] Longobardo, A. et al., LPSC abstract, #2239, 2016 [4] De Sanctis, M.C. et al., LPSC abstract, #1832, 2016 [5] De Sanctis, M.C. et al., Nature, 528, 241-244, 2015 [6] Palomba, E. et al., LPSC abstract, #2166, 2016 [7] Ammannito, E. et al., LPSC abstract, #3020, 2016 [8] Johansen, A. et al., Sci. Adv. 1, 1500109, 2015 [9] McKinnon, W.B. et al., Proc. Conf. Asteroids, Comets, Meteors, # 6475, 2012

Gravity with a cosmological constant from rational curves

NASA Astrophysics Data System (ADS)

Adamo, Tim

2015-11-01

We give a new formula for all tree-level correlators of boundary field insertions in gauged N=8 supergravity in AdS4; this is an analogue of the tree-level S-matrix in anti-de Sitter space. The formula is written in terms of rational maps from the Riemann sphere to twistor space, with no reference to bulk perturbation theory. It is polynomial in the cosmological constant, and equal to the classical scattering amplitudes of supergravity in the flat space limit. The formula is manifestly supersymmetric, independent of gauge choices on twistor space, and equivalent to expressions computed via perturbation theory at 3-point overline{MHV} and n-point MHV. We also show that the formula factorizes and obeys BCFW recursion in twistor space.

A reference consensus genetic map for molecular markers and economically important traits in faba bean (Vicia faba L.)

PubMed Central

2013-01-01

Background Faba bean (Vicia faba L.) is among the earliest domesticated crops from the Near East. Today this legume is a key protein feed and food worldwide and continues to serve an important role in culinary traditions throughout Middle East, Mediterranean region, China and Ethiopia. Adapted to a wide range of soil types, the main faba bean breeding objectives are to improve yield, resistance to biotic and abiotic stresses, seed quality and other agronomic traits. Genomic approaches aimed at enhancing faba bean breeding programs require high-quality genetic linkage maps to facilitate quantitative trait locus analysis and gene tagging for use in a marker-assisted selection. The objective of this study was to construct a reference consensus map in faba bean by joining the information from the most relevant maps reported so far in this crop. Results A combination of two approaches, increasing the number of anchor loci in diverse mapping populations and joining the corresponding genetic maps, was used to develop a reference consensus map in faba bean. The map was constructed from three main recombinant inbreed populations derived from four parental lines, incorporates 729 markers and is based on 69 common loci. It spans 4,602 cM with a range from 323 to 1041 loci in six main linkage groups or chromosomes, and an average marker density of one locus every 6 cM. Locus order is generally well maintained between the consensus map and the individual maps. Conclusion We have constructed a reliable and fairly dense consensus genetic linkage map that will serve as a basis for genomic approaches in faba bean research and breeding. The core map contains a larger number of markers than any previous individual map, covers existing gaps and achieves a wider coverage of the large faba bean genome as a whole. This tool can be used as a reference resource for studies in different genetic backgrounds, and provides a framework for transferring genetic information when using different marker technologies. Combined with syntenic approaches, the consensus map will increase marker density in selected genomic regions and will be useful for future faba bean molecular breeding applications. PMID:24377374

Bathymetry and acoustic backscatter of the mid and outer continental shelf, head of De Soto Canyon, northeastern Gulf of Mexico: data, images, and GIS

USGS Publications Warehouse

Gardner, James V.; Hughes-Clarke, John E.; Mayer, Larry A.; Dartnell, Peter

2003-01-01

The mid to outer continental shelf off Mississippi-Alabama and off northwest Florida were the focus of U.S. Geological Survey (USGS) multibeam echosounder (MBES) mapping cruises in 2000 and 2001, respectively. These areas were mapped to investigate the extent of "deep-water reefs" first suggested by Ludwig and Walton (1957). The reefs off Mississippi and Alabama were initially described in water depths of 60 to 120 m (Ludwig and Walton, 1957) but the 2000 mapping found reef and hardgrounds to be much more extensive than previously thought (Gardner et al., 2001). The persistent trend of reef-like features along the outer shelf of Mississippi-Alabama suggested the trend might continue along the northwest Florida mid and outer shelf so a MBES-mapping effort was mounted in 2001 to test this suggestion. It is critical to determine the accurate location, geomorphology, and types of the ridges and reefs that occur in this region to understand the Quaternary history of the area and to assess their importance as benthic habitats for fisheries. The area known as the "Head of De Soto Canyon" is the large unmapped region between the 2000 and 2001 mapped areas. It was unknown whether the reefs of the Mississippi-Alabama shelf continue eastward into the head of De Soto Canyon and connect with the ridges and reefs mapped on the northwest Florida outer shelf. The existence of carbonate-cemented Quaternary to Holocene sandstones along the western wall of the head of De Soto Canyon (Shipp and Hopkins, 1978; Benson et al., 1997; W.W. Schroeder, personal commun., 2002) is of interest because of the potential benthic habitats they may represent. In the summer of 2002, the USGS, in cooperation with Minerals Management Service (MMS), the University of New Hampshire, and the University of New Brunswick, conducted a MBES survey of the Head of De Soto Canyon Region connecting the 2000 and 2001 mapped regions.

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

PubMed Central

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

2017-01-01

Increasing grain yield is the ultimate goal for maize breeding. High resolution quantitative trait loci (QTL) mapping can help us understand the molecular basis of phenotypic variation of yield and thus facilitate marker assisted breeding. The aim of this study is to use genotyping-by-sequencing (GBS) for large-scale SNP discovery and simultaneous genotyping of all F2 individuals from a cross between two varieties of maize that are in clear contrast in yield and related traits. A set of 199 F2 progeny derived from the cross of varieties SG-5 and SG-7 were generated and genotyped by GBS. A total of 1,046,524,604 reads with an average of 5,258,918 reads per F2 individual were generated. This number of reads represents an approximately 0.36-fold coverage of the maize reference genome Zea_mays.AGPv3.29 for each F2 individual. A total of 68,882 raw SNPs were discovered in the F2 population, which, after stringent filtering, led to a total of 29,927 high quality SNPs. Comparative analysis using these physically mapped marker loci revealed a higher degree of synteny with the reference genome. The SNP genotype data were utilized to construct an intra-specific genetic linkage map of maize consisting of 3,305 bins on 10 linkage groups spanning 2,236.66 cM at an average distance of 0.68 cM between consecutive markers. From this map, we identified 28 QTLs associated with yield traits (100-kernel weight, ear length, ear diameter, cob diameter, kernel row number, corn grains per row, ear weight, and grain weight per plant) using the composite interval mapping (CIM) method and 29 QTLs using the least absolute shrinkage selection operator (LASSO) method. QTLs identified by the CIM method account for 6.4% to 19.7% of the phenotypic variation. Small intervals of three QTLs (qCGR-1, qKW-2, and qGWP-4) contain several genes, including one gene (GRMZM2G139872) encoding the F-box protein, three genes (GRMZM2G180811, GRMZM5G828139, and GRMZM5G873194) encoding the WD40-repeat protein, and one gene (GRMZM2G019183) encoding the UDP-Glycosyltransferase. The work will not only help to understand the mechanisms that control yield traits of maize, but also provide a basis for marker-assisted selection and map-based cloning in further studies. PMID:28533786

Landsat maps (phase V, deliverable 60), ASTER maps (phase V, deliverable 62), ASTER_DEM maps (phase V, deliverable 63), and spectral remote sensing in support of PRISM-II mineral resource assessment project, Islamic Republic of Mauritania (phase V, deliverables 61 and 64): Chapter E in Second projet de renforcement institutionnel du secteur minier de la République Islamique de Mauritanie (PRISM-II)

USGS Publications Warehouse

Rockwell, Barnaby W.; Knepper, Daniel H.; Horton, John D.

2015-01-01

The image products derived from Landsat TM and ASTER data enable the delineation of mineral groups across wide areas based on color response. Guides are provided that allow users to interpret these colors as to mineral group occurrence over lithologic units and known deposits. This information can be extrapolated to other geologically permissive tracts for various deposit types in the search for similar mineralogic responses that may be indicative of concealed deposits.

Forest Biomass Mapping From Lidar and Radar Synergies

NASA Technical Reports Server (NTRS)

Sun, Guoqing; Ranson, K. Jon; Guo, Z.; Zhang, Z.; Montesano, P.; Kimes, D.

2011-01-01

The use of lidar and radar instruments to measure forest structure attributes such as height and biomass at global scales is being considered for a future Earth Observation satellite mission, DESDynI (Deformation, Ecosystem Structure, and Dynamics of Ice). Large footprint lidar makes a direct measurement of the heights of scatterers in the illuminated footprint and can yield accurate information about the vertical profile of the canopy within lidar footprint samples. Synthetic Aperture Radar (SAR) is known to sense the canopy volume, especially at longer wavelengths and provides image data. Methods for biomass mapping by a combination of lidar sampling and radar mapping need to be developed. In this study, several issues in this respect were investigated using aircraft borne lidar and SAR data in Howland, Maine, USA. The stepwise regression selected the height indices rh50 and rh75 of the Laser Vegetation Imaging Sensor (LVIS) data for predicting field measured biomass with a R(exp 2) of 0.71 and RMSE of 31.33 Mg/ha. The above-ground biomass map generated from this regression model was considered to represent the true biomass of the area and used as a reference map since no better biomass map exists for the area. Random samples were taken from the biomass map and the correlation between the sampled biomass and co-located SAR signature was studied. The best models were used to extend the biomass from lidar samples into all forested areas in the study area, which mimics a procedure that could be used for the future DESDYnI Mission. It was found that depending on the data types used (quad-pol or dual-pol) the SAR data can predict the lidar biomass samples with R2 of 0.63-0.71, RMSE of 32.0-28.2 Mg/ha up to biomass levels of 200-250 Mg/ha. The mean biomass of the study area calculated from the biomass maps generated by lidar- SAR synergy 63 was within 10% of the reference biomass map derived from LVIS data. The results from this study are preliminary, but do show the potential of the combined use of lidar samples and radar imagery for forest biomass mapping. Various issues regarding lidar/radar data synergies for biomass mapping are discussed in the paper.

Prevalence of and factors associated with self-reported high blood pressure in Brazilian adults.

PubMed

Malta, Deborah Carvalho; Bernal, Regina Tomie Ivata; Andrade, Silvânia Suely Caribé de Araújo; Silva, Marta Maria Alves da; Velasquez-Melendez, Gustavo

2017-06-01

To analyze factors associated with self-reported high blood pressure among adults in Brazilian state capitals. The study uses data from Sistema de Vigilância de Fatores de Risco e Proteção para Doenças Crônicas por Inquérito Telefônico (Vigitel - Surveillance System of Risk and Protection Factors of Noncommunicable Diseases by Telephone Survey) collected in 2013. Prevalence rates and their respective 95% confidence intervals by gender were estimated according to sociodemographic variables, lifestyle, reported noncommunicable diseases and self-rated health status. Multivariate logistic regression modeling was used to identify variables associated with self-reported high blood pressure with α < 0.05. Prevalence of self-reported high blood pressure among adults living in Brazilian state capitals and the Federal District was 24.1%. The following variables were associated with self-reported high blood pressure: age group, taking 18-24 as reference (all age groups presented increased risk - from 25-34 years [OR = 2.6; 95%CI 2.0-3.4] up to 65 years or more [OR = 28.1; 95%CI 21.7-36.4]); low education level (9 to 11 years of study [OR = 0.8; 95%CI 0.7-0.9] and 12 years or more [OR = 0.6; 95%CI 0.6-0.7]); Black race or skin color (OR = 1.3; 95%CI 1.1-1.5); being a former smoker (OR = 1.2; 95%CI 1.1-1.3); obesity (OR = 2.7; 95%CI 2.4-3.0); diabetes (OR = 2.9; 95%CI 2.5-3.5%), and high cholesterol (OR = 1.9; 95%CI 1.8-2.2). Approximately one quarter of the adult population living in Brazilian state capitals reported having high blood pressure. Information from Vigitel is useful to monitor high blood pressure and identity its associated factors, supporting public policies for health promotion, surveillance and care. Analisar os fatores associados à hipertensão arterial autorreferida entre adultos nas capitais brasileiras. Estudo com os dados do Sistema de Vigilância de Fatores de Risco e Proteção para Doenças Crônicas por Inquérito Telefônico (Vigitel) coletados no ano de 2013. Foram estimadas as prevalências e seus respectivos intervalos de confiança 95% por sexo segundo variáveis sociodemográficas, estilos de vida, doenças crônicas relatadas e avaliação do estado de saúde. Modelagem de regressão logística multivariada foi utilizada para identificar as variáveis associadas à hipertensão arterial autorreferida com α < 0,05. A prevalência de hipertensão arterial autorreferida entre os adultos residentes nas capitais brasileiras e Distrito Federal foi de 24,1%. Foram identificadas as seguintes associações com hipertensão arterial autorreferida: faixa etária, tomando 18 a 24 anos como referência, todas as faixas etárias apresentaram maior chance - de 25 a 34 anos (RC = 2,6; IC95% 2,0-3,4) até 65 anos ou mais (RC = 28,1; IC95% 21,7-36,4); baixa escolaridade (9 a 11 anos de estudo - RC = 0,8; IC95% 0,7-0,9; e 12 anos ou mais - RC = 0,6; IC95% 0,6-0,7); raça/cor da pele preta (RC = 1,3; IC95% 1,1-1,5); ser ex-fumante (RC = 1,2; IC95% 1,1-1,3); obesidade (RC = 2,7; IC95% 2,4-3,0); diabetes (RC = 2,9; IC95% 2,5-3,5); e colesterol elevado (RC = 1,9; IC95% 1,8-2,2). Cerca de um quarto da população adulta residente nas capitais brasileiras refere ter hipertensão arterial. As informações do Vigitel são úteis para o monitoramento da hipertensão arterial e identificação de seus fatores associados, subsidiando políticas públicas de promoção, vigilância e atenção à saúde.

Trees in the Landscape.

ERIC Educational Resources Information Center

Webb, Richard; Forbatha, Ann

1982-01-01

Strategies for using trees in classroom instruction are provided. Includes: (1) activities (such as tree identification, mapping, measuring tree height/width); (2) list of asthetic, architectural, engineering, climate, and wildlife functions of trees; (3) tree discussion questions; and (4) references. (JN)

Flood mapping with multitemporal MODIS data

NASA Astrophysics Data System (ADS)

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

2014-05-01

Flood is one of the most devastating and frequent disasters resulting in loss of human life and serve damage to infrastructure and agricultural production. Flood is phenomenal in the Mekong River Delta (MRD), Vietnam. It annually lasts from July to November. Information on spatiotemporal flood dynamics is thus important for planners to devise successful strategies for flood monitoring and mitigation of its negative effects. The main objective of this study is to develop an approach for weekly mapping flood dynamics with the Moderate Resolution Imaging Spectroradiometer data in MRD using the water fraction model (WFM). The data processed for 2009 comprises three main steps: (1) data pre-processing to construct smooth time series of the difference in the values (DVLE) between land surface water index (LSWI) and enhanced vegetation index (EVI) using the empirical mode decomposition (EMD), (2) flood derivation using WFM, and (3) accuracy assessment. The mapping results were compared with the ground reference data, which were constructed from Envisat Advanced Synthetic Aperture Radar (ASAR) data. As several error sources, including mixed-pixel problems and low-resolution bias between the mapping results and ground reference data, could lower the level of classification accuracy, the comparisons indicated satisfactory results with the overall accuracy of 80.5% and Kappa coefficient of 0.61, respectively. These results were reaffirmed by a close correlation between the MODIS-derived flood area and that of the ground reference map at the provincial level, with the correlation coefficients (R2) of 0.93. Considering the importance of remote sensing for monitoring floods and mitigating the damage caused by floods to crops and infrastructure, this study eventually leads to the realization of the value of using time-series MODIS DVLE data for weekly flood monitoring in MRD with the aid of EMD and WFM. Such an approach that could provide quantitative information on spatiotemporal flood dynamics for monitoring purposes was completely transferable to other regions in the world.

Genome-wide SNP identification and QTL mapping for black rot resistance in cabbage.

PubMed

Lee, Jonghoon; Izzah, Nur Kholilatul; Jayakodi, Murukarthick; Perumal, Sampath; Joh, Ho Jun; Lee, Hyeon Ju; Lee, Sang-Choon; Park, Jee Young; Yang, Ki-Woung; Nou, Il-Sup; Seo, Joodeok; Yoo, Jaeheung; Suh, Youngdeok; Ahn, Kyounggu; Lee, Ji Hyun; Choi, Gyung Ja; Yu, Yeisoo; Kim, Heebal; Yang, Tae-Jin

2015-02-03

Black rot is a destructive bacterial disease causing large yield and quality losses in Brassica oleracea. To detect quantitative trait loci (QTL) for black rot resistance, we performed whole-genome resequencing of two cabbage parental lines and genome-wide SNP identification using the recently published B. oleracea genome sequences as reference. Approximately 11.5 Gb of sequencing data was produced from each parental line. Reference genome-guided mapping and SNP calling revealed 674,521 SNPs between the two cabbage lines, with an average of one SNP per 662.5 bp. Among 167 dCAPS markers derived from candidate SNPs, 117 (70.1%) were validated as bona fide SNPs showing polymorphism between the parental lines. We then improved the resolution of a previous genetic map by adding 103 markers including 87 SNP-based dCAPS markers. The new map composed of 368 markers and covers 1467.3 cM with an average interval of 3.88 cM between adjacent markers. We evaluated black rot resistance in the mapping population in three independent inoculation tests using F2:3 progenies and identified one major QTL and three minor QTLs. We report successful utilization of whole-genome resequencing for large-scale SNP identification and development of molecular markers for genetic map construction. In addition, we identified novel QTLs for black rot resistance. The high-density genetic map will promote QTL analysis for other important agricultural traits and marker-assisted breeding of B. oleracea.

Draft genome and reference transcriptomic resources for the urticating pine defoliator Thaumetopoea pityocampa (Lepidoptera: Notodontidae).

PubMed

Gschloessl, B; Dorkeld, F; Berges, H; Beydon, G; Bouchez, O; Branco, M; Bretaudeau, A; Burban, C; Dubois, E; Gauthier, P; Lhuillier, E; Nichols, J; Nidelet, S; Rocha, S; Sauné, L; Streiff, R; Gautier, M; Kerdelhué, C

2018-05-01

The pine processionary moth Thaumetopoea pityocampa (Lepidoptera: Notodontidae) is the main pine defoliator in the Mediterranean region. Its urticating larvae cause severe human and animal health concerns in the invaded areas. This species shows a high phenotypic variability for various traits, such as phenology, fecundity and tolerance to extreme temperatures. This study presents the construction and analysis of extensive genomic and transcriptomic resources, which are an obligate prerequisite to understand their underlying genetic architecture. Using a well-studied population from Portugal with peculiar phenological characteristics, the karyotype was first determined and a first draft genome of 537 Mb total length was assembled into 68,292 scaffolds (N50 = 164 kb). From this genome assembly, 29,415 coding genes were predicted. To circumvent some limitations for fine-scale physical mapping of genomic regions of interest, a 3X coverage BAC library was also developed. In particular, 11 BACs from this library were individually sequenced to assess the assembly quality. Additionally, de novo transcriptomic resources were generated from various developmental stages sequenced with HiSeq and MiSeq Illumina technologies. The reads were de novo assembled into 62,376 and 63,175 transcripts, respectively. Then, a robust subset of the genome-predicted coding genes, the de novo transcriptome assemblies and previously published 454/Sanger data were clustered to obtain a high-quality and comprehensive reference transcriptome consisting of 29,701 bona fide unigenes. These sequences covered 99% of the cegma and 88% of the busco highly conserved eukaryotic genes and 84% of the busco arthropod gene set. Moreover, 90% of these transcripts could be localized on the draft genome. The described information is available via a genome annotation portal (http://bipaa.genouest.org/sp/thaumetopoea_pityocampa/). © 2018 John Wiley & Sons Ltd.

Genetics Home Reference: SATB2-associated syndrome

MedlinePlus

... factor Satb2 interacts with matrix attachment region DNA elements in a tissue-specific manner and demonstrates cell- ... Citation on PubMed or Free article on PubMed Central Britanova O, de Juan Romero C, Cheung A, ...

The algebra of supertraces for 2+1 super de Sitter gravity

NASA Technical Reports Server (NTRS)

Urrutia, L. F.; Waelbroeck, H.; Zertuche, F.

1993-01-01

The algebra of the observables for 2+1 super de Sitter gravity, for one genus of the spatial surface is calculated. The algebra turns out to be an infinite Lie algebra subject to non-linear constraints. The constraints are solved explicitly in terms of five independent complex supertraces. These variables are the true degrees of freedom of the system and their quantized algebra generates a new structure which is referred to as a 'central extension' of the quantum algebra SU(2)q.

