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Sample records for high-resolution comparative map

  1. A high-resolution comparative radiation hybrid map of equine chromosome 4q12-q22.

    PubMed

    Dierks, C; Mömke, S; Drögemüller, C; Leeb, T; Chowdhary, B P; Distl, O

    2006-10-01

    In this study, we present a comprehensive 5000-rad radiation hybrid map of a 40-cM region on equine chromosome 4 (ECA4) that contains quantitative trait loci for equine osteochondrosis. We mapped 29 gene-associated sequence tagged site markers using primers designed from equine expressed sequence tags or BAC clones in the ECA4q12-q22 region. Three blocks of conserved synteny, showing two chromosomal breakpoints, were identified in the segment of ECA4q12-q22. Markers from other segments of HSA7q mapped to ECA13p and ECA4p, and a region of HSA7p was homologous to ECA13p. Therefore, we have improved the resolution of the human-equine comparative map, which allows the identification of candidate genes underlying traits of interest.

  2. A high-resolution whole-genome cattle-human comparative map reveals details of mammalian chromosome evolution.

    PubMed

    Everts-van der Wind, Annelie; Larkin, Denis M; Green, Cheryl A; Elliott, Janice S; Olmstead, Colleen A; Chiu, Readman; Schein, Jacqueline E; Marra, Marco A; Womack, James E; Lewin, Harris A

    2005-12-20

    Approximately 3,000 cattle bacterial artificial chromosome (BAC)-end sequences were added to the Illinois-Texas 5,000-rad RH (RH, radiation hybrid) map. The BAC-end sequences selected for mapping are approximately 1 Mbp apart on the human chromosomes as determined by blastn analysis. The map has 3,484 ordered markers, of which 3,204 are anchored in the human genome. Two hundred-and-one homologous synteny blocks (HSBs) were identified, of which 27 are previously undiscovered, 79 are extended, 26 were formed by previously unrecognized breakpoints in 18 previously defined HSBs, and 23 are the result of fusions. The comparative coverage relative to the human genome is approximately 91%, or 97% of the theoretical maximum. The positions of 64% of all cattle centromeres and telomeres were reassigned relative to their positions on the previous map, thus facilitating a more detailed comparative analysis of centromere and telomere evolution. As an example of the utility of the high-resolution map, 22 cattle BAC fingerprint contigs were directly anchored to cattle chromosome 19 [Bos taurus, (BTA) 19]. The order of markers on the cattle RH and fingerprint maps of BTA19 and the sequence-based map of human chromosome 17 [Homo sapiens, (HSA) 17] were found to be highly consistent, with only two minor ordering discrepancies between the RH map and fingerprint contigs. The high-resolution Illinois-Texas 5,000-rad RH and comparative maps will facilitate identification of candidate genes for economically important traits, the phylogenomic analysis of mammalian chromosomes, proofing of the BAC fingerprint map and, ultimately, aid the assembly of cattle whole-genome sequence.

  3. Zooming in on the human-mouse comparative map: genome conservation re-examined on a high-resolution scale.

    PubMed

    Carver, E A; Stubbs, L

    1997-12-01

    Over the past decade, conservation of genetic linkage groups has been shown in mammals and used to great advantage, fueling significant exchanges of gene mapping and functional information especially between the genomes of humans and mice. As human physical maps increase in resolution from chromosome bands to nucleotide sequence, comparative alignments of mouse and human regions have revealed striking similarities and surprising differences between the genomes of these two best-mapped mammalian species. Whereas, at present, very few mouse and human regions have been compared on the physical level, existing studies provide intriguing insights to genome evolution, including the observation of recent duplications and deletions of genes that may play significant roles in defining some of the biological differences between the two species. Although high-resolution conserved marker-based maps are currently available only for human and mouse, a variety of new methods and resources are speeding the development of comparative maps of additional organisms. These advances mark the first step toward establishment of the human genome as a reference map for vertebrate species, providing evolutionary and functional annotation to human sequence and vast new resources for genetic analysis of a variety of commercially, medically, and ecologically important animal models.

  4. Construction of high-resolution genetic maps of Zoysia matrella (L.) Merrill and applications to comparative genomic analysis and QTL mapping of resistance to fall armyworm.

    PubMed

    Huang, Xiaoen; Wang, Fangfang; Singh, Ratnesh; Reinert, James A; Engelke, M C; Genovesi, Anthony D; Chandra, Ambika; Yu, Qingyi

    2016-08-08

    Zoysia matrella, widely used in lawns and sports fields, is of great economic and ecological value. Z. matrella is an allotetraploid species (2n = 4x = 40) in the genus zoysia under the subfamily Chloridoideae. Despite its ecological impacts and economic importance, the subfamily Chloridoideae has received little attention in genomics studies. As a result, limited genetic and genomic information are available for this subfamily, which have impeded progress in understanding evolutionary history of grasses in this important lineage. The lack of a high-resolution genetic map has hampered efforts to improve zoysiagrass using molecular genetic tools. We used restriction site-associated DNA sequencing (RADSeq) approach and a segregating population developed from the cross between Z. matrella cultivars 'Diamond' and 'Cavalier' to construct high-resolution genetic maps of Z. matrella. The genetic map of Diamond consists of 2,375 Single Nucleotide Polymorphism (SNP) markers mapped on 20 linkage groups (LGs) with a total length of 1754.48 cM and an average distance between adjacent markers at 0.74 cM. The genetic map of Cavalier contains 3,563 SNP markers on 20 LGs, covering 1824.92 cM, with an average distance between adjacent markers at 0.51 cM. A higher level of genome collinearity between Z. matrella and rice than that between Z. matrella and sorghum was revealed by comparative genomic analysis. Pairwise comparison revealed that two independent nested chromosome fusion events occurred after Z. matrella and sorghum split from a common ancestor. The high-resolution linkage maps were applied into mapping QTLs associated with fall armyworm (FAW) resistance and six loci located on LGs 8 and 20 were detected to be significantly associated with FAW resistance. The high-resolution linkage maps provide anchor points for comparative genomics analysis between Z. matrella and other grass species. Our comparative genomic analysis suggested that the chromosome number

  5. High resolution optical DNA mapping

    NASA Astrophysics Data System (ADS)

    Baday, Murat

    Many types of diseases including cancer and autism are associated with copy-number variations in the genome. Most of these variations could not be identified with existing sequencing and optical DNA mapping methods. We have developed Multi-color Super-resolution technique, with potential for high throughput and low cost, which can allow us to recognize more of these variations. Our technique has made 10--fold improvement in the resolution of optical DNA mapping. Using a 180 kb BAC clone as a model system, we resolved dense patterns from 108 fluorescent labels of two different colors representing two different sequence-motifs. Overall, a detailed DNA map with 100 bp resolution was achieved, which has the potential to reveal detailed information about genetic variance and to facilitate medical diagnosis of genetic disease.

  6. High-Resolution Global Soil Moisture Map

    NASA Image and Video Library

    2015-05-19

    High-resolution global soil moisture map from NASA SMAP combined radar and radiometer instruments, acquired between May 4 and May 11, 2015 during SMAP commissioning phase. The map has a resolution of 5.6 miles (9 kilometers). The data gap is due to turning the instruments on and off during testing. http://photojournal.jpl.nasa.gov/catalog/PIA19337

  7. Venus gravity - A high-resolution map

    NASA Technical Reports Server (NTRS)

    Reasenberg, R. D.; Goldberg, Z. M.; Macneil, P. E.; Shapiro, I. I.

    1981-01-01

    The Doppler data from the radio tracking of the Pioneer Venus Orbiter (PVO) have been used in a two-stage analysis to develop a high-resolution map of the gravitational potential of Venus, represented by a central mass and a surface mass density. The two-stage procedure invokes a Kalman filter-smoother to determine the orbit of the spacecraft, and a stabilized linear inverter to estimate the surface mass density. The resultant gravity map is highly correlated with the topographic map derived from the PVO radar altimeter data. However, the magnitudes of the gravity variations are smaller than would be expected if the topography were uncompensated, indicating that at least partial compensation has taken place.

  8. High Resolution Camera for Mapping Titan Surface

    NASA Technical Reports Server (NTRS)

    Reinhardt, Bianca

    2011-01-01

    Titan, Saturn's largest moon, has a dense atmosphere and is the only object besides Earth to have stable liquids at its surface. The Cassini/Huygens mission has revealed the extraordinary breadth of geological processes shaping its surface. Further study requires high resolution imaging of the surface, which is restrained by light absorption by methane and scattering from aerosols. The Visual and Infrared Mapping Spectrometer (VIMS) onboard the Cassini spacecraft has demonstrated that Titan's surface can be observed within several windows in the near infrared, allowing us to process several regions in order to create a geological map and to determine the morphology. Specular reflections monitored on the lakes of the North Pole show little scattering at 5 microns, which, combined with the present study of Titan's northern pole area, refutes the paradigm that only radar can achieve high resolution mapping of the surface. The present data allowed us to monitor the evolution of lakes, to identify additional lakes at the Northern Pole, to examine Titan's hypothesis of non-synchronous rotation and to analyze the albedo of the North Pole surface. Future missions to Titan could carry a camera with 5 micron detectors and a carbon fiber radiator for weight reduction.

  9. High-Resolution Mapping in Manus Basin

    NASA Astrophysics Data System (ADS)

    Roman, C. N.; Ferrini, V. L.

    2006-12-01

    Near-bottom seafloor mapping with precisely navigated deep submergence vehicles has become increasingly common in a range of oceanographic settings. Recent mapping efforts at deep-water hydrothermal vent sites have resulted in high-resolution (sub-meter) bathymetry datasets that can be used to identify morphological features associated with volcanic, tectonic, and hydrothermal processes. The resolution of these maps, and our ability to accurately quantify the complex morphologic details of hydrothermal structures has been limited by a number of variables including navigational accuracy, sonar settings (e.g. acoustic wavelength, sonar orientation, ping rate), survey parameters (e.g. altitude, speed), data density, and data processing techniques (e.g. gridding algorithms). We present the results of two near-bottom surveys conducted in August 2006 at the PACMANUS (Papua New Guinea-Australia-Canada Manus) hydrothermal field in the eastern Manus Basin of the Bismarck Sea, south of New Ireland, Papua New Guinea. Data were simultaneously acquired with two high-resolution multibeam sonar systems mounted on the Remote Operated Vehicle (ROV) Jason 2. A Simrad SM2000 (200 kHz) multibeam system was mounted in down-looking mode, and an Imagenex DeltaT (675 kHz) multibeam system was mounted on the brow of the vehicle in a forward-looking orientation. Surveys were conducted in parallel survey lines at 15 m altitude (15 m line spacing), and the can be used to generate sub-meter resolution maps of the seafloor. The maps were assembled using a terrain registration algorithm designed to minimize the affects of navigation error. Together, these sonars provide a complementary dataset that allows us to better quantify the 3-dimensional morphological characteristics of complex hydrothermal vent structures. This information can be used to more accurately estimate the volume of hydrothermal deposits, and render a more complete environmental picture that is less hindered by occlusions and

  10. High-resolution mapping of genotype-phenotype relationships in cri du chat syndrome using array comparative genomic hybridization.

    PubMed

    Zhang, Xiaoxiao; Snijders, Antoine; Segraves, Richard; Zhang, Xiuqing; Niebuhr, Anita; Albertson, Donna; Yang, Huanming; Gray, Joe; Niebuhr, Erik; Bolund, Lars; Pinkel, Dan

    2005-02-01

    We have used array comparative genomic hybridization to map DNA copy-number changes in 94 patients with cri du chat syndrome who had been carefully evaluated for the presence of the characteristic cry, speech delay, facial dysmorphology, and level of mental retardation (MR). Most subjects had simple deletions involving 5p (67 terminal and 12 interstitial). Genotype-phenotype correlations localized the region associated with the cry to 1.5 Mb in distal 5p15.31, between bacterial artificial chromosomes (BACs) containing markers D5S2054 and D5S676; speech delay to 3.2 Mb in 5p15.32-15.33, between BACs containing D5S417 and D5S635; and the region associated with facial dysmorphology to 2.4 Mb in 5p15.2-15.31, between BACs containing D5S208 and D5S2887. These results overlap and refine those reported in previous publications. MR depended approximately on the 5p deletion size and location, but there were many cases in which the retardation was disproportionately severe, given the 5p deletion. All 15 of these cases, approximately two-thirds of the severely retarded patients, were found to have copy-number aberrations in addition to the 5p deletion. Restriction of consideration to patients with only 5p deletions clarified the effect of such deletions and suggested the presence of three regions, MRI-III, with differing effect on retardation. Deletions including MRI, a 1.2-Mb region overlapping the previously defined cri du chat critical region but not including MRII and MRIII, produced a moderate level of retardation. Deletions restricted to MRII, located just proximal to MRI, produced a milder level of retardation, whereas deletions restricted to the still-more proximal MRIII produced no discernible phenotype. However, MR increased as deletions that included MRI extended progressively into MRII and MRIII, and MR became profound when all three regions were deleted.

  11. High-resolution mapping of genotype-phenotype relationships in cridu chat syndrome using array comparative genomic hybridization

    SciTech Connect

    Zhang, Xiaoxiao; Snijders, Antoine; Segraves, Richard; Zhang,Xiuqing; Niebuhr, Anita; Albertson, Donna; Yang, Huanming; Gray, Joe; Niebuhr, Erik; Bolund, Lars; Pinkel, Dan

    2007-07-03

    We have used array comparative genomic hybridization to map DNA copy-number changes in 94 patients with cri du chat syndrome who had been carefully evaluated for the presence of the characteristic cry, speech delay, facial dysmorphology, and level of mental retardation (MR). Most subjects had simple deletions involving 5p (67 terminal and 12 interstitial). Genotype-phenotype correlations localized the region associated with the cry to 1.5 Mb in distal 5p15.31, between bacterial artificial chromosomes (BACs) containing markers D5S2054 and D5S676; speech delay to 3.2 Mb in 5p15.32-15.33, between BACs containing D5S417 and D5S635; and the region associated with facial dysmorphology to 2.4 Mb in 5p15.2-15.31, between BACs containing D5S208 and D5S2887. These results overlap and refine those reported in previous publications. MR depended approximately on the 5p deletion size and location, but there were many cases in which the retardation was disproportionately severe, given the 5p deletion. All 15 of these cases, approximately two-thirds of the severely retarded patients, were found to have copy-number aberrations in addition to the 5p deletion. Restriction of consideration to patients with only 5p deletions clarified the effect of such deletions and suggested the presence of three regions, MRI-III, with differing effect on retardation. Deletions including MRI, a 1.2-Mb region overlapping the previously defined cri du chat critical region but not including MRII and MRIII, produced a moderate level of retardation. Deletions restricted to MRII, located just proximal to MRI, produced a milder level of retardation, whereas deletions restricted to the still-more proximal MRIII produced no discernible phenotype. However, MR increased as deletions that included MRI extended progressively into MRII and MRIII, and MR became profound when all three regions were deleted.

  12. High Resolution Mapping of Pluto's Albedo Distribution

    NASA Astrophysics Data System (ADS)

    Stern, S.

    1994-01-01

    This proposal requests time to map Pluto's albedo distribution, using the highest possible resolution of the CYCLE 4 HST. Maps will be made in several key UV and visible bandpasses. Our scientific objectives are to (a) study the distribution of light and dark areas, (b) make the first disk-resolved estimates of Pluto's limb darkening, and (c) compositional discriminate pure from contaminated frost regions. These objectives have not been previously achievable, but are essential to understanding the surface morphology, volatile transport, and the root cause of Pluto's secular lightcurve variations. It may also be possible to detect evidence of the reported limb haze layer(s) in Pluto's atmosphere. These maps will also provide the first direct check on Pluto maps made through indirect techniques. Owing to Pluto's elliptic orbit, we expect the distribution of albedo to change (on a years-to-decade timescale) as Pluto draws away from perihelion and volatile transport proceeds. The proposed observations will document the albedo state at three rotational epochs near the time of perihelion. These maps will be obtained in two colors, by the FOC. No other astronomical instrument has sufficient resolution to accomplish these important scientific objectives.

  13. High Resolution Airborne Shallow Water Mapping

    NASA Astrophysics Data System (ADS)

    Steinbacher, F.; Pfennigbauer, M.; Aufleger, M.; Ullrich, A.

    2012-07-01

    In order to meet the requirements of the European Water Framework Directive (EU-WFD), authorities face the problem of repeatedly performing area-wide surveying of all kinds of inland waters. Especially for mid-sized or small rivers this is a considerable challenge imposing insurmountable logistical efforts and costs. It is therefore investigated if large-scale surveying of a river system on an operational basis is feasible by employing airborne hydrographic laser scanning. In cooperation with the Bavarian Water Authority (WWA Weilheim) a pilot project was initiated by the Unit of Hydraulic Engineering at the University of Innsbruck and RIEGL Laser Measurement Systems exploiting the possibilities of a new LIDAR measurement system with high spatial resolution and high measurement rate to capture about 70 km of riverbed and foreland for the river Loisach in Bavaria/Germany and the estuary and parts of the shoreline (about 40km in length) of lake Ammersee. The entire area surveyed was referenced to classic terrestrial cross-section surveys with the aim to derive products for the monitoring and managing needs of the inland water bodies forced by the EU-WFD. The survey was performed in July 2011 by helicopter and airplane and took 3 days in total. In addition, high resolution areal images were taken to provide an optical reference, offering a wide range of possibilities on further research, monitoring, and managing responsibilities. The operating altitude was about 500 m to maintain eye-safety, even for the aided eye, the airspeed was about 55 kts for the helicopter and 75 kts for the aircraft. The helicopter was used in the alpine regions while the fixed wing aircraft was used in the plains and the urban area, using appropriate scan rates to receive evenly distributed point clouds. The resulting point density ranged from 10 to 25 points per square meter. By carefully selecting days with optimum water quality, satisfactory penetration down to the river bed was achieved

  14. High resolution mapping of martian neutron albedo

    NASA Astrophysics Data System (ADS)

    Sanin, A.

    It is known from data of High Energy Neutron Detector (HEND) on Mars Odyssey that there is very large regional variation of leakage flux of epithermal neutrons on the surface of Mars. The factor of regional variations is about 10 for mapping with linear resolution of about 200-300 km. Two circumpolar depressions of epithermal neutrons emission were found above latitudes of 50 - 60, which correspond to Northern and Southern permafrost regions with very high (up to 50 wt%) content of water ice. Also, according to the HEND mapping data, there are two opposite equatorial regions Arabia Terra and Memnonia, which contain about 10 wt% of water under the top layer of dry soil with a column density of about 30 g/cm2. The surface resolution of orbital data about 300 km is determined by natural collimation of neutrons in the subsurface and in the atmosphere. For a territory larger than this size, the average content of water could be estimated by the large area approximation. In this case the comparison is performed between the average counts of neutrons over the territory and predicted counts for the planet with the same model of the entire surface. The content of water is found, as the best fitting parameter of this model. For local spots of depression with much smaller sizes this procedure underestimates the content of water. Thus, according this approximation, the spot with largest depression in the Arabia Terra at 10-12 N and 30-32 E contains at least 16 wt% of water, but in reality this value could be much larger. The content of water at this spot will be obtained with better spatial resolution by so-called inverse projection procedure. This model-dependent procedure allows to test water content for areas much smaller than the size of HEND surface resolution. The results of water content according to this procedure will be presented for the Arabia spot with the greatest depression of epithermal neutrons.

  15. Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis

    PubMed Central

    Shao, Changwei; Niu, Yongchao; Rastas, Pasi; Liu, Yang; Xie, Zhiyuan; Li, Hengde; Wang, Lei; Jiang, Yong; Tai, Shuaishuai; Tian, Yongsheng; Sakamoto, Takashi; Chen, Songlin

    2015-01-01

    High-resolution genetic maps are essential for fine mapping of complex traits, genome assembly, and comparative genomic analysis. Single-nucleotide polymorphisms (SNPs) are the primary molecular markers used for genetic map construction. In this study, we identified 13,362 SNPs evenly distributed across the Japanese flounder (Paralichthys olivaceus) genome. Of these SNPs, 12,712 high-confidence SNPs were subjected to high-throughput genotyping and assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 3,497.29 cM with an average distance of 0.47 cM between loci, thereby representing the densest genetic map currently reported for Japanese flounder. Nine positive quantitative trait loci (QTLs) forming two main clusters for Vibrio anguillarum disease resistance were detected. All QTLs could explain 5.1–8.38% of the total phenotypic variation. Synteny analysis of the QTL regions on the genome assembly revealed 12 immune-related genes, among them 4 genes strongly associated with V. anguillarum disease resistance. In addition, 246 genome assembly scaffolds with an average size of 21.79 Mb were anchored onto the LGs; these scaffolds, comprising 522.99 Mb, represented 95.78% of assembled genomic sequences. The mapped assembly scaffolds in Japanese flounder were used for genome synteny analyses against zebrafish (Danio rerio) and medaka (Oryzias latipes). Flounder and medaka were found to possess almost one-to-one synteny, whereas flounder and zebrafish exhibited a multi-syntenic correspondence. The newly developed high-resolution genetic map, which will facilitate QTL mapping, scaffold assembly, and genome synteny analysis of Japanese flounder, marks a milestone in the ongoing genome project for this species. PMID:25762582

  16. Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis.

    PubMed

    Shao, Changwei; Niu, Yongchao; Rastas, Pasi; Liu, Yang; Xie, Zhiyuan; Li, Hengde; Wang, Lei; Jiang, Yong; Tai, Shuaishuai; Tian, Yongsheng; Sakamoto, Takashi; Chen, Songlin

    2015-04-01

    High-resolution genetic maps are essential for fine mapping of complex traits, genome assembly, and comparative genomic analysis. Single-nucleotide polymorphisms (SNPs) are the primary molecular markers used for genetic map construction. In this study, we identified 13,362 SNPs evenly distributed across the Japanese flounder (Paralichthys olivaceus) genome. Of these SNPs, 12,712 high-confidence SNPs were subjected to high-throughput genotyping and assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 3,497.29 cM with an average distance of 0.47 cM between loci, thereby representing the densest genetic map currently reported for Japanese flounder. Nine positive quantitative trait loci (QTLs) forming two main clusters for Vibrio anguillarum disease resistance were detected. All QTLs could explain 5.1-8.38% of the total phenotypic variation. Synteny analysis of the QTL regions on the genome assembly revealed 12 immune-related genes, among them 4 genes strongly associated with V. anguillarum disease resistance. In addition, 246 genome assembly scaffolds with an average size of 21.79 Mb were anchored onto the LGs; these scaffolds, comprising 522.99 Mb, represented 95.78% of assembled genomic sequences. The mapped assembly scaffolds in Japanese flounder were used for genome synteny analyses against zebrafish (Danio rerio) and medaka (Oryzias latipes). Flounder and medaka were found to possess almost one-to-one synteny, whereas flounder and zebrafish exhibited a multi-syntenic correspondence. The newly developed high-resolution genetic map, which will facilitate QTL mapping, scaffold assembly, and genome synteny analysis of Japanese flounder, marks a milestone in the ongoing genome project for this species. © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  17. Updating Maps Using High Resolution Satellite Imagery

    NASA Astrophysics Data System (ADS)

    Alrajhi, Muhamad; Shahzad Janjua, Khurram; Afroz Khan, Mohammad; Alobeid, Abdalla

    2016-06-01

    Kingdom of Saudi Arabia is one of the most dynamic countries of the world. We have witnessed a very rapid urban development's which are altering Kingdom's landscape on daily basis. In recent years a substantial increase in urban populations is observed which results in the formation of large cities. Considering this fast paced growth, it has become necessary to monitor these changes, in consideration with challenges faced by aerial photography projects. It has been observed that data obtained through aerial photography has a lifecycle of 5-years because of delay caused by extreme weather conditions and dust storms which acts as hindrances or barriers during aerial imagery acquisition, which has increased the costs of aerial survey projects. All of these circumstances require that we must consider some alternatives that can provide us easy and better ways of image acquisition in short span of time for achieving reliable accuracy and cost effectiveness. The approach of this study is to conduct an extensive comparison between different resolutions of data sets which include: Orthophoto of (10 cm) GSD, Stereo images of (50 cm) GSD and Stereo images of (1 m) GSD, for map updating. Different approaches have been applied for digitizing buildings, roads, tracks, airport, roof level changes, filling stations, buildings under construction, property boundaries, mosques buildings and parking places.

  18. High resolution fire risk mapping in Italy

    NASA Astrophysics Data System (ADS)

    Fiorucci, Paolo; Biondi, Guido; Campo, Lorenzo; D'Andrea, Mirko

    2014-05-01

    extinguishing actions, leaving more resources to improve safety in areas at risk. With the availability of fire perimeters mapped over a period spanning from 5 to 10 years, depending by the region, a procedure was defined in order to assess areas at risk with high spatial resolution (900 m2) based on objective criteria by observing past fire events. The availability of fire perimeters combined with a detailed knowledge of topography and land cover allowed to understand which are the main features involved in forest fire occurrences and their behaviour. The seasonality of the fire regime was also considered, partitioning the analysis in two macro season (November- April and May- October). In addition, the total precipitation obtained from the interpolation of 30 years-long time series from 460 raingauges and the average air temperature obtained downscaling 30 years ERA-INTERIM data series were considered. About 48000 fire perimeters which burnt about 5500 km2 were considered in the analysis. The analysis has been carried out at 30 m spatial resolution. Some important considerations relating to climate and the territorial features that characterize the fire regime at national level contribute to better understand the forest fire phenomena. These results allow to define new strategies for forest fire prevention and management extensible to other geographical areas.

  19. High resolution thermal infrared mapping of Martian channels

    NASA Technical Reports Server (NTRS)

    Craddock, R. A.; Greeley, R.; Christensen, P. R.

    1987-01-01

    Viking Infrared Thermal Mapper (IRTM) high resolution (2 to 5 km) data were compiled and compared to Viking Visual Imaging Subsystem (VIS) data and available 1:5M geologic maps for several Martian channels including Dao, Harmakhis, Mangala, Shalbatana, and Simud Valles in an effort to determine the surface characteristics and the processes active during and after the formation of these channels. Results show a dominance of aeolian processes active in and around the channels. These processes have left materials thick enough to mask any genuine channel deposits. Results also indicate that very comparable Martian channels and their surrounding terrain are blanketed by deposits which are homogeneous in their thermal inertia values. However, optimum IRTM data does not cover the entire Martian surface and because local deposits of high thermal inertia material may not be large enough in areal extent or may be in an unfavorable location on the planet, a high resolution data track may not always occur over these deposits. Therefore, aeolian processes may be even more active than the IRTM data tracts can always show.

  20. Mapping Mexico's Forest Lands with Advanced Very High Resolution Radiometer

    Treesearch

    David J. Evans; Zhiliang Zhu; Susan Eggen-McIntosh; Pedro García Mayoral; Jose Luis Ornelas de Anda

    1992-01-01

    Data from the Advanced Very High Resolution Radiometer (AVHRR) were used in a program sponsored by the U.S. Department of Agriculture, Forest Service, and the United Nations Food and Agriculture Organization to help scientists from Mexico generate forest-cover maps of that country. Two near-cloud-free composite images were generated for December and March 1990 from...

  1. High-Resolution Land Use and Land Cover Mapping

    USGS Publications Warehouse

    ,

    1999-01-01

    As the Nation?s population grows, quantifying, monitoring, and managing land use becomes increasingly important. The U.S. Geological Survey (USGS) has a long heritage of leadership and innovation in land use and land cover (LULC) mapping that has been the model both nationally and internationally for over 20 years. At present, the USGS is producing high-resolution LULC data for several watershed and urban areas within the United States. This high-resolution LULC mapping is part of an ongoing USGS Land Cover Characterization Program (LCCP). The four components of the LCCP are global (1:2,000,000-scale), national (1:100,000-scale), urban (1:24,000-scale), and special projects (various scales and time periods). Within the urban and special project components, the USGS Rocky Mountain Mapping Center (RMMC) is collecting historical as well as contemporary high-resolution LULC data. RMMC?s high-resolution LULC mapping builds on the heritage and success of previous USGS LULC programs and provides LULC information to meet user requirements.

  2. High resolution data base for use with MAP

    SciTech Connect

    Tapley, W.C.; Harris, D.B.

    1987-05-05

    A high resolution cartographic data base of thw World is available from the CIA. We obtained this data, extracted portions of the data, and produced cartographic files of varying resolutions. The resulting data files are of the proper format for use with MAP (2), our in-house cartographic plotting program.

  3. Tamarisk Mapping and Monitoring Using High Resolution Satellite Imagery

    Treesearch

    Jason W. San Souci; John T. Doyle

    2006-01-01

    QuickBird high resolution multispectral satellite imagery (60 cm GSD, 4 spectral bands) and calibrated products from DigitalGlobe’s AgroWatch program were used as inputs to Visual Learning System’s Feature Analyst automated feature extraction software to map localized occurrences of pervasive and aggressive Tamarisk (Tamarix ramosissima), an invasive...

  4. Full-sky, High-resolution Maps of Interstellar Dust

    NASA Astrophysics Data System (ADS)

    Meisner, Aaron Michael

    We present full-sky, high-resolution maps of interstellar dust based on data from the Wide-field Infrared Survey Explorer (WISE) and Planck missions. We describe our custom processing of the entire WISE 12 micron All-Sky imaging data set, and present the resulting 15 arcsecond resolution, full-sky map of diffuse Galactic dust emission, free of compact sources and other contaminating artifacts. Our derived 12 micron dust map offers angular resolution far superior to that of all other existing full-sky, infrared dust emission maps, revealing a wealth of small-scale filamentary structure. We also apply the Finkbeiner et al. (1999) two-component thermal dust emission model to the Planck HFI maps. We derive full-sky 6.1 arcminute resolution maps of dust optical depth and temperature by fitting this two-component model to Planck 217-857 GHz along with DIRBE/IRAS 100 micron data. In doing so, we obtain the first ever full-sky 100-3000 GHz Planck-based thermal dust emission model, as well as a dust temperature correction with ~10 times enhanced angular resolution relative to DIRBE-based temperature maps. Analyzing the joint Planck/DIRBE dust spectrum, we show that two-component models provide a better fit to the 100-3000 GHz emission than do single-MBB models, though by a lesser margin than found by Finkbeiner et al. (1999) based on FIRAS and DIRBE. We find that, in diffuse sky regions, our two-component 100-217 GHz predictions are on average accurate to within 2.2%, while extrapolating the Planck Collaboration (2013) single-MBB model systematically underpredicts emission by 18.8% at 100 GHz, 12.6% at 143 GHz and 7.9% at 217 GHz. We calibrate our two-component optical depth to reddening, and compare with reddening estimates based on stellar spectra. We find the dominant systematic problems in our temperature/reddening maps to be zodiacal light on large angular scales and the cosmic infrared background anisotropy on small angular scales. Future work will focus on combining

  5. High-resolution mapping of motor vehicle carbon dioxide emissions

    NASA Astrophysics Data System (ADS)

    McDonald, Brian C.; McBride, Zoe C.; Martin, Elliot W.; Harley, Robert A.

    2014-05-01

    A fuel-based inventory for vehicle emissions is presented for carbon dioxide (CO2) and mapped at various spatial resolutions (10 km, 4 km, 1 km, and 500 m) using fuel sales and traffic count data. The mapping is done separately for gasoline-powered vehicles and heavy-duty diesel trucks. Emission estimates from this study are compared with the Emissions Database for Global Atmospheric Research (EDGAR) and VULCAN. All three inventories agree at the national level within 5%. EDGAR uses road density as a surrogate to apportion vehicle emissions, which leads to 20-80% overestimates of on-road CO2 emissions in the largest U.S. cities. High-resolution emission maps are presented for Los Angeles, New York City, San Francisco-San Jose, Houston, and Dallas-Fort Worth. Sharp emission gradients that exist near major highways are not apparent when emissions are mapped at 10 km resolution. High CO2 emission fluxes over highways become apparent at grid resolutions of 1 km and finer. Temporal variations in vehicle emissions are characterized using extensive day- and time-specific traffic count data and are described over diurnal, day of week, and seasonal time scales. Clear differences are observed when comparing light- and heavy-duty vehicle traffic patterns and comparing urban and rural areas. Decadal emission trends were analyzed from 2000 to 2007 when traffic volumes were increasing and a more recent period (2007-2010) when traffic volumes declined due to recession. We found large nonuniform changes in on-road CO2 emissions over a period of 5 years, highlighting the importance of timely updates to motor vehicle emission inventories.

  6. 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

    2017-08-24

    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 x DBA/2J, ILS/IbgTejJ x ISS/IbgTejJ, C57BL/6J x A/J) and chromosome substitution strain panels (C57BL/6J-Chr#, C57BL/6J-Chr#, C57BL/6J-Chr#). We genotyped all samples using the Affymetrix Mouse Diversity Array with an average inter-marker spacing of 4.3kb. 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 21kb to 8.4Mb. 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, G3: Genes, Genomes, Genetics.

  7. High Resolution Ionospheric Mapping Using Spaceborne Synthetic Aperture Radars

    NASA Astrophysics Data System (ADS)

    Meyer, F. J.; Chotoo, K.; Roth, A. P.

    2012-12-01

    properties, and (if applicable) geographic location. Three case studies will be presented to highlight the type and quality of ionospheric information that can be retrieved: (1) The high spatial resolution of SAR-derived TEC maps is emphasized in a case study that focuses on high resolution mapping of aurora arcs in central Alaska. Here, TEC enhancements associated with aurora activity are mapped and compared to reference observations from sky cameras and GPS; (2) observations of mid-latitudal traveling ionospheric disturbances are shown to showcase the accuracy of SAR-derived TEC maps. Several SAR-based TEC mapping methods are compared to highlight their respective advantages and disadvantages regarding processing complexity and estimation accuracy; (3) a third example focuses on analyzing post-sunset scintillation phenomena in equatorial regions. SAR is used to assess the frequency of occurrence of scintillation and analyze their associated power spectra. To conclude the paper, the temporal and spatial sampling of the ionosphere provided by the fleet of current and future spaceborne SAR sensors is analyzed to provide an assessment of the global ionospheric mapping capabilities of SAR.

  8. Clickstream Data Yields High-Resolution Maps of Science

    PubMed Central

    Bollen, Johan; Van de Sompel, Herbert; Rodriguez, Marko A.; Balakireva, Lyudmila

    2009-01-01

    Background Intricate maps of science have been created from citation data to visualize the structure of scientific activity. However, most scientific publications are now accessed online. Scholarly web portals record detailed log data at a scale that exceeds the number of all existing citations combined. Such log data is recorded immediately upon publication and keeps track of the sequences of user requests (clickstreams) that are issued by a variety of users across many different domains. Given these advantages of log datasets over citation data, we investigate whether they can produce high-resolution, more current maps of science. Methodology Over the course of 2007 and 2008, we collected nearly 1 billion user interactions recorded by the scholarly web portals of some of the most significant publishers, aggregators and institutional consortia. The resulting reference data set covers a significant part of world-wide use of scholarly web portals in 2006, and provides a balanced coverage of the humanities, social sciences, and natural sciences. A journal clickstream model, i.e. a first-order Markov chain, was extracted from the sequences of user interactions in the logs. The clickstream model was validated by comparing it to the Getty Research Institute's Architecture and Art Thesaurus. The resulting model was visualized as a journal network that outlines the relationships between various scientific domains and clarifies the connection of the social sciences and humanities to the natural sciences. Conclusions Maps of science resulting from large-scale clickstream data provide a detailed, contemporary view of scientific activity and correct the underrepresentation of the social sciences and humanities that is commonly found in citation data. PMID:19277205

  9. Clickstream data yields high-resolution maps of science

    SciTech Connect

    Bollen, Johan; Van De Sompel, Herbert; Hagberg, Aric; Bettencourt, Luis; Chute, Ryan; Rodriguez, Marko A; Balakireva, Lyudmila

    2009-01-01

    Intricate maps of science have been created from citation data to visualize the structure of scientific activity. However, most scientific publications are now accessed online. Scholarly web portals record detailed log data at a scale that exceeds the number of all existing citations combined. Such log data is recorded immediately upon publication and keeps track of the sequences of user requests (clickstreams) that are issued by a variety of users across many different domains. Given these advantagees of log datasets over citation data, we investigate whether they can produce high-resolution, more current maps of science.

  10. High resolution map of light pollution over Poland

    NASA Astrophysics Data System (ADS)

    Netzel, Henryka; Netzel, Paweł

    2016-09-01

    In 1976 Berry introduced a simple mathematical equation to calculate artificial night sky brightness at zenith. In the original model cities, considered as points with given population, are only sources of light emission. In contrary to Berry's model, we assumed that all terrain surface can be a source of light. Emission of light depends on percent of built up area in a given cell. We based on Berry's model. Using field measurements and high-resolution data we obtained the map of night sky brightness over Poland in 100-m resolution. High resolution input data, combined with a very simple model, makes it possible to obtain detailed structures of the night sky brightness without complicating the calculations.

  11. Mapping Crop Yield and Sow Date Using High Resolution Imagery

    NASA Astrophysics Data System (ADS)

    Royal, K.

    2015-12-01

    Keitasha Royal, Meha Jain, Ph.D., David Lobell, Ph.D Mapping Crop Yield and Sow Date Using High Resolution ImageryThe use of satellite imagery in agriculture is becoming increasingly more significant and valuable. Due to the emergence of new satellites, such as Skybox, these satellites provide higher resolution imagery (e.g 1m) therefore improving the ability to map smallholder agriculture. For the smallholder farm dominated area of northern India, Skybox high-resolution satellite imagery can aid in understanding how to improve farm yields. In particular, we are interested in mapping winter wheat in India, as this region produces approximately 80% of the country's wheat crop, which is important given that wheat is a staple crop that provides approximately 20% of household calories. In northeast India, the combination of increased heat stress, limited irrigation access, and the difficulty for farmers to access advanced farming technologies results in farmers only producing about 50% of their potential crop yield. The use of satellite imagery can aid in understanding wheat yields through time and help identify ways to increase crop yields in the wheat belt of India. To translate Skybox satellite data into meaningful information about wheat fields, we examine vegetation indices, such as the normalized difference vegetation index (NDVI), to measure the "greenness" of plants to help determine the health of the crops. We test our ability to predict crop characteristics, like sow date and yield, using vegetation indices of 59 fields for which we have field data in Bihar, India.

  12. High resolution physical mapping of single gene fragments on pachytene chromosome 4 and 7 of Rosa.

    PubMed

    Kirov, Ilya V; Van Laere, Katrijn; Khrustaleva, Ludmila I

    2015-07-02

    Rosaceae is a family containing many economically important fruit and ornamental species. Although fluorescence in situ hybridization (FISH)-based physical mapping of plant genomes is a valuable tool for map-based cloning, comparative genomics and evolutionary studies, no studies using high resolution physical mapping have been performed in this family. Previously we proved that physical mapping of single-copy genes as small as 1.1 kb is possible on mitotic metaphase chromosomes of Rosa wichurana using Tyramide-FISH. In this study we aimed to further improve the physical map of Rosa wichurana by applying high resolution FISH to pachytene chromosomes. Using high resolution Tyramide-FISH and multicolor Tyramide-FISH, 7 genes (1.7-3 kb) were successfully mapped on pachytene chromosomes 4 and 7 of Rosa wichurana. Additionally, by using multicolor Tyramide-FISH three closely located genes were simultaneously visualized on chromosome 7. A detailed map of heterochromatine/euchromatine patterns of chromosome 4 and 7 was developed with indication of the physical position of these 7 genes. Comparison of the gene order between Rosa wichurana and Fragaria vesca revealed a poor collinearity for chromosome 7, but a perfect collinearity for chromosome 4. High resolution physical mapping of short probes on pachytene chromosomes of Rosa wichurana was successfully performed for the first time. Application of Tyramide-FISH on pachytene chromosomes allowed the mapping resolution to be increased up to 20 times compared to mitotic metaphase chromosomes. High resolution Tyramide-FISH and multicolor Tyramide-FISH might become useful tools for further physical mapping of single-copy genes and for the integration of physical and genetic maps of Rosa wichurana and other members of the Rosaceae.

  13. High-Resolution Underwater Mapping Using Side-Scan Sonar

    PubMed Central

    2016-01-01

    The goal of this study is to generate high-resolution sea floor maps using a Side-Scan Sonar(SSS). This is achieved by explicitly taking into account the SSS operation as follows. First, the raw sensor data is corrected by means of a physics-based SSS model. Second, the data is projected to the sea-floor. The errors involved in this projection are thoroughfully analysed. Third, a probabilistic SSS model is defined and used to estimate the probability of each sea-floor region to be observed. This probabilistic information is then used to weight the contribution of each SSS measurement to the map. Because of these models, arbitrary map resolutions can be achieved, even beyond the sensor resolution. Finally, a geometric map building method is presented and combined with the probabilistic approach. The resulting map is composed of two layers. The echo intensity layer holds the most likely echo intensities at each point in the sea-floor. The probabilistic layer contains information about how confident can the user or the higher control layers be about the echo intensity layer data. Experimental results have been conducted in a large subsea region. PMID:26821379

  14. High-Resolution Underwater Mapping Using Side-Scan Sonar.

    PubMed

    Burguera, Antoni; Oliver, Gabriel

    2016-01-01

    The goal of this study is to generate high-resolution sea floor maps using a Side-Scan Sonar(SSS). This is achieved by explicitly taking into account the SSS operation as follows. First, the raw sensor data is corrected by means of a physics-based SSS model. Second, the data is projected to the sea-floor. The errors involved in this projection are thoroughfully analysed. Third, a probabilistic SSS model is defined and used to estimate the probability of each sea-floor region to be observed. This probabilistic information is then used to weight the contribution of each SSS measurement to the map. Because of these models, arbitrary map resolutions can be achieved, even beyond the sensor resolution. Finally, a geometric map building method is presented and combined with the probabilistic approach. The resulting map is composed of two layers. The echo intensity layer holds the most likely echo intensities at each point in the sea-floor. The probabilistic layer contains information about how confident can the user or the higher control layers be about the echo intensity layer data. Experimental results have been conducted in a large subsea region.

  15. Spatial-temperature high resolution map for early cancer diagnosis

    NASA Astrophysics Data System (ADS)

    Gavriloaia, Gheorghe V.; Hurduc, Anca; Ghimigean, Ana-Maria; Fumarel, Radu

    2009-02-01

    Heat is one of the most important parameters of living beings. Skin temperature is not the same on the entire body and so, a thermal signature can be got. Infrared map on serial imaging can constitute an early sign of an abnormality. Thermography detects changes in tissue that appear before and accompany many diseases including cancer. As this map has a better resolution an early cancer diagnosis can be done. The temperature of neoplasic tissue is different up to 1.5 °C than that of the healthy tissue as a result of the specific metabolic rate. The infrared camera images show very quickly the heat transferred by radiation. A lot of factors disturb the temperature conversion to pixel intensity. A sensitive temperature sensor with a 10 Mpixels video camera, showing its spatial position, and a computer fusion program were used for the map with high spatial-temperature resolution. A couple of minutes are necessary to get a high resolution map. The asymmetry and borders were the main parameters analyzed. The right cancer diagnosis was for about 78.4% of patients with thyroid cancer, and more than 89.6% from patients with breast cancer. In the near future, the medical prognosis will be improved by fractal analysis.

  16. Mars 1:500k high resolution map bases

    NASA Astrophysics Data System (ADS)

    Lee, E. M.; Edwards, K.; Grecu, A.; Redding, B.; Wasserman, A.; Bennett, A.

    1997-03-01

    The Mars 1:500k map bases are high-resolution black and white digital photomosaics generated to support the Mars Geologic Mapping Program. The Viking Orbiter images are used to map areas of scientific interest. The final products provided to the mapper include a cutline plot indicating image location and resolution, digital files, and a package consisting of a brownline, cronapaque, cronaflex, ozalid, and continuous tone photographic print. The mosaics are compiled by digital methods. The Planetary Imaging Cartography System (PICS) software, developed by the U.S. Geological Survey, was used to process the digital mosaics. The Integrated Software for Imaging Spectrometers (ISIS) software within the UNIX environment will be used starting this year to replace PICS. Currently, ISIS runs on SUN and Alpha platforms. The images are processed through reseau mark, and systematic and random noise artifact removal, radiometric correction, geometric control, and tone matching, to produce an even-toned controlled photomosaic. The maps are geometrically controlled to the Mars Digital Image Model and mosaicked at a resolution of 1024 pixels/deg or 58 m/pixel.

  17. EMODnet High Resolution Seabed Mapping - further developing a high resolution digital bathymetry for European seas

    NASA Astrophysics Data System (ADS)

    Schaap, Dick M. A.; Schmitt, Thierry

    2017-04-01

    Access to marine data is a key issue for the EU Marine Strategy Framework Directive and the EU Marine Knowledge 2020 agenda and includes the European Marine Observation and Data Network (EMODnet) initiative. EMODnet aims at assembling European marine data, data products and metadata from diverse sources in a uniform way. The EMODnet data infrastructure is developed through a stepwise approach in three major phases. Currently EMODnet is entering its 3rd phase with operational portals providing access to marine data for bathymetry, geology, physics, chemistry, biology, seabed habitats and human activities, complemented by checkpoint projects, analysing the fitness for purpose of data provision. The EMODnet Bathymetry project has developed Digital Terrain Models (DTM) for the European seas. These have been produced from survey and aggregated data sets that are indexed with metadata by adopting the SeaDataNet Catalogue services. SeaDataNet is a network of major oceanographic data centres around the European seas that manage, operate and further develop a pan-European infrastructure for marine and ocean data management. The latest EMODnet Bathymetry DTM release has a resolution of 1/8 arcminute * 1/8 arcminute and covers all European sea regions. Use has been made of circa 7800 gathered survey datasets and composite DTMs from 27 European data providers from 15 countries. For areas without coverage use has been made of the latest GEBCO DTM. The catalogue services and the generated EMODnet DTM have been published at the dedicated EMODnet Bathymetry portal which includes a versatile DTM viewing service that also supports downloading in various formats. End December 2016 the Bathymetry project has been succeeded by EMODnet High Resolution Seabed Mapping (HRSM) as part of the third phase of EMODnet. This new project will continue gathering of bathymetric in-situ data sets with extra efforts for near coastal waters and coastal zones. In addition Satellite Derived Bathymetry

  18. High-resolution mapping of bifurcations in nonlinear biochemical circuits

    NASA Astrophysics Data System (ADS)

    Genot, A. J.; Baccouche, A.; Sieskind, R.; Aubert-Kato, N.; Bredeche, N.; Bartolo, J. F.; Taly, V.; Fujii, T.; Rondelez, Y.

    2016-08-01

    Analog molecular circuits can exploit the nonlinear nature of biochemical reaction networks to compute low-precision outputs with fewer resources than digital circuits. This analog computation is similar to that employed by gene-regulation networks. Although digital systems have a tractable link between structure and function, the nonlinear and continuous nature of analog circuits yields an intricate functional landscape, which makes their design counter-intuitive, their characterization laborious and their analysis delicate. Here, using droplet-based microfluidics, we map with high resolution and dimensionality the bifurcation diagrams of two synthetic, out-of-equilibrium and nonlinear programs: a bistable DNA switch and a predator-prey DNA oscillator. The diagrams delineate where function is optimal, dynamics bifurcates and models fail. Inverse problem solving on these large-scale data sets indicates interference from enzymatic coupling. Additionally, data mining exposes the presence of rare, stochastically bursting oscillators near deterministic bifurcations.

  19. High Resolution Mapping of Protein Sequence–Function Relationships

    PubMed Central

    Fowler, Douglas M.; Araya, Carlos L.; Fleishman, Sarel J.; Kellogg, Elizabeth H.; Stephany, Jason J.; Baker, David; Fields, Stanley

    2010-01-01

    We present a large-scale approach to investigate the functional consequences of sequence variation in a protein. The approach entails the display of hundreds of thousands of protein variants, moderate selection for activity, and high throughput DNA sequencing to quantify the performance of each variant. Using this strategy, we tracked the performance of >600,000 variants of a human WW domain after three and six rounds of selection by phage display for binding to its peptide ligand. Binding properties of these variants defined a high-resolution map of mutational preference across the WW domain; each position possessed unique features that could not be captured by a few representative mutations. Our approach could be applied to many in vitro or in vivo protein assays, providing a general means for understanding how protein function relates to sequence. PMID:20711194

  20. The high resolution mapping of the Venice Lagoon tidal network

    NASA Astrophysics Data System (ADS)

    Madricardo, Fantina; Foglini, Federica; Kruss, Aleksandra; Bellafiore, Debora; Trincardi, Fabio

    2017-04-01

    One of the biggest challenges of the direct observation of the ocean is to achieve a high resolution mapping of its seafloor morphology and benthic habitats. So far, sonars have mapped just 0.05% of the ocean floor with less than ten-meter resolution. The recent efforts of the scientific community have been devoted towards the mapping of both Deep Ocean and very shallow coastal areas. Coastal and transitional environments in particular undergo strong morphological changes due to natural and anthropogenic pressure. Nowadays, only about 5% of the seafloor of these environments † have been mapped: the shallowness of these environments has prevented the use of underwater acoustics to reveal their morphological features. The recent technological development of multibeam echosounder systems, however, enables these instruments to achieve very high performances also in such shallow environments. In this work, we present results and case studies of an extensive multibeam survey carried out in the Lagoon of Venice in 2013. The Lagoon of Venice is the biggest lagoon in the Mediterranean Sea with a surface of about 550 km2 and with an average depth of about 1 m. In the last century, the morphological and ecological properties of the lagoon changed dramatically: the surface of the salt marshes was reduced by 60% and some parts of the lagoon are deepening with a net sediment flux exiting from the inlets. Moreover, major engineering interventions are currently ongoing at the inlets (MOSE project). These changes at the inlets could affect substantially the lagoon environment. To understand and monitor the future evolution of the Lagoon of Venice, ISMAR within the project RITMARE (a National Research Programme funded by the Italian Ministry of University and Research) carried out an extensive survey, involving a team of more than 25 scientists, to collect high resolution (0.5 m) bathymetry of key study areas such as the tidal inlets and channels. Following a broad

  1. Exploring for subtle traps with high-resolution paleogeographic maps

    SciTech Connect

    Bulling, T.B.; Breyer, J.A.

    1988-01-01

    High-resolution paleogeographic maps depicting the depositional history of the Reklaw 1 interval provide a basis for prospecting for subtle traps in the updip Reklaw trend in south Texas. The Reklaw 1 interval began with sand being carried southwest by longshore currents to form the barrier bar that forms the reservoir in Atkinson field. The hydrocarbons are trapped by the updip pinch-out of barrier-bar sand into lagoonal mud. Stratigraphic traps similar to Atkinson field could be present along depositional strike if the sand in the field were part of a more extensive-bar system. After the barrier bar formed, distributary-mouth bars prograded seaward depositing the bar-finger sands that are the reservoirs in Hysaw and Flax fields. Subtle structural traps could be present where small down-to-the-north faults associated with the Sample fault system cut the bar-finger sands downdip from the established production. Farther down paleoslope, the distributary channels began to bifurcate and the distributary-mouth bar coalesced to form a broad delt-front sheet sand. Burnell, Hondo Creek, and Runge West fields produce from this sheet sand near the unstable shelf margin. A rapid rise in relative sea level terminated deposition of the Reklaw 1 interval. Many of the oil and gas fields remaining to be discovered in the United States are in mature petroleum provinces where much of the remaining oil and gas probably resides in subtle traps. High-resolution paleogeographic maps may be a key to finding these subtle traps.

  2. Mapping detailed 3D information onto high resolution SAR signatures

    NASA Astrophysics Data System (ADS)

    Anglberger, H.; Speck, R.

    2017-05-01

    Due to challenges in the visual interpretation of radar signatures or in the subsequent information extraction, a fusion with other data sources can be beneficial. The most accurate basis for a fusion of any kind of remote sensing data is the mapping of the acquired 2D image space onto the true 3D geometry of the scenery. In the case of radar images this is a challenging task because the coordinate system is based on the measured range which causes ambiguous regions due to layover effects. This paper describes a method that accurately maps the detailed 3D information of a scene to the slantrange-based coordinate system of imaging radars. Due to this mapping all the contributing geometrical parts of one resolution cell can be determined in 3D space. The proposed method is highly efficient, because computationally expensive operations can be directly performed on graphics card hardware. The described approach builds a perfect basis for sophisticated methods to extract data from multiple complimentary sensors like from radar and optical images, especially because true 3D information from whole cities will be available in the near future. The performance of the developed methods will be demonstrated with high resolution radar data acquired by the space-borne SAR-sensor TerraSAR-X.

  3. Application of laser microdissection ICP-MS for high resolution elemental mapping in mouse brain tissue: a comparative study with laser ablation ICP-MS.

    PubMed

    Sussulini, Alessandra; Becker, J Sabine

    2015-01-01

    Mapping of elements in biological tissue by laser induced mass spectrometry is a fast growing analytical methodology in life sciences. This method provides a multitude of useful information of metal, nonmetal, metalloid and isotopic distribution at major, minor and trace concentration ranges, usually with a lateral resolution of 12-160 µm. Selected applications in medical research require an improved lateral resolution of laser induced mass spectrometric technique at the low micrometre scale and below. The present work demonstrates the applicability of a recently developed analytical methodology - laser microdissection associated to inductively coupled plasma mass spectrometry (LMD ICP-MS) - to obtain elemental images of different solid biological samples at high lateral resolution. LMD ICP-MS images of mouse brain tissue samples stained with uranium and native are shown, and a direct comparison of LMD and laser ablation (LA) ICP-MS imaging methodologies, in terms of elemental quantification, is performed. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. Construction of high-resolution recombination maps in Asian seabass.

    PubMed

    Wang, Le; Bai, Bin; Liu, Peng; Huang, Shu Qing; Wan, Zi Yi; Chua, Elaine; Ye, Baoqing; Yue, Gen Hua

    2017-01-10

    A high-density genetic map is essential for de novo genome assembly, fine mapping QTL for important complex traits, comparative genomic studies and understanding the mechanisms of genome evolution. Although a number of genomic resources are available in Asian seabass (Lates calcarifer), a high-density linkage map is still lacking. To facilitate QTL mapping for marker-assisted selection and genome assembly, and to understand the genome-wide recombination rates, we constructed high density linkage maps using three families and genotyping by sequencing. A high-density consensus linkage map consisting of 8, 274 markers was constructed based on sex-averaged genetic maps. The genetic maps were then aligned and integrated with the current genome assembly of Asian seabass. More than 90% of the genome contig sequences were anchored onto the consensus genetic map. Evidence of assembly errors in the current genome assembly was identified. A fragment of up to 2.5 Mb belonging to LG14 was assembled into Chr15. The length of family-specific sex-averaged maps ranged from 1348.96 to 1624.65 cM. Female maps were slightly longer than male maps using common markers. Female-to-male ratios were highly variable both across chromosomes within each family and throughout three families for each chromosome. However, the distribution patterns of recombination along chromosomes were similar between sexes across the whole genome. The overall recombination rates were significantly correlated with genome-wide GC content and the correlations were revealed to be stronger in females than in males. These high-density genetic maps provide not only essential tools for facilitating de novo genome assembly and comparative genomic studies in teleosts, but also critical resources for fine mapping QTL and genome-wide association mapping for economically important traits in Asian seabass.

  5. High-Resolution Geologic Mapping in the Eastern Manus Basin

    NASA Astrophysics Data System (ADS)

    Thal, J.; Bach, W.; Tivey, M.; Yoerger, D. R.