A two-dimensional proteome map of the aflatoxigenic fungus Aspergillus flavus.

PubMed

Pechanova, Olga; Pechan, Tibor; Rodriguez, Jose M; Williams, W Paul; Brown, Ashli E

2013-05-01

The filamentous fungus Aspergillus flavus is an opportunistic soil-borne pathogen that produces aflatoxins, the most potent naturally occurring carcinogenic compounds known. This work represents the first gel-based profiling analysis of A. flavus proteome and establishes a 2D proteome map. Using 2DE and MALDI-TOF-MS/MS, we identified 538 mycelial proteins of the aflatoxigenic strain NRRL 3357, the majority of which were functionally annotated as related to various cellular metabolic and biosynthetic processes. Additionally, a few enzymes from the aflatoxin synthesis pathway were also identified. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

APPLICATION OF A "VITURAL FIELD REFERENCE DATABASE" TO ASSESS LAND-COVER MAP ACCURACIES

EPA Science Inventory

An accuracy assessment was performed for the Neuse River Basin, NC land-cover/use
(LCLU) mapping results using a "Virtual Field Reference Database (VFRDB)". The VFRDB was developed using field measurement and digital imagery (camera) data collected at 1,409 sites over a perio...

GRASS 3.0 Programmer’s Manual

DTIC Science & Technology

1989-09-01

cedcecer.amymil. §1 Introducticm -5- -5- Dnomet Ge~ de GRASS continues its development with several key objectives as a guide. Tie programmer should be awme of...They do NOT assurne anything about byte ordering in the cpu. : This neans that tie value is stored using as nmy bytes as required by an integer on de ...mimum likelihood classifier to produce a landcover map. 2 Derived cell files can be the results of image classfication procedues such as clustering

Design and update of a classification system: the UCSD map of science.

PubMed

Börner, Katy; Klavans, Richard; Patek, Michael; Zoss, Angela M; Biberstine, Joseph R; Light, Robert P; Larivière, Vincent; Boyack, Kevin W

2012-01-01

Global maps of science can be used as a reference system to chart career trajectories, the location of emerging research frontiers, or the expertise profiles of institutes or nations. This paper details data preparation, analysis, and layout performed when designing and subsequently updating the UCSD map of science and classification system. The original classification and map use 7.2 million papers and their references from Elsevier's Scopus (about 15,000 source titles, 2001-2005) and Thomson Reuters' Web of Science (WoS) Science, Social Science, Arts & Humanities Citation Indexes (about 9,000 source titles, 2001-2004)-about 16,000 unique source titles. The updated map and classification adds six years (2005-2010) of WoS data and three years (2006-2008) from Scopus to the existing category structure-increasing the number of source titles to about 25,000. To our knowledge, this is the first time that a widely used map of science was updated. A comparison of the original 5-year and the new 10-year maps and classification system show (i) an increase in the total number of journals that can be mapped by 9,409 journals (social sciences had a 80% increase, humanities a 119% increase, medical (32%) and natural science (74%)), (ii) a simplification of the map by assigning all but five highly interdisciplinary journals to exactly one discipline, (iii) a more even distribution of journals over the 554 subdisciplines and 13 disciplines when calculating the coefficient of variation, and (iv) a better reflection of journal clusters when compared with paper-level citation data. When evaluating the map with a listing of desirable features for maps of science, the updated map is shown to have higher mapping accuracy, easier understandability as fewer journals are multiply classified, and higher usability for the generation of data overlays, among others.

Design and Update of a Classification System: The UCSD Map of Science

PubMed Central

Börner, Katy; Klavans, Richard; Patek, Michael; Zoss, Angela M.; Biberstine, Joseph R.; Light, Robert P.; Larivière, Vincent; Boyack, Kevin W.

2012-01-01

Global maps of science can be used as a reference system to chart career trajectories, the location of emerging research frontiers, or the expertise profiles of institutes or nations. This paper details data preparation, analysis, and layout performed when designing and subsequently updating the UCSD map of science and classification system. The original classification and map use 7.2 million papers and their references from Elsevier’s Scopus (about 15,000 source titles, 2001–2005) and Thomson Reuters’ Web of Science (WoS) Science, Social Science, Arts & Humanities Citation Indexes (about 9,000 source titles, 2001–2004)–about 16,000 unique source titles. The updated map and classification adds six years (2005–2010) of WoS data and three years (2006–2008) from Scopus to the existing category structure–increasing the number of source titles to about 25,000. To our knowledge, this is the first time that a widely used map of science was updated. A comparison of the original 5-year and the new 10-year maps and classification system show (i) an increase in the total number of journals that can be mapped by 9,409 journals (social sciences had a 80% increase, humanities a 119% increase, medical (32%) and natural science (74%)), (ii) a simplification of the map by assigning all but five highly interdisciplinary journals to exactly one discipline, (iii) a more even distribution of journals over the 554 subdisciplines and 13 disciplines when calculating the coefficient of variation, and (iv) a better reflection of journal clusters when compared with paper-level citation data. When evaluating the map with a listing of desirable features for maps of science, the updated map is shown to have higher mapping accuracy, easier understandability as fewer journals are multiply classified, and higher usability for the generation of data overlays, among others. PMID:22808037

From a 2DE-gel spot to protein function: lesson learned from HS1 in chronic lymphocytic leukemia.

PubMed

Apollonio, Benedetta; Bertilaccio, Maria Teresa Sabrina; Restuccia, Umberto; Ranghetti, Pamela; Barbaglio, Federica; Ghia, Paolo; Caligaris-Cappio, Federico; Scielzo, Cristina

2014-10-19

The identification of molecules involved in tumor initiation and progression is fundamental for understanding disease's biology and, as a consequence, for the clinical management of patients. In the present work we will describe an optimized proteomic approach for the identification of molecules involved in the progression of Chronic Lymphocytic Leukemia (CLL). In detail, leukemic cell lysates are resolved by 2-dimensional Electrophoresis (2DE) and visualized as "spots" on the 2DE gels. Comparative analysis of proteomic maps allows the identification of differentially expressed proteins (in terms of abundance and post-translational modifications) that are picked, isolated and identified by Mass Spectrometry (MS). The biological function of the identified candidates can be tested by different assays (i.e. migration, adhesion and F-actin polymerization), that we have optimized for primary leukemic cells.

A Single Molecule Scaffold for the Maize Genome

PubMed Central

Zhou, Shiguo; Wei, Fusheng; Nguyen, John; Bechner, Mike; Potamousis, Konstantinos; Goldstein, Steve; Pape, Louise; Mehan, Michael R.; Churas, Chris; Pasternak, Shiran; Forrest, Dan K.; Wise, Roger; Ware, Doreen; Wing, Rod A.; Waterman, Michael S.; Livny, Miron; Schwartz, David C.

2009-01-01

About 85% of the maize genome consists of highly repetitive sequences that are interspersed by low-copy, gene-coding sequences. The maize community has dealt with this genomic complexity by the construction of an integrated genetic and physical map (iMap), but this resource alone was not sufficient for ensuring the quality of the current sequence build. For this purpose, we constructed a genome-wide, high-resolution optical map of the maize inbred line B73 genome containing >91,000 restriction sites (averaging 1 site/∼23 kb) accrued from mapping genomic DNA molecules. Our optical map comprises 66 contigs, averaging 31.88 Mb in size and spanning 91.5% (2,103.93 Mb/∼2,300 Mb) of the maize genome. A new algorithm was created that considered both optical map and unfinished BAC sequence data for placing 60/66 (2,032.42 Mb) optical map contigs onto the maize iMap. The alignment of optical maps against numerous data sources yielded comprehensive results that proved revealing and productive. For example, gaps were uncovered and characterized within the iMap, the FPC (fingerprinted contigs) map, and the chromosome-wide pseudomolecules. Such alignments also suggested amended placements of FPC contigs on the maize genetic map and proactively guided the assembly of chromosome-wide pseudomolecules, especially within complex genomic regions. Lastly, we think that the full integration of B73 optical maps with the maize iMap would greatly facilitate maize sequence finishing efforts that would make it a valuable reference for comparative studies among cereals, or other maize inbred lines and cultivars. PMID:19936062

Ontology and diversity of transcript-associated microsatellites mined from a globe artichoke EST database

PubMed Central

Scaglione, Davide; Acquadro, Alberto; Portis, Ezio; Taylor, Christopher A; Lanteri, Sergio; Knapp, Steven J

2009-01-01

Background The globe artichoke (Cynara cardunculus var. scolymus L.) is a significant crop in the Mediterranean basin. Despite its commercial importance and its both dietary and pharmaceutical value, knowledge of its genetics and genomics remains scant. Microsatellite markers have become a key tool in genetic and genomic analysis, and we have exploited recently acquired EST (expressed sequence tag) sequence data (Composite Genome Project - CGP) to develop an extensive set of microsatellite markers. Results A unigene assembly was created from over 36,000 globe artichoke EST sequences, containing 6,621 contigs and 12,434 singletons. Over 12,000 of these unigenes were functionally assigned on the basis of homology with Arabidopsis thaliana reference proteins. A total of 4,219 perfect repeats, located within 3,308 unigenes was identified and the gene ontology (GO) analysis highlighted some GO term's enrichments among different classes of microsatellites with respect to their position. Sufficient flanking sequence was available to enable the design of primers to amplify 2,311 of these microsatellites, and a set of 300 was tested against a DNA panel derived from 28 C. cardunculus genotypes. Consistent amplification and polymorphism was obtained from 236 of these assays. Their polymorphic information content (PIC) ranged from 0.04 to 0.90 (mean 0.66). Between 176 and 198 of the assays were informative in at least one of the three available mapping populations. Conclusion EST-based microsatellites have provided a large set of de novo genetic markers, which show significant amounts of polymorphism both between and within the three taxa of C. cardunculus. They are thus well suited as assays for phylogenetic analysis, the construction of genetic maps, marker-assisted breeding, transcript mapping and other genomic applications in the species. PMID:19785740

22 CFR 1102.2 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-04-01

... FREEDOM OF INFORMATION ACT § 1102.2 Definitions. Act means the Freedom of Information Act, 5 U.S.C. 552, as amended. Commercial-use request refers to a request from or on behalf of one who seeks information.... Records and/or information are defined as all books, papers, manuals, maps, photographs, or other...

22 CFR 1102.2 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-04-01

... FREEDOM OF INFORMATION ACT § 1102.2 Definitions. Act means the Freedom of Information Act, 5 U.S.C. 552, as amended. Commercial-use request refers to a request from or on behalf of one who seeks information.... Records and/or information are defined as all books, papers, manuals, maps, photographs, or other...

22 CFR 1102.2 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-04-01

... FREEDOM OF INFORMATION ACT § 1102.2 Definitions. Act means the Freedom of Information Act, 5 U.S.C. 552, as amended. Commercial-use request refers to a request from or on behalf of one who seeks information.... Records and/or information are defined as all books, papers, manuals, maps, photographs, or other...

22 CFR 1102.2 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-04-01

... FREEDOM OF INFORMATION ACT § 1102.2 Definitions. Act means the Freedom of Information Act, 5 U.S.C. 552, as amended. Commercial-use request refers to a request from or on behalf of one who seeks information.... Records and/or information are defined as all books, papers, manuals, maps, photographs, or other...

Altitude, depth, and thickness of the Galena-Platteville Bedrock Unit in the subcrop area of Illinois and Wisconsin

USGS Publications Warehouse

Brown, Timothy A.; Dunning, Charles P.; Sharpe, Jennifer B.

2000-01-01

The report series will enable investigators involved in site-specific studies within the subcrop area to understand the regional geologic framework of the unit and to find additional reference sources. This report consists of four sheets that show the altitude (sheet 1), depth from land surface (sheet 2), total thickness (sheet 3), and location of altitude data (sheet 4) of the lithologic units that constitute the Galena-Platteville bedrock unit within the subcrop area. The sheets also show major known geologic features within the Galena-Platteville study area in Illinois and Wisconsin. A geographic information system (GIS) was used to generate data layers (coverages) from point data and from published and unpublished contour maps at various scales and detail. Standard GIS procedures were used to change the coverages into the maps shown on the sheets presented in this report. A list of references for the data used to prepare the maps is provided. 

Spectroscopic parallaxes of MAP region stars from UBVRI, DDO, and uvbyH-beta photometry. [Multichannel Astrometric Photometer for astronomical observation

NASA Technical Reports Server (NTRS)

Persinger, Tim; Castelaz, Michael W.

1990-01-01

This paper presents the results of spectral type and luminosity classification of reference stars in the Allegheny Observatory MAP parallax program, using broadband and intermediate-band photometry. In addition to the use of UBVRI and DDO photometric systems, the uvbyH-beta photometric system was included for classification of blue (B - V less than 0.6) reference stars. The stellar classifications made from the photometry are used to determine spectroscopic parallaxes. The spectroscopic parallaxes are used in turn to adjust the relative parallaxes measured with the MAP to absolute parallaxes. A new method for dereddening stars using more than one photometric system is presented. In the process of dereddening, visual extinctions, spectral types, and luminosity classes are determined, as well as a measure of the goodness of fit. The measure of goodness of fit quantifies confidence in the stellar classifications. It is found that the spectral types are reliable to within 2.5 spectral subclasses.

The development of fast-mapping and novel word retention strategies in monolingual and bilingual infants.

PubMed

Kalashnikova, Marina; Escudero, Paola; Kidd, Evan

2018-04-30

The mutual exclusivity (ME) assumption is proposed to facilitate early word learning by guiding infants to map novel words to novel referents. This study assessed the emergence and use of ME to both disambiguate and retain the meanings of novel words across development in 18-month-old monolingual and bilingual children (Experiment 1; N = 58), and in a sub-group of these children again at 24 months of age (Experiment 2: N = 32). Both monolinguals and bilinguals employed ME to select the referent of a novel label to a similar extent at 18 and 24 months. At 18 months, there were also no differences in novel word retention between the two language-background groups. However, at 24 months, only monolinguals showed the ability to retain these label-object mappings. These findings indicate that the development of the ME assumption as a reliable word-learning strategy is shaped by children's individual language exposure and experience with language use. © 2018 John Wiley & Sons Ltd.

Clinical-Functional Vulnerability Index-20 (IVCF-20): rapid recognition of frail older adults.

PubMed

Moraes, Edgar Nunes de; Carmo, Juliana Alves do; Moraes, Flávia Lanna de; Azevedo, Raquel Souza; Machado, Carla Jorge; Montilla, Dalia Elena Romero

2016-12-22

To evaluate the adequacy of the Clinical-Functional Vulnerability Index-20, a rapid triage instrument to test vulnerability in Brazilian older adults, for the use in primary health care. The study included convenience sample of 397 patients aged older than or equal to 60 years attended at Centro de Referência para o Idoso (Reference Center for Older Adults) and of 52 older adults the same age attended at the community. The results of the questionnaire, consisting of 20 questions, were compared with those of the Comprehensive Geriatric Assessment, considered a reference for identifying frail older adults. Spearman's correlation was evaluated in the Clinical-Functional Vulnerability Index-20 with the Comprehensive Geriatric Assessment; the validity was verified by the area under the ROC curve; reliability was estimated by the percentage of agreement among evaluators and by the kappa coefficient, both with quadratic weighted. The cut-off point was obtained based on the higher accuracy criterion. Cronbach's alpha, a measure of internal consistency, was estimated. The Spearman's correlation coefficient was high and positive for both groups (0.792 for older adults attended at the Reference Center and 0.305 for older adults from the community [p < 0.001]). The area under the ROC curve for older adults attended at the Reference Center was substantial (0.903). The cut-off point obtained was six, and older adults with scores in Clinical-Functional Vulnerability Index-20 above that value had strong possibility of being frail. For older adults from the community, the quadratic weighted agreement among evaluators was 99.5%, and the global quadratic weighted kappa coefficient was 0.94. Cronbach's alpha was high for older adults attended at the Reference Center (0.861) and those attended at the community (0.740). The Clinical-Functional Vulnerability Index-20 questionnaire, in the sample examined, turned out to be positively correlated with the Comprehensive Geriatric Assessment, in addition to the results indicating a high degree of validity and reliability. Thus, the Clinical-Functional Vulnerability Index-20 proves to be viable as a triage instrument in the primary health care that identifies frail older adults (older adults at risk of weakening and frail older adults). Avaliar a adequação do Índice de Vulnerabilidade Clínico-Funcional-20 , instrumento de triagem rápida de vulnerabilidade em idosos brasileiros, para utilização pela atenção básica. O estudo incluiu amostra de conveniência de 397 pacientes com idade maior ou igual a 60 anos atendidos em um Centro de Referência para o Idoso e de 52 idosos da mesma idade atendidos na comunidade. Os resultados do questionário, constituído por 20 perguntas, foram comparados com aqueles da Avaliação Geriátrica Ampla, considerada referência para identificação do idoso frágil. Foi avaliada a correlação de Spearman do Índice de Vulnerabilidade Clínico-Funcional-20 com a Avaliação Geriátrica Ampla; a validade foi verificada pela área sob a curva ROC; a confiabilidade foi estimada pelo percentual de concordância entre avaliadores e coeficiente kappa, ambos com ponderação quadrática. Obteve-se ponto de corte com base no critério de maior acurácia. O alfa de Cronbach, medida de consistência interna, foi calculado. O coeficiente de correlação de Spearman foi elevado e positivo em ambos os grupos (0,792 para idosos atendidos no Centro de Referência para o Idoso e 0,305 para idosos da comunidade [p < 0,001]). A área sob a curva ROC para idosos atendidos no Centro de Referência para o Idoso foi substancial (0,903). O ponto de corte obtido foi seis e idosos com pontuação no Índice de Vulnerabilidade Clínico-Funcional-20 acima desse valor tinham forte possibilidade de serem frágeis. Para idosos da comunidade, a concordância ponderada quadrática entre avaliadores foi 99,5% e o coeficiente kappa ponderado quadrático global, 0,94. O alfa de Cronbach foi elevado para idosos atendidos no Centro de Referência para o Idoso (0,861) e da comunidade (0,740). O questionário do Índice de Vulnerabilidade Clínico-Funcional-20, na amostra analisada, mostrou ser positivamente correlacionado com a Avaliação Geriátrica Ampla, além de os resultados indicarem alto grau de validade e confiabilidade. Assim, o Índice de Vulnerabilidade Clínico-Funcional-20 se mostra viável como instrumento de rastreio na atenção básica que identifica o idoso com fragilidade (idoso em risco de fragilização e idoso frágil).

Mapping Typha Domingensis in the Cienega de Santa Clara Using Satellite Images, Global Positioning System, and Spectrometry

USGS Publications Warehouse

Sanchez, Richard D.; Burnett, Earl E.; Croxen, Fred

2000-01-01

The Cienega de Santa Clara, Sonora, Mexico, a brackish wetland area created near the delta of the Colorado River from drainage effluent flowing from the United States since 1977, may undergo changes owing to the operation of the Yuma Desalting Plant in the United States. This has become the largest wetland in the delta region containing rare and endangered species, yet little is known about the environmental impact of these changes. The water quality of the marsh is of growing concern to the Bureau of Reclamation (BOR) which operates the Desalting Plant. Consequently, the BOR solicited the U.S. Geological Survey to investigate the limits and usefulness of satellite, global positioning system (GPS), and spectra data to map the Typha domingensis (cattail) of the Cienega de Santa Clara. Typha domingensis was selected by the BOR as the Cienega de Santa Clara indicator species to best predict the environmental effects of effl uent from the Yuma Desalting Plant. The successful base mapping of Typha domingensis will provide a viable tool for long-term monitoring and stress detection in the Cienega de Santa Clara.

Geologic Map of The Volcanoes Quadrangle, Bernalillo and Sandoval Counties, New Mexico

USGS Publications Warehouse

Thompson, Ren A.; Shroba, Ralph R.; Menges, Christopher M.; Schmidt, Dwight L.; Personius, Stephen F.; Brandt, Theodore R.