    2011-12-01

    AUV-based microbathymetry combined with ROV video data was used to create the first high-resolution geologic maps of two hydrothermal active areas in the eastern Manus Basin: North Su volcano and PACManus hydrothermal field on Pual Ridge. The data were recorded in 2006 and 2011 during the research cruises Magellan-06 operated by the Woods Hole Oceanographic Institution and BAMBUS (SO-216) operated by MARUM / University Bremen. High accuracy underwater navigation transponder-based and Posidonia systems allowed us to combine video data with bathymetry. The navigation on both cruises was very precise (m-scale) and navigation offsets were less than 10 m. We conducted detailed geologic mapping and sampling to identify the seafloor volcanic and hydrothermal features and created highly detailed maps that provide a comprehensive picture of the seafloor and vent distribution in the eastern Manus Basin. Several different types of dacite lava morphology were mapped, including pillow lava, lobate flows and massive block lava. We have compiled all available information on rock chemistry, fluid and temperature measurements, video data, bathymetry and navigation data into a GIS database. We find that, in contrast to the tectonic control on vent distribution at slow spreading mid-ocean ridges, the pathways of upwelling hydrothermal vent fluids at PACManus are dominated by volcanic features, such as lava domes and thick, massive block lava flows. Vent fields are developed preferentially along the margins of major flow units, probably because the cores of these units are impermeable to fluid flow, while the autobrecciated outer parts of the flows are not. In the North Su area, a comparison of seafloor maps from 2006 and 2011 reveals recent volcanic activity, which has strongly modified the bathymetry and hydrothermal vent distribution on the southern flank of the volcano. An ash cone with multiple small craters on the SW flank of the North-Su volcano that didn't exist in 2006 was

  6. High resolution mapping of flood hazard for South Korea

    NASA Astrophysics Data System (ADS)

    Ghosh, Sourima; Nzerem, Kechi; Zovi, Francesco; Li, Shuangcai; Mei, Yi; Assteerawatt, Anongnart; Hilberts, Arno; Tillmanns, Stephan; Mitas, Christos

    2015-04-01

    Floods are one of primary natural hazards that affect South Korea. During the past 15 years, catastrophic flood events which mainly have occurred during the rainy and typhoon seasons - especially under condition where soils are already saturated, have triggered substantial property damage with an average annual loss of around US1.2 billion (determined from WAter Management Information System's flood damage database for years 2002-2011) in South Korea. According to Seoul Metropolitan Government, over 16,000 households in the capital city Seoul were inundated during 2010 flood events. More than 10,000 households in Seoul were apparently flooded during one major flood event due to torrential rain in July 2011. Recently in August 2014, a serious flood event due to heavy rainfall hit the Busan region in the south east of South Korea. Addressing the growing needs, RMS has recently released country-wide high resolution combined flood return period maps for post-drainage local "pluvial" inundation and undefended large-scale "fluvial" inundation to aid the government and the insurance industry in the evaluation of comprehensive flood risk. RMS has developed a flood hazard model for South Korea to generate inundation depths and extents for a range of flood return periods. The model is initiated with 30 years of historical meteorological forcing data and calibrated to daily observations at over 100 river gauges across the country. Simulations of hydrologic processes are subsequently performed based on a 2000 year set of stochastic forcing. Floodplain inundation processes are modelled by numerically solving the shallow water equations using finite volume method on GPUs. Taking into account the existing stormwater drainage standards, economic exposure densities, etc., reasonable flood maps are created from inundation model output. Final hazard maps at one arcsec grid resolution can be the basis for both evaluating and managing flood risk, its economic impacts, and insured flood

  7. A high-resolution map of transcriptional repression

    PubMed Central

    Liang, Ziwei; Brown, Karen E; Carroll, Thomas; Taylor, Benjamin; Vidal, Isabel Ferreirós; Hendrich, Brian; Rueda, David; Fisher, Amanda G; Merkenschlager, Matthias

    2017-01-01

    Turning genes on and off is essential for development and homeostasis, yet little is known about the sequence and causal role of chromatin state changes during the repression of active genes. This is surprising, as defective gene silencing underlies developmental abnormalities and disease. Here we delineate the sequence and functional contribution of transcriptional repression mechanisms at high temporal resolution. Inducible entry of the NuRD-interacting transcriptional regulator Ikaros into mouse pre-B cell nuclei triggered immediate binding to target gene promoters. Rapid RNAP2 eviction, transcriptional shutdown, nucleosome invasion, and reduced transcriptional activator binding required chromatin remodeling by NuRD-associated Mi2beta/CHD4, but were independent of HDAC activity. Histone deacetylation occurred after transcriptional repression. Nevertheless, HDAC activity contributed to stable gene silencing. Hence, high resolution mapping of transcriptional repression reveals complex and interdependent mechanisms that underpin rapid transitions between transcriptional states, and elucidates the temporal order, functional role and mechanistic separation of NuRD-associated enzymatic activities. DOI: http://dx.doi.org/10.7554/eLife.22767.001 PMID:28318487

  8. Towards a Global High Resolution Peatland Map in 2020

    NASA Astrophysics Data System (ADS)

    Barthelmes, Alexandra; Barthelmes, Karen-Doreen; Joosten, Hans; Dommain, Rene; Margalef, Olga

    2015-04-01

    Some 3% of land area on planet Earth (approx. 4 million km2) is covered by peatlands. About 10% (~ 0.3 % of the land area) are drained and responsible for a disproportional 5 % of the global anthropogenic CO2 emissions (Victoria et al., 2012). Additionally, peatland drainage and degradation lead to land subsidence, soil degradation, water pollution, and enhanced susceptibility to fire (Holden et al., 2004; Joosten et al., 2012). The global importance of peatlands for carbon storage and climate change mitigation has currently been recognized in international policy - since 2008 organic soils are subject of discussion in the UN Framework Convention on Climate Change (UNFCCC) (Joosten, 2011). In May 2013 the European Parliament decided that the global post 2020 climate agreement should include the obligation to report emissions and removals from peatland drainage and rewetting. Implementation of such program, however, necessitates the rapid availability of reliable, comprehensive, high resolution, spatially explicit data on the extent and status of peatlands. For many reporting countries this requires an innovation in peatland mapping, i.e. the better and integrative use of novel, but already available methods and technologies. We developed an approach that links various science networks, methodologies and data bases, including those of peatland/landscape ecology for understanding where and how peatlands may occur, those of remote sensing for identifying possible locations, and those of pedology (legacy soil maps) and (palaeo-)ecology for ground truthing. Such integration of old field data, specialized knowledge, and modern RS and GIS technologies enables acquiring a rapid, comprehensive, detailed and rather reliable overview, even on a continental scale. We illustrate this approach with a high resolution overview of peatland distribution, area, status and greenhouse gas fluxes e.g. for the East African countries Rwanda, Burundi, Uganda and Zambia. Furthermore, we

  9. Towards a Global High Resolution Peatland Map in 2020

    NASA Astrophysics Data System (ADS)

    Barthelmes, Alexandra; Barthelmes, Karen-Doreen; Dommain, Rene; Margalef, Olga; Joosten, Hans

    2014-05-01

    Some 3% of land area on planet Earth (approx. 4 million km2) is covered by peatlands. About 10% (~ 0.3 % of the land area) are drained and responsible for a disproportional 5 % of the global anthropogenic CO2 emissions (Victoria et al., 2012). Additionally, peatland drainage and degradation lead to land subsidence, soil degradation, water pollution, and enhanced susceptibility to fire (Holden et al., 2004; Joosten et al., 2012). The global importance of peatlands for carbon storage and climate change mitigation has only recently been recognized in international policy - only since 2008 organic soils are subject of discussion in the UN Framework Convention on Climate Change (UNFCCC) (Joosten, 2011). In May 2013 the European Parliament decided that the global post 2020 climate agreement should include the obligation to report emissions and removals from peatland drainage and rewetting. Implementation of such program, however, necessitates the rapid availability of reliable, comprehensive, high resolution, spatially explicit data on the extent and status of peatlands. For many reporting countries this requires an innovation in peatland mapping, i.e. the better and integrative use of novel, but already available methods and technologies. We developed an approach that links various science networks, methodologies and data bases, including those of peatland/landscape ecology for understanding where and how peatlands may occur, those of remote sensing for identifying possible locations, and those of pedology (legacy soil maps) and (palaeo-)ecology for ground truthing. Such integration of old field data, specialized knowledge, and modern RS and GIS technologies enables acquiring a rapid, comprehensive, detailed and rather reliable overview, even on a continental scale. We illustrate this approach with a high resolution overview of peatland distribution, area, status and greenhouse gas fluxes for East Africa (including the Horn of Africa, the African Great Lakes region and

  10. Visualizing sediment dynamics through repeated high-resolution multibeam mapping

    NASA Astrophysics Data System (ADS)

    de Vries, J. J.; Greinert, J.; Maierhofer, T.

    2013-12-01

    abundance of smaller ripples and different net-transport rates of sediment into the Wadden Sea. Vertical stratification in the Marsdiep is determined by salinity with stronger vertical stratification in winter time. The Texelstroom channel is ebb-dominant with an outflow over the entire water column. However, during more vertically stratified conditions, the residual circulation is smaller at the bottom because the outflow at the surface is balanced at the bottom resulting in more symmetrical sand waves in summer. The repeated high-resolution multibeam surveys shed light on the highly dynamic seasonal behavior of sand waves in the Texelstroom channel and corroborates the high value of repeated multibeam surveys to visualize these dynamics.

  11. With high resolution DEM to enhanced maps of Dominant Runoff Processes (DRP)

    NASA Astrophysics Data System (ADS)

    Margreth, Michael; Naef, Felix

    2010-05-01

    . Erosion ditches indicate the generation of quick SOF, caused by limited soil depth. In 20 catchments of different sizes, with different topography and different geology, the automatically derived DRP maps were compared with manually developed ones. In 80% to 99%, the automatically derived DRP areas match the manually developed ones or differ by 1 step in process intensity. As this method allows the derivation of enhanced DRP maps in high resolution, the DRP maps can also be used to forecast the runoff reaction of small catchments.

  12. High Resolution Velocity Map Imaging Photoelectron Spectroscopy of the Beryllium Oxide Anion, BeO-

    NASA Astrophysics Data System (ADS)

    Dermer, Amanda Reed; Mascaritolo, Kyle; Heaven, Michael

    2016-06-01

    The photodetachment spectrum of BeO- has been studied using high resolution velocity map imaging photoelectron spectroscopy. The vibrational contours were imaged and compared with Franck-Condon simulations for the ground and excited states of the neutral. The electron affinity of BeO was measured for the first time, and anisotropies of several transitions were determined. Experimental findings are compared to high level ab initio calculations.

  13. Remotely sensed high resolution irrigated area mapping in India for 2000 to 2015

    PubMed Central

    Ambika, Anukesh Krishnankutty; Wardlow, Brian; Mishra, Vimal

    2016-01-01

    India is among the countries that uses a significant fraction of available water for irrigation. Irrigated area in India has increased substantially after the Green revolution and both surface and groundwater have been extensively used. Under warming climate projections, irrigation frequency may increase leading to increased irrigation water demands. Water resources planning and management in agriculture need spatially-explicit irrigated area information for different crops and different crop growing seasons. However, annual, high-resolution irrigated area maps for India for an extended historical record that can be used for water resources planning and management are unavailable. Using 250 m normalized difference vegetation index (NDVI) data from Moderate Resolution Imaging Spectroradiometer (MODIS) and 56 m land use/land cover data, high-resolution irrigated area maps are developed for all the agroecological zones in India for the period of 2000–2015. The irrigated area maps were evaluated using the agricultural statistics data from ground surveys and were compared with the previously developed irrigation maps. High resolution (250 m) irrigated area maps showed satisfactory accuracy (R2=0.95) and can be used to understand interannual variability in irrigated area at various spatial scales. PMID:27996974

  14. Remotely sensed high resolution irrigated area mapping in India for 2000 to 2015

    NASA Astrophysics Data System (ADS)

    Ambika, Anukesh Krishnankutty; Wardlow, Brian; Mishra, Vimal

    2016-12-01

    India is among the countries that uses a significant fraction of available water for irrigation. Irrigated area in India has increased substantially after the Green revolution and both surface and groundwater have been extensively used. Under warming climate projections, irrigation frequency may increase leading to increased irrigation water demands. Water resources planning and management in agriculture need spatially-explicit irrigated area information for different crops and different crop growing seasons. However, annual, high-resolution irrigated area maps for India for an extended historical record that can be used for water resources planning and management are unavailable. Using 250 m normalized difference vegetation index (NDVI) data from Moderate Resolution Imaging Spectroradiometer (MODIS) and 56 m land use/land cover data, high-resolution irrigated area maps are developed for all the agroecological zones in India for the period of 2000-2015. The irrigated area maps were evaluated using the agricultural statistics data from ground surveys and were compared with the previously developed irrigation maps. High resolution (250 m) irrigated area maps showed satisfactory accuracy (R2=0.95) and can be used to understand interannual variability in irrigated area at various spatial scales.

  15. High-Resolution Cryo-EM Maps and Models: A Crystallographer's Perspective.

    PubMed

    Wlodawer, Alexander; Li, Mi; Dauter, Zbigniew

    2017-08-10

    The appearance of ten high-resolution cryoelectron microscopy (cryo-EM) maps of proteins, ribosomes, and viruses was compared with the experimentally phased crystallographic electron density maps of four proteins. We found that maps calculated at a similar resolution by the two techniques are quite comparable in their appearance, although cryo-EM maps, even when sharpened, seem to be a little less detailed. An analysis of models fitted to the cryo-EM maps indicated the presence of significant problems in almost all of them, including incorrect geometry, clashes between atoms, and discrepancies between the map density and the fitted models. In particular, the treatment of the atomic displacement (B) factors was meaningless in almost all analyzed cryo-EM models. Stricter cryo-EM structure deposition standards and their better enforcement are needed. Published by Elsevier Ltd.

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

    NASA Astrophysics Data System (ADS)

    Juvela, M.; Montillaud, J.

    2013-09-01

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

  17. High resolution digital soil mapping as a future instrument for developing sustainable landuse strategies

    NASA Astrophysics Data System (ADS)

    Gries, Philipp; Funke, Lisa-Marie; Baumann, Frank; Schmidt, Karsten; Behrens, Thorsten; Scholten, Thomas

    2016-04-01

    Climate change, increase in population and intensification of land use pose a great challenge for sustainable handling of soils. Intelligent landuse systems are able to minimize and/or avoid soil erosion and loss of soil fertility. A successful application of such systems requires area-wide soil information with high resolution. Containing three consecutive steps, the project INE-2-H („innovative sustainable landuse") at the University of Tuebingen is about creating high-resolution soil information using Digital Soil Mapping (DSM) techniques to develop sustainable landuse strategies. Input data includes soil data from fieldwork (texture and carbon content), the official digital soil and geological map (1:50.000) as well as a wide selection of local, complex and combined terrain parameters. First, soil maps have been created using the DSM approach and Random Forest (RF). Due to high resolution (10x10 m pixels), those maps show a more detailed spatial variability of soil information compared to the official maps used. Root mean square errors (RMSE) of the modelled maps vary from 2.11 % to 6.87 % and the coefficients of determination (R²) go from 0.42 to 0.68. Second, soil erosion potentials have been estimated according to the Universal Soil Loss Equation (USLE). Long-term average annual soil loss ranges from 0.56 to 24.23 [t/ha/a]. Third, combining high-resolution erosion potentials with expert-knowledge of local farmers will result in a landuse system adapted to local conditions. This system will include sustainable strategies reducing soil erosion and conserving soil fertility.

  18. Towards high resolution soil property maps for Austria

    NASA Astrophysics Data System (ADS)

    Schürz, Christoph; Klotz, Daniel; Herrnegger, Mathew; Schulz, Karsten

    2015-04-01

    Soil hydraulic properties, such as soil texture, soil water retention characteristics, hydraulic conductivity, or soil depth are important inputs for hydrologic catchment modelling. However, the availability of such data in Austria is often insufficient to fulfill requirements of well-established hydrological models. Either, soil data is available in sufficient spatial resolution but only covers a small extent of the considered area, or the data is comprehensive but rather coarse in its spatial resolution. Furthermore, the level of detail and quality of the data differs between the available data sets. In order to generate a comprehensive soil data set for whole Austria that includes main soil physical properties, as well as soil depth and organic carbon content in a high spatial resolution (10x10 to 100x100m²) several available soil data bases are merged and harmonized. Starting point is a high resolution soil texture map that only covers agricultural areas and is available due to Austrian land appraisal. Soil physical properties for those areas are derived by applying pedotransfer functions (e.g. Saxton and Rawls, 2006) resulting in expectation values and quantiles of the respective property for each soil texture class. For agricultural areas where no texture information is available, the most likely soil texture is assigned applying a Bayesian network approach incorporating information such as elevation, soil slope, soil type, or hydro-geology at different spatial scales. Soil data for forested areas, that cover a large extent of the state territory, are rather sparse in Austria. For such areas a similar approach as for agricultural areas is applied by using a Bayesian network for prediction of the soil texture. Additionally, information to various soil parameters taken from literature is incorporated. For areas that are covered by land use different to agriculture or forestry, such as bare rock surfaces, or wetland areas, solely literature information is used

  19. Comparative Assessment of Very High Resolution Satellite and Aerial Orthoimagery

    NASA Astrophysics Data System (ADS)

    Agrafiotis, P.; Georgopoulos, A.

    2015-03-01

    This paper aims to assess the accuracy and radiometric quality of orthorectified high resolution satellite imagery from Pleiades-1B satellites through a comparative evaluation of their quantitative and qualitative properties. A Pleiades-B1 stereopair of high resolution images taken in 2013, two adjacent GeoEye-1 stereopairs from 2011 and aerial orthomosaic (LSO) provided by NCMA S.A (Hellenic Cadastre) from 2007 have been used for the comparison tests. As control dataset orthomosaic from aerial imagery provided also by NCMA S.A (0.25m GSD) from 2012 was selected. The process for DSM and orthoimage production was performed using commercial digital photogrammetric workstations. The two resulting orthoimages and the aerial orthomosaic (LSO) were relatively and absolutely evaluated for their quantitative and qualitative properties. Test measurements were performed using the same check points in order to establish their accuracy both as far as the single point coordinates as well as their distances are concerned. Check points were distributed according to JRC Guidelines for Best Practice and Quality Checking of Ortho Imagery and NSSDA standards while areas with different terrain relief and land cover were also included. The tests performed were based also on JRC and NSSDA accuracy standards. Finally, tests were carried out in order to assess the radiometric quality of the orthoimagery. The results are presented with a statistical analysis and they are evaluated in order to present the merits and demerits of the imaging sensors involved for orthoimage production. The results also serve for a critical approach for the usability and cost efficiency of satellite imagery for the production of Large Scale Orthophotos.

  20. High-resolution EEG mapping: an equivalent charge-layer approach

    NASA Astrophysics Data System (ADS)

    Yao, Dezhong

    2003-07-01

    Brain electrical signal is one of the windows to understanding neural activities. Various high-resolution imaging techniques have been developed to reveal the electrical activities underneath the cortical surface from scalp electroencephalographic recordings, such as scalp Laplacian, cortical surface potential, equivalent charge layer (ECL) and equivalent dipole layer (EDL). In this work, we develop forward density formulae for the ECL and the EDL of neural electric sources in a 4-concentric-sphere head model, and compare ECL with EDL in theory, simulation and real evoked data tests. The results confirm that the ECL map may be of higher spatial resolution than the EDL map.

  1. Large-scale, high-resolution neurophysiological maps underlying FMRI of macaque temporal lobe.

    PubMed

    Issa, Elias B; Papanastassiou, Alex M; DiCarlo, James J

    2013-09-18

    Maps obtained by functional magnetic resonance imaging (fMRI) are thought to reflect the underlying spatial layout of neural activity. However, previous studies have not been able to directly compare fMRI maps to high-resolution neurophysiological maps, particularly in higher level visual areas. Here, we used a novel stereo microfocal x-ray system to localize thousands of neural recordings across monkey inferior temporal cortex (IT), construct large-scale maps of neuronal object selectivity at subvoxel resolution, and compare those neurophysiology maps with fMRI maps from the same subjects. While neurophysiology maps contained reliable structure at the sub-millimeter scale, fMRI maps of object selectivity contained information at larger scales (>2.5 mm) and were only partly correlated with raw neurophysiology maps collected in the same subjects. However, spatial smoothing of neurophysiology maps more than doubled that correlation, while a variety of alternative transforms led to no significant improvement. Furthermore, raw spiking signals, once spatially smoothed, were as predictive of fMRI maps as local field potential signals. Thus, fMRI of the inferior temporal lobe reflects a spatially low-passed version of neurophysiology signals. These findings strongly validate the widespread use of fMRI for detecting large (>2.5 mm) neuronal domains of object selectivity but show that a complete understanding of even the most pure domains (e.g., faces vs nonface objects) requires investigation at fine scales that can currently only be obtained with invasive neurophysiological methods.

  2. THEMIS high-resolution digital terrain: Topographic and thermophysical mapping of Gusev Crater, Mars

    USGS Publications Warehouse

    Cushing, G.E.; Titus, T.N.; Soderblom, L.A.; Kirk, R.L.

    2009-01-01

    We discuss a new technique to generate high-resolution digital terrain models (DTMs) and to quantitatively derive and map slope-corrected thermophysical properties such as albedo, thermal inertia, and surface temperatures. This investigation is a continuation of work started by Kirk et al. (2005), who empirically deconvolved Thermal Emission Imaging System (THEMIS) visible and thermal infrared data of this area, isolating topographic information that produced an accurate DTM. Surface temperatures change as a function of many variables such as slope, albedo, thermal inertia, time, season, and atmospheric opacity. We constrain each of these variables to construct a DTM and maps of slope-corrected albedo, slope- and albedo-corrected thermal inertia, and surface temperatures across the scene for any time of day or year and at any atmospheric opacity. DTMs greatly facilitate analyses of the Martian surface, and the MOLA global data set is not finely scaled enough (128 pixels per degree, ???0.5 km per pixel near the equator) to be combined with newer data sets (e.g., High Resolution Imaging Science Experiment, Context Camera, and Compact Reconnaissance Imaging Spectrometer for Mars at ???0.25, ???6, and ???20 m per pixel, respectively), so new techniques to derive high-resolution DTMs are always being explored. This paper discusses our technique of combining a set of THEMIS visible and thermal infrared observations such that albedo and thermal inertia variations within the scene are eliminated and only topographic variations remain. This enables us to produce a high-resolution DTM via photoclinometry techniques that are largely free of albedo-induced errors. With this DTM, THEMIS observations, and a subsurface thermal diffusion model, we generate slope-corrected maps of albedo, thermal inertia, and surface temperatures. In addition to greater accuracy, these products allow thermophysical properties to be directly compared with topography.

  3. A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A

    PubMed Central

    Balcárková, Barbora; Frenkel, Zeev; Škopová, Monika; Abrouk, Michael; Kumar, Ajay; Chao, Shiaoman; Kianian, Shahryar F.; Akhunov, Eduard; Korol, Abraham B.; Doležel, Jaroslav; Valárik, Miroslav

    2017-01-01

    Bread wheat has a large and complex allohexaploid genome with low recombination level at chromosome centromeric and peri-centromeric regions. This significantly hampers ordering of markers, contigs of physical maps and sequence scaffolds and impedes obtaining of high-quality reference genome sequence. Here we report on the construction of high-density and high-resolution radiation hybrid (RH) map of chromosome 4A supported by high-density chromosome deletion map. A total of 119 endosperm-based RH lines of two RH panels and 15 chromosome deletion bin lines were genotyped with 90K iSelect single nucleotide polymorphism (SNP) array. A total of 2316 and 2695 markers were successfully mapped to the 4A RH and deletion maps, respectively. The chromosome deletion map was ordered in 19 bins and allowed precise identification of centromeric region and verification of the RH panel reliability. The 4A-specific RH map comprises 1080 mapping bins and spans 6550.9 cR with a resolution of 0.13 Mb/cR. Significantly higher mapping resolution in the centromeric region was observed as compared to recombination maps. Relatively even distribution of deletion frequency along the chromosome in the RH panel was observed and putative functional centromere was delimited within a region characterized by two SNP markers. PMID:28119729

  4. High resolution comparative genomic hybridisation in clinical cytogenetics

    PubMed Central

    Kirchhoff, M.; Rose, H.; Lundsteen, C.

    2001-01-01

    High resolution comparative genomic hybridisation (HR-CGH) is a diagnostic tool in our clinical cytogenetics laboratory. The present survey reports the results of 253 clinical cases in which 47 abnormalities were detected. Among 144 dysmorphic and mentally retarded subjects with a normal conventional karyotype, 15 (10%) had small deletions or duplications, of which 11 were interstitial. In addition, a case of mosaic trisomy 9 was detected. Among 25 dysmorphic and mentally retarded subjects carrying apparently balanced de novo translocations, four had deletions at translocation breakpoints and two had deletions elsewhere in the genome. Seventeen of 19 complex rearrangements were clarified by HR-CGH. A small supernumerary marker chromosome occurring with low frequency and the breakpoint of a mosaic r(18) case could not be clarified. Three of 19 other abnormalities could not be confirmed by HR-CGH. One was a Williams syndrome deletion and two were DiGeorge syndrome deletions, which were apparently below the resolution of HR-CGH. However, we were able to confirm Angelman and Prader-Willi syndrome deletions, which are about 3-5 Mb. We conclude that HR-CGH should be used for the evaluation of (1) dysmorphic and mentally retarded subjects where normal karyotyping has failed to show abnormalities, (2) dysmorphic and mentally retarded subjects carrying apparently balanced de novo translocations, (3) apparently balanced de novo translocations detected prenatally, and (4) for clarification of complex structural rearrangements.


Keywords: comparative genomic hybridisation; chromosome analysis; chromosome aberrations; dysmorphism PMID:11694545

  5. Creating High-Resolution Maps of Leaf Water Isotopes Using IM-CRDS and IRMS Techniques

    NASA Astrophysics Data System (ADS)

    Gerlein-Safdi, C.; Sinkler, C. J.; Caylor, K. K.

    2014-12-01

    Since the development of isotope ratio infrared spectroscopy (IRIS), the applications of water isotope analysis have been increasing. Here, we present a new protocol to create high-resolution maps of leaf water isotopes 18O and 2H. We use the Picarro induction module (IM-CRDS) combined with an isotope analyzer (L2130-i) to sample up to 25 locations in one half of each leaf. Each sampling location corresponds to four samples (6 mm outside diameter punched-holes) punched next to each other. In the induction module, an induction coil heats a metal holder containing the leaf sample. The sample will release water vapor that is then sent to the isotope analyzer. The IM-CRDS allows us to significantly reduce the sample size and therefore increase the sample density, compared to the traditional cryogenic extraction method. Using spatial analysis tools, we create high-resolution spatial maps of each isotope as well as d-excess maps. The water in the second half of the leaf is extracted by cryogenic extraction and analyzed using both IRIS and isotope ratio mass spectroscopy. The isotopic composition of the extracted water is compared to the average composition calculated from the maps and used for calibration. We present applications of this protocol to the analysis of the spatio-temporal evolution of foliar uptake in Colocasia esculenta under laboratory conditions.

  6. High-resolution terrain map from multiple sensor data

    NASA Technical Reports Server (NTRS)

    Kweon, In S.; Kanade, Takeo

    1992-01-01

    The authors present 3-D vision techniques for incrementally building an accurate 3-D representation of rugged terrain using multiple sensors. They have developed the locus method to model the rugged terrain. The locus method exploits sensor geometry to efficiently build a terrain representation from multiple sensor data. The locus method is used to estimate the vehicle position in the digital elevation map (DEM) by matching a sequence of range images with the DEM. Experimental results from large-scale real and synthetic terrains demonstrate the feasibility and power of the 3-D mapping techniques for rugged terrain. In real world experiments, a composite terrain map was built by merging 125 real range images. Using synthetic range images, a composite map of 150 m was produced from 159 images. With the proposed system, mobile robots operating in rugged environments can build accurate terrain models from multiple sensor data.

  7. High-resolution terrain map from multiple sensor data

    NASA Technical Reports Server (NTRS)

    Kweon, In S.; Kanade, Takeo

    1992-01-01

    The authors present 3-D vision techniques for incrementally building an accurate 3-D representation of rugged terrain using multiple sensors. They have developed the locus method to model the rugged terrain. The locus method exploits sensor geometry to efficiently build a terrain representation from multiple sensor data. The locus method is used to estimate the vehicle position in the digital elevation map (DEM) by matching a sequence of range images with the DEM. Experimental results from large-scale real and synthetic terrains demonstrate the feasibility and power of the 3-D mapping techniques for rugged terrain. In real world experiments, a composite terrain map was built by merging 125 real range images. Using synthetic range images, a composite map of 150 m was produced from 159 images. With the proposed system, mobile robots operating in rugged environments can build accurate terrain models from multiple sensor data.

  8. High resolution hybrid optical and acoustic sea floor maps (Invited)

    NASA Astrophysics Data System (ADS)

    Roman, C.; Inglis, G.

    2013-12-01

    This abstract presents a method for creating hybrid optical and acoustic sea floor reconstructions at centimeter scale grid resolutions with robotic vehicles. Multibeam sonar and stereo vision are two common sensing modalities with complementary strengths that are well suited for data fusion. We have recently developed an automated two stage pipeline to create such maps. The steps can be broken down as navigation refinement and map construction. During navigation refinement a graph-based optimization algorithm is used to align 3D point clouds created with both the multibeam sonar and stereo cameras. The process combats the typical growth in navigation error that has a detrimental affect on map fidelity and typically introduces artifacts at small grid sizes. During this process we are able to automatically register local point clouds created by each sensor to themselves and to each other where they overlap in a survey pattern. The process also estimates the sensor offsets, such as heading, pitch and roll, that describe how each sensor is mounted to the vehicle. The end results of the navigation step is a refined vehicle trajectory that ensures the points clouds from each sensor are consistently aligned, and the individual sensor offsets. In the mapping step, grid cells in the map are selectively populated by choosing data points from each sensor in an automated manner. The selection process is designed to pick points that preserve the best characteristics of each sensor and honor some specific map quality criteria to reduce outliers and ghosting. In general, the algorithm selects dense 3D stereo points in areas of high texture and point density. In areas where the stereo vision is poor, such as in a scene with low contrast or texture, multibeam sonar points are inserted in the map. This process is automated and results in a hybrid map populated with data from both sensors. Additional cross modality checks are made to reject outliers in a robust manner. The final

  9. High Resolution Maps of the Moon Surface with AMIE/SMART-1

    NASA Astrophysics Data System (ADS)

    Despan, Daniela; Erard, S.; Barucci, A.; Josset, J. L.; Beauvivre, S.; Chevrel, S.; Pinet, P.; Koschny, D.; Almeida, M.; Grieger, B.; Foing, B.; AMIE Team

    2008-09-01

    The Advanced Moon micro-Imager Experiment (AMIE) on board the ESA lunar mission Smart-1 has performed colour imaging of the lunar surface using various filters in the visible and NIR range. This micro-camera provided high resolution images of selected parts of the lunar surface, including the North and South pole areas. Being give that the SMART-1 mission was in a 300km x 300km orbit with perilune over the South pole, the coverage between the North and the South regions is different. The AMIE images were obtained using a tele-objective with 5.3° x 5.3° field of view and a sensor of 1024 x 1024 pixels. The output images have resolution 45m/pixel at 500km, and are encoded with 10 bits/pixel. The data for the North pole were obtained at a much higher altitude than the South pole data. From the 300 Km pericenter altitude, the same field of view corresponds to a spatial resolution about 27 m/pixel. The high resolution imaging of the Moon surface makes possible detailed analysis of the morphological features and physical characteristics of the lunar surface. In order to construct AMIE data maps, systematic analysis and processing is being carried on using the whole data set. Geometrical analysis of AMIE images relies on the SPICE system: image coordinates are computed to get precise projection at the surface, and illumination angles are computed to analyze the photometric sequences. Using this method, high resolution mosaics were constructed then compared to lower resolution Clementine UV-Vis and NIR images. Maps of both North and South pole were obtained as well as other regions of interest. Eventually, this method will be applied in all areas where AMIE has provided high resolution observations of the surface, typically a factor of 3 higher than the Clementine UV-Vis camera. New results will be presented at the conference.

  10. A System and Method for Online High-Resolution Mapping of Gastric Slow-Wave Activity

    PubMed Central

    Bull, Simon H.; O’Grady, Gregory; Du, Peng

    2015-01-01

    High-resolution (HR) mapping employs multielectrode arrays to achieve spatially detailed analyses of propagating bioelectrical events. A major current limitation is that spatial analyses must currently be performed “off-line” (after experiments), compromising timely recording feedback and restricting experimental interventions. These problems motivated development of a system and method for “online” HR mapping. HR gastric recordings were acquired and streamed to a novel software client. Algorithms were devised to filter data, identify slow-wave events, eliminate corrupt channels, and cluster activation events. A graphical user interface animated data and plotted electrograms and maps. Results were compared against off-line methods. The online system analyzed 256-channel serosal recordings with no unexpected system terminations with a mean delay 18 s. Activation time marking sensitivity was 0.92; positive predictive value was 0.93. Abnormal slow-wave patterns including conduction blocks, ectopic pacemaking, and colliding wave fronts were reliably identified. Compared to traditional analysis methods, online mapping had comparable results with equivalent coverage of 90% of electrodes, average RMS errors of less than 1 s, and CC of activation maps of 0.99. Accurate slow-wave mapping was achieved in near real-time, enabling monitoring of recording quality and experimental interventions targeted to dysrhythmic onset. This work also advances the translation of HR mapping toward real-time clinical application. PMID:24860024

  11. High-resolution Geophysical Mapping of Submarine Glacial Landforms

    NASA Astrophysics Data System (ADS)

    Jakobsson, M.; Dowdeswell, J. A.; Canals, M.; Todd, B. J.; Dowdeswell, E. K.; Hogan, K. A.; Mayer, L. A.

    2014-12-01

    Glacial landforms are generated from the activity of glaciers and display spatial dimensions ranging from below one meter up to tens of kilometers. Glacial landforms are used as diagnostic features of past activity of ice sheets and glaciers; they are specifically important in the field of palaeoglaciology. Mapping of submarine glacial landforms is largely dependent on geophysical survey methods capable of imaging the seafloor and sub-bottom through the water column. Full "global" seafloor mapping coverage, equivalent to what exists for land elevation, is to-date only achieved by the powerful method of deriving bathymetry from altimeters on satellites like GEOSAT and ERS-1. The lateral resolution of satellite derived bathymetry is, however, limited by the footprint of the satellite and the need to average out local wave and wind effects resulting in values of around 15 km. Consequently, mapping submarine glacial landforms requires for the most part higher resolution than is achievable by satellite derived bathymetry. The most widely-used methods for mapping submarine glacial landforms are based on echo-sounding principles. This presentation shows how the evolution of marine geophysical mapping techniques, in particular the advent of side-scan and multibeam bathymetric sonars, has made it possible to study submarine glacial landforms in unprecedented detail. Examples are shown from the Atlas of Submarine Glacial Landforms: Modern, Quaternary and Ancient, which will be published in late 2015 in the Memoir Series of the Geological Society of London.

  12. Mapping ET at high resolution in an advective semi-arid environment with airborne multispectral imagery

    USDA-ARS?s Scientific Manuscript database

    Periodic and accurate estimates of spatially distributed evapotranspiration (ET) are essential for managing water in irrigated regions and in hydrologic modeling. In this study, METRIC (Mapping ET at high Resolution with Internalized Calibration), an energy balance algorithm originally developed for...

  13. High resolution weak lensing mass mapping combining shear and flexion

    NASA Astrophysics Data System (ADS)

    Lanusse, F.; Starck, J.-L.; Leonard, A.; Pires, S.

    2016-06-01

    Aims: We propose a new mass mapping algorithm, specifically designed to recover small-scale information from a combination of gravitational shear and flexion. Including flexion allows us to supplement the shear on small scales in order to increase the sensitivity to substructures and the overall resolution of the convergence map without relying on strong lensing constraints. Methods: To preserve all available small scale information, we avoid any binning of the irregularly sampled input shear and flexion fields and treat the mass mapping problem as a general ill-posed inverse problem, which is regularised using a robust multi-scale wavelet sparsity prior. The resulting algorithm incorporates redshift, reduced shear, and reduced flexion measurements for individual galaxies and is made highly efficient by the use of fast Fourier estimators. Results: We tested our reconstruction method on a set of realistic weak lensing simulations corresponding to typical HST/ACS cluster observations and demonstrate our ability to recover substructures with the inclusion of flexion, which are otherwise lost if only shear information is used. In particular, we can detect substructures on the 15'' scale well outside of the critical region of the clusters. In addition, flexion also helps to constrain the shape of the central regions of the main dark matter halos. Our mass mapping software, called Glimpse2D, is made freely available at http://www.cosmostat.org/software/glimpse

  14. Urban cover mapping using digital, high-resolution aerial imagery

    Treesearch

    Soojeong Myeong; David J. Nowak; Paul F. Hopkins; Robert H. Brock

    2003-01-01

    High-spatial resolution digital color-infrared aerial imagery of Syracuse, NY was analyzed to test methods for developing land cover classifications for an urban area. Five cover types were mapped: tree/shrub, grass/herbaceous, bare soil, water and impervious surface. Challenges in high-spatial resolution imagery such as shadow effect and similarity in spectral...

  15. High-resolution Mapping of Offshore and Onshore Glaciogenic Features in Melville Bay, Northwestern Greenland

    NASA Astrophysics Data System (ADS)

    Freire, F.; Gyllencreutz, R.; Greenwood, S.; Mayer, L. A.; Jakobsson, M.

    2014-12-01

    This study presents results from high resolution mapping in the northwestern part of Greenland's continental shelf, offshore from the Greenland Ice Sheet. The study area is located at about 74o30'N and 58 o40'W where high-resolution seafloor imagery were collected from ~200-500 m water depth. These data were analyzed and compared to existing high-resolution satellite imagery of exposed glacial landforms from the nearby coastal areas. Offshore geophysical mapping equipment consisted of a Kongsberg EM2040 multibeam that was bow-mounted on the sailing vessel Explorer of Sweden together with a Seatex MRU5+ motion sensor and GPS antennas. In addition, a GAVIA autonomous underwater vehicle (AUV) from University of Iceland with installed Geoswath interfometric sonar and Marine Sonic side-scan was used. The data from these systems permitted the production of both 5-m (for the EM2040) and 2-m (for the Geoswath) resolution bathymetric grids for landform analyzes. Sediment characterization analysis was also undertaken using the co-registered backscatter data. The exposed onshore landforms were studied using data from the high-res QuickBird satellite images with a 2-m pixel resolution. Geomorphic analysis of the data shows that past tectonic and glacial scouring processes have shaped the present-day landscape in both the offshore and onshore study areas. The terrain consists of glacially eroded bedrock covered with very thin surficial sediments resembling a 'cnoc-and-lochan' terrain, although the degree of erosion varies spatially, probably as a result of local variations in the rock properties. Different glacially influenced features are identified and described in the study. These features have been used to understand and infer past ice-sheet processes, particularly ice-flow direction and the extent of ice-cover on the continental shelves from previous extreme glaciation events. The backscatter information from the high-resolution interferometric sonar show fine

  16. High Resolution Urban Feature Extraction for Global Population Mapping using High Performance Computing

    SciTech Connect

    Vijayaraj, Veeraraghavan; Bright, Eddie A; Bhaduri, Budhendra L

    2007-01-01

    The advent of high spatial resolution satellite imagery like Quick Bird (0.6 meter) and IKONOS (1 meter) has provided a new data source for high resolution urban land cover mapping. Extracting accurate urban regions from high resolution images has many applications and is essential to the population mapping efforts of Oak Ridge National Laboratory's (ORNL) LandScan population distribution program. This paper discusses an automated parallel algorithm that has been implemented on a high performance computing environment to extract urban regions from high resolution images using texture and spectral features

  17. High-resolution genome-wide mapping of histone modifications.

    PubMed

    Roh, Tae-young; Ngau, Wing Chi; Cui, Kairong; Landsman, David; Zhao, Keji

    2004-08-01

    The expression patterns of eukaryotic genomes are controlled by their chromatin structure, consisting of nucleosome subunits in which DNA of approximately 146 bp is wrapped around a core of 8 histone molecules. Post-translational histone modifications play an essential role in modifying chromatin structure. Here we apply a combination of SAGE and chromatin immunoprecipitation (ChIP) protocols to determine the distribution of hyperacetylated histones H3 and H4 in the Saccharomyces cerevisiae genome. We call this approach genome-wide mapping technique (GMAT). Using GMAT, we find that the highest acetylation levels are detected in the 5' end of a gene's coding region, but not in the promoter. Furthermore, we show that the histone acetyltransferase, GCN5p, regulates H3 acetylation in the promoter and 5' end of the coding regions. These findings indicate that GMAT should find valuable applications in mapping target sites of chromatin-modifying enzymes.

  18. High resolution regional elasticity mapping of the human prostate.

    PubMed

    Murayama, Yoshinobu; Omata, Sadao; Yajima, Toshikuni; Peng, Qiyu; Shishido, Keiichi; Peehl, Donna M; Constantinou, Christos E

    2007-01-01

    What is it that the clinician "feels" during a digital rectal examination? To answer this question, it is necessary to measure the elastic properties of the prostate and verify the stiffness values with histological examination. Therefore, we devised an Elasticity Mapping System to evaluate the elastic properties of various histopathological grades of prostate cancer in relation to benign prostatic hyperplasia (BPH) and normal tissue. The system consists of a micro tactile sensor, a three-axis (XYZ) with one (fine Z) micromanipulation stage, a stereoscope camera and a measurement chamber. Using this methodology we mapped the elasticity of human prostate cancer (CaP) and it was obviously observed that the node was significantly harder than surrounding normal tissues and had some textures.

  19. High Resolution Aircraft Scanner Mapping of Geothermal and Volcanic Areas

    SciTech Connect

    Mongillo, M.A.; Cochrane, G.R.; Wood, C.P.; Shibata, Y.

    1995-01-01

    High spectral resolution GEOSCAN Mkll multispectral aircraft scanner imagery has been acquired, at 3-6 m spatial resolutions, over much of the Taupo Volcanic Zone as part of continuing investigations aimed at developing remote sensing techniques for exploring and mapping geothermal and volcanic areas. This study examined the 24-band: visible, near-IR (NIR), mid-IR (MIR) and thermal-IR (TIR) imagery acquired over Waiotapu geothermal area (3 m spatial resolution) and White Island volcano (6 m resolution). Results show that color composite images composed of visible and NIR wavelengths that correspond to color infrared (CIR) photographic wavelengths can be useful for distinguishing among bare ground, water and vegetation features and, in certain cases, for mapping various vegetation types. However, combinations which include an MIR band ({approx} 2.2 {micro}m) with either visible and NIR bands, or two NIR bands, are the most powerful for mapping vegetation types, water bodies, and bare and hydrothermally altered ground. Combinations incorporating a daytime TIR band with NIR and MIR bands are also valuable for locating anomalously hot features and distinguishing among different types of surface hydrothermal alteration.

  20. Improving dust emission characterization in dust models using dynamic high-resolution geomorphic erodibility map

    NASA Astrophysics Data System (ADS)

    Parajuli, S. P.; Yang, Z.; Kocurek, G.

    2013-12-01

    Dust is known to affect the earth radiation budget, biogeochemical cycle, precipitation, human health and visibility. Despite the increased research effort, dust emission modeling remains challenging because dust emission is affected by complex geomorphological processes. Existing dust models overestimate dust emission and rely on tuning and a static erodibility factor in order to make simulated results comparable to remote sensing and ground-based observations. In most of current models, dust emission is expressed in terms of threshold friction speed, which ultimately depends mainly upon the percentage clay content and soil moisture. Unfortunately, due to the unavailability of accurate and high resolution input data of the clay content and soil moisture, estimated threshold friction speed commonly does not represent the variability in field condition. In this work, we attempt to improve dust emission characterization by developing a high resolution geomorphic map of the Middle East and North Africa (MENA), which is responsible for more than 50% of global dust emission. We develop this geomorphic map by visually examining high resolution satellite images obtained from Google Earth Pro and ESRI base map. Albeit subjective, our technique is more reliable compared to automatic image classification technique because we incorporate knowledge of geological/geographical setting in identifying dust sources. We hypothesize that the erodibility is unique for different geomorphic landforms and that it can be quantified by the correlation between observed wind speed and satellite retrieved aerosol optical depth (AOD). We classify the study area into several key geomorphological categories with respect to their dust emission potential. Then we quantify their dust emission potential using the correlation between observed wind speed and satellite retrieved AOD. The dynamic, high-resolution geomorphic erodibility map thus prepared will help to reduce the uncertainty in current

  1. Large-Scale, High-Resolution Neurophysiological Maps Underlying fMRI of Macaque Temporal Lobe

    PubMed Central

    Papanastassiou, Alex M.; DiCarlo, James J.

    2013-01-01

    Maps obtained by functional magnetic resonance imaging (fMRI) are thought to reflect the underlying spatial layout of neural activity. However, previous studies have not been able to directly compare fMRI maps to high-resolution neurophysiological maps, particularly in higher level visual areas. Here, we used a novel stereo microfocal x-ray system to localize thousands of neural recordings across monkey inferior temporal cortex (IT), construct large-scale maps of neuronal object selectivity at subvoxel resolution, and compare those neurophysiology maps with fMRI maps from the same subjects. While neurophysiology maps contained reliable structure at the sub-millimeter scale, fMRI maps of object selectivity contained information at larger scales (>2.5 mm) and were only partly correlated with raw neurophysiology maps collected in the same subjects. However, spatial smoothing of neurophysiology maps more than doubled that correlation, while a variety of alternative transforms led to no significant improvement. Furthermore, raw spiking signals, once spatially smoothed, were as predictive of fMRI maps as local field potential signals. Thus, fMRI of the inferior temporal lobe reflects a spatially low-passed version of neurophysiology signals. These findings strongly validate the widespread use of fMRI for detecting large (>2.5 mm) neuronal domains of object selectivity but show that a complete understanding of even the most pure domains (e.g., faces vs nonface objects) requires investigation at fine scales that can currently only be obtained with invasive neurophysiological methods. PMID:24048850

  2. Airborne LIDAR: high resolution shallow water bathymetric mapping

    NASA Astrophysics Data System (ADS)

    Carter, W. E.; Shrestha, R. L.; Glennie, C. L.; Dietrich, W. E.

    2011-12-01

    The primary goals of the National Center for Airborne Laser Mapping (NCALM) include collecting research quality airborne LIDAR observations for projects funded by NSF through proposal/peer review, and improving airborne LIDAR technology/products to enable new applications. To extend NCALM capabilities to shallow water bathymetric mapping, as inexpensively and quickly as possible, we contracted for the development of a new sensor head compatible with the electronics rack of our near infrared (NIR) sensor, but operates at a wavelength of 0.532 micrometers. The new sensor head utilizes the same laser pump diodes, control electronics, waveform digitizer (currently 8 bit, with a 12 bit unit under development), and high capacity data storage units as the NIR sensor, but the optics are designed and coated for the green light produced by the frequency doubled NdYAG laser. The green sensor has a sufficient field of view to receive returns from the surface of a body of water, and allowing for refraction, from the underlying terrain. The laser operates at selected pulse rates up to 70 kHz, and has a nominal pulse width of approximately 5 nanoseconds. Laboratory and initial engineering field tests indicate that the system can detect bottom returns in 10 meters or greater depths of water with 0.1 loss of signal per meter of water and a bottom reflectivity of 0.1, and that it should be possible, with proper processing of the digitized waveform data, to resolve surface and bottom returns in water as shallow as 10 to 15 cm. Operating from an altitude of 400 meters hundred meters, ground-speed of 80 meters per second, scan angle of 15 degrees, and a pulse rate of 70 kHz, yields a single-pass point density of about 5 points per m2, which will yield bathymetric maps of shallow lakes, streams and coastal waters with previously unavailable spatial resolutions.

  3. Mapping Urban Ecosystem Services Using High Resolution Aerial Photography

    NASA Astrophysics Data System (ADS)

    Pilant, A. N.; Neale, A.; Wilhelm, D.

    2010-12-01

    Ecosystem services (ES) are the many life-sustaining benefits we receive from nature: e.g., clean air and water, food and fiber, cultural-aesthetic-recreational benefits, pollination and flood control. The ES concept is emerging as a means of integrating complex environmental and economic information to support informed environmental decision making. The US EPA is developing a web-based National Atlas of Ecosystem Services, with a component for urban ecosystems. Currently, the only wall-to-wall, national scale land cover data suitable for this analysis is the National Land Cover Data (NLCD) at 30 m spatial resolution with 5 and 10 year updates. However, aerial photography is acquired at higher spatial resolution (0.5-3 m) and more frequently (1-5 years, typically) for most urban areas. Land cover was mapped in Raleigh, NC using freely available USDA National Agricultural Imagery Program (NAIP) with 1 m ground sample distance to test the suitability of aerial photography for urban ES analysis. Automated feature extraction techniques were used to extract five land cover classes, and an accuracy assessment was performed using standard techniques. Results will be presented that demonstrate applications to mapping ES in urban environments: greenways, corridors, fragmentation, habitat, impervious surfaces, dark and light pavement (urban heat island). Automated feature extraction results mapped over NAIP color aerial photograph. At this scale, we can look at land cover and related ecosystem services at the 2-10 m scale. Small features such as individual trees and sidewalks are visible and mappable. Classified aerial photo of Downtown Raleigh NC Red: impervious surface Dark Green: trees Light Green: grass Tan: soil

  4. High resolution spatial map imaging of a gaseous target

    NASA Astrophysics Data System (ADS)

    Stei, Martin; von Vangerow, Johannes; Otto, Rico; Kelkar, Aditya H.; Carrascosa, Eduardo; Best, Thorsten; Wester, Roland

    2013-06-01

    Electrostatic ion imaging with the velocity map imaging mode is a widely used method in atomic and molecular physics and physical chemistry. In contrast, the spatial map imaging (SMI) mode has received very little attention, despite the fact that it has been proposed earlier [A. T. J. B. Eppink and D. H. Parker, Rev. Sci. Instrum. 68, 3477 (1997)], 10.1063/1.1148310. Here, we present a detailed parametric characterization of SMI both by simulation and experiment. One-, two- and three-dimensional imaging modes are described. The influence of different parameters on the imaging process is described by means of a Taylor expansion. To experimentally quantify elements of the Taylor expansion and to infer the spatial resolution of our spectrometer, photoionization of toluene with a focused laser beam has been carried out. A spatial resolution of better than 4 μm out of a focal volume of several mm in diameter has been achieved. Our results will be useful for applications of SMI to the characterization of laser beams, the overlap control of multiple particle or light beams, and the determination of absolute collision cross sections.

  5. High-resolution electroencephalogram (EEG) mapping: scalp charge layer

    NASA Astrophysics Data System (ADS)

    Yao, Dezhong; Yin, Zhong Ke; Tang, Xiang Hong; Arendt-Nielsen, Lars; Chen, Andrew C. N.

    2004-11-01

    The neural electrical signal related to the human brain function is one of the tracks to understanding ourselves. Various electroencephalogram imaging techniques have been developed to reveal spatial information on neural activities in the brain from scalp recordings, such as Laplacian, equivalent source layer and potential. Physically, these methods may be classified into two categories: scalp surface or cortical surface based techniques. In this work, the focus is on the scalp surface based equivalent charge layer (ECL), with a comparison to the scalp potential with different references and scalp Laplacian (SL). The contents include theoretical analysis and numeric evaluation of simulated data and real alpha (8-12 Hz) data. The results confirm the fact that SL and ECL are of higher spatial resolution than various scalp potential maps, and for SL and ECL, SL is of higher resolution but more sensitive to noise.

  6. DNA fiber mapping techniques for the assembly of high-resolution physical maps.

    PubMed

    Weier, H U

    2001-08-01

    High-resolution physical maps are indispensable for directed sequencing projects or the finishing stages of shotgun sequencing projects. These maps are also critical for the positional cloning of disease genes and genetic elements that regulate gene expression. Typically, physical maps are based on ordered sets of large insert DNA clones from cosmid, P1/PAC/BAC, or yeast artificial chromosome (YAC) libraries. Recent technical developments provide detailed information about overlaps or gaps between clones and precisely locate the position of sequence tagged sites or expressed sequences, and thus support efforts to determine the complete sequence of the human genome and model organisms. Assembly of physical maps is greatly facilitated by hybridization of non-isotopically labeled DNA probes onto DNA molecules that were released from interphase cell nuclei or recombinant DNA clones, stretched to some extent and then immobilized on a solid support. The bound DNA, collectively called "DNA fibers," may consist of single DNA molecules in some experiments or bundles of chromatin fibers in others. Once released from the interphase nuclei, the DNA fibers become more accessible to probes and detection reagents. Hybridization efficiency is therefore increased, allowing the detection of DNA targets as small as a few hundred base pairs. This review summarizes different approaches to DNA fiber mapping and discusses the detection sensitivity and mapping accuracy as well as recent achievements in mapping expressed sequence tags and DNA replication sites.

  7. High-resolution habitat mapping on mud fields: new approach to quantitative mapping of Ocean quahog.

    PubMed

    Isachenko, Artem; Gubanova, Yana; Tzetlin, Alexander; Mokievsky, Vadim

    2014-12-01

    During 2009-2012 stocks of the bivalve Arctica islandica (Linnaeus, 1767) (Ocean quahog) in Kandalaksha Bay (the White Sea) has been assessed using a side-scan sonar, grab sampling and underwater photo imaging. Structurally uniform localities were highlighted on the basis of side-scan signal. Each type of a signal reflects combination of sediment type, microtopography and structural characteristics of benthic community. The distribution of A. islandica was the predominant factor in determining community structure. Seabed attributes considered most significant were defined for each type of substrate type. Relations of sonar signal and sediment type were used for landscape mapping based on sonar data. Community characteristics at known localities were reliably interpolated to the area of survey using statistical processing of geophysical data. A method of integrated sonar and sampling data interpretation for high-resolution mapping of A. islandica by biomass groups, benthic faunal groups and associated habitats was developed. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. A high-resolution radiation hybrid map of the bovine genome

    USDA-ARS?s Scientific Manuscript database

    We are building high-resolution radiation hybrid maps of all 29 bovine autosomes and chromosome X, using a 58,000-marker genotyping assay, and a 12,000-rad whole-genome radiation hybrid (RH) panel. To accommodate the large number of markers, and to automate the map building procedure, a software pip...

  9. HetMappsS: Heterozygous mapping strategy for high resolution Genotyping-by-Sequencing Markers

    USDA-ARS?s Scientific Manuscript database

    Reduced representation genotyping approaches, such as genotyping-by-sequencing (GBS), provide opportunities to generate high-resolution genetic maps at a low per-sample cost. However, missing data and non-uniform sequence coverage can complicate map creation in highly heterozygous species. To facili...

  10. A new map of the vegetation of central European Russia based on high-resolution satellite data.

    PubMed

    Ershov, D V; Gavrilyuk, E A; Karpukhina, D A; Kovganko, K A

    2015-01-01

    The scientific basis of and approaches to regional thematic mapping of vegetation based on high-resolution satellite data have been elaborated. A vegetation map of central European Russia has been compiled. The map includes 12 thematic classes, six of which pertain to forest ecosystems. The map has been compared to the data of the GFC project (University of Maryland, United States) and the official data of the Rosstat Federal Service of State Statistics (Russia). The new vegetation map is currently used in the information system of the remote monitoring of forest fires in Russia.

  11. Risk assessment of ventricular arrhythmia using new parameters based on high resolution body surface potential mapping.

    PubMed

    Fereniec, Malgorzata; Stix, Gunter; Kania, Michal; Mroczka, Tomasz; Janusek, Dariusz; Maniewski, Roman

    2011-02-25

    The effective screening of myocardial infarction (MI) patients threatened by ventricular tachycardia (VT) is an important issue in clinical practice, especially in the process of implantable cardioverter-defibrillator (ICD) therapy recommendation. This study proposes new parameters describing depolarization and repolarization inhomogeneity in high resolution body surface potential maps (HR BSPM) to identify MI patients threatened by VT. High resolution ECGs were recorded from 64 surface leads. Time-averaged HR BSPMs were used. Several parameters for arrhythmia risk assessment were calculated in 2 groups of MI patients: those with and without documented VT. Additionally, a control group of healthy subjects was studied. To assess the risk of VT, the following parameters were proposed: correlation coefficient between STT and QRST integral maps (STT_QRST_CORR), departure index of absolute value of STT integral map (STT_DI), and departure index of absolute value of T-wave shape index (TSI_DI). These new parameters were compared to known parameters: QRS width, QT interval, QT dispersion, Tpeak-Tend interval, total cosines between QRS complex and T wave, and non-dipolar content of QRST integral maps. STT_DI, TSI_DI, STT_QRST_CORR, QRS width, and QT interval parameters were statistically significant (p ≤ 0.05) in arrhythmia risk assessment. The highest sensitivity was found for the STT_DI parameter (0.77) and the highest specificity for TSI_DI (0.79). Arrhythmia risk is demonstrated by both abnormal spatial distribution of the repolarization phase and changed relationship between depolarization and repolarization phases, as well as their prolongation. The proposed new parameters might be applied for risk stratification of cardiac arrhythmia.

  12. Risk assessment of ventricular arrhythmia using new parameters based on high resolution body surface potential mapping

    PubMed Central

    Fereniec, Malgorzata; Stix, Gunter; Kania, Michal; Mroczka, Tomasz; Janusek, Dariusz; Maniewski, Roman

    2011-01-01

    Summary Background The effective screening of myocardial infarction (MI) patients threatened by ventricular tachycardia (VT) is an important issue in clinical practice, especially in the process of implantable cardioverter-defibrillator (ICD) therapy recommendation. This study proposes new parameters describing depolarization and repolarization inhomogeneity in high resolution body surface potential maps (HR BSPM) to identify MI patients threatened by VT. Material/Methods High resolution ECGs were recorded from 64 surface leads. Time-averaged HR BSPMs were used. Several parameters for arrhythmia risk assessment were calculated in 2 groups of MI patients: those with and without documented VT. Additionally, a control group of healthy subjects was studied. To assess the risk of VT, the following parameters were proposed: correlation coefficient between STT and QRST integral maps (STT_QRST_CORR), departure index of absolute value of STT integral map (STT_DI), and departure index of absolute value of T-wave shape index (TSI_DI). These new parameters were compared to known parameters: QRS width, QT interval, QT dispersion, Tpeak-Tend interval, total cosines between QRS complex and T wave, and non-dipolar content of QRST integral maps. Results STT_DI, TSI_DI, STT_QRST_CORR, QRS width, and QT interval parameters were statistically significant (p≤0.05) in arrhythmia risk assessment. The highest sensitivity was found for the STT_DI parameter (0.77) and the highest specificity for TSI_DI (0.79). Conclusions Arrhythmia risk is demonstrated by both abnormal spatial distribution of the repolarization phase and changed relationship between depolarization and repolarization phases, as well as their prolongation. The proposed new parameters might be applied for risk stratification of cardiac arrhythmia. PMID:21358612

  13. High-resolution fracture aperture mapping using optical profilometry

    NASA Astrophysics Data System (ADS)

    Ameli, Pasha; Elkhoury, Jean E.; Detwiler, Russell L.

    2013-10-01

    Fractures play an important role in the Earth's crust, often controlling both mechanical and transport processes. Developing a mechanistic understanding of these processes requires quantifying the roughness of fracture surfaces and the contacts and void spaces between fracture surfaces at high spatial resolution (10s of microns) over a broad range of scales (centimeters to meters). Here we present a scalable method for measuring fracture surfaces and reconstructing fracture aperture fields using an optical profilometer. We evaluate the method by measuring two fractured limestone cores; one is a tensile fracture with strong cross correlation between the surfaces and the other is a saw-cut, sand-blasted fracture with negligible cross correlation between the surfaces. Results of repeated measurements of these two fractures suggest that well-correlated surfaces, where the correlation between the surfaces can aid reconstruction, can be reproduced with local uncertainties with median standard deviation of 8 μm . Poorly correlated surfaces, where reconstruction relies solely upon the precision of the placement of the halves of the core on the profilometer stage, can be reproduced with local uncertainties with median standard deviation of 20 μm . Additionally, we quantified the accuracy of the technique by comparing calculated aperture profiles of a fractured concrete core to thin sections cut from the core after impregnating it with epoxy. The median deviation between the two measurements, which includes errors due to residual misalignment of the profiles, was 29 μm supporting the accuracy of the method. Our results emphasize the potential for using noncontact surface measurement techniques to accurately and precisely reconstruct fracture apertures over a wide range of length scales.

  14. Fine resolution topographic mapping of the Jovian moons: a Ka-band high resolution topographic mapping interferometric synthetic aperture radar

    NASA Technical Reports Server (NTRS)

    Madsen, Soren N.; Carsey, Frank D.; Turtle, Elizabeth P.

    2003-01-01

    The topographic data set obtained by MOLA has provided an unprecedented level of information about Mars' geologic features. The proposed flight of JIMO provides an opportunity to accomplish a similar mapping of and comparable scientific discovery for the Jovian moons through us of an interferometric imaging radar analogous to the Shuttle radar that recently generated a new topographic map of Earth. A Ka-band single pass across-track synthetic aperture radar (SAR) interferometer can provide very high resolution surface elevation maps. The concept would use two antennas mounted at the ends of a deployable boom (similar to the Shuttle Radar Topographic Mapper) extended orthogonal to the direction of flight. Assuming an orbit altitude of approximately 100 km and a ground velocity of approximately 1.5 km/sec, horizontal resolutions at the 10 meter level and vertical resolutions at the sub-meter level are possible.

  15. Fine Resolution Topographic Mapping of the Jovian Moons: A Ka-Band High Resolution Topographic Mapping Interferometric Synthetic Aperture Radar

    NASA Technical Reports Server (NTRS)

    Madsen, S. N.; Carsey, F. D.; Turtle, E. P.

    2003-01-01

    The topographic data set obtained by MOLA has provided an unprecedented level of information about Mars' geologic features. The proposed flight of JIMO provides an opportunity to accomplish a similar mapping of and comparable scientific discovery for the Jovian moons through use of an interferometric imaging radar analogous to the Shuttle radar that recently generated a new topographic map of Earth. A Ka-band single pass across-track synthetic aperture radar (SAR) interferometer can provide very high resolution surface elevation maps. The concept would use two antennas mounted at the ends of a deployable boom (similar to the Shuttle Radar Topographic Mapper) extended orthogonal to the direction of flight. Assuming an orbit altitude of approximately 100km and a ground velocity of approximately 1.5 km/sec, horizontal resolutions at the 10 meter level and vertical resolutions at the sub-meter level are possible.

  16. Mangrove species mapping in Kuala Sepetang Mangrove Forest, Perak using high resolution airborne data

    NASA Astrophysics Data System (ADS)

    Beh, B. C.; MatJafri, M. Z.; Lim, H. S.

    2015-10-01

    Mangrove vegetation is widely employed and studied as it is a unique ecosystem which is able to provide plenty of goods and applications to our country. In this paper, high resolution airborne image data obtained the flight mission on Kuala Sepetang Mangrove Forest Reserve, Perak, Malaysia will be used for mangrove species mapping. Supervised classification using the retrieved surface reflectance will be performed to classify the airborne data using Geomatica 2013 software package. The ground truth data will be used to validate the classification accuracy. High correlation of R2=0.873 was achieved in this study indicate that high resolution airborne data is reliable and suitable used for mangrove species mapping.

  17. Geospatial mapping of vegetation in the Antarctic environment using very high-resolution WorldView-2 imagery

    NASA Astrophysics Data System (ADS)

    Jawak, Shridhar D.; Udhayaraj, A. D.; Alvarinho, Luis J.

    2016-05-01

    A robust monitoring of the changes in the distribution and density of cryospheric plant species requires accurate and high-resolution baseline maps of vegetation. Mapping such change at the landscape scale is often problematic, particularly in remote areas, such as Antarctica. Vegetation mapping of plant communities at fine spatial scales is increasingly supported by remote sensing technology in cryospheric regions. Less frequent imaging with high spatial resolution satellite sensors enable more detailed analyses of vegetation change frequently. This study is the first to use high-resolution WorldView-2 (WV-2) imagery to classify vegetation communities on Antarctic oases and to provide semi-automated means to map vegetation, as an imperative indicator for environmental change. Multispectral imagery (MSI) and panchromatic imagery (PAN) from very high resolution WV-2 have been used for mapping of vegetation in different forms in Antarctic environment. A range of supervised classification methods have been executed using pan-sharpened WV-2 data. This study comparatively and statistically evaluates vegetation mapping results using supervised and unsupervised classification methods to extract vegetation in Larsemann Hills and Schirmacher oasis, east Antarctica. We also discuss on the use of supervised pixel-based classifiers and textural measures, in addition to standard multispectral information, to improve the classification of Antarctic vegetation communities. Classification results were validated with independent reference datasets. This work indicates that the overall accuracy of mapping vegetation using WV-2 imagery and semi-automated target extraction methods ranged from 90% to 94%.

  18. Using Artificial Neural Network model to produce high resolution forest soil property maps

    NASA Astrophysics Data System (ADS)

    Meng, F.-R.; Zhao, Z.; Xing, Z.; Li, S.

    2012-04-01

    Soil property maps are considered as the most important input information for decision support and policy making in agriculture, forestry, flood control as well as environmental protection. Traditionally, soil property maps are mainly obtained from field surveys. Field soil survey is generally time consuming and expensive, which limited it application over a large area. As such, high resolution soil property maps are only available for small areas, very often, being obtained for research purposes. In this research, artificial neural network technology was used to generate high resolutions soil property maps. Hydrological parameters derived from digital elevation maps combined with information extracted from existing coarse resolution soil maps were used as input for the proposed model. Detailed soil survey information from Black Brook Watershed in Northern New Brunswick was used to test the model performance. We found that ANN models base model can be used to predict soil texture, soil drainage classes and soil organic matter content across landscape with reasonable accuracy. The high resolution soil maps derived with this method could be used for growth and yield assessment, silviculture design and making forest management plans.

  19. High Resolution QTL Maps Of 31 Traits in Contemporary U.S. Holstein Cows

    USDA-ARS?s Scientific Manuscript database

    High-resolution QTL maps of 1586 SNPs affecting 31 dairy traits (top 100 effects per trait)were constructed based on a genome-wide association analysis of 1,654 contemporary U.S. Holstein cows genotyped with 45,878 SNPs. The 31 traits include net merit and its 8 compnent traits, 4 calving traits, an...

  20. Grapevine powdery mildew resistance and susceptibility loci identified on a high-resolution SNP map

    USDA-ARS?s Scientific Manuscript database

    Improved efficacy and durability of powdery mildew resistance requires knowledge of the genetics of resistance and susceptibility and high resolution maps to facilitate combining of multiple resistance genes with desirable traits. In the current study, we studied the inheritance of resistance and s...

  1. High-resolution mapping of the Palos outflow channel: Preliminary results.

    NASA Astrophysics Data System (ADS)

    Rauhala, A. I.; Kukkonen, S.; Kostama, V.-P.

    2013-09-01

    We have begun a high-resolution geomorphic mapping of the "Palos outflow channel" in order to further characterize the paleofluvial activity in the Amenthes region. Preliminary findings, such as multiple instances of hanging valleys, suggest a complex history of flooding.

  2. ET mapping with high-resolution airborne remote sensing data in an advective semiarid environment

    USDA-ARS?s Scientific Manuscript database

    Accurate estimates of spatially distributed vegetation evapotranspiration (ET) are essential for managing water in irrigated regions and for hydrologic modeling. The METRIC**TM (Mapping ET at high Resolutions with Internal Calibration) energy balance algorithm was applied to derive ET from six very ...

  3. High Resolution QTL Maps Of 31 Traits in Contemporary U.S. Holstein Cows

    USDA-ARS?s Scientific Manuscript database

    High-resolution QTL maps of 1586 SNPs affecting 31 dairy traits (top 100 effects per trait)were constructed based on a genome-wide association analysis of 1,654 contemporary U.S. Holstein cows genotyped with 45,878 SNPs. The 31 traits include net merit and its 8 compnent traits, 4 calving traits, an...

  4. Rapid, High-Resolution Forest Structure and Terrain Mapping over Large Areas using Single Photon Lidar

    NASA Astrophysics Data System (ADS)

    Swatantran, Anu; Tang, Hao; Barrett, Terence; Decola, Phil; Dubayah, Ralph

    2016-06-01

    Single photon lidar (SPL) is an innovative technology for rapid forest structure and terrain characterization over large areas. Here, we evaluate data from an SPL instrument - the High Resolution Quantum Lidar System (HRQLS) that was used to map the entirety of Garrett County in Maryland, USA (1700 km2). We develop novel approaches to filter solar noise to enable the derivation of forest canopy structure and ground elevation from SPL point clouds. SPL attributes are compared with field measurements and an existing leaf-off, low-point density discrete return lidar dataset as a means of validation. We find that canopy and ground characteristics from SPL are similar to discrete return lidar despite differences in wavelength and acquisition periods but the higher point density of the SPL data provides more structural detail. Our experience suggests that automated noise removal may be challenging, particularly over high albedo surfaces and rigorous instrument calibration is required to reduce ground measurement biases to accepted mapping standards. Nonetheless, its efficiency of data collection, and its ability to produce fine-scale, three-dimensional structure over large areas quickly strongly suggests that SPL should be considered as an efficient and potentially cost-effective alternative to existing lidar systems for large area mapping.

  5. Rapid, High-Resolution Forest Structure and Terrain Mapping over Large Areas using Single Photon Lidar

    PubMed Central

    Swatantran, Anu; Tang, Hao; Barrett, Terence; DeCola, Phil; Dubayah, Ralph

    2016-01-01

    Single photon lidar (SPL) is an innovative technology for rapid forest structure and terrain characterization over large areas. Here, we evaluate data from an SPL instrument - the High Resolution Quantum Lidar System (HRQLS) that was used to map the entirety of Garrett County in Maryland, USA (1700 km2). We develop novel approaches to filter solar noise to enable the derivation of forest canopy structure and ground elevation from SPL point clouds. SPL attributes are compared with field measurements and an existing leaf-off, low-point density discrete return lidar dataset as a means of validation. We find that canopy and ground characteristics from SPL are similar to discrete return lidar despite differences in wavelength and acquisition periods but the higher point density of the SPL data provides more structural detail. Our experience suggests that automated noise removal may be challenging, particularly over high albedo surfaces and rigorous instrument calibration is required to reduce ground measurement biases to accepted mapping standards. Nonetheless, its efficiency of data collection, and its ability to produce fine-scale, three-dimensional structure over large areas quickly strongly suggests that SPL should be considered as an efficient and potentially cost-effective alternative to existing lidar systems for large area mapping. PMID:27329078

  6. Rapid, High-Resolution Forest Structure and Terrain Mapping over Large Areas using Single Photon Lidar.

    PubMed

    Swatantran, Anu; Tang, Hao; Barrett, Terence; DeCola, Phil; Dubayah, Ralph

    2016-06-22

    Single photon lidar (SPL) is an innovative technology for rapid forest structure and terrain characterization over large areas. Here, we evaluate data from an SPL instrument - the High Resolution Quantum Lidar System (HRQLS) that was used to map the entirety of Garrett County in Maryland, USA (1700 km(2)). We develop novel approaches to filter solar noise to enable the derivation of forest canopy structure and ground elevation from SPL point clouds. SPL attributes are compared with field measurements and an existing leaf-off, low-point density discrete return lidar dataset as a means of validation. We find that canopy and ground characteristics from SPL are similar to discrete return lidar despite differences in wavelength and acquisition periods but the higher point density of the SPL data provides more structural detail. Our experience suggests that automated noise removal may be challenging, particularly over high albedo surfaces and rigorous instrument calibration is required to reduce ground measurement biases to accepted mapping standards. Nonetheless, its efficiency of data collection, and its ability to produce fine-scale, three-dimensional structure over large areas quickly strongly suggests that SPL should be considered as an efficient and potentially cost-effective alternative to existing lidar systems for large area mapping.

  7. High-resolution, three-dimensional mapping of gene expression using GeneExpressMap (GEM).

    PubMed

    Flynn, C J; Sharma, T; Ruffins, S W; Guerra, S L; Crowley, J C; Ettensohn, C A

    2011-09-15

    The analysis of temporal and spatial patterns of gene expression is critically important for many kinds of developmental studies, including the construction of gene regulatory networks. Recently, multiplex, fluorescent, whole mount in situ hybridization (multiplex F-WMISH), applied in combination with confocal microscopy, has emerged as the method of choice for high-resolution, three-dimensional (3D) mapping of gene expression patterns in developing tissues. We have developed an image analysis tool, GeneExpressMap (GEM), that facilitates the rapid, 3D analysis of multiplex F-WMISH data at single-cell resolution. GEM assigns F-WMISH signal to individual cells based upon the proximity of cytoplasmic hybridization signal to cell nuclei. Here, we describe the features of GEM and, as a test of its utility, we use GEM to analyze patterns of regulatory gene expression in the non-skeletogenic mesoderm of the early sea urchin embryo. GEM greatly extends the power of multiplex F-WMISH for analyzing patterns of gene expression and is a valuable tool for gene network analysis and many other kinds of developmental studies. Copyright © 2011 Elsevier Inc. All rights reserved.

  8. High-resolution MRI velocimetry compared with numerical simulations

    NASA Astrophysics Data System (ADS)

    Edelhoff, Daniel; Walczak, Lars; Henning, Stefan; Weichert, Frank; Suter, Dieter

    2013-10-01

    Alterations of the blood flow are associated with various cardiovascular diseases. Precise knowledge of the velocity distribution is therefore important for understanding these diseases and predicting the effect of different medical intervention schemes. The goal of this work is to estimate the precision with which the velocity field can be measured and predicted by studying two simple model geometries with NMR micro imaging and computational fluid dynamics. For these initial experiments, we use water as an ideal test medium. The phantoms consist of tubes simulating a straight blood vessel and a step between two tubes of different diameters, which can be seen as a minimal model of the situation behind a stenosis. For both models, we compare the experimental data with the numerical prediction, using the experimental boundary conditions. For the simpler model, we also compare the data to the analytical solution. As an additional validation, we determine the divergence of the velocity field and verify that it vanishes within the experimental uncertainties. We discuss the resulting precision of the simulation and the outlook for extending this approach to the analysis of specific cases of arteriovascular problems.

  9. High-resolution comparative modeling with RosettaCM.

    PubMed

    Song, Yifan; DiMaio, Frank; Wang, Ray Yu-Ruei; Kim, David; Miles, Chris; Brunette, Tj; Thompson, James; Baker, David

    2013-10-08

    We describe an improved method for comparative modeling, RosettaCM, which optimizes a physically realistic all-atom energy function over the conformational space defined by homologous structures. Given a set of sequence alignments, RosettaCM assembles topologies by recombining aligned segments in Cartesian space and building unaligned regions de novo in torsion space. The junctions between segments are regularized using a loop closure method combining fragment superposition with gradient-based minimization. The energies of the resulting models are optimized by all-atom refinement, and the most representative low-energy model is selected. The CASP10 experiment suggests that RosettaCM yields models with more accurate side-chain and backbone conformations than other methods when the sequence identity to the templates is greater than ∼15%.

  10. Origin and propagation of human gastric slow-wave activity defined by high-resolution mapping

    PubMed Central

    Du, Peng; Cheng, Leo K.; Egbuji, John U.; Lammers, Wim J. E. P.; Windsor, John A.; Pullan, Andrew J.

    2010-01-01

    Slow waves coordinate gastric motility, and abnormal slow-wave activity is thought to contribute to motility disorders. The current understanding of normal human gastric slow-wave activity is based on extrapolation from data derived from sparse electrode recordings and is therefore potentially incomplete. This study employed high-resolution (HR) mapping to reevaluate human gastric slow-wave activity. HR mapping was performed in 12 patients with normal stomachs undergoing upper abdominal surgery, using flexible printed circuit board (PCB) arrays (interelectrode distance 7.6 mm). Up to six PCBs (192 electrodes; 93 cm2) were used simultaneously. Slow-wave activity was characterized by spatiotemporal mapping, and regional frequencies, amplitudes, and velocities were defined and compared. Slow-wave activity in the pacemaker region (mid to upper corpus, greater curvature) was of greater amplitude (mean 0.57 mV) and higher velocity (8.0 mm/s) than the corpus (0.25 mV, 3.0 mm/s) (P < 0.001) and displayed isotropic propagation. A marked transition to higher amplitude and velocity activity occurred in the antrum (0.52 mV, 5.9 mm/s) (P < 0.001). Multiple (3–4) wavefronts were found to propagate simultaneously in the organoaxial direction. Frequencies were consistent between regions (2.83 ± 0.35 cycles per min). HR mapping has provided a more complete understanding of normal human gastric slow-wave activity. The pacemaker region is associated with high-amplitude, high-velocity activity, and multiple wavefronts propagate simultaneously. These data provide a baseline for future HR mapping studies in disease states and will inform noninvasive diagnostic strategies. PMID:20595620

  11. Direct Push Optical Screening Tool for High-Resolution, Real-Time Mapping of Chlorinated Solvent DNAPL Architecture

    DTIC Science & Technology

    2016-04-01

    FINAL REPORT Direct Push Optical Screening Tool for High-Resolution, Real- Time Mapping of Chlorinated Solvent DNAPL Architecture ESTCP Project ER...Direct Push Optical Screening Tool for High Resolution, Real-time Mapping of Chlorinated Solvent DNAPL Architecture Murray Einarson Haley...for real-time, high-resolution mapping of petroleum hydrocarbon and coal tar-based NAPL source zones. The objective of this project is to demonstrate

  12. Direct Push Optical Screening Tool for High Resolution, Real-Time Mapping of Chlorinated Solvent DNAPL Architecture

    DTIC Science & Technology

    2016-07-01

    ER-201121) Direct Push Optical Screening Tool for High- Resolution, Real-Time Mapping of Chlorinated Solvent DNAPL Architecture July 2016 This...Report April 2011 - March 2016 Direct Push Optical Screening Tool for High Resolution, Real-time Mapping of Chlorinated Solvent DNAPL Architecture...tools are currently available for real-time, high-resolution mapping of petroleum hydrocarbon and coal tar-based NAPL source zones. The objective of

  13. High-resolution mirror temperature mapping in GaN-based diode lasers by thermoreflectance spectroscopy

    NASA Astrophysics Data System (ADS)

    Pierścińska, Dorota; Marona, Łucja; Pierściński, Kamil; Wiśniewski, Przemysław; Perlin, Piotr; Bugajski, Maciej

    2017-02-01

    In this paper accurate measurements of temperature distribution on the facet of GaN-based diode lasers are presented as well as development of the instrumentation for high-resolution thermal imaging based on thermoreflectance. It is shown that thermoreflectance can be successfully applied to provide information on heat dissipation in these devices. We demonstrate the quantitative measurements of the temperature profiles and high-resolution temperature maps on the front facet of nitride lasers and prove that thermoreflectance spectroscopy can be considered as the accurate and fast nondestructive tool for investigation of thermally induced degradation modes of GaN lasers.

  14. High-Resolution Mapping of H1 Linker Histone Variants in Embryonic Stem Cells

    PubMed Central

    Cao, Kaixiang; Lee, Eva K.; Wu, Hongwei; Medrzycki, Magdalena; Pan, Chenyi; Ho, Po-Yi; Cooper, Guy P.; Dong, Xiao; Bock, Christoph; Bouhassira, Eric E.; Fan, Yuhong

    2013-01-01

    H1 linker histones facilitate higher-order chromatin folding and are essential for mammalian development. To achieve high-resolution mapping of H1 variants H1d and H1c in embryonic stem cells (ESCs), we have established a knock-in system and shown that the N-terminally tagged H1 proteins are functionally interchangeable to their endogenous counterparts in vivo. H1d and H1c are depleted from GC- and gene-rich regions and active promoters, inversely correlated with H3K4me3, but positively correlated with H3K9me3 and associated with characteristic sequence features. Surprisingly, both H1d and H1c are significantly enriched at major satellites, which display increased nucleosome spacing compared with bulk chromatin. While also depleted at active promoters and enriched at major satellites, overexpressed H10 displays differential binding patterns in specific repetitive sequences compared with H1d and H1c. Depletion of H1c, H1d, and H1e causes pericentric chromocenter clustering and de-repression of major satellites. These results integrate the localization of an understudied type of chromatin proteins, namely the H1 variants, into the epigenome map of mouse ESCs, and we identify significant changes at pericentric heterochromatin upon depletion of this epigenetic mark. PMID:23633960

  15. Land use/land cover mapping using multi-scale texture processing of high resolution data

    NASA Astrophysics Data System (ADS)

    Wong, S. N.; Sarker, M. L. R.

    2014-02-01

    Land use/land cover (LULC) maps are useful for many purposes, and for a long time remote sensing techniques have been used for LULC mapping using different types of data and image processing techniques. In this research, high resolution satellite data from IKONOS was used to perform land use/land cover mapping in Johor Bahru city and adjacent areas (Malaysia). Spatial image processing was carried out using the six texture algorithms (mean, variance, contrast, homogeneity, entropy, and GLDV angular second moment) with five difference window sizes (from 3×3 to 11×11). Three different classifiers i.e. Maximum Likelihood Classifier (MLC), Artificial Neural Network (ANN) and Supported Vector Machine (SVM) were used to classify the texture parameters of different spectral bands individually and all bands together using the same training and validation samples. Results indicated that texture parameters of all bands together generally showed a better performance (overall accuracy = 90.10%) for land LULC mapping, however, single spectral band could only achieve an overall accuracy of 72.67%. This research also found an improvement of the overall accuracy (OA) using single-texture multi-scales approach (OA = 89.10%) and single-scale multi-textures approach (OA = 90.10%) compared with all original bands (OA = 84.02%) because of the complementary information from different bands and different texture algorithms. On the other hand, all of the three different classifiers have showed high accuracy when using different texture approaches, but SVM generally showed higher accuracy (90.10%) compared to MLC (89.10%) and ANN (89.67%) especially for the complex classes such as urban and road.

  16. Application of high-resolution multispectral data for mapping blue ice areas in the Antarctic environment

    NASA Astrophysics Data System (ADS)

    Jawak, Shridhar D.; Luis, Alvarinho J.

    2016-05-01

    High resolution calibrated PAN-sharpened images from WorldView-2 (WV-2) were used for extracting blue ice areas in Schirmacher Oasis, east Antarctica. The Schirmacher oasis extends from 70°45' S to 70° 75' S and 11°38' E to 11° 38' E. Blue ice areas represents long-term ablation. The amplitude of blue ice is lower than that of snow, because the ice surface is smoother than the latter. But the difference is not so obvious when applying automatic extraction techniques. To achieve desirable results and support comparative analysis, multiband image combinations were generated from atmospherically-corrected WV-2 data. For feature extraction process, regions of interest (ROI) were considered in which blue ice was used as target and white snow/ice appearing on the blue ice was considered as non-target. Various semiautomatic feature extraction methods, such as, target detection, mapping methods, etc, and many trials were used for extracting blue ice areas. Surface patterns of alternating snow and blue ice bands were found in east Antarctica which becomes obstacle to clearly extract blue ice feature. From the high resolution WV-2 data, reference data (digitized data) were prepared for blue ice area. By comparing reference data and extracted data, bias and root mean square (RMS) error values were calculated. Accuracy assessment was done considering the entire necessary prior results of the blue ice area. Our results indicate that the pixel-based supervised classification methods yielded an overall accuracy ranging from 82%-89% for extraction of blue ice areas.

  17. Aircraft Detection in High-Resolution SAR Images Based on a Gradient Textural Saliency Map

    PubMed Central

    Tan, Yihua; Li, Qingyun; Li, Yansheng; Tian, Jinwen

    2015-01-01

    This paper proposes a new automatic and adaptive aircraft target detection algorithm in high-resolution synthetic aperture radar (SAR) images of airport. The proposed method is based on gradient textural saliency map under the contextual cues of apron area. Firstly, the candidate regions with the possible existence of airport are detected from the apron area. Secondly, directional local gradient distribution detector is used to obtain a gradient textural saliency map in the favor of the candidate regions. In addition, the final targets will be detected by segmenting the saliency map using CFAR-type algorithm. The real high-resolution airborne SAR image data is used to verify the proposed algorithm. The results demonstrate that this algorithm can detect aircraft targets quickly and accurately, and decrease the false alarm rate. PMID:26378543

  18. Aircraft Detection in High-Resolution SAR Images Based on a Gradient Textural Saliency Map.

    PubMed

    Tan, Yihua; Li, Qingyun; Li, Yansheng; Tian, Jinwen

    2015-09-11

    This paper proposes a new automatic and adaptive aircraft target detection algorithm in high-resolution synthetic aperture radar (SAR) images of airport. The proposed method is based on gradient textural saliency map under the contextual cues of apron area. Firstly, the candidate regions with the possible existence of airport are detected from the apron area. Secondly, directional local gradient distribution detector is used to obtain a gradient textural saliency map in the favor of the candidate regions. In addition, the final targets will be detected by segmenting the saliency map using CFAR-type algorithm. The real high-resolution airborne SAR image data is used to verify the proposed algorithm. The results demonstrate that this algorithm can detect aircraft targets quickly and accurately, and decrease the false alarm rate.

  19. New approaches to high-resolution mapping of marine vertical structures.

    PubMed

    Robert, Katleen; Huvenne, Veerle A I; Georgiopoulou, Aggeliki; Jones, Daniel O B; Marsh, Leigh; D O Carter, Gareth; Chaumillon, Leo

    2017-08-21

    Vertical walls in marine environments can harbour high biodiversity and provide natural protection from bottom-trawling activities. However, traditional mapping techniques are usually restricted to down-looking approaches which cannot adequately replicate their 3D structure. We combined sideways-looking multibeam echosounder (MBES) data from an AUV, forward-looking MBES data from ROVs and ROV-acquired videos to examine walls from Rockall Bank and Whittard Canyon, Northeast Atlantic. High-resolution 3D point clouds were extracted from each sonar dataset and structure from motion photogrammetry (SfM) was applied to recreate 3D representations of video transects along the walls. With these reconstructions, it was possible to interact with extensive sections of video footage and precisely position individuals. Terrain variables were derived on scales comparable to those experienced by megabenthic individuals. These were used to show differences in environmental conditions between observed and background locations as well as explain spatial patterns in ecological characteristics. In addition, since the SfM 3D reconstructions retained colours, they were employed to separate and quantify live coral colonies versus dead framework. The combination of these new technologies allows us, for the first time, to map the physical 3D structure of previously inaccessible habitats and demonstrates the complexity and importance of vertical structures.

  20. High-Resolution Debris Flow Volume Mapping with Unmanned Aerial Systems (uas) and Photogrammetric Techniques

    NASA Astrophysics Data System (ADS)

    Adams, M. S.; Fromm, R.; Lechner, V.

    2016-06-01

    Debris flows cause an average € 30 million damages and 1-2 fatalities every year in Austria. Detailed documentation of their extent and magnitude is essential for understanding, preventing and mitigating these natural hazard events. The recent development of unmanned aerial systems (UAS) has provided a new possibility for on-demand high-resolution monitoring and mapping. Here, we present a study, where the spatial extent and volume of a large debris flow event were mapped with different UAS, fitted with commercial off-the-shelf sensors. Orthophotos and digital terrain models (DTM) were calculated using structure-from-motion photogrammetry software. Terrain height differences caused by the debris flow in the catchment and valley floor were derived by subtracting the pre-event airborne laser scanning (ALS) DTM from a post-event UAS-DTM. The analysis of the volumetric sediment budget showed, that approximately 265,000 m³ material was mobilised in the catchment, of which 45,000 m³ settled there; of the material, which reached the valley floor, 120,000 m³ was deposited, while another 10,000 m³ was eroded from there. The UAS-results were validated against ALS data and imagery from a traditional manned-aircraft photogrammetry campaign. In conclusion, the UAS-data can reach an accuracy and precision comparable to manned aircraft data, but with the added benefits of higher flexibility, easier repeatability, less operational constraints and higher spatial resolution.

  1. High-resolution hydraulic parameter maps for surface soils in tropical South America

    NASA Astrophysics Data System (ADS)

    Marthews, T. R.; Quesada, C. A.; Galbraith, D. R.; Malhi, Y.; Mullins, C. E.; Hodnett, M. G.; Dharssi, I.

    2014-05-01

    Modern land surface model simulations capture soil profile water movement through the use of soil hydraulics sub-models, but good hydraulic parameterisations are often lacking, especially in the tropics. We present much-improved gridded data sets of hydraulic parameters for surface soil for the critical area of tropical South America, describing soil profile water movement across the region to 30 cm depth. Optimal hydraulic parameter values are given for the Brooks and Corey, Campbell, van Genuchten-Mualem and van Genuchten-Burdine soil hydraulic models, which are widely used hydraulic sub-models in land surface models. This has been possible through interpolating soil measurements from several sources through the SOTERLAC soil and terrain data base and using the most recent pedotransfer functions (PTFs) derived for South American soils. All soil parameter data layers are provided at 15 arcsec resolution and available for download, this being 20x higher resolution than the best comparable parameter maps available to date. Specific examples are given of the use of PTFs and the importance highlighted of using PTFs that have been locally parameterised and that are not just based on soil texture. We discuss current developments in soil hydraulic modelling and how high-resolution parameter maps such as these can improve the simulation of vegetation development and productivity in land surface models.

  2. High-resolution hydraulic parameter maps for surface soils in tropical South America

    NASA Astrophysics Data System (ADS)

    Marthews, T. R.; Quesada, C. A.; Galbraith, D. R.; Malhi, Y.; Mullins, C. E.; Hodnett, M. G.; Dharssi, I.

    2013-12-01

    Modern land surface model simulations capture soil profile water movement through the use of soil hydraulics sub-models, but good hydraulic parameterisations are often lacking, especially in the tropics. We present much-improved gridded datasets of hydraulic parameters for surface soil for the critical area of tropical South America, describing soil profile water movement across the region to 30 cm depth. Optimal hydraulic parameter values are given for the Brooks and Corey, Campbell, van Genuchten-Mualem and van Genuchten-Burdine soil hydraulic models, which are widely-used hydraulic sub-models in Land Surface Models. This has been possible through interpolating soil measurements from several sources through the SOTERLAC soil and terrain database and using the most recent pedotransfer functions (PTFs) derived for South American soils. All soil parameter data layers are provided at 15 arcsec resolution and available for download, this being 20 × higher resolution than the best comparable parameter maps available to date. Specific examples are given of the use of PTFs and the importance highlighted of using PTFs that have been locally-parameterised and that are not just based on soil texture. Details are provided specifically on how to assemble the ancillary data files required for grid-based vegetation simulation using the Joint UK Land Environment Simulator (JULES). We discuss current developments in soil hydraulic modelling and how high-resolution parameter maps such as these can improve the simulation of vegetation development and productivity in land surface models.

  3. Ecosystem services of boreal forests - Carbon budget mapping at high resolution.

    PubMed

    Akujärvi, Anu; Lehtonen, Aleksi; Liski, Jari

    2016-10-01

    The carbon (C) cycle of forests produces ecosystem services (ES) such as climate regulation and timber production. Mapping these ES using simple land cover -based proxies might add remarkable inaccuracy to the estimates. A framework to map the current status of the C budget of boreal forested landscapes was developed. The C stocks of biomass and soil and the annual change in these stocks were quantified in a 20 × 20 m resolution at the regional level on mineral soils in southern Finland. The fine-scale variation of the estimates was analyzed geo-statistically. The reliability of the estimates was evaluated by comparing them to measurements from the national multi-source forest inventory. The C stocks of forests increased slightly from the south coast to inland whereas the changes in these stocks were more uniform. The spatial patches of C stocks were larger than those of C stock changes. The patch size of the C stocks reflected the spatial variation in the environmental conditions, and that of the C stock changes the typical area of forest management compartments. The simulated estimates agreed well with the measurements indicating a good mapping framework performance. The mapping framework is the basis for evaluating the effects of forest management alternatives on C budget at high resolution across large spatial scales. It will be coupled with the assessment of other ES and biodiversity to study their relationships. The framework integrated a wide suite of simulation models and extensive inventory data. It provided reliable estimates of the human influence on C cycle in forested landscapes.

  4. Soil Erosion map of Europe based on high resolution input datasets

    NASA Astrophysics Data System (ADS)

    Panagos, Panos; Borrelli, Pasquale; Meusburger, Katrin; Ballabio, Cristiano; Alewell, Christine

    2015-04-01

    Modelling soil erosion in European Union is of major importance for agro-environmental policies. Soil erosion estimates are important inputs for the Common Agricultural Policy (CAP) and the implementation of the Soil Thematic Strategy. Using the findings of a recent pan-European data collection through the EIONET network, it was concluded that most Member States are applying the empirical Revised Universal Soil Loss Equation (RUSLE) for the modelling soil erosion at National level. This model was chosen for the pan-European soil erosion risk assessment and it is based on 6 input factors. Compared to past approaches, each of the factors is modelled using the latest pan-European datasets, expertise and data from Member states and high resolution remote sensing data. The soil erodibility (K-factor) is modelled using the recently published LUCAS topsoil database with 20,000 point measurements and incorporating the surface stone cover which can reduce K-factor by 15%. The rainfall erosivity dataset (R-factor) has been implemented using high temporal resolution rainfall data from more than 1,500 precipitation stations well distributed in Europe. The cover-management (C-factor) incorporates crop statistics and management practices such as cover crops, tillage practices and plant residuals. The slope length and steepness (combined LS-factor) is based on the first ever 25m Digital Elevation Model (DEM) of Europe. Finally, the support practices (P-factor) is modelled for first time at this scale taking into account the 270,000 LUCAS earth observations and the Good Agricultural and Environmental Condition (GAEC) that farmers have to follow in Europe. The high resolution input layers produce the final soil erosion risk map at 100m resolution and allow policy makers to run future land use, management and climate change scenarios.

  5. Automated high resolution mapping of coffee in Rwanda using an expert Bayesian network

    NASA Astrophysics Data System (ADS)

    Mukashema, A.; Veldkamp, A.; Vrieling, A.

    2014-12-01

    African highland agro-ecosystems are dominated by small-scale agricultural fields that often contain a mix of annual and perennial crops. This makes such systems difficult to map by remote sensing. We developed an expert Bayesian network model to extract the small-scale coffee fields of Rwanda from very high resolution data. The model was subsequently applied to aerial orthophotos covering more than 99% of Rwanda and on one QuickBird image for the remaining part. The method consists of a stepwise adjustment of pixel probabilities, which incorporates expert knowledge on size of coffee trees and fields, and on their location. The initial naive Bayesian network, which is a spectral-based classification, yielded a coffee map with an overall accuracy of around 50%. This confirms that standard spectral variables alone cannot accurately identify coffee fields from high resolution images. The combination of spectral and ancillary data (DEM and a forest map) allowed mapping of coffee fields and associated uncertainties with an overall accuracy of 87%. Aggregated to district units, the mapped coffee areas demonstrated a high correlation with the coffee areas reported in the detailed national coffee census of 2009 (R2 = 0.92). Unlike the census data our map provides high spatial resolution of coffee area patterns of Rwanda. The proposed method has potential for mapping other perennial small scale cropping systems in the East African Highlands and elsewhere.

  6. High-resolution Ceres High Altitude Mapping Orbit atlas derived from Dawn Framing Camera images

    NASA Astrophysics Data System (ADS)

    Roatsch, Th.; Kersten, E.; Matz, K.-D.; Preusker, F.; Scholten, F.; Jaumann, R.; Raymond, C. A.; Russell, C. T.

    2016-09-01

    The Dawn spacecraft Framing Camera (FC) acquired over 2400 clear filter images of Ceres with a resolution of about 140 m/pixel during the six cycles in the High Altitude Mapping Orbit (HAMO) phase between August 18 and October 21, 2015. We ortho-rectified the images from the first cycle and produced a global, high-resolution, controlled photomosaic of Ceres. This global mosaic is the basis for a high-resolution Ceres atlas that consists of 15 tiles mapped at a scale of 1:750,000. The nomenclature used in this atlas was proposed by the Dawn team and was approved by the International Astronomical Union (IAU). The full atlas is available to the public through the Dawn Geographical Information System (GIS) web page

  7. High-resolution Ceres Low Altitude Mapping Orbit Atlas derived from Dawn Framing Camera images

    NASA Astrophysics Data System (ADS)

    Roatsch, Th.; Kersten, E.; Matz, K.-D.; Preusker, F.; Scholten, F.; Jaumann, R.; Raymond, C. A.; Russell, C. T.

    2017-06-01

    The Dawn spacecraft Framing Camera (FC) acquired over 31,300 clear filter images of Ceres with a resolution of about 35 m/pxl during the eleven cycles in the Low Altitude Mapping Orbit (LAMO) phase between December 16 2015 and August 8 2016. We ortho-rectified the images from the first four cycles and produced a global, high-resolution, uncontrolled photomosaic of Ceres. This global mosaic is the basis for a high-resolution Ceres atlas that consists of 62 tiles mapped at a scale of 1:250,000. The nomenclature used in this atlas was proposed by the Dawn team and was approved by the International Astronomical Union (IAU). The full atlas is available to the public through the Dawn Geographical Information System (GIS) web page [http://dawngis.dlr.de/atlas] and will become available through the NASA Planetary Data System (PDS) (http://pdssbn.astro.umd.edu/).

  8. Upsampling range camera depth maps using high-resolution vision camera and pixel-level confidence classification

    NASA Astrophysics Data System (ADS)

    Tian, Chao; Vaishampayan, Vinay; Zhang, Yifu

    2011-03-01

    We consider the problem of upsampling a low-resolution depth map generated by a range camera, by using information from one or more additional high-resolution vision cameras. The goal is to provide an accurate high resolution depth map from the viewpoint of one of the vision cameras. We propose an algorithm that first converts the low resolution depth map into a depth/disparity map through coordinate mappings into the coordinate frame of one vision camera, then classifies the pixels into regions according to whether the range camera depth map is trustworthy, and finally refine the depth values for the pixels in the untrustworthy regions. For the last refinement step, both a method based on graph cut optimization and that based on bilateral filtering are examined. Experimental results show that the proposed methods using classification are able to upsample the depth map by a factor of 10 x 10 with much improved depth details, with significantly better accuracy comparing to those without the classification. The improvements are visually perceptible on a 3D auto-stereoscopic display.

  9. High-resolution mapping of mass loss from highly evolved carbon stars

    NASA Technical Reports Server (NTRS)

    Ball, R.

    1986-01-01

    The molecular component of the mass outflow at high resolution was mapped with the Owens Valley Millimeter-Wave Interferometer in two well-known objects, CRL 2688 and CIT 6. Interferometric observations of a pair of carbon stars which are evolving toward the planetary nebula stage have revealed evidence of episodic, nonspherically symmetric mass loss, and may lead to a fuller understanding of shielding properties of the dust grains involved in these flows.

  10. Advanced Ecosystem Mapping Techniques for Large Arctic Study Domains Using Calibrated High-Resolution Imagery

    NASA Astrophysics Data System (ADS)

    Macander, M. J.; Frost, G. V., Jr.

    2015-12-01

    Regional-scale mapping of vegetation and other ecosystem properties has traditionally relied on medium-resolution remote sensing such as Landsat (30 m) and MODIS (250 m). Yet, the burgeoning availability of high-resolution (<=2 m) imagery and ongoing advances in computing power and analysis tools raises the prospect of performing ecosystem mapping at fine spatial scales over large study domains. Here we demonstrate cutting-edge mapping approaches over a ~35,000 km² study area on Alaska's North Slope using calibrated and atmospherically-corrected mosaics of high-resolution WorldView-2 and GeoEye-1 imagery: (1) an a priori spectral approach incorporating the Satellite Imagery Automatic Mapper (SIAM) algorithms; (2) image segmentation techniques; and (3) texture metrics. The SIAM spectral approach classifies radiometrically-calibrated imagery to general vegetation density categories and non-vegetated classes. The SIAM classes were developed globally and their applicability in arctic tundra environments has not been previously evaluated. Image segmentation, or object-based image analysis, automatically partitions high-resolution imagery into homogeneous image regions that can then be analyzed based on spectral, textural, and contextual information. We applied eCognition software to delineate waterbodies and vegetation classes, in combination with other techniques. Texture metrics were evaluated to determine the feasibility of using high-resolution imagery to algorithmically characterize periglacial surface forms (e.g., ice-wedge polygons), which are an important physical characteristic of permafrost-dominated regions but which cannot be distinguished by medium-resolution remote sensing. These advanced mapping techniques provide products which can provide essential information supporting a broad range of ecosystem science and land-use planning applications in northern Alaska and elsewhere in the circumpolar Arctic.

  11. Connecting geomorphology to dust emission through high-resolution mapping of global land cover and sediment supply

    NASA Astrophysics Data System (ADS)

    Parajuli, Sagar Prasad; Zender, Charles S.

    2017-08-01

    A key challenge in modeling dust emissions is to represent the location and strength of dust sources. One critical aspect of dust sources that is not well understood and thus not represented in dust models is their geomorphology. In this work, we investigate the geomorphology of global dust sources by developing two high-resolution (∼500 m), seamless, global maps. First is a land surface map in which landforms are classified into different categories based on geomorphology using an image classification technique. The land surface map shows the distribution of landforms in dust source regions and is useful in defining the boundaries of different dust sources in dust models. Second is the sediment supply map developed by combining the upstream drainage area with the visible reflectance retrieved by the Moderate-resolution Imaging Spectroradiometer (MODIS). This map, due to the inclusion of surface reflectance, highlights dust sources such as playa/sabkha and sand dunes and anthropogenic dust sources such as agricultural areas, that may not be captured by the commonly used elevation-based erodibility maps. We establish the connection between geomorphology and dust emission by comparing the sediment supply map with the land surface map and dust frequency map, qualitatively and quantitatively. We show that the sediment supply is linked to the land surface type and that playa/sabkha corresponds to the greatest inferred sediment supply. The sediment supply map is largely consistent with the land surface map and correlates well with the frequency of occurrence map derived from high-resolution MODIS level-2 aerosol optical depth (AOD) data.

  12. Mapping trees in high resolution imagery across large areas using locally variable thresholds guided by medium resolution tree maps

    NASA Astrophysics Data System (ADS)

    Fisher, Adrian; Danaher, Tim; Gill, Tony

    2017-06-01

    Large area tree maps, important for environmental monitoring and natural resource management, are often based on medium resolution satellite imagery. These data have difficulty in detecting trees in fragmented woodlands, and have significant omission errors in modified agricultural areas. High resolution imagery can better detect these trees, however, as most high resolution imagery is not normalised it is difficult to automate a tree classification method over large areas. The method developed here used an existing medium resolution map derived from either Landsat or SPOT5 satellite imagery to guide the classification of the high resolution imagery. It selected a spatially-variable threshold on the green band, calculated based on the spatially-variable percentage of trees in the existing map of tree cover. The green band proved more consistent at classifying trees across different images than several common band combinations. The method was tested on 0.5 m resolution imagery from airborne digital sensor (ADS) imagery across New South Wales (NSW), Australia using both Landsat and SPOT5 derived tree maps to guide the threshold selection. Accuracy was assessed across 6 large image mosaics revealing a more accurate result when the more accurate tree map from SPOT5 imagery was used. The resulting maps achieved an overall accuracy with 95% confidence intervals of 93% (90-95%), while the overall accuracy of the previous SPOT5 tree map was 87% (86-89%). The method reduced omission errors by mapping more scattered trees, although it did increase commission errors caused by dark pixels from water, building shadows, topographic shadows, and some soils and crops. The method allows trees to be automatically mapped at 5 m resolution from high resolution imagery, provided a medium resolution tree map already exists.

  13. A hyper-temporal remote sensing protocol for high-resolution mapping of ecological sites

    PubMed Central

    Karl, Jason W.

    2017-01-01

    sites) spectral variability through time, 2) field sampling protocols that accurately characterize key soil properties (e.g., texture, depth) need to be adopted, and 3) additional environmental covariates (e.g. terrain attributes) need to be evaluated that may help further differentiate sites with similar spectral signals. Finally, the proposed hyper-temporal remote sensing framework may provide a standardized approach to evaluate and test our ecological site concepts through examining differences in vegetation dynamics in response to climatic variability and other drivers of land-use change. Results from this study demonstrate the efficacy of the hyper-temporal remote sensing approach for high resolution mapping of ecological sites, and highlights its utility in terms of reduced cost and time investment relative to traditional manual mapping approaches. PMID:28414731

  14. A hyper-temporal remote sensing protocol for high-resolution mapping of ecological sites.

    PubMed

    Maynard, Jonathan J; Karl, Jason W

    2017-01-01

    ) spectral variability through time, 2) field sampling protocols that accurately characterize key soil properties (e.g., texture, depth) need to be adopted, and 3) additional environmental covariates (e.g. terrain attributes) need to be evaluated that may help further differentiate sites with similar spectral signals. Finally, the proposed hyper-temporal remote sensing framework may provide a standardized approach to evaluate and test our ecological site concepts through examining differences in vegetation dynamics in response to climatic variability and other drivers of land-use change. Results from this study demonstrate the efficacy of the hyper-temporal remote sensing approach for high resolution mapping of ecological sites, and highlights its utility in terms of reduced cost and time investment relative to traditional manual mapping approaches.

  15. Correlation of scar in cardiac MRI and high-resolution contact mapping of left ventricle in a chronic infarct model.

    PubMed

    Thajudeen, Anees; Jackman, Warren M; Stewart, Brian; Cokic, Ivan; Nakagawa, Hiroshi; Shehata, Michael; Amorn, Allen M; Kali, Avinash; Liu, Ezh; Harlev, Doron; Bennett, Nathan; Dharmakumar, Rohan; Chugh, Sumeet S; Wang, Xunzhang

    2015-06-01

    Endocardial mapping for scars and abnormal electrograms forms the most essential component of ventricular tachycardia ablation. The utility of ultra-high resolution mapping of ventricular scar was assessed using a multielectrode contact mapping system in a chronic canine infarct model. Chronic infarcts were created in five anesthetized dogs by ligating the left anterior descending coronary artery. Late gadolinium-enhanced magnetic resonance imaging (LGE MRI) was obtained 4.9 ± 0.9 months after infarction, with three-dimensional (3D) gadolinium enhancement signal intensity maps at 1-mm and 5-mm depths from the endocardium. Ultra-high resolution electroanatomical maps were created using a novel mapping system (Rhythmia Mapping System, Rhythmia Medical/Boston Scientific, Marlborough, MA, USA) Rhythmia Medical, Boston Scientific, Marlborough, MA, USA with an 8.5F catheter with mini-basket electrode array (64 tiny electrodes, 2.5-mm spacing, center-to-center). The maps contained 7,754 ± 1,960 electrograms per animal with a mean resolution of 2.8 ± 0.6 mm. Low bipolar voltage (<2 mV) correlated closely with scar on the LGE MRI and the 3D signal intensity map (1-mm depth). The scar areas between the MRI signal intensity map and electroanatomic map matched at 87.7% of sites. Bipolar and unipolar voltages, compared in 592 electrograms from four MRI-defined scar types (endocardial scar, epicardial scar, mottled transmural scar, and dense transmural scar) as well as normal tissue, were significantly different. A unipolar voltage of <13 mV correlated with transmural extension of scar in MRI. Electrograms exhibiting isolated late potentials (ILPs) were manually annotated and ILP maps were created showing ILP location and timing. ILPs were identified in 203 ± 159 electrograms per dog (within low-voltage areas) and ILP maps showed gradation in timing of ILPs at different locations in the scar. Ultra-high resolution contact electroanatomical mapping accurately localizes

  16. High resolution critical habitat mapping and classification of tidal freshwater wetlands in the ACE Basin

    NASA Astrophysics Data System (ADS)

    Strickland, Melissa Anne

    In collaboration with the South Carolina Department of Natural Resources ACE Basin National Estuarine Research Reserve (ACE Basin NERR), the tidal freshwater ecosystems along the South Edisto River in the ACE Basin are being accurately mapped and classified using a LIDAR-Remote Sensing Fusion technique that integrates LAS LIDAR data into texture images and then merges the elevation textures and multispectral imagery for very high resolution mapping. This project discusses the development and refinement of an ArcGIS Toolbox capable of automating protocols and procedures for marsh delineation and microhabitat identification. The result is a high resolution habitat and land use map used for the identification of threatened habitat. Tidal freshwater wetlands are also a critical habitat for colonial wading birds and an accurate assessment of community diversity and acreage of this habitat type in the ACE Basin will support SCDNR's conservation and protection efforts. The maps developed by this study will be used to better monitor the freshwater/saltwater interface and establish a baseline for an ACE NERR monitoring program to track the rates and extent of alterations due to projected environmental stressors. Preliminary ground-truthing in the field will provide information about the accuracy of the mapping tool.

  17. Contamination-free transmission electron microscopy for high-resolution carbon elemental mapping of polymers.

    PubMed

    Horiuchi, Shin; Hanada, Takeshi; Ebisawa, Masaharu; Matsuda, Yasuhiro; Kobayashi, Motoyasu; Takahara, Atsushi

    2009-05-26

    Specimen contamination induced by electron beam irradiation has long been a serious problem for high-resolution imaging and analysis by a transmission electron microscope (TEM). It creates a deposition of carbonaceous compounds on a region under study, causing the loss of resolution. We developed a method to reduce the beam-induced specimen contamination by cleaning a TEM with activated oxygen radicals. The hydrocarbon contaminants accumulated inside the microscope's chamber can be etched away by gentle chemical oxidation without causing any damage to the microscope. The "contamination-free TEM" can effectively suppress the deposition of carbon-rich products on a specimen and therefore enables us to perform high-resolution carbon elemental mapping by energy-filtering transmission electron microscopy (EFTEM). In this study, we investigated the structure of polymer brushes immobilized on a silica nanoparticle (SiNP), of which molecular weight, length, and density of the brushes had been characterized in detail. The isolated particle showed the stretched formations of the polymer chains growing from the surface, while the densely distributed particles showed the connection of the polymer chains between neighboring particles. Moreover, the polymer brush layer and the surface initiator could be differentiated from each other by the component-specific contrast achieved by electron spectroscopic imaging (ESI). The contamination-free TEM can allow us to perform high-resolution carbon mapping and is expected to provide deep insights of soft materials' nanostructures.

  18. Structural Mapping and Geomorphology of Ireland's Southwest Continental Shelf Using High Resolution Sonar

    NASA Astrophysics Data System (ADS)

    Bowden, S.; Wireman, R.

    2016-02-01

    Bathymetric surveys were conducted on the continental shelf off the southwest coast of County Cork, Ireland by the Marine Institute of Ireland, the Geological Survey of Ireland, and the INFOMAR project. Data were collected from July 2006 through September 2014 using a Kongsberg EM2040 multibeam echosounder aboard the R/Vs Celtic Voyager and Keary, and a Kongsberg EM1002 on the R/V Celtic Explorer. Sonar data were post-processed with CARIS HIPS and SIPS 9.0 to create 2D and 3D bathymetric and backscatter intensity surfaces with a resolution of 1 m. The offshore study site is part of the 286 Ma western Variscian orogenic front and has several massive outcrops, exhibiting 5 to 20 m of near-vertical relief. These outcrops were structurally mapped and relatively aged, and exhibit significant folding, rotation, tilting, and joint systems. Google Earth, ArcGIS, and previous terrestrial studies were used to further analyze how geomorphology is controlled by seafloor composition and structural features. Rock type and age were interpreted by comparing fracture analysis of the joints and fold trends to similar onshore outcrops documented previously, to determine an age of 416-299 Ma for the shelf's outcropping strata and associated structural features. The oldest features observed are regional anticlines and synclines containing Upper Devonian Old Red Sandstone and Lower Carboniferous shales. Within the shale layers are NE-SW plunging parasitic chevron folds. Jointing is observed in both sandstone and shale layers and is superimposed on chevron folding, with cross joints appearing to influence shallow current patterns. Rotation of the regional folds is the youngest structural feature, as both the parasitic folds and joint systems are warped. Our study shows that high resolution sonar is an effective tool for offshore structural mapping and is an important resource for understanding the geomorphology and geologic history of submerged outcrops on continental shelf systems.

  19. High Resolution Mapping of Reference ET for the State of Wyoming

    NASA Astrophysics Data System (ADS)

    Rasmussen, R. W.; Park, G.

    2010-12-01

    Accurate estimation of Consumptive Use (CU) and Consumptive Irrigation Requirement (CIR) are essential components for water resources planning and management. The Wyoming State Engineer’s Office currently determines monthly reference evapotranspiration (ET) with an Excel Spreadsheet ET model using average monthly data from a nearby weather station (usually an airport weather station) for the irrigated area of interest. The monthly reference ET is then interpolated into daily reference ET using either linear or cubic functions. The purpose of this project is to enhance the current Excel model with a GIS-based ET calculator. Our approach will use daily weather data to calculate reference ET and actual ET, and then aggregate them into monthly and seasonal ET. Among the many reference ET equations available, the ASCE Standardized Reference Evapotranspiration Equation (ASCE-ET) and the Hargreaves-Samani equations were selected to calculate daily reference ET. Data needed for the equations (minimum and maximum temperatures, wind speed, and dew point temperature) was gathered at various resolutions from several sources, such as weather stations in Wyoming and from the National Centers for Environmental Prediction (NCEP). High resolution (1km x 1km) gridded reference ET maps were produced from interpolated weather data for the three major river basins in southern Wyoming (North Platte River, Green River, and Bear River basins). Monthly and seasonal reference ET values will be determined using daily reference ET. Gridded reference ET values from the two methods will be compared with the reference ET using data from a single weather station. These reference ET maps will then be used to develop a GIS-based ET calculator.

  20. Towards a Full-sky, High-resolution Dust Extinction Map with WISE and Planck

    NASA Astrophysics Data System (ADS)

    Meisner, Aaron M.; Finkbeiner, D. P.

    2014-01-01

    We have recently completed a custom processing of the entire WISE 12 micron All-sky imaging data set. The result is a full-sky map of diffuse, mid-infrared Galactic dust emission with angular resolution of 15 arcseconds, and with contaminating artifacts such as compact sources removed. At the same time, the 2013 Planck HFI maps represent a complementary data set in the far-infrared, with zero-point relatively immune to zodiacal contamination and angular resolution superior to previous full-sky data sets at similar frequencies. Taken together, these WISE and Planck data products present an opportunity to improve upon the SFD (1998) dust extinction map, by virtue of enhanced angular resolution and potentially better-controlled systematics on large scales. We describe our continuing efforts to construct and test high-resolution dust extinction and temperature maps based on our custom WISE processing and Planck HFI data.

  1. RAVEN - High-resolution Mapping of Venus within a Discovery Mission Budget

    NASA Astrophysics Data System (ADS)

    Sharpton, V. L.; Herrick, R. R.; Rogers, F.; Waterman, S.

    2009-12-01

    It has been more than 15 years since the Magellan mission mapped Venus with S-band synthetic aperture radar (SAR) images at ~100-m resolution. Advances in radar technology are such that current Earth-orbiting SAR instruments are capable of providing images at meter-scale resolution. RAVEN (RAdar at VENus) is a mission concept that utilizes the instrument developed for the RADARSAT Constellation Mission (RCM) to map Venus in an economical, highly capable, and reliable way. RCM relies on a C-band SAR that can be tuned to generate images at a wide variety of resolutions and swath widths, ranging from ScanSAR mode (broad swaths at 30-m resolution) to strip-map mode (resolutions as fine as 3 m), as well as a spotlight mode that can image patches at 1-m resolution. In particular, the high-resolution modes allow the landing sites of previous missions to be pinpointed and characterized. Repeat-pass interferometric SAR (InSAR) and stereo radargrammetry provide options for constraining topography to better than 100-m horizontal and 10-m vertical resolution. InSAR also provides the potential for detecting surface deformation at centimeter precision. Performing InSAR requires precise knowledge and control of the orbital geometry, and for this reason a 600-km circular polar orbit is favored. This configuration causes the equatorial nadir point to move ~9 km per orbit. Considering both ascending and descending passes, the spacecraft will pass over every point on the planet in half a Venus day (~4 Earth months). The ability to transmit data back to Earth via the Deep Space Network is the primary limiting factor on the volume of data that can be collected. Our current estimates indicate that within an imaging cycle of one Venus day we can image 20-30 percent of the planet at 20-30-m resolution and several percent at 3-5 m resolution. These figures compare favorably to the coverage provided by recent imaging systems orbiting Mars. Our strategy calls for the first cycle of coverage

  2. National scale high-resolution mapping of coastal wave overtopping risk in England and Wales

    NASA Astrophysics Data System (ADS)

    Alexandre, Rebecca; Hird, Matthew

    2015-04-01

    The coastal flooding associated with the 2013-2014 UK winter storms caused widespread property damage and one fatality along the coastlines of south-west England and Wales. High spring tides and large waves combined to unexpectedly overtop coastal flood defences. The increasing risk of waves overtopping sea defences coupled with the rise in property development along the coast highlights the need for new and innovative tools for understanding coastal flood risk. Until now, broad-scale coastal hazard maps have overlooked coastal wave overtopping inundation, thereby underestimating flood risk. Recognising this gap has led to the development of the first nation-wide wave overtopping flood map for England and Wales, which we present here. Aimed primarily at the re/insurance sector, JBA has established a methodology for rapidly modelling large-scale wave overtopping flooding. An inception study investigated a range of modelling approaches for national scale modelling and the most suitable design computed general peak wave overtopping rates representative of four separate return period events. Hydrographs were calculated to reflect the changes in the overtopping rate as a result of changes to the water levels throughout the tidal cycle. Overtopping volumes were then computed from the overtopping rates and defence polylines digitised in ArcGIS. Finally, topographically controlled inundation was simulated across a high-resolution digital terrain model using a 2D hydrodynamic flood model. Results from the selected methodology compared well against test areas modelled in detail using additional data on bathymetry, beach profiles, and defence geometry. Sensibility checks were performed using extreme sea level value data to ensure that the model outputs were consistent with the sea level heights expected during a storm event of a particular return period. Moreover, model results corroborated well with media reports on flood extents experienced by communities during the 2013

  3. Daily High-Resolution Flood Maps of Africa: 1992-present with Near Real Time Updates

    NASA Astrophysics Data System (ADS)

    Picton, J.; Galantowicz, J. F.; Root, B.

    2016-12-01

    The ability to characterize past and current flood extents frequently, accurately, and at high resolution is needed for many applications including risk assessment, wetlands monitoring, and emergency management. However, remote sensing methods have not been capable of meeting all of these requirements simultaneously. Cloud cover too often obscures the surface for visual and infrared sensors and observations from radar sensors are too infrequent to create consistent historical databases or monitor evolving events. Lower-resolution (10-50 km) passive microwave sensors, such as SSM/I, AMSR-E, and AMSR2, are sensitive to water cover, acquire useful data during clear and cloudy conditions, have revisit periods of up to twice daily, and provide a continuous record of data from 1992 to the present. What they lack most is the resolution needed to map flood extent. We will present results from a flood mapping system capable of producing high-resolution (90-m) flood extent depictions from lower resolution microwave data. The system uses the strong sensitivity of microwave data to surface water coverage combined with land surface and atmospheric data to derive daily flooded fraction estimates on a sensor-footprint basis. The system downscales flooded fraction to make high-resolution Boolean flood extent depictions that are spatially continuous and consistent with the lower resolution data. The downscaling step is based on a relative floodability (RF) index derived from higher-resolution topographic and hydrological data. We process RF to create a flooded fraction threshold map that relates each 90-m grid point to the surrounding terrain at the microwave scale. We have derived daily, 90-m resolution flood maps for Africa covering 1992-present using SSM/I, AMSR-E, and AMSR2 data and we are now producing new daily maps in near real time. The flood maps are being used by the African Risk Capacity (ARC) Agency to underpin an intergovernmental river flood insurance program in

  4. Improving the process of geological mapping in sedimentary terrain by using high-resolution topography in 3D environments

    NASA Astrophysics Data System (ADS)

    Chan, Yu-Chang; Shih, Nai-Cih; Chiu, Chia-Hung; Hsieh, Yu-Chung

    2017-04-01

    Traditional geologic maps were basically produced by field geologists through direct field investigations and interpretations from 2D topographic maps. However, the quality of traditional geologic maps was knowingly compromised by field conditions, particularly, when the mapping area is largely inaccessible or covered by heavy forest canopies. Recent advancement in airborne LiDAR technology can virtually remove trees or buildings, thus, providing a useful high-resolution topographic data set for the bare ground surface. The high-resolution topography still needs to be interpreted in terms of geology, and fundamental questions regarding how to apply the high-resolution topography remain to be answered for improving the process and quality of geological mapping. In this study, we aim to test the quality and reliability of high-resolution geologic maps produced by recently developed methods by an example from the fold-and-thrust belt in northern Taiwan. We performed the geological mapping by applying the LiDAR-derived DEM, self-developed Python program tools and many layers of relevant information at interactive 3D environments on a computer. Our mapping results indicate that the proposed mapping methods will significantly raise the quality and consistency of the geologic maps. Our study also shows that in order to gain consistent mapping results, future high-resolution geologic maps should be produced in 3D environments based on existing geologic maps and a few field checks for verification.