2009-01-01

This geologic map, in support of the U.S. Geological Survey Middle Rio Grande Basin Geologic Mapping Project, shows the spatial distribution of surficial deposits, lava flows, and related sediments of the Albuquerque volcanoes, upper Santa Fe Group sediments, faults, and fault-related structural features. These deposits are on, along, and beneath the Llano de Albuquerque (West Mesa) west of Albuquerque, New Mexico. Some of these deposits are in the western part of Petroglyph National Monument. Artificial fill deposits are mapped chiefly beneath and near the City of Albuquerque Soil Amendment Facility and the Double Eagle II Airport. Alluvial deposits were mapped in and along stream channels, beneath terrace surfaces, and on the Llano de Albuquerque and its adjacent hill slopes. Deposits composed of alluvium and colluvium are also mapped on hill slopes. Wedge-shaped deposits composed chiefly of sandy sheetwash deposits, eolian sand, and intercalated calcic soils have formed on the downthrown-sides of faults. Deposits of active and inactive eolian sand and sandy sheetwash deposits mantle the Llano de Albuquerque. Lava flows and related sediments of the Albuquerque volcanoes were mapped near the southeast corner of the map area. They include eleven young lava flow units and, where discernable, associated vent and near-vent pyroclastic deposits associated with cinder cones. Upper Santa Fe Group sediments are chiefly fluvial in origin, and are well exposed near the western boundary of the map area. From youngest to oldest they include a gravel unit, pebbly sand unit, tan sand and mud unit, tan sand unit, tan sand and clay unit, and silty sand unit. Undivided upper Santa Fe Group sediments are mapped in the eastern part of the map area. Faults were identified on the basis of surface expression determined from field mapping and interpretation of aeromagnetic data where concealed beneath surficial deposits. Fault-related structural features are exposed and were mapped near the western boundary of the map area.

Uneven recombination rate and linkage disequilibrium across a reference SNP map for common bean (Phaseolus vulgaris L.)

PubMed Central

Farmer, Andrew D.; Huang, Wei; Ambachew, Daniel; Penmetsa, R. Varma; Carrasquilla-Garcia, Noelia; Assefa, Teshale; Cannon, Steven B.

2018-01-01

Recombination (R) rate and linkage disequilibrium (LD) analyses are the basis for plant breeding. These vary by breeding system, by generation of inbreeding or outcrossing and by region in the chromosome. Common bean (Phaseolus vulgaris L.) is a favored food legume with a small sequenced genome (514 Mb) and n = 11 chromosomes. The goal of this study was to describe R and LD in the common bean genome using a 768-marker array of single nucleotide polymorphisms (SNP) based on Trans-legume Orthologous Group (TOG) genes along with an advanced-generation Recombinant Inbred Line reference mapping population (BAT93 x Jalo EEP558) and an internationally available diversity panel. A whole genome genetic map was created that covered all eleven linkage groups (LG). The LGs were linked to the physical map by sequence data of the TOGs compared to each chromosome sequence of common bean. The genetic map length in total was smaller than for previous maps reflecting the precision of allele calling and mapping with SNP technology as well as the use of gene-based markers. A total of 91.4% of TOG markers had singleton hits with annotated Pv genes and all mapped outside of regions of resistance gene clusters. LD levels were found to be stronger within the Mesoamerican genepool and decay more rapidly within the Andean genepool. The recombination rate across the genome was 2.13 cM / Mb but R was found to be highly repressed around centromeres and frequent outside peri-centromeric regions. These results have important implications for association and genetic mapping or crop improvement in common bean. PMID:29522524

De novo and inherited private variants in MAP1B in periventricular nodular heterotopia.

PubMed

Heinzen, Erin L; O'Neill, Adam C; Zhu, Xiaolin; Allen, Andrew S; Bahlo, Melanie; Chelly, Jamel; Chen, Ming Hui; Dobyns, William B; Freytag, Saskia; Guerrini, Renzo; Leventer, Richard J; Poduri, Annapurna; Robertson, Stephen P; Walsh, Christopher A; Zhang, Mengqi

2018-05-01

Periventricular nodular heterotopia (PVNH) is a malformation of cortical development commonly associated with epilepsy. We exome sequenced 202 individuals with sporadic PVNH to identify novel genetic risk loci. We first performed a trio-based analysis and identified 219 de novo variants. Although no novel genes were implicated in this initial analysis, PVNH cases were found overall to have a significant excess of nonsynonymous de novo variants in intolerant genes (p = 3.27x10-7), suggesting a role for rare new alleles in genes yet to be associated with the condition. Using a gene-level collapsing analysis comparing cases and controls, we identified a genome-wide significant signal driven by four ultra-rare loss-of-function heterozygous variants in MAP1B, including one de novo variant. In at least one instance, the MAP1B variant was inherited from a parent with previously undiagnosed PVNH. The PVNH was frontally predominant and associated with perisylvian polymicrogyria. These results implicate MAP1B in PVNH. More broadly, our findings suggest that detrimental mutations likely arising in immediately preceding generations with incomplete penetrance may also be responsible for some apparently sporadic diseases.

Construction of a reference genetic linkage map for carnation (Dianthus caryophyllus L.)

PubMed Central

2013-01-01

Background Genetic linkage maps are important tools for many genetic applications including mapping of quantitative trait loci (QTLs), identifying DNA markers for fingerprinting, and map-based gene cloning. Carnation (Dianthus caryophyllus L.) is an important ornamental flower worldwide. We previously reported a random amplified polymorphic DNA (RAPD)-based genetic linkage map derived from Dianthus capitatus ssp. andrezejowskianus and a simple sequence repeat (SSR)-based genetic linkage map constructed using data from intraspecific F2 populations; however, the number of markers was insufficient, and so the number of linkage groups (LGs) did not coincide with the number of chromosomes (x = 15). Therefore, we aimed to produce a high-density genetic map to improve its usefulness for breeding purposes and genetic research. Results We improved the SSR-based genetic linkage map using SSR markers derived from a genomic library, expression sequence tags, and RNA-seq data. Linkage analysis revealed that 412 SSR loci (including 234 newly developed SSR loci) could be mapped to 17 linkage groups (LGs) covering 969.6 cM. Comparison of five minor LGs covering less than 50 cM with LGs in our previous RAPD-based genetic map suggested that four LGs could be integrated into two LGs by anchoring common SSR loci. Consequently, the number of LGs corresponded to the number of chromosomes (x = 15). We added 192 new SSRs, eight RAPD, and two sequence-tagged site loci to refine the RAPD-based genetic linkage map, which comprised 15 LGs consisting of 348 loci covering 978.3 cM. The two maps had 125 SSR loci in common, and most of the positions of markers were conserved between them. We identified 635 loci in carnation using the two linkage maps. We also mapped QTLs for two traits (bacterial wilt resistance and anthocyanin pigmentation in the flower) and a phenotypic locus for flower-type by analyzing previously reported genotype and phenotype data. Conclusions The improved genetic linkage maps and SSR markers developed in this study will serve as reference genetic linkage maps for members of the genus Dianthus, including carnation, and will be useful for mapping QTLs associated with various traits, and for improving carnation breeding programs. PMID:24160306

Construction of a reference genetic linkage map for carnation (Dianthus caryophyllus L.).

PubMed

Yagi, Masafumi; Yamamoto, Toshiya; Isobe, Sachiko; Hirakawa, Hideki; Tabata, Satoshi; Tanase, Koji; Yamaguchi, Hiroyasu; Onozaki, Takashi

2013-10-26

Genetic linkage maps are important tools for many genetic applications including mapping of quantitative trait loci (QTLs), identifying DNA markers for fingerprinting, and map-based gene cloning. Carnation (Dianthus caryophyllus L.) is an important ornamental flower worldwide. We previously reported a random amplified polymorphic DNA (RAPD)-based genetic linkage map derived from Dianthus capitatus ssp. andrezejowskianus and a simple sequence repeat (SSR)-based genetic linkage map constructed using data from intraspecific F2 populations; however, the number of markers was insufficient, and so the number of linkage groups (LGs) did not coincide with the number of chromosomes (x = 15). Therefore, we aimed to produce a high-density genetic map to improve its usefulness for breeding purposes and genetic research. We improved the SSR-based genetic linkage map using SSR markers derived from a genomic library, expression sequence tags, and RNA-seq data. Linkage analysis revealed that 412 SSR loci (including 234 newly developed SSR loci) could be mapped to 17 linkage groups (LGs) covering 969.6 cM. Comparison of five minor LGs covering less than 50 cM with LGs in our previous RAPD-based genetic map suggested that four LGs could be integrated into two LGs by anchoring common SSR loci. Consequently, the number of LGs corresponded to the number of chromosomes (x = 15). We added 192 new SSRs, eight RAPD, and two sequence-tagged site loci to refine the RAPD-based genetic linkage map, which comprised 15 LGs consisting of 348 loci covering 978.3 cM. The two maps had 125 SSR loci in common, and most of the positions of markers were conserved between them. We identified 635 loci in carnation using the two linkage maps. We also mapped QTLs for two traits (bacterial wilt resistance and anthocyanin pigmentation in the flower) and a phenotypic locus for flower-type by analyzing previously reported genotype and phenotype data. The improved genetic linkage maps and SSR markers developed in this study will serve as reference genetic linkage maps for members of the genus Dianthus, including carnation, and will be useful for mapping QTLs associated with various traits, and for improving carnation breeding programs.

High-Resolution Forest Carbon Monitoring and Modeling: Continued Prototype Development and Deployment Across The Tri-state Area (MD, PA, DE), USA

NASA Astrophysics Data System (ADS)

Hurtt, G. C.; Birdsey, R.; Campbell, E.; Dolan, K. A.; Dubayah, R.; Escobar, V. M.; Finley, A. O.; Flanagan, S.; Huang, W.; Johnson, K.; Lister, A.; ONeil-Dunne, J.; Sepulveda Carlo, E.; Zhao, M.

2017-12-01

Local, national and international programs have increasing need for precise and accurate estimates of forest carbon and structure to support greenhouse gas reduction plans, climate initiatives, and other international climate treaty frameworks. In 2010 Congress directed NASA to initiate research towards the development of Carbon Monitoring Systems (CMS). In response, our team has worked to develop a robust, replicable framework to produce maps of high-resolution carbon stocks and future carbon sequestration potential. High-resolution (30m) maps of carbon stocks and uncertainty were produced by linking national 1m-resolution imagery and existing wall-to-wall airborne lidar to spatially explicit in-situ field observations such as the USFS Forest Inventory and Analysis (FIA) network. These same data, characterizing forest extent and vertical structure, were used to drive a prognostic ecosystem model to predict carbon fluxes and carbon sequestration potential at unprecedented spatial resolution and scale (90m), more than 100,000 times the spatial resolution of standard global models. Through project development, the domain of this research has expanded from two counties in MD (2,181 km2), to the entire state (32,133 km2), to the tri-state region of MD, PA, and DE (157,868 km2), covering forests in four major USDA ecological providences (Eastern Broadleaf, Northeastern Mixed, Outer Coastal Plain, and Central Appalachian). Across the region, we estimate 694 Tg C (14 DE, 113 MD, 567 PA) in above ground biomass, and estimate a carbon sequestration potential more than twice that amount. Empirical biomass products enhance existing approaches though high resolution accounting for trees outside traditional forest maps. Modeling products move beyond traditional MRV, and map future afforestation and reforestation potential for carbon at local actionable spatial scales. These products are relevant to multiple stakeholder needs in the region as discussed through the Tri-sate Working Group, and are actively being used to inform the state of MD's Greenhouse Gas Reduction Act. The approach is scalable, and provides a protoype framework for application in other domains and for future spaceborne lidar missions.

World Map Showing Surface and Subsurface Distribution, and Lithologic Character of Middle and Late Neoproterozoic Rocks

USGS Publications Warehouse

Stewart, John H.

2007-01-01

INTRODUCTION The map was prepared to outline the basic information on where Neoproterozoic rocks are present in the World, and of the lithologic character of these rocks. The information provides a better understanding of major Neoproterozoic tectonic subdivisions useful in paleogeographic and plate tectonic reconstructions. The time frame of the map is within the middle and late Neoproterozoic from approximately 870 to 540 Ma and is after widespread Mesoproterozoic Grenville-age collisional events that are considered to have formed the hypothetical supercontinent of Rodinia. Much of the time represented by the map is interpreted to be during the fragmentation of Rodinia. The recognition of Neoproterozoic rocks is commonly difficult because of limited isotopic or paloeontological dating. Thus, some rocks shown on the map could be older or younger than the age indicated. However, at the scale of the map the the problem may be minor. Enough information seems to be available to indicate the general age of the rocks. Many of the successions contain diamictite deposits considered to be glaciogenic and dated as middle or late Neoproterozoic. These deposits thus show a rough correlation of middle and late Neoproterozoic rocks of the world. The map is a Richardson map projection, except for Antarctica which is a polar projection. The map was prepared from about 650 references, shown in the text linked below under 'Sources of Information', used to outline distribution patterns, determine rock types, and provide information on the regional and local geologic framework of the rocks. The focus of the references is on the geologic information needed to prepare the map. Other information, such as plate tectonic reconstructions or paleomagnetic studies is generally not included. The 'Sources of Information' lists references alphabetically for each of 14 regions. In brackets is a code for each area. These codes provide help in locating the specific regions in the references.

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-01-01

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

Digitising the Past: The Beginning of a New Future at the Royal Tropical Institute of The Netherlands

ERIC Educational Resources Information Center

Levi, Peter

2010-01-01

Purpose: The purpose of this paper is to describe a project to digitise maps at the Royal Tropical Institute, or Koninklijk Instituut voor de Tropen (KIT), of The Netherlands. KIT has an extensive collection of maps and nautical charts of (sub-) tropical regions, including general maps and topographical map series, city maps, thematic maps and…

Satellite Remote Sensing of Cropland Characteristics in 30m Resolution: The First North American Continental-Scale Classification on High Performance Computing Platforms

NASA Astrophysics Data System (ADS)

Massey, Richard

Cropland characteristics and accurate maps of their spatial distribution are required to develop strategies for global food security by continental-scale assessments and agricultural land use policies. North America is the major producer and exporter of coarse grains, wheat, and other crops. While cropland characteristics such as crop types are available at country-scales in North America, however, at continental-scale cropland products are lacking at fine sufficient resolution such as 30m. Additionally, applications of automated, open, and rapid methods to map cropland characteristics over large areas without the need of ground samples are needed on efficient high performance computing platforms for timely and long-term cropland monitoring. In this study, I developed novel, automated, and open methods to map cropland extent, crop intensity, and crop types in the North American continent using large remote sensing datasets on high-performance computing platforms. First, a novel method was developed in this study to fuse pixel-based classification of continental-scale Landsat data using Random Forest algorithm available on Google Earth Engine cloud computing platform with an object-based classification approach, recursive hierarchical segmentation (RHSeg) to map cropland extent at continental scale. Using the fusion method, a continental-scale cropland extent map for North America at 30m spatial resolution for the nominal year 2010 was produced. In this map, the total cropland area for North America was estimated at 275.2 million hectares (Mha). This map was assessed for accuracy using randomly distributed samples derived from United States Department of Agriculture (USDA) cropland data layer (CDL), Agriculture and Agri-Food Canada (AAFC) annual crop inventory (ACI), Servicio de Informacion Agroalimentaria y Pesquera (SIAP), Mexico's agricultural boundaries, and photo-interpretation of high-resolution imagery. The overall accuracies of the map are 93.4% with a producer's accuracy for crop class at 85.4% and user's accuracy of 74.5% across the continent. The sub-country statistics including state-wise and county-wise cropland statistics derived from this map compared well in regression models resulting in R2 > 0.84. Secondly, an automated phenological pattern matching (PPM) method to efficiently map cropping intensity was also developed in this study. This study presents a continental-scale cropping intensity map for the North American continent at 250m spatial resolution for 2010. In this map, the total areas for single crop, double crop, continuous crop, and fallow were estimated to be 123.5 Mha, 11.1 Mha, 64.0 Mha, and 83.4 Mha, respectively. This map was assessed using limited country-level reference datasets derived from United States Department of Agriculture cropland data layer and Agriculture and Agri-Food Canada annual crop inventory with overall accuracies of 79.8% and 80.2%, respectively. Third, two novel and automated decision tree classification approaches to map crop types across the conterminous United States (U.S.) using MODIS 250 m resolution data: 1) generalized, and 2) year-specific classification were developed. The classification approaches use similarities and dissimilarities in crop type phenology derived from NDVI time-series data for the two approaches. Annual crop type maps were produced for 8 major crop types in the United States using the generalized classification approach for 2001-2014 and the year-specific approach for 2008, 2010, 2011 and 2012. The year-specific classification had overall accuracies greater than 78%, while the generalized classifier had accuracies greater than 75% for the conterminous U.S. for 2008, 2010, 2011, and 2012. The generalized classifier enables automated and routine crop type mapping without repeated and expensive ground sample collection year after year with overall accuracies > 70% across all independent years. Taken together, these cropland products of extent, cropping intensity, and crop types, are significantly beneficial in agricultural and water use planning and monitoring to formulate policies towards global and North American food security issues.

BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences, and Perspectives for Genetic Mapping

PubMed Central

Hulse-Kemp, Amanda M.; Ashrafi, Hamid; Stoffel, Kevin; Zheng, Xiuting; Saski, Christopher A.; Scheffler, Brian E.; Fang, David D.; Chen, Z. Jeffrey; Van Deynze, Allen; Stelly, David M.

2015-01-01

A bacterial artificial chromosome library and BAC-end sequences for cultivated cotton (Gossypium hirsutum L.) have recently been developed. This report presents genome-wide single nucleotide polymorphism (SNP) mining utilizing resequencing data with BAC-end sequences as a reference by alignment of 12 G. hirsutum L. lines, one G. barbadense L. line, and one G. longicalyx Hutch and Lee line. A total of 132,262 intraspecific SNPs have been developed for G. hirsutum, whereas 223,138 and 470,631 interspecific SNPs have been developed for G. barbadense and G. longicalyx, respectively. Using a set of interspecific SNPs, 11 randomly selected and 77 SNPs that are putatively associated with the homeologous chromosome pair 12 and 26, we mapped 77 SNPs into two linkage groups representing these chromosomes, spanning a total of 236.2 cM in an interspecific F2 population (G. barbadense 3-79 × G. hirsutum TM-1). The mapping results validated the approach for reliably producing large numbers of both intraspecific and interspecific SNPs aligned to BAC-ends. This will allow for future construction of high-density integrated physical and genetic maps for cotton and other complex polyploid genomes. The methods developed will allow for future Gossypium resequencing data to be automatically genotyped for identified SNPs along the BAC-end sequence reference for anchoring sequence assemblies and comparative studies. PMID:25858960

References from Brazilian medical journals in national publications.

PubMed

Teixeira, Renan Kleber Costa; Botelho, Nara Macedo; Petroianu, Andy

2013-01-01

To assess whether there is a preference for international journal citation to the detriment of national ones in ten Brazilian medical journals, in two different periods. All references in the articles published in Arquivos Brasileiros de Oftalmologia, Revista Brasileira de Cirurgia Cardiovascular, Revista da Associação Médica Brasileira, São Paulo Medical Journal, Arquivos Brasileiros de Endocrinologia e Metabologia, Clinics, Jornal Brasileiro de Pneumologia, Revista da Sociedade Brasileira de Medicina Tropical, Revista Brasileira de Psiquiatria e Acta Ortopédica Brasileira in the years 2011 and 2007 were analyzed, assessing the number of articles published in national and international journals. A total of 36,125 references from 1,462 articles published in the 10 aforementioned journals were analyzed. Of the total number, 4.242 (11.74%) were from Brazilian journals. There was no significant difference between the two analyzed periods. A total of 453 (30,98%) of the articles studied non-cited brazilian papers,and 81 (5.54%) articles had more Brazilian than international references. Of total references analyzed, 11.74% were related to articles published in Brazilian journals. This number, when compared to the percentage of Brazilian articles published in the medical area, demonstrates a good number of citations of national articles. Copyright © 2012 Elsevier Editora Ltda. All rights reserved.

Exploring New Command and Control Concepts and Capabilities (Exploration de Nouveaux Concepts de Commandement et Controle et de Leurs Capacites)

DTIC Science & Technology

2007-04-01

Anthropology Genetics, Physiology Cognition Knowledge Skills IndividualI i i l Team Personality & Values Dynamic Factors & Behaviors Organizational...better support that group, one should therefore have an eye upon the flow of benefits to the right. The four uses relating to learning more about C2 are...from the scenario evolution discussion outlines above and coloured blue in the figure) with the Reference Model equivalent variables and linkages

A successful development of subtle traps: Chihuido de la Sierra Negra, Neuquen Basin

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

Comeron, R.; Valenzuela, M.W.