  5. Mapping the Fresh-Salt Water Interaction in the Coastal Zone Using High Resolution Airborne Electromagnetics

    NASA Astrophysics Data System (ADS)

    Auken, E.; Pedersen, J. B. B.; Christiansen, A. V.; Foged, N.; Schaars, F.; Rolf, H.

    2016-12-01

    During the last decade airborne electromagnetics (AEM) and the accompanying data processing and inversion algorithms have undergone huge developments in terms of technology, costs, and reliability. This has expanded the scope of AEM from mainly mineral exploration to geotechnical applications and groundwater resource mapping. In this abstract we present a case with generally applicable results where AEM is used to map saltwater intrusion as well as outflow of fresh water to the sea. The survey took place on the Dutch coast in 2011 and is composed of a detailed inland coastal mapping as well as lines extending kilometres into the North Sea. It adds further complications that the area has a dense infrastructure and rapid varying dune topography causing the need for cautious data processing. We use the high resolution AEM system SkyTEM and data processing and inversion in the Aarhus Workbench. On the inland side, the results show a high resolution image of the fresh water interface and the interaction with clay layers acting as barriers. On the sea side they show a picture of freshwater plumes being pushed several hundred meters under the sea. The last mentioned information was actually the main purpose of the survey as this information could hardly be obtained by other methods and it is decisive for the total water balance of the system. The case shows an example of an AEM survey resulting in a high resolution image of the entire coastal zone. The technology is applicable in all coastal zones in the world and if applied it would lead to much improved management of the water resources in these landscapes.

  6. Very High Resolution Mapping of Tree Cover Using Scalable Deep Learning Architectures

    NASA Astrophysics Data System (ADS)

    ganguly, sangram; basu, saikat; nemani, ramakrishna; mukhopadhyay, supratik; michaelis, andrew; votava, petr; saatchi, sassan

    2016-04-01

    Several studies to date have provided an extensive knowledge base for estimating forest aboveground biomass (AGB) and recent advances in space-based modeling of the 3-D canopy structure, combined with canopy reflectance measured by passive optical sensors and radar backscatter, are providing improved satellite-derived AGB density mapping for large scale carbon monitoring applications. A key limitation in forest AGB estimation from remote sensing, however, is the large uncertainty in forest cover estimates from the coarse-to-medium resolution satellite-derived land cover maps (present resolution is limited to 30-m of the USGS NLCD Program). As part of our NASA Carbon Monitoring System Phase II activities, we have demonstrated that uncertainties in forest cover estimates at the Landsat scale result in high uncertainties in AGB estimation, predominantly in heterogeneous forest and urban landscapes. We have successfully tested an approach using scalable deep learning architectures (Feature-enhanced Deep Belief Networks and Semantic Segmentation using Convolutional Neural Networks) and High-Performance Computing with NAIP air-borne imagery data for mapping tree cover at 1-m over California and Maryland. Our first high resolution satellite training label dataset from the NAIP data can be found here at http://csc.lsu.edu/~saikat/deepsat/ . In a comparison with high resolution LiDAR data available over selected regions in the two states, we found our results to be promising both in terms of accuracy as well as our ability to scale nationally. In this project, we propose to estimate very high resolution forest cover for the continental US at spatial resolution of 1-m in support of reducing uncertainties in the AGB estimation. The proposed work will substantially contribute to filling the gaps in ongoing carbon monitoring research and help quantifying the errors and uncertainties in related carbon products.

  7. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

    PubMed Central

    Skene, Peter J; Henikoff, Steven

    2017-01-01

    We describe Cleavage Under Targets and Release Using Nuclease (CUT&RUN), a chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. Unlike Chromatin Immunoprecipitation (ChIP), which fragments and solubilizes total chromatin, CUT&RUN is performed in situ, allowing for both quantitative high-resolution chromatin mapping and probing of the local chromatin environment. When applied to yeast and human nuclei, CUT&RUN yielded precise transcription factor profiles while avoiding crosslinking and solubilization issues. CUT&RUN is simple to perform and is inherently robust, with extremely low backgrounds requiring only ~1/10th the sequencing depth as ChIP, making CUT&RUN especially cost-effective for transcription factor and chromatin profiling. When used in conjunction with native ChIP-seq and applied to human CTCF, CUT&RUN mapped directional long range contact sites at high resolution. We conclude that in situ mapping of protein-DNA interactions by CUT&RUN is an attractive alternative to ChIP-seq. DOI: http://dx.doi.org/10.7554/eLife.21856.001 PMID:28079019

  8. GERLUMPH DATA RELEASE 1: HIGH-RESOLUTION COSMOLOGICAL MICROLENSING MAGNIFICATION MAPS AND eResearch TOOLS

    SciTech Connect

    Vernardos, G.; Fluke, C. J.; Croton, D.; Bate, N. F.

    2014-03-01

    As synoptic all-sky surveys begin to discover new multiply lensed quasars, the flow of data will enable statistical cosmological microlensing studies of sufficient size to constrain quasar accretion disk and supermassive black hole properties. In preparation for this new era, we are undertaking the GPU-Enabled, High Resolution cosmological MicroLensing parameter survey (GERLUMPH). We present here the GERLUMPH Data Release 1, which consists of 12,342 high resolution cosmological microlensing magnification maps and provides the first uniform coverage of the convergence, shear, and smooth matter fraction parameter space. We use these maps to perform a comprehensive numerical investigation of the mass-sheet degeneracy, finding excellent agreement with its predictions. We study the effect of smooth matter on microlensing induced magnification fluctuations. In particular, in the minima and saddle-point regions, fluctuations are enhanced only along the critical line, while in the maxima region they are always enhanced for high smooth matter fractions (≈0.9). We describe our approach to data management, including the use of an SQL database with a Web interface for data access and online analysis, obviating the need for individuals to download large volumes of data. In combination with existing observational databases and online applications, the GERLUMPH archive represents a fundamental component of a new microlensing eResearch cloud. Our maps and tools are publicly available at http://gerlumph.swin.edu.au/.

  9. High-resolution mapping of a 130-kb core region of the MYCN amplicon in neuroblastomas

    SciTech Connect

    Reiter, J.L.; Brodeur, G.M.

    1996-02-15

    This article reports on a high-resolution restriction map containing the MYCN locus. the exon-intron structure and tissue distribution of the laminin {gamma}2 chain (LAMC2) gene, which is mutated in some cases of junctional epidermolysis bullosa. The article also discusses the transcription and splicing of this gene, which result in alternative uses of the last two exons of the gene. The different tissue distributions of the transcripts indicate different functions for the gene in vivo. 36 refs., 8 figs., 3 tabs.

  10. High-Resolution Geologic Mapping of the Inner Continental Shelf: Cape Ann to Salisbury Beach, Massachusetts

    USGS Publications Warehouse

    Barnhardt, Walter A.; Andrews, Brian D.; Ackerman, Seth D.; Baldwin, Wayne E.; Hein, Christopher J.

    2009-01-01

    The geologic framework of the Massachusetts inner continental shelf between Cape Ann and Salisbury Beach has been shaped by a complicated history of glaciation, deglaciation, and changes in relative sea level. New geophysical data (swath bathymetry, sidescan sonar and seismic-reflection profiling), sediment samples, and seafloor photography provide insight into the geomorphic and stratigraphic record generated by these processes. High-resolution spatial data and geologic maps in this report support coastal research and efforts to understand the type, distribution, and quality of subtidal marine habitats in the Massachusetts coastal ocean.

  11. High-resolution geologic mapping of the inner continental shelf: Nahant to Gloucester, Massachusetts

    USGS Publications Warehouse

    Barnhardt, Walter A.; Andrews, Brian D.; Butman, Bradford

    2006-01-01

    This report presents high-resolution maps of the seafloor offshore of Massachusetts, from Nahant to Gloucester. Approximately 134 km² of the inner shelf were mapped with a focus on the nearshore region in water depths less than 40 m (fig. 1.1). The maps were prepared as part of a cooperative mapping program between the U.S. Geological Survey (USGS) and the Massachusetts Office of Coastal Zone Management (CZM). They are based on marine geophysical data, sediment sampling, and bottom photography obtained on two research cruises carried out in 2003 and 2004. The primary objective of this program is to develop a suite of seafloor maps that provide geologic information for management of coastal and marine resources. Accurate maps of seafloor geology are important first steps toward protecting fish habitat, delineating marine reserves, and assessing environmental changes due to natural or human impacts. The maps also provide a geologic framework for scientific research, industry and the public. The organization of this report is outlined in the navigation bar along the left-hand margin of the page. This is section 1, the introduction. Section 2 briefly describes the mapping products contained in this report and has links to large-format map sheets, that can be viewed on line or downloaded. Section 3 is a description of the data collection, processing, and analysis procedures used to create the map products. Section 4 examines the geologic framework and late Quaternary evolution of the region, and presents two different strategies for mapping the complex seafloor. This report also contains four appendices that include GIS layers of all data collected in this study, and copies of the sample and photographic data used to validate the interpretations.

  12. High-Resolution Association Mapping of Quantitative Trait Loci: A Population-Based Approach

    PubMed Central

    Fan, Ruzong; Jung, Jeesun; Jin, Lei

    2006-01-01

    In this article, population-based regression models are proposed for high-resolution linkage disequilibrium mapping of quantitative trait loci (QTL). Two regression models, the “genotype effect model” and the “additive effect model,” are proposed to model the association between the markers and the trait locus. The marker can be either diallelic or multiallelic. If only one marker is used, the method is similar to a classical setting by Nielsen and Weir, and the additive effect model is equivalent to the haplotype trend regression (HTR) method by Zaykin et al. If two/multiple marker data with phase ambiguity are used in the analysis, the proposed models can be used to analyze the data directly. By analytical formulas, we show that the genotype effect model can be used to model the additive and dominance effects simultaneously; the additive effect model takes care of the additive effect only. On the basis of the two models, F-test statistics are proposed to test association between the QTL and markers. By a simulation study, we show that the two models have reasonable type I error rates for a data set of moderate sample size. The noncentrality parameter approximations of F-test statistics are derived to make power calculation and comparison. By a simulation study, it is found that the noncentrality parameter approximations of F-test statistics work very well. Using the noncentrality parameter approximations, we compare the power of the two models with that of the HTR. In addition, a simulation study is performed to make a comparison on the basis of the haplotype frequencies of 10 SNPs of angiotensin-1 converting enzyme (ACE) genes. PMID:16172503

  13. Exploring the high-resolution mapping of gender-disaggregated development indicators.

    PubMed

    Bosco, C; Alegana, V; Bird, T; Pezzulo, C; Bengtsson, L; Sorichetta, A; Steele, J; Hornby, G; Ruktanonchai, C; Ruktanonchai, N; Wetter, E; Tatem, A J

    2017-04-01

    Improved understanding of geographical variation and inequity in health status, wealth and access to resources within countries is increasingly being recognized as central to meeting development goals. Development and health indicators assessed at national or subnational scale can often conceal important inequities, with the rural poor often least well represented. The ability to target limited resources is fundamental, especially in an international context where funding for health and development comes under pressure. This has recently prompted the exploration of the potential of spatial interpolation methods based on geolocated clusters from national household survey data for the high-resolution mapping of features such as population age structures, vaccination coverage and access to sanitation. It remains unclear, however, how predictable these different factors are across different settings, variables and between demographic groups. Here we test the accuracy of spatial interpolation methods in producing gender-disaggregated high-resolution maps of the rates of literacy, stunting and the use of modern contraceptive methods from a combination of geolocated demographic and health surveys cluster data and geospatial covariates. Bayesian geostatistical and machine learning modelling methods were tested across four low-income countries and varying gridded environmental and socio-economic covariate datasets to build 1×1 km spatial resolution maps with uncertainty estimates. Results show the potential of the approach in producing high-resolution maps of key gender-disaggregated socio-economic indicators, with explained variance through cross-validation being as high as 74-75% for female literacy in Nigeria and Kenya, and in the 50-70% range for many other variables. However, substantial variations by both country and variable were seen, with many variables showing poor mapping accuracies in the range of 2-30% explained variance using both geostatistical and machine

  14. Exploring the high-resolution mapping of gender-disaggregated development indicators

    PubMed Central

    Alegana, V.; Bird, T.; Pezzulo, C.; Bengtsson, L.; Sorichetta, A.; Hornby, G.; Ruktanonchai, C.; Ruktanonchai, N.; Wetter, E.; Tatem, A. J.

    2017-01-01

    Improved understanding of geographical variation and inequity in health status, wealth and access to resources within countries is increasingly being recognized as central to meeting development goals. Development and health indicators assessed at national or subnational scale can often conceal important inequities, with the rural poor often least well represented. The ability to target limited resources is fundamental, especially in an international context where funding for health and development comes under pressure. This has recently prompted the exploration of the potential of spatial interpolation methods based on geolocated clusters from national household survey data for the high-resolution mapping of features such as population age structures, vaccination coverage and access to sanitation. It remains unclear, however, how predictable these different factors are across different settings, variables and between demographic groups. Here we test the accuracy of spatial interpolation methods in producing gender-disaggregated high-resolution maps of the rates of literacy, stunting and the use of modern contraceptive methods from a combination of geolocated demographic and health surveys cluster data and geospatial covariates. Bayesian geostatistical and machine learning modelling methods were tested across four low-income countries and varying gridded environmental and socio-economic covariate datasets to build 1×1 km spatial resolution maps with uncertainty estimates. Results show the potential of the approach in producing high-resolution maps of key gender-disaggregated socio-economic indicators, with explained variance through cross-validation being as high as 74–75% for female literacy in Nigeria and Kenya, and in the 50–70% range for many other variables. However, substantial variations by both country and variable were seen, with many variables showing poor mapping accuracies in the range of 2–30% explained variance using both geostatistical and

  15. A novel technique for visualizing high-resolution 3D terrain maps

    NASA Astrophysics Data System (ADS)

    Dammann, John

    2007-02-01

    A new technique is presented for visualizing high-resolution terrain elevation data. It produces realistic images at small scales on the order of the data resolution and works particularly well when natural objects are present. Better visualization at small scales opens up new applications, like site surveillance for security and Google Earth-type local search and exploration tasks that are now done with 2-D maps. The large 3-D maps are a natural for high-resolution stereo display. The traditional technique drapes a continuous surface over the regularly spaced elevation values. This technique works well when displaying large areas or in cities with large buildings, but falls apart at small scales or for natural objects like trees. The new technique visualizes the terrain as a set of disjoint square patches. It is combined with an algorithm that identifies smooth areas within the scene. Where the terrain is smooth, such as in grassy areas, roads, parking lots and rooftops, it warps the patches to create a smooth surface. For trees or shrubs or other areas where objects are under-sampled, however, the patches are left disjoint. This has the disadvantage of leaving gaps in the data, but the human mind is very adept at filling in this missing information. It has the strong advantage of making natural terrain look realistic, trees and bushes look stylized but still look natural and are easy to interpret. Also, it does not add artifacts to the map, like filling in blank vertical walls where there are alcoves and other structure and extending bridges and overpasses down to the ground. The new technique is illustrated using very large 1-m resolution 3-D maps from the Rapid Terrain Visualization (RTV) program, and comparisons are made with traditional visualizations using these maps.

  16. High-Resolution 3D Bathymetric Mapping for Small Streams Using Low-Altitude Aerial Photography

    NASA Astrophysics Data System (ADS)

    Dietrich, J. T.; Duffin, J.

    2015-12-01

    Geomorphic monitoring of river restoration projects is a critical component of measuring their success. In smaller streams, with depths less than 2 meters, one of the more difficult variables to map at high-resolution is bathymetry. In larger rivers, bathymetry can be measured with instruments like multi-beam sonar, bathymetric airborne LiDAR, or acoustic doppler current profilers (ADCP). However, these systems are often limited by their minimum operating depths, which makes them ineffective in shallow water. Remote sensing offers several potential solutions for collecting bathymetry, spectral depth mapping and photogrammetric measurement (e.g. Structure-from-Motion (SfM) multi-view photogrammetry). In this case study, we use SfM to produce both high-resolution above water topography and below water bathymetry for two reaches of a stream restoration project on the Middle Fork of the John Day River in eastern Oregon and one reach on the White River in Vermont. We collected low-allitude multispectral (RGB+NIR) aerial photography at all of the sites at altitudes of 30 to 50 meters. The SfM survey was georeferenced with RTK-GPS ground control points and the bathymetry was refraction-corrected using additional RTK-GPS sample points. The resulting raster data products have horizontal resolutions of ~4-8 centimeters for the topography and ~8-15 cm for the bathymetry. This methodology, like many fluvial remote sensing methods, will only work under ideal conditions (e.g. clear water), but it provides an additional tool for collecting high-resolution bathymetric datasets for geomorphic monitoring efforts.

  17. REAL-TIME high-resolution urban surface water flood mapping to support flood emergency management

    NASA Astrophysics Data System (ADS)

    Guan, M.; Yu, D.; Wilby, R.

    2016-12-01

    Strong evidence has shown that urban flood risks will substantially increase because of urbanisation, economic growth, and more frequent weather extremes. To effectively manage these risks require not only traditional grey engineering solutions, but also a green management solution. Surface water flood risk maps based on return period are useful for planning purposes, but are limited for application in flood emergencies, because of the spatiotemporal heterogeneity of rainfall and complex urban topography. Therefore, a REAL-TIME urban surface water mapping system is highly beneficial to increasing urban resilience to surface water flooding. This study integrated numerical weather forecast and high-resolution urban surface water modelling into a real-time multi-level surface water mapping system for Leicester City in the UK. For rainfall forecast, the 1km composite rain radar from the Met Office was used, and we used the advanced rainfall-runoff model - FloodMap to predict urban surface water at both city-level (10m-20m) and street-level (2m-5m). The system is capable of projecting 3-hour urban surface water flood, driven by rainfall derived from UK Met Office radar. Moreover, this system includes real-time accessibility mapping to assist the decision-making of emergency responders. This will allow accessibility (e.g. time to travel) from individual emergency service stations (e.g. Fire & Rescue; Ambulance) to vulnerable places to be evaluated. The mapping results will support contingency planning by emergency responders ahead of potential flood events.

  18. High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly.

    PubMed

    Bartholomé, Jérôme; Mandrou, Eric; Mabiala, André; Jenkins, Jerry; Nabihoudine, Ibouniyamine; Klopp, Christophe; Schmutz, Jeremy; Plomion, Christophe; Gion, Jean-Marc

    2015-06-01

    Genetic maps are key tools in genetic research as they constitute the framework for many applications, such as quantitative trait locus analysis, and support the assembly of genome sequences. The resequencing of the two parents of a cross between Eucalyptus urophylla and Eucalyptus grandis was used to design a single nucleotide polymorphism (SNP) array of 6000 markers evenly distributed along the E. grandis genome. The genotyping of 1025 offspring enabled the construction of two high-resolution genetic maps containing 1832 and 1773 markers with an average marker interval of 0.45 and 0.5 cM for E. grandis and E. urophylla, respectively. The comparison between genetic maps and the reference genome highlighted 85% of collinear regions. A total of 43 noncollinear regions and 13 nonsynthetic regions were detected and corrected in the new genome assembly. This improved version contains 4943 scaffolds totalling 691.3 Mb of which 88.6% were captured by the 11 chromosomes. The mapping data were also used to investigate the effect of population size and number of markers on linkage mapping accuracy. This study provides the most reliable linkage maps for Eucalyptus and version 2.0 of the E. grandis genome.

  19. A high-resolution PAC and BAC map of the SCA2 region.

    PubMed

    Nechiporuk, T; Nechiporuk, A; Sahba, S; Figueroa, K; Shibata, H; Chen, X N; Korenberg, J R; de Jong, P; Pulst, S M

    1997-09-15

    The spinocerebellar ataxia type 2 (SCA2) gene has been localized to chromosome 12q24.1. To characterize this region and to aid in the identification of the SCA2 gene, we have constructed a 3.9-Mb physical map, which covers markers D12S1328 and D12S1329 known to flank the gene. The map comprises a contig of 84 overlapping yeast artificial chromosomes (YACs), P1 artificial chromosomes (PACs), and bacterial artificial chromosomes (BACs) onto which we placed 82 PCR markers. We localized eight genes and expressed sequence tags on this map, many of which had not been precisely mapped before. In contrast to YACs, which showed a high degree of chimerism and deletions in this region, PACs and BACs were stable. Only 1 in 65 PACs contained a small deletion, and 2 in 18 BACs were chimeric. The high-resolution physical map, which was used in the identification of the SCA2 gene, will be useful for the positional cloning of other disease genes mapped to this region.

  20. High-resolution crossover maps for each bivalent of Zea mays using recombination nodules.

    PubMed Central

    Anderson, Lorinda K; Doyle, Gregory G; Brigham, Brian; Carter, Jenna; Hooker, Kristina D; Lai, Ann; Rice, Mindy; Stack, Stephen M

    2003-01-01

    Recombination nodules (RNs) are closely correlated with crossing over, and, because they are observed by electron microscopy of synaptonemal complexes (SCs) in extended pachytene chromosomes, RNs provide the highest-resolution cytological marker currently available for defining the frequency and distribution of crossovers along the length of chromosomes. Using the maize inbred line KYS, we prepared an SC karyotype in which each SC was identified by relative length and arm ratio and related to the proper linkage group using inversion heterozygotes. We mapped 4267 RNs on 2080 identified SCs to produce high-resolution maps of RN frequency and distribution on each bivalent. RN frequencies are closely correlated with both chiasma frequencies and SC length. The total length of the RN recombination map is about twofold shorter than that of most maize linkage maps, but there is good correspondence between the relative lengths of the different maps when individual bivalents are considered. Each bivalent has a unique distribution of crossing over, but all bivalents share a high frequency of distal RNs and a severe reduction of RNs at and near kinetochores. The frequency of RNs at knobs is either similar to or higher than the average frequency of RNs along the SCs. These RN maps represent an independent measure of crossing over along maize bivalents. PMID:14573493

  1. High-resolution crossover maps for each bivalent of Zea mays using recombination nodules.

    PubMed

    Anderson, Lorinda K; Doyle, Gregory G; Brigham, Brian; Carter, Jenna; Hooker, Kristina D; Lai, Ann; Rice, Mindy; Stack, Stephen M

    2003-10-01

    Recombination nodules (RNs) are closely correlated with crossing over, and, because they are observed by electron microscopy of synaptonemal complexes (SCs) in extended pachytene chromosomes, RNs provide the highest-resolution cytological marker currently available for defining the frequency and distribution of crossovers along the length of chromosomes. Using the maize inbred line KYS, we prepared an SC karyotype in which each SC was identified by relative length and arm ratio and related to the proper linkage group using inversion heterozygotes. We mapped 4267 RNs on 2080 identified SCs to produce high-resolution maps of RN frequency and distribution on each bivalent. RN frequencies are closely correlated with both chiasma frequencies and SC length. The total length of the RN recombination map is about twofold shorter than that of most maize linkage maps, but there is good correspondence between the relative lengths of the different maps when individual bivalents are considered. Each bivalent has a unique distribution of crossing over, but all bivalents share a high frequency of distal RNs and a severe reduction of RNs at and near kinetochores. The frequency of RNs at knobs is either similar to or higher than the average frequency of RNs along the SCs. These RN maps represent an independent measure of crossing over along maize bivalents.

  2. High resolution genetic mapping by genome sequencing reveals genome duplication and tetraploid genetic structure of the diploid Miscanthus sinensis.

    PubMed

    Ma, Xue-Feng; Jensen, Elaine; Alexandrov, Nickolai; Troukhan, Maxim; Zhang, Liping; Thomas-Jones, Sian; Farrar, Kerrie; Clifton-Brown, John; Donnison, Iain; Swaller, Timothy; Flavell, Richard

    2012-01-01

    We have created a high-resolution linkage map of Miscanthus sinensis, using genotyping-by-sequencing (GBS), identifying all 19 linkage groups for the first time. The result is technically significant since Miscanthus has a very large and highly heterozygous genome, but has no or limited genomics information to date. The composite linkage map containing markers from both parental linkage maps is composed of 3,745 SNP markers spanning 2,396 cM on 19 linkage groups with a 0.64 cM average resolution. Comparative genomics analyses of the M. sinensis composite linkage map to the genomes of sorghum, maize, rice, and Brachypodium distachyon indicate that sorghum has the closest syntenic relationship to Miscanthus compared to other species. The comparative results revealed that each pair of the 19 M. sinensis linkages aligned to one sorghum chromosome, except for LG8, which mapped to two sorghum chromosomes (4 and 7), presumably due to a chromosome fusion event after genome duplication. The data also revealed several other chromosome rearrangements relative to sorghum, including two telomere-centromere inversions of the sorghum syntenic chromosome 7 in LG8 of M. sinensis and two paracentric inversions of sorghum syntenic chromosome 4 in LG7 and LG8 of M. sinensis. The results clearly demonstrate, for the first time, that the diploid M. sinensis is tetraploid origin consisting of two sub-genomes. This complete and high resolution composite linkage map will not only serve as a useful resource for novel QTL discoveries, but also enable informed deployment of the wealth of existing genomics resources of other species to the improvement of Miscanthus as a high biomass energy crop. In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the Miscanthus genus.

  3. Transfer of Technology for Cadastral Mapping in Tajikistan Using High Resolution Satellite Data

    NASA Astrophysics Data System (ADS)

    Kaczynski, R.

    2012-07-01

    European Commission funded project entitled: "Support to the mapping and certification capacity of the Agency of Land Management, Geodesy and Cartography" in Tajikistan was run by FINNMAP FM-International and Human Dynamics from Nov. 2006 to June 2011. The Agency of Land Management, Geodesy and Cartography is the state agency responsible for development, implementation, monitoring and evaluation of state policies on land tenure and land management, including the on-going land reform and registration of land use rights. The specific objective was to support and strengthen the professional capacity of the "Fazo" Institute in the field of satellite geodesy, digital photogrammetry, advanced digital satellite image processing of high resolution satellite data and digital cartography. Lectures and on-the-job trainings for the personnel of "Fazo" and Agency in satellite geodesy, digital photogrammetry, cartography and the use of high resolution satellite data for cadastral mapping have been organized. Standards and Quality control system for all data and products have been elaborated and implemented in the production line. Technical expertise and trainings in geodesy, photogrammetry and satellite image processing to the World Bank project "Land Registration and Cadastre System for Sustainable Agriculture" has also been completed in Tajikistan. The new map projection was chosen and the new unclassified geodetic network has been established for all of the country in which all agricultural parcel boundaries are being mapped. IKONOS, QuickBird and WorldView1 panchromatic data have been used for orthophoto generation. Average accuracy of space triangulation of non-standard (long up to 90km) satellite images of QuickBird Pan and IKONOS Pan on ICPs: RMSEx = 0.5m and RMSEy = 0.5m have been achieved. Accuracy of digital orthophoto map is RMSExy = 1.0m. More then two and half thousands of digital orthophoto map sheets in the scale of 1:5000 with pixel size 0.5m have been produced

  4. Exploring for subtle traps with high-resolution paleogeographic maps: Reklaw 1 interval (Eocene), south Texas

    SciTech Connect

    Bulling, T.P.; Breyer, J.A.

    1989-01-01

    High-resolution paleogeographic maps depicting the depositional history of the Reklaw 1 interval provide a basis for prospecting for subtle traps in the updip Reklaw trend in south Texas. The Reklaw 1 interval began with sand being carried southwestward by longshore currents to form the barrier bar that became Atkinson field. The hydrocarbons were trapped by the updip pinch-out of barrier-bar sand into lagoonal mud. Stratigraphic traps similar to Atkinson field could be present along depositional strike if the sand in the field were part of an extensive barrier-bar system. After the barrier bar formed, distributary mouth bars prograded seaward, depositing the bar-finger sands that became the Hysaw and Flax fields. Subtle structural traps could be present today where small up-to-the-coast faults associated with the sample fault system cut the bar-finger sands downdip from established production. Farther down paleoslope, the distributary channels began to bifurcate and the distributary mouth bars coalesced to form a broad delta-front sheet sand. Burnell, Hondo Creek, and Runge West fields produce from this sheet sand at the unstable shelf margin. A rapid rise in relative sea level terminated the Reklaw 1 interval. Many of the oil and gas fields still to be discovered in the US are in mature petroleum provinces where much of the remaining oil and gas probably resides in subtle traps. High-resolution paleogeographic maps are the key to finding these subtle traps. 11 figures, 2 tables.

  5. High-resolution, genome-wide mapping of chromatin modifications by GMAT.

    PubMed

    Roh, Tae-Young; Zhao, Keji

    2008-01-01

    One major postgenomic challenge is to characterize the epigenomes that control genome functions. The epigenomes are mainly defined by the specific association of nonhistone proteins with chromatin and the covalent modifications of chromatin, including DNA methylation and posttranslational histone modifications. The in vivo protein-binding and chromatin-modification patterns can be revealed by the chromatin immunoprecipitation assay (ChIP). By combining the ChIP assays and the serial analysis of gene expression (SAGE) protocols, we have developed an unbiased and high-resolution genome-wide mapping technique (GMAT) to determine the genome-wide protein-targeting and chromatin-modification patterns. GMAT has been successfully applied to mapping the target sites of the histone acetyltransferase, Gcn5p, in yeast and to the discovery of the histone acetylation islands as an epigenetic mark for functional regulatory elements in the human genome.

  6. USGS advances in integrated, high-resolution sea-floor mapping: inner continental shelf to estuaries

    USGS Publications Warehouse

    Denny, J.F.; Schwab, W.C.; Twichell, D.C.; O'Brien, T.F.; Danforth, W.W.; Foster, D.S.; Bergeron, E.; Worley, C.W.; Irwin, B.J.; Butman, B.; Valentine, P.C.; Baldwin, W.E.; Morton, R.A.; Thieler, E.R.; Nichols, D.R.; Andrews, B.D.

    2007-01-01

    The U.S. Geological Survey (USGS) has been involved in geological mapping of the sea floor for the past thirty years. Early geophysical and acoustic mapping efforts using GLORIA (Geologic LOng Range Inclined ASDIC) a long-range sidescan-sonar system, provided broad-scale imagery of deep waters within the U.S. Exclusive Economic Zone (EEZ). In the early 1990's, research emphasis shifted from deep- to shallow-water environments to address pertinent coastal research and resource management issues. Use of shallow-water, high-resolution geophysical systems has enhanced our understanding of the processes shaping shallow marine environments. However, research within these shallow-water environments continues to present technological challenges.

  7. Rockfall susceptibility mapping of Yosemite Valley (USA) using a high-resolution digital elevation model

    NASA Astrophysics Data System (ADS)

    Pannatier, A.; Oppikofer, T.; Jaboyedoff, M.; Stock, G. M.

    2009-04-01

    In Yosemite National Park (California, USA) rockfalls from the steep valley flanks are frequent (>600 documented events in 150 years) and threaten infrastructure in this popular tourist area. This study focuses on a methodology to map the susceptibility to rockfall initiation based on a high-resolution digital elevation model (HRDEM) obtained from aerial laser scanning (1 meter cell size). This methodology is based on geometric factors derived from the HRDEM, i.e., the steepness of the topography, the presence of joints or fractures enabling either a planar or a wedge failure mechanism, and a high denudation potential. The slope angle histogram computed using standard GIS routines was simulated using Gaussian distributions, which were attributed to different parts of the topography, i.e., the cliffs, the valley flanks and the valley floor. Slopes steeper than 36° are found to form cliffs and thus potentially lead to rockfalls. A morpho-structural analysis of the HRDEM was performed in Coltop3D software to determine the major discontinuity sets that shape the topography. Kinematic analyses were made for each of these 7 discontinuity sets in order to determine the HRDEM cells that fulfil the geometric criteria for a planar or wedge failure mechanism. Most of the cliffs in Yosemite Valley enable one or both of these failure mechanisms. The denudation potential was assessed using the sloping local base level (SLBL) concept. The SLBL defines a basal erosion surface and the above lying rock masses (up to 400 m in some of the vertical cliffs) are susceptible to erosion by mass wasting. A thickness of 20 m above the SLBL surface was chosen as lower limit for the denudation potential criterion. The HRDEM cells that satisfy 1, 2 or all 3 criteria are considered having low, moderate and high susceptibility to rockfall initiation. The areas with highest susceptibility (El Capitan, Glacier Point, Yosemite Falls and Half Dome) coincide well with post-glacial talus accumulations

  8. Lunar Topographic Mapping Using a New High Resolution Mode for the GSSR Radar

    NASA Technical Reports Server (NTRS)

    Hensley, Scott; Gurrola, Eric; Slade, Martin; Quirk, Kevin; Srinivasan, Meera; Lee, Clement; Yun, Sang-Ho; Jao, Joseph; Wilson, Barbara; De Jong, Eric; Marechal, Nick; Weintraub, Lawrence; Dickinson, Richard; Bloom, Ronald; Karamyan, Grant; Lilje, Anneliese; Harcke, Leif

    2010-01-01

    Mapping the Moon's topography using Earth based radar interferometric measurements by the Goldstone Solar System Radar (GSSR) has been done several times since the mid 1990s. In 2008 we reported at this conference the generation of lunar topographic maps having approximately 4 m height accuracy at a horizontal posting of 40 m. Since then GSSR radar has been improved to allow 40 MHz bandwidth imaging and consequently obtained images and interferograms with a resolution of about 4 m in range by 5 m in azimuth. The long synthetic aperture times of approximately 90 minutes in duration necessitated a migration from range/Doppler image formation techniques to spotlight mode processing and autofocusing methods. The improved resolution imagery should permit the generation of topographic maps with a factor of two better spatial resolution with about same height accuracy. Coupled the with the recent availability of new lidar topography maps of the lunar surface made by orbiting satellites of Japan and the United States the geodetic control of the radar generated maps products can be improved dramatically. This paper will discuss the hardware and software improvements made to the GSSR and present some of the new high resolution products.

  9. The need for sustained and integrated high-resolution mapping of dynamic coastal environments

    USGS Publications Warehouse

    Stockdon, Hilary F.; Lillycrop, Jeff W.; Howd, Peter A.; Wozencraft, Jennifer M.

    2007-01-01

    The evolution of the United States' coastal zone response to both human activities and natural processes is dynamic. Coastal resource and population protection requires understanding, in detail, the processes needed for change as well as the physical setting. Sustained coastal area mapping allows change to be documented and baseline conditions to be established, as well as future behavior to be predicted in conjunction with physical process models. Hyperspectral imagers and airborne lidars, as well as other recent mapping technology advances, allow rapid national scale land use information and high-resolution elevation data collection. Coastal hazard risk evaluation has critical dependence on these rich data sets. A fundamental storm surge model parameter in predicting flooding location, for example, is coastal elevation data, and a foundation in identifying the most vulnerable populations and resources is land use maps. A wealth of information for physical change process study, coastal resource and community management and protection, and coastal area hazard vulnerability determination, is available in a comprehensive national coastal mapping plan designed to take advantage of recent mapping technology progress and data distribution, management, and collection.

  10. High-resolution mapping of the 1998 lava flows at Axial Seamount

    NASA Astrophysics Data System (ADS)

    Chadwick, B.; Clague, D. A.; Embley, R. W.; Caress, D. W.; Paduan, J. B.; Sasnett, P.

    2011-12-01

    Axial Seamount (an active hotspot volcano on the Juan de Fuca Ridge) last erupted in 1998 and produced two lava flows (a "northern" and a "southern" flow) along the upper south rift zone separated by a distance of 4 km. Geologic mapping of the 1998 lava flows has been carried out with a combination of visual observations from multiple submersible dives since 1998, and with high-resolution bathymetry, most recently collected with the MBARI mapping AUV (the D. Allan B.) since 2007. The new mapping results revise and update the previous preliminary flow outlines, areas, and volumes. The high-resolution bathymetry (1-m grid cell size) allows eruptive fissures fine-scale morphologic features to be resolved with new and remarkable clarity. The morphology of both lava flows can be interpreted as a consequence of a specific sequence of events during their emplacement. The northern sheet flow is long (4.6 km) and narrow (500 m), and erupted in the SE part of Axial caldera, where it temporarily ponded and inflated on relatively flat terrain before draining out southward toward steeper slopes. The inflation and drain-out of this sheet flow by ~ 3.5 m over 2.5 hours was previously documented by a monitoring instrument that was caught in the lava flow. Our geologic mapping shows that the morphology of the northern sheet flow varies along its length primarily due to gradients in the underlying slope and processes active during flow emplacement. The original morphology of the sheet flow where it ponded is lobate, with pillows near the margins, whereas the central axis of drain-out and collapse is floored with lineated, ropy, and jumbled lava morphologies. The southern lava flow, in contrast, is mostly pillow lava where it cascaded down the steep slope on the east flank of the south rift zone, but also has a major area of collapse where lava ponded temporarily near the rift axis. These results show that submarine lava flows have more subsurface hydraulic connectivity than has

  11. A new ant based distributed framework for urban road map updating from high resolution satellite imagery

    NASA Astrophysics Data System (ADS)

    Zarrinpanjeh, Nima; Samadzadegan, Farhad; Schenk, Toni

    2013-04-01

    Receiving updated information about the network of roads from high resolution satellite imagery is a crucially important issue in continuously changing developing urban regions. Considering experiences in road extraction and also exploiting distributed evolutionary computational approaches, in this paper a new framework for road map updating from remotely sensed data is proposed. Three main computational entities of ant-agent, seed extractor and algorithm library are designed and road map updating is performed through three main stages of verification of the old map, extraction of possible roads and grouping of the results of both stages. Extracting corresponding pixels to each road element in the map, an object level supervised classification or any available road verification algorithm from the library capable of producing a road likeliness value is applied. Since road extraction is a simple and also a complex problem, more comprehensive algorithms are chosen from library iteratively by ant-agents so the decision about verification and rejection of each road element is finally made. Ant-agents facilitate choosing road elements and moving of ant agents via stigmergic communication by pheromone cast and evaporation. The proposed method is developed and tested using GeoEye-1 pan-sharpen imagery and 1:2000 corresponding digital vector map of the region. As observed, the results are satisfactory in terms of detection, verification and extraction of roads and generation of the updated map specifically in case of inspection of main roads. Besides, some missed road items are reported in case of inspection of bystreets and alleys specially when situated at the margin of the image. Completeness, correctness and quality measures are computed for evaluation of the initial and the resulted updated maps. The computed measures verify the improvement of the updated map.

  12. Evaluation of the use of very high resolution aerial imagery for accurate ice-wedge polygon mapping (Adventdalen, Svalbard).

    PubMed

    Lousada, Maura; Pina, Pedro; Vieira, Gonçalo; Bandeira, Lourenço; Mora, Carla

    2017-09-24

    The main objective of this paper is to verify the accuracy of delineating and characterizing ice-wedge polygonal networks with features exclusively extracted from remotely sensed images of very high resolution. This kind of mapping plays a key role for quantifying ice-wedge degradation in warming permafrost. The evaluation of mapping a network is performed in this study with two sets of aerial images that are compared to ground reference data determined by fieldwork on the same network, located in Adventdalen, Svalbard (78°N). One aerial dataset is obtained from a photogrammetric survey with RGB+NIR imagery of 20cm/pixel, the other from an UAV (Unmanned Aerial Vehicle) survey that acquired RGB images of 6cm/pixel of spatial resolution. Besides evaluating the degree of matching between the delineations, the morphometric and topological features computed for the differently mapped versions of the network are also confronted, to have a more solid basis of comparison. The results obtained are similar enough to admit that remotely sensed images of very high resolution are an adequate support to provide extensive characterizations and classifications of this kind of patterned ground. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Fast Mean-Shift Based Classification of Very High Resolution Images: Application to Forest Cover Mapping

    NASA Astrophysics Data System (ADS)

    Boukir, S.; Jones, S.; Reinke, K.

    2012-07-01

    This paper presents a new unsupervised classification method which aims to effectively and efficiently map remote sensing data. The Mean-Shift (MS) algorithm, a non parametric density-based clustering technique, is at the core of our method. This powerful clustering algorithm has been successfully used for both the classification and the segmentation of gray scale and color images during the last decade. However, very little work has been reported regarding the performance of this technique on remotely sensed images. The main disadvantage of the MS algorithm lies on its high computational costs. Indeed, it is based on an optimization procedure to determine the modes of the pixels density. To investigate the MS algorithm in the difficult context of very high resolution remote sensing imagery, we use a fast version of this algorithm which has been recently proposed, namely the Path-Assigned Mean Shift (PAMS). This algorithm is up to 5 times faster than other fast MS algorithms while inducing a low loss in quality compared to the original MS version. To compensate for this loss, we propose to use the K modes (cluster centroids) obtained after convergence of the PAMS algorithm as an initialization of a K-means clustering algorithm. The latter converges very quickly to a refined solution to the underlying clustering problem. Furthermore, it does not suffer the main drawback of the classic K-means algorithm (the number of clusters K needs to be specified) as K is automatically determined via the MS mode-seeking procedure. We demonstrate the effectiveness of this two-stage clustering method in performing automatic classification of aerial forest images. Both individual bands and band combination trails are presented. When compared to the classical PAMS algorithm, our technique is better in terms of classification quality. The improvement in classification is significant both visually and statistically. The whole classification process is performed in a few seconds on

  14. High-Resolution Mapping of Complex Traits with a Four-Parent Advanced Intercross Yeast Population

    PubMed Central

    Cubillos, Francisco A.; Parts, Leopold; Salinas, Francisco; Bergström, Anders; Scovacricchi, Eugenio; Zia, Amin; Illingworth, Christopher J. R.; Mustonen, Ville; Ibstedt, Sebastian; Warringer, Jonas; Louis, Edward J.; Durbin, Richard; Liti, Gianni

    2013-01-01

    A large fraction of human complex trait heritability is due to a high number of variants with small marginal effects and their interactions with genotype and environment. Such alleles are more easily studied in model organisms, where environment, genetic makeup, and allele frequencies can be controlled. Here, we examine the effect of natural genetic variation on heritable traits in a very large pool of baker’s yeast from a multiparent 12th generation intercross. We selected four representative founder strains to produce the Saccharomyces Genome Resequencing Project (SGRP)-4X mapping population and sequenced 192 segregants to generate an accurate genetic map. Using these individuals, we mapped 25 loci linked to growth traits under heat stress, arsenite, and paraquat, the majority of which were best explained by a diverging phenotype caused by a single allele in one condition. By sequencing pooled DNA from millions of segregants grown under heat stress, we further identified 34 and 39 regions selected in haploid and diploid pools, respectively, with most of the selection against a single allele. While the most parsimonious model for the majority of loci mapped using either approach was the effect of an allele private to one founder, we could validate examples of pleiotropic effects and complex allelic series at a locus. SGRP-4X is a deeply characterized resource that provides a framework for powerful and high-resolution genetic analysis of yeast phenotypes and serves as a test bed for testing avenues to attack human complex traits. PMID:24037264

  15. Whole-Genome Mapping as a Novel High-Resolution Typing Tool for Legionella pneumophila.

    PubMed

    Bosch, Thijs; Euser, Sjoerd M; Landman, Fabian; Bruin, Jacob P; IJzerman, Ed P; den Boer, Jeroen W; Schouls, Leo M

    2015-10-01

    Legionella is the causative agent for Legionnaires' disease (LD) and is responsible for several large outbreaks in the world. More than 90% of LD cases are caused by Legionella pneumophila, and studies on the origin and transmission routes of this pathogen rely on adequate molecular characterization of isolates. Current typing of L. pneumophila mainly depends on sequence-based typing (SBT). However, studies have shown that in some outbreak situations, SBT does not have sufficient discriminatory power to distinguish between related and nonrelated L. pneumophila isolates. In this study, we used a novel high-resolution typing technique, called whole-genome mapping (WGM), to differentiate between epidemiologically related and nonrelated L. pneumophila isolates. Assessment of the method by various validation experiments showed highly reproducible results, and WGM was able to confirm two well-documented Dutch L. pneumophila outbreaks. Comparison of whole-genome maps of the two outbreaks together with WGMs of epidemiologically nonrelated L. pneumophila isolates showed major differences between the maps, and WGM yielded a higher discriminatory power than SBT. In conclusion, WGM can be a valuable alternative to perform outbreak investigations of L. pneumophila in real time since the turnaround time from culture to comparison of the L. pneumophila maps is less than 24 h.

  16. Recent Advancements in DNA Damage-Transcription Crosstalk and High-Resolution Mapping of DNA Breaks.

    PubMed

    Vitelli, Valerio; Galbiati, Alessandro; Iannelli, Fabio; Pessina, Fabio; Sharma, Sheetal; d'Adda di Fagagna, Fabrizio

    2017-08-31

    Until recently, DNA damage arising from physiological DNA metabolism was considered a detrimental by-product for cells. However, an increasing amount of evidence has shown that DNA damage could have a positive role in transcription activation. In particular, DNA damage has been detected in transcriptional elements following different stimuli. These physiological DNA breaks are thought to be instrumental for the correct expression of genomic loci through different mechanisms. In this regard, although a plethora of methods are available to precisely map transcribed regions and transcription start sites, commonly used techniques for mapping DNA breaks lack sufficient resolution and sensitivity to draw a robust correlation between DNA damage generation and transcription. Recently, however, several methods have been developed to map DNA damage at single-nucleotide resolution, thus providing a new set of tools to correlate DNA damage and transcription. Here, we review how DNA damage can positively regulate transcription initiation, the current techniques for mapping DNA breaks at high resolution, and how these techniques can benefit future studies of DNA damage and transcription.

  17. High-resolution mapping of vehicle emissions in China in 2008

    NASA Astrophysics Data System (ADS)

    Zheng, B.; Huo, H.; Zhang, Q.; Yao, Z. L.; Wang, X. T.; Yang, X. F.; Liu, H.; He, K. B.

    2014-09-01

    This study is the first in a series of papers that aim to develop high-resolution emission databases for different anthropogenic sources in China. Here we focus on on-road transportation. Because of the increasing impact of on-road transportation on regional air quality, developing an accurate and high-resolution vehicle emission inventory is important for both the research community and air quality management. This work proposes a new inventory methodology to improve the spatial and temporal accuracy and resolution of vehicle emissions in China. We calculate, for the first time, the monthly vehicle emissions for 2008 in 2364 counties (an administrative unit one level lower than city) by developing a set of approaches to estimate vehicle stock and monthly emission factors at county-level, and technology distribution at provincial level. We then introduce allocation weights for the vehicle kilometers traveled to assign the county-level emissions onto 0.05° × 0.05° grids based on the China Digital Road-network Map (CDRM). The new methodology overcomes the common shortcomings of previous inventory methods, including neglecting the geographical differences between key parameters and using surrogates that are weakly related to vehicle activities to allocate vehicle emissions. The new method has great advantages over previous methods in depicting the spatial distribution characteristics of vehicle activities and emissions. This work provides a better understanding of the spatial representation of vehicle emissions in China and can benefit both air quality modeling and management with improved spatial accuracy.

  18. Hydropower potential mapping in mountain basins by high-resolution hydrological and GIS analysis

    NASA Astrophysics Data System (ADS)

    Claps, P.; Gallo, E.; Ganora, D.; Laio, F.; Masoero, A.

    2013-12-01

    Even in regions with mature hydropower development, needs for stable renewable power sources suggest to revise plans of exploitation of water resources, in compliance to the framework of international and national environmental regulations. This goal requires high-resolution hydrological analysis, that allows to : i) comply with the effects of existing hydropower plants or of other types of water withdrawals; ii) to assist the planner to figure out potential of new plants with still high marginal efficiency; iii) to assist the regulator in the process of comparing projects based on different solutions and different underlying hydrologic estimation methods. Flow duration curves (FDC) are the tool usually adopted to represent water availability and variability for hydropower purposes. They are usually determined in ungauged basins by means of regional statistical analysis. For this study, a 'spatially smooth' regional estimation method (SSEM) has been developed for FDC estimation, with some evolutions from a previous version: i) the method keeps the estimates of mean annual runoff congruent in the confluences by considering only raster-summable explanatory variables; ii) the presence of existing reservoirs and hydropower plants is taken into account by restoring the ';natural' statistics of the curve. The SSEM reconstructs the the FDC in ungauged basins using its L-moments from regressions on geomorphoclimatic descriptors. Relations are obtained on more than 100 gauged basins located in Northwestern Italy. To support the assessment of residual hydropower potential on two specific mountain watersheds the model has been applied extensively (Hi-Res) by mapping the estimated mean flow for each pixel of a DEM-derived river network raster model. 25000 sections were then identified over the network extracted from a 50m-resolution DTM. Spatial algorithms and data management were developed using Free&OpenSource Software (FOSS) (GRASS GIS and PostgreSQL/PostGIS), with the

  19. Mapping Small Intestine Bioelectrical Activity Using High-Resolution Printed-Circuit-Board Electrodes

    PubMed Central

    Angeli, Timothy R.; O’Grady, Gregory; Erickson, Jonathan C.; Du, Peng; Paskaranandavadivel, Niranchan; Bissett, Ian P.; Cheng, Leo K.; Pullan, Andrew J.

    2014-01-01

    In this study, novel methods were developed for the in-vivo high-resolution recording and analysis of small intestine bioelectrical activity, using flexible printed-circuit-board (PCB) electrode arrays. Up to 256 simultaneous recordings were made at multiple locations along the porcine small intestine. Data analysis was automated through the application and tuning of the Falling-Edge Variable-Threshold algorithm, achieving 92% sensitivity and a 94% positive-predictive value. Slow wave propagation patterns were visualized through the automated generation of animations and isochronal maps. The methods developed and validated in this study are applicable for use in humans, where future studies will serve to improve the clinical understanding of small intestine motility in health and disease. PMID:22255449

  20. Mapping small intestine bioelectrical activity using high-resolution printed-circuit-board electrodes.

    PubMed

    Angeli, Timothy R; O'Grady, Gregory; Erickson, Jonathan C; Du, Peng; Paskaranandavadivel, Niranchan; Bissett, Ian P; Cheng, Leo K; Pullan, Andrew J

    2011-01-01

    In this study, novel methods were developed for the in-vivo high-resolution recording and analysis of small intestine bioelectrical activity, using flexible printed-circuit-board (PCB) electrode arrays. Up to 256 simultaneous recordings were made at multiple locations along the porcine small intestine. Data analysis was automated through the application and tuning of the Falling-Edge Variable-Threshold algorithm, achieving 92% sensitivity and a 94% positive-predictive value. Slow wave propagation patterns were visualized through the automated generation of animations and isochronal maps. The methods developed and validated in this study are applicable for use in humans, where future studies will serve to improve the clinical understanding of small intestine motility in health and disease.

  1. BrainMaps.org - Interactive High-Resolution Digital Brain Atlases and Virtual Microscopy.

    PubMed

    Mikula, Shawn; Stone, James M; Jones, Edward G

    2008-01-01

    BrainMaps.org is an interactive high-resolution digital brain atlas and virtual microscope that is based on over 20 million megapixels of scanned images of serial sections of both primate and non-primate brains and that is integrated with a high-speed database for querying and retrieving data about brain structure and function over the internet. Complete brain datasets for various species, including Homo sapiens, Macaca mulatta, Chlorocebus aethiops, Felis catus, Mus musculus, Rattus norvegicus, and Tyto alba, are accessible online. The methods and tools we describe are useful for both research and teaching, and can be replicated by labs seeking to increase accessibility and sharing of neuroanatomical data. These tools offer the possibility of visualizing and exploring completely digitized sections of brains at a sub-neuronal level, and can facilitate large-scale connectional tracing, histochemical and stereological analyses.

  2. Exploiting crowdsourced observations: High-resolution mapping of real-time urban air quality throughout Europe

    NASA Astrophysics Data System (ADS)

    Schneider, Philipp; Castell, Nuria; Vallejo, Islen; van den Bossche, Joris; Lahoz, William; Bartonova, Alena

    2016-04-01

    With the technology of air quality sensors improving rapidly in recent years and with an increasing number of initiatives for collecting air quality information being established worldwide, there is a rapidly increasing amount of information on air quality. Such datasets can provide unprecedented spatial detail and thus exhibit a significant potential for allowing to create observation-based high-resolution maps of air quality in the urban environment. However, most datasets of observations made within a citizen science or crowdsourcing framework tend to have highly variable characteristics in terms of quantity, accuracy, measured parameters, and representativeness, and many more. It is therefore currently unknown how to best exploit this information for mapping purposes. In order to address this challenge we present a novel approach for combining crowdsourced observations of urban air quality with model information, allowing us to produce near-real-time, high-resolution maps of air quality in the urban environment. The approach is based on data fusion techniques, which allow for combining observations with model data in a mathematically objective way and therefore provide a means of adding value to both the observations and the model. The observations are improved by filling spatio-temporal gaps in the data and the model is improved by constraining it with observations. The model further provides detailed spatial patterns in areas where no observations are available. As such, data fusion of observations from high-density low-cost sensor networks together with air quality models can contribute to significantly improving urban-scale air quality mapping. The system has been implemented to run in an automated fashion in near real-time (once every hour) for several cities in Europe. Evaluation of the methodology is being carried out using the leave-one-out cross validation technique and simulated datasets. We present case studies demonstrating the methodology for

  3. High-resolution aeromagnetic mapping of volcanic terrain, Yellowstone National Park

    USGS Publications Warehouse

    Finn, C.A.; Morgan, L.A.

    2002-01-01

    High-resolution aeromagnetic data acquired over Yellowstone National Park (YNP) show contrasting patterns reflecting differences in rock composition, types and degree of alteration, and crustal structures that mirror the variable geology of the Yellowstone Plateau. The older, Eocene, Absaroka Volcanic Supergroup, a series of mostly altered, andesitic volcanic and volcaniclastic rocks partially exposed in mountains on the eastern margin of YNP, produces high-amplitude, positive magnetic anomalies, strongly contrasting with the less magnetic, younger, latest Cenozoic, Yellowstone Plateau Group, primarily a series of fresh and variably altered rhyolitic rocks covering most of YNP. The Yellowstone caldera is the centerpiece of the Yellowstone Plateau; part of its boundary can be identified on the aeromagnetic map as a series of discontinuous, negative magnetic anomalies that reflect faults or zones along which extensive hydrothermal alteration is localized. The large-volume rhyolitic ignimbrite deposits of the 0.63-Ma Lava Creek Tuff and the 2.1-Ma Huckleberry Ridge Tuff, which are prominent lithologies peripheral to the Yellowstone caldera, produce insignificant magnetic signatures. A zone of moderate amplitude positive anomalies coincides with the mapped extent of several post-caldera rhyolitic lavas. Linear magnetic anomalies reflect the rectilinear fault systems characteristic of resurgent domes in the center of the caldera. Peripheral to the caldera, the high-resolution aeromagnetic map clearly delineates flow unit boundaries of pre- and post-caldera basalt flows, which occur stratigraphically below the post-caldera rhyolitic lavas and are not exposed extensively at the surface. All of the hot spring and geyser basins, such as Norris, Upper and Lower Geyser Basins, West Thumb, and Gibbon, are associated with negative magnetic anomalies, reflecting hydrothermal alteration that has destroyed the magnetic susceptibility of minerals in the volcanic rocks. Within

  4. High-Resolution Thermal Inertia Mapping from the Mars Global Surveyor Thermal Emission Spectrometer

    USGS Publications Warehouse

    Mellon, M.T.; Jakosky, B.M.; Kieffer, H.H.; Christensen, P.R.

    2000-01-01

    High-resolution thermal inertia mapping results are presented, derived from Mars Global Surveyor (MGS) Thermal Emission Spectrometer (TES) observations of the surface temperature of Mars obtained during the early portion of the MGS mapping mission. Thermal inertia is the key property controlling the diurnal surface temperature variations, and is dependent on the physical character of the top few centimeters of the surface. It represents a complex combination of particle size, rock abundance, exposures of bedrock, and degree of induration. In this work we describe the derivation of thermal inertia from TES data, present global scale analysis, and place these results into context with earlier work. A global map of nighttime thermal-bolometer-based thermal inertia is presented at 14?? per pixel resolution, with approximately 63% coverage between 50??S and 70??N latitude. Global analysis shows a similar pattern of high and low thermal inertia as seen in previous Viking low-resolution mapping. Significantly more detail is present in the high-resolution TES thermal inertia. This detail represents horizontal small-scale variability in the nature of the surface. Correlation with albedo indicates the presence of a previously undiscovered surface unit of moderate-to-high thermal inertia and intermediate albedo. This new unit has a modal peak thermal inertia of 180-250 J m-2 K-1 s-12 and a narrow range of albedo near 0.24. The unit, covering a significant fraction of the surface, typically surrounds the low thermal inertia regions and may comprise a deposit of indurated fine material. Local 3-km-resolution maps are also presented as examples of eolian, fluvial, and volcanic geology. Some impact crater rims and intracrater dunes show higher thermal inertias than the surrounding terrain; thermal inertia of aeolian deposits such as intracrater dunes may be related to average particle size. Outflow channels and valleys consistently show higher thermal inertias than the

  5. High-resolution aeromagnetic mapping of volcanic terrain, Yellowstone National Park

    NASA Astrophysics Data System (ADS)

    Finn, Carol A.; Morgan, Lisa A.

    2002-06-01

    High-resolution aeromagnetic data acquired over Yellowstone National Park (YNP) show contrasting patterns reflecting differences in rock composition, types and degree of alteration, and crustal structures that mirror the variable geology of the Yellowstone Plateau. The older, Eocene, Absaroka Volcanic Supergroup, a series of mostly altered, andesitic volcanic and volcaniclastic rocks partially exposed in mountains on the eastern margin of YNP, produces high-amplitude, positive magnetic anomalies, strongly contrasting with the less magnetic, younger, latest Cenozoic, Yellowstone Plateau Group, primarily a series of fresh and variably altered rhyolitic rocks covering most of YNP. The Yellowstone caldera is the centerpiece of the Yellowstone Plateau; part of its boundary can be identified on the aeromagnetic map as a series of discontinuous, negative magnetic anomalies that reflect faults or zones along which extensive hydrothermal alteration is localized. The large-volume rhyolitic ignimbrite deposits of the 0.63-Ma Lava Creek Tuff and the 2.1-Ma Huckleberry Ridge Tuff, which are prominent lithologies peripheral to the Yellowstone caldera, produce insignificant magnetic signatures. A zone of moderate amplitude positive anomalies coincides with the mapped extent of several post-caldera rhyolitic lavas. Linear magnetic anomalies reflect the rectilinear fault systems characteristic of resurgent domes in the center of the caldera. Peripheral to the caldera, the high-resolution aeromagnetic map clearly delineates flow unit boundaries of pre- and post-caldera basalt flows, which occur stratigraphically below the post-caldera rhyolitic lavas and are not exposed extensively at the surface. All of the hot spring and geyser basins, such as Norris, Upper and Lower Geyser Basins, West Thumb, and Gibbon, are associated with negative magnetic anomalies, reflecting hydrothermal alteration that has destroyed the magnetic susceptibility of minerals in the volcanic rocks. Within

  6. High-resolution charge carrier mobility mapping of heterogeneous organic semiconductors

    NASA Astrophysics Data System (ADS)

    Button, Steven W.; Mativetsky, Jeffrey M.

    2017-08-01

    Organic electronic device performance is contingent on charge transport across a heterogeneous landscape of structural features. Methods are therefore needed to unravel the effects of local structure on overall electrical performance. Using conductive atomic force microscopy, we construct high-resolution out-of-plane hole mobility maps from arrays of 5000 to 16 000 current-voltage curves. To demonstrate the efficacy of this non-invasive approach for quantifying and mapping local differences in electrical performance due to structural heterogeneities, we investigate two thin film test systems, one bearing a heterogeneous crystal structure [solvent vapor annealed 5,11-Bis(triethylsilylethynyl)anthradithiophene (TES-ADT)—a small molecule organic semiconductor] and one bearing a heterogeneous chemical composition [p-DTS(FBTTh2)2:PC71BM—a high-performance organic photovoltaic active layer]. TES-ADT shows nearly an order of magnitude difference in hole mobility between semicrystalline and crystalline areas, along with a distinct boundary between the two regions, while p-DTS(FBTTh2)2:PC71BM exhibits subtle local variations in hole mobility and a nanoscale domain structure with features below 10 nm in size. We also demonstrate mapping of the built-in potential, which plays a significant role in organic light emitting diode and organic solar cell operation.

  7. Creating High-Resolution Multiscale Maps of Human Tissue Using Multi-beam SEM

    PubMed Central

    Hageman, Daniel J.; Garbowski, Tomasz; Riedesel, Christof; Knothe, Ulf; Zeidler, Dirk; Knothe Tate, Melissa L.

    2016-01-01

    Multi-beam scanning electron microscopy (mSEM) enables high-throughput, nano-resolution imaging of macroscopic tissue samples, providing an unprecedented means for structure-function characterization of biological tissues and their cellular inhabitants, seamlessly across multiple length scales. Here we describe computational methods to reconstruct and navigate a multitude of high-resolution mSEM images of the human hip. We calculated cross-correlation shift vectors between overlapping images and used a mass-spring-damper model for optimal global registration. We utilized the Google Maps API to create an interactive map and provide open access to our reconstructed mSEM datasets to both the public and scientific communities via our website www.mechbio.org. The nano- to macro-scale map reveals the tissue’s biological and material constituents. Living inhabitants of the hip bone (e.g. osteocytes) are visible in their local extracellular matrix milieu (comprising collagen and mineral) and embedded in bone’s structural tissue architecture, i.e. the osteonal structures in which layers of mineralized tissue are organized in lamellae around a central blood vessel. Multi-beam SEM and our presented methodology enable an unprecedented, comprehensive understanding of health and disease from the molecular to organ length scale. PMID:27870847

  8. Digital terrain mapping from multispectral and high-resolution satellite data for defense studies

    NASA Astrophysics Data System (ADS)

    Pandey, Suraj

    2007-04-01

    Multi spectral and high resolution satellite imageries enhancing their resolution capabilities in terms of spatial and spectral reflectance time to time such as LANDSAT, IRS, IKONOS and Digital Globe, these imageries are being used effectively and efficiently in certain applications, whereas to register spectral reflectance in different channels of electromagnetic spectrum is the principal characteristic of multi spectral satellite imageries. The real time nature of remotely sensed data can be of high value for mapping and analyzing surface features. This paper explores the broader application of remote sensing analysis for terrain mapping from multi-spectral satellite data, the accuracy of digital elevation model has been verified from various surface interpolation algorithms in which contouring and point interpolation techniques were extensively used. The study reveals that digital interpretation has become more sharpened on a large scale and terrain mapping with high and multi-spectral satellite data along with GPS Mobile Mapper can be done for any region, on some extent this research work has confirmed that sensor on a satellite can navigate army movements.

  9. Quantitative analysis of anthropogenic relief features: automated mapping of charcoal kiln sites from high-resolution ALS data

    NASA Astrophysics Data System (ADS)

    Schneider, Anna; Takla, Melanie; Nicolay, Alexander; Raab, Alexandra; Raab, Thomas

    2014-05-01

    High-resolution digital elevation data from airborne laser scanning (ALS) allow for identification and mapping of so far unknown small-scale relief features that are hidden by forest cover. Especially as a result of historic land use, small anthropogenic landforms can occur, e.g., remains of charcoal kilns on sites that were used for charcoal production or ridge and furrow systems in former farmland areas. Mapping such relief features and analyzing their spatial distribution patterns can help to understand past land-use systems and their effects on landscapes. To efficiently detect and quantify small-scale relief features from high-resolution DEMs for larger areas, (semi-) automated mapping routines are required. In order to describe the number and spatial distribution of historic charcoal kiln sites in the area around Cottbus, Germany, we developed a GIS-based routine for the detection and mapping of kiln remnants from ALS elevation models with a resolution of 1 or 2 meters. The method is based on a template matching algorithm, using a combination of morphometric parameters, and is implemented within ArcGIS. The mapping results could be validated against a comprehensive database of kiln sites and diameters recorded from archaeological excavations in the forefield of the opencast mine Jänschwalde and from manual digitization of kiln remnants from Shaded Relief maps for the Jänschwalder Heide and the Tauersche Forst, north of Cottbus. A considerably high number of charcoal kiln sites could be detected in ALS data, and the diameters of the identified charcoal kilns are remarkable large in the area. For the Jänschwalder Heide, more than 5000 kiln sites in an area of 32 km2 were detected by manual digitization, with 1355 kiln sites that are wider than 12 m. These relatively large kiln sites could be mapped with detection rates that are close to those of manual digitization using the automated mapping routine. Detection quality was improved by the combination of

  10. Calculating High Resolution CWSI Maps for Entire Growing Season of a Cultivated Barley Field with UAV-Collected Surface Temperatures.

    NASA Astrophysics Data System (ADS)

    Hoffmann, H.; Jensen, R.; Nieto Solana, H.; Friborg, T.; Thomsen, A.

    2015-12-01

    With agriculture as the largest consumer of freshwater and an overall increasing pressure on water resources, developing more efficient irrigation systems is important. Combining the crop water stress index (CWSI) with unmanned aerial vehicles (UAVs) enables detection of which specific areas within a cultivated field that requires irrigation to ensure healthy growing plants. In this study remotely sensed, high resolution surface temperatures are collected with a thermal camera onboard an UAV. Temperatures are used to calculate spatially distributed, high resolution CWSI maps over a barley field during growing seasons 2014 and 2015. In early stages of the barley growing season, surface temperatures are an ensemble of both soil and canopy temperatures. Canopy temperatures are extracted using leaf area index and the two source energy balance modelling scheme. This approach enables CWSI calculations for homogeneous and evenly distributed crops (such as barley) during early as well as late stages of a growing season. CWSI maps are calculated using both an empirical and an analytical approach and are compared and validated against modelled canopy conductance and transpiration rates.

  11. High-resolution geologic mapping of the inner continental shelf: Boston Harbor and approaches, Massachusetts

    USGS Publications Warehouse

    Ackerman, Seth D.; Butman, Bradford; Barnhardt, Walter A.; Danforth, William W.; Crocker, James M.

    2006-01-01

    This report presents the surficial geologic framework data and information for the sea floor of Boston Harbor and Approaches, Massachusetts (fig. 1.1). This mapping was conducted as part of a cooperative program between the U.S. Geological Survey (USGS), the Massachusetts Office of Coastal Zone Management (CZM), and the National Oceanic and Atmospheric Administration (NOAA). The primary objective of this project was to provide sea floor geologic information and maps of Boston Harbor to aid resource management, scientific research, industry and the public. A secondary objective was to test the feasibility of using NOAA hydrographic survey data, normally collected to update navigation charts, to create maps of the sea floor suitable for geologic and habitat interpretations. Defining sea-floor geology is the first steps toward managing ocean resources and assessing environmental changes due to natural or human activity. The geophysical data for these maps were collected as part of hydrographic surveys carried out by NOAA in 2000 and 2001 (fig. 1.2). Bottom photographs, video, and samples of the sediments were collected in September 2004 to help in the interpretation of the geophysical data. Included in this report are high-resolution maps of the sea floor, at a scale of 1:25,000; the data used to create these maps in Geographic Information Systems (GIS) format; a GIS project; and a gallery of photographs of the sea floor. Companion maps of sea floor to the north Boston Harbor and Approaches are presented by Barnhardt and others (2006) and to the east by Butman and others (2003a,b,c). See Butman and others (2004) for a map of Massachusetts Bay at a scale of 1:125,000. The sections of this report are listed in the navigation bar along the left-hand margin of this page. Section 1 (this section) introduces the report. Section 2 presents the large-format map sheets. Section 3 describes data collection, processing, and analysis. Section 4 summarizes the geologic history of

  12. Heterozygous mapping strategy (HetMapps)for high resolution genotyping-by-sequencing markers: a case study in grapevine

    USDA-ARS?s Scientific Manuscript database

    Genotyping by sequencing (GBS) provides opportunities to generate high-resolution genetic maps at a low per-sample genotyping cost, but missing data and under-calling of heterozygotes complicate the creation of GBS linkage maps for highly heterozygous species. To overcome these issues, we developed ...

  13. Comparative Analysis of two Methods for High-Resolution Differential Conductance Measurement

    NASA Astrophysics Data System (ADS)

    Cusick, David; Naito, Michio; Ramos, Roberto

    We compare two methods of differential conductance measurement. The first is a traditional method in which current and voltage data is acquired via four-wire measurement, then averaged and differentiated numerically. The second method calculates dI / dV in real time by superimposing a small DC signal dI on the input step function, alternating between addition and subtraction of the signal with each step, then averaging the small signal voltage response over three steps to obtain dV . This requires two instruments: a DC current source and a high-resolution voltmeter. Keithley Instruments has commercially promoted the Keithley 622x current source and 2182A nanovoltmeter as means to achieve this measurement; we therefore refer to it as the Keithley method. We compare the two methods by performing high-resolution measurements of the energy gap of MgB2 thin film Josephson junctions. We show that the Keithley method has advantages of cleaner data, easier implementation, and overall faster data collection, but may lack the traditional method's high resolution. R.C.R. acknowledges support from National Science Foundation Grant # DMR-1555775.

  14. Estimation of Stand Height and Forest Volume Using High Resolution Stereo Photography and Forest Type Map

    NASA Astrophysics Data System (ADS)

    Kim, K. M.

    2016-06-01

    Traditional field methods for measuring tree heights are often too costly and time consuming. An alternative remote sensing approach is to measure tree heights from digital stereo photographs which is more practical for forest managers and less expensive than LiDAR or synthetic aperture radar. This work proposes an estimation of stand height and forest volume(m3/ha) using normalized digital surface model (nDSM) from high resolution stereo photography (25cm resolution) and forest type map. The study area was located in Mt. Maehwa model forest in Hong Chun-Gun, South Korea. The forest type map has four attributes such as major species, age class, DBH class and crown density class by stand. Overlapping aerial photos were taken in September 2013 and digital surface model (DSM) was created by photogrammetric methods(aerial triangulation, digital image matching). Then, digital terrain model (DTM) was created by filtering DSM and subtracted DTM from DSM pixel by pixel, resulting in nDSM which represents object heights (buildings, trees, etc.). Two independent variables from nDSM were used to estimate forest stand volume: crown density (%) and stand height (m). First, crown density was calculated using canopy segmentation method considering live crown ratio. Next, stand height was produced by averaging individual tree heights in a stand using Esri's ArcGIS and the USDA Forest Service's FUSION software. Finally, stand volume was estimated and mapped using aerial photo stand volume equations by species which have two independent variables, crown density and stand height. South Korea has a historical imagery archive which can show forest change in 40 years of successful forest rehabilitation. For a future study, forest volume change map (1970s-present) will be produced using this stand volume estimation method and a historical imagery archive.

  15. High-resolution entrainment mapping of gastric pacing: a new analytical tool.

    PubMed

    O'Grady, Gregory; Du, Peng; Lammers, Wim J E P; Egbuji, John U; Mithraratne, Pulasthi; Chen, Jiande D Z; Cheng, Leo K; Windsor, John A; Pullan, Andrew J

    2010-02-01

    Gastric pacing has been investigated as a potential treatment for gastroparesis. New pacing protocols are required to improve symptom and motility outcomes; however, research progress has been constrained by a limited understanding of the effects of electrical stimulation on slow-wave activity. This study introduces high-resolution (HR) "entrainment mapping" for the analysis of gastric pacing and presents four demonstrations. Gastric pacing was initiated in a porcine model (typical amplitude 4 mA, pulse width 400 ms, period 17 s). Entrainment mapping was performed using flexible multielectrode arrays (mapped in HR, revealing an ectopic slow-wave focus and uncoupled propagations. In the fourth demonstration, differences were observed between paced and native slow-wave amplitudes (0.24 +/- 0.08 vs. 0.38 +/- 0.14 mV; P < 0.001), velocities (6.2 +/- 2.8 vs. 11.5 +/- 4.7 mm/s; P < 0.001), and activated areas (20.6 +/- 1.9 vs. 32.8 +/- 2.6 cm(2); P < 0.001). Entrainment mapping enables an accurate quantification of the effects of gastric pacing on slow-wave activity, offering an improved method to assess whether pacing protocols are likely to achieve physiologically and clinically useful outcomes.

  16. A high-resolution physically-based global flood hazard map

    NASA Astrophysics Data System (ADS)

    Kaheil, Y.; Begnudelli, L.; McCollum, J.

    2016-12-01

    We present the results from a physically-based global flood hazard model. The model uses a physically-based hydrologic model to simulate river discharges, and 2D hydrodynamic model to simulate inundation. The model is set up such that it allows the application of large-scale flood hazard through efficient use of parallel computing. For hydrology, we use the Hillslope River Routing (HRR) model. HRR accounts for surface hydrology using Green-Ampt parameterization. The model is calibrated against observed discharge data from the Global Runoff Data Centre (GRDC) network, among other publicly-available datasets. The parallel-computing framework takes advantage of the river network structure to minimize cross-processor messages, and thus significantly increases computational efficiency. For inundation, we implemented a computationally-efficient 2D finite-volume model with wetting/drying. The approach consists of simulating flood along the river network by forcing the hydraulic model with the streamflow hydrographs simulated by HRR, and scaled up to certain return levels, e.g. 100 years. The model is distributed such that each available processor takes the next simulation. Given an approximate criterion, the simulations are ordered from most-demanding to least-demanding to ensure that all processors finalize almost simultaneously. Upon completing all simulations, the maximum envelope of flood depth is taken to generate the final map. The model is applied globally, with selected results shown from different continents and regions. The maps shown depict flood depth and extent at different return periods. These maps, which are currently available at 3 arc-sec resolution ( 90m) can be made available at higher resolutions where high resolution DEMs are available. The maps can be utilized by flood risk managers at the national, regional, and even local levels to further understand their flood risk exposure, exercise certain measures of mitigation, and/or transfer the residual

  17. Flexible fitting of high-resolution x-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations.

    PubMed

    Orzechowski, Marek; Tama, Florence

    2008-12-15

    A methodology for flexible fitting of all-atom high-resolution structures into low-resolution cryoelectron microscopy (cryo-EM) maps is presented. Flexibility of the modeled structure is simulated by classical molecular dynamics and an additional effective potential is introduced to enhance the fitting process. The additional potential is proportional to the correlation coefficient between the experimental cryo-EM map and a synthetic map generated for an all-atom structure being fitted to the map. The additional forces are calculated as a gradient of the correlation coefficient. During the molecular dynamics simulations under the additional forces, the molecule undergoes a conformational transition that maximizes the correlation coefficient, which results in a high-accuracy fit of all-atom structure into a cryo-EM map. Using five test proteins that exhibit structural rearrangement during their biological activity, we demonstrate performance of our method. We also test our method on the experimental cryo-EM of elongation factor G and show that the model obtained is comparable to previous studies. In addition, we show that overfitting can be avoided by assessing the quality of the fitted model in terms of correlation coefficient and secondary structure preservation.

  18. Mapping evapotranspiration with high resolution aircraft imagery over vineyards using one and two source modeling schemes

    NASA Astrophysics Data System (ADS)

    Xia, T.; Kustas, W. P.; Anderson, M. C.; Alfieri, J. G.; Gao, F.; McKee, L.; Prueger, J. H.; Geli, H. M. E.; Neale, C. M. U.; Sanchez, L.; Mar Alsina, M.; Wang, Z.

    2015-11-01

    Thermal and multispectral remote sensing data from low-altitude aircraft can provide high spatial resolution necessary for sub-field (≤ 10 m) and plant canopy (≤ 1m) scale evapotranspiration (ET) monitoring. In this study, high resolution aircraft sub-meter scale thermal infrared and multispectral shortwave data are used to map ET over vineyards in central California with the Two Source Energy Balance (TSEB) model and with a simple model called DATTUTDUT (Deriving Atmosphere Turbulent Transport Useful To Dummies Using Temperature) which uses contextual information within the image to scale between radiometric land surface temperature (TR) values representing hydrologic limits of potential ET and a non-evaporative surface. Imagery from five days throughout the growing season is used for mapping ET at the sub-field scale. The performance of the two models is evaluated using tower-based energy flux measurements of sensible (H) and latent heat (LE) or ET. The comparison indicates that TSEB was able to derive reasonable ET estimates under varying conditions, likely due to the physically based treatment of the energy and the surface temperature partitioning between the soil/cover crop inter-row and vine canopy elements. On the other hand, DATTUTDUT performance was somewhat degraded presumably because the simple scaling scheme does not consider differences in the two sources (vine and inter-row) of heat and temperature contributions or the effect of surface roughness on the efficiency of heat exchange. Maps of the evaporative fraction (EF = LE/(H + LE)) from the two models had similar spatial patterns but different magnitudes in some areas within the fields on certain days. Large EF discrepancies between the models were found on two of the five days (DOY 162 and 219) when there were significant differences with the tower-based ET measurements, particularly using the DATTUTDUT model. These differences in EF between the models translate to significant variations in

  19. High resolution mapping of dust sources in Central Asia using MODIS imagery

    NASA Astrophysics Data System (ADS)

    Nobakht, Mohamad; Shahgedanova, Maria; White, Kevin

    2015-04-01

    Dust impacts the energy balance of the Earth via absorption and scattering of radiation in the atmosphere and through the mechanism by which aerosols modify the optical properties of clouds and land surfaces. It is now established that the deposition of mineral dust significantly affects high-altitude environments, including both snow pack and glacier ice. Central Asia is a region where large deserts are located in close proximity to the mountains whose extensive glaciers and snow pack provide runoff supporting agriculture in the densely populated foothills. More than 75% of the territory in Central Asia is desert lowland varying from sandy to stony, salt, and clay deserts. Significant amounts of wind-blown desert dust, originating from these deserts, are deposited on glaciers of Tian Shan Mountains in Central Asia. Satellite remote sensing using optical imagery has provided us with a powerful tool for identification and characterization of dust emission sources. In this study we investigated the spatial distribution and seasonal pattern of dust emissions in surrounding lowlands of the Tian Shan Mountains using Moderate Resolution Imaging Spectroradiometer (MODIS) imagery. Seasonality of dust emission is studied by analyzing MODIS Deep Blue aerosol optical depth, acquired over a period of 12 years from January 2003 to December 2014. We analyzed the spatial distribution and frequency of occurrence of dust optical depth to identify the main dust sources in this region. In order to produce a detailed map of dust emission sources, we also employed a dust enhancement algorithm to obtain high resolution (1km) dust enhancement products from MODIS imageries. The high resolution of MODIS dust enhancement products enabled us to identify several small, eroding point sources within the dust source areas. Different seasonal patterns of dust emissions were observed in northern, western and southern deserts around the Tian Shan Mountains and their relation to climatological

  20. High-Resolution Temperature Mapping of Mesospheric Gravity Waves and Breaking Events

    NASA Astrophysics Data System (ADS)

    Taylor, Michael J.; Pautet, Pierre-Dominique; Zhao, Yucheng; Yuan, Tao; Pendleon, William R.; Fritts, David; Esplin, Roy; McLain, David; Stober, Gunter

    2016-04-01

    This presentation highlights new research capabilities and recent results using a novel infra-red imaging system operating at high-latitudes at the ALOMAR Arctic Observatory, Norway (69°N), and at Amundsen-Scott South Pole Station, Antarctica (90°S). The Advanced Mesospheric Temperature Mapper (AMTM) is a high-performance digital imaging system that measures selected emission lines in the mesospheric OH (3,1) band (at ~1.55 μm) to create high-quality intensity and temperature maps of a broad spectrum of gravity waves at the ~87 km level (with periods ranging from several minutes to many hours). The temperature data are obtained with an unprecedented spatial (~0.5 km) and temporal (typically 30 sec) resolution over a large 120° field of view enabling detailed studies of gravity wave propagation and breaking events in the Mesosphere and Lower Thermosphere (MLT) region, even in the presence of strong aurora and moonlight. New results include high-resolution wintertime studies of continuous (24-hr) gravity wave activity and spectral evolution, and first evidence of gravity wave "self-acceleration" in the MLT region using coordinated lidar and radar measurements. These results are complemented by very high resolution (~4 sec) gravity wave observations using a third AMTM developed for airborne measurements on the National Science Foundation (NSF) Gulfstream V aircraft as part of the DEEPWAVE program. This mission was successfully conducted from New Zealand during the Austral winter, June-July 2014, and obtained spectacular new data on mesospheric mountain waves, including large amplitude breaking events associated with variable orographic forcing over the Southern Alps.

  1. Urban air pollution model based on a high-resolution digital elevation map

    NASA Astrophysics Data System (ADS)

    Antonacci, G.; Tubino, M.

    2003-04-01

    The availability of a high resolution map of the town of Trento, which provides information on the height of buildings within the urban area and of traffic data continuosly monitored in several points, allow the development of a dispersion model which is suitable for the estimate of traffic-derived air pollution. In the present case a large amount of traffic data is available, together with concentration data of several pollutants measured through air quality stations located within the urban area. On the other hand only one reliable weather station is presently active within the urban area. However, for the kind of analysis which refers to low level emission sources, traffic conditions turn out to be much more important than meteorological factors in determining air pollution. It is then possible to develop a numerical model, which takes advantage of the high resolution description of the urban structure and of the transit of vehicles. The calculus domain along the vertical direction is divided in two parts: in the lower layer the pollutant is assumed to spread only due to diffusion, while in the upper layer, whose lower limit is fixed by the average height of the buildings, advection is also taken into account. The average wind speed above the buildings' level is supposed to be uniform in space. The diffusion coefficient in the lower layer results from three contributions: the first is the turbulence induced by solar forcing, the second is the mechanical turbulence induced by the transit of motorvehicles, and the last term arises from a globl estimate of the effect of the flow field within the urban fabric, which is not directly computed due to the lack of spatially distributed wind data. The model is applicable only when a large amount of data describing traffic and streets layout is available.

  2. High-Resolution Plasmodium falciparum Malaria Risk Mapping in Mutasa District, Zimbabwe: Implications for Regaining Control.

    PubMed

    Kanyangarara, Mufaro; Mamini, Edmore; Mharakurwa, Sungano; Munyati, Shungu; Gwanzura, Lovemore; Kobayashi, Tamaki; Shields, Timothy; Mullany, Luke C; Mutambu, Susan; Mason, Peter R; Curriero, Frank C; Moss, William J

    2016-07-06

    In Zimbabwe, more than half of malaria cases are concentrated in Manicaland Province, where seasonal malaria epidemics occur despite intensified control strategies. The objectives of this study were to develop a prediction model based on environmental risk factors and obtain seasonal malaria risk maps for Mutasa District, one of the worst affected districts in Manicaland Province. From October 2012 to September 2015, 483 households were surveyed, and 104 individuals residing within 69 households had positive rapid diagnostic test results. Logistic regression was used to model the probability of household positivity as a function of the environmental covariates extracted from high-resolution remote sensing data sources. Model predictions and prediction standard errors were generated for the rainy and dry seasons. The resulting maps predicted elevated risk during the rainy season, particularly in low-lying areas bordering Mozambique. In contrast, the risk of malaria was low across the study area during the dry season with foci of malaria risk scattered along the northern and western peripheries of the study area. These findings underscore the need for strong cross-border malaria control initiatives to complement country-specific interventions. © The American Society of Tropical Medicine and Hygiene.

  3. High resolution mapping of interstitial long arm deletions of chromosome 16: relationship to phenotype.

    PubMed Central

    Callen, D F; Eyre, H; Lane, S; Shen, Y; Hansmann, I; Spinner, N; Zackai, E; McDonald-McGinn, D; Schuffenhauer, S; Wauters, J

    1993-01-01

    The breakpoints of seven interstitial deletions of the long arm of chromosome 16 and two ring chromosomes of this chromosome were mapped by in situ hybridisation or by analysis of mouse/human somatic cell hybrids containing the deleted chromosome 16. Use of a high resolution cytogenetic based physical map of chromosome 16 enabled breakpoints to be assigned to an average resolution of at least 1.6 Mb. In general, interstitial deletions involving q12 or q22.1 have broadly similar phenotypes though there are differences in specific abnormalities. Deletions involving regions more distal, from 16q22.1 to 16q24.1, were associated with relatively mild dysmorphism. One region of the long arm, q24.2 to q24.3, was not involved in any deletion, either in this study or in any previous report. Presumably, monosomy for this region is lethal. In contrast, patients with deletions of 16q21 have a normal phenotype. These results are consistent with the proposed distribution of genes, frequent in telomeric Giesma light band regions but infrequent in G positive bands. Images PMID:8230159

  4. High-resolution mapping of glacial landforms in the North Alpine Foreland, Austria

    NASA Astrophysics Data System (ADS)

    Salcher, Bernhard C.; Hinsch, Ralph; Wagreich, Michael

    2010-10-01

    In this study results from traditional field mapping were merged with precise elevation information from airborne LiDAR (Light detection and ranging) surveys. Morphological and sedimentological data provide new results from the Austrian (eastern) part of the Salzach piedmont glacier during times of and shortly after the Last Glacial Maximum (LGM). The variations in meltwater discharge had a major impact on the development of glacial landforms. In areas with high meltwater supply erosional or debris reworking processes play a major role, represented by drainage channels, drumlins and kettled, low relief hummocky moraine with low slope angles. Low discharge areas are associated with distinct depositional forms such as high relief end moraines (up to 30 m) and hummocky moraine (averaging 20 m) with high slope angles. Isolated conical kames may reach heights up to 45 m. Fluvial activity is supposed to rise towards the end of the glacial cycle causing high melting rates and comprehensive debris reworking. The formation of terminal lakes and associated widespread, inorganic lake clays are the last deposits within the study area before the Salzach Glacier completely receded to its main valley. The survey of glacial landforms through the combination of field mapping and high-resolution DEM derived from airborne LiDAR missions gives precise information on transport and deposition during the last glacial cycle of the eastern Salzach Glacier piedmont lobe.

  5. Combination of AUV high resolution mapping and submersible visual observations on the Guaymas Hydrothermal Fields (Southern Trough Ridge)

    NASA Astrophysics Data System (ADS)

    Ondreas, H.; Fouquet, Y.; Normand, A.; Rouxel, O.; Godfroy, A.

    2011-12-01

    The BIG cruise -leg I- was carried out on the Guaymas basin in June 2010 on board the French research vessel L'Atalante. An AUV high-resolution survey was made on the southern trough ridge to gather fine-scale bathymetry and acoustic imagery data. The results of the high resolution survey were used, the next days, to explore the vent's area during several Nautile dives. The southern trough hydrothermal fields of the Guaymas basin have often been studied. However, the local geological context was not really well-defined. During the AUV surveys, maps at 70 m above the seafloor were done over the hydrothermal area. The data were gridded at 2 m spacing. During the same cruise, Nautile dives help us to compare the field observations and the geological features revealed by the high resolution mapping and to investigate the fine-scale relationships between the vents and their geological environment. Integration of these data is made easier by the use of the GIS software technology. It helps us perpetuate data, undertake comparisons, combine different types of data, realize fine-scale geological mapping. Even if some problems are recurrent (precision of positioning, integration of old data...), such combinations of high resolution mapping and visual observations and sampling have changed our vision of hydrothermal geological context. In the Guaymas sedimented spreading axis, our new data show that major hydrothermal sites, in the south part of the southern trough only, are located inside or at the border of 100 to 250 m long, 60 to 150 m wide, 6 to 12 m deep small collapsed sub-circular depressions. The direction of the collapse is variable. Curved faults at the outer border of these depressions control the largest and mature edifices. Smaller, possibly younger, immature chimneys are located at the centre of some depressions. The mature hydrothermal structures appear as mounds up to 80 m in diameter, 20 m in high, each hydrothermal edifice being very-well identified on the

  6. Comparison of Methods to Map and Measure River Terraces using High-Resolution Airborne LiDAR Data

    NASA Astrophysics Data System (ADS)

    Hopkins, A. J.; Snyder, N. P.

    2013-12-01

    Fluvial terraces are important recorders of land-use, climate, and tectonic history that form in both erosional and depositional landscapes and consist of a flat surface bounded by valley walls and a steep-sloping scarp adjacent to the river channel. Combining these defining characteristics with high-resolution digital elevation models (DEMs) derived from airborne light detection and ranging (lidar) surveys, several methods have been developed to identify and map terraces. The goals of this research are to compare some of these existing techniques and develop an objective approach to map terraces over entire watersheds using lidar DEMs. Additionally, we aim to quantify the thickness and volume of fill terrace deposits. Our preliminary application is to the Sheepscot River watershed, Maine, where strath and fill terraces are present and record Pleistocene deglaciation, Holocene eustatic forcing, and Anthropocene land-use change. We identify terraces along the longitudinal profile using an algorithm developed by Finnegan and Balco (2013), that computes the elevation frequency distribution at regularly spaced cross-sections normal to the channel. Next, we delineate terrace spatial extent using three separate methodologies: (1) image processing using Matlab, (2) feature classification algorithms developed by Wood (1996), and (3) image interpretation using manually placed points on known terraces to construct interpolated surfaces (Walter and Merritts, 2008). Lastly, we determine the thickness and volume of fill terrace sediments by subtracting an interpolated, adjacent water surface elevation from the defined terrace points. We compare our LiDAR-based results with field mapping, stratigraphic columns of terrace landforms, and ground penetrating radar over terrace surfaces. These findings suggest powerful new ways to rapidly analyze landscape history over large regions using high-resolution lidar DEMs, with less reliance on detailed and costly field data collection.

  7. High-resolution Pleiades DEMs and improved mapping methods for the E-Corinth marine terraces

    NASA Astrophysics Data System (ADS)

    de Gelder, Giovanni; Fernández-Blanco, David; Delorme, Arthur; Jara-Muñoz, Julius; Melnick, Daniel; Lacassin, Robin; Armijo, Rolando

    2016-04-01

    The newest generation of satellite imagery provides exciting new possibilities for highly detailed mapping, with ground resolution of sub-metric pixels and absolute accuracy within a few meters. This opens new venues for the analysis of geologic and geomorphic landscape features, especially since photogrammetric methods allow the extraction of detailed topographic information from these satellite images. We used tri-stereo imagery from the Pleiades platform of the CNES in combination with Euclidium software for image orientation, and Micmac software for dense matching, to develop state-of-the-art, 2m-resolution digital elevation models (DEMs) for eight areas in Greece. Here, we present our mapping results for an area in the eastern Gulf of Corinth, which contains one of the most extensive and well-preserved flights of marine terraces world-wide. The spatial extent of the terraces has been determined by an iterative combination of an automated surface classification model for terrain slope and roughness, and qualitative assessment of satellite imagery, DEM hillshade maps, slope maps, as well as detailed topographic analyses of profiles and contours. We determined marine terrace shoreline angles by means of swath profiles that run perpendicularly to the paleo-seacliffs, using the graphical interface TerraceM. Our analysis provided us with a minimum and maximum estimate of the paleoshoreline location on ~750 swath profiles, by using the present-day cliff slope as an approximation for its paleo-cliff counterpart. After correlating the marine terraces laterally we obtained 16 different terrace-levels, recording Quaternary sea-level highstands of both major interglacial and several interstadial periods. Our high-resolution Pleiades-DEMs and improved method for paleoshoreline determination allowed us to produce a marine terrace map of unprecedented detail, containing more terrace sub-levels than hitherto. Our mapping demonstrates that we are no longer limited by the

  8. The interaction of high-resolution electrophoresis and computational analysis in genome mapping

    SciTech Connect

    Carrano, A.V.; Branscomb, E.W.; de Jong, P.J.; Mohrenweiser, H.; Olsen, A.; Slezak, T.

    1990-07-26

    The construction of physical maps and the determination of the DNA sequence of chromosome-size segments of the human genome is a complex, multidisciplinary undertaking. The approach we have taken to construct a physical map and sequence of human chromosome 19 typifies these interactions. We exploit the power of both acrylamide and agarose gel electrophoresis to provide a simple and versatile method for DNA fingerprinting and the creation of contigs or sets of overlapping genomic clones. Cosmid libraries are constructed from Yeast Artificial Chromosomes (YAC) clones or from flow-sorted chromosomes. Cosmid DNA isolated from the screened library array is cut with a combination of five restriction enzymes and the fragment ends labeled with one of four different fluorochromes. Our approach to contig construction uses a robotic system to label restriction fragments from cosmids with fluorochromes, use of an automated DNA sequencer to capture fragment mobility data in a high resolution multiplex mode processes the mobility data to determine fragment length and provide a statistical measure of overlap among cosmids; and display the contigs and underlying cosmids for operator interaction and access to a database. Data analyses and interactions are conducted over a network of SUN workstations using a set of software tools that we developed and coupled to a commercially available database. Applying these methods, we have analyzed 5154 cosmid clones and assembled 515 contigs for chromosome 19. Some of these contigs have been identified with known genes and many have been mapped to the chromosome by fluorescence in situ hybridization. Existing contigs are being extended by a combination of walking and fingerprinting. 21 refs., 2 figs.

  9. High resolution wetland mapping in West Siberian taiga zone for methane emission inventory

    NASA Astrophysics Data System (ADS)

    Terentieva, I. E.; Glagolev, M. V.; Lapshina, E. D.; Sabrekov, A. F.; Maksyutov, S. S.

    2015-12-01

    High latitude wetlands are important for understanding climate change risks because these environments sink carbon and emit methane. Fine scale heterogeneity of wetland landscapes pose challenges for producing the greenhouse gas flux inventories based on point observations. To reduce uncertainties at the regional scale, we mapped wetlands and water bodies in the taiga zone of West Siberia on a scene-by-scene basis using a supervised classification of Landsat imagery. The training dataset was based on high-resolution images and field data that were collected at 28 test areas. Classification scheme was aimed at methane inventory applications and included 7 wetland ecosystem types composing 9 wetland complexes in different proportions. Accuracy assessment based on 1082 validation polygons of 10 × 10 pixels indicated an overall map accuracy of 79 %. The total area of the wetlands and water bodies was estimated to be 52.4 Mha or 4-12 % of the global wetland area. Ridge-hollow complexes prevail in WS's taiga, occupying 33 % of the domain, followed by forested bogs or "ryams" (23 %), ridge-hollow-lake complexes (16 %), open fens (8 %), palsa complexes (7 %), open bogs (5 %), patterned fens (4 %), and swamps (4 %). Various oligotrophic environments are dominant among the wetland ecosystems, while fens cover only 14 % of the area. Because of the significant update in the wetland ecosystem coverage, a considerable revaluation of the total CH4 emissions from the entire region is expected. A new Landsat-based map of WS's taiga wetlands provides a benchmark for validation of coarse-resolution global land cover products and wetland datasets in high latitudes.

  10. A hybrid CPU-GPU accelerated framework for fast mapping of high-resolution human brain connectome.

    PubMed

    Wang, Yu; Du, Haixiao; Xia, Mingrui; Ren, Ling; Xu, Mo; Xie, Teng; Gong, Gaolang; Xu, Ningyi; Yang, Huazhong; He, Yong

    2013-01-01

    Recently, a combination of non-invasive neuroimaging techniques and graph theoretical approaches has provided a unique opportunity for understanding the patterns of the structural and functional connectivity of the human brain (referred to as the human brain connectome). Currently, there is a very large amount of brain imaging data that have been collected, and there are very high requirements for the computational capabilities that are used in high-resolution connectome research. In this paper, we propose a hybrid CPU-GPU framework to accelerate the computation of the human brain connectome. We applied this framework to a publicly available resting-state functional MRI dataset from 197 participants. For each subject, we first computed Pearson's Correlation coefficient between any pairs of the time series of gray-matter voxels, and then we constructed unweighted undirected brain networks with 58 k nodes and a sparsity range from 0.02% to 0.17%. Next, graphic properties of the functional brain networks were quantified, analyzed and compared with those of 15 corresponding random networks. With our proposed accelerating framework, the above process for each network cost 80∼150 minutes, depending on the network sparsity. Further analyses revealed that high-resolution functional brain networks have efficient small-world properties, significant modular structure, a power law degree distribution and highly connected nodes in the medial frontal and parietal cortical regions. These results are largely compatible with previous human brain network studies. Taken together, our proposed framework can substantially enhance the applicability and efficacy of high-resolution (voxel-based) brain network analysis, and have the potential to accelerate the mapping of the human brain connectome in normal and disease states.

  11. High-Resolution Regional Biomass Map of Siberia from Glas, Palsar L-Band Radar and Landsat Vcf Data

    NASA Astrophysics Data System (ADS)

    Sun, G.; Ranson, K.; Montesano, P.; Zhang, Z.; Kharuk, V.

    2015-12-01

    N to 75oN, and 80oE to 145oE. The spatial patterns of the new biomass map is much better than the previous maps due to spatially specific mapping in high resolution. The uncertainties of field/GLAS and GLAS/imagery models were investigated using bootstrap procedure, and the final biomass map was compared with previous maps.

  12. Vegetation mapping from high-resolution satellite images in the heterogeneous arid environments of Socotra Island (Yemen)

    NASA Astrophysics Data System (ADS)

    Malatesta, Luca; Attorre, Fabio; Altobelli, Alfredo; Adeeb, Ahmed; De Sanctis, Michele; Taleb, Nadim M.; Scholte, Paul T.; Vitale, Marcello

    2013-01-01

    Socotra Island (Yemen), a global biodiversity hotspot, is characterized by high geomorphological and biological diversity. In this study, we present a high-resolution vegetation map of the island based on combining vegetation analysis and classification with remote sensing. Two different image classification approaches were tested to assess the most accurate one in mapping the vegetation mosaic of Socotra. Spectral signatures of the vegetation classes were obtained through a Gaussian mixture distribution model, and a sequential maximum a posteriori (SMAP) classification was applied to account for the heterogeneity and the complex spatial pattern of the arid vegetation. This approach was compared to the traditional maximum likelihood (ML) classification. Satellite data were represented by a RapidEye image with 5 m pixel resolution and five spectral bands. Classified vegetation relevés were used to obtain the training and evaluation sets for the main plant communities. Postclassification sorting was performed to adjust the classification through various rule-based operations. Twenty-eight classes were mapped, and SMAP, with an accuracy of 87%, proved to be more effective than ML (accuracy: 66%). The resulting map will represent an important instrument for the elaboration of conservation strategies and the sustainable use of natural resources in the island.

  13. A High-Resolution Map of Synteny Disruptions in Gibbon and Human Genomes

    PubMed Central

    Hallers, Boudewijn F.H. ten; Zhu, Baoli; Osoegawa, Kazutoyo; Mootnick, Alan; Kofler, Andrea; Wienberg, Johannes; Rogers, Jane; Humphray, Sean; Scott, Carol; Harris, R. Alan; Milosavljevic, Aleksandar; de Jong, Pieter J

    2006-01-01

    Gibbons are part of the same superfamily (Hominoidea) as humans and great apes, but their karyotype has diverged faster from the common hominoid ancestor. At least 24 major chromosome rearrangements are required to convert the presumed ancestral karyotype of gibbons into that of the hominoid ancestor. Up to 28 additional rearrangements distinguish the various living species from the common gibbon ancestor. Using the northern white-cheeked gibbon (2n = 52) (Nomascus leucogenys leucogenys) as a model, we created a high-resolution map of the homologous regions between the gibbon and human. The positions of 100 synteny breakpoints relative to the assembled human genome were determined at a resolution of about 200 kb. Interestingly, 46% of the gibbon–human synteny breakpoints occur in regions that correspond to segmental duplications in the human lineage, indicating a common source of plasticity leading to a different outcome in the two species. Additionally, the full sequences of 11 gibbon BACs spanning evolutionary breakpoints reveal either segmental duplications or interspersed repeats at the exact breakpoint locations. No specific sequence element appears to be common among independent rearrangements. We speculate that the extraordinarily high level of rearrangements seen in gibbons may be due to factors that increase the incidence of chromosome breakage or fixation of the derivative chromosomes in a homozygous state. PMID:17196042

  14. Subsurface Feature Mapping of Mars using a High Resolution Ground Penetrating Radar System

    NASA Astrophysics Data System (ADS)

    Wu, T. S.; Persaud, D. M.; Preudhomme, M. A.; Jurg, M.; Smith, M. K.; Buckley, H.; Tarnas, J.; Chalumeau, C.; Lombard-Poirot, N.; Mann, B.

    2015-12-01

    As the closest Earth-like, potentially life-sustaining planet in the solar system, Mars' future of human exploration is more a question of timing than possibility. The Martian surface remains hostile, but its subsurface geology holds promise for present or ancient astrobiology and future habitation, specifically lava tube (pyroduct) systems, whose presence has been confirmed by HiRISE imagery.The location and characterization of these systems could provide a basis for understanding the evolution of the red planet and long-term shelters for future manned missions on Mars. To detect and analyze the subsurface geology of terrestrial bodies from orbit, a novel compact (smallsat-scale) and cost-effective approach called the High-resolution Orbiter for Mapping gEology by Radar (HOMER) has been proposed. Adapting interferometry techniques with synthetic aperture radar (SAR) to a ground penetrating radar system, a small satellite constellation is able to achieve a theoretical resolution of 50m from low-Mars orbit (LMO). Alongside this initial prototype design of HOMER, proposed data processing methodology and software and a Mars mission design are presented. This project was developed as part of the 2015 NASA Ames Academy for Space Exploration.

  15. Bow Shocks Around Runaway Stars.III.The High Resolution Maps

    NASA Astrophysics Data System (ADS)

    Noriega-Crespo, Alberto; van Buren, Dave; Dgani, Ruth

    1997-02-01

    In a recent survey for bow shock structures around OB runaway stars using the ISSA/IRAS archival data and excess maps at 60 \\mum, 58 candidates were found. These objects are surrounded by extended infrared emission at 60 \\mum, characteristic of warm dust heated by ultraviolet photons, a signature of wind bow shocks. High resolution IRAS (HiRes) images have been produced for these 58 objects and some of those spatially resolved are presented in this study. The images were used to distinguish between multiple confused IR sources, possible artifacts and unambiguous bow shocks, as the sources of the extended 60 \\mum emission. Six new bow shocks have been identified using this method, and three have been rejected. Twenty two of the targets, however, remain spatially unresolved even at the nominal HiRes resolution of ~ 1arcmin . For the larger and better defined bow shocks some internal substructure is discernible. The length of these features suggest that they arise as the result of a subtle dynamical instability. It can not be ruled out, however, that some of the bow shock morphology could be imprinted by the surrounding medium.

  16. High-Resolution Mapping and Functional Analysis of se2.1

    PubMed Central

    Chen, Kai-Yi; Tanksley, Steven D.

    2004-01-01

    The degree to which stigmas are exserted above the stamen in flowers is a key determinant of cross-pollination (and hence allogamy) in many plant species. Most species in the genus Lycopersicon are obligate or facultative outcrossers and bear flowers with highly exserted stigmas. In contrast, the cultivated tomato (Lycopersicon esculentum) bears flowers with flush or inserted stigmas promoting self-fertilization. It has been observed that a major QTL, se2.1, on chromosome 2 is responsible for a large portion of phenotypic variation for this trait and that mutation(s) at this locus were likely involved in the evolution from allogamy to autogamy in this genus. To understand the genetic and molecular basis of stigma exsertion, we have conducted a high-resolution mapping at the chromosome region harboring the se2.1 QTL. The results indicate that this is a compound locus, comprising at least five tightly linked genes, one controlling style length, three controlling stamen length, and the other affecting anther dehiscence, a taxonomic character used to distinguish Lycopersicon species from other solanaceous species. This cluster of genes may represent the vestiges of an ancient coadapted gene complex in controlling mating behavior. PMID:15579707

  17. High resolution aeromagnetic anomaly map of Mount Etna volcano, Southern Italy

    NASA Astrophysics Data System (ADS)

    D'Ajello Caracciolo, F.; Nicolosi, I.; Carluccio, R.; Chiappini, S.; De Ritis, R.; Giuntini, A.; Materni, V.; Messina, A.; Chiappini, M.

    2014-05-01

    A high resolution aeromagnetic survey of Mount Etna Volcano was carried out by the Airborne Geophysics Science Team of Istituto Nazionale di Geofisica e Vulcanologia (INGV), aimed at producing the most detailed magnetic anomaly map existing so far for this area. Two datasets of the total intensity of the Earth's Magnetic Field were collected at different altitudes to take into account the huge topographic variations of Etna volcano, that reaches elevations above 3300 m asl. One level was flown at the altitude of 2200 m whereas a second one over the central part, at about 3500 m of altitude. Since the region is characterized by a large presence of strongly magnetized volcanic products, the survey was carried out acquiring profile lines only, in order to optimize the resources. From the residual magnetic anomaly analysis we inferred two main trending lineaments (- 35°N and 0°N) that are related to regional tectonic stress field and we interpret the main magnetic anomaly as the effect of thickness variation of magnetized volcanic products due to the complex pre-volcanic basement morphology of Etna.

  18. A high-resolution map of synteny disruptions in gibbon and human genomes.

    PubMed

    Carbone, Lucia; Vessere, Gery M; ten Hallers, Boudewijn F H; Zhu, Baoli; Osoegawa, Kazutoyo; Mootnick, Alan; Kofler, Andrea; Wienberg, Johannes; Rogers, Jane; Humphray, Sean; Scott, Carol; Harris, R Alan; Milosavljevic, Aleksandar; de Jong, Pieter J

    2006-12-29

    Gibbons are part of the same superfamily (Hominoidea) as humans and great apes, but their karyotype has diverged faster from the common hominoid ancestor. At least 24 major chromosome rearrangements are required to convert the presumed ancestral karyotype of gibbons into that of the hominoid ancestor. Up to 28 additional rearrangements distinguish the various living species from the common gibbon ancestor. Using the northern white-cheeked gibbon (2n = 52) (Nomascus leucogenys leucogenys) as a model, we created a high-resolution map of the homologous regions between the gibbon and human. The positions of 100 synteny breakpoints relative to the assembled human genome were determined at a resolution of about 200 kb. Interestingly, 46% of the gibbon-human synteny breakpoints occur in regions that correspond to segmental duplications in the human lineage, indicating a common source of plasticity leading to a different outcome in the two species. Additionally, the full sequences of 11 gibbon BACs spanning evolutionary breakpoints reveal either segmental duplications or interspersed repeats at the exact breakpoint locations. No specific sequence element appears to be common among independent rearrangements. We speculate that the extraordinarily high level of rearrangements seen in gibbons may be due to factors that increase the incidence of chromosome breakage or fixation of the derivative chromosomes in a homozygous state.

  19. ATLAS: an airborne active linescan system for high-resolution topographic mapping

    NASA Astrophysics Data System (ADS)

    Willetts, David V.; Kightley, Peter J.; Mole, S. G.; Pearson, Guy N.; Pearson, P.; Coffey, Adrian S.; Stokes, Tim J.; Tapster, Paul R.; Westwood, M.

    2004-12-01

    High resolution ground mapping is of interest for survey and management of long linear features such as roads, railways and pipelines, and for georeferencing of areas such as flood plains for hydrological purposes. ATLAS (Airborne Topographic Laser System) is an active linescan system operating at the eyesafe wavelength of 1.5μm. Built for airborne survey, it is currently certified for use on a Twin Squirrel helicopter for operation from low levels to heights above 500 feet allowing commercial survey in built up areas. The system operates at a pulse repetition frequency of 56kHz with a line completed in 15ms, giving 36 points/m2 at the surface at the design flight speed. At each point the range to the ground is measured together with the scan angle of the system. This data is combined with a system attitude measurement from an integrated inertial navigation system and with system position derived from differential GPS data aboard the platform. A recording system captures the data with a synchronised time-stamp to enable post-processed reconstruction of a cloud of data points that will give a three-dimensional representation of the terrain, allowing the points to be located with respect to absolute Earth referenced coordinates to a precision of 5cm in three axes. This paper summarises the design, harmonisation, evaluation and performance of the system, and shows examples of survey data.

  20. Machine Learning Approaches for High-resolution Urban Land Cover Classification: A Comparative Study

    SciTech Connect

    Vatsavai, Raju; Chandola, Varun; Cheriyadat, Anil M; Bright, Eddie A; Bhaduri, Budhendra L; Graesser, Jordan B

    2011-01-01

    The proliferation of several machine learning approaches makes it difficult to identify a suitable classification technique for analyzing high-resolution remote sensing images. In this study, ten classification techniques were compared from five broad machine learning categories. Surprisingly, the performance of simple statistical classification schemes like maximum likelihood and Logistic regression over complex and recent techniques is very close. Given that these two classifiers require little input from the user, they should still be considered for most classification tasks. Multiple classifier systems is a good choice if the resources permit.

  1. High resolution mapping of combustion processes and implications for CO2 emissions

    NASA Astrophysics Data System (ADS)

    Wang, R.; Tao, S.; Ciais, P.; Shen, H. Z.; Huang, Y.; Chen, H.; Shen, G. F.; Wang, B.; Li, W.; Zhang, Y. Y.; Lu, Y.; Zhu, D.; Chen, Y. C.; Liu, X. P.; Wang, W. T.; Wang, X. L.; Liu, W. X.; Li, B. G.; Piao, S. L.

    2012-08-01

    High-resolution mapping of fuel combustion and CO2 emission provides valuable information for inferring terrestrial carbon balance, modeling pollutant transport, and developing mitigation strategies. Previous inventories included only a limited number of fuel types and anthropogenic emissions were mapped using national population proxies which may distort the geographical distribution within countries. In this study, a sub-national disaggregation method (SDM) was applied to establish a global 0.1°×0.1° geo-referenced inventory of fuel combustion (PKU-FUEL) and a corresponding CO2 emission inventory (PKU-CO2) based upon 64 fuel sub-types for the year 2007. Uncertainties of the new inventories were evaluated using a Monte Carlo method. The total combustion CO2 emission in 2007 was 11.2 (9.11 and 13.3 as 5th and 95th percentiles) Pg C yr-1. By replacing national disaggregation with sub-national disaggregation in this study, the average 95th minus 5th percentile ranges of CO2 emission for all grids can be reduced from 417 to 68.2 Mg km-2 yr-1, indicating a significant reduction in uncertainty, because the uneven distribution of per-capita fuel consumptions within countries has been taken into account by using the sub-national fuel consumption data directly. Significant difference in per-capita CO2 emissions between urban and rural areas was found in developing nations (2.09 vs. 0.600 Mg C cap-1 yr-1), but not in developed ones (3.57 vs. 3.42 Mg C cap-1 yr-1), suggesting strong influence of the rapid urbanization of these countries on the carbon emission. By using the CO2 emission product, a new spatial pattern of terrestrial carbon sink was derived and the impact of sub-national disaggregation is discussed.

  2. Hazard Mapping of Structurally Controlled Landslide in Southern Leyte, Philippines Using High Resolution Digital Elevation Model

    NASA Astrophysics Data System (ADS)

    Luzon, Paul Kenneth; Rochelle Montalbo, Kristina; Mahar Francisco Lagmay, Alfredo

    2014-05-01

    The 2006 Guinsaugon landslide in St. Bernard, Southern Leyte is the largest known mass movement of soil in the Philippines. It consisted of a 15 million m3 rockslide-debris avalanche from an approximately 700 m high escarpment produced by continuous movement of the Philippine fault at approximately 2.5 cm/year. The landslide was preceded by continuous heavy rainfall totaling 571.2 mm from February 8 to 12, 2006. The catastrophic landslide killed more than 1,000 people and displaced 19,000 residents over its 6,400 km path. To investigate the present-day morphology of the scar and potential failure that may occur, an analysis of a high-resolution digital elevation model (10 m resolution Synthetic Aperture Radar images in 2013) was conducted, leading to the generation of a structurally controlled landslide hazard map of the area. Discontinuity sets that could contribute to any failure mechanism were identified using Coltop 3D software which uses a unique lower Schmidt-Lambert color scheme for any given dip and dip direction. Thus, finding main morpho-structural orientations became easier. Matterocking, a software designed for structural analysis, was used to generate possible planes that could slide due to the identified discontinuity sets. Conefall was then utilized to compute the extent to which the rock mass will run out. The results showed potential instabilities in the scarp area of the 2006 Guinsaguon landslide and in adjacent slopes because of the presence of steep discontinuities that range from 45-60°. Apart from the 2006 Guinsaugon potential landslides, conefall simulation generated farther rock mass extent in adjacent slopes. In conclusion, there is a high probability of landslides in the municipality of St. Bernard Leyte, where the 2006 Guinsaugon Landslide occurred. Concerned agencies may use maps produced from this study for disaster preparedness and to facilitate long-term recovery planning for hazardous areas.

  3. Grapevine powdery mildew resistance and susceptibility loci identified on a high-resolution SNP map.

    PubMed

    Barba, Paola; Cadle-Davidson, Lance; Harriman, James; Glaubitz, Jeffrey C; Brooks, Siraprapa; Hyma, Katie; Reisch, Bruce

    2014-01-01

    Improved efficacy and durability of powdery mildew resistance can be enhanced via knowledge of the genetics of resistance and susceptibility coupled with the development of high-resolution maps to facilitate the stacking of multiple resistance genes and other desirable traits. We studied the inheritance of powdery mildew (Erysiphe necator) resistance and susceptibility of wild Vitis rupestris B38 and cultivated V. vinifera 'Chardonnay', finding evidence for quantitative variation. Molecular markers were identified using genotyping-by-sequencing, resulting in 16,833 single nucleotide polymorphisms (SNPs) based on alignment to the V. vinifera 'PN40024' reference genome sequence. With an average density of 36 SNPs/Mbp and uniform coverage of the genome, this 17K set was used to identify 11 SNPs on chromosome 7 associated with a resistance locus from V. rupestris B38 and ten SNPs on chromosome 9 associated with a locus for susceptibility from 'Chardonnay' using single marker association and linkage disequilibrium analysis. Linkage maps for V. rupestris B38 (1,146 SNPs) and 'Chardonnay' (1,215 SNPs) were constructed and used to corroborate the 'Chardonnay' locus named Sen1 (Susceptibility to Erysiphe necator 1), providing the first insight into the genetics of susceptibility to powdery mildew from V. vinifera. The identification of markers associated with a susceptibility locus in a V. vinifera background can be used for negative selection among breeding progenies. This work improves our understanding of the nature of powdery mildew resistance in V. rupestris B38 and 'Chardonnay', while applying next-generation sequencing tools to advance grapevine genomics and breeding.