1996-08-01

Using new traps search concepts in the Chihuido de la Sierra Negra oil field, it was possible to substantially increase production from 4400 bbl/day in 1984 to 125,000 bbl/day in 1995. Oil reserves are located within an 8000 ha area situated on the Chihuido de la Sierra Negra anticlinal flank. Success was achieved by using different techniques for subtle traps detection, namely seismic amplitude mapping, individualization of different production facies and its predictive mapping. This reduced the search and development toward low structural areas which had not been considered before. The production layers are formed by two lower Cretaceous eolianmore » sandstones called the Avile Member and the Troncoso Lower Member, with thicknesses ranging from 5 to 30 meters. 2D seismic made it possible to individualize the thickest sand areas, some of which turned out to be productive. Using 3D seismic, by means of azimuth and dip maps, fractured areas were detected where fault throws range from 5 to 10 meters. In many of these fractured zones, thin igneous intrusives are emplaced forming seals. Such determinations make it possible for different oil-water contacts and static pressures to be delimited. Due to the small fault throws, the different blocks could not be detected by conventional mapping methods. The delineation of the field compartmentalization becomes important in the waterflooding stage as well as for the detection of new traps in surrounding areas. The combination of seismic and stratigraphic methods made it possible to discover and develop Argentina`s main oil field.« less

Establishing a leaf proteome reference map for Ginkgo biloba provides insight into potential ethnobotanical uses

USDA-ARS?s Scientific Manuscript database

Although ginkgo (Maidenhair tree, Ginkgo biloba L.) is an ancient medicinal and ornamental tree, there has not previously been any systematic proteomic study of the leaves. Herein we describe results from the initial study identifying abundant ginkgo leaf proteins and present a gel reference map. Pr...

78 FR 19355 - Noise Exposure Map Notice: Receipt of Noise Compatibility Program and Request for Review

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-29

... of 49 U.S.C. 47501 et. seq (the Aviation Safety and Noise Abatement Act, hereinafter referred to as.... 47503 (the Aviation Safety and Noise Abatement Act, hereinafter referred to as ``the Act''), an airport... DEPARTMENT OF TRANSPORTATION Federal Aviation Administration Noise Exposure Map Notice: Receipt of...

Construction of an integrated genetic map for Capsicum baccatum L.

PubMed

Moulin, M M; Rodrigues, R; Ramos, H C C; Bento, C S; Sudré, C P; Gonçalves, L S A; Viana, A P

2015-06-18

Capsicum baccatum L. is one of the five Capsicum domesticated species and has multiple uses in the food, pharmaceutical and cosmetic industries. This species is also a valuable source of genes for chili pepper breeding, especially genes for disease resistance and fruit quality. However, knowledge of the genetic structure of C. baccatum is limited. A reference map for C. baccatum (2n = 2x = 24) based on 42 microsatellite, 85 inter-simple sequence repeat, and 56 random amplified polymorphic DNA markers was constructed using an F2 population consisting of 203 individuals. The map was generated using the JoinMap software (version 4.0) and the linkage groups were formed and ordered using a LOD score of 3.0 and maximum of 40% recombination. The genetic map consisted of 12 major and four minor linkage groups covering a total genome distance of 2547.5 cM with an average distance of 14.25 cM between markers. Of the 152 pairs of microsatellite markers available for Capsicum annuum, 62 were successfully transferred to C. baccatum, generating polymorphism. Forty-two of these markers were mapped, allowing the introduction of C. baccatum in synteny studies with other species of the genus Capsicum.

The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing

PubMed Central

2010-01-01

Background Food supply from the ocean is constrained by the shortage of domesticated and selected fish. Development of genomic models of economically important fishes should assist with the removal of this bottleneck. European sea bass Dicentrarchus labrax L. (Moronidae, Perciformes, Teleostei) is one of the most important fishes in European marine aquaculture; growing genomic resources put it on its way to serve as an economic model. Results End sequencing of a sea bass genomic BAC-library enabled the comparative mapping of the sea bass genome using the three-spined stickleback Gasterosteus aculeatus genome as a reference. BAC-end sequences (102,690) were aligned to the stickleback genome. The number of mappable BACs was improved using a two-fold coverage WGS dataset of sea bass resulting in a comparative BAC-map covering 87% of stickleback chromosomes with 588 BAC-contigs. The minimum size of 83 contigs covering 50% of the reference was 1.2 Mbp; the largest BAC-contig comprised 8.86 Mbp. More than 22,000 BAC-clones aligned with both ends to the reference genome. Intra-chromosomal rearrangements between sea bass and stickleback were identified. Size distributions of mapped BACs were used to calculate that the genome of sea bass may be only 1.3 fold larger than the 460 Mbp stickleback genome. Conclusions The BAC map is used for sequencing single BACs or BAC-pools covering defined genomic entities by second generation sequencing technologies. Together with the WGS dataset it initiates a sea bass genome sequencing project. This will allow the quantification of polymorphisms through resequencing, which is important for selecting highly performing domesticated fish. PMID:20105308

Preliminary Geologic Map of the Vermejo Peak area, Colfax and Taos Counties, New Mexico and Las Animas and Costilla Counties, Colorado

USGS Publications Warehouse

Fridrich, Christopher J.; Shroba, Ralph R.; Pillmore, Charles L.; Hudson, Adam M.

2009-01-01

This geologic map covers four 7.5-minute quadrangles-The Wall, NM-CO (New Mexico-Colorado), Vermejo Park, NM-CO, Ash Mountain, NM, and Van Bremmer Park, NM. The study area straddles the boundary between the eastern flank of the Sangre de Cristo Mountains and the western margin of the Raton Basin, with about two-thirds of the map area in the basin. The Raton Basin is a foreland basin that formed immediately eastward of the Sangre de Cristo Mountains during their initial uplift, in the Late Cretaceous through early Eocene Laramide orogeny. Subsequently, these mountains have been extensively modified during formation of the Rio Grande rift, from late Oligocene to present. The map area is within that part of the Sangre de Cristo Mountains that is called the Culebra Range. Additionally, the map covers small parts of the Devil's Park graben and the Valle Vidal half-graben, in the northwestern and southwestern parts of the map area, respectively. These two grabens are small intermontaine basins, that are satellitic to the main local basin of the Rio Grande rift, the San Luis Basin, that are an outlying, early- formed part of the rift, and that separate the Culebra Range from the Taos Range, to the southwest.

Not all memories are the same: Situational context influences spatial recall within one's city of residency.

PubMed

Meilinger, Tobias; Frankenstein, Julia; Simon, Nadine; Bülthoff, Heinrich H; Bresciani, Jean-Pierre

2016-02-01

Reference frames in spatial memory encoding have been examined intensively in recent years. However, their importance for recall has received considerably less attention. In the present study, passersby used tags to arrange a configuration map of prominent city center landmarks. It has been shown that such configurational knowledge is memorized within a north-up reference frame. However, participants adjusted their maps according to their body orientations. For example, when participants faced south, the maps were likely to face south-up. Participants also constructed maps along their location perspective-that is, the self-target direction. If, for instance, they were east of the represented area, their maps were oriented west-up. If the location perspective and body orientation were in opposite directions (i.e., if participants faced away from the city center), participants relied on location perspective. The results indicate that reference frames in spatial recall depend on the current situation rather than on the organization in long-term memory. These results cannot be explained by activation spread within a view graph, which had been used to explain similar results in the recall of city plazas. However, the results are consistent with forming and transforming a spatial image of nonvisible city locations from the current location. Furthermore, prior research has almost exclusively focused on body- and environment-based reference frames. The strong influence of location perspective in an everyday navigational context indicates that such a reference frame should be considered more often when examining human spatial cognition.

Nursing interventions for rehabilitation in Parkinson's disease: cross mapping of terms.

PubMed

Tosin, Michelle Hyczy de Siqueira; Campos, Débora Moraes; Andrade, Leonardo Tadeu de; Oliveira, Beatriz Guitton Renaud Baptista de; Santana, Rosimere Ferreira

2016-08-08

to perform a cross-term mapping of nursing language in the patient record with the Nursing Interventions Classification system, in rehabilitation patients with Parkinson's disease. a documentary research study to perform cross mapping. A probabilistic, simple random sample composed of 67 records of patients with Parkinson's disease who participated in a rehabilitation program, between March of 2009 and April of 2013. The research was conducted in three stages, in which the nursing terms were mapped to natural language and crossed with the Nursing Interventions Classification. a total of 1,077 standard interventions that, after crossing with the taxonomy and refinement performed by the experts, resulted in 32 interventions equivalent to the Nursing Interventions Classification (NIC) system. The NICs, "Education: The process of the disease.", "Contract with the patient", and "Facilitation of Learning" were present in 100% of the records. For these interventions, 40 activities were described, representing 13 activities by intervention. the cross mapping allowed for the identification of corresponding terms with the nursing interventions used every day in rehabilitation nursing, and compared them to the Nursing Interventions Classification. realizar o mapeamento cruzado de termos da linguagem de Enfermagem, com o sistema de Classificação das Intervenções de Enfermagem, em prontuários de pacientes com doença de Parkinson em reabilitação. estudo de pesquisa documental, para realização de mapeamento cruzado. Amostra probabilística, do tipo aleatória simples, composta por 67 prontuários de pacientes com doença de Parkinson que participaram de programa de reabilitação, entre março de 2009 e abril de 2013. Pesquisa realizada em três etapas onde foram mapeados os termos de Enfermagem em linguagem livre e cruzados com o sistema de Classificação das Intervenções de Enfermagem. foram identificadas 1.077 intervenções normalizadas que, após o cruzamento com a taxonomia e o refinamento feito pelos especialistas, resultaram em 32 intervenções equivalentes ao sistema de Classificação das Intervenções de Enfermagem. "Ensino: Processo da doença", "Contrato com o Paciente" e "Facilitação da Aprendizagem" estiveram presentes em 100% dos prontuários. Para essas, foram descritas 40 atividades, representando 13 atividades por intervenção prescrita. o mapeamento cruzado permitiu levantar os termos correspondentes às Intervenções de Enfermagem utilizados no cotidiano dos enfermeiros de reabilitação e compará-los ao sistema de Classificação das Intervenções de Enfermagem. realizar el mapeo cruzado de términos del lenguaje de Enfermería con el Sistema de Clasificación de las Intervenciones de Enfermería en historias clínicas de pacientes con enfermedad de Parkinson en rehabilitación. estudio de investigación documental para realización de mapeo cruzado. Muestra probabilística de tipo aleatoria simple, compuesta por 67 historias clínicas de pacientes con enfermedad de Parkinson que participaron del programa de rehabilitación entre marzo de 2009 y abril de 2013. Investigación realizada en tres etapas donde fueron mapeados los términos de Enfermería en lenguaje libre y cruzados con el sistemas de Clasificación de Intervenciones de Enfermería. se identificaron 1077 intervenciones normalizadas que, después del cruzamiento con la taxonomía y el refinamiento hecho por los especialistas, resultaron en 32 intervenciones equivalentes al sistema de Clasificación de Intervenciones de Enfermería. "Enseñanza: Proceso de la enfermedad", "Contrato con el paciente" y "Facilitación del aprendizaje" estuvieron presentes en 100% de las historias clínicas. Para éstas, se describieron 40 actividades, representando 13 actividades por cada intervención prescripta. el mapeo cruzado permitió encontrar los términos correspondientes a las Intervenciones en Enfermería utilizados en el día a día de los enfermeros de rehabilitación y compararlos con el sistema de Clasificación de Intervenciones de Enfermería.

One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies

PubMed Central

Yuan, Shuai; Johnston, H. Richard; Zhang, Guosheng; Li, Yun; Hu, Yi-Juan; Qin, Zhaohui S.

2015-01-01

With rapid decline of the sequencing cost, researchers today rush to embrace whole genome sequencing (WGS), or whole exome sequencing (WES) approach as the next powerful tool for relating genetic variants to human diseases and phenotypes. A fundamental step in analyzing WGS and WES data is mapping short sequencing reads back to the reference genome. This is an important issue because incorrectly mapped reads affect the downstream variant discovery, genotype calling and association analysis. Although many read mapping algorithms have been developed, the majority of them uses the universal reference genome and do not take sequence variants into consideration. Given that genetic variants are ubiquitous, it is highly desirable if they can be factored into the read mapping procedure. In this work, we developed a novel strategy that utilizes genotypes obtained a priori to customize the universal haploid reference genome into a personalized diploid reference genome. The new strategy is implemented in a program named RefEditor. When applying RefEditor to real data, we achieved encouraging improvements in read mapping, variant discovery and genotype calling. Compared to standard approaches, RefEditor can significantly increase genotype calling consistency (from 43% to 61% at 4X coverage; from 82% to 92% at 20X coverage) and reduce Mendelian inconsistency across various sequencing depths. Because many WGS and WES studies are conducted on cohorts that have been genotyped using array-based genotyping platforms previously or concurrently, we believe the proposed strategy will be of high value in practice, which can also be applied to the scenario where multiple NGS experiments are conducted on the same cohort. The RefEditor sources are available at https://github.com/superyuan/refeditor. PMID:26267278

Beyond the double banana: improved recognition of temporal lobe seizures in long-term EEG.

PubMed

Rosenzweig, Ivana; Fogarasi, András; Johnsen, Birger; Alving, Jørgen; Fabricius, Martin Ejler; Scherg, Michael; Neufeld, Miri Y; Pressler, Ronit; Kjaer, Troels W; van Emde Boas, Walter; Beniczky, Sándor

2014-02-01

To investigate whether extending the 10-20 array with 6 electrodes in the inferior temporal chain and constructing computed montages increases the diagnostic value of ictal EEG activity originating in the temporal lobe. In addition, the accuracy of computer-assisted spectral source analysis was investigated. Forty EEG samples were reviewed by 7 EEG experts in various montages (longitudinal and transversal bipolar, common average, source derivation, source montage, current source density, and reference-free montages) using 2 electrode arrays (10-20 and the extended one). Spectral source analysis used source montage to calculate density spectral array, defining the earliest oscillatory onset. From this, phase maps were calculated for localization. The reference standard was the decision of the multidisciplinary epilepsy surgery team on the seizure onset zone. Clinical performance was compared with the double banana (longitudinal bipolar montage, 10-20 array). Adding the inferior temporal electrode chain, computed montages (reference free, common average, and source derivation), and voltage maps significantly increased the sensitivity. Phase maps had the highest sensitivity and identified ictal activity at earlier time-point than visual inspection. There was no significant difference concerning specificity. The findings advocate for the use of these digital EEG technology-derived analysis methods in clinical practice.

Genetics and fine mapping of a purple leaf gene, BoPr, in ornamental kale (Brassica oleracea L. var. acephala).

PubMed

Liu, Xiao-Ping; Gao, Bao-Zhen; Han, Feng-Qing; Fang, Zhi-Yuan; Yang, Li-Mei; Zhuang, Mu; Lv, Hong-Hao; Liu, Yu-Mei; Li, Zhan-Sheng; Cai, Cheng-Cheng; Yu, Hai-Long; Li, Zhi-Yuan; Zhang, Yang-Yong

2017-03-14

Due to its variegated and colorful leaves, ornamental kale (Brassica oleracea L. var. acephala) has become a popular ornamental plant. In this study, we report the fine mapping and analysis of a candidate purple leaf gene using a backcross population and an F 2 population derived from two parental lines: W1827 (with white leaves) and P1835 (with purple leaves). Genetic analysis indicated that the purple leaf trait is controlled by a single dominant gene, which we named BoPr. Using markers developed based on the reference genome '02-12', the BoPr gene was preliminarily mapped to a 280-kb interval of chromosome C09, with flanking markers M17 and BoID4714 at genetic distances of 4.3 cM and 1.5 cM, respectively. The recombination rate within this interval is almost 12 times higher than the usual level, which could be caused by assembly error for reference genome '02-12' at this interval. Primers were designed based on 'TO1000', another B. oleracea reference genome. Among the newly designed InDel markers, BRID485 and BRID490 were found to be the closest to BoPr, flanking the gene at genetic distances of 0.1 cM and 0.2 cM, respectively; the interval between the two markers is 44.8 kb (reference genome 'TO1000'). Seven annotated genes are located within the 44.8 kb genomic region, of which only Bo9g058630 shows high homology to AT5G42800 (dihydroflavonol reductase), which was identified as a candidate gene for BoPr. Blast analysis revealed that this 44.8 kb interval is located on an unanchored scaffold (Scaffold000035_P2) of '02-12', confirming the existence of assembly error at the interval between M17 and BoID4714 for reference genome '02-12'. This study identified a candidate gene for BoPr and lays a foundation for the cloning and functional analysis of this gene.

The Conterminous United States Mineral Appraisal Program; background information to accompany folio of geologic, geochemical, geophysical, and mineral resources maps of the Tonopah 1 by 2 degree Quadrangle, Nevada

USGS Publications Warehouse

John, David A.; Nash, J.T.; Plouff, Donald; Whitebread, D.H.

1991-01-01

The Tonopah 1 ? by 2 ? quadrangle in south-central Nevada was studied by an interdisciplinary research team to appraise its mineral resources. The appraisal is based on geological, geochemical, and geophysical field and laboratory investigations, the results of which are published as a folio of maps, figures, and tables, with accompanying discussions. This circular provides background information on the investigations and integrates the information presented in the folio. The selected bibliography lists references to the geology, geochemistry, geophysics, and mineral deposits of the Tonopah 1 ? by 2 ? quadrangle.

Performance Evaluation and Control of Distributed Computer Communication Networks.

DTIC Science & Technology

1984-09-01

including: L. Clare, L.A. De Moraes, J. Baker, M. Zuckerman, S. Katz, P. Rodrigues, R. Pazos , S. Resheff. Other participants are the following visiting...investigations have been reported in reference (1) and (2) below. References (1) M. Gerla, R. Pazos -Rangel "Bandwidth Allocation and Routing in ISDN’s," IEEE...and efficient methods for its solution are presented. (2) R.A. Pazos -Rangel "Evaluation and Design of Integrated Packet Switching and Circuit Switching

Online, automatic, ionospheric maps: IRI-PLAS-MAP

NASA Astrophysics Data System (ADS)

Arikan, F.; Sezen, U.; Gulyaeva, T. L.; Cilibas, O.

2015-04-01

Global and regional behavior of the ionosphere is an important component of space weather. The peak height and critical frequency of ionospheric layer for the maximum ionization, namely, hmF2 and foF2, and the total number of electrons on a ray path, Total Electron Content (TEC), are the most investigated and monitored values of ionosphere in capturing and observing ionospheric variability. Typically ionospheric models such as International Reference Ionosphere (IRI) can provide electron density profile, critical parameters of ionospheric layers and Ionospheric electron content for a given location, date and time. Yet, IRI model is limited by only foF2 STORM option in reflecting the dynamics of ionospheric/plasmaspheric/geomagnetic storms. Global Ionospheric Maps (GIM) are provided by IGS analysis centers for global TEC distribution estimated from ground-based GPS stations that can capture the actual dynamics of ionosphere and plasmasphere, but this service is not available for other ionospheric observables. In this study, a unique and original space weather service is introduced as IRI-PLAS-MAP from http://www.ionolab.org

De novo modeling of the F420-reducing [NiFe]-hydrogenase from a methanogenic archaeon by cryo-electron microscopy

PubMed Central

Mills, Deryck J; Vitt, Stella; Strauss, Mike; Shima, Seigo; Vonck, Janet

2013-01-01

Methanogenic archaea use a [NiFe]-hydrogenase, Frh, for oxidation/reduction of F420, an important hydride carrier in the methanogenesis pathway from H2 and CO2. Frh accounts for about 1% of the cytoplasmic protein and forms a huge complex consisting of FrhABG heterotrimers with each a [NiFe] center, four Fe-S clusters and an FAD. Here, we report the structure determined by near-atomic resolution cryo-EM of Frh with and without bound substrate F420. The polypeptide chains of FrhB, for which there was no homolog, was traced de novo from the EM map. The 1.2-MDa complex contains 12 copies of the heterotrimer, which unexpectedly form a spherical protein shell with a hollow core. The cryo-EM map reveals strong electron density of the chains of metal clusters running parallel to the protein shell, and the F420-binding site is located at the end of the chain near the outside of the spherical structure. DOI: http://dx.doi.org/10.7554/eLife.00218.001 PMID:23483797

Patellar cartilage lesions: comparison of magnetic resonance imaging and T2 relaxation-time mapping.

PubMed

Hannila, I; Nieminen, M T; Rauvala, E; Tervonen, O; Ojala, R

2007-05-01

To evaluate the detection and the size of focal patellar cartilage lesions in T2 mapping as compared to standard clinical magnetic resonance imaging (MRI) at 1.5T. Fifty-five consecutive clinical patients referred to knee MRI were imaged both with a standard knee MRI protocol (proton-density-weighted sagittal and axial series, T2-weighted sagittal and coronal series, and T1-weighted coronal series) and with an axial multislice multi-echo spin-echo measurement to determine the T2 relaxation time of the patellar cartilage. MR images and T2 maps of patellar cartilage were evaluated for focal lesions. The lesions were evaluated for lesion width (mm), lesion depth (1/3, 2/3, or 3/3 of cartilage thickness), and T2 value (20-40 ms, 40-60 ms, or 60-80 ms) based on visual evaluation. Altogether, 36 focal patellar cartilage lesions were detected from 20 human subjects (11 male, nine female, mean age 40+/-15 years). Twenty-eight lesions were detected both on MRI and T2 maps, while eight lesions were only visible on T2 maps. Cartilage lesions were significantly wider (P = 0.001) and thicker (P<0.001) on T2 maps as compared to standard knee MRI. Most lesions 27 had moderately (T2 40-60 ms) increased T2 values, while two lesions had slightly (T2 20-40 ms) and seven lesions remarkably (T2 60-80 ms) increased T2 relaxation times. T2 mapping of articular cartilage is feasible in the clinical setting and may reveal early cartilage lesions not visible with standard clinical MRI.