  4. Mapping and delineating wetlands of Huntington Wildlife Forest using very high resolution digital color-infrared imagery

    NASA Astrophysics Data System (ADS)

    Yavuz, Mehmet

    The effectiveness of off-site wetland delineation methods using very high resolution digital color-infrared aerial imagery (the color-IR imagery) is compared to the traditional on-site wetland delineation method. The on-site delineation results created using the US Fish and Wildlife Service's National Wetland Inventory (NWI map procedures are compared to the following mapping techniques; heads-up digitizing, hybrid classification, Normalized Difference Vegetation Index (NDVI) and unsupervised classifications (ISODATA) using the same image source. Each of the mapping techniques was applied using the seasonal color-IR imagery. Pair-wise significance tests of the closest mean distances indicated that heads-up digitizing was significantly more accurate than other classification techniques for the color-IR imagery. A combination of the heads-up digitizing and the hybrid classification showed that emergent wetland and scrub-shrub wetlands can be delineated without visiting the ground from the color-IR imagery. Applying logarithmic and hyperbolic sine algorithms to enhance the radiometric property of the color-IR imagery increased delineation accuracy 98% in the spring color-IR imagery and 28% in the fall color-IR imagery. Methods for measuring the accuracy of linear features are reviewed and a new method Points-in-Buffer Analysis (PIBA) is proposed. Keywords. Wetland boundary delineation, heads-up digitizing, radiometric enhancement, wetland boundary accuracy, point-in-buffer analysis (PIBA)

  5. Experimental and Automated Analysis Techniques for High-resolution Electrical Mapping of Small Intestine Slow Wave Activity

    PubMed Central

    Angeli, Timothy R; O'Grady, Gregory; Paskaranandavadivel, Niranchan; Erickson, Jonathan C; Du, Peng; Pullan, Andrew J; Bissett, Ian P

    2013-01-01

    Background/Aims Small intestine motility is governed by an electrical slow wave activity, and abnormal slow wave events have been associated with intestinal dysmotility. High-resolution (HR) techniques are necessary to analyze slow wave propagation, but progress has been limited by few available electrode options and laborious manual analysis. This study presents novel methods for in vivo HR mapping of small intestine slow wave activity. Methods Recordings were obtained from along the porcine small intestine using flexible printed circuit board arrays (256 electrodes; 4 mm spacing). Filtering options were compared, and analysis was automated through adaptations of the falling-edge variable-threshold (FEVT) algorithm and graphical visualization tools. Results A Savitzky-Golay filter was chosen with polynomial-order 9 and window size 1.7 seconds, which maintained 94% of slow wave amplitude, 57% of gradient and achieved a noise correction ratio of 0.083. Optimized FEVT parameters achieved 87% sensitivity and 90% positive-predictive value. Automated activation mapping and animation successfully revealed slow wave propagation patterns, and frequency, velocity, and amplitude were calculated and compared at 5 locations along the intestine (16.4 ± 0.3 cpm, 13.4 ± 1.7 mm/sec, and 43 ± 6 µV, respectively, in the proximal jejunum). Conclusions The methods developed and validated here will greatly assist small intestine HR mapping, and will enable experimental and translational work to evaluate small intestine motility in health and disease. PMID:23667749

  6. A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination.

    PubMed

    Li, Gang; Hillier, LaDeana W; Grahn, Robert A; Zimin, Aleksey V; David, Victor A; Menotti-Raymond, Marilyn; Middleton, Rondo; Hannah, Steven; Hendrickson, Sher; Makunin, Alex; O'Brien, Stephen J; Minx, Pat; Wilson, Richard K; Lyons, Leslie A; Warren, Wesley C; Murphy, William J

    2016-06-01

    High-resolution genetic and physical maps are invaluable tools for building accurate genome assemblies, and interpreting results of genome-wide association studies (GWAS). Previous genetic and physical maps anchored good quality draft assemblies of the domestic cat genome, enabling the discovery of numerous genes underlying hereditary disease and phenotypes of interest to the biomedical science and breeding communities. However, these maps lacked sufficient marker density to order thousands of shorter scaffolds in earlier assemblies, which instead relied heavily on comparative mapping with related species. A high-resolution map would aid in validating and ordering chromosome scaffolds from existing and new genome assemblies. Here, we describe a high-resolution genetic linkage map of the domestic cat genome based on genotyping 453 domestic cats from several multi-generational pedigrees on the Illumina 63K SNP array. The final maps include 58,055 SNP markers placed relative to 6637 markers with unique positions, distributed across all autosomes and the X chromosome. Our final sex-averaged maps span a total autosomal length of 4464 cM, the longest described linkage map for any mammal, confirming length estimates from a previous microsatellite-based map. The linkage map was used to order and orient the scaffolds from a substantially more contiguous domestic cat genome assembly (Felis catus v8.0), which incorporated ∼20 × coverage of Illumina fragment reads. The new genome assembly shows substantial improvements in contiguity, with a nearly fourfold increase in N50 scaffold size to 18 Mb. We use this map to report probable structural errors in previous maps and assemblies, and to describe features of the recombination landscape, including a massive (∼50 Mb) recombination desert (of virtually zero recombination) on the X chromosome that parallels a similar desert on the porcine X chromosome in both size and physical location.

  7. A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination

    PubMed Central

    Li, Gang; Hillier, LaDeana W.; Grahn, Robert A.; Zimin, Aleksey V.; David, Victor A.; Menotti-Raymond, Marilyn; Middleton, Rondo; Hannah, Steven; Hendrickson, Sher; Makunin, Alex; O’Brien, Stephen J.; Minx, Pat; Wilson, Richard K.; Lyons, Leslie A.; Warren, Wesley C.; Murphy, William J.

    2016-01-01

    High-resolution genetic and physical maps are invaluable tools for building accurate genome assemblies, and interpreting results of genome-wide association studies (GWAS). Previous genetic and physical maps anchored good quality draft assemblies of the domestic cat genome, enabling the discovery of numerous genes underlying hereditary disease and phenotypes of interest to the biomedical science and breeding communities. However, these maps lacked sufficient marker density to order thousands of shorter scaffolds in earlier assemblies, which instead relied heavily on comparative mapping with related species. A high-resolution map would aid in validating and ordering chromosome scaffolds from existing and new genome assemblies. Here, we describe a high-resolution genetic linkage map of the domestic cat genome based on genotyping 453 domestic cats from several multi-generational pedigrees on the Illumina 63K SNP array. The final maps include 58,055 SNP markers placed relative to 6637 markers with unique positions, distributed across all autosomes and the X chromosome. Our final sex-averaged maps span a total autosomal length of 4464 cM, the longest described linkage map for any mammal, confirming length estimates from a previous microsatellite-based map. The linkage map was used to order and orient the scaffolds from a substantially more contiguous domestic cat genome assembly (Felis catus v8.0), which incorporated ∼20 × coverage of Illumina fragment reads. The new genome assembly shows substantial improvements in contiguity, with a nearly fourfold increase in N50 scaffold size to 18 Mb. We use this map to report probable structural errors in previous maps and assemblies, and to describe features of the recombination landscape, including a massive (∼50 Mb) recombination desert (of virtually zero recombination) on the X chromosome that parallels a similar desert on the porcine X chromosome in both size and physical location. PMID:27172201

  8. Photon-counting lidars for contiguous high resolution topographic mapping of planets and moons

    NASA Astrophysics Data System (ADS)

    Degnan, John J.

    2007-08-01

    Planetary scientists have long expressed interest in obtaining globally contiguous, high resolution (few meter horizontal, decimeter vertical) 3D topographic maps of planets and moons. For example, the goal of NASA's LIST mission, scheduled for launch in the 2016-2020 time frame, is a globally contiguous, 5 meter resolution, topographic map of the Earth. Unfortunately, achieving such a capability through a simple scaling of the laser power and/or telescope aperture from prior art NASA laser altimeters (e.g. MOLA, GLAS, and MLA) is not practical. This is especially true of laser altimeters destined for orbit about distant planets or moons where instrument mass and prime power usage is severely constrained. Photon counting receivers permit each range measurement to be made with a single received photon, even in daylight, and the surface sampling rate of an orbiting altimeter can be increased by three to four orders of magnitude by emitting the available laser photons in a high frequency train of low energy pulses instead of a low frequency train of high energy pulses typical of past spaceborne lidars. The feasibility of the photon-counting approach in the presence of a strong solar background was first successfully demonstrated from a high altitude aircraft under NASA's Instrument Incubator Program in 2001. Sigma Space Corporation has subsequently developed a second generation of scanning 3D imaging and polarimetric lidars for use in small aircraft and Unmanned Aerial Vehicles (UAV's). Future space applications include: (1) decimeter vertical resolution topographic mapping of extraterrestrial terrain from orbiters, balloons, or other aerial vehicles for determining safe landing sites; (2) monitoring the terrain in real time and increasingly higher resolution during spacecraft descent; or (3) for truly contiguous few meter resolution imaging of planetary terrain on a global scale from orbit. Targets of particular interest to NASA are the Earth, Moon, Mars, the Jovian

  9. High-resolution mapping of combustion processes and implications for CO2 emissions

    NASA Astrophysics Data System (ADS)

    Wang, R.; Tao, S.; Ciais, P.; Shen, H. Z.; Huang, Y.; Chen, H.; Shen, G. F.; Wang, B.; Li, W.; Zhang, Y. Y.; Lu, Y.; Zhu, D.; Chen, Y. C.; Liu, X. P.; Wang, W. T.; Wang, X. L.; Liu, W. X.; Li, B. G.; Piao, S. L.

    2013-05-01

    High-resolution mapping of fuel combustion and CO2 emission provides valuable information for modeling pollutant transport, developing mitigation policy, and for inverse modeling of CO2 fluxes. Previous global emission maps included only few fuel types, and emissions were estimated on a grid by distributing national fuel data on an equal per capita basis, using population density maps. This process distorts the geographical distribution of emissions within countries. In this study, a sub-national disaggregation method (SDM) of fuel data is applied to establish a global 0.1° × 0.1° geo-referenced inventory of fuel combustion (PKU-FUEL) and corresponding CO2 emissions (PKU-CO2) based upon 64 fuel sub-types for the year 2007. Uncertainties of the emission maps are evaluated using a Monte Carlo method. It is estimated that CO2 emission from combustion sources including fossil fuel, biomass, and solid wastes in 2007 was 11.2 Pg C yr-1 (9.1 Pg C yr-1 and 13.3 Pg C yr-1 as 5th and 95th percentiles). Of this, emission from fossil fuel combustion is 7.83 Pg C yr-1, which is very close to the estimate of the International Energy Agency (7.87 Pg C yr-1). By replacing national data disaggregation with sub-national data in this study, the average 95th minus 5th percentile ranges of CO2 emission for all grid points can be reduced from 417 to 68.2 Mg km-2 yr-1. The spread is reduced because the uneven distribution of per capita fuel consumptions within countries is better taken into account by using sub-national fuel consumption data directly. Significant difference in per capita CO2 emissions between urban and rural areas was found in developing countries (2.08 vs. 0.598 Mg C/(cap. × yr)), but not in developed countries (3.55 vs. 3.41 Mg C/(cap. × yr)). This implies that rapid urbanization of developing countries is very likely to drive up their emissions in the future.

  10. Pan-Tropical Forest Mapping by Exploiting Textures of Multi-Temporal High Resolution SAR Data

    NASA Astrophysics Data System (ADS)

    Knuth, R.; Eckardt, R.; Richter, N.; Schmullius, C.

    2012-12-01

    radar images were processed using an operational processing chain that includes radiometric transformation, noise reduction, and georeferencing of the SAR data. In places with pronounced topography both satellites were used as single pass interferometer to derive a digital surface model in order to perform an orthorectification followed by a topographic normalization of the SAR backscatter values. As prescribed by the FAO, the final segment-based classification algorithm was fed by multi-temporal backscatter information, a set of textural features, and information on the degree of coherence between the multi-temporal acquisitions. Validation with available high resolution optical imagery suggests that the produced forest maps possess an overall accuracy of 75 percent or higher.

  11. High-resolution mapping and spatial variability of soil organic carbon storage of permafrost-affected soils

    NASA Astrophysics Data System (ADS)

    Siewert, Matthias; Hugelius, Gustaf

    2017-04-01

    Permafrost-affected soils store large amounts of soil organic carbon (SOC). Mapping of this SOC provides a first order spatial input variable for research that relates carbon stored in permafrost regions to carbon cycle dynamics. High-resolution satellite imagery is becoming increasingly available even in circum-polar regions. The presented research highlights findings of high-resolution mapping efforts of SOC from five study areas in the northern circum-polar permafrost region. These study areas are located in Siberia (Kytalyk, Spasskaya Pad /Neleger, Lena delta), Northern Sweden (Abisko) and Northwestern Canada (Herschel Island). Our high spatial resolution analyses show how geomorphology has a strong influence on the distribution of SOC. This is organized at different spatial scales. Periglacial landforms and processes dictate local scale SOC distribution due to patterned ground. Such landforms are non-sorted circles and ice-wedge polygons of different age and scale. Palsas and peat plateaus are formed and can cover larger areas in Sub-Arctic environments. Study areas that have not been affected by Pleistocene glaciation feature ice-rich Yedoma sediments that dominate the local relief through thermokarst formation and create landscape scale macro environments that dictate the distribution of SOC. A general trend indicates higher SOC storage in Arctic tundra soils compared to forested Boreal or Sub-Arctic taiga soils. Yet, due to the shallower active layer depth in the Arctic, much of the SOC may be permanently frozen and thus not be available to ecosystem processes. Significantly more SOC is stored in soils compared to vegetation, indicating that vegetation growth and incorporation of the carbon into the plant phytomass alone will not be able to offset SOC released from permafrost. This contribution also addresses advances in thematic mapping methods and digital soil mapping of SOC in permafrost terrain. In particular machine-learning methods, such as support

  12. Will it Blend? Visualization and Accuracy Evaluation of High-Resolution Fuzzy Vegetation Maps

    NASA Astrophysics Data System (ADS)

    Zlinszky, A.; Kania, A.

    2016-06-01

    Instead of assigning every map pixel to a single class, fuzzy classification includes information on the class assigned to each pixel but also the certainty of this class and the alternative possible classes based on fuzzy set theory. The advantages of fuzzy classification for vegetation mapping are well recognized, but the accuracy and uncertainty of fuzzy maps cannot be directly quantified with indices developed for hard-boundary categorizations. The rich information in such a map is impossible to convey with a single map product or accuracy figure. Here we introduce a suite of evaluation indices and visualization products for fuzzy maps generated with ensemble classifiers. We also propose a way of evaluating classwise prediction certainty with "dominance profiles" visualizing the number of pixels in bins according to the probability of the dominant class, also showing the probability of all the other classes. Together, these data products allow a quantitative understanding of the rich information in a fuzzy raster map both for individual classes and in terms of variability in space, and also establish the connection between spatially explicit class certainty and traditional accuracy metrics. These map products are directly comparable to widely used hard boundary evaluation procedures, support active learning-based iterative classification and can be applied for operational use.

  13. Structure and Evolution of Hawaii's Loihi Seamount from High-resolution Mapping

    NASA Astrophysics Data System (ADS)

    Clague, D. A.; Paduan, J. B.; Moyer, C. L.; Glazer, B. T.; Caress, D. W.; Yoerger, D.; Kaiser, C. L.

    2016-12-01

    Loihi Seamount has been mapped repeatedly using shipboard multibeam sonars with improving resolution over time. Simrad EM302 data with 25m resolution at the 950m summit and 90m at the 5000m base of the volcano were collected from Schmidt Ocean Institute's R/V Falkor in 2014. A contracted multibeam survey in 1997 employing a deep-towed vehicle has 7m resolution for the summit and upper north and south rift zones, but suffered from poor navigation. Woods Hole Oceanographic Institution's AUV Sentry surveyed most of the summit and low-T hydrothermal vents on the base of the south rift in 2013 and 2014. The 2m resolution of most data is more precise than the navigation. The 6 summit surveys were reprocessed using MB-System to remove abundant bad bottom picks and adjust the navigation to produce a spatially accurate map. The 3 summit pits, including Pele's Pit that formed in 1996, are complex collapse structures and nested inside a larger caldera that was modified by large landslides on the east and west summit flanks. The pits cut low shields that once formed a complex of overlapping summit shields, similar to Kilauea before the current caldera formed 1500 to 1790 CE. An 11m section of ash deposits crops out on the east rim of the summit along a caldera-bounding fault and is analogous to Kilauea where the caldera-bounding faults expose ash erupted as the present caldera formed. Most of the Loihi ash section is 3300 to 5880 yr BP, indicating that the larger caldera structure at Loihi is younger than 3300 yr BP. The landslides on the east and west edges of the summit are therefore younger 3300 yr BP. The uppermost south rift has several small pit craters between cones and pillow ridges, also analogous to Kilauea. Two cones near the deep low-T vents are steep pillow mounds with slopes of talus. High-resolution mapping reveals, for the first time, the many similarities between the structure and evolution of submarine Loihi Seamount and subaerial Kilauea Volcano.

  14. Mapping high-resolution soil moisture and properties using distributed temperature sensing data and an adaptive particle batch smoother

    USDA-ARS?s Scientific Manuscript database

    This study demonstrated a new method for mapping high-resolution (spatial: 1 m, and temporal: 1 h) soil moisture by assimilating distributed temperature sensing (DTS) observed soil temperatures at intermediate scales. In order to provide robust soil moisture and property estimates, we first proposed...

  15. Mapping Urban Tree Canopy Coverage and Structure using Data Fusion of High Resolution Satellite Imagery and Aerial Lidar

    NASA Astrophysics Data System (ADS)

    Elmes, A.; Rogan, J.; Williams, C. A.; Martin, D. G.; Ratick, S.; Nowak, D.

    2015-12-01

    Urban tree canopy (UTC) coverage is a critical component of sustainable urban areas. Trees provide a number of important ecosystem services, including air pollution mitigation, water runoff control, and aesthetic and cultural values. Critically, urban trees also act to mitigate the urban heat island (UHI) effect by shading impervious surfaces and via evaporative cooling. The cooling effect of urban trees can be seen locally, with individual trees reducing home HVAC costs, and at a citywide scale, reducing the extent and magnitude of an urban areas UHI. In order to accurately model the ecosystem services of a given urban forest, it is essential to map in detail the condition and composition of these trees at a fine scale, capturing individual tree crowns and their vertical structure. This paper presents methods for delineating UTC and measuring canopy structure at fine spatial resolution (<1m). These metrics are essential for modeling the HVAC benefits from UTC for individual homes, and for assessing the ecosystem services for entire urban areas. Such maps have previously been made using a variety of methods, typically relying on high resolution aerial or satellite imagery. This paper seeks to contribute to this growing body of methods, relying on a data fusion method to combine the information contained in high resolution WorldView-3 satellite imagery and aerial lidar data using an object-based image classification approach. The study area, Worcester, MA, has recently undergone a large-scale tree removal and reforestation program, following a pest eradication effort. Therefore, the urban canopy in this location provides a wide mix of tree age class and functional type, ideal for illustrating the effectiveness of the proposed methods. Early results show that the object-based classifier is indeed capable of identifying individual tree crowns, while continued research will focus on extracting crown structural characteristics using lidar-derived metrics. Ultimately

  16. High-resolution mapping of gastric slow-wave recovery profiles: biophysical model, methodology, and demonstration of applications.

    PubMed

    Paskaranandavadivel, N; Cheng, L K; Du, P; Rogers, J M; O'Grady, G

    2017-09-01

    Slow waves play a central role in coordinating gastric motor activity. High-resolution mapping of extracellular potentials from the stomach provides spatiotemporal detail on normal and dysrhythmic slow-wave patterns. All mapping studies to date have focused exclusively on tissue activation; however, the recovery phase contains vital information on repolarization heterogeneity, the excitable gap, and refractory tail interactions but has not been investigated. Here, we report a method to identify the recovery phase in slow-wave mapping data. We first developed a mathematical model of unipolar extracellular potentials that result from slow-wave propagation. These simulations showed that tissue repolarization in such a signal is defined by the steepest upstroke beyond the activation phase (activation was defined by accepted convention as the steepest downstroke). Next, we mapped slow-wave propagation in anesthetized pigs by recording unipolar extracellular potentials from a high-resolution array of electrodes on the serosal surface. Following the simulation result, a wavelet transform technique was applied to detect repolarization in each signal by finding the maximum positive slope beyond activation. Activation-recovery (ARi) and recovery-activation (RAi) intervals were then computed. We hypothesized that these measurements of recovery profile would differ for slow waves recorded during normal and spatially dysrhythmic propagation. We found that the ARi of normal activity was greater than dysrhythmic activity (5.1 ± 0.8 vs. 3.8 ± 0.7 s; P < 0.05), whereas RAi was lower (9.7 ± 1.3 vs. 12.2 ± 2.5 s; P < 0.05). During normal propagation, RAi and ARi were linearly related with negative unit slope indicating entrainment of the entire mapped region. This relationship was weakened during dysrhythmia (slope: -0.96 ± 0.2 vs -0.71 ± 0.3; P < 0.05).NEW & NOTEWORTHY The theoretical basis of the extracellular gastric slow-wave recovery phase was

  17. aMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data

    PubMed Central

    Niedworok, Christian J.; Brown, Alexander P. Y.; Jorge Cardoso, M.; Osten, Pavel; Ourselin, Sebastien; Modat, Marc; Margrie, Troy W.

    2016-01-01

    The validation of automated image registration and segmentation is crucial for accurate and reliable mapping of brain connectivity and function in three-dimensional (3D) data sets. While validation standards are necessarily high and routinely met in the clinical arena, they have to date been lacking for high-resolution microscopy data sets obtained from the rodent brain. Here we present a tool for optimized automated mouse atlas propagation (aMAP) based on clinical registration software (NiftyReg) for anatomical segmentation of high-resolution 3D fluorescence images of the adult mouse brain. We empirically evaluate aMAP as a method for registration and subsequent segmentation by validating it against the performance of expert human raters. This study therefore establishes a benchmark standard for mapping the molecular function and cellular connectivity of the rodent brain. PMID:27384127

  18. High-resolution AUV mapping and lava flow ages at Axial Seamount

    NASA Astrophysics Data System (ADS)

    Clague, D. A.; Paduan, J. B.; Dreyer, B. M.; Caress, D. W.; Martin, J.

    2011-12-01

    Mapping along mid-ocean ridges, as on land, requires identification of flow boundaries and sequence, and ages of some flows to understand eruption history. Multibeam sonars on autonomous underwater vehicles (AUV) now generate 1-m resolution maps that resolve lava pillars, internal flow structures and boundaries, and lava flow emplacement sequences using crosscutting relations and abundance of fissures. MBARI has now mapped the summit caldera floor and rims and the upper south rift zone on Axial Seamount on the Juan de Fuca Ridge. With the advent of the high-resolution bathymetry and the ability to observe flow contacts to determine superposition using ROVs and submersibles, the missing component has been determining absolute ages of the flows. We used the MBARI ROV Doc Ricketts to collect short push cores (<30 cm) of the thin sediment nestled between pillow lava lobes and sieve and then hand-pick planktic foraminifera from the base of the cores to date by AMS 14C. Ages of planktic foraminifera are marine-calibrated in years before present, and provide minimum ages for the underlying flows, as there is probably some basal sediment that is not recovered. 14C ages have been determined for 10 cores near the summit of Axial Seamount and for 6 from the lowermost south rift. Ages of nearby samples commonly yield statistically identical ages, and 2 cores near the center of the caldera had multiple layers dated. These ages systematically increase with depth, indicating that redistribution of sediment by bottom currents does not significantly affect the stratigraphy. We will expand these collections in summer 2011. The coring is accompanied by collection of flow samples for chemistry and video observations to confirm contact locations and flow superposition inferred from the mapping data. Six ages from the lowermost part of the south rift of Axial Seamount include samples on a cone with deep summit crater that is ~16,580 aBP and on 5 flows between 950 and 1510 aBP. Two

  19. High Resolution Map of Water Supply and Demand for North East United States

    NASA Astrophysics Data System (ADS)

    Ehsani, N.; Vorosmarty, C. J.; Fekete, B. M.

    2012-12-01

    Accurate estimates of water supply and demand are crucial elements in water resources management and modeling. As part of our NSF-funded EaSM effort to build a Northeast Regional Earth System Model (NE-RESM) as a framework to improve our understanding and capacity to forecast the implications of planning decisions on the region's environment, ecosystem services, energy and economic systems through the 21st century, we are producing a high resolution map (3' x 3' lat/long) of estimated water supply and use for the north east region of United States. Focusing on water demand, results from this study enables us to quantify how demand sources affect the hydrology and thermal-chemical water pollution across the region. In an attempt to generate this 3-minute resolution map in which each grid cell has a specific estimated monthly domestic, agriculture, thermoelectric and industrial water use. Estimated Use of Water in the United States in 2005 (Kenny et al., 2009) is being coupled to high resolution land cover and land use, irrigation, power plant and population data sets. In addition to water demands, we tried to improve estimates of water supply from the WBM model by improving the way it controls discharge from reservoirs. Reservoirs are key characteristics of the modern hydrologic system, with a particular impact on altering the natural stream flow, thermal characteristics, and biogeochemical fluxes of rivers. Depending on dam characteristics, watershed characteristics and the purpose of building a dam, each reservoir has a specific optimum operating rule. It means that literally 84,000 dams in the National Inventory of Dams potentially follow 84,000 different sets of rules for storing and releasing water which must somehow be accounted for in our modeling exercise. In reality, there is no comprehensive observational dataset depicting these operating rules. Thus, we will simulate these rules. Our perspective is not to find the optimum operating rule per se but to find

  20. High-resolution mapping of biomass burning emissions in tropical regions across three continents

    NASA Astrophysics Data System (ADS)

    Shi, Yusheng; Matsunaga, Tsuneo; Saito, Makoto

    2015-04-01

    Biomass burning emissions from open vegetation fires (forest fires, savanna fires, agricultural waste burning), human waste and biofuel combustion contain large amounts of trace gases (e.g., CO2, CH4, and N2O) and aerosols (BC and OC), which significantly impact ecosystem productivity, global atmospheric chemistry, and climate . With the help of recently released satellite products, biomass density based on satellite and ground-based observation data, and spatial variable combustion factors, this study developed a new high-resolution emissions inventory for biomass burning in tropical regions across three continents in 2010. Emissions of trace gases and aerosols from open vegetation burning are estimated from burned areas, fuel loads, combustion factors, and emission factors. Burned areas were derived from MODIS MCD64A1 burned area product, fuel loads were mapped from biomass density data sets for herbaceous and tree-covered land based on satellite and ground-based observation data. To account for spatial heterogeneity in combustion factors, global fractional tree cover (MOD44B) and vegetation cover maps (MCD12Q1) were introduced to estimate the combustion factors in different regions by using their relationship with tree cover under less than 40%, between 40-60% and above 60% conditions. For emission factors, the average values for each fuel type from field measurements are used. In addition to biomass burning from open vegetation fires, the emissions from human waste (residential and dump) burning and biofuel burning in 2010 were also estimated for 76 countries in tropical regions across the three continents and then allocated into each pixel with 1 km grid based on the population density (Gridded Population of the World v3). Our total estimates for the tropical regions across the three continents in 2010 were 17744.5 Tg CO2, 730.3 Tg CO, 32.0 Tg CH4, 31.6 Tg NOx, 119.2 Tg NMOC, 6.3 Tg SO2, 9.8 NH3 Tg, 81.8 Tg PM2.5, 48.0 Tg OC, and 5.7 Tg BC, respectively. Open

  1. Mapping intra-urban malaria risk using high resolution satellite imagery: a case study of Dar es Salaam.

    PubMed

    Kabaria, Caroline W; Molteni, Fabrizio; Mandike, Renata; Chacky, Frank; Noor, Abdisalan M; Snow, Robert W; Linard, Catherine

    2016-07-30

    With more than half of Africa's population expected to live in urban settlements by 2030, the burden of malaria among urban populations in Africa continues to rise with an increasing number of people at risk of infection. However, malaria intervention across Africa remains focused on rural, highly endemic communities with far fewer strategic policy directions for the control of malaria in rapidly growing African urban settlements. The complex and heterogeneous nature of urban malaria requires a better understanding of the spatial and temporal patterns of urban malaria risk in order to design effective urban malaria control programs. In this study, we use remotely sensed variables and other environmental covariates to examine the predictability of intra-urban variations of malaria infection risk across the rapidly growing city of Dar es Salaam, Tanzania between 2006 and 2014. High resolution SPOT satellite imagery was used to identify urban environmental factors associated malaria prevalence in Dar es Salaam. Supervised classification with a random forest classifier was used to develop high resolution land cover classes that were combined with malaria parasite prevalence data to identify environmental factors that influence localized heterogeneity of malaria transmission and develop a high resolution predictive malaria risk map of Dar es Salaam. Results indicate that the risk of malaria infection varied across the city. The risk of infection increased away from the city centre with lower parasite prevalence predicted in administrative units in the city centre compared to administrative units in the peri-urban suburbs. The variation in malaria risk within Dar es Salaam was shown to be influenced by varying environmental factors. Higher malaria risks were associated with proximity to dense vegetation, inland water and wet/swampy areas while lower risk of infection was predicted in densely built-up areas. The predictive maps produced can serve as valuable resources for

  2. Genome-Wide Mapping of Nucleosome Positions in Yeast Using High-Resolution MNase ChIP-Seq

    PubMed Central

    Wal, Megha

    2016-01-01

    Eukaryotic DNA is packaged into chromatin where nucleosomes form the basic building unit. Knowing the precise positions of nucleosomes is important because they determine the accessibility of underlying regulatory DNA sequences. Here we describe a detailed method to map on a genomic scale the locations of nucleosomes with very high resolution. Micrococcal nuclease (MNase) digestion followed by chromatin immunoprecipitation and facilitated library construction for deep sequencing provides a simple and accurate map of nucleosome positions. PMID:22929772

  3. High-resolution mapping of global surface water and its long-term changes

    NASA Astrophysics Data System (ADS)

    Pekel, J. F.; Cottam, A.; Gorelick, N.; Belward, A.

    2016-12-01

    The location and persistence of surface water is both affected by climate and human activity and affects climate, biological diversity and human wellbeing. Global datasets documenting surface water location and seasonality have been produced but measuring long-term changes at high resolution remains a challenge.To address the dynamic nature of water, the European Commission's Joint Research Centre (JRC), working with the Google Earth Engine (GEE) team has processed each single pixel acquired by Landsat 5, 7, and 8 between 16th March 1984 to 10th October 2015 (> 3.000.000 Landsat scenes, representing > 1823 Terabytes of data).The produced dataset record months and years when water was present across 32 year, were occurrence changed and what form changes took in terms of seasonality and persistence, and document intra-annual persistence, inter-annual variability, and trends.This validated dataset shows that impacts of climate change and climate oscillations on surface water occurrence can be measured and that evidence can be gathered showing how surface water is altered by human activities.Freely available, we anticipate that this dataset will provide valuable information to those working in areas linked to security of water supply for agriculture, industry and human consumption, for assessing water-related disaster reduction and recovery and for the study of waterborne pollution and disease spread. The maps will also improve surface boundary condition setting in climate and weather models, improve carbon emissions estimates, inform regional climate change impact studies, delimit wetlands for biodiversity and determine desertification trends. Issues such as dam building (and less widespread dam removal), disappearing rivers, the geopolitics of water distribution and coastal erosion are also addressed.

  4. A new Concept for High Resolution Benthic Mapping and Data Aquisition: MANSIO-VIATOR

    NASA Astrophysics Data System (ADS)

    Flögel, S.

    2015-12-01

    Environmental conditions within sensitive seafloor ecosystems such as cold-seep provinces or cold-water coral reef communities vary temporally and spatially over a wide range of scales. Some of these are regularly monitored via short periods of intense shipborne activity or low resolution, fixed location studies by benthic lander systems. Long term measurements of larger areas and volumes are ususally coupled to costly infrastructure investments such as cabled observatories. In space exploration, a combination of fixed and mobile systems working together are commonly used, e.g. lander systems coupled to rovers, to tackle observational needs that are very similar to deep-sea data aquisition. The analogies between space and deep-sea research motivated the German Helmholtz Association to setup the joint research program ROBEX (Robotic Exploration under extreme conditions). The program objectives are to identify, develop and verify technological synergies between the robotic exploration of e.g. the moon and the deep-sea. Within ROBEX, the mobility of robots is a vital element for research missions due to valuable scientifice return potential from different sites as opposed to static landers. Within this context, we developed a new mobile crawler system (VIATOR, latin for traveller) and a fixed lander component for energy and data transfer (MANSIO, latin for housing/shelter). This innovative MANSIO-VIATOR system has been developed during the past 2.5 years. The caterpillar driven component is developed to conduct high resolution opitcal mapping and repeated monitoring of physical and biogeochemical parameters along transects. The system operates fully autonomously including navigational components such as camera and laser scanners, as well as marker based near-field navigation used in space technology. This new concept of data aquisition by a submarine crawler in combination with a fixed lander further opens up marine exploration possibilities.

  5. High resolution mapping of oxygen reduction reaction kinetics at polycrystalline platinum electrodes.

    PubMed

    Chen, Chang-Hui; Meadows, Katherine E; Cuharuc, Anatolii; Lai, Stanley C S; Unwin, Patrick R

    2014-09-14

    The scanning droplet-based technique, scanning electrochemical cell microscopy (SECCM), combined with electron backscatter diffraction (EBSD), is demonstrated as a powerful approach for visualizing surface structure effects on the rate of the oxygen reduction reaction (ORR) at polycrystalline platinum electrodes. Elucidating the effect of electrode structure on the ORR is of major interest in connection to electrocatalysis for energy-related applications. The attributes of the approach herein stem from: (i) the ease with which the polycrystalline substrate electrode can be prepared; (ii) the wide range of surface character open to study; (iii) the possibility of mapping reactivity within a particular facet (or grain), in a pseudo-single-crystal approach, and acquiring a high volume of data as a consequence; (iv) the ready ability to measure the activity at grain boundaries; and (v) an experimental arrangement (SECCM) that mimics the three-phase boundary in low temperature fuel cells. The kinetics of the ORR was analyzed and a finite element method model was developed to explore the effect of the three-phase boundary, in particular to examine pH variations in the droplet and the differential transport rates of the reactants and products. We have found a significant variation of activity across the platinum substrate, inherently linked to the crystallographic orientation, but do not detect any enhanced activity at grain boundaries. Grains with (111) and (100) contributions exhibit considerably higher activity than those with (110) and (100) contributions. These results, which can be explained by reference to previous single-crystal measurements, enhance our understanding of ORR structure-activity relationships on complex high-index platinum surfaces, and further demonstrate the power of high resolution flux imaging techniques to visualize and understand complex electrocatalyst materials.

  6. High resolution gradient fingerprint mapping and its impact on urban planning.

    NASA Astrophysics Data System (ADS)

    Larour, Eric; Adhikari, Surendra; Ivins, Erik

    2017-04-01

    Local sea level rise is a measure of several competing processes, such as the contribution of melting ice from polar ice sheets, short-term processes related to ocean and atmospheric circulation, vertical land motion, viscoelastic adjustment of the mantle and crust and intense storm flooding. Of all these components, polar ice sheets will contribute most in the near to long-term future. It is therefore paramount to understand how sensitive local sea level is to spatio-temporally variable patterns of ice thickness in glaciated areas around the world. Here, we propose a new tool to assess this sensitivity based on gradient fingerprint mapping (GFM). This method quantifies exactly the derivative dS/dH, where S is local sea level and H ice thickness around the world. This derivative can be used to compute local projections of sea level using the following approach: S = dS/dH * DH + deltaS, where dS/dH is the gradient fingerprint (as it relates to ice) and DH any projected change in ice thickness (be it from observations extrapolated in time, or semi-empirical approaches, or model-based projections). deltaS encompasses other time variable components (assumed of a lower order) described above. Using high-resolution GFM, urban planners can assess which glaciated areas around the world will be of relevance to sea level change at their specific location, and how to instantly transfer projections of polar ice sheet evolution into localized sea-level change projections, along with associated uncertainties. This work was performed at the California Institute of Technology's Jet Propulsion Laboratory under a contract with the National Aeronautics and Space Administration's Cryosphere Science Program.

  7. High-resolution Surface Correlation Maps for Improved Resolution and Retrieval of Aerosols Over Urban Scenes

    NASA Astrophysics Data System (ADS)

    Oo, M. M.; Hernandez, E.; Jerg, M.; Gross, B. M.; Moshary, F.; Ahmed, S. A.

    2008-12-01

    Determination of Aerosol Optical Depth (AOD) by satellite remote sensing measurements over land is complicated by the fact that the Top of Atmosphere (TOA) reflectance is a combination of the desired atmospheric path reflectance as well as the ground reflectance. In this paper, we focus on the use of simultaneous MODIS and AERONET sky radiometer data to refine the surface albedo models regionally and improve on the current AOD operational retrieval. In particular, over New York City, we show that the correlation coefficient assumption used in the MODIS Collection (5) model between the VIS and MIR channels used for surface reflection parameterization are still severely underestimated in comparison with high spatial imagery data from Hyperion thereby leading to an underestimate in the VIS ground albedos and explaining the subsequent overestimate of the VIS optical depth. Furthermore, we find that the VIS/MIR ratios depend only weakly on the scattering geometry allowing us to generate a regional VIS/MIR surface reflectance correlation coefficient map at spatial resolutions down to 1.5km. When applying the new VIS/MIR surface reflectance ratio model, we show the MODIS and AERONET derived optical thickness agreement is significantly improved for the operational 10km resolution product. Moreover, we also show the high resolution surface model allows us to improve the resolution of the retrieved AOD to 3km. Although direct comparisons for a given day can only be made at the AERONET site, we find the AOD spatial variability from the improved MODIS retrievals is in far better agreement with temporal statistics seen in the AERONET time series retrievals. In addition to that, we also process and validate with another urban area, Mexico City, and the result is also significantly improved by using refined regional VIS/MIR surface reflectance ratio model.

  8. Glaciotectonic structures mapped by GPR, geoelectrical, high-resolution seismic and airborne transient electromagnetic methods

    NASA Astrophysics Data System (ADS)

    Høyer, Anne-Sophie; Møller, Ingelise; Jørgensen, Flemming

    2013-04-01

    Glaciotectonic structures have traditionally been recognized through observations in the landscape or exposures like cliffs. However, mapping of these structures can highly benefit from geophysical data, which can give information on buried glaciotectonic complexes. In the current study, we focus on the appearance of glaciotectonic structures in data from four commonly used geophysical methods: Ground penetrating radar (GPR), geoelectrical, high-resolution seismic and airborne transient electromagnetic (SkyTEM). The data are collected within a study area that covers 100 km2 and is located in the western part of Denmark. The study area is characterized by a highly heterogeneous geological setting, which has been influenced by multiple glacial deformation phases resulting in a buried glaciotectonic complex. The glaciotectonic structures appear as folds and faults and are recognizable at all scales. As a consequence of the different resolution capabilities of the methods, different degrees of detail are observed: Large-scale structures are recognized based on the seismic and airborne transient electromagnetic data, whereas small-scale structures are interpreted based on the GPR and geoelectrical data. At the same time, the nature of the methods results in different types of information from the data: The GPR and the seismic data generally provide detailed structural information, whereas the electric and electromagnetic data provide a more 'blurred' resistivity image of the subsurface. In order to recognize geological structures on the electric and electromagnetic data, the structures therefore need to influence sediments with contrasting resistivities to the surroundings. The structures are recognizable on all the different data sets, but the understanding and thus, the interpretation, of the geological environment strongly benefits from the combined observations from the different types of data.

  9. Comparative visualization of protein conformations using large high resolution displays with gestures and body tracking

    NASA Astrophysics Data System (ADS)

    Marangoni, Matt; Wischgoll, Thomas

    2015-01-01

    Automatically identifying protein conformations can yield multiple candidate structures. Potential candidates are examined further to cull false positives. Individual conformations and the collection are compared when seeking flaws. Desktop displays are ineffective due to limited size and resolution. Thus a user must sacrifice large scale content by viewing the micro level with high detail or view the macro level while forfeiting small details. We address this ultimatum by utilizing multiple, high resolution displays. Using 27, 50", high resolution displays with active, stereoscopic 3D, and modified virtual environment software, each display presents a protein users can manipulate. Such an environment enables users to gain extensive insight both at the micro and macro levels when performing structural comparisons among the candidate structures. Integrating stereoscopic 3D improves the user's ability to judge conformations spatial relationships. In order to facilitate intuitive interaction, gesture recognition as well as body tracking are used. The user is able to look at the protein of interest, select a modality via gesture, and the user's motions provide intuitive navigation functions such as panning, rotating, and zooming. Using this approach, users are able to perform protein structure comparison through intuitive controls without sacrificing important visual details at any scale.

  10. High resolution computed tomographic assessment of asbestosis and cryptogenic fibrosing alveolitis: a comparative study.

    PubMed Central

    al-Jarad, N; Strickland, B; Pearson, M C; Rubens, M B; Rudd, R M

    1992-01-01

    BACKGROUND: The aim of this study was to compare the distribution and configuration of lung opacities in patients with cryptogenic fibrosing alveolitis and asbestosis by high resolution computed tomography. METHODS: Eighteen patients with cryptogenic fibrosing alveolitis and 24 with asbestosis were studied. Two independent observers assessed the type and distributions of opacities in the upper, middle, and lower zones of the computed tomogram. RESULTS: Upper zone fibrosis occurred in 10 of the 18 patients with cryptogenic fibrosing alveolitis and in six of the 24 patients with asbestosis. A specific pattern in which fibrosis was distributed posteriorly in the lower zones, laterally in the middle zones, and anteriorly in the upper zones was seen in 11 patients with cryptogenic fibrosing alveolitis and in four with asbestosis. Band like intrapulmonary opacities, often merging with the pleura, were seen in 19 patients with asbestosis but in only two with cryptogenic fibrosing alveolitis. Areas with a reticular pattern and a confluent or ground glass pattern were the commonest features of cryptogenic fibrosing alveolitis (15 and 14 patients respectively) but were uncommon in asbestosis (four and three patients). Pleural thickening or plaques were seen in 21 patients with asbestosis and in none with cryptogenic fibrosing alveolitis. CONCLUSION: Apart from showing pleural disease high resolution computed tomography showed that confluent (ground glass) opacities are common in cryptogenic fibrosing alveolitis and rare in asbestosis whereas thick, band like opacities are common in asbestosis and rare in cryptogenic fibrosing alveolitis. Images PMID:1412123

  11. Fine-scale mapping of vector habitats using very high resolution satellite imagery: a liver fluke case-study.

    PubMed

    De Roeck, Els; Van Coillie, Frieke; De Wulf, Robert; Soenen, Karen; Charlier, Johannes; Vercruysse, Jozef; Hantson, Wouter; Ducheyne, Els; Hendrickx, Guy

    2014-12-01

    The visualization of vector occurrence in space and time is an important aspect of studying vector-borne diseases. Detailed maps of possible vector habitats provide valuable information for the prediction of infection risk zones but are currently lacking for most parts of the world. Nonetheless, monitoring vector habitats from the finest scales up to farm level is of key importance to refine currently existing broad-scale infection risk models. Using Fasciola hepatica, a parasite liver fluke, as a case in point, this study illustrates the potential of very high resolution (VHR) optical satellite imagery to efficiently and semi-automatically detect detailed vector habitats. A WorldView2 satellite image capable of <5m resolution was acquired in the spring of 2013 for the area around Bruges, Belgium, a region where dairy farms suffer from liver fluke infections transmitted by freshwater snails. The vector thrives in small water bodies (SWBs), such as ponds, ditches and other humid areas consisting of open water, aquatic vegetation and/or inundated grass. These water bodies can be as small as a few m2 and are most often not present on existing land cover maps because of their small size. We present a classification procedure based on object-based image analysis (OBIA) that proved valuable to detect SWBs at a fine scale in an operational and semi-automated way. The classification results were compared to field and other reference data such as existing broad-scale maps and expert knowledge. Overall, the SWB detection accuracy reached up to 87%. The resulting fine-scale SWB map can be used as input for spatial distribution modelling of the liver fluke snail vector to enable development of improved infection risk mapping and management advice adapted to specific, local farm situations.

  12. GlobalSoilMap France: High-resolution spatial modelling the soils of France up to two meter depth.

    PubMed

    Mulder, V L; Lacoste, M; Richer-de-Forges, A C; Arrouays, D

    2016-12-15

    This work presents the first GlobalSoilMap (GSM) products for France. We developed an automatic procedure for mapping the primary soil properties (clay, silt, sand, coarse elements, pH, soil organic carbon (SOC), cation exchange capacity (CEC) and soil depth). The procedure employed a data-mining technique and a straightforward method for estimating the 90% confidence intervals (CIs). The most accurate models were obtained for pH, sand and silt. Next, CEC, clay and SOC were found reasonably accurate predicted. Coarse elements and soil depth were the least accurate of all models. Overall, all models were considered robust; important indicators for this were 1) the small difference in model diagnostics between the calibration and cross-validation set, 2) the unbiased mean predictions, 3) the smaller spatial structure of the prediction residuals in comparison to the observations and 4) the similar performance compared to other developed GlobalSoilMap products. Nevertheless, the confidence intervals (CIs) were rather wide for all soil properties. The median predictions became less reliable with increasing depth, as indicated by the increase of CIs with depth. In addition, model accuracy and the corresponding CIs varied depending on the soil variable of interest, soil depth and geographic location. These findings indicated that the CIs are as informative as the model diagnostics. In conclusion, the presented method resulted in reasonably accurate predictions for the majority of the soil properties. End users can employ the products for different purposes, as was demonstrated with some practical examples. The mapping routine is flexible for cloud-computing and provides ample opportunity to be further developed when desired by its users. This allows regional and international GSM partners with fewer resources to develop their own products or, otherwise, to improve the current routine and work together towards a robust high-resolution digital soil map of the world

  13. Modeling Foliar Uptake in Colocasia Esculenta Using High Resolution Maps of Leaf Water Isotopes

    NASA Astrophysics Data System (ADS)

    Sinkler, C. J.; Gerlein-Safdi, C.; Caylor, K. K.

    2014-12-01

    The uptake of carbon dioxide by vegetation is a major sink of CO2 and a factor that will determine future climate. Some studies predict a decrease in CO2 uptake from vegetation because of a general drying of the Amazon Basin. Because of the tight linkage between water availability and plant carbon uptake, a comprehensive model of plant water use at the individual scale is necessary to build a complete carbon budget at the global scale. Foliar uptake of non-meteoric water is a common process used by plants to alleviate water stress. However the occurrence of this process in tropical ecosystems, as well as its interaction with other physiological parameters, is not well understood. We present a model of leaf water balance that includes foliar uptake. The isotopic composition of the different sources as well as the leaf water are also included. The model is tested against a series of experiments on Colocasia esculenta, under two different water availability conditions: drought and artificial dew. The artificial dew is spiked with stable isotopes of water (δ18O = 8.56 permil, δ2H = 709.7 permil) that allow us to trace the partition of dew uptake within a leaf. We create high-resolution maps of the distribution of isotopes in one half of each leaf using a Picarro IM-CRDS. The maps show a clear enrichment due to foliar uptake for the artificial dew treatment. The water in the second half of the leaf is extracted by cryogenic extraction and analyzed using both IRIS and IRMS for quality control of the IM-CRDS data. Soil water is collected for isotope analysis and water content measurement. Finally, stomatal conductance data collected every two days shows no significant decrease due to either treatment over the course of the experiment. We conclude that foliar uptake of dew water is an important water acquisition mechanism for C. esculenta, even under high soil water content conditions, and we propose guidelines for further improvement of models of leaf-scale water

  14. High-resolution spatiotemporal strain mapping reveals non-uniform deformation in micropatterned elastomers

    NASA Astrophysics Data System (ADS)

    Aksoy, B.; Rehman, A.; Bayraktar, H.; Alaca, B. E.

    2017-04-01

    Micropatterns are generated on a vast selection of polymeric substrates for various applications ranging from stretchable electronics to cellular mechanobiological systems. When these patterned substrates are exposed to external loading, strain field is primarily affected by the presence of microfabricated structures and similarly by fabrication-related defects. The capturing of such nonhomogeneous strain fields is of utmost importance in cases where study of the mechanical behavior with a high spatial resolution is necessary. Image-based non-contact strain measurement techniques are favorable and have recently been extended to scanning tunneling microscope and scanning electron microscope images for the characterization of mechanical properties of metallic materials, e.g. steel and aluminum, at the microscale. A similar real-time analysis of strain heterogeneity in elastomers is yet to be achieved during the entire loading sequence. The available measurement methods for polymeric materials mostly depend on cross-head displacement or precalibrated strain values. Thus, they suffer either from the lack of any real-time analysis, spatiotemporal distribution or high resolution in addition to a combination of these factors. In this work, these challenges are addressed by integrating a tensile stretcher with an inverted optical microscope and developing a subpixel particle tracking algorithm. As a proof of concept, the patterns with a critical dimension of 200 µm are generated on polydimethylsiloxane substrates and strain distribution in the vicinity of the patterns is captured with a high spatiotemporal resolution. In the field of strain measurement, there is always a tradeoff between minimum measurable strain value and spatial resolution. Current noncontact techniques on elastomers can deliver a strain resolution of 0.001% over a minimum length of 5 cm. More importantly, inhomogeneities within this quite large region cannot be captured. The proposed technique can

  15. High-resolution linkage map in the proximity of the host resistance locus Cmv1

    SciTech Connect

    Depatie, C.; Muise, E.; Gros, P.

    1997-01-15

    The mouse chromosome 6 locus Cmv1 controls replication of mouse Cytomegalovirus (MCMV) in the spleen of the infected host. In our effort to clone Cmv1, we have constructed a high-resolution genetic linkage map in the proximity of the gene. For this, a total of 45 DNA markers corresponding to either cloned genes or microsatellites were mapped within a 7.9-cM interval overlapping the Cmv1 region. We have followed the cosegregation of these markers with respect to Cmv1 in a total of 2248 backcross mice from a preexisting interspecific backcross panel of 281 (Mus spretus X C57BL/6J)F1 X C57BL/6J and 2 novel panels of 989 (A/J X C57BL6)F1 X A/J and 978 (BALB/c X C57BL/6J)F1 X BALB/c segregating Cmv1. Combined pedigree analysis allowed us to determine the following gene order and intergene distances (in cM) on the distal region of mouse chromosome 6: D6Mit216-(1.9)-D6Mit336-(2.2)-D6Mit218-(1.0)-D6Mit52-(0.5)-D6Mit194-(0.2)-Nkrp1/D6Mit61/135/257/289/338-(0.4)-Cmv1/Ly49A/D6Mit370-(0.3)-Prp/Kap/D6Mit13/111/219-(0.3)-Tel/D6Mit374/290/220/196/195/110-(1.1)-D6Mit25. Therefore, the minimal genetic interval for Cmv1 of 0.7 cM is defined by 13 tightly linked markers including 2 markers, Ly49A and D6Mit370, that did not show recombination with Cmv1 in 1967 meioses analyzed; the proximal limit of the Cmv1 domain was defined by 8 crossovers between Nkrp1/D6Mit61/135/257/289/338 and Cmv1/Ly49A/D6Mit370, and the distal limit was defined by 5 crossovers between Cmv1/Ly49A/D6Mit370 and Prp/Kap/D6Mit13/111/219. This work demonstrates tight linkage between Cmv1 and genes from the natural killer complex (NKC), such as Nkrp1 and Ly49A suggesting that Cmv1 may represent an NK cell recognition structure encoded in the NKC region. 54 refs., 4 figs., 2 tabs.

  16. Mapping temporal changes in connectivity using high-resolution aerial data and object based image analysis

    NASA Astrophysics Data System (ADS)

    Masselink, Rens; Anders, Niels; Keesstra, Saskia; Seeger, Manuel

    2014-05-01

    Within the field of geomorphology mapping has always been an important tool to interpret spatial and temporal distributions of phenomena and processes at the surface. In the field of connectivity however, although throughout the past decade many articles have been published, there are only very few that go into the mapping of connectivity. This study aimed at developing a new, automated method for mapping connectivity within agricultural catchments. The method, which is a combination of Object-Based Image Analysis (OBIA) and traditional geomorphological field mapping, was applied to two agricultural catchments in Navarre, Spain, both with an area of approximately 2 sq.km. An unmanned aerial vehicle (UAV) was used to take aerial photographs with a resolution of 6 cm, of which a DEM with a 12 cm resolution was created using structure-from-motion photogrammetry. Connectivity was mapped within the study areas using OBIA using a top down method, meaning that connectivity was mapped at different scale levels, starting at the largest scale. Firstly sub-catchments were automatically delineated, after which several characteristics and features that affect connectivity within the sub-catchments were classified, e.g. landuse, landslides, rills, gullies, riparian vegetation, changes in slope, ploughing direction etc. In two consecutive years (2013-2014) photographs were taken and connectivity of both catchments of both years will be compared. Future work will include a quantification of the mapped connectivity (highly connected years vs. low connected years), causes and consequences of these differences in connectivity, comparison to existing connectivity indices and comparison of mapped connectivity in sub-catchments and measured discharge.

  17. A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs

    PubMed Central

    2012-01-01

    Background The Nile tilapia (Oreochromis niloticus) is the second most farmed fish species worldwide. It is also an important model for studies of fish physiology, particularly because of its broad tolerance to an array of environments. It is a good model to study evolutionary mechanisms in vertebrates, because of its close relationship to haplochromine cichlids, which have undergone rapid speciation in East Africa. The existing genomic resources for Nile tilapia include a genetic map, BAC end sequences and ESTs, but comparative genome analysis and maps of quantitative trait loci (QTL) are still limited. Results We have constructed a high-resolution radiation hybrid (RH) panel for the Nile tilapia and genotyped 1358 markers consisting of 850 genes, 82 markers corresponding to BAC end sequences, 154 microsatellites and 272 single nucleotide polymorphisms (SNPs). From these, 1296 markers could be associated in 81 RH groups, while 62 were not linked. The total size of the RH map is 34,084 cR3500 and 937,310 kb. It covers 88% of the entire genome with an estimated inter-marker distance of 742 Kb. Mapping of microsatellites enabled integration to the genetic map. We have merged LG8 and LG24 into a single linkage group, and confirmed that LG16-LG21 are also merged. The orientation and association of RH groups to each chromosome and LG was confirmed by chromosomal in situ hybridizations (FISH) of 55 BACs. Fifty RH groups were localized on the 22 chromosomes while 31 remained small orphan groups. Synteny relationships were determined between Nile tilapia, stickleback, medaka and pufferfish. Conclusion The RH map and associated FISH map provide a valuable gene-ordered resource for gene mapping and QTL studies. All genetic linkage groups with their corresponding RH groups now have a corresponding chromosome which can be identified in the karyotype. Placement of conserved segments indicated that multiple inter-chromosomal rearrangements have occurred between Nile tilapia

  18. High resolution synoptic salinity mapping to identify groundwater--surface water discharges in lowland rivers.

    PubMed

    Pai, Henry; Villamizar, Sandra R; Harmon, Thomas C

    2015-04-21

    Quantifying distributed lateral groundwater contributions to surface water (GW-SW discharges) is a key aspect of tracking nonpoint-source pollution (NPSP) within a watershed. In this study, we characterized distributed GW-SW discharges and associated salt loading using elevated GW specific conductance (SC) as a tracer along a 38 km reach of the Lower Merced River in Central California. High resolution longitudinal surveys for multiple flows (1.3-150 m(3) s(-1)) revealed river SC gradients that mainly decreased with increasing flow, suggesting a dilution effect and/or reduced GW-SW discharges due to hydraulic gradient reductions. However, exceptions occurred (gradients increasing with increasing flow), pointing to complex spatiotemporal influences on GW-SW dynamics. The surveys revealed detailed variability in salinity gradients, from which we estimated distributed GW-SW discharge and salt loading using a simple mixing model. Modeled cumulative GW discharges for two surveys unaffected by ungauged SW discharges were comparable in magnitude to differential gauging-based discharge estimates and prior GW-SW studies along the same river reach. Ungauged lateral inlets and sparse GW data limited the study, and argue for enhancing monitoring efforts. Our approach provides a rapid and economical method for characterizing NPSP for gaining rivers in the context of integrated watershed modeling and management.

  19. High resolution mapping of riffle-pool dynamics based on ADCP and close-range remote sensing data

    NASA Astrophysics Data System (ADS)

    Salmela, Jouni; Kasvi, Elina; Alho, Petteri

    2017-04-01

    Present development of mobile laser scanning (MLS) and close-range photogrammetry with unmanned aerial vehicle (UAV) enable us to create seamless digital elevation models (DEMs) of the riverine environment. Remote-controlled flow measurement platforms have also improved spatio-temporal resolution of the flow field data. In this study, acoustic Doppler current profiler (ADCP) attached to remote-controlled mini-boat, UAV-based bathymetry and MLS techniques were utilized to create the high-resolution DEMs of the river channel. These high-resolution measurements can be used in many fluvial applications such as computational fluid dynamics, channel change detection, habitat mapping or hydro-electric power plant planning. In this study we aim: 1) to analyze morphological changes of river channel especially riffle and pool formations based on fine-scale DEMs and ADCP measurements, 2) to analyze flow fields and their effect on morphological changes. The interest was mainly focused on reach-scale riffle-pool dynamics within two-year period of 2013 and 2014. The study was performed in sub-arctic meandering Pulmankijoki River located in Northern Finland. The river itself has shallow and clear water and sandy bed sediment. Discharge remains typically below 10 m3s-1 most of the year but during snow melt period in spring the discharge may exceed 70 m3s-1. We compared DEMs and ADCP measurements to understand both magnitude and spatio-temporal change of the river bed. Models were accurate enough to study bed form changes and locations and persistence of riffles and pools. We analyzed their locations with relation to flow during the peak and low discharge. Our demonstrated method has improved significantly spatio-temporal resolution of riverine DEMs compared to other cross-sectional and photogrammetry based models. Together with flow field measurements we gained better understanding of riverbed-water interaction

  20. High-resolution seafloor mapping surveys over the San Gregorio-Palo Colorado Fault

    NASA Astrophysics Data System (ADS)

    Paull, C. K.; Caress, D. W.; Thomas, H.; Lundsten, E.; Anderson, K.; Gwiazda, R.

    2011-12-01

    The San Gregorio-Palo Colorado Fault (SGPCF) is mapped as traversing the outer end of Monterey Bay and crossing Monterey Canyon near its intersection with Carmel Canyon. The location of the fault is based on offsets in seismic reflection profiles, lineations in the bathymetry, and locations of epicenters associated with small earthquakes. However, much of the offshore area where the trace of the SGPCF is postulated to be located is sediment bare, making it difficult to determine if there has been recent movement along this segment of the fault. High-resolution multibeam bathymetry (vertical precision of 0.15 m and horizontal resolution of 1.0 m) and 1-4.5 kHz chirp seismic reflection profiles have recently been collected in up to 1.6 km water depths on the northern flank of Monterey Canyon where the SGPCF is thought to cut across the canyon wall. The objective of these surveys was to look for indications of recent deformation associated with the SGPCF where accumulations of sediments could provide evidence of seafloor displacement along this segment of the fault since these sediments have been deposited. The surveys were conducted using an autonomous underwater vehicle (AUV) during two 17.5-hour-long dives. An inertial navigation system combined with a Doppler velocity sonar allowed the AUV to fly pre-programmed grids at 3 knots while maintaining an altitude of 50 m above the seafloor. These surveys are in addition to other recently published AUV surveys of the floor of Monterey Canyon extending out to 2.2 km water depths and including the zone where the SGPCF is mapped to cross the canyon floor. The lack of clear evidence of fault deformation along the SGPCF trace on the canyon floor is easily attributable to frequent sediment transport events within the canyon's channel, which would presumably overwrite sediment deformation associated with the SGPCF. The surveys presented here extend above the active canyon floor and cover the northern flank of Monterey Canyon

  1. High Resolution Mapping of the Lunar South Pole-Aitken Basin Interior

    NASA Astrophysics Data System (ADS)

    Archinal, B. A.; Gaddis, L. R.; Hare, T. M.; Rosiek, M.; Howington-Kraus, E.; Lee, E.; Weller, L.; Kirk, R. L.; Edmundson, K.; Becker, T.; Jolliff, B. L.; Tran, T.; Robinson, M.; LROC Science Team

    2010-12-01

    We are making geodetically controlled high-resolution digital terrain models (DTMs) and image orthomosaics of the Constellation (Cx) Program region of interest (ROI) in the lunar South Pole-Aitken Basin interior (“SAB”) (center at 200.06° E, 60.00° S). This work is part of the Lunar Mapping and Modeling Program (LMMP), a NASA-funded effort to create useful cartographic products from past and current lunar datasets and to serve them on a web portal. The SAB is one of 50 ROIs chosen by Cx as potential sites for future robotic or human landings or analogs thereof. Source data for our products includes publically released ~50 cm/pixel Lunar Reconnaissance Orbiter Camera (LROC) Narrow Angle Camera images and Lunar Orbiter Laser Altimeter (LOLA) spot elevation measurements and preliminary global 16 posts/° DTM. Products generated so far include: a) a preliminary stereo DTM covering ~25% of the center 20 km square area of the ROI, with post spacing (resolution) of 1.5 m and ~86x10^6 posts; b) a preliminary mosaic of 90% of the 40 km square ROI, with a resolution of 2 m, orthorectified with LOLA data or, where possible, the stereo DTM; c) preliminary DTMs generated via the use of photoclinometry (“shape from shading”), covering small areas with post spacing of 50 cm; and d) slope and roughness maps derived from a and c. All products are in the lunar mean Earth/polar axis coordinate system and the preliminary global reference frame of the current LOLA DTM. The absolute accuracy of these products is limited by the horizontal and vertical accuracy of the LOLA DTM, to which they are tied (DTMs and mosaics) or on which they are projected (mosaics). The expected vertical precision of the stereo DTM is ~20 cm. The products will soon be publically available via the LMMP portal and also via the USGS planetary GIS site, http://webgis.wr.usgs.gov/. Final versions tied to the LOLA nominal mission global DTM will be available in 2011 October. Preliminary analyses of these

  2. Comparing XRF core scan data to conventional geochemical analyses for high resolution paleoenvironmental studies

    NASA Astrophysics Data System (ADS)

    Hennekam, Rick; De Lange, Gert J.

    2013-04-01

    X-ray fluorescence (XRF) core scanning is becoming an increasingly common method to rapidly obtain paleo-environmental data from untreated (marine) sediments. There is a large potential for this method, being cheap, rapid, and non-destructive. However, the sediment surface is not an ideal substrate for XRF-analysis, thus measurement artefacts may occur relating to water content, grain size, surface roughness, film formation, and sediment inhomogeneity. A high resolution analysis of an Eastern Mediterranean sediment core is used to compare such potential artefacts and signal-to-noise ratio of XRF core scan measurements to those of traditional analyses using XRF glass bead and ICP-AES on distinct samples. A suit of major elements (and elemental ratios), often used as paleo-proxies, have been examined in this way so as to compare the robustness of the more 'relative' XRF-scan method compared to these more 'absolute' measurements. XRF core scan data only reflect the chemical composition of a thin (5-500 µm) layer of the sediment surface. Any inhomogeneity in this surface can cause large deviations thus may result in large 'deduced' paleo-environmental variability. It is shown that (random) water-rich spots can form underneath the Ultralene covering foil, having a substantial effect on the lighter elements with shallow response depths. This can create non-existing peaks in the XRF core scan -produced paleo-environmental record. Such deviations especially occur for elemental ratios when various elements are measured in different runs (e.g. other tube-voltage settings). This study urges to verify high/low amplitudinal variability observed in XRF corescans by means of (destructive) conventional geochemical analyses prior to their interpretation.. Reference: Hennekam R. and G. de Lange. X-ray fluorescence core scanning of wet marine sediments: methods to improve quality and reproducibility of high-resolution paleoenvironmental records. Limnology and Oceanography: Methods

  3. Using high-resolution digital aerial imagery to map land cover

    USGS Publications Warehouse

    Dieck, J.J.; Robinson, Larry

    2014-01-01

    The Upper Midwest Environmental Sciences Center (UMESC) has used aerial photography to map land cover/land use on federally owned and managed lands for over 20 years. Until recently, that process used 23- by 23-centimeter (9- by 9-inch) analog aerial photos to classify vegetation along the Upper Mississippi River System, on National Wildlife Refuges, and in National Parks. With digital aerial cameras becoming more common and offering distinct advantages over analog film, UMESC transitioned to an entirely digital mapping process in 2009. Though not without challenges, this method has proven to be much more accurate and efficient when compared to the analog process.

  4. High-resolution Mapping of In Vivo Gastrointestinal Slow Wave Activity Using Flexible Printed Circuit Board Electrodes: Methodology and Validation

    PubMed Central

    DU, PENG; O'GRADY, G.; EGBUJI, J. U.; LAMMERS, W. J.; BUDGETT, D.; NIELSEN, P.; WINDSOR, J. A.; PULLAN, A. J.; CHENG, L. K.

    2014-01-01

    High-resolution, multi-electrode mapping is providing valuable new insights into the origin, propagation, and abnormalities of gastrointestinal (GI) slow wave activity. Construction of high-resolution mapping arrays has previously been a costly and time-consuming endeavor, and existing arrays are not well suited for human research as they cannot be reliably and repeatedly sterilized. The design and fabrication of a new flexible printed circuit board (PCB) multi-electrode array that is suitable for GI mapping is presented, together with its in vivo validation in a porcine model. A modified methodology for characterizing slow waves and forming spatiotemporal activation maps showing slow waves propagation is also demonstrated. The validation study found that flexible PCB electrode arrays are able to reliably record gastric slow wave activity with signal quality near that achieved by traditional epoxy resin-embedded silver electrode arrays. Flexible PCB electrode arrays provide a clinically viable alternative to previously published devices for the high-resolution mapping of GI slow wave activity. PCBs may be mass-produced at low cost, and are easily sterilized and potentially disposable, making them ideally suited to intra-operative human use. PMID:19224368

  5. High-resolution mapping of in vivo gastrointestinal slow wave activity using flexible printed circuit board electrodes: methodology and validation.

    PubMed

    Du, Peng; O'Grady, G; Egbuji, J U; Lammers, W J; Budgett, D; Nielsen, P; Windsor, J A; Pullan, A J; Cheng, L K

    2009-04-01

    High-resolution, multi-electrode mapping is providing valuable new insights into the origin, propagation, and abnormalities of gastrointestinal (GI) slow wave activity. Construction of high-resolution mapping arrays has previously been a costly and time-consuming endeavor, and existing arrays are not well suited for human research as they cannot be reliably and repeatedly sterilized. The design and fabrication of a new flexible printed circuit board (PCB) multi-electrode array that is suitable for GI mapping is presented, together with its in vivo validation in a porcine model. A modified methodology for characterizing slow waves and forming spatiotemporal activation maps showing slow waves propagation is also demonstrated. The validation study found that flexible PCB electrode arrays are able to reliably record gastric slow wave activity with signal quality near that achieved by traditional epoxy resin-embedded silver electrode arrays. Flexible PCB electrode arrays provide a clinically viable alternative to previously published devices for the high-resolution mapping of GI slow wave activity. PCBs may be mass-produced at low cost, and are easily sterilized and potentially disposable, making them ideally suited to intra-operative human use.

  6. Mapping Sub-Antarctic Cushion Plants Using Random Forests to Combine Very High Resolution Satellite Imagery and Terrain Modelling

    PubMed Central

    Bricher, Phillippa K.; Lucieer, Arko; Shaw, Justine; Terauds, Aleks; Bergstrom, Dana M.

    2013-01-01

    Monitoring changes in the distribution and density of plant species often requires accurate and high-resolution baseline maps of those species. Detecting such change at the landscape scale is often problematic, particularly in remote areas. We examine a new technique to improve accuracy and objectivity in mapping vegetation, combining species distribution modelling and satellite image classification on a remote sub-Antarctic island. In this study, we combine spectral data from very high resolution WorldView-2 satellite imagery and terrain variables from a high resolution digital elevation model to improve mapping accuracy, in both pixel- and object-based classifications. Random forest classification was used to explore the effectiveness of these approaches on mapping the distribution of the critically endangered cushion plant Azorellamacquariensis Orchard (Apiaceae) on sub-Antarctic Macquarie Island. Both pixel- and object-based classifications of the distribution of Azorella achieved very high overall validation accuracies (91.6–96.3%, κ = 0.849–0.924). Both two-class and three-class classifications were able to accurately and consistently identify the areas where Azorella was absent, indicating that these maps provide a suitable baseline for monitoring expected change in the distribution of the cushion plants. Detecting such change is critical given the threats this species is currently facing under altering environmental conditions. The method presented here has applications to monitoring a range of species, particularly in remote and isolated environments. PMID:23940805

  7. Mapping sub-antarctic cushion plants using random forests to combine very high resolution satellite imagery and terrain modelling.

    PubMed

    Bricher, Phillippa K; Lucieer, Arko; Shaw, Justine; Terauds, Aleks; Bergstrom, Dana M

    2013-01-01

    Monitoring changes in the distribution and density of plant species often requires accurate and high-resolution baseline maps of those species. Detecting such change at the landscape scale is often problematic, particularly in remote areas. We examine a new technique to improve accuracy and objectivity in mapping vegetation, combining species distribution modelling and satellite image classification on a remote sub-Antarctic island. In this study, we combine spectral data from very high resolution WorldView-2 satellite imagery and terrain variables from a high resolution digital elevation model to improve mapping accuracy, in both pixel- and object-based classifications. Random forest classification was used to explore the effectiveness of these approaches on mapping the distribution of the critically endangered cushion plant Azorella macquariensis Orchard (Apiaceae) on sub-Antarctic Macquarie Island. Both pixel- and object-based classifications of the distribution of Azorella achieved very high overall validation accuracies (91.6-96.3%, κ = 0.849-0.924). Both two-class and three-class classifications were able to accurately and consistently identify the areas where Azorella was absent, indicating that these maps provide a suitable baseline for monitoring expected change in the distribution of the cushion plants. Detecting such change is critical given the threats this species is currently facing under altering environmental conditions. The method presented here has applications to monitoring a range of species, particularly in remote and isolated environments.

  8. High resolution mapping of hyporheic fluxes using streambed temperatures: Recommendations and limitations

    NASA Astrophysics Data System (ADS)

    Irvine, Dylan J.; Lautz, Laura K.

    2015-05-01

    Analytical solutions to the 1D heat transport equation can be used to derive point measurements of flux between surface water and groundwater from streambed temperature time series. Recent studies have used empirical relationships between measured flux and point-in-time observations of streambed temperatures to produce detailed plan view maps of flux from instantaneous temperature maps. Here, the accuracy of such flux maps, derived using streambed temperatures as a quantitative proxy, was assessed from synthetic streambed temperature data generated by numerical flow and transport simulations. The use of numerical simulations is advantageous because maps of flux from the temperature proxy method can be compared to known flux maps to quantify error. Empirical flux-temperature relationships are most accurate if developed from data collected when stream temperatures are at a maximum. The true relationship between flux and streambed temperature will generally be non-linear and well approximated as a cubic function, although linear relationships may be applied when data density is low. Intermediate fluxes (±1.0 m/day) returned by the temperature proxy method have errors typically less than ±0.1 m/day. Errors in estimated flux increase for strong upwelling (>1.0 m/day) or downwelling (<-1.0 m/day), although the direction of flux is still accurate.

  9. A high-resolution radiation hybrid map of rhesus macaque chromosome 5 identifies rearrangements in the genome assembly

    PubMed Central

    Karere, Genesio M.; Froenicke, Lutz; Millon, Lee; Womack, James E.; Lyons, Leslie A.

    2008-01-01

    A 10,000-rad radiation hybrid cell panel of the rhesus macaque was generated to construct a comprehensive RH map of chromosome 5. The map represents 218 markers typed in 185 RH clones. The 4,846 cR length map has an average marker spacing of 798 kb. Alignments of the RH map to macaque and human genome sequences confirm a large inversion and reveal a previously unreported telomeric inversion. The macaque genome sequence indicates small translocations from the ancestral homolog of macaque chromosome 5 to macaque chromosome 1 and 6. The RH map suggests that these are likely assembly artifacts. Unlike the genome sequence, the RH mapping data indicate the conservation of synteny between macaque chromosome 5 and human chromosome 4. This study shows that the 10,000-rad panel is appropriate for the generation of a high-resolution whole genome RH map suitable for the verification of the rhesus genome assembly. PMID:18601997

  10. Resonant x-ray emission spectroscopy of liquid water: novel instrumentation, high resolution, and the"map" approach

    SciTech Connect

    Weinhardt, L.; Fuchs, O.; Blum, M.; Bär, M.; Weigand, M.; Denlinger, J.D.; Zubavichus, Y.; Zharnikov, M.; Grunze, M.; Heske, C.; Umbach, E.

    2008-06-17

    Techniques to study the electronic structure of liquids are rare. Most recently, resonant x-ray emission spectroscopy (XES) has been shown to be an extremely versatile spectroscopy to study both occupied and unoccupied electronic states for liquids in thermodynamic equilibrium. However, XES requires high-brilliance soft x-ray synchrotron radiation and poses significant technical challenges to maintain a liquid sample in an ultra-high vacuum environment. Our group has therefore developed and constructed a novel experimental setup for the study of liquids, with the long-term goal of investigating the electronic structure of biological systems in aqueous environments. We have developed a flow-through liquid cell in which the liquid is separated from vacuum by a thin Si3N4 or SiC window and which allows a precise control of temperature. This approach has significant advantages compared to static liquids cells used in the past. Furthermore, we have designed a dedicated high-transmission, high-resolution soft x-ray spectrometer. The high transmission makes it possible to measure complete resonant XES"maps" in less than an hour, giving unprecedented detailed insight into the electronic structure of the investigated sample. Using this new equipment we have investigated the electronic structure of liquid water. Furthermore, our XES spectra and maps give information about ultra-fast dissociation on the timescale of the O 1s core hole lifetime, which is strongly affected by the initial state hydrogen bonding configuration.

  11. Using High Resolution Aeromagnetic Data to Map Pervasive Folding in the Lithologically Indistinct Franciscan Coastal Belt

    NASA Astrophysics Data System (ADS)

    Phelps, G. A.; McLaughlin, R. J.; Jachens, R. C.; Wentworth, C. M.

    2008-12-01

    We use high-resolution aeromagnetic data to map magnetic bodies of graywacke of limited exposure that are either interbedded or structurally emplaced within broader areas of non-magnetic graywacke within the Franciscan Complex Coastal belt in northern California, which is bounded by the San Andreas Fault on the west and the Franciscan Complex Central belt on the south and east. Previous work has not extensively subdivided the Coastal belt because of the poor exposure and the fact that the exposed lithology is primarily graywacke indistinguishable in outcrop and hand sample and is thus difficult to map in the field. A hand-held magnetic susceptibility meter, however, in combination with thin-section analysis, reveals that some Coastal belt graywackes are magnetic. The thin-section analysis shows that the magnetic samples have a significant component of andesitic grains, whereas the non-magnetic samples do not. Further, the locations of these magnetic rocks correspond to elongate regions of high magnetic intensity (magnetic anomalies) kilometers to tens of kilometers in length. Previous 2D modeling showed that the bodies of magnetic graywacke can be modeled as a folded sheet, with antiformal limbs near or exposed at the surface and synformal limbs reaching a depth of about 1 km. Locations of edges of magnetic source bodies can be extracted from their magnetic anomalies. Near surface, steeply dipping edges lie beneath local maxima in the horizontal gradient of the magnetic potential surface. The edges are demarcated by locating discrete points along the local maxima. We connected these points, using an algorithm with a specific set of parameters, to delineate the edges of the magnetic graywacke bodies. Together with the previous 2D modeling, the anomalies and their edges show that the Coastal belt contains antiformal structures 5 to 20 km in length and 1.5 km in width, with a wavelength approximately 1.5 km. The modal direction of elongation is oriented approximately

  12. Mapping human brain capillary water lifetime: high-resolution metabolic neuroimaging.

    PubMed

    Rooney, William D; Li, Xin; Sammi, Manoj K; Bourdette, Dennis N; Neuwelt, Edward A; Springer, Charles S

    2015-06-01

    Shutter-speed analysis of dynamic-contrast-agent (CA)-enhanced normal, multiple sclerosis (MS), and glioblastoma (GBM) human brain data gives the mean capillary water molecule lifetime (τ(b)) and blood volume fraction (v(b); capillary density-volume product (ρ(†)V)) in a high-resolution (1)H2O MRI voxel (40 μL) or ROI. The equilibrium water extravasation rate constant, k(po) (τ(b)(-1)), averages 3.2 and 2.9 s(-1) in resting-state normal white matter (NWM) and gray matter (NGM), respectively (n = 6). The results (italicized) lead to three major conclusions. (A) k(po) differences are dominated by capillary water permeability (P(W)(†)), not size, differences. NWM and NGM voxel k(po) and v(b) values are independent. Quantitative analyses of concomitant population-averaged k(po), v(b) variations in normal and normal-appearing MS brain ROIs confirm P(W)(†) dominance. (B) P(W)(†) is dominated (>95%) by a trans(endothelial)cellular pathway, not the P(CA)(†) paracellular route. In MS lesions and GBM tumors, P(CA)(†) increases but P(W)(†) decreases. (C) k(po) tracks steady-state ATP production/consumption flux per capillary. In normal, MS, and GBM brain, regional k(po) correlates with literature MRSI ATP (positively) and Na(+) (negatively) tissue concentrations. This suggests that the P(W)(†) pathway is metabolically active. Excellent agreement of the relative NGM/NWM k(po)v(b) product ratio with the literature (31)PMRSI-MT CMR(oxphos) ratio confirms the flux property. We have previously shown that the cellular water molecule efflux rate constant (k(io)) is proportional to plasma membrane P-type ATPase turnover, likely due to active trans-membrane water cycling. With synaptic proximities and synergistic metabolic cooperativities, polar brain endothelial, neuroglial, and neuronal cells form "gliovascular units." We hypothesize that a chain of water cycling processes transmits brain metabolic activity to k(po), letting it report neurogliovascular unit Na

  13. Carbonado revisited: Insights from neutron diffraction, high resolution orientation mapping and numerical simulations

    NASA Astrophysics Data System (ADS)

    Piazolo, Sandra; Kaminsky, Felix V.; Trimby, Patrick; Evans, Lynn; Luzin, V.

    2016-11-01

    One of the most controversial diamond types is carbonado, as its origin and geological history are still under debate. Here, we investigate selected carbonado samples using neutron diffraction and high resolution orientation mapping in combination with numerical simulations. Neutron diffraction analyses show that fine grained carbonado samples exhibit a distinct lack of crystallographic preferred orientation. Quantitative crystallographic orientation analyses performed on transmission electron microscope (TEM) sections reveal that the 2-10 μm grains exhibit locally significant internal deformation. Such features are consistent with crystal plastic deformation of a grain aggregate that initially formed by rapid nucleation, characterized by a high number of nucleation sites and no crystallographic preferred orientation. Crystal plastic deformation resulted in high stress heterogeneities close to grain boundaries, even at low bulk strains, inducing a high degree of lattice distortion without significant grain size reduction and the development of a crystallographic preferred orientation. Observed differences in the character of the grain boundary network and internal deformation structures can be explained by significant post-deformation annealing occurring to variable degrees in the carbonado samples. Differences in intensity of crystal bending and subgrain boundary sharpness can be explained by dislocation annihilation and rearrangement, respectively. During annealing grain energy is reduced resulting in distinct changes to the grain boundary geometry. Grain scale numerical modelling shows that anisotropic grain growth, where grain boundary energy is determined by the orientation of a boundary segment relative to the crystallographic orientation of adjacent grains results in straight boundary segments with abrupt changes in orientation even if the boundary is occurring between two triple junctions forming a ;zigzag; pattern. In addition, in diamond anisotropic

  14. High resolution mapping of Normalized Difference Vegetation Indices (NDVI) of biological soil crusts

    NASA Astrophysics Data System (ADS)

    Fischer, T.; Veste, M.; Eisele, A.; Bens, O.; Spyra, W.; Hüttl, R. F.

    2012-04-01

    Normalized Difference Vegetation Indices (NDVI) are typically determined using satellite or airborne remote sensing, or field portable spectrometers, which give an averaged signal on centimetre to meter scale plots. Biological soil crust (BSC) patches may have smaller sizes, and ecophysiological, hydrological as well as pedological processes may be heterogeneously distributed within this level of resolution. A ground-based NDVI imaging procedure using low-cost equipment (Olympus Camedia 5000z digital camera equipped with a Hoya R72 infrared filter) was developed in this study to fill this gap at the level of field research, where carrying costly and bulky equipment to remote locations is often the limiting factor for data collection. A commercially available colour rendition chart (GretagMacbeth ColorChecker®) with known red (600-700 nm) and NIR (800-900 nm) reflectances was placed into each scene and used for calibration purposes on a per-image basis. Generation of NDVI images involved (i) determination of red and NIR reflectances from the pixel values of the red and NIR channels, respectively, and (ii) calculation and imaging of the NDVI, where NDVI values of -1 to +1 were mapped to grey values of 0 to 255. The correlation between NDVI values retrieved from these images and NDVI values determined using conventional field spectrometry (ASD FieldSpec 3 portable spectroradiometer) was close (r2 =0.91), the 95% confidence interval amounted to 0.10 NDVI units. The pixel resolution was 0.8 mm in the field and 0.2 mm in the laboratory, but can still be improved significantly with closer distance to the crust or with higher camera resolution. Geostatistical analysis revealed that both spatial variability as well as size of individual objects characterized by the NDVI increased with crust development. The latter never exceeded 4 mm in the investigated crusts, which points to the necessity of high resolution imaging for linking remote sensing with ecophysiology

  15. Application of high resolution aeromagnetic data for basement topography mapping of Siluko and environs, southwestern Nigeria

    NASA Astrophysics Data System (ADS)

    Osinowo, Olawale O.; Akanji, Adesoji O.; Olayinka, Abel I.

    2014-11-01

    The discovery of hydrocarbon in commercial quantity in the Niger Delta, southern Nigeria, has since the early fifties shifted the attention of exploration/active geological studies from the Dahomey basin and the adjacent basement terrain in south-western Nigeria towards the south and this has left some gaps in information required for the discovery and exploitation of the economic potential of the region. This study mapped the Siluko transition zone in south-western Nigeria in terms of structures, geometry and basement topography with the object of providing requisite geological information that will engender interest in the exploration and exploitation of the numerous economic potentials of south-western part of Nigeria. Acquired high resolution aeromagnetic data were filtered, processed and enhanced, the resultant data were subjected to qualitative and quantitative magnetic interpretation, depth weighting analyses and modelling to generate the subsurface basement topography across the study area. The obtained results indicate regions of high and low magnetic anomalies with residual magnetic intensity values ranging from -100.8 nT to 100.9 nT. Euler Deconvolution indicates generally undulating basement topography with depth range of 125-1812 m. The basement relief is generally gentle and flat lying within the basement terrain with depth ranging from 125 to 500 m. However the sedimentary terrain is undulating and generally steeps south, down the basin with depth range of 300-1812 m. A basement topography model of the magnetic data constrained by Euler solutions correlate positively with the geology of the study area and indicates a generally increasing sedimentary deposits' thickness southward toward the western part of Dahomey basin. The revealed basement topography and structures as well as the delineated direction of continuous increase in thickness of sedimentary deposit provide insight to the controlling factor responsible for tar sand deposit and bitumen

  16. Comparison of High Resolution Topographic Data Sources (SAR, IfSAR, and LiDAR) for Storm Surge Hazard Maps

    NASA Astrophysics Data System (ADS)

    Suarez, J. K. B.; Santiago, J. T.; Muldong, T. M. M.; Lagmay, A. M. A.; Caro, C. V.; Ramos, M.

    2014-12-01

    As an archipelagic country, the Philippines has experienced multiple storm surge threats. Moreover, the country's location, adjacent to the Pacific Ocean, results in an average of eight to nine typhoons that make landfall in a year. Storm surge hazard maps require high resolution topographic data to illustrate water inflow in the event of storm surges in vulnerable coastal areas and for accurate boundaries and coastline. Furthermore, potential hazard areas tend to be generalized in lower resolution data. The objective of this research is to compare three sources where accurate and quality storm surge hazard maps will draw bases from. For this purpose, the researcher used and compared SAR, IfSAR and LiDAR. The study involved comparing maps from different topographic data sources in Tacloban, in the province of Leyte. This area was one of the most heavily stricken areas during typhoon Haiyan where more than 6,000 people died and P34.37 billion worth of property was destroyed. In the comparison of the three sources, the following had be taken into consideration: cost of acquiring data, processing time, purpose, and the results. The research learned the following: Synthetic Aperture Radar or SAR produces data with a 30 meter resolution, while Interferometric Synthetic Aperture Radar (IfSAR) offers a resolution of 5 meters. Light Detection and Ranging (LiDAR) has the highest resolution of the three with 1 meter. In addition, higher costs are paid for more detailed topographic data. Also, processing time takes longer for finer details due to the memory of the computer units used for modelling. The sources were also evaluated on the necessity of the scale at which the maps are needed for specific purposes such as practicality and direct disaster response. Results from the maps have been validated through interviews with the locals on the experience of actual storm surges. Through this study, the researcher concluded that although LiDAR can offer a more detailed and

  17. Short-term forecasting of high resolution local DNI maps with multiple fish-eye cameras in stereoscopic mode

    NASA Astrophysics Data System (ADS)

    Blanc, Philippe; Massip, Pierre; Kazantzidis, Andreas; Tzoumanikas, Panagiotis; Kuhn, Pascal; Wilbert, Stefan; Schüler, David; Prahl, Christoph

    2017-06-01

    Nowcasting of high resolution maps of direct normal irradiance (DNI) is of interest to efficiently operate Concentrated Solar Power plants. The paper presents a state-of-the-art and innovative methodology, developed in the framework of the FP7 DNICast project, to derive nowcasting of DNI maps from fish-eye cameras in stereoscopic mode. This methodology has been applied at the Plataforma Solar de Almeria: fish-eye cameras at distances from each other between 500 m and 900 m have been used in stereoscopic mode to produce nowcasted 1-min time series of decametric DNI maps.

  18. Mapping an Extended Neurochemical Profile at 3 and 7 T Using Accelerated High-Resolution Proton Magnetic Resonance Spectroscopic Imaging.

    PubMed

    Gruber, Stephan; Heckova, Eva; Strasser, Bernhard; Považan, Michal; Hangel, Gilbert J; Minarikova, Lenka; Trattnig, Siegfried; Bogner, Wolfgang

    2017-10-01

    The aim of this study was to compare high-resolution free induction decay magnetic resonance spectroscopic imaging (FID-MRSI) at 3 T and 7 T in the brain of healthy subjects and to showcase the clinical potential of accelerated FID-MRSI at 7 T in 2 brain tumor cases. In this institutional review board-approved study, 10 healthy volunteers (8 men/2 women; age: 31 ± 6 years) were measured at 3 T and 7 T (Trio and 7T-Magnetom; Siemens Healthcare, Germany) and 2 patients (a 38-year-old man and a 37-year-old man), 1 with an anaplastic oligoastrocytoma (grade III) and 1 with a low-grade glioma (oligodendroglioma), were measured at 7 T.Free induction decay MR spectroscopic imaging with 3.4 × 3.4 mm in-plane resolution was acquired in 30 minutes/6 minutes (nonaccelerated/accelerated) at both field strengths. In addition, single-slice or multi-slice FID-MRSI at 7 T was measured in the 2 tumor patients at 7 T within 6 minutes/13.3 minutes. Signal-to-noise ratio, Cramer-Rao lower bounds, and parallel imaging efficiency were assessed. High-resolution maps were created for 9 different brain metabolites. At 7 T, 7 of 9 metabolites were reliably mapped over the whole slice but only 3 at 3 T. Parallel imaging efficiency was significantly improved at 7 T. Signal-to-noise ratios were +75%/+66% (P < 0.05) for N-acetylaspartate and +97%/+74%(P < 0.05) for glutamine + glutamate [Glx], and full-widths at half maximum were +112%/+109%(P < 0.05) higher at 7 T than at 3 T (nonaccelerated/accelerated) for N-acetylaspartate. Cramer-Rao lower bounds were more than double at 3 T (P < 0.05). At 7 T, FID-MRSI allowed the assessment of an extended neurochemical profile and yielded better metabolic maps in only approximately 6 minutes at 7 T than in approximately 30 minutes at 3 T. We found several potentially therapy-relevant neurochemical alterations in brain tumors that highlighted the potential of fast clinical FID-MRSI at 7 T.

  19. High Speed High Resolution Current Comparator and its Application to Analog to Digital Converter

    NASA Astrophysics Data System (ADS)

    Sridhar, Ranjana; Pandey, Neeta; Bhattacharyya, Asok; Bhatia, Veepsa

    2016-06-01

    This paper introduces a high speed high resolution current comparator which includes the current differencing stage and employs non linear feedback in the gain stage. The usefulness of the proposed comparator is demonstrated by implementing a 3-bit current mode flash analog-to-digital converter (ADC). Simulation program with integrated circuit emphasis (SPICE) simulations have been carried out to verify theoretical proposition and performance parameters of both comparator and ADC are obtained using TSMC 0.18 µm CMOS technology parameters. The current comparator shows a resolution of ±5 nA and a delay of 0.86 ns for current difference of ±1 µA. The impact of process variation on proposed comparator propagation delay has been studied through Monte Carlo simulation and it is found that percentage change in propagation delay in best case is 1.3 % only and in worst case is 9 % only. The ADC exhibits an offset, gain error, differential nonlinearity (DNL) and integral nonlinearity (INL) of 0.102 µA, 0.99, -0.34 LSB and 0.0267 LSB, respectively. The impact of process variation on ADC has also been studied at different process corners.

  20. Three very high resolution optical images for land use mapping of a suburban catchment: input to distributed hydrological models

    NASA Astrophysics Data System (ADS)

    Jacqueminet, Christine; Kermadi, Saïda; Michel, Kristell; Jankowfsky, Sonja; Braud, Isabelle; Branger, Flora; Beal, David; Gagnage, Matthieu

    2010-05-01

    resampled in the same low resolution of 2.5 m and compared in order to evaluate the accuracy of different image processing methods and to determine for each cover type, the more appropriate image and/or method. This comparison provides hydrologists with a synthetic land cover map. Four parameters affect the accuracy of land cover mapping: firstly the addition of the NIR band improves vegetation classification such as the distinction between coniferous forest and broad-leaved forest. Moreover the intensity of chlorophyllian activity allows us to characterize the use of agricultural fields. Secondly, the images were taken at three dates in the agricultural calendar. This multi-date data allows the discrimination between permanently vegetalized pastures, and temporarily bare crops, a useful information for hydrologists who study surfaces hydraulic properties. Thirdly, the high resolution of the BD Ortho IGN image emphasizes the heterogeneity inside the spatial entities. Thus, in urbanised areas, high-resolution imagery allows the precise identification of objects > 5 m2 and consequently the quantification of impervious and pervious surfaces. However, the continuity of forest areas is not maintained because of the presence of small entities with sparser tree cover that were classified as herbaceous areas. Finally, image characteristics are more crucial than classification methods for the accuracy of land cover mapping. However, object based approach improves the classification of mixed pixels on the edge between different objects. It's particularly true for buildings and roads.

  1. Dynamics of the MAP IOP 15 severe Mistral event: Observations and high-resolution numerical simulations

    NASA Astrophysics Data System (ADS)

    Guénard, V.; Drobinski, P.; Caccia, J. L.; Tedeschi, G.; Currier, P.

    2006-04-01

    This paper investigates the fundamental processes involved in a severe Mistral event that occurred during the Mesoscale Alpine Program (from 6 to 9 November 1999). The Mistral refers to a violent north/north-westerly wind blowing in south-eastern France from the Rhône valley to the French Riviera. The study is based on measurements from radiosoundings launched from Lyon and Nîmes and from two UHF wind profilers located near Marseille and Toulon allowing a good description of the flow in the complex terrain formed by the south-western Alps. Observational results are compared with RAMS non-hydrostatic numerical simulations performed with 27 km, 9 km and 3 km nested grids. The numerical simulations capture the flow complexity both upstream of the Alps and in the coastal area affected by the Mistral. They correctly reproduce horizontal wind speeds and directions, vertical velocities, virtual potential temperature and relative humidity documented by the observational network. The simulations are used to point out the main dynamical processes generating the Mistral. It is found that flow splitting around the Alps and around the isolated peaks bordering the south-eastern part of the Rhône valley (Mont Ventoux 1909 m, Massif du Lubéron 1425 m) induces the low-level jet observed near Marseille that lasts for 36 hours. The high-resolution simulation indicates that the transient low-level jet lasting for only 9 hours observed at Toulon is due to a gravity wave breaking over local topography (the Sainte Baume 1147 m) where hydraulic jumps are involved. A mountain wake with two opposite-sign potential-vorticity banners is generated. The mesoscale wake explains the westward progression of the large-scale Alpine wake.

  2. Fiber Optic Distributed Sensors for High-resolution Temperature Field Mapping

    PubMed Central

    Lomperski, Stephen; Gerardi, Craig; Lisowski, Darius

    2016-01-01

    The reliability of computational fluid dynamics (CFD) codes is checked by comparing simulations with experimental data. A typical data set consists chiefly of velocity and temperature readings, both ideally having high spatial and temporal resolution to facilitate rigorous code validation. While high resolution velocity data is readily obtained through optical measurement techniques such as particle image velocimetry, it has proven difficult to obtain temperature data with similar resolution. Traditional sensors such as thermocouples cannot fill this role, but the recent development of distributed sensing based on Rayleigh scattering and swept-wave interferometry offers resolution suitable for CFD code validation work. Thousands of temperature measurements can be generated along a single thin optical fiber at hundreds of Hertz. Sensors function over large temperature ranges and within opaque fluids where optical techniques are unsuitable. But this type of sensor is sensitive to strain and humidity as well as temperature and so accuracy is affected by handling, vibration, and shifts in relative humidity. Such behavior is quite unlike traditional sensors and so unconventional installation and operating procedures are necessary to ensure accurate measurements. This paper demonstrates implementation of a Rayleigh scattering-type distributed temperature sensor in a thermal mixing experiment involving two air jets at 25 and 45 °C. We present criteria to guide selection of optical fiber for the sensor and describe installation setup for a jet mixing experiment. We illustrate sensor baselining, which links readings to an absolute temperature standard, and discuss practical issues such as errors due to flow-induced vibration. This material can aid those interested in temperature measurements having high data density and bandwidth for fluid dynamics experiments and similar applications. We highlight pitfalls specific to these sensors for consideration in experiment design

  3. Fiber Optic Distributed Sensors for High-resolution Temperature Field Mapping.

    PubMed

    Lomperski, Stephen; Gerardi, Craig; Lisowski, Darius

    2016-11-07

    The reliability of computational fluid dynamics (CFD) codes is checked by comparing simulations with experimental data. A typical data set consists chiefly of velocity and temperature readings, both ideally having high spatial and temporal resolution to facilitate rigorous code validation. While high resolution velocity data is readily obtained through optical measurement techniques such as particle image velocimetry, it has proven difficult to obtain temperature data with similar resolution. Traditional sensors such as thermocouples cannot fill this role, but the recent development of distributed sensing based on Rayleigh scattering and swept-wave interferometry offers resolution suitable for CFD code validation work. Thousands of temperature measurements can be generated along a single thin optical fiber at hundreds of Hertz. Sensors function over large temperature ranges and within opaque fluids where optical techniques are unsuitable. But this type of sensor is sensitive to strain and humidity as well as temperature and so accuracy is affected by handling, vibration, and shifts in relative humidity. Such behavior is quite unlike traditional sensors and so unconventional installation and operating procedures are necessary to ensure accurate measurements. This paper demonstrates implementation of a Rayleigh scattering-type distributed temperature sensor in a thermal mixing experiment involving two air jets at 25 and 45 °C. We present criteria to guide selection of optical fiber for the sensor and describe installation setup for a jet mixing experiment. We illustrate sensor baselining, which links readings to an absolute temperature standard, and discuss practical issues such as errors due to flow-induced vibration. This material can aid those interested in temperature measurements having high data density and bandwidth for fluid dynamics experiments and similar applications. We highlight pitfalls specific to these sensors for consideration in experiment design

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

    USDA-ARS?s Scientific Manuscript database

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

  5. Global High Resolution Mapping and Assimilation of Soil Moisture Observations for the SMAP Radar and Radiometer

    USDA-ARS?s Scientific Manuscript database

    The Soil Moisture Active and Passive (SMAP) mission is being developed by NASA for launch in 2015. The primary science objectives of SMAP are to enhance understanding of land surface controls on the water, energy and carbon cycles, and to determine their linkages. Moreover, SMAP high-resolution so...

  6. Mapping evapotranspiration with high resolution aircraft imagery over vineyards using one and two source modeling schemes

    USDA-ARS?s Scientific Manuscript database

    Thermal and multispectral remote sensing data from low-altitude aircraft can provide high spatial resolution necessary for sub-field (= 10 m) and plant canopy (= 1 m) scale evapotranspiration (ET) monitoring. In this study, high resolution aircraft sub-meter scale thermal infrared and multispectral...

  7. Expert system designed to assist in the interpretation and evaluation of thoracic surface maps produced by high-resolution electrocardiography

    SciTech Connect

    Johnson, J.K.

    1988-01-01

    An expert system is an artificial intelligence program that relies on a knowledge base composed of information derived from an expert and is designed to perform a difficult task. The system is usually domain specific and provides an interactive consultation with the user in problem solving. High-resolution electrocardiography is a technique for acquiring information about the heart's electrical activity with the use of multilead electrodes. Thoracic surface maps are presented at precise intervals during the depolarization/repolarization stages of a heartbeat. Cardiologists have determined methods for relating the thoracic maps to the actual tissue condition of the heart giving a basis for diagnoses. This work shows the anatomy of the heart, techniques for measuring that activity, and in detail, the techniques used with High Resolution Electrocardiography. The field of artificial intelligence is explored with an emphasis on expert systems. An expert system developed to diagnose the HRE record is presented.

  8. Gaussian Multiple Instance Learning Approach for Mapping the Slums of the World Using Very High Resolution Imagery

    SciTech Connect

    Vatsavai, Raju

    2013-01-01

    In this paper, we present a computationally efficient algo- rithm based on multiple instance learning for mapping infor- mal settlements (slums) using very high-resolution remote sensing imagery. From remote sensing perspective, infor- mal settlements share unique spatial characteristics that dis- tinguish them from other urban structures like industrial, commercial, and formal residential settlements. However, regular pattern recognition and machine learning methods, which are predominantly single-instance or per-pixel classi- fiers, often fail to accurately map the informal settlements as they do not capture the complex spatial patterns. To overcome these limitations we employed a multiple instance based machine learning approach, where groups of contigu- ous pixels (image patches) are modeled as generated by a Gaussian distribution. We have conducted several experi- ments on very high-resolution satellite imagery, represent- ing four unique geographic regions across the world. Our method showed consistent improvement in accurately iden- tifying informal settlements.

  9. High resolution population distribution maps for Southeast Asia in 2010 and 2015.

    PubMed

    Gaughan, Andrea E; Stevens, Forrest R; Linard, Catherine; Jia, Peng; Tatem, Andrew J

    2013-01-01

    Spatially accurate, contemporary data on human population distributions are vitally important to many applied and theoretical researchers. The Southeast Asia region has undergone rapid urbanization and population growth over the past decade, yet existing spatial population distribution datasets covering the region are based principally on population count data from censuses circa 2000, with often insufficient spatial resolution or input data to map settlements precisely. Here we outline approaches to construct a database of GIS-linked circa 2010 census data and methods used to construct fine-scale (∼100 meters spatial resolution) population distribution datasets for each country in the Southeast Asia region. Landsat-derived settlement maps and land cover information were combined with ancillary datasets on infrastructure to model population distributions for 2010 and 2015. These products were compared with those from two other methods used to construct commonly used global population datasets. Results indicate mapping accuracies are consistently higher when incorporating land cover and settlement information into the AsiaPop modelling process. Using existing data, it is possible to produce detailed, contemporary and easily updatable population distribution datasets for Southeast Asia. The 2010 and 2015 datasets produced are freely available as a product of the AsiaPop Project and can be downloaded from: www.asiapop.org.

  10. Mapping the electrostatic force field of single molecules from high-resolution scanning probe images

    PubMed Central

    Hapala, Prokop; Švec, Martin; Stetsovych, Oleksandr; van der Heijden, Nadine J.; Ondráček, Martin; van der Lit, Joost; Mutombo, Pingo; Swart, Ingmar; Jelínek, Pavel

    2016-01-01

    How electronic charge is distributed over a molecule determines to a large extent its chemical properties. Here, we demonstrate how the electrostatic force field, originating from the inhomogeneous charge distribution in a molecule, can be measured with submolecular resolution. We exploit the fact that distortions typically observed in high-resolution atomic force microscopy images are for a significant part caused by the electrostatic force acting between charges of the tip and the molecule of interest. By finding a geometrical transformation between two high-resolution AFM images acquired with two different tips, the electrostatic force field or potential over individual molecules and self-assemblies thereof can be reconstructed with submolecular resolution. PMID:27230940

  11. Using dynamical interpolation to map high-resolution altimeter data in the Western Mediterranean Sea

    NASA Astrophysics Data System (ADS)

    Roge, M.; Morrow, R.; Gerald, D.

    2016-12-01

    The main oceanographic objective of the future SWOT mission is to characterize the ocean mesoscale and submesoscale circulation by observing the fine range of ocean dynamics (from 15-300 km). However it will not capture the time evolution of short mesoscale signals. Despite the very high spatial resolution of the future satellite, the temporal resolution is not sufficient to track the evolution of the small, rapid features (exact repeat cycle of 21 days, with near repeats around 5-10 days, depending on the latitude). High resolution SWOT sea surface height snapshots alone will not allow us to follow the dynamics of ocean variability at these scales, such as the formation and evolution of small eddies. Here, we investigate a means to reconstruct the missing SSH signal in time between two satellite revisits. We use a shallow water quasi-geostrophic model developed by Ubelmann et al (2015). Based on potential vorticity conservation, it dynamically advects the SSH field, assuming that the quasi-geostrophic dynamics are principally captured by the first baroclinic mode. This model has been tested in energetic open ocean regions such as the Gulf Stream and the Californian Current, and has given improved results. Here we test this model in the Western Mediterranean Sea, where the first radius of deformation of Rossby is small (5-15 km), where the dynamics have a strong topographic control and strong spatial and seasonal variability. In this region, the technique provides a small improvement over linear interpolation in the coastal boundary current systems. The simple dynamical model is missing some physical mechanisms, needed to correctly represent the mesoscale circulation in this region, including a significant barotropic mode. We investigate modifications to the 1.5 layer model in this regional study, to include a topographic-beta effect and small-scale dissipation and an extension to a two-layer model. The results show an improved performance compared to simple linear

  12. High-resolution NO2 maps of Rotterdam and Zürich retrieved from the APEX imaging spectrometer

    NASA Astrophysics Data System (ADS)

    Kuhlmann, Gerrit; Hueni, Andreas; Brunner, Dominik

    2016-04-01

    In urban areas, nitrogen dioxide (NO_2) concentrations have high spatial and temporal variability making high-resolution NO2 maps an important tool for air pollution assessment and epidemiological studies. We retrieved high-resolution NO2 maps from the Airborne Prism Experiment (APEX) imaging spectrometer measured over Zürich on 30. August 2013 (11:24--12:05 UTC) and Rotterdam on 17. September 2014 (8:53--10:18 UTC). Our updated retrieval fits NO_2, O_3, O_4, H_2O and the Ring effect between 440 and 510 nm using Differential Optical Absorption Spectroscopy (DOAS). The radiance spectra were spectrally calibrated using a high-resolution solar reference spectrum to correct spectral shifts in across- and along-track direction. Air mass factors were computed using the SCIATRAN radiative transfer model. The retrieved NO2 maps have 50×50m2 resolution and cover an area of 10×26 km2 for Zürich and 10×50 km2 for Rotterdam. The maps show enhanced NO2 values in populated areas and at least three strong plumes from oil refineries in Rotterdam. A comparison with ground measurements in Rotterdam shows only weak correlation, because most of the NO2 is found in elevated plumes. In conclusion, airborne observations allow mapping of the NO2 distribution in urban areas providing a different perspective on urban air quality which cannot be acquired by ground-based observations. The obtained maps will be used for further analysis such as estimating NOX emissions from oil refineries and comparison with urban-scale chemistry transport modelling.

  13. High-resolution seismic reflection profiling for mapping shallow aquifers in Lee County, Florida

    USGS Publications Warehouse

    Missimer, T.M.; Gardner, Richard Alfred

    1976-01-01

    High-resolution continuous seismic reflection profiling equipment was utilized to define the configuration of sedimentary layers underlying part of Lee County, Florida. About 45 miles (72 kilometers) of profile were made on the Caloosahatchee River Estuary and San Carlos Bay. Two different acoustic energy sources, a high resolution boomer and a 45-electrode high resolution sparker, both having a power input of 300 joules, were used to obtain both adequate penetration and good resolution. The seismic profiles show that much of the strata of middle Miocene to Holocene age apparently are extensively folded but not faulted. Initial interpretations indicate that: (1) the top of the Hawthorn Formation (which contains the upper Hawthorn aquifer) has much relief due chiefly to apparent folding; (2) the limestone, sandstone, and unconsolidated sand and phosphorite, which together compose the sandstone aquifer, appear to be discontinuous; (3) the green clay unit of the Tamiami Formation contains large scale angular beds dipping eastward; and (4) numerous deeply cut alluvium-filled paleochannels underlie the Caloosahatchee River. (Woodard-USGS)

  14. Mapping trees outside forests using high-resolution aerial imagery: a comparison of pixel- and object-based classification approaches.

    PubMed

    Meneguzzo, Dacia M; Liknes, Greg C; Nelson, Mark D

    2013-08-01

    Discrete trees and small groups of trees in nonforest settings are considered an essential resource around the world and are collectively referred to as trees outside forests (ToF). ToF provide important functions across the landscape, such as protecting soil and water resources, providing wildlife habitat, and improving farmstead energy efficiency and aesthetics. Despite the significance of ToF, forest and other natural resource inventory programs and geospatial land cover datasets that are available at a national scale do not include comprehensive information regarding ToF in the United States. Additional ground-based data collection and acquisition of specialized imagery to inventory these resources are expensive alternatives. As a potential solution, we identified two remote sensing-based approaches that use free high-resolution aerial imagery from the National Agriculture Imagery Program (NAIP) to map all tree cover in an agriculturally dominant landscape. We compared the results obtained using an unsupervised per-pixel classifier (independent component analysis-[ICA]) and an object-based image analysis (OBIA) procedure in Steele County, Minnesota, USA. Three types of accuracy assessments were used to evaluate how each method performed in terms of: (1) producing a county-level estimate of total tree-covered area, (2) correctly locating tree cover on the ground, and (3) how tree cover patch metrics computed from the classified outputs compared to those delineated by a human photo interpreter. Both approaches were found to be viable for mapping tree cover over a broad spatial extent and could serve to supplement ground-based inventory data. The ICA approach produced an estimate of total tree cover more similar to the photo-interpreted result, but the output from the OBIA method was more realistic in terms of describing the actual observed spatial pattern of tree cover.

  15. Self-Powered High-Resolution and Pressure-Sensitive Triboelectric Sensor Matrix for Real-Time Tactile Mapping.

    PubMed

    Wang, Xiandi; Zhang, Hanlu; Dong, Lin; Han, Xun; Du, Weiming; Zhai, Junyi; Pan, Caofeng; Wang, Zhong Lin

    2016-04-20

    A triboelectric sensor matrix (TESM) can accurately track and map 2D tactile sensing. A self-powered, high-resolution, pressure-sensitive, flexible and durable TESM with 16 × 16 pixels is fabricated for the fast detection of single-point and multi-point touching. Using cross-locating technology, a cross-type TESM with 32 × 20 pixels is developed for more rapid tactile mapping, which significantly reduces the addressing lines from m × n to m + n. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Mapping cold seeps with high-resolution deep water multibeam echosounders in the Black Sea

    NASA Astrophysics Data System (ADS)

    Wintersteller, P.; dos Santos Ferreira, C.; Klaucke, I.; Ivanov, M.; Sahling, H.; Bohrmann, G.

    2011-12-01

    Cold seeps are locations at the seafloor where gas and/or fluids are emitting. In contrast to mud volcanoes, which distinctly change the seafloor morphology, cold seeps often lack significant relief. However, in comparison with surrounding sediments seep locations on the sea floor are often characterized by high acoustic backscatter intensity. This was documented during several investigations with deep towed side-scan sonar (SSS) systems in recent years. Authigenic carbonates, free gas and gas hydrates, as evidenced by ground truthing, are responsible for the high backscatter values. Last year's upgrade of the 1°x2° KONGSBERG deep water echosounder EM120 to EM122 on RV Meteor enhanced the system to almost 4 times the previous resolution due to multi-ping and high density signal processing. Based on the physics of sound propagation in the water column, multibeam echosounders (MBES) for deep water use relatively low frequencies of about 12-15 kHz. Apparently highly water-saturated sediments are penetrated by these signals and can cause artificial offsets in bottom detection in comparison to high-frequency echosounders. Nevertheless the effect of the slightly penetrating signal has a useful side effect on the backscatter. Investigations on several seep sites in the Black Sea, carried out with both EM122 and EM710 during Meteror cruise M84-2, resulted in maps of remarkable bathymetric resolution but also showed multibeam backscatter information of a 12 kHz signal to be an excellent tool to map seep-influenced seafloor areas. New seep locations have been mapped in regions of the western Turkish continental margin close to Eregli and of the eastern Turkish margin off Samsun. In both areas high backscatter patches were mapped with nearly comparable resolution as achieved by deep-tow SSS systems. At Eregli the new data is compared with data from a deep-towed EdgeTech SSS system recorded with a frequency of 75 kHz. At Samsun the results are compared with data from a MAK-1

  17. Object-based locust habitat mapping using high-resolution multispectral satellite data in the southern Aral Sea basin

    NASA Astrophysics Data System (ADS)

    Navratil, Peter; Wilps, Hans

    2013-01-01

    Three different object-based image classification techniques are applied to high-resolution satellite data for the mapping of the habitats of Asian migratory locust (Locusta migratoria migratoria) in the southern Aral Sea basin, Uzbekistan. A set of panchromatic and multispectral Système Pour l'Observation de la Terre-5 satellite images was spectrally enhanced by normalized difference vegetation index and tasseled cap transformation and segmented into image objects, which were then classified by three different classification approaches: a rule-based hierarchical fuzzy threshold (HFT) classification method was compared to a supervised nearest neighbor classifier and classification tree analysis by the quick, unbiased, efficient statistical trees algorithm. Special emphasis was laid on the discrimination of locust feeding and breeding habitats due to the significance of this discrimination for practical locust control. Field data on vegetation and land cover, collected at the time of satellite image acquisition, was used to evaluate classification accuracy. The results show that a robust HFT classifier outperformed the two automated procedures by 13% overall accuracy. The classification method allowed a reliable discrimination of locust feeding and breeding habitats, which is of significant importance for the application of the resulting data for an economically and environmentally sound control of locust pests because exact spatial knowledge on the habitat types allows a more effective surveying and use of pesticides.

  18. Thick-lens velocity-map imaging spectrometer with high resolution for high-energy charged particles

    NASA Astrophysics Data System (ADS)

    Kling, N. G.; Paul, D.; Gura, A.; Laurent, G.; De, S.; Li, H.; Wang, Z.; Ahn, B.; Kim, C. H.; Kim, T. K.; Litvinyuk, I. V.; Cocke, C. L.; Ben-Itzhak, I.; Kim, D.; Kling, M. F.

    2014-05-01

    A novel design for a velocity-map imaging (VMI) spectrometer with high resolution over a wide energy range surpassing a standard VMI design is reported. The main difference to a standard three-electrode VMI is the spatial extension of the applied field using 11 electrodes forming a thick-lens. This permits measurements of charged particles with higher energies while achieving excellent resolving power over a wide range of energies. Using SIMION simulations, the thick-lens VMI is compared to a standard design for up to 360 eV electrons. The simulations also show that the new spectrometer design is suited for charged-particle detection with up to 1 keV using a repeller-electrode voltage of -30 kV. The experimental performance is tested by laser-induced ionization of rare gases producing electrons up to about 70 eV. The thick-lens VMI is useful for a wide variety of studies on atoms, molecules and nanoparticles in intense laser fields and high-photon-energy fields from high-harmonic-generation or free-electron lasers.

  19. Magellan radar image compared to high resolution Earth-based image of Venus

    NASA Technical Reports Server (NTRS)

    1990-01-01

    A strip of a Magellan radar image (left) is compared to a high resolution Earth-based radar image of Venus, obtained by the U.S. National Astronomy and Ionosphere Center's Arecibo Observatory in Puerto Rico. The small white box in the Arecibo image corresponds to the Magellan image. This portion of the Magellan imagery shows a small region on the east flank of a major volcanic upland called Beta Regio. The image is centered at 23 degrees north latitude and 286.7 degrees east longitude. The ridge and valley network in the middle part of the image is formed by intersecting faults which have broken the Venusian crust into a complex deformed type of surface called tessera, the Latin word for tile. The parallel mountains and valleys resemble the Basin and Range Province in the western United States. The irregular dark patch near the top of the image is a smooth surface, probably formed, according to scientists, by lava flows in a region about 10 kilometers (6 miles) across. Similar dark sur

  20. High resolution mapping of development in the wildland-urban interface using object based image extraction.

    PubMed

    Caggiano, Michael D; Tinkham, Wade T; Hoffman, Chad; Cheng, Antony S; Hawbaker, Todd J

    2016-10-01

    The wildland-urban interface (WUI), the area where human development encroaches on undeveloped land, is expanding throughout the western United States resulting in increased wildfire risk to homes and communities. Although census based mapping efforts have provided insights into the pattern of development and expansion of the WUI at regional and national scales, these approaches do not provide sufficient detail for fine-scale fire and emergency management planning, which requires maps of individual building locations. Although fine-scale maps of the WUI have been developed, they are often limited in their spatial extent, have unknown accuracies and biases, and are costly to update over time. In this paper we assess a semi-automated Object Based Image Analysis (OBIA) approach that utilizes 4-band multispectral National Aerial Image Program (NAIP) imagery for the detection of individual buildings within the WUI. We evaluate this approach by comparing the accuracy and overall quality of extracted buildings to a building footprint control dataset. In addition, we assessed the effects of buffer distance, topographic conditions, and building characteristics on the accuracy and quality of building extraction. The overall accuracy and quality of our approach was positively related to buffer distance, with accuracies ranging from 50 to 95% for buffer distances from 0 to 100 m. Our results also indicate that building detection was sensitive to building size, with smaller outbuildings (footprints less than 75 m(2)) having detection rates below 80% and larger residential buildings having detection rates above 90%. These findings demonstrate that this approach can successfully identify buildings in the WUI in diverse landscapes while achieving high accuracies at buffer distances appropriate for most fire management applications while overcoming cost and time constraints associated with traditional approaches. This study is unique in that it evaluates the ability of an OBIA

  1. High resolution mapping of development in the wildland-urban interface using object based image extraction

    USGS Publications Warehouse

    Caggiano, Michael D.; Tinkham, Wade T.; Hoffman, Chad; Cheng, Antony S.; Hawbaker, Todd J.

    2016-01-01

    The wildland-urban interface (WUI), the area where human development encroaches on undeveloped land, is expanding throughout the western United States resulting in increased wildfire risk to homes and communities. Although census based mapping efforts have provided insights into the pattern of development and expansion of the WUI at regional and national scales, these approaches do not provide sufficient detail for fine-scale fire and emergency management planning, which requires maps of individual building locations. Although fine-scale maps of the WUI have been developed, they are often limited in their spatial extent, have unknown accuracies and biases, and are costly to update over time. In this paper we assess a semi-automated Object Based Image Analysis (OBIA) approach that utilizes 4-band multispectral National Aerial Image Program (NAIP) imagery for the detection of individual buildings within the WUI. We evaluate this approach by comparing the accuracy and overall quality of extracted buildings to a building footprint control dataset. In addition, we assessed the effects of buffer distance, topographic conditions, and building characteristics on the accuracy and quality of building extraction. The overall accuracy and quality of our approach was positively related to buffer distance, with accuracies ranging from 50 to 95% for buffer distances from 0 to 100 m. Our results also indicate that building detection was sensitive to building size, with smaller outbuildings (footprints less than 75 m2) having detection rates below 80% and larger residential buildings having detection rates above 90%. These findings demonstrate that this approach can successfully identify buildings in the WUI in diverse landscapes while achieving high accuracies at buffer distances appropriate for most fire management applications while overcoming cost and time constraints associated with traditional approaches. This study is unique in that it evaluates the ability of an OBIA

  2. High Resolution Mapping of Modafinil Induced Changes in Glutamate Level in Rat Brain

    PubMed Central

    Haris, Mohammad; Singh, Anup; Cai, Kejia; Nath, Kavindra; Verma, Gaurav; Nanga, Ravi Prakash Reddy; Hariharan, Hari; Detre, John A.; Epperson, Neill; Reddy, Ravinder

    2014-01-01

    Modafinil is marketed in the United States for the treatment of narcolepsy and daytime somnolence due to shift-work or sleep apnea. Investigations of this drug in the treatment of cocaine and nicotine dependence in addition to disorders of executive function are also underway. Modafinil has been known to increase glutamate levels in rat brain models. Proton magnetic resonance spectroscopy (1HMRS) has been commonly used to detect the glutamate (Glu) changes in vivo. In this study, we used a recently described glutamate chemical exchange saturation transfer (GluCEST) imaging technique to measure Modafinil induced regional Glu changes in rat brain and compared the results with Glu concentration measured by single voxel 1HMRS. No increases in either GluCEST maps or 1HMRS were observed after Modafinil injection over a period of 5 hours. However, a significant increase in GluCEST (19±4.4%) was observed 24 hours post Modafinil administration, which is consistent with results from previous biochemical studies. This change was not consistently seen with 1HMRS. GluCEST mapping allows regional cerebral Glu changes to be measured and may provide a useful clinical biomarker of Modafinil effects for the management of patients with sleep disorders and addiction. PMID:25068408

  3. High resolution mapping of modafinil induced changes in glutamate level in rat brain.

    PubMed

    Haris, Mohammad; Singh, Anup; Cai, Kejia; Nath, Kavindra; Verma, Gaurav; Nanga, Ravi Prakash Reddy; Hariharan, Hari; Detre, John A; Epperson, Neill; Reddy, Ravinder

    2014-01-01

    Modafinil is marketed in the United States for the treatment of narcolepsy and daytime somnolence due to shift-work or sleep apnea. Investigations of this drug in the treatment of cocaine and nicotine dependence in addition to disorders of executive function are also underway. Modafinil has been known to increase glutamate levels in rat brain models. Proton magnetic resonance spectroscopy (1HMRS) has been commonly used to detect the glutamate (Glu) changes in vivo. In this study, we used a recently described glutamate chemical exchange saturation transfer (GluCEST) imaging technique to measure Modafinil induced regional Glu changes in rat brain and compared the results with Glu concentration measured by single voxel 1HMRS. No increases in either GluCEST maps or 1HMRS were observed after Modafinil injection over a period of 5 hours. However, a significant increase in GluCEST (19 ± 4.4%) was observed 24 hours post Modafinil administration, which is consistent with results from previous biochemical studies. This change was not consistently seen with 1HMRS. GluCEST mapping allows regional cerebral Glu changes to be measured and may provide a useful clinical biomarker of Modafinil effects for the management of patients with sleep disorders and addiction.