183. Photocopy of map (Twin Falls Canal Company). TOPOGRAPHICAL MAP ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

183. Photocopy of map (Twin Falls Canal Company). TOPOGRAPHICAL MAP OF MILNER DAM SITE, TWIN FALLS COUNTY, MILNER, IDAHO; MAP, LEFT SIDE ONLY. CROSS REFERENCE: ID-15-192. - Milner Dam & Main Canal: Twin Falls Canal Company, On Snake River, 11 miles West of city of Burley, Idaho, Twin Falls, Twin Falls County, ID

Publications - Beikman, H.M., 1980 | Alaska Division of Geological &

Science.gov Websites

main content USGS Beikman, H.M., 1980 Publication Details Title: Geologic map of Alaska Authors Warehouse Bibliographic Reference Beikman, H.M., 1980, Geologic map of Alaska: U.S. Geological Survey, 1 USGS website Maps & Other Oversized Sheets Maps & Other Oversized Sheets Sheet 1 Geologic Map

A proteome-scale map of the human interactome network

PubMed Central

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

2014-01-01

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

Dual-reference digital holographic interferometry for analyzing high-density gradients in fluid mechanics.

PubMed

Desse, Jean-Michel; Olchewsky, François

2018-04-15

This Letter proposes a dual-reference digital holographic interferometer for analyzing the high refractive index encountered in transonic and supersonic flows. For that, a Wollaston prism is inserted in the reference arm in order to simultaneously generate two orthogonally polarized reference waves. As a consequence, recorded interferograms contain two crossed and perpendicular interference patterns that give two orders fully separated in the Fourier spectrum. It is then possible to analyze a transparent object regardless of the orientation of the refractive index gradient using the two phase maps reconstructed with each of the two first interference orders. Fusion of the phase maps yields a single phase map in which the phase singularities are removed. Experimental results demonstrate the suitability of the proposed approach for analyzing shock waves in the unsteady wake flow around a circular cylinder at Mach 0.75.

Characteristics of Marine Gravity Anomaly Reference Maps and Accuracy Analysis of Gravity Matching-Aided Navigation.

PubMed

Wang, Hubiao; Wu, Lin; Chai, Hua; Xiao, Yaofei; Hsu, Houtse; Wang, Yong

2017-08-10

The variation of a marine gravity anomaly reference map is one of the important factors that affect the location accuracy of INS/Gravity integrated navigation systems in underwater navigation. In this study, based on marine gravity anomaly reference maps, new characteristic parameters of the gravity anomaly were constructed. Those characteristic values were calculated for 13 zones (105°-145° E, 0°-40° N) in the Western Pacific area, and simulation experiments of gravity matching-aided navigation were run. The influence of gravity variations on the accuracy of gravity matching-aided navigation was analyzed, and location accuracy of gravity matching in different zones was determined. Studies indicate that the new parameters may better characterize the marine gravity anomaly. Given the precision of current gravimeters and the resolution and accuracy of reference maps, the location accuracy of gravity matching in China's Western Pacific area is ~1.0-4.0 nautical miles (n miles). In particular, accuracy in regions around the South China Sea and Sulu Sea was the highest, better than 1.5 n miles. The gravity characteristic parameters identified herein and characteristic values calculated in various zones provide a reference for the selection of navigation area and planning of sailing routes under conditions requiring certain navigational accuracy.

Characteristics of Marine Gravity Anomaly Reference Maps and Accuracy Analysis of Gravity Matching-Aided Navigation

PubMed Central

Wang, Hubiao; Chai, Hua; Xiao, Yaofei; Hsu, Houtse; Wang, Yong

2017-01-01

The variation of a marine gravity anomaly reference map is one of the important factors that affect the location accuracy of INS/Gravity integrated navigation systems in underwater navigation. In this study, based on marine gravity anomaly reference maps, new characteristic parameters of the gravity anomaly were constructed. Those characteristic values were calculated for 13 zones (105°–145° E, 0°–40° N) in the Western Pacific area, and simulation experiments of gravity matching-aided navigation were run. The influence of gravity variations on the accuracy of gravity matching-aided navigation was analyzed, and location accuracy of gravity matching in different zones was determined. Studies indicate that the new parameters may better characterize the marine gravity anomaly. Given the precision of current gravimeters and the resolution and accuracy of reference maps, the location accuracy of gravity matching in China’s Western Pacific area is ~1.0–4.0 nautical miles (n miles). In particular, accuracy in regions around the South China Sea and Sulu Sea was the highest, better than 1.5 n miles. The gravity characteristic parameters identified herein and characteristic values calculated in various zones provide a reference for the selection of navigation area and planning of sailing routes under conditions requiring certain navigational accuracy. PMID:28796158

Decoding 2D-PAGE complex maps: relevance to proteomics.

PubMed

Pietrogrande, Maria Chiara; Marchetti, Nicola; Dondi, Francesco; Righetti, Pier Giorgio

2006-03-20

This review describes two mathematical approaches useful for decoding the complex signal of 2D-PAGE maps of protein mixtures. These methods are helpful for interpreting the large amount of data of each 2D-PAGE map by extracting all the analytical information hidden therein by spot overlapping. Here the basic theory and application to 2D-PAGE maps are reviewed: the means for extracting information from the experimental data and their relevance to proteomics are discussed. One method is based on the quantitative theory of statistical model of peak overlapping (SMO) using the spot experimental data (intensity and spatial coordinates). The second method is based on the study of the 2D-autocovariance function (2D-ACVF) computed on the experimental digitised map. They are two independent methods that are able to extract equal and complementary information from the 2D-PAGE map. Both methods permit to obtain fundamental information on the sample complexity and the separation performance and to single out ordered patterns present in spot positions: the availability of two independent procedures to compute the same separation parameters is a powerful tool to estimate the reliability of the obtained results. The SMO procedure is an unique tool to quantitatively estimate the degree of spot overlapping present in the map, while the 2D-ACVF method is particularly powerful in simply singling out the presence of order in the spot position from the complexity of the whole 2D map, i.e., spot trains. The procedures were validated by extensive numerical computation on computer-generated maps describing experimental 2D-PAGE gels of protein mixtures. Their applicability to real samples was tested on reference maps obtained from literature sources. The review describes the most relevant information for proteomics: sample complexity, separation performance, overlapping extent, identification of spot trains related to post-translational modifications (PTMs).

Cumulative Total Middle East/North Africa Freshwater Losses as Seen by NASA GRACE, 2002-15

NASA Image and Video Library

2015-12-08

Cumulative total freshwater losses in North Africa and the Middle East from 2002 to 2015 (in inches) observed by NASA's Gravity Recovery and Climate Experiment (GRACE) mission. Total water refers to all of the snow, surface water, soil water and groundwater combined. Groundwater depletion in Turkey, Syria, Iraq and Iran, and along the Arabian Peninsula, are leading to large changes in total water storage in the region. Likewise, drought and groundwater pumping is contributing to the drying of the Caspian Sea Region. The Northwest Sahara Aquifer System, which underlies Tunisia and Libya, is also experiencing increasing water stress as shown in the map. Image updated from Voss et al., 2013. Citation of Record: Voss, K. A., J. S. Famiglietti, M. Lo, C. R. de Linage, M. Rodell and S. C. Swenson, Groundwater depletion in the Middle East from GRACE with Implications for Transboundary Water Management in the Tigris-Euphrates-Western Iran Region, Wat. Resour. Res., 49(2), 904-914, DOI: 10.1002/wrcr.20078. http://photojournal.jpl.nasa.gov/catalog/PIA20207

[Bibliometric study of scientific output published by the Revista Panamericana de Salud Pública/Pan American Journal of Public Health from 1997-2012].

PubMed

Sanz-Valero, Javier; Casterá, Vicente Tomás; Wanden-Berghe, Carmina

2014-02-01

To characterize the scientific output of the Revista Panamericana de Salud Pública/Pan American Journal of Public Health (RPSP) as a scientific publication of reference in the public health sector in the Americas. A descriptive cross-sectional study was conducted based on the articles published in the RPSP from 1997-2012. Bibliometric indicators of productivity (documents published, languages, authorship, and indices of productivity and collaboration); impact (impact factor according to the SciELO Network, Journal Citation Report and SCImago); key words; and bibliographic references, their structure (document type and main nucleus of Bradford) and degree of obsolescence (Burton and Kebler half-life, and Price index), were analyzed. A total of 2 815 articles with a median of 3 authors and 2 institutions per article were published. The percentage of original research articles increased in 2008-2012 compared to 2003-2007 and 1997-2002 (P < 0.001). The predominant language was Spanish, displaced by English in the last 5 years. A total of 88.76% of the key words referred to the Health Sciences Descriptors (DeCS) and had a public health and community orientation related to the Americas. The Burton and Kebler half-life of bibliographic references was 8 years, although it decreased to 5 years in 2012. The Price index was 20.47% and the nucleus of Bradford was made up of 20 mainstream journals. The percentage of self-citation was low (2.07%). The RPSP is an international publication with bibliometric indicators similar to those of the most representative Latin American health science journals, with improvements in the recent years studied that lead it to fully meet international publishing criteria.

Department of Defense Strategy to Support Multi-Agency Bat Conservation Initiative within the State of Utah

DTIC Science & Technology

2008-02-28

Range, and Section are entered. Datum: Geometric reference surface. Original Site Location datum is defined by user’s map datum; e.g. NAD27...Section are entered. Datum: Geometric reference surface. Original Site Location datum is defined by user’s map datum; e.g. NAD27 Conus or NAD83...Calculated and recorded automatically if the fields UTM_N and UTM_E or Township, Range, and Section are entered. 41 Datum: Geometric reference surface

MPEG-4 AVC saliency map computation

NASA Astrophysics Data System (ADS)

Ammar, M.; Mitrea, M.; Hasnaoui, M.

2014-02-01

A saliency map provides information about the regions inside some visual content (image, video, ...) at which a human observer will spontaneously look at. For saliency maps computation, current research studies consider the uncompressed (pixel) representation of the visual content and extract various types of information (intensity, color, orientation, motion energy) which are then fusioned. This paper goes one step further and computes the saliency map directly from the MPEG-4 AVC stream syntax elements with minimal decoding operations. In this respect, an a-priori in-depth study on the MPEG-4 AVC syntax elements is first carried out so as to identify the entities appealing the visual attention. Secondly, the MPEG-4 AVC reference software is completed with software tools allowing the parsing of these elements and their subsequent usage in objective benchmarking experiments. This way, it is demonstrated that an MPEG-4 saliency map can be given by a combination of static saliency and motion maps. This saliency map is experimentally validated under a robust watermarking framework. When included in an m-QIM (multiple symbols Quantization Index Modulation) insertion method, PSNR average gains of 2.43 dB, 2.15dB, and 2.37 dB are obtained for data payload of 10, 20 and 30 watermarked blocks per I frame, i.e. about 30, 60, and 90 bits/second, respectively. These quantitative results are obtained out of processing 2 hours of heterogeneous video content.

Validation of real-time three-dimensional echocardiography for quantifying left ventricular volumes in the presence of a left ventricular aneurysm: in vitro and in vivo studies

NASA Technical Reports Server (NTRS)

Qin, J. X.; Jones, M.; Shiota, T.; Greenberg, N. L.; Tsujino, H.; Firstenberg, M. S.; Gupta, P. C.; Zetts, A. D.; Xu, Y.; Ping Sun, J.;

Comparing physiographic maps with different categorisations

NASA Astrophysics Data System (ADS)

Zawadzka, J.; Mayr, T.; Bellamy, P.; Corstanje, R.

2015-02-01

This paper addresses the need for a robust map comparison method suitable for finding similarities between thematic maps with different forms of categorisations. In our case, the requirement was to establish the information content of newly derived physiographic maps with regards to set of reference maps for a study area in England and Wales. Physiographic maps were derived from the 90 m resolution SRTM DEM, using a suite of existing and new digital landform mapping methods with the overarching purpose of enhancing the physiographic unit component of the Soil and Terrain database (SOTER). Reference maps were seven soil and landscape datasets mapped at scales ranging from 1:200,000 to 1:5,000,000. A review of commonly used statistical methods for categorical comparisons was performed and of these, the Cramer's V statistic was identified as the most appropriate for comparison of maps with different legends. Interpretation of multiple Cramer's V values resulting from one-by-one comparisons of the physiographic and baseline maps was facilitated by multi-dimensional scaling and calculation of average distances between the maps. The method allowed for finding similarities and dissimilarities amongst physiographic maps and baseline maps and informed the recommendation of the most suitable methodology for terrain analysis in the context of soil mapping.

Integrative transcriptome, proteome, phosphoproteome and genetic mapping reveals new aspects in a fiberless mutant of cotton

PubMed Central

Ma, Qi-Feng; Wu, Chun-Hui; Wu, Man; Pei, Wen-Feng; Li, Xing-Li; Wang, Wen-Kui; Zhang, Jinfa; Yu, Ji-Wen; Yu, Shu-Xun

2016-01-01

To investigate the molecular mechanisms of fiber initiation in cotton (Gossypium spp.), an integrated approach combining transcriptome, iTRAQ-based proteome and genetic mapping was taken to compare the ovules of the Xuzhou 142 wild type (WT) with its fuzzless-lintless (fl) mutant at −3 and 0 day post-anthesis. A total of 1,953 mRNAs, 187 proteins, and 131 phosphoproteins were differentially expressed (DE) between WT and fl, and the levels of transcripts and their encoded proteins and phosphoproteins were highly congruent. A functional analysis suggested that the abundance of proteins were mainly involved in amino sugar, nucleotide sugar and fatty acid metabolism, one carbon pool for folate metabolism and flavonoid biosynthesis. qRT-PCR, Western blotting, and enzymatic assays were performed to confirm the regulation of these transcripts and proteins. A molecular mapping located the lintless gene li3 in the fl mutant on chromosome 26 for the first time. A further in-silico physical mapping of DE genes with sequence variations between fl and WT identified one and four candidate genes in the li3 and n2 regions, respectively. Taken together, the transcript abundance, phosphorylation status of proteins at the fiber initiation stage and candidate genes have provided insights into regulatory processes underlying cotton fiber initiation. PMID:27075604

Referred Pain Patterns Provoked on Intra-Pelvic Structures among Women with and without Chronic Pelvic Pain: A Descriptive Study

PubMed Central

Butler, Stephen; Peterson, Magnus; Eriksson, Margaretha

2015-01-01

Objectives To describe referred pain patterns provoked from intra-pelvic structures in women with chronic pelvic pain (CPP) persisting after childbirth with the purpose to improve diagnostics and give implications for treatment. Materials and Methods In this descriptive and comparative study 36 parous women with CPP were recruited from a physiotherapy department waiting list and by advertisements in newspapers. A control group of 29 parous women without CPP was consecutively assessed for eligibility from a midwifery surgery. Inclusion criterion for CPP was: moderate pain in the sacral region persisting at least six months after childbirth confirmed by pelvic pain provocation tests. Exclusion criteria in groups with and without CPP were: persistent back or pelvic pain with onset prior to pregnancy, previous back surgery and positive neurological signs. Pain was provoked by palpation of 13 predetermined intra-pelvic anatomical landmarks. The referred pain distribution was expressed in pain drawings and described in pain maps and calculated referred pain areas. Results Pain provoked by palpation of the posterior intra-pelvic landmarks was mostly referred to the sacral region and pain provoked by palpation of the ischial and pubic bones was mostly referred to the groin and pubic regions, with or without pain referred down the ipsilateral leg. The average pain distribution area provoked by palpation of all 13 anatomical landmarks was 30.3 mm² (19.2 to 53.7) in women with CPP as compared to 3.2 mm² (1.0 to 5.1) in women without CPP, p< 0.0001. Conclusions Referred pain patterns provoked from intra-pelvic landmarks in women with CPP are consistent with sclerotomal sensory innervation. Magnification of referred pain patterns indicates allodynia and central sensitization. The results suggest that pain mapping can be used to evaluate and confirm the pain experience among women with CPP and contribute to diagnosis. PMID:25793999

Effect of Dipole Perturbation on a Good Confining Surface Near X Point

NASA Astrophysics Data System (ADS)

Prakash, Sushant; Witmer, Lisa; Punjabi, Alkesh; Ali, Halima

2002-11-01

We analyze effects of dipole perturbation on a good magnetic surface of a single null divertor tokamak using the method of maps developed by Punjabi and Boozer /1/. Unperturbed fields are represented by the Symmetric Simple Map /2/. Effects of high MN perturbation are represented by the Dipole Map (DM) /2/ given by: x_n+1 = x_n+2δ s^3x_n[(y_n-y_s+s) / [x_n+1^2+(y_n-y_s+s)^2]^2], y_n+1 = y_n+δ s^3x_n[[(y_n-y_s+s)^2-x_n+1^2] / [x_n+1^2+(y_n-y_s+s)^2]^2] The good surface is x_0=0 and y_0=0.952873. We start with the strength of perturbation, δ=0, increase it slowly, and observe how the surface changes. The results will be presented. This project is supported by the QEM network NASA Sharp Plus program and by DE-FG02-02ER54673. The work is done on the FUSION1 server under Profs. Ali and Punjabi 1. Punjabi A., Verma A. and Boozer A., Phys. Rev. Lett., 69, 3322 (1992) 2. Ali H., Punjabi A. and Boozer A., Dipole Map for Single-null Divertor Tokamak, 2002 International Congress on Plasma Physics, Manly, Australia.

Landslide Susceptibility Analysis by the comparison and integration of Random Forest and Logistic Regression methods; application to the disaster of Nova Friburgo - Rio de Janeiro, Brasil (January 2011)

NASA Astrophysics Data System (ADS)

Esposito, Carlo; Barra, Anna; Evans, Stephen G.; Scarascia Mugnozza, Gabriele; Delaney, Keith

2014-05-01

The study of landslide susceptibility by multivariate statistical methods is based on finding a quantitative relationship between controlling factors and landslide occurrence. Such studies have become popular in the last few decades thanks to the development of geographic information systems (GIS) software and the related improved data management. In this work we applied a statistical approach to an area of high landslide susceptibility mainly due to its tropical climate and geological-geomorphological setting. The study area is located in the south-east region of Brazil that has frequently been affected by flood and landslide hazard, especially because of heavy rainfall events during the summer season. In this work we studied a disastrous event that occurred on January 11th and 12th of 2011, which involved Região Serrana (the mountainous region of Rio de Janeiro State) and caused more than 5000 landslides and at least 904 deaths. In order to produce susceptibility maps, we focused our attention on an area of 93,6 km2 that includes Nova Friburgo city. We utilized two different multivariate statistic methods: Logistic Regression (LR), already widely used in applied geosciences, and Random Forest (RF), which has only recently been applied to landslide susceptibility analysis. With reference to each mapping unit, the first method (LR) results in a probability of landslide occurrence, while the second one (RF) gives a prediction in terms of % of area susceptible to slope failure. With this aim in mind, a landslide inventory map (related to the studied event) has been drawn up through analyses of high-resolution GeoEye satellite images, in a GIS environment. Data layers of 11 causative factors have been created and processed in order to be used as continuous numerical or discrete categorical variables in statistical analysis. In particular, the logistic regression method has frequent difficulties in managing numerical continuous and discrete categorical variables together; therefore in our work we tried different methods to process categorical variables , until we obtained a statistically significant model. The outcomes of the two statistical methods (RF and LR) have been tested with a spatial validation and gave us two susceptibility maps. The significance of the models is quantified in terms of Area Under ROC Curve (AUC resulted in 0.81 for RF model and in 0.72 for LR model). In the first instance, a graphical comparison of the two methods shows a good correspondence between them. Further, we integrated results in a unique susceptibility map which maintains both information of probability of occurrence and % of area of landslide detachment, resulting from LR and RF respectively. In fact, in view of a landslide susceptibility classification of the study area, the former is less accurate but gives easily classifiable results, while the latter is more accurate but the results can be only subjectively classified. The obtained "integrated" susceptibility map preserves information about the probability that a given % of area could fail for each mapping unit.

Border collie comprehends object names as verbal referents.