  4. High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates

    PubMed Central

    Förstner, Konrad U.; Heidrich, Nadja; Reinhardt, Richard; Nieselt, Kay; Sharma, Cynthia M.

    2013-01-01

    Campylobacter jejuni is currently the leading cause of bacterial gastroenteritis in humans. Comparison of multiple Campylobacter strains revealed a high genetic and phenotypic diversity. However, little is known about differences in transcriptome organization, gene expression, and small RNA (sRNA) repertoires. Here we present the first comparative primary transcriptome analysis based on the differential RNA–seq (dRNA–seq) of four C. jejuni isolates. Our approach includes a novel, generic method for the automated annotation of transcriptional start sites (TSS), which allowed us to provide genome-wide promoter maps in the analyzed strains. These global TSS maps are refined through the integration of a SuperGenome approach that allows for a comparative TSS annotation by mapping RNA–seq data of multiple strains into a common coordinate system derived from a whole-genome alignment. Considering the steadily increasing amount of RNA–seq studies, our automated TSS annotation will not only facilitate transcriptome annotation for a wider range of pro- and eukaryotes but can also be adapted for the analysis among different growth or stress conditions. Our comparative dRNA–seq analysis revealed conservation of most TSS, but also single-nucleotide-polymorphisms (SNP) in promoter regions, which lead to strain-specific transcriptional output. Furthermore, we identified strain-specific sRNA repertoires that could contribute to differential gene regulation among strains. In addition, we identified a novel minimal CRISPR-system in Campylobacter of the type-II CRISPR subtype, which relies on the host factor RNase III and a trans-encoded sRNA for maturation of crRNAs. This minimal system of Campylobacter, which seems active in only some strains, employs a unique maturation pathway, since the crRNAs are transcribed from individual promoters in the upstream repeats and thereby minimize the requirements for the maturation machinery. Overall, our study provides new insights into

  5. Comparing Magnetic Resonance Imaging and High-Resolution Dynamic Ultrasonography for Diagnosis of Plantar Plate Pathology: A Case Series.

    PubMed

    Donegan, Ryan J; Stauffer, Anthony; Heaslet, Michael; Poliskie, Michael

    Plantar plate pathology has gained noticeable attention in recent years as an etiology of lesser metatarsophalangeal joint pain. The heightened clinical awareness has led to the need for more effective diagnostic imaging accuracy. Numerous reports have established the accuracy of both magnetic resonance imaging and ultrasonography for the diagnosis of plantar plate pathology. However, no conclusions have been made regarding which is the superior imaging modality. The present study reports a case series directly comparing high-resolution dynamic ultrasonography and magnetic resonance imaging. A multicenter retrospective comparison of magnetic resonance imaging versus high-resolution dynamic ultrasonography to evaluate plantar plate pathology with surgical confirmation was conducted. The sensitivity, specificity, and positive and negative predictive values for magnetic resonance imaging were 60%, 100%, 100%, and 33%, respectively. The overall diagnostic accuracy compared with the intraoperative findings was 66%. The sensitivity, specificity, and positive and negative predictive values for high-resolution dynamic ultrasound imaging were 100%, 100%, 100%, and 100%, respectively. The overall diagnostic accuracy compared with the intraoperative findings was 100%. The p value using Fisher's exact test for magnetic resonance imaging and high-resolution dynamic ultrasonography was p = .45, a difference that was not statistically significant. High-resolution dynamic ultrasonography had greater accuracy than magnetic resonance imaging in diagnosing lesser metatarsophalangeal joint plantar plate pathology, although the difference was not statistically significant. The present case series suggests that high-resolution dynamic ultrasonography can be considered an equally accurate imaging modality for plantar plate pathology at a potential cost savings compared with magnetic resonance imaging. Therefore, high-resolution dynamic ultrasonography warrants further investigation in

  6. High resolution mapping and classification of oyster habitats in nearshore Louisiana using sidescan sonar

    USGS Publications Warehouse

    Allen, Y.C.; Wilson, C.A.; Roberts, H.H.; Supan, J.

    2005-01-01

    Sidescan sonar holds great promise as a tool to quantitatively depict the distribution and extent of benthic habitats in Louisiana's turbid estuaries. In this study, we describe an effective protocol for acoustic sampling in this environment. We also compared three methods of classification in detail: mean-based thresholding, supervised, and unsupervised techniques to classify sidescan imagery into categories of mud and shell. Classification results were compared to ground truth results using quadrat and dredge sampling. Supervised classification gave the best overall result (kappa = 75%) when compared to quadrat results. Classification accuracy was less robust when compared to all dredge samples (kappa = 21-56%), but increased greatly (90-100%) when only dredge samples taken from acoustically homogeneous areas were considered. Sidescan sonar when combined with ground truth sampling at an appropriate scale can be effectively used to establish an accurate substrate base map for both research applications and shellfish management. The sidescan imagery presented here also provides, for the first time, a detailed presentation of oyster habitat patchiness and scale in a productive oyster growing area.

  7. Screening of genomic imbalances in glioblastoma multiforme using high-resolution comparative genomic hybridization.

    PubMed

    Vranová, Vladimíra; Necesalová, Eva; Kuglík, Petr; Cejpek, Pavel; Pesáková, Martina; Budínská, Eva; Relichová, Jirina; Veselská, Renata

    2007-02-01

    Comparative genomic hybridization (CGH) is a molecular cytogenetic technique that allows the genome-wide analysis of DNA sequence copy number differences. We applied conventional CGH and the recently developed high-resolution CGH (HR-CGH) to tumour samples from 18 patients with glioblastoma multiforme (GBM) in order to compare the sensitivity of CGH and HR-CGH in the screening of chromosomal abnormalities. The abnormalities were studied in topologically different central and peripheral tumour parts. A total of 78 different changes were observed using CGH (0-16 per tumour, median 3.5) and 154 using HR-CGH (0-21 per tumour, median 6). Using HR-CGH, losses were more frequent than gains. The representation of the most prominent changes revealed by both methods was similar and was comprised of the amplification of 7q12 and 12q13-q15, the gain of 7, 3q and 19, and the loss of 10, 9p, and 13q. However, HR-CGH detected certain other abnormalities (the loss of 6, 14q, 15q and 18q, and the gain of 19), which were rarely revealed by CGH. Using HR-CGH, the numbers and types of chromosomal changes detected in the central and peripheral parts of GBM were almost the same. The loss of chromosomes 10 and 9p and the gain of chromosomes 7 and 19 were the most frequent chromosomal alterations in both tumour parts. Our results from the GBM analysis show that HR-CGH technology can reveal new, recurrent genetic alterations involving the genes known to participate in tumorigenesis and in the progression of several human malignancies, thus allowing for a more accurate genetic characterization of these tumours.

  8. High-Resolution Comparative Genomic Hybridization of Inflammatory Breast Cancer and Identification of Candidate Genes

    PubMed Central

    Adelaïde, José; Ferrari, Anthony; Tarpin, Carole; Charafe-Jauffret, Emmanuelle; Charpin, Colette; Houvenaeghel, Gilles; Jacquemier, Jocelyne; Bidaut, Ghislain; Birnbaum, Daniel; Viens, Patrice; Chaffanet, Max; Bertucci, François

    2011-01-01

    Background Inflammatory breast cancer (IBC) is an aggressive form of BC poorly defined at the molecular level. We compared the molecular portraits of 63 IBC and 134 non-IBC (nIBC) clinical samples. Methodology/Findings Genomic imbalances of 49 IBCs and 124 nIBCs were determined using high-resolution array-comparative genomic hybridization, and mRNA expression profiles of 197 samples using whole-genome microarrays. Genomic profiles of IBCs were as heterogeneous as those of nIBCs, and globally relatively close. However, IBCs showed more frequent “complex” patterns and a higher percentage of genes with CNAs per sample. The number of altered regions was similar in both types, although some regions were altered more frequently and/or with higher amplitude in IBCs. Many genes were similarly altered in both types; however, more genes displayed recurrent amplifications in IBCs. The percentage of genes whose mRNA expression correlated with CNAs was similar in both types for the gained genes, but ∼7-fold lower in IBCs for the lost genes. Integrated analysis identified 24 potential candidate IBC-specific genes. Their combined expression accurately distinguished IBCs and nIBCS in an independent validation set, and retained an independent prognostic value in a series of 1,781 nIBCs, reinforcing the hypothesis for a link with IBC aggressiveness. Consistent with the hyperproliferative and invasive phenotype of IBC these genes are notably involved in protein translation, cell cycle, RNA processing and transcription, metabolism, and cell migration. Conclusions Our results suggest a higher genomic instability of IBC. We established the first repertory of DNA copy number alterations in this tumor, and provided a list of genes that may contribute to its aggressiveness and represent novel therapeutic targets. PMID:21339811

  9. A high resolution genetic map anchoring scaffolds of the sequenced watermelon genome

    USDA-ARS?s Scientific Manuscript database

    As part of our ongoing efforts to sequence and map the watermelon (Citrullus spp.) genome, we have constructed a high-density genetic linkage map. The map positioned 234 watermelon genome sequence scaffolds (an average size of 1.41 Mb) that cover about 330 Mb and account for 93.5% of the 353 Mb of ...

  10. High resolution coherence domain depth-resolved nailfold capillaroscopy based on correlation mapping optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Subhash, Hrebesh M.; O'Gorman, Sean; Neuhaus, Kai; Leahy, Martin

    2014-03-01

    In this paper we demonstrate a novel application of correlation mapping optical coherence tomography (cm-OCT) for volumetric nailfold capillaroscopy (NFC). NFC is a widely used non-invasive diagnostic method to analyze capillary morphology and microvascular abnormalities of nailfold area for a range of disease conditions. However, the conventional NFC is incapable of providing volumetric imaging, when volumetric quantitative microangiopathic parameters such as plexus morphology, capillary density, and morphologic anomalies of the end row loops most critical. cm-OCT is a recently developed well established coherence domain magnitude based angiographic modality, which takes advantage of the time-varying speckle effect, which is normally dominant in the vicinity of vascular regions compared to static tissue region. It utilizes the correlation coefficient as a direct measurement of decorrelation between two adjacent B-frames to enhance the visibility of depth-resolved microcirculation.

  11. Exceptional conservation of horse-human gene order on X chromosome revealed by high-resolution radiation hybrid mapping.

    PubMed

    Raudsepp, Terje; Lee, Eun-Joon; Kata, Srinivas R; Brinkmeyer, Candice; Mickelson, James R; Skow, Loren C; Womack, James E; Chowdhary, Bhanu P

    2004-02-24

    Development of a dense map of the horse genome is key to efforts aimed at identifying genes controlling health, reproduction, and performance. We herein report a high-resolution gene map of the horse (Equus caballus) X chromosome (ECAX) generated by developing and typing 116 gene-specific and 12 short tandem repeat markers on the 5,000-rad horse x hamster whole-genome radiation hybrid panel and mapping 29 gene loci by fluorescence in situ hybridization. The human X chromosome sequence was used as a template to select genes at 1-Mb intervals to develop equine orthologs. Coupled with our previous data, the new map comprises a total of 175 markers (139 genes and 36 short tandem repeats, of which 53 are fluorescence in situ hybridization mapped) distributed on average at approximately 880-kb intervals along the chromosome. This is the densest and most uniformly distributed chromosomal map presently available in any mammalian species other than humans and rodents. Comparison of the horse and human X chromosome maps shows remarkable conservation of gene order along the entire span of the chromosomes, including the location of the centromere. An overview of the status of the horse map in relation to mouse, livestock, and companion animal species is also provided. The map will be instrumental for analysis of X linked health and fertility traits in horses by facilitating identification of targeted chromosomal regions for isolation of polymorphic markers, building bacterial artificial chromosome contigs, or sequencing.

  12. A high-resolution linkage map of human 9q34. 1

    SciTech Connect

    Henske, E.P.; Kwiatkowski, D.J. ); Ozelius, L.; Gusella, J.F.; Haines, J.L. )

    1993-09-01

    A map comprising 16 distinct markers with heterozygosities of 0.61-0.92 for a 10-cM region of human 9q34.1 is presented. The map incorporates four genes and has a maximum intermarker interval of 2.1 cM. Markers were analyzed in the Venezuelan reference pedigrees and all were placed uniquely in the map with a minimum likelihood of 676:1. The map should prove useful in analysis of families segregating dystonia and tuberous sclerosis, as the DYT1 and TSC1 loci map within this region. 18 refs., 2 figs., 2 tabs.

  13. Surface Temperature Mapping of the University of Northern Iowa Campus Using High Resolution Thermal Infrared Aerial Imageries.

    PubMed

    Savelyev, Alexander; Sugumaran, Ramanathan

    2008-08-25

    The goal of this project was to map the surface temperature of the University of Northern Iowa campus using high-resolution thermal infrared aerial imageries. A thermal camera with a spectral bandwidth of 3.0-5.0 μm was flown at the average altitude of 600 m, achieving ground resolution of 29 cm. Ground control data was used to construct the pixelto-temperature conversion model, which was later used to produce temperature maps of the entire campus and also for validation of the model. The temperature map then was used to assess the building rooftop conditions and steam line faults in the study area. Assessment of the temperature map revealed a number of building structures that may be subject to insulation improvement due to their high surface temperatures leaks. Several hot spots were also identified on the campus for steam pipelines faults. High-resolution thermal infrared imagery proved highly effective tool for precise heat anomaly detection on the campus, and it can be used by university facility services for effective future maintenance of buildings and grounds.

  14. A high-resolution linkage map of the vicinity of the rice submergence tolerance locus Sub1.

    PubMed

    Xu, K; Xu, X; Ronald, P C; Mackill, D J

    2000-05-01

    Resistance to submergence stress is an important breeding objective in areas where rice cultivars are subjected to complete inundation for a week or more. The present study was conducted to develop a high-resolution map of the region surrounding the submergence tolerance gene Sub1 in rice, which derives from the Indian cultivar FR13A. Submergence screening of 8-day-old plants of F3 families kept for 14 days submerged in 60 cm of water allowed an accurate classification of Sub1 phenotypes. Bulked segregant analysis was used to identify AFLP markers linked to Sub1. A population of 2950 F2 plants segregating for Sub1 was screened with two RFLP markers flanking the Sub1 locus, 2.4 and 4.9 cM away. Submergence tolerance was measured in the recombinant plants, and AFLP markers closely linked to Sub1 were mapped. Two AFLP markers cosegregated with Sub1 in this large population, and other markers were localized within 0.2 cM of Sub1. The high-resolution map should serve as the basis for map-based cloning of this important locus, as it will permit the identification of BAC clones spanning the region.

  15. High-resolution tree canopy mapping for New York City using LIDAR and object-based image analysis

    NASA Astrophysics Data System (ADS)

    MacFaden, Sean W.; O'Neil-Dunne, Jarlath P. M.; Royar, Anna R.; Lu, Jacqueline W. T.; Rundle, Andrew G.

    2012-01-01

    Urban tree canopy is widely believed to have myriad environmental, social, and human-health benefits, but a lack of precise canopy estimates has hindered quantification of these benefits in many municipalities. This problem was addressed for New York City using object-based image analysis (OBIA) to develop a comprehensive land-cover map, including tree canopy to the scale of individual trees. Mapping was performed using a rule-based expert system that relied primarily on high-resolution LIDAR, specifically its capacity for evaluating the height and texture of aboveground features. Multispectral imagery was also used, but shadowing and varying temporal conditions limited its utility. Contextual analysis was a key part of classification, distinguishing trees according to their physical and spectral properties as well as their relationships to adjacent, nonvegetated features. The automated product was extensively reviewed and edited via manual interpretation, and overall per-pixel accuracy of the final map was 96%. Although manual editing had only a marginal effect on accuracy despite requiring a majority of project effort, it maximized aesthetic quality and ensured the capture of small, isolated trees. Converting high-resolution LIDAR and imagery into usable information is a nontrivial exercise, requiring significant processing time and labor, but an expert system-based combination of OBIA and manual review was an effective method for fine-scale canopy mapping in a complex urban environment.

  16. Surface Temperature Mapping of the University of Northern Iowa Campus Using High Resolution Thermal Infrared Aerial Imageries

    PubMed Central

    Savelyev, Alexander; Sugumaran, Ramanathan

    2008-01-01

    The goal of this project was to map the surface temperature of the University of Northern Iowa campus using high-resolution thermal infrared aerial imageries. A thermal camera with a spectral bandwidth of 3.0-5.0 μm was flown at the average altitude of 600 m, achieving ground resolution of 29 cm. Ground control data was used to construct the pixel- to-temperature conversion model, which was later used to produce temperature maps of the entire campus and also for validation of the model. The temperature map then was used to assess the building rooftop conditions and steam line faults in the study area. Assessment of the temperature map revealed a number of building structures that may be subject to insulation improvement due to their high surface temperatures leaks. Several hot spots were also identified on the campus for steam pipelines faults. High-resolution thermal infrared imagery proved highly effective tool for precise heat anomaly detection on the campus, and it can be used by university facility services for effective future maintenance of buildings and grounds. PMID:27873800

  17. A comparative verification of high resolution precipitation forecasts using model output statistics

    NASA Astrophysics Data System (ADS)

    van der Plas, Emiel; Schmeits, Maurice; Hooijman, Nicolien; Kok, Kees

    2017-04-01

    Verification of localized events such as precipitation has become even more challenging with the advent of high-resolution meso-scale numerical weather prediction (NWP). The realism of a forecast suggests that it should compare well against precipitation radar imagery with similar resolution, both spatially and temporally. Spatial verification methods solve some of the representativity issues that point verification gives rise to. In this study a verification strategy based on model output statistics is applied that aims to address both double penalty and resolution effects that are inherent to comparisons of NWP models with different resolutions. Using predictors based on spatial precipitation patterns around a set of stations, an extended logistic regression (ELR) equation is deduced, leading to a probability forecast distribution of precipitation for each NWP model, analysis and lead time. The ELR equations are derived for predictands based on areal calibrated radar precipitation and SYNOP observations. The aim is to extract maximum information from a series of precipitation forecasts, like a trained forecaster would. The method is applied to the non-hydrostatic model Harmonie (2.5 km resolution), Hirlam (11 km resolution) and the ECMWF model (16 km resolution), overall yielding similar Brier skill scores for the 3 post-processed models, but larger differences for individual lead times. Besides, the Fractions Skill Score is computed using the 3 deterministic forecasts, showing somewhat better skill for the Harmonie model. In other words, despite the realism of Harmonie precipitation forecasts, they only perform similarly or somewhat better than precipitation forecasts from the 2 lower resolution models, at least in the Netherlands.

  18. High-Resolution Mapping of Lunar Crustal Magnetic Fields: Correlations with Albedo Markings of the Reiner Gamma Class

    NASA Technical Reports Server (NTRS)

    Hood, L. L.; Yingst, A.; Mitchell, D. L.; Lin, R. P.; Acuna, M.; Binder, A.

    1999-01-01

    During the last eight months of the Lunar Prospector mission (December 1999-July 1999), the spacecraft was placed in a relatively low-altitude (15-30-km perapsis), near-polar orbit that allowed high-resolution mapping of crustal magnetic fields. We report here initial studies of the correlation of locally strong magnetic anomalies with unusual, swirl-like albedo markings of the Reiner Gamma class. Based on this correlation, which is known from earlier studies of Apollo subsatellite magnetometer data, it has been proposed that the swirls represent regions whose higher albedos have been preserved via deflection of the solar-wind ion bombardment by strong crustal fields. This model in turn depends on the hypothesis that solar-wind implanted H is at least one component of the process that optically matures exposed silicate surfaces in the inner solar system . Specifically, it is hypothesized that implanted H acts as an effective reducing agent to enhance the rate of production of nanophase metallic Fe particles from preexisting silicates during micrometeoroid impacts. According to the model, the curvilinear shapes of these albedo markings are caused, at least in part, by the geometry of ion deflections in a magnetic field. The improved resolution and coverage of the Prospector data allow more detailed mapping of the fields, especially on the lunar farside. This permits a more quantitative test of whether all albedo markings of this class are associated with strong local magnetic fields.Only if the latter condition is met can the solar-wind deflection hypothesis he valid. The basic procedure for mapping crustal magnetic fields using Lunar Prospector magnetometer data follows that developed for analysis of Apollo subsatellite magnetometer data. The specific mapping steps are (1) selection of mission time intervals suitable for mapping crustal fields; these are limited essentially either to times when the Moon is in a lobe of the geomagnetic tail or to times when the Moon

  19. High-Resolution Mapping of Lunar Crustal Magnetic Fields: Correlations with Albedo Markings of the Reiner Gamma Class

    NASA Technical Reports Server (NTRS)

    Hood, L. L.; Yingst, A.; Mitchell, D. L.; Lin, R. P.; Acuna, M.; Binder, A.

    1999-01-01

    During the last eight months of the Lunar Prospector mission (December 1999-July 1999), the spacecraft was placed in a relatively low-altitude (15-30-km perapsis), near-polar orbit that allowed high-resolution mapping of crustal magnetic fields. We report here initial studies of the correlation of locally strong magnetic anomalies with unusual, swirl-like albedo markings of the Reiner Gamma class. Based on this correlation, which is known from earlier studies of Apollo subsatellite magnetometer data, it has been proposed that the swirls represent regions whose higher albedos have been preserved via deflection of the solar-wind ion bombardment by strong crustal fields. This model in turn depends on the hypothesis that solar-wind implanted H is at least one component of the process that optically matures exposed silicate surfaces in the inner solar system . Specifically, it is hypothesized that implanted H acts as an effective reducing agent to enhance the rate of production of nanophase metallic Fe particles from preexisting silicates during micrometeoroid impacts. According to the model, the curvilinear shapes of these albedo markings are caused, at least in part, by the geometry of ion deflections in a magnetic field. The improved resolution and coverage of the Prospector data allow more detailed mapping of the fields, especially on the lunar farside. This permits a more quantitative test of whether all albedo markings of this class are associated with strong local magnetic fields.Only if the latter condition is met can the solar-wind deflection hypothesis he valid. The basic procedure for mapping crustal magnetic fields using Lunar Prospector magnetometer data follows that developed for analysis of Apollo subsatellite magnetometer data. The specific mapping steps are (1) selection of mission time intervals suitable for mapping crustal fields; these are limited essentially either to times when the Moon is in a lobe of the geomagnetic tail or to times when the Moon

  20. A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification

    PubMed Central

    Fulop, Daniel; Ranjan, Aashish; Ofner, Itai; Covington, Michael F.; Chitwood, Daniel H.; West, Donelly; Ichihashi, Yasunori; Headland, Lauren; Zamir, Daniel; Maloof, Julin N.; Sinha, Neelima R.

    2016-01-01

    Quantitative Trait Loci (QTL) mapping is a powerful technique for dissecting the genetic basis of traits and species differences. Established tomato mapping populations between domesticated tomato (Solanum lycopersicum) and its more distant interfertile relatives typically follow a near isogenic line (NIL) design, such as the S. pennellii Introgression Line (IL) population, with a single wild introgression per line in an otherwise domesticated genetic background. Here, we report on a new advanced backcross QTL mapping resource for tomato, derived from a cross between the M82 tomato cultivar and S. pennellii. This so-called Backcrossed Inbred Line (BIL) population is comprised of a mix of BC2 and BC3 lines, with domesticated tomato as the recurrent parent. The BIL population is complementary to the existing S. pennellii IL population, with which it shares parents. Using the BILs, we mapped traits for leaf complexity, leaflet shape, and flowering time. We demonstrate the utility of the BILs for fine-mapping QTL, particularly QTL initially mapped in the ILs, by fine-mapping several QTL to single or few candidate genes. Moreover, we confirm the value of a backcrossed population with multiple introgressions per line, such as the BILs, for epistatic QTL mapping. Our work was further enabled by the development of our own statistical inference and visualization tools, namely a heterogeneous hidden Markov model for genotyping the lines, and by using state-of-the-art sparse regression techniques for QTL mapping. PMID:27510891

  1. From maps to movies: High resolution time-varying sensitivity analysis for spatially distributed watershed models

    NASA Astrophysics Data System (ADS)

    Herman, J. D.; Kollat, J. B.; Reed, P. M.; Wagener, T.

    2013-12-01

    Distributed watershed models are now widely used in practice to simulate runoff responses at high spatial and temporal resolutions. Counter to this purpose, diagnostic analyses of distributed models currently aggregate performance measures in space and/or time and are thus disconnected from the models' operational and scientific goals. To address this disconnect, this study contributes a novel approach for computing and visualizing time-varying global sensitivity indices for spatially distributed model parameters. The high-resolution model diagnostics employ the method of Morris to identify evolving patterns in dominant model processes at sub-daily timescales over a six-month period. The method is demonstrated on the United States National Weather Service's Hydrology Laboratory Research Distributed Hydrologic Model (HL-RDHM) in the Blue River watershed, Oklahoma, USA. Three hydrologic events are selected from within the six-month period to investigate the patterns in spatiotemporal sensitivities that emerge as a function of forcing patterns as well as wet-to-dry transitions. Surprisingly, events with similar magnitudes and durations exhibit significantly different performance controls in space and time, indicating that the diagnostic inferences drawn from representative events will be heavily biased by the a priori selection of those events. By contrast, this study demonstrates high-resolution time-varying sensitivity analysis, requiring no assumptions regarding representative events and allowing modelers to identify transitions between modeled hydrologic regimes a posteriori. The proposed approach details the dynamics of parameter sensitivity in nearly continuous time, providing critical diagnostic insights into the underlying model processes driving predictions. Furthermore, the approach offers the potential to identify transition points between hydrologic regimes under nonstationarity.

  2. From maps to movies: high resolution time-varying sensitivity analysis for spatially distributed watershed models

    NASA Astrophysics Data System (ADS)

    Herman, J. D.; Kollat, J. B.; Reed, P. M.; Wagener, T.

    2013-08-01

    Distributed watershed models are now widely used in practice to simulate runoff responses at high spatial and temporal resolutions. Counter to this purpose, diagnostic analyses of distributed models currently aggregate performance measures in space and/or time and are thus disconnected from the models' operational and scientific goals. To address this disconnect, this study contributes a novel approach for computing and visualizing time-varying global sensitivity indices for spatially distributed model parameters. The high-resolution model diagnostics employ the method of Morris to identify evolving patterns in dominant model processes at sub-daily timescales over a six-month period. The method is demonstrated on the United States National Weather Service's Hydrology Laboratory Research Distributed Hydrologic Model (HL-RDHM) in the Blue River watershed, Oklahoma, USA. Three hydrologic events are selected from within the six-month period to investigate the patterns in spatiotemporal sensitivities that emerge as a function of forcing patterns as well as wet-to-dry transitions. Surprisingly, events with similar magnitudes and durations exhibit significantly different performance controls in space and time, indicating that the diagnostic inferences drawn from representative events will be heavily biased by the a priori selection of those events. By contrast, this study demonstrates high-resolution time-varying sensitivity analysis, requiring no assumptions regarding representative events and allowing modelers to identify transitions between modeled hydrologic regimes a posteriori. The proposed approach details the dynamics of parameter sensitivity in nearly continuous time, providing critical diagnostic insights into the underlying model processes driving predictions. Furthermore, the approach offers the potential to identify transition points between hydrologic regimes under nonstationarity.

  3. Satellite-based high-resolution mapping of rainfall over southern Africa

    NASA Astrophysics Data System (ADS)

    Meyer, Hanna; Drönner, Johannes; Nauss, Thomas

    2017-06-01

    A spatially explicit mapping of rainfall is necessary for southern Africa for eco-climatological studies or nowcasting but accurate estimates are still a challenging task. This study presents a method to estimate hourly rainfall based on data from the Meteosat Second Generation (MSG) Spinning Enhanced Visible and Infrared Imager (SEVIRI). Rainfall measurements from about 350 weather stations from 2010-2014 served as ground truth for calibration and validation. SEVIRI and weather station data were used to train neural networks that allowed the estimation of rainfall area and rainfall quantities over all times of the day. The results revealed that 60 % of recorded rainfall events were correctly classified by the model (probability of detection, POD). However, the false alarm ratio (FAR) was high (0.80), leading to a Heidke skill score (HSS) of 0.18. Estimated hourly rainfall quantities were estimated with an average hourly correlation of ρ = 0. 33 and a root mean square error (RMSE) of 0.72. The correlation increased with temporal aggregation to 0.52 (daily), 0.67 (weekly) and 0.71 (monthly). The main weakness was the overestimation of rainfall events. The model results were compared to the Integrated Multi-satellitE Retrievals for GPM (IMERG) of the Global Precipitation Measurement (GPM) mission. Despite being a comparably simple approach, the presented MSG-based rainfall retrieval outperformed GPM IMERG in terms of rainfall area detection: GPM IMERG had a considerably lower POD. The HSS was not significantly different compared to the MSG-based retrieval due to a lower FAR of GPM IMERG. There were no further significant differences between the MSG-based retrieval and GPM IMERG in terms of correlation with the observed rainfall quantities. The MSG-based retrieval, however, provides rainfall in a higher spatial resolution. Though estimating rainfall from satellite data remains challenging, especially at high temporal resolutions, this study showed promising results

  4. High-resolution forest mapping for behavioural studies in the Nature Reserve ‘Les Nouragues’, French Guiana

    PubMed Central

    Ringler, Max; Mangione, Rosanna; Pašukonis, Andrius; Rainer, Gerhard; Gyimesi, Kristin; Felling, Julia; Kronaus, Hannes; Réjou-Méchain, Maxime; Chave, Jérôme; Reiter, Karl; Ringler, Eva

    2015-01-01

    For animals with spatially complex behaviours at relatively small scales, the resolution of a global positioning system (GPS) receiver location is often below the resolution needed to correctly map animals’ spatial behaviour. Natural conditions such as canopy cover, canyons or clouds can further degrade GPS receiver reception. Here we present a detailed, high-resolution map of a 4.6 ha Neotropical river island and a 8.3 ha mainland plot with the location of every tree >5 cm DBH and all structures on the forest floor, which are relevant to our study species, the territorial frog Allobates femoralis (Dendrobatidae). The map was derived using distance- and compass-based survey techniques, rooted on dGPS reference points, and incorporates altitudinal information based on a LiDAR survey of the area. PMID:27053943

  5. Objective landslide detection and surface morphology mapping using high-resolution airborne laser altimetry

    Treesearch

    J. McKean; J. Roering

    2004-01-01

    A map of extant slope failures is the most basic element of any landslide assessment. Without an accurate inventory of slope instability, it is not possible to analyze the controls on the spatial and temporal patterns of mass movement or the environmental, human, or geomorphic consequences of slides. Landslide inventory maps are tedious to compile, difficult to make in...

  6. Combining Proximal and Penetrating Soil Electrical Conductivity Sensors for High Resolution Digital Soil Mapping

    USDA-ARS?s Scientific Manuscript database

    Proximal ground conductivity sensors produce high spatial resolution maps that integrate the bulk electrical conductivity (ECa) of the soil profile. Variability in conductivity maps must either be inverted to profile conductivity, or be directly calibrated to profile properties for meaningful interp...

  7. High-precision three-dimensional field mapping of a high resolution magnetic spectrometer for hypernuclear spectroscopy at JLab

    SciTech Connect

    Fujii, Yuu; Hashimoto, Osamu; Miyoshi, Toshinobu; Nakamura, Satoshi N.; Ohtani, Atsushi; Okayasu, Yuichi; Oyamada, Masamichi; Yamamoto, Yosuke; Kato, Seigo; Matsui, Jumei; Sako, Katsuhisa; Brindza, Paul

    2015-09-01

    The High Resolution Kaon Spectrometer (HKS), which consists of two quadrupole magnets and one dipole magnet, was designed and constructed for high-resolution spectroscopy of hypernuclei using the (e,e'K+) reaction in Hall C, Jefferson Lab (JLab). It was used to analyze momenta of around 1.2 GeV/c K^+ s with a resolution of 2 ×10^-4 (FWHM). To achieve the target resolution, a full three-dimensional magnetic field measurement of each magnet was successfully performed, and a full three-dimensional magnetic field map of the HKS magnets was reconstructed. Using the measured field map, the initial reconstruction function was generated. The target resolution would be achieved via careful tuning of the reconstruction function of HKS with the p(e,e'K+)Lambda,Sigma^0 and C-12 (e,e'K+)12_Lambda B_g.s. reactions. After tuning of the initial reconstruction function generated from the measured map, the estimated HKS momentum resolution was 2.2×10^-4 (FWHM).

  8. High-resolution three-dimensional quantitative map of the macromolecular proton fraction distribution in the normal rat brain.

    PubMed

    Naumova, Anna V; Akulov, Andrey E; Khodanovich, Marina Yu; Yarnykh, Vasily L

    2017-02-01

    The presented dataset provides a normative high-resolution three-dimensional (3D) macromolecular proton fraction (MPF) map of the healthy rat brain in vivo and source images used for its reconstruction. The images were acquired using the protocol described elsewhere (Naumova, et al. High-resolution three-dimensional macromolecular proton fraction mapping for quantitative neuroanatomical imaging of the rodent brain in ultra-high magnetic fields. Neuroimage (2016) doi: 10.1016/j.neuroimage.2016.09.036). The map was reconstructed from three source images with different contrast weightings (proton density, T1, and magnetization transfer) using the single-point algorithm with a synthetic reference image. Source images were acquired from a living animal on an 11.7 T small animal MRI scanner with isotropic spatial resolution of 170 µm(3) and total acquisition time about 1.5 h. The 3D dataset can be used for multiple purposes including interactive viewing of rat brain anatomy, measurements of reference MPF values in various brain structures, and development of image processing techniques for the rodent brain segmentation. It also can serve as a gold standard image for implementation and optimization of rodent brain MRI protocols.

  9. Portable Piezospectroscopy system: non-contact in-situ stress sensing through high resolution photo-luminescent mapping

    NASA Astrophysics Data System (ADS)

    Hanhan, I.; Durnberg, E.; Freihofer, G.; Akin, P.; Raghavan, S.

    2014-11-01

    Through the piezospectroscopic effect, certain photo-luminescent materials, once excited with a laser, produce spectral emissions which are sensitive to the stress or strain that the material experiences. A system that utilizes the piezospectroscopic effect for non-contact stress detection over a material's surface can capture important information on the evolution of mechanical response under various conditions. Therefore, the components necessary for piezospectroscopic mapping and analysis have now been integrated into a versatile and transportable system that can be used with photo-luminescent materials in any load frame or on a variety of structures. This system combines compact hardware components such as a portable laser source, fiber optics, spectrograph, charge-coupled device (CCD), and an X-Y-Z stage (with focusing capabilities) with a series of data analysis algorithms capable of analyzing and outputting high resolution photo-luminescent (PL) maps on-site. Through a proof of concept experiment using a compressed polycrystalline alumina sample with sharp machined corners, this system successfully captured high resolution PL maps with a step size of 28.86μm/pixel and located high stress concentrations in critical areas, which correlated closely with the results of a finite element model. This work represents an important step in advancing the portability of piezospectroscopy for in-situ and non-contact stress detection. The instrumentation developed here has strong implications for the future of non-destructive evaluation and non-invasive structural health monitoring.

  10. High-Resolution Cytogenetic Map for the African Malaria Vector Anopheles gambiae

    PubMed Central

    George, Phillip; Sharakhova, Maria V.; Sharakhov, Igor V.

    2010-01-01

    Cytogenetic and physical maps are indispensible for precise assembly of genome sequences, functional characterization of chromosomal regions, and population genetic and taxonomic studies. We have created a new cytogenetic map for Anopheles gambiae by using a high-pressure squash technique that increases overall band clarity. To link chromosomal regions to the genome sequence, we attached genome coordinates, based on 302 markers of BAC, cDNA clones, and PCR-amplified gene fragments, to the chromosomal bands and interbands at approximately a 0.5-1 Mb interval. In addition, we placed the breakpoints of seven common polymorphic inversions on the map and described the chromosomal landmarks for the arm and inversion identification. The map's improved resolution can be used to further enhance physical mapping, improve genome assembly, and stimulate epigenomic studies of malaria vectors. PMID:20609021

  11. 3-Dimentional Mapping Coastal Zone using High Resolution Satellite Stereo Imageries

    NASA Astrophysics Data System (ADS)

    Hong, Zhonghua; Liu, Fengling; Zhang, Yun

    2014-03-01

    The metropolitan coastal zone mapping is critical for coastal resource management, coastal environmental protection, and coastal sustainable development and planning. The results of geometric processing of a Shanghai coastal zone from 0.7-m-resolution QuickBird Geo stereo images are presented firstly. The geo-positioning accuracy of ground point determination with vendor-provided rigorous physical model (RPM) parameters is evaluated and systematic errors are found when compared with ground control points surveyed by GPS real-time kinematic (GPS-RTK) with 5cm accuracy. A bias-compensation process in image space that applies a RPM bundle adjustment to the RPM-calculated 3D ground points to correct the systematic errors is used to improve the geo-positioning accuracy. And then, a area-based matching (ABM) method is used to generated the densely corresponding points of left and right QuickBird images. With the densely matching points, the 3-dimentinal coordinates of ground points can be calculated by using the refined geometric relationship between image and ground points. At last step, digital surface model (DSM) can be achieved automatically using interpolation method. Accuracies of the DSM as assessed from independent checkpoints (ICPs) are approximately 1.2 m in height.

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

    NASA Astrophysics Data System (ADS)

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

    2017-06-01

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

  13. A High-Resolution Map of Segmental DNA Copy Number Variation in the Mouse Genome

    PubMed Central

    Graubert, Timothy A; Selzer, Rebecca R; Richmond, Todd A; Eis, Peggy S; Shannon, William D; Li, Xia; McLeod, Howard L; Cheverud, James M; Ley, Timothy J

    2007-01-01

    Submicroscopic (less than 2 Mb) segmental DNA copy number changes are a recently recognized source of genetic variability between individuals. The biological consequences of copy number variants (CNVs) are largely undefined. In some cases, CNVs that cause gene dosage effects have been implicated in phenotypic variation. CNVs have been detected in diverse species, including mice and humans. Published studies in mice have been limited by resolution and strain selection. We chose to study 21 well-characterized inbred mouse strains that are the focus of an international effort to measure, catalog, and disseminate phenotype data. We performed comparative genomic hybridization using long oligomer arrays to characterize CNVs in these strains. This technique increased the resolution of CNV detection by more than an order of magnitude over previous methodologies. The CNVs range in size from 21 to 2,002 kb. Clustering strains by CNV profile recapitulates aspects of the known ancestry of these strains. Most of the CNVs (77.5%) contain annotated genes, and many (47.5%) colocalize with previously mapped segmental duplications in the mouse genome. We demonstrate that this technique can identify copy number differences associated with known polymorphic traits. The phenotype of previously uncharacterized strains can be predicted based on their copy number at these loci. Annotation of CNVs in the mouse genome combined with sequence-based analysis provides an important resource that will help define the genetic basis of complex traits. PMID:17206864

  14. High-resolution mapping of nonuniform carrier transport at contacts to polycrystalline CdTe/CdS solar cells

    NASA Astrophysics Data System (ADS)

    Sutter, P.; Sutter, E.; Ohno, T. R.

    2004-03-01

    We demonstrate a spectroscopic technique based on scanning tunneling microscopy that provides high-resolution maps of local carrier transport across contacts to polycrystalline thin-film solar cells. Using this technique, preferential transport channels across a p+-ZnTe/p-CdTe back contact of a p-CdTe/n-CdS solar cell are imaged with 20 nm spatial resolution. Transport across this contact is highly nonuniform. Large areas of high resistance coexist with nanoscale low-resistance regions that are strongly correlated with grain boundaries in the CdTe absorber. These results suggest an important role of grain boundaries as near-contact conducting channels.

  15. Comparing supervised and unsupervised multiresolution segmentation approaches for extracting buildings from very high resolution imagery

    NASA Astrophysics Data System (ADS)

    Belgiu, Mariana; ǎguţ, Lucian, , Dr

    2014-10-01

    Although multiresolution segmentation (MRS) is a powerful technique for dealing with very high resolution imagery, some of the image objects that it generates do not match the geometries of the target objects, which reduces the classification accuracy. MRS can, however, be guided to produce results that approach the desired object geometry using either supervised or unsupervised approaches. Although some studies have suggested that a supervised approach is preferable, there has been no comparative evaluation of these two approaches. Therefore, in this study, we have compared supervised and unsupervised approaches to MRS. One supervised and two unsupervised segmentation methods were tested on three areas using QuickBird and WorldView-2 satellite imagery. The results were assessed using both segmentation evaluation methods and an accuracy assessment of the resulting building classifications. Thus, differences in the geometries of the image objects and in the potential to achieve satisfactory thematic accuracies were evaluated. The two approaches yielded remarkably similar classification results, with overall accuracies ranging from 82% to 86%. The performance of one of the unsupervised methods was unexpectedly similar to that of the supervised method; they identified almost identical scale parameters as being optimal for segmenting buildings, resulting in very similar geometries for the resulting image objects. The second unsupervised method produced very different image objects from the supervised method, but their classification accuracies were still very similar. The latter result was unexpected because, contrary to previously published findings, it suggests a high degree of independence between the segmentation results and classification accuracy. The results of this study have two important implications. The first is that object-based image analysis can be automated without sacrificing classification accuracy, and the second is that the previously accepted idea

  16. Comparing supervised and unsupervised multiresolution segmentation approaches for extracting buildings from very high resolution imagery.

    PubMed

    Belgiu, Mariana; Dr Guţ, Lucian

    2014-10-01

    Although multiresolution segmentation (MRS) is a powerful technique for dealing with very high resolution imagery, some of the image objects that it generates do not match the geometries of the target objects, which reduces the classification accuracy. MRS can, however, be guided to produce results that approach the desired object geometry using either supervised or unsupervised approaches. Although some studies have suggested that a supervised approach is preferable, there has been no comparative evaluation of these two approaches. Therefore, in this study, we have compared supervised and unsupervised approaches to MRS. One supervised and two unsupervised segmentation methods were tested on three areas using QuickBird and WorldView-2 satellite imagery. The results were assessed using both segmentation evaluation methods and an accuracy assessment of the resulting building classifications. Thus, differences in the geometries of the image objects and in the potential to achieve satisfactory thematic accuracies were evaluated. The two approaches yielded remarkably similar classification results, with overall accuracies ranging from 82% to 86%. The performance of one of the unsupervised methods was unexpectedly similar to that of the supervised method; they identified almost identical scale parameters as being optimal for segmenting buildings, resulting in very similar geometries for the resulting image objects. The second unsupervised method produced very different image objects from the supervised method, but their classification accuracies were still very similar. The latter result was unexpected because, contrary to previously published findings, it suggests a high degree of independence between the segmentation results and classification accuracy. The results of this study have two important implications. The first is that object-based image analysis can be automated without sacrificing classification accuracy, and the second is that the previously accepted idea

  17. Comparing Individual Tree Segmentation Based on High Resolution Multispectral Image and Lidar Data

    NASA Astrophysics Data System (ADS)

    Xiao, P.; Kelly, M.; Guo, Q.

    2014-12-01

    This study compares the use of high-resolution multispectral WorldView images and high density Lidar data for individual tree segmentation. The application focuses on coniferous and deciduous forests in the Sierra Nevada Mountains. The tree objects are obtained in two ways: a hybrid region-merging segmentation method with multispectral images, and a top-down and bottom-up region-growing method with Lidar data. The hybrid region-merging method is used to segment individual tree from multispectral images. It integrates the advantages of global-oriented and local-oriented region-merging strategies into a unified framework. The globally most-similar pair of regions is used to determine the starting point of a growing region. The merging iterations are constrained within the local vicinity, thus the segmentation is accelerated and can reflect the local context. The top-down region-growing method is adopted in coniferous forest to delineate individual tree from Lidar data. It exploits the spacing between the tops of trees to identify and group points into a single tree based on simple rules of proximity and likely tree shape. The bottom-up region-growing method based on the intensity and 3D structure of Lidar data is applied in deciduous forest. It segments tree trunks based on the intensity and topological relationships of the points, and then allocate other points to exact tree crowns according to distance. The accuracies for each method are evaluated with field survey data in several test sites, covering dense and sparse canopy. Three types of segmentation results are produced: true positive represents a correctly segmented individual tree, false negative represents a tree that is not detected and assigned to a nearby tree, and false positive represents that a point or pixel cluster is segmented as a tree that does not in fact exist. They respectively represent correct-, under-, and over-segmentation. Three types of index are compared for segmenting individual tree

  18. Comparing supervised and unsupervised multiresolution segmentation approaches for extracting buildings from very high resolution imagery

    PubMed Central

    Belgiu, Mariana; Drǎguţ, Lucian

    2014-01-01

    Although multiresolution segmentation (MRS) is a powerful technique for dealing with very high resolution imagery, some of the image objects that it generates do not match the geometries of the target objects, which reduces the classification accuracy. MRS can, however, be guided to produce results that approach the desired object geometry using either supervised or unsupervised approaches. Although some studies have suggested that a supervised approach is preferable, there has been no comparative evaluation of these two approaches. Therefore, in this study, we have compared supervised and unsupervised approaches to MRS. One supervised and two unsupervised segmentation methods were tested on three areas using QuickBird and WorldView-2 satellite imagery. The results were assessed using both segmentation evaluation methods and an accuracy assessment of the resulting building classifications. Thus, differences in the geometries of the image objects and in the potential to achieve satisfactory thematic accuracies were evaluated. The two approaches yielded remarkably similar classification results, with overall accuracies ranging from 82% to 86%. The performance of one of the unsupervised methods was unexpectedly similar to that of the supervised method; they identified almost identical scale parameters as being optimal for segmenting buildings, resulting in very similar geometries for the resulting image objects. The second unsupervised method produced very different image objects from the supervised method, but their classification accuracies were still very similar. The latter result was unexpected because, contrary to previously published findings, it suggests a high degree of independence between the segmentation results and classification accuracy. The results of this study have two important implications. The first is that object-based image analysis can be automated without sacrificing classification accuracy, and the second is that the previously accepted idea

  19. TRMM Precipitation Radar Reflectivity Profiles Compared to High-Resolution Airborne and Ground-Based Radar Measurements

    NASA Technical Reports Server (NTRS)

    Heymsfield, G. M.; Geerts, B.; Tian, L.

    1999-01-01

    In this paper, TRMM (Tropical Rainfall Measuring Mission Satellite) Precipitation Radar (PR) products are evaluated by means of simultaneous comparisons with data from the high-altitude ER-2 Doppler Radar (EDOP), as well as ground-based radars. The comparison is aimed primarily at the vertical reflectivity structure, which is of key importance in TRMM rain type classification and latent heating estimation. The radars used in this study have considerably different viewing geometries and resolutions, demanding non-trivial mapping procedures in common earth-relative coordinates. Mapped vertical cross sections and mean profiles of reflectivity from the PR, EDOP, and ground-based radars are compared for six cases. These cases cover a stratiform frontal rainband, convective cells of various sizes and stages, and a hurricane. For precipitating systems that are large relative to the PR footprint size, PR reflectivity profiles compare very well to high-resolution measurements thresholded to the PR minimum reflectivity, and derived variables such as bright band height and rain types are accurate, even at high PR incidence angles. It was found that for, the PR reflectivity of convective cells small relative to the PR footprint is weaker than in reality. Some of these differences can be explained by non-uniform beam filling. For other cases where strong reflectivity gradients occur within a PR footprint, the reflectivity distribution is spread out due to filtering by the PR antenna illumination pattern. In these cases, rain type classification may err and be biased towards the stratiform type, and the average reflectivity tends to be underestimated. The limited sensitivity of the PR implies that the upper regions of precipitation systems remain undetected and that the PR storm top height estimate is unreliable, usually underestimating the actual storm top height. This applies to all cases but the discrepancy is larger for smaller cells where limited sensitivity is compounded

  20. High-resolution maps of forest-urban watersheds present an opportunity for ecologists and managers

    EPA Science Inventory

    Dense populations of people and abundant impervious surfaces contribute to poor water quality and increased flooding in forest-urban watersheds. Green infrastructure mitigates these effects, but precisely quantifying benefits is difficult because most land cover maps rely on coar...

  1. High-resolution maps of forest-urban watersheds present an opportunity for ecologists and managers

    EPA Science Inventory

    Dense populations of people and abundant impervious surfaces contribute to poor water quality and increased flooding in forest-urban watersheds. Green infrastructure mitigates these effects, but precisely quantifying benefits is difficult because most land cover maps rely on coar...

  2. High-resolution mapping of quantum efficiency of silicon photodiode via optical-feedback laser microthermography

    SciTech Connect

    Cemine, Vernon Julius; Blanca, Carlo Mar; Saloma, Caesar

    2006-09-20

    We map the external quantum efficiency (QE) distribution of a silicon photodiode (PD) sample via a thermographic imaging technique based on optical-feedback laser confocal microscopy. An image pair consisting of the confocal reflectance image and the 2D photocurrent map is simultaneously acquired to delineate the following regions of interest on the sample: the substrate, the n-type region, the pn overlay, and the bonding pad. The 2D QE distribution is derived from the photocurrent map to quantify the optical performance of these sites. The thermal integrity of the sample is then evaluated by deriving the rate of change of QE with temperature T at each point on the silicon PD. These gradient maps function not only as stringent measures of local thermal QE activity but they also expose probable defect locations on the sample at high spatial resolution - a capability that is not feasible with existing bulk measurement techniques.

  3. Hierarchical object-based classification of ultra-high-resolution digital mapping camera (DMC) imagery for rangeland mapping and assessment

    USDA-ARS?s Scientific Manuscript database

    Ultra high resolution digital aerial photography has great potential to complement or replace ground measurements of vegetation cover for rangeland monitoring and assessment. We investigated object-based image analysis (OBIA) techniques for classifying vegetation in southwestern U.S. arid rangelands...

  4. The 1998 eruption of Axial Seamount: New insights on submarine lava flow emplacement from high-resolution mapping

    NASA Astrophysics Data System (ADS)

    Chadwick, W. W.; Clague, D. A.; Embley, R. W.; Perfit, M. R.; Butterfield, D. A.; Caress, D. W.; Paduan, J. B.; Martin, J. F.; Sasnett, P.; Merle, S. G.; Bobbitt, A. M.

    2013-10-01

    Axial Seamount, an active submarine volcano on the Juan de Fuca Ridge at 46°N, 130°W, erupted in January 1998 along 11 km of its upper south rift zone. We use ship-based multibeam sonar, high-resolution (1 m) bathymetry, sidescan sonar imagery, and submersible dive observations to map four separate 1998 lava flows that were fed from 11 eruptive fissures. These new mapping results give an eruption volume of 31 × 106 m3, 70% of which was in the northern-most flow, 23% in the southern-most flow, and 7% in two smaller flows in between. We introduce the concept of map-scale submarine lava flow morphology (observed at a scale of hundreds of meters, as revealed by the high-resolution bathymetry), and an interpretive model in which two map-scale morphologies are produced by high effusion-rate eruptions: "inflated lobate flows" are formed near eruptive vents, and where they drain downslope more than 0.5-1.0 km, they transition to "inflated pillow flows." These two morphologies are observed on the 1998 lava flows at Axial. A third map-scale flow morphology that was not produced during this eruption, "pillow mounds," is formed by low effusion-rate eruptions in which pillow lava piles up directly over the eruptive vents. Axial Seamount erupted again in April 2011 and there are remarkable similarities between the 1998 and 2011 eruptions, particularly the locations of eruptive vents and lava flow morphologies. Because the 2011 eruption reused most of the same eruptive fissures, 58% of the area of the 1998 lava flows is now covered by 2011 lava.

  5. High resolution electron energy loss spectroscopy with two-dimensional energy and momentum mapping.

    PubMed

    Zhu, Xuetao; Cao, Yanwei; Zhang, Shuyuan; Jia, Xun; Guo, Qinlin; Yang, Fang; Zhu, Linfan; Zhang, Jiandi; Plummer, E W; Guo, Jiandong

    2015-08-01

    High resolution electron energy loss spectroscopy (HREELS) is a powerful technique to probe vibrational and electronic excitations at surfaces. The dispersion relation of surface excitations, i.e., energy as a function of momentum, has in the past, been obtained by measuring the energy loss at a fixed angle (momentum) and then rotating sample, monochromator, or analyzer. Here, we introduce a new strategy for HREELS, utilizing a specially designed lens system with a double-cylindrical Ibach-type monochromator combined with a commercial VG Scienta hemispherical electron energy analyzer, which can simultaneously measure the energy and momentum of the scattered electrons. The new system possesses high angular resolution (<0.1°), detecting efficiency and sampling density. The capabilities of this system are demonstrated using Bi2Sr2CaCu2O(8+δ). The time required to obtain a complete dispersion spectrum is at least one order of magnitude shorter than conventional spectrometers, with improved momentum resolution and no loss in energy resolution.

  6. High resolution electron energy loss spectroscopy with two-dimensional energy and momentum mapping

    SciTech Connect

    Zhu, Xuetao; Cao, Yanwei; Zhang, Shuyuan; Jia, Xun; Guo, Qinlin; Yang, Fang; Zhu, Linfan; Zhang, Jiandi; Plummer, E. W.; Guo, Jiandong

    2015-08-15

    High resolution electron energy loss spectroscopy (HREELS) is a powerful technique to probe vibrational and electronic excitations at surfaces. The dispersion relation of surface excitations, i.e., energy as a function of momentum, has in the past, been obtained by measuring the energy loss at a fixed angle (momentum) and then rotating sample, monochromator, or analyzer. Here, we introduce a new strategy for HREELS, utilizing a specially designed lens system with a double-cylindrical Ibach-type monochromator combined with a commercial VG Scienta hemispherical electron energy analyzer, which can simultaneously measure the energy and momentum of the scattered electrons. The new system possesses high angular resolution (<0.1°), detecting efficiency and sampling density. The capabilities of this system are demonstrated using Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8+δ}. The time required to obtain a complete dispersion spectrum is at least one order of magnitude shorter than conventional spectrometers, with improved momentum resolution and no loss in energy resolution.

  7. High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species

    PubMed Central

    Schumer, Molly; Cui, Rongfeng; Powell, Daniel L; Dresner, Rebecca; Rosenthal, Gil G; Andolfatto, Peter

    2014-01-01

    Hybridization is increasingly being recognized as a common process in both animal and plant species. Negative epistatic interactions between genes from different parental genomes decrease the fitness of hybrids and can limit gene flow between species. However, little is known about the number and genome-wide distribution of genetic incompatibilities separating species. To detect interacting genes, we perform a high-resolution genome scan for linkage disequilibrium between unlinked genomic regions in naturally occurring hybrid populations of swordtail fish. We estimate that hundreds of pairs of genomic regions contribute to reproductive isolation between these species, despite them being recently diverged. Many of these incompatibilities are likely the result of natural or sexual selection on hybrids, since intrinsic isolation is known to be weak. Patterns of genomic divergence at these regions imply that genetic incompatibilities play a significant role in limiting gene flow even in young species. DOI: http://dx.doi.org/10.7554/eLife.02535.001 PMID:24898754

  8. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions

    PubMed Central

    Ernst, Jason; Melnikov, Alexandre; Zhang, Xiaolan; Wang, Li; Rogov, Peter; Mikkelsen, Tarjei S.; Kellis, Manolis

    2016-01-01

    Massively parallel reporter assays (MPRA) enable nucleotide-resolution dissection of transcriptional regulatory regions, such as enhancers, but only few regions at a time. Here, we present a combined experimental and computational approach, Sharpr-MPRA, that allows high-resolution analysis of thousands of regions simultaneously. Sharpr-MPRA combines dense tiling of overlapping MPRA constructs with a probabilistic graphical model to recognize functional regulatory nucleotides, and to distinguish activating and repressive nucleotides, using their inferred contribution to reporter gene expression. We use Sharpr-MPRA to test 4.6 million nucleotides spanning 15,000 putative regulatory regions tiled at 5-nucleotide resolution in two human cell types. Our results recover known cell type-specific regulatory motifs and evolutionarily-conserved nucleotides, and distinguish known activating and repressive motifs. Our results also show that endogenous chromatin state and DNA accessibility are both predictive of regulatory function in reporter assays, identify retroviral elements with activating roles, and uncover ‘attenuator’ motifs with repressive roles in active chromatin. PMID:27701403

  9. High Resolution Spatial and Temporal Mapping of Traffic-Related Air Pollutants

    PubMed Central

    Batterman, Stuart; Ganguly, Rajiv; Harbin, Paul

    2015-01-01

    Vehicle traffic is one of the most significant emission sources of air pollutants in urban areas. While the influence of mobile source emissions is felt throughout an urban area, concentrations from mobile emissions can be highest near major roadways. At present, information regarding the spatial and temporal patterns and the share of pollution attributable to traffic-related air pollutants is limited, in part due to concentrations that fall sharply with distance from roadways, as well as the few monitoring sites available in cities. This study uses a newly developed dispersion model (RLINE) and a spatially and temporally resolved emissions inventory to predict hourly PM2.5 and NOx concentrations across Detroit (MI, USA) at very high spatial resolution. Results for annual averages and high pollution days show contrasting patterns, the need for spatially resolved analyses, and the limitations of surrogate metrics like proximity or distance to roads. Data requirements, computational and modeling issues are discussed. High resolution pollutant data enable the identification of pollutant “hotspots”, “project-level” analyses of transportation options, development of exposure measures for epidemiology studies, delineation of vulnerable and susceptible populations, policy analyses examining risks and benefits of mitigation options, and the development of sustainability indicators integrating environmental, social, economic and health information. PMID:25837345

  10. High resolution mapping of genetic factors affecting abdominal bristle number in Drosophila melanogaster

    SciTech Connect

    Long, A.D. |; Mullaney, S.L.; Langley, C.H.; Reid, L.A.; Fry, J.D.; Mackay, T.F.C.

    1995-03-01

    Factors responsible for selection response for abdominal bristle number and correlated responses in sternopleural