PubMed

Pilley, John W; Reid, Alliston K

2011-02-01

Four experiments investigated the ability of a border collie (Chaser) to acquire receptive language skills. Experiment 1 demonstrated that Chaser learned and retained, over a 3-year period of intensive training, the proper-noun names of 1022 objects. Experiment 2 presented random pair-wise combinations of three commands and three names, and demonstrated that she understood the separate meanings of proper-noun names and commands. Chaser understood that names refer to objects, independent of the behavior directed toward those objects. Experiment 3 demonstrated Chaser's ability to learn three common nouns--words that represent categories. Chaser demonstrated one-to-many (common noun) and many-to-one (multiple-name) name-object mappings. Experiment 4 demonstrated Chaser's ability to learn words by inferential reasoning by exclusion--inferring the name of an object based on its novelty among familiar objects that already had names. Together, these studies indicate that Chaser acquired referential understanding of nouns, an ability normally attributed to children, which included: (a) awareness that words may refer to objects, (b) awareness of verbal cues that map words upon the object referent, and (c) awareness that names may refer to unique objects or categories of objects, independent of the behaviors directed toward those objects. Copyright © 2010 Elsevier B.V. All rights reserved.

Crystalline basement map of Mauritania derived from filtered aeromagnetic data (deliverable 54_1), Aeromagnetic and geological structure map of Mauritania (phase V, deliverable 54_2), Maximum depth to basement map of Mauritania derived from Euler analysis of Aeromagnetic data (phase V, deliverable 54_3), and color composite image of radioelement data (added value): Chapter B1 in Second projet de renforcement institutionnel du secteur minier de la République Islamique de Mauritanie (PRISM-II)

USGS Publications Warehouse

Finn, Carol A.; Horton, John D.

2015-01-01

This report contains the USGS results of the PRISM-II Mauritania Minerals Project and is presented in cooperation with the Ministry of Petroleum, Energy, and Mines of the Islamic Republic of Mauritania. The Report is composed of separate chapters consisting of multidisciplinary interpretive reports with accompanying plates on the geology, structure, geochronology, geophysics, hydrogeology, geochemistry, remote sensing (Landsat TM and ASTER), and SRTM and ASTER digital elevation models of Mauritania. The syntheses of these multidisciplinary data formed the basis for additional chapters containing interpretive reports on 12 different commodities and deposit types known to occur in Mauritania, accompanied by countrywide mineral resource potential maps of each commodity/deposit type. The commodities and deposit types represented include: (1) Ni, Cu, PGE, and Cr deposits hosted in ultramafic rocks; (2) orogenic, Carlin-like, and epithermal gold deposits; (3) polymetallic Pb-Zn-Cu vein deposits; (4) sediment-hosted Pb-Zn-Ag deposits of the SEDEX and Mississippi Valley-type; (5) sediment-hosted copper deposits; ( 6) volcanogenic massive sulfide deposits; (7) iron oxide copper-gold deposits; (8) uranium deposits; (9) Algoma-, Superior-, and oolitic-type iron deposits; (10) shoreline Ti-Zr placer deposits; (11) incompatible element deposits hosted in pegmatites, alkaline rocks, and carbonatites, and; (12) industrial mineral deposits. Additional chapters include the Mauritanian National Mineral Deposits Database are accompanied by an explanatory text and the Mauritania Minerals Project GIS that contains all of the interpretive layers created by USGS scientists. Raw data not in the public domain may be obtained from the Ministry of Petroleum, Energy, and Mines in Nouakchott, Mauritania.

Effects of Concreteness and Contiguity on Learning from Computer-Based Reference Maps

ERIC Educational Resources Information Center

Srinivasan, Sribhagyam; Lewis, Daphne D.; Crooks, Steven M.

2006-01-01

Today's technology has reached new heights that have not been fully implemented. One of the areas where technology has not yet reached its full potential is in education. This study examined the effects of concreteness of location names and contiguity of location names with textual information on learning from computer-based reference maps. The…

The role of reference in cross-situational word learning.

PubMed

Wang, Felix Hao; Mintz, Toben H

2018-01-01

Word learning involves massive ambiguity, since in a particular encounter with a novel word, there are an unlimited number of potential referents. One proposal for how learners surmount the problem of ambiguity is that learners use cross-situational statistics to constrain the ambiguity: When a word and its referent co-occur across multiple situations, learners will associate the word with the correct referent. Yu and Smith (2007) propose that these co-occurrence statistics are sufficient for word-to-referent mapping. Alternative accounts hold that co-occurrence statistics alone are insufficient to support learning, and that learners are further guided by knowledge that words are referential (e.g., Waxman & Gelman, 2009). However, no behavioral word learning studies we are aware of explicitly manipulate subjects' prior assumptions about the role of the words in the experiments in order to test the influence of these assumptions. In this study, we directly test whether, when faced with referential ambiguity, co-occurrence statistics are sufficient for word-to-referent mappings in adult word-learners. Across a series of cross-situational learning experiments, we varied the degree to which there was support for the notion that the words were referential. At the same time, the statistical information about the words' meanings was held constant. When we overrode support for the notion that words were referential, subjects failed to learn the word-to-referent mappings, but otherwise they succeeded. Thus, cross-situational statistics were useful only when learners had the goal of discovering mappings between words and referents. We discuss the implications of these results for theories of word learning in children's language acquisition. Copyright © 2017 Elsevier B.V. All rights reserved.

CLOCS (Computer with Low Context-Switching Time) Architecture Reference Documents

DTIC Science & Technology

1988-05-06

Peculiarities The only state inside the central processing unit(CPU) is a program status word. All data operations are memory to memory. One result of this... to the challenge "if I whore to design RISC, this is how I would do it." The architecture was designed by Mark Davis and Bill Gallmeister. 1.2...are memory to memory. Any special devices added should be memory mapped. The program counter is even memory mapped. 1.3.1 Working storage There is no

Team VaCAS Design and Development of Cooperative UGV System

DTIC Science & Technology

2011-02-04

Mapping ( SLAM ) [24]. Similar to such work, the technique to be used in the project will also (1) use the last reliably available data as the reference...Losada1, D., Matia1, F., Pedraza1, L., Jimenez A. and Galan, R., Consistency of SLAM -EKF Algorithms for Indoor Environments, Journal of Intelligent and...mounted on the UGV 1 include GPS for outdoor navigation, LiDAR for obstacle avoidance and mapping and camera for OOI detection and localization. UGVs 2

Geological Mapping of the Ac-H-3 Dantu Quadrangle of Ceres from NASA's Dawn Mission.

NASA Astrophysics Data System (ADS)

Kneissl, Thomas; Schmedemann, Nico; Neesemann, Adrian; Williams, David A.; Crown, David A.; Mest, Scott C.; Buczkowski, Debra L.; Scully, Jennifer E. C.; Frigeri, Allessandro; Ruesch, Ottaviano; Hiesinger, Harald; Walter, Sebastian H. G.; Jaumann, Ralf; Roatsch, Thomas; Preusker, Frank; Kersten, Elke; Naß, Andrea; Nathues, Andreas; Platz, Thomas; Russell, Chistopher T.

2016-04-01

The Dawn Science Team is conducting a geologic mapping campaign for Ceres similar to that done for Vesta [1,2], including production of a Survey- and High Altitude Mapping Orbit (HAMO)-based global map and a series of 15 Low Altitude Mapping Orbit (LAMO)-based quadrangle maps. In this abstract we discuss the geologic evolution of the Ac-H-3 Dantu Quadrangle. The current map is based on a Framing Camera (FC) clear-filter image mosaic from HAMO data (~140 m/px) as well as a digital terrain model (DTM) derived from imagery of the Survey phase [3]. Albedo variations were identified and mapped using a mosaic of photometrically corrected HAMO images provided by DLR. FC color images provided further context for map unit identification. LAMO images (35m/pixel), which have just become available at the time of writing, will be used to update the map to be presented as a poster. The quadrangle is located between 21-66°N and 90-180°E in a large-scale depression north of the impact basin Kerwan. The northern and southeastern parts of the quadrangle are characterized by cratered terrain while the south and southwest are dominated by the partially smooth ejecta blankets of craters Dantu and Gaue. East-west oriented pit/crater chains in the southern half of the quadrangle might be related to tectonic processes [4,5]. Dantu crater (d=~126 km) is a complex impact crater showing slump terraces and a partially smooth crater floor with concentric and radial fractures. Furthermore, Dantu shows a central pit structure with pitted terrain on its floor as well as several bright spots in the interior and exterior of the crater. High-resolution measurements of crater size-frequency distributions (CSFDs) superposed on Dantu indicate a formation/modification age of ~200 - 700 Ma. Most of the ejecta appear to be relatively bright and correspond to parts of the #2 high albedo region observed with the Hubble Space Telescope [6]. However, the southwestern portion of the ejecta blanket is characterized by relatively dark ejecta material. The albedo variations and differences in color data indicate materials of different compositions in the subsurface. Interestingly, Dantu is located in a longitude range where the Herschel space telescope might have observed the release of water vapor [7]. In the course of the mission, analyses of LAMO imagery as well as VIR spectral data will help to identify potential water sources, constrain the compositional variations, and the overall geologic history of the Dantu crater region. Further CSFD measurements we will help to determine the formation ages of other impact structures in the quadrangle. Acknowledgements: We acknowledge the support of M. Hoffmann, M. Schaefer, M.C. De Sanctis, C.A. Raymond, and the Dawn Instrument, Operations, and Science Teams. This work is partly supported by the German Space Agency (DLR), grant 50 OW 1101. References: [1] Williams D.A. et al. (2014) Icarus, 244, 1-12. [2] Yingst R.A. et al. (2014) PSS, 103, 2-23. [3] Preusker, F. et al. (2016), LPSC abstract. [4] Scully, J.E.C. et al. (2016), this meeting. [5] Buczkowski D. L. et al. (2015), AGU abstract #P44B-05. [6] Li, J-Y. et al. (2006), Icarus, 182, 143-160. [7] Küppers, M., et al. (2014), Nature, v. 505, 525-527.

Nigel: A Systemic Grammar for Text Generation.

DTIC Science & Technology

1983-02-01

presumed. Basic references on the systemic framework include [Berry 75, Berry 77, Halliday 76a, Halliday 76b, Hudson 76, Halliday 81, de Joia 80...Edinburgh, 1979. [do Joia 80] de Joia , A., and A. Stanton, Terms in Systemic Linguistics, Batsford Academic and Educational, Ltd., London, 1980. -’C...1 A Grammar for Text Generation- -The Challenge ................................. 1 *1.2 A Grammar for Text Generation--The Design

International Celestial Reference Frame (ICRF): mantenimiento y extensión

NASA Astrophysics Data System (ADS)

Ma, C.; Arias, E. F.; Eubanks, T.; Fey, A. L.; Gontier, A.-M.; Jacobs, C. S.; Sovers, O. J.; Archinal, B. A.; Charlot, P.

A partir de enero de 1998 el sistema de referencia celeste convencional está representado por el International Celestial Reference System (ICRS) y materializado a través de las coordenadas VLBI del conjunto de radiofuentes extragalácticas que conforman el International Celestial Reference Frame (ICRF). La primera realización del ICRF, fue elaborada en 1995 por un grupo de expertos designado por la IAU, la que encomendó al International Earth Rotation Service el mantenimiento del ICRS, del ICRF y del vínculo con marcos de referencia en otras frecuencias. Una primera extensión del ICRF se realizó entre abril y junio de 1999, con el objetivo primario de proveer posiciones de radiofuentes extragalácticas observadas a partir de julio de 1995 y de mejorar las posiciones de las fuentes ``candidatas" con la inclusión de observaciones adicionales. Objetivos secundarios fueron monitorear a las radiofuentes para verificar que siguen siendo adecuadas para realizar al ICRF y mejorar las técnicas de análisis de datos. Como resultado del nuevo análisis se obtuvo una solución a partir de la cual se construyó la primera extensión del ICRF, denominada ICRF - Ext.1. Ella representa al ICRS, sus fuentes de definición se mantienen con las mismas posiciones y errores que en la primera realización del ICRF; las demás radiofuentes tienen coordenadas mejor determinadas que en ICRF; el marco de referencia se densificó con el agregado de 59 nuevas radiofuentes.

Analysis of the Bovine Monocyte-Derived Macrophage Response to Mycobacterium avium Subspecies Paratuberculosis Infection Using RNA-seq.

PubMed

Casey, Maura E; Meade, Kieran G; Nalpas, Nicolas C; Taraktsoglou, Maria; Browne, John A; Killick, Kate E; Park, Stephen D E; Gormley, Eamonn; Hokamp, Karsten; Magee, David A; MacHugh, David E

2015-01-01

Johne's disease, caused by infection with Mycobacterium avium subsp. paratuberculosis, (MAP), is a chronic intestinal disease of ruminants with serious economic consequences for cattle production in the United States and elsewhere. During infection, MAP bacilli are phagocytosed and subvert host macrophage processes, resulting in subclinical infections that can lead to immunopathology and dissemination of disease. Analysis of the host macrophage transcriptome during infection can therefore shed light on the molecular mechanisms and host-pathogen interplay associated with Johne's disease. Here, we describe results of an in vitro study of the bovine monocyte-derived macrophage (MDM) transcriptome response during MAP infection using RNA-seq. MDM were obtained from seven age- and sex-matched Holstein-Friesian cattle and were infected with MAP across a 6-h infection time course with non-infected controls. We observed 245 and 574 differentially expressed (DE) genes in MAP-infected versus non-infected control samples (adjusted P value ≤0.05) at 2 and 6 h post-infection, respectively. Functional analyses of these DE genes, including biological pathway enrichment, highlighted potential functional roles for genes that have not been previously described in the host response to infection with MAP bacilli. In addition, differential expression of pro- and anti-inflammatory cytokine genes, such as those associated with the IL-10 signaling pathway, and other immune-related genes that encode proteins involved in the bovine macrophage response to MAP infection emphasize the balance between protective host immunity and bacilli survival and proliferation. Systematic comparisons of RNA-seq gene expression results with Affymetrix(®) microarray data generated from the same experimental samples also demonstrated that RNA-seq represents a superior technology for studying host transcriptional responses to intracellular infection.

Analysis of the Bovine Monocyte-Derived Macrophage Response to Mycobacterium avium Subspecies Paratuberculosis Infection Using RNA-seq

PubMed Central

Casey, Maura E.; Meade, Kieran G.; Nalpas, Nicolas C.; Taraktsoglou, Maria; Browne, John A.; Killick, Kate E.; Park, Stephen D. E.; Gormley, Eamonn; Hokamp, Karsten; Magee, David A.; MacHugh, David E.

2015-01-01

Johne’s disease, caused by infection with Mycobacterium avium subsp. paratuberculosis, (MAP), is a chronic intestinal disease of ruminants with serious economic consequences for cattle production in the United States and elsewhere. During infection, MAP bacilli are phagocytosed and subvert host macrophage processes, resulting in subclinical infections that can lead to immunopathology and dissemination of disease. Analysis of the host macrophage transcriptome during infection can therefore shed light on the molecular mechanisms and host-pathogen interplay associated with Johne’s disease. Here, we describe results of an in vitro study of the bovine monocyte-derived macrophage (MDM) transcriptome response during MAP infection using RNA-seq. MDM were obtained from seven age- and sex-matched Holstein-Friesian cattle and were infected with MAP across a 6-h infection time course with non-infected controls. We observed 245 and 574 differentially expressed (DE) genes in MAP-infected versus non-infected control samples (adjusted P value ≤0.05) at 2 and 6 h post-infection, respectively. Functional analyses of these DE genes, including biological pathway enrichment, highlighted potential functional roles for genes that have not been previously described in the host response to infection with MAP bacilli. In addition, differential expression of pro- and anti-inflammatory cytokine genes, such as those associated with the IL-10 signaling pathway, and other immune-related genes that encode proteins involved in the bovine macrophage response to MAP infection emphasize the balance between protective host immunity and bacilli survival and proliferation. Systematic comparisons of RNA-seq gene expression results with Affymetrix® microarray data generated from the same experimental samples also demonstrated that RNA-seq represents a superior technology for studying host transcriptional responses to intracellular infection. PMID:25699042

A new automatic SAR-based flood mapping application hosted on the European Space Agency's grid processing on demand fast access to imagery environment

NASA Astrophysics Data System (ADS)

Hostache, Renaud; Chini, Marco; Matgen, Patrick; Giustarini, Laura

2013-04-01

There is a clear need for developing innovative processing chains based on earth observation (EO) data to generate products supporting emergency response and flood management at a global scale. Here an automatic flood mapping application is introduced. The latter is currently hosted on the Grid Processing on Demand (G-POD) Fast Access to Imagery (Faire) environment of the European Space Agency. The main objective of the online application is to deliver flooded areas using both recent and historical acquisitions of SAR data in an operational framework. It is worth mentioning that the method can be applied to both medium and high resolution SAR images. The flood mapping application consists of two main blocks: 1) A set of query tools for selecting the "crisis image" and the optimal corresponding pre-flood "reference image" from the G-POD archive. 2) An algorithm for extracting flooded areas using the previously selected "crisis image" and "reference image". The proposed method is a hybrid methodology, which combines histogram thresholding, region growing and change detection as an approach enabling the automatic, objective and reliable flood extent extraction from SAR images. The method is based on the calibration of a statistical distribution of "open water" backscatter values inferred from SAR images of floods. Change detection with respect to a pre-flood reference image helps reducing over-detection of inundated areas. The algorithms are computationally efficient and operate with minimum data requirements, considering as input data a flood image and a reference image. Stakeholders in flood management and service providers are able to log onto the flood mapping application to get support for the retrieval, from the rolling archive, of the most appropriate pre-flood reference image. Potential users will also be able to apply the implemented flood delineation algorithm. Case studies of several recent high magnitude flooding events (e.g. July 2007 Severn River flood, UK and March 2010 Red River flood, US) observed by high-resolution SAR sensors as well as airborne photography highlight advantages and limitations of the online application. A mid-term target is the exploitation of ESA SENTINEL 1 SAR data streams. In the long term it is foreseen to develop a potential extension of the application for systematically extracting flooded areas from all SAR images acquired on a daily, weekly or monthly basis. On-going research activities investigate the usefulness of the method for mapping flood hazard at global scale using databases of historic SAR remote sensing-derived flood inundation maps.

Geomorphological map of glaciated gorges in a granitic massif (Gredos range, Central Spain).

NASA Astrophysics Data System (ADS)

Campos, Néstor; Tanarro, Luis Miguel; Palacios, David

2017-04-01

A detailed geomorphological map on a 1:10,000 scale is presented for a high mountain area in Gredos range (Iberian Central System), this area is located in a granitic massif 160 km West of Madrid and comprises three gorges : La Vega, Taheña-Honda and La Nava. Only few detailed geomorphological maps of the Gredos range are available despite the wide diversity of landforms, in order to improve the understanding of this zone, this geomorphological map of the area has been produced, showing in detail the geomorphologic diversity of these gorges. The map was created with the aid of 25 cm resolution aerial photographs, 25 cm resolution satellite images, Iberpix 3D images provided by the Spanish National Geographic Institute and verified with field work. The landforms were delimitated with a stereoscope and satellite image pairs and digitized using GIS and CAD software, in some areas 3D glasses has been used with 3D images and the software Esri ArcScene. The landforms resulting from interpretation of aerial photographs and satellite images were classified using the IGUL (Institute of Geography, University of Lausanne) legend system (developed at the end of the 1980s) combined with the legend proposed by Peña et al. (1997) and some personal adaptations. The map legend includes 45 landforms divided into seven sections: structural, hydrography, fluvial, gravitative, glacial, nival and anthropic landforms. The use of both legend systems allows us to represent the landform types distributed over an area of 40 km2 and to identify the geomorphic processes involved in their morphogenesis, this variety of processes and landforms identified demonstrated that geomorphological cartography obtained by combining traditional image interpretation and GIS technology facilitates the production of geomorphological maps and the obtaining of valuable data for identify and understand surface processes and landforms. References: Maillard, B., Lambiel, C., Martin, S., Pellitero, R., Reynard, E., & Schoeneich, P. (2011). The ArcGIS version of the geomorphological mapping legend of the University of Lausanne. Technical report, Université de Lausanne. Peña, J., Pellicer, F., Chueca, J., & Julián, A. (1997). Leyenda para mapas geomorfológicos a escalas 1:25.000/1:50.000. In J. L. Peña (Ed.), Cartografía Geomorfológica Básica y Aplicada. Geoforma Ed. Logroño. Research funded by Deglaciation project (CGL2015-65813-R), Government of Spain

What is an evidence map? A systematic review of published evidence maps and their definitions, methods, and products.

PubMed

Miake-Lye, Isomi M; Hempel, Susanne; Shanman, Roberta; Shekelle, Paul G

2016-02-10

The need for systematic methods for reviewing evidence is continuously increasing. Evidence mapping is one emerging method. There are no authoritative recommendations for what constitutes an evidence map or what methods should be used, and anecdotal evidence suggests heterogeneity in both. Our objectives are to identify published evidence maps and to compare and contrast the presented definitions of evidence mapping, the domains used to classify data in evidence maps, and the form the evidence map takes. We conducted a systematic review of publications that presented results with a process termed "evidence mapping" or included a figure called an "evidence map." We identified publications from searches of ten databases through 8/21/2015, reference mining, and consulting topic experts. We abstracted the research question, the unit of analysis, the search methods and search period covered, and the country of origin. Data were narratively synthesized. Thirty-nine publications met inclusion criteria. Published evidence maps varied in their definition and the form of the evidence map. Of the 31 definitions provided, 67 % described the purpose as identification of gaps and 58 % referenced a stakeholder engagement process or user-friendly product. All evidence maps explicitly used a systematic approach to evidence synthesis. Twenty-six publications referred to a figure or table explicitly called an "evidence map," eight referred to an online database as the evidence map, and five stated they used a mapping methodology but did not present a visual depiction of the evidence. The principal conclusion of our evaluation of studies that call themselves "evidence maps" is that the implied definition of what constitutes an evidence map is a systematic search of a broad field to identify gaps in knowledge and/or future research needs that presents results in a user-friendly format, often a visual figure or graph, or a searchable database. Foundational work is needed to better standardize the methods and products of an evidence map so that researchers and policymakers will know what to expect of this new type of evidence review. Although an a priori protocol was developed, no registration was completed; this review did not fit the PROSPERO format.

A Large Maize (Zea mays L.) SNP Genotyping Array: Development and Germplasm Genotyping, and Genetic Mapping to Compare with the B73 Reference Genome

PubMed Central

Ganal, Martin W.; Durstewitz, Gregor; Polley, Andreas; Bérard, Aurélie; Buckler, Edward S.; Charcosset, Alain; Clarke, Joseph D.; Graner, Eva-Maria; Hansen, Mark; Joets, Johann; Le Paslier, Marie-Christine; McMullen, Michael D.; Montalent, Pierre; Rose, Mark; Schön, Chris-Carolin; Sun, Qi; Walter, Hildrun; Martin, Olivier C.; Falque, Matthieu

2011-01-01

SNP genotyping arrays have been useful for many applications that require a large number of molecular markers such as high-density genetic mapping, genome-wide association studies (GWAS), and genomic selection. We report the establishment of a large maize SNP array and its use for diversity analysis and high density linkage mapping. The markers, taken from more than 800,000 SNPs, were selected to be preferentially located in genes and evenly distributed across the genome. The array was tested with a set of maize germplasm including North American and European inbred lines, parent/F1 combinations, and distantly related teosinte material. A total of 49,585 markers, including 33,417 within 17,520 different genes and 16,168 outside genes, were of good quality for genotyping, with an average failure rate of 4% and rates up to 8% in specific germplasm. To demonstrate this array's use in genetic mapping and for the independent validation of the B73 sequence assembly, two intermated maize recombinant inbred line populations – IBM (B73×Mo17) and LHRF (F2×F252) – were genotyped to establish two high density linkage maps with 20,913 and 14,524 markers respectively. 172 mapped markers were absent in the current B73 assembly and their placement can be used for future improvements of the B73 reference sequence. Colinearity of the genetic and physical maps was mostly conserved with some exceptions that suggest errors in the B73 assembly. Five major regions containing non-colinearities were identified on chromosomes 2, 3, 6, 7 and 9, and are supported by both independent genetic maps. Four additional non-colinear regions were found on the LHRF map only; they may be due to a lower density of IBM markers in those regions or to true structural rearrangements between lines. Given the array's high quality, it will be a valuable resource for maize genetics and many aspects of maize breeding. PMID:22174790

Costs of Public Pharmaceutical Services in Rio de Janeiro Compared to Farmácia Popular Program

PubMed Central

da Silva, Rondineli Mendes; Caetano, Rosângela

2016-01-01

ABSTRACT OBJECTIVE To analyze the costs of public pharmaceutical services compared to Farmácia Popular Program (Popular Pharmacy Program). METHODS Comparison between prices paid by Aqui Tem Farmácia Popular Program (Farmácia Popular is available here) with the full costs of medicine provision by the Municipal Health Department of Rio de Janeiro. The comparison comprised 25 medicines supplied by both the municipal pharmaceutical service and Aqui Tem Farmácia Popular Program. Calculating the cost per pharmaceutical unit of each medicine included expenditure by Municipal Health Department of Rio de Janeiro with procurement (price), logistics, and local dispensation. The reference price of medicines paid by Aqui Tem Farmácia Popular was taken from the Brazilian Ministry of Health standard in force in 2012. Comparisons included full reference price; reference price minus 10.0% copayment by users; and maximum reference paid by the Ministry of Health (minus copayment and taxes). Simulations were carried out of the differences between the costs of Municipal Health Department of Rio de Janeiro with the common medicines and those potentially incurred based on the reference price of Aqui Tem Farmácia Popular. RESULTS The Municipal Health Department of Rio de Janeiro spent R$28,526,526.57 with 25 medicines of the common list in 2012; 58.7% accounted for direct procurement costs. The estimated costs of the Health Department were generally lower than the reference prices of the Aqui Tem Farmácia Popular Program for 20 medicines, regardless of reference prices. The potential costs incurred by Health Department if expenditure of its consumption pattern were based on the reference prices of Aqui Tem Farmácia Popular would be R$124,170,777.76, considering the best scenario of payment by the Brazilian Ministry of Health (90.0% of the reference price, minus taxes). CONCLUSIONS The difference in costs between public provision by Municipal Health Department of Rio de Janeiro and Farmácia Popular Program indicates that some reference prices could be reviewed aiming at their reduction. PMID:28099664

Enhancing genome assemblies by integrating non-sequence based data

PubMed Central

2011-01-01

Introduction Many genome projects were underway before the advent of high-throughput sequencing and have thus been supported by a wealth of genome information from other technologies. Such information frequently takes the form of linkage and physical maps, both of which can provide a substantial amount of data useful in de novo sequencing projects. Furthermore, the recent abundance of genome resources enables the use of conserved synteny maps identified in related species to further enhance genome assemblies. Methods The tammar wallaby (Macropus eugenii) is a model marsupial mammal with a low coverage genome. However, we have access to extensive comparative maps containing over 14,000 markers constructed through the physical mapping of conserved loci, chromosome painting and comprehensive linkage maps. Using a custom Bioperl pipeline, information from the maps was aligned to assembled tammar wallaby contigs using BLAT. This data was used to construct pseudo paired-end libraries with intervals ranging from 5-10 MB. We then used Bambus (a program designed to scaffold eukaryotic genomes by ordering and orienting contigs through the use of paired-end data) to scaffold our libraries. To determine how map data compares to sequence based approaches to enhance assemblies, we repeated the experiment using a 0.5× coverage of unique reads from 4 KB and 8 KB Illumina paired-end libraries. Finally, we combined both the sequence and non-sequence-based data to determine how a combined approach could further enhance the quality of the low coverage de novo reconstruction of the tammar wallaby genome. Results Using the map data alone, we were able order 2.2% of the initial contigs into scaffolds, and increase the N50 scaffold size to 39 KB (36 KB in the original assembly). Using only the 0.5× paired-end sequence based data, 53% of the initial contigs were assigned to scaffolds. Combining both data sets resulted in a further 2% increase in the number of initial contigs integrated into a scaffold (55% total) but a 35% increase in N50 scaffold size over the use of sequence-based data alone. Conclusions We provide a relatively simple pipeline utilizing existing bioinformatics tools to integrate map data into a genome assembly which is available at http://www.mcb.uconn.edu/fac.php?name=paska. While the map data only contributed minimally to assigning the initial contigs to scaffolds in the new assembly, it greatly increased the N50 size. This process added structure to our low coverage assembly, greatly increasing its utility in further analyses. PMID:21554765

Enhancing genome assemblies by integrating non-sequence based data.

PubMed

Heider, Thomas N; Lindsay, James; Wang, Chenwei; O'Neill, Rachel J; Pask, Andrew J

2011-05-28

Many genome projects were underway before the advent of high-throughput sequencing and have thus been supported by a wealth of genome information from other technologies. Such information frequently takes the form of linkage and physical maps, both of which can provide a substantial amount of data useful in de novo sequencing projects. Furthermore, the recent abundance of genome resources enables the use of conserved synteny maps identified in related species to further enhance genome assemblies. The tammar wallaby (Macropus eugenii) is a model marsupial mammal with a low coverage genome. However, we have access to extensive comparative maps containing over 14,000 markers constructed through the physical mapping of conserved loci, chromosome painting and comprehensive linkage maps. Using a custom Bioperl pipeline, information from the maps was aligned to assembled tammar wallaby contigs using BLAT. This data was used to construct pseudo paired-end libraries with intervals ranging from 5-10 MB. We then used Bambus (a program designed to scaffold eukaryotic genomes by ordering and orienting contigs through the use of paired-end data) to scaffold our libraries. To determine how map data compares to sequence based approaches to enhance assemblies, we repeated the experiment using a 0.5× coverage of unique reads from 4 KB and 8 KB Illumina paired-end libraries. Finally, we combined both the sequence and non-sequence-based data to determine how a combined approach could further enhance the quality of the low coverage de novo reconstruction of the tammar wallaby genome. Using the map data alone, we were able order 2.2% of the initial contigs into scaffolds, and increase the N50 scaffold size to 39 KB (36 KB in the original assembly). Using only the 0.5× paired-end sequence based data, 53% of the initial contigs were assigned to scaffolds. Combining both data sets resulted in a further 2% increase in the number of initial contigs integrated into a scaffold (55% total) but a 35% increase in N50 scaffold size over the use of sequence-based data alone. We provide a relatively simple pipeline utilizing existing bioinformatics tools to integrate map data into a genome assembly which is available at http://www.mcb.uconn.edu/fac.php?name=paska. While the map data only contributed minimally to assigning the initial contigs to scaffolds in the new assembly, it greatly increased the N50 size. This process added structure to our low coverage assembly, greatly increasing its utility in further analyses.

Role of hand dominance in mapping preferences for emotional-valence words to keypress responses.

PubMed

Song, Xiaolei; Chen, Jing; Proctor, Robert W

2017-10-01

When a crossed-hands placement (right hand presses left key; left hand presses right key) is used in a two-choice spatial reaction task, the mapping of left stimulus to left key and right stimulus to right key yields faster responses than the opposite mapping. In contrast, de la Vega, Dudschig, De Filippis, Lachmair, and Kaup (2013) reported that when right-handed individuals classified words as having positive or negative affect, there was a benefit for mapping positive affect to the right hand (left key) and negative affect to the left hand (right key). The goal of the present study was to replicate and extend this seemingly distinct finding. Experiment 1 duplicated the design of that study without including nonword "no-go" trials but including a condition in which participants performed with an uncrossed hand placement. Results corroborated the benefit for mapping positive to the right hand and negative to the left hand with the hands crossed, and this benefit was as large as that obtained with the hands uncrossed. Experiment 2 confirmed the importance of the dominant/subordinate hand distinction with left-handed participants, and Experiment 3 showed, with right-handed participants, that it does not depend on which limb is placed over the other. The results verify that the mapping advantage for positive→right/negative→left is indeed due to the distinction between dominant and subordinate hands. Possible reasons for the difference between these results and those obtained with spatial-location stimuli are considered. Copyright © 2017 Elsevier B.V. All rights reserved.

Drug-coated balloon angioplasty for de novo small vessel disease including chronic total occlusion and bifurcation in real-world clinical practice.

PubMed

Onishi, Takayuki; Onishi, Yuko; Kobayashi, Isshi; Umezawa, Shigeo; Niwa, Akihiro

2018-06-18

The aim of this study is to validate the efficacy of drug-coated balloons (DCBs) for real-world de novo small vessel diseases including chronic total occlusion and bifurcation. DCB angioplasty has been reported to be effective in the treatment of de novo small vessel disease. However, the number of reports that have focused on complex lesions is limited. This observational study comprised consecutive patients who underwent DCB angioplasty for de novo small vessel disease with a reference diameter of less than 2.5 mm by visual estimation. Outcome parameters included late lumen loss, restenosis rate, and major adverse cardiac events, such as cardiac death, non-fatal myocardial infarction, and target lesion revascularization (TLR). Fifty-two patients underwent DCB angioplasty for 59 lesions with a reference vessel diameter of 1.93 ± 0.63 mm. Thirty-eight of the lesions (69%) were classified as type B2/C, including chronic total occlusions (20%) and bifurcations (33%). At the 8-month follow-up, late lumen loss was - 0.01 ± 0.44 mm with a restenosis rate of 20%. No cardiac deaths or myocardial infarctions were reported and only 5 (9%) angiographically driven TLRs were reported. DCB angioplasty offered an acceptable 8-month lumen patency and a stable clinical outcome for real-world complex de novo coronary diseases.

Genetics Home Reference: CLN2 disease

MedlinePlus

... Z, Mole SE, Noher de Halac I, Pearce DA, Poupetova H, Schulz A, Specchio N, Xin W, ... Jul 25. Citation on PubMed Getty AL, Pearce DA. Interactions of the proteins of neuronal ceroid lipofuscinosis: ...

Enhancement of snow cover change detection with sparse representation and dictionary learning

NASA Astrophysics Data System (ADS)

Varade, D.; Dikshit, O.

2014-11-01

Sparse representation and decoding is often used for denoising images and compression of images with respect to inherent features. In this paper, we adopt a methodology incorporating sparse representation of a snow cover change map using the K-SVD trained dictionary and sparse decoding to enhance the change map. The pixels often falsely characterized as "changes" are eliminated using this approach. The preliminary change map was generated using differenced NDSI or S3 maps in case of Resourcesat-2 and Landsat 8 OLI imagery respectively. These maps are extracted into patches for compressed sensing using Discrete Cosine Transform (DCT) to generate an initial dictionary which is trained by the K-SVD approach. The trained dictionary is used for sparse coding of the change map using the Orthogonal Matching Pursuit (OMP) algorithm. The reconstructed change map incorporates a greater degree of smoothing and represents the features (snow cover changes) with better accuracy. The enhanced change map is segmented using kmeans to discriminate between the changed and non-changed pixels. The segmented enhanced change map is compared, firstly with the difference of Support Vector Machine (SVM) classified NDSI maps and secondly with a reference data generated as a mask by visual interpretation of the two input images. The methodology is evaluated using multi-spectral datasets from Resourcesat-2 and Landsat-8. The k-hat statistic is computed to determine the accuracy of the proposed approach.

Children's Understanding of Large-Scale Mapping Tasks: An Analysis of Talk, Drawings, and Gesture

ERIC Educational Resources Information Center

Kotsopoulos, Donna; Cordy, Michelle; Langemeyer, Melanie

2015-01-01

This research examined how children represent motion in large-scale mapping tasks that we referred to as "motion maps". The underlying mathematical content was transformational geometry. In total, 19 children, 8- to 10-year-old, created motion maps and captured their motion maps with accompanying verbal description digitally. Analysis of…

Preference mapping of dulce de leche commercialized in Brazilian markets.

PubMed

Gaze, L V; Oliveira, B R; Ferrao, L L; Granato, D; Cavalcanti, R N; Conte Júnior, C A; Cruz, A G; Freitas, M Q

2015-03-01

Dulce de leche samples available in the Brazilian market were submitted to sensory profiling by quantitative descriptive analysis and acceptance test, as well sensory evaluation using the just-about-right scale and purchase intent. External preference mapping and the ideal sensory characteristics of dulce de leche were determined. The results were also evaluated by principal component analysis, hierarchical cluster analysis, partial least squares regression, artificial neural networks, and logistic regression. Overall, significant product acceptance was related to intermediate scores of the sensory attributes in the descriptive test, and this trend was observed even after consumer segmentation. The results obtained by sensometric techniques showed that optimizing an ideal dulce de leche from the sensory standpoint is a multidimensional process, with necessary adjustments on the appearance, aroma, taste, and texture attributes of the product for better consumer acceptance and purchase. The optimum dulce de leche was characterized by high scores for the attributes sweet taste, caramel taste, brightness, color, and caramel aroma in accordance with the preference mapping findings. In industrial terms, this means changing the parameters used in the thermal treatment and quantitative changes in the ingredients used in formulations. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Mapping dominant runoff processes: an evaluation of different approaches using similarity measures and synthetic runoff simulations

NASA Astrophysics Data System (ADS)

Antonetti, Manuel; Buss, Rahel; Scherrer, Simon; Margreth, Michael; Zappa, Massimiliano

2016-07-01

The identification of landscapes with similar hydrological behaviour is useful for runoff and flood predictions in small ungauged catchments. An established method for landscape classification is based on the concept of dominant runoff process (DRP). The various DRP-mapping approaches differ with respect to the time and data required for mapping. Manual approaches based on expert knowledge are reliable but time-consuming, whereas automatic GIS-based approaches are easier to implement but rely on simplifications which restrict their application range. To what extent these simplifications are applicable in other catchments is unclear. More information is also needed on how the different complexities of automatic DRP-mapping approaches affect hydrological simulations. In this paper, three automatic approaches were used to map two catchments on the Swiss Plateau. The resulting maps were compared to reference maps obtained with manual mapping. Measures of agreement and association, a class comparison, and a deviation map were derived. The automatically derived DRP maps were used in synthetic runoff simulations with an adapted version of the PREVAH hydrological model, and simulation results compared with those from simulations using the reference maps. The DRP maps derived with the automatic approach with highest complexity and data requirement were the most similar to the reference maps, while those derived with simplified approaches without original soil information differed significantly in terms of both extent and distribution of the DRPs. The runoff simulations derived from the simpler DRP maps were more uncertain due to inaccuracies in the input data and their coarse resolution, but problems were also linked with the use of topography as a proxy for the storage capacity of soils. The perception of the intensity of the DRP classes also seems to vary among the different authors, and a standardised definition of DRPs is still lacking. Furthermore, we argue not to use expert knowledge for only model building and constraining, but also in the phase of landscape classification.

46 CFR 162.050-4 - Incorporation by reference: Where can I get a copy of the publications mentioned in this part?

Code of Federal Regulations, 2011 CFR

2011-10-01

... Standardization (ISO) 1, rue de Varembé, Case postale 56, CH-1211 Geneva 20, Switzerland (Internet: http://www.iso.org): (1) International Standard ISO 8217 Third edition 2005-11-01, Petroleum products—Fuels (class F)—Specifications of marine fuels (“ISO 8217”), incorporation by reference approved for § 162.050-20. (2...

46 CFR 162.050-4 - Incorporation by reference: Where can I get a copy of the publications mentioned in this part?

Code of Federal Regulations, 2010 CFR

2010-10-01

... Standardization (ISO) 1, rue de Varembé, Case postale 56, CH-1211 Geneva 20, Switzerland (Internet: http://www.iso.org): (1) International Standard ISO 8217 Third edition 2005-11-01, Petroleum products—Fuels (class F)—Specifications of marine fuels (“ISO 8217”), incorporation by reference approved for § 162.050-20. (2...

Multiple active myofascial trigger points and pressure pain sensitivity maps in the temporalis muscle are related in women with chronic tension type headache.

PubMed

Fernández-de-las-Peñas, César; Caminero, Ana B; Madeleine, Pascal; Guillem-Mesado, Amparo; Ge, Hong-You; Arendt-Nielsen, Lars; Pareja, Juan A

2009-01-01

To describe the common locations of active trigger points (TrPs) in the temporalis muscle and their referred pain patterns in chronic tension type headache (CTTH), and to determine if pressure sensitivity maps of this muscle can be used to describe the spatial distribution of active TrPs. Forty women with CTTH were included. An electronic pressure algometer was used to assess pressure pain thresholds (PPT) from 9 points over each temporalis muscle: 3 points in the anterior, medial and posterior part, respectively. Both muscles were examined for the presence of active TrPs over each of the 9 points. The referred pain pattern of each active TrP was assessed. Two-way analysis of variance detected significant differences in mean PPT levels between the measurement points (F=30.3; P<0.001), but not between sides (F=2.1; P=0.2). PPT scores decreased from the posterior to the anterior column (P<0.001). No differences were found in the number of active TrPs (F=0.3; P=0.9) between the dominant side the nondominant side. Significant differences were found in the distribution of the active TrPs (chi2=12.2; P<0.001): active TrPs were mostly found in the anterior column and in the middle of the muscle belly. The analysis of variance did not detect significant differences in the referred pain pattern between active TrPs (F=1.1, P=0.4). The topographical pressure pain sensitivity maps showed the distinct distribution of the TrPs indicated by locations with low PPTs. Multiple active TrPs in the temporalis muscle were found, particularly in the anterior column and in the middle of the muscle belly. Bilateral posterior to anterior decreased distribution of PPTs in the temporalis muscle in women with CTTH was found. The locations of active TrPs in the temporalis muscle corresponded well to the muscle areas with lower PPT, supporting the relationship between multiple active muscle TrPs and topographical pressure sensitivity maps in the temporalis muscle in women with CTTH.

Clinical Impact and Implication of Real-Time Oscillation Analysis for Language Mapping.

PubMed

Ogawa, Hiroshi; Kamada, Kyousuke; Kapeller, Christoph; Prueckl, Robert; Takeuchi, Fumiya; Hiroshima, Satoru; Anei, Ryogo; Guger, Christoph

2017-01-01

We developed a functional brain analysis system that enabled us to perform real-time task-related electrocorticography (ECoG) and evaluated its potential in clinical practice. We hypothesized that high gamma activity (HGA) mapping would provide better spatial and temporal resolution with high signal-to-noise ratios. Seven awake craniotomy patients were evaluated. ECoG was recorded during language tasks using subdural grids, and HGA (60-170 Hz) maps were obtained in real time. The patients also underwent electrocortical stimulation (ECS) mapping to validate the suspected functional locations on HGA mapping. The results were compared and calculated to assess the sensitivity and specificity of HGA mapping. For reference, bedside HGA-ECS mapping was performed in 5 epilepsy patients. HGA mapping demonstrated functional brain areas in real time and was comparable with ECS mapping. Sensitivity and specificity for the language area were 90.1% ± 11.2% and 90.0% ± 4.2%, respectively. Most HGA-positive areas were consistent with ECS-positive regions in both groups, and there were no statistical between-group differences. Although this study included a small number of subjects, it showed real-time HGA mapping with the same setting and tasks under different conditions. This study demonstrates the clinical feasibility of real-time HGA mapping. Real-time HGA mapping enabled simple and rapid detection of language functional areas in awake craniotomy. The mapping results were highly accurate, although the mapping environment was noisy. Further studies of HGA mapping may provide the potential to elaborate complex brain functions and networks. Copyright © 2016 Elsevier Inc. All rights reserved.

Interstitial duplication 8q22-q24: Report of a case proven by FISH with mapped cosmid probes

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

Wakui, Keiko; Ohashi, Hirofumi; Yamagishi, Akira

We report on a 6-month-old malformed female infant with a de novo interstitial duplication of an 8q22-q24 segment. She had an excess dark-band on the 8q distal region by GTG-banded chromosome analysis, which was likely to be 8q23. We performed FISH analysis using cosmid probes mapped to 8q23 and proved that the patient had an 8q duplication including the 8q23 region. 20 refs., 2 figs., 1 tab.

Smiles2Monomers: a link between chemical and biological structures for polymers.

PubMed

Dufresne, Yoann; Noé, Laurent; Leclère, Valérie; Pupin, Maude

2015-01-01

The monomeric composition of polymers is powerful for structure comparison and synthetic biology, among others. Many databases give access to the atomic structure of compounds but the monomeric structure of polymers is often lacking. We have designed a smart algorithm, implemented in the tool Smiles2Monomers (s2m), to infer efficiently and accurately the monomeric structure of a polymer from its chemical structure. Our strategy is divided into two steps: first, monomers are mapped on the atomic structure by an efficient subgraph-isomorphism algorithm ; second, the best tiling is computed so that non-overlapping monomers cover all the structure of the target polymer. The mapping is based on a Markovian index built by a dynamic programming algorithm. The index enables s2m to search quickly all the given monomers on a target polymer. After, a greedy algorithm combines the mapped monomers into a consistent monomeric structure. Finally, a local branch and cut algorithm refines the structure. We tested this method on two manually annotated databases of polymers and reconstructed the structures de novo with a sensitivity over 90 %. The average computation time per polymer is 2 s. s2m automatically creates de novo monomeric annotations for polymers, efficiently in terms of time computation and sensitivity. s2m allowed us to detect annotation errors in the tested databases and to easily find the accurate structures. So, s2m could be integrated into the curation process of databases of small compounds to verify the current entries and accelerate the annotation of new polymers. The full method can be downloaded or accessed via a website for peptide-like polymers at http://bioinfo.lifl.fr/norine/smiles2monomers.jsp.Graphical abstract:.

Map Classification: A Comparison of Schemes with Special Reference to the Continent of Africa. Occasional Papers, Number 154.

ERIC Educational Resources Information Center

Merrett, Christopher E.

This guide to the theory and practice of map classification begins with a discussion of the filing of maps and the function of map classification based on area and theme as illustrated by four maps of Africa. The description of the various classification systems which follows is divided into book schemes with provision for maps (including Dewey…

De novo transcriptome sequencing of the Octopus vulgaris hemocytes using Illumina RNA-Seq technology: response to the infection by the gastrointestinal parasite Aggregata octopiana.

PubMed

Castellanos-Martínez, Sheila; Arteta, David; Catarino, Susana; Gestal, Camino

2014-01-01

Octopus vulgaris is a highly valuable species of great commercial interest and excellent candidate for aquaculture diversification; however, the octopus' well-being is impaired by pathogens, of which the gastrointestinal coccidian parasite Aggregata octopiana is one of the most important. The knowledge of the molecular mechanisms of the immune response in cephalopods, especially in octopus is scarce. The transcriptome of the hemocytes of O. vulgaris was de novo sequenced using the high-throughput paired-end Illumina technology to identify genes involved in immune defense and to understand the molecular basis of octopus tolerance/resistance to coccidiosis. A bi-directional mRNA library was constructed from hemocytes of two groups of octopus according to the infection by A. octopiana, sick octopus, suffering coccidiosis, and healthy octopus, and reads were de novo assembled together. The differential expression of transcripts was analysed using the general assembly as a reference for mapping the reads from each condition. After sequencing, a total of 75,571,280 high quality reads were obtained from the sick octopus group and 74,731,646 from the healthy group. The general transcriptome of the O. vulgaris hemocytes was assembled in 254,506 contigs. A total of 48,225 contigs were successfully identified, and 538 transcripts exhibited differential expression between groups of infection. The general transcriptome revealed genes involved in pathways like NF-kB, TLR and Complement. Differential expression of TLR-2, PGRP, C1q and PRDX genes due to infection was validated using RT-qPCR. In sick octopuses, only TLR-2 was up-regulated in hemocytes, but all of them were up-regulated in caecum and gills. The transcriptome reported here de novo establishes the first molecular clues to understand how the octopus immune system works and interacts with a highly pathogenic coccidian. The data provided here will contribute to identification of biomarkers for octopus resistance against pathogens, which could improve octopus farming in the near future.

De Novo Transcriptome Sequencing of the Octopus vulgaris Hemocytes Using Illumina RNA-Seq Technology: Response to the Infection by the Gastrointestinal Parasite Aggregata octopiana

PubMed Central

Castellanos-Martínez, Sheila; Arteta, David; Catarino, Susana; Gestal, Camino

2014-01-01

Background Octopus vulgaris is a highly valuable species of great commercial interest and excellent candidate for aquaculture diversification; however, the octopus’ well-being is impaired by pathogens, of which the gastrointestinal coccidian parasite Aggregata octopiana is one of the most important. The knowledge of the molecular mechanisms of the immune response in cephalopods, especially in octopus is scarce. The transcriptome of the hemocytes of O. vulgaris was de novo sequenced using the high-throughput paired-end Illumina technology to identify genes involved in immune defense and to understand the molecular basis of octopus tolerance/resistance to coccidiosis. Results A bi-directional mRNA library was constructed from hemocytes of two groups of octopus according to the infection by A. octopiana, sick octopus, suffering coccidiosis, and healthy octopus, and reads were de novo assembled together. The differential expression of transcripts was analysed using the general assembly as a reference for mapping the reads from each condition. After sequencing, a total of 75,571,280 high quality reads were obtained from the sick octopus group and 74,731,646 from the healthy group. The general transcriptome of the O. vulgaris hemocytes was assembled in 254,506 contigs. A total of 48,225 contigs were successfully identified, and 538 transcripts exhibited differential expression between groups of infection. The general transcriptome revealed genes involved in pathways like NF-kB, TLR and Complement. Differential expression of TLR-2, PGRP, C1q and PRDX genes due to infection was validated using RT-qPCR. In sick octopuses, only TLR-2 was up-regulated in hemocytes, but all of them were up-regulated in caecum and gills. Conclusion The transcriptome reported here de novo establishes the first molecular clues to understand how the octopus immune system works and interacts with a highly pathogenic coccidian. The data provided here will contribute to identification of biomarkers for octopus resistance against pathogens, which could improve octopus farming in the near future. PMID:25329466

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

PubMed Central

Degner, Jacob F.; Marioni, John C.; Pai, Athma A.; Pickrell, Joseph K.; Nkadori, Everlyne; Gilad, Yoav; Pritchard, Jonathan K.

2009-01-01

Motivation: Next-generation sequencing has become an important tool for genome-wide quantification of DNA and RNA. However, a major technical hurdle lies in the need to map short sequence reads back to their correct locations in a reference genome. Here, we investigate the impact of SNP variation on the reliability of read-mapping in the context of detecting allele-specific expression (ASE). Results: We generated 16 million 35 bp reads from mRNA of each of two HapMap Yoruba individuals. When we mapped these reads to the human genome we found that, at heterozygous SNPs, there was a significant bias toward higher mapping rates of the allele in the reference sequence, compared with the alternative allele. Masking known SNP positions in the genome sequence eliminated the reference bias but, surprisingly, did not lead to more reliable results overall. We find that even after masking, ∼5–10% of SNPs still have an inherent bias toward more effective mapping of one allele. Filtering out inherently biased SNPs removes 40% of the top signals of ASE. The remaining SNPs showing ASE are enriched in genes previously known to harbor cis-regulatory variation or known to show uniparental imprinting. Our results have implications for a variety of applications involving detection of alternate alleles from short-read sequence data. Availability: Scripts, written in Perl and R, for simulating short reads, masking SNP variation in a reference genome and analyzing the simulation output are available upon request from JFD. Raw short read data were deposited in GEO (http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE18156. Contact: jdegner@uchicago.edu; marioni@uchicago.edu; gilad@uchicago.edu; pritch@uchicago.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19808877

Mapping the Archives: 2

ERIC Educational Resources Information Center

Jackson, Anthony

2012-01-01

With this issue, "RiDE" continues its new occasional series of short informational pieces on archives in the field of drama and theatre education and applied theatre and performance. Each instalment includes summaries of one or more collections of significant material in the field. Over time this will build into a readily accessible…

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

PubMed Central

Beier, Sebastian; Himmelbach, Axel; Colmsee, Christian; Zhang, Xiao-Qi; Barrero, Roberto A.; Zhang, Qisen; Li, Lin; Bayer, Micha; Bolser, Daniel; Taudien, Stefan; Groth, Marco; Felder, Marius; Hastie, Alex; Šimková, Hana; Staňková, Helena; Vrána, Jan; Chan, Saki; Muñoz-Amatriaín, María; Ounit, Rachid; Wanamaker, Steve; Schmutzer, Thomas; Aliyeva-Schnorr, Lala; Grasso, Stefano; Tanskanen, Jaakko; Sampath, Dharanya; Heavens, Darren; Cao, Sujie; Chapman, Brett; Dai, Fei; Han, Yong; Li, Hua; Li, Xuan; Lin, Chongyun; McCooke, John K.; Tan, Cong; Wang, Songbo; Yin, Shuya; Zhou, Gaofeng; Poland, Jesse A.; Bellgard, Matthew I.; Houben, Andreas; Doležel, Jaroslav; Ayling, Sarah; Lonardi, Stefano; Langridge, Peter; Muehlbauer, Gary J.; Kersey, Paul; Clark, Matthew D.; Caccamo, Mario; Schulman, Alan H.; Platzer, Matthias; Close, Timothy J.; Hansson, Mats; Zhang, Guoping; Braumann, Ilka; Li, Chengdao; Waugh, Robbie; Scholz, Uwe; Stein, Nils; Mascher, Martin

2017-01-01

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. ‘Morex’ was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX). PMID:28448065

Improving Signal-to-Noise Ratio in Scanning Transmission Electron Microscopy Energy-Dispersive X-Ray (STEM-EDX) Spectrum Images Using Single-Atomic-Column Cross-Correlation Averaging.

PubMed

Jeong, Jong Seok; Mkhoyan, K Andre

2016-06-01

Acquiring an atomic-resolution compositional map of crystalline specimens has become routine practice, thus opening possibilities for extracting subatomic information from such maps. A key challenge for achieving subatomic precision is the improvement of signal-to-noise ratio (SNR) of compositional maps. Here, we report a simple and reliable solution for achieving high-SNR energy-dispersive X-ray (EDX) spectroscopy spectrum images for individual atomic columns. The method is based on standard cross-correlation aided by averaging of single-column EDX maps with modifications in the reference image. It produces EDX maps with minimal specimen drift, beam drift, and scan distortions. Step-by-step procedures to determine a self-consistent reference map with a discussion on the reliability, stability, and limitations of the method are presented here.

78 FR 45941 - Changes in Flood Hazard Determinations

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-30

... (hereinafter referred to as flood hazard determinations) as shown on the indicated Letter of Map Revision (LOMR... Insurance Rate Maps (FIRMs), and in some cases the Flood Insurance Study (FIS) reports, currently in effect... respective Community Map Repository address listed in the table below and online through the FEMA Map Service...

High School Biology: A Group Approach to Concept Mapping.

ERIC Educational Resources Information Center

Brown, David S.

2003-01-01

Explains concept mapping as an instructional method in cooperative learning environments, and describes a study investigating the effectiveness of concept mapping on student learning during a photosynthesis and cellular respiration unit. Reports on the positive effects of concept mapping in the experimental group. (Contains 16 references.) (YDS)

Ammonium on Ceres

NASA Astrophysics Data System (ADS)

Ammannito, E.; De Sanctis, M. C.; Carrorro, F. G.; Ciarniello, M.; Combe, J. P.; De Angelis, S.; Ehlmann, B. L.; Frigeri, A.; Longobardo, A.; Mugnuolo, R.; Marchi, S.; Palomba, E.; Raymond, C. A.; Salatti, M.; Tosi, F.; Zambon, F.; Russell, C. T.

2017-12-01

Since January 2015, the surface of Ceres has been studied by the Dawn spacecraft through the measurements from the three instruments on board (1). The VIR imaging spectrometer, sensitive to the spectral range 0.25 -5.0 μm, provided information on the surficial composition of Ceres at resolutions ranging from few kilometers to about one hundred meters (2). Analysis of VIR reflectance data revealed that the average spectrum of Ceres is compatible with a mixture of low-albedo minerals, Mg- phyllosilicates, ammoniated clays, and Mg- carbonates, (3) confirming previous studies based on ground based spectra (4, 5). Mineralogical maps of the surface at about 1 km/px show that the components identified in the average spectrum are present all across the surface with variations in their relative abundance and chemical composition (6, 7). While the ammoniated clays have been already studied (6), the presence nature and distribution of additional ammoniated species has never been investigated in detail, although the spectral analysis of the bright faculae within Occator crater already revealed the potential presence of ammonium salts (8). Since the position and shape of the ammonium absorption in the VIS-NIR region are function of the hosting mineral specie (8), we did an inventory and characterization of the ammonium-rich regions, in order to analyze their spectral properties. In addition to the presence of ammonium, also the identification of the hosting species has implication for the evolution of Ceres. Our study, therefore, is a step forward in understanding of evolutionary pathway of Ceres. References: (1) Russell, C. T. et al., Science, 2016. (2) De Sanctis M.C. et al., Space Science Reviews, 2011. (3) De Sanctis M.C. et al., Nature, 2015. (4) King T. et al. Science, 1992. (5) Rivkin A.S. et al. Icarus, 2006. (6) Ammannito E. et al., Science, 2016. (7) Carrozzo F.G. et al., Science Advances, in revision. (8) De Sanctis et al., Nature, 2016. (9) Berg et al., Icarus, 2016.

The Release 6 reference sequence of the Drosophila melanogaster genome

DOE PAGES

Hoskins, Roger A.; Carlson, Joseph W.; Wan, Kenneth H.; ...

2015-01-14

Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy andmore » middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. In conclusion, further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.« less

The Release 6 reference sequence of the Drosophila melanogaster genome

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

Hoskins, Roger A.; Carlson, Joseph W.; Wan, Kenneth H.

Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy andmore » middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. In conclusion, further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.« less

Mapping the Fetomaternal Peripheral Immune System at Term Pregnancy

PubMed Central

Fragiadakis, Gabriela K.; Baca, Quentin J.; Gherardini, Pier Federico; Ganio, Edward A.; Gaudilliere, Dyani K.; Tingle, Martha; Lancero, Hope L.; McNeil, Leslie S.; Spitzer, Matthew H.; Wong, Ronald J.; Shaw, Gary M.; Darmstadt, Gary L.; Sylvester, Karl G.; Winn, Virginia D.; Carvalho, Brendan; Lewis, David B.; Stevenson, David K.; Nolan, Garry P.; Aghaeepour, Nima; Angst, Martin S.; Gaudilliere, Brice L.

2016-01-01

Preterm labor and infections are the leading causes of neonatal deaths worldwide. During pregnancy, immunological cross talk between the mother and her fetus are critical for the maintenance of pregnancy and the delivery of an immuno-competent neonate. A precise understanding of healthy fetomaternal immunity is the important first step to identifying dysregulated immune mechanisms driving adverse maternal or neonatal outcomes. This study combined single-cell mass cytometry of paired peripheral and umbilical cord blood samples from mothers and their neonates with a graphical approach developed for the visualization of high-dimensional data to provide a high-resolution reference map of the cellular composition and functional organization of the healthy fetal and maternal immune systems at birth. The approach enabled mapping of known phenotypical and functional characteristics of fetal immunity (including the functional hyper-responsiveness of CD4+ and CD8+ T cells and the global blunting of innate immune responses). It also allowed discovery of new properties that distinguish the fetal and maternal immune systems. For example, examination of paired samples revealed differences in endogenous signaling tone that are unique to a mother and her offspring, including increased ERK1/2, MAPKAPK2, rpS6, and CREB phosphorylation in fetal Tbet+CD4+ T cells, CD8+ T cells, B cells and CD56loCD16+ NK cells and decreased ERK1/2, MAPKAPK2, and STAT1 phosphorylation in fetal intermediate and non-classical monocytes. This highly interactive functional map of healthy fetomaternal immunity builds the core reference for a growing data repository that will allow inferring deviations from normal associated with adverse maternal and neonatal outcomes. PMID:27793998

Mapping the Fetomaternal Peripheral Immune System at Term Pregnancy.

PubMed

Fragiadakis, Gabriela K; Baca, Quentin J; Gherardini, Pier Federico; Ganio, Edward A; Gaudilliere, Dyani K; Tingle, Martha; Lancero, Hope L; McNeil, Leslie S; Spitzer, Matthew H; Wong, Ronald J; Shaw, Gary M; Darmstadt, Gary L; Sylvester, Karl G; Winn, Virginia D; Carvalho, Brendan; Lewis, David B; Stevenson, David K; Nolan, Garry P; Aghaeepour, Nima; Angst, Martin S; Gaudilliere, Brice L

2016-12-01

Preterm labor and infections are the leading causes of neonatal deaths worldwide. During pregnancy, immunological cross talk between the mother and her fetus is critical for the maintenance of pregnancy and the delivery of an immunocompetent neonate. A precise understanding of healthy fetomaternal immunity is the important first step to identifying dysregulated immune mechanisms driving adverse maternal or neonatal outcomes. This study combined single-cell mass cytometry of paired peripheral and umbilical cord blood samples from mothers and their neonates with a graphical approach developed for the visualization of high-dimensional data to provide a high-resolution reference map of the cellular composition and functional organization of the healthy fetal and maternal immune systems at birth. The approach enabled mapping of known phenotypical and functional characteristics of fetal immunity (including the functional hyperresponsiveness of CD4 + and CD8 + T cells and the global blunting of innate immune responses). It also allowed discovery of new properties that distinguish the fetal and maternal immune systems. For example, examination of paired samples revealed differences in endogenous signaling tone that are unique to a mother and her offspring, including increased ERK1/2, MAPK-activated protein kinase 2, rpS6, and CREB phosphorylation in fetal Tbet + CD4 + T cells, CD8 + T cells, B cells, and CD56 lo CD16 + NK cells and decreased ERK1/2, MAPK-activated protein kinase 2, and STAT1 phosphorylation in fetal intermediate and nonclassical monocytes. This highly interactive functional map of healthy fetomaternal immunity builds the core reference for a growing data repository that will allow inferring deviations from normal associated with adverse maternal and neonatal outcomes. Copyright © 2016 by The American Association of Immunologists, Inc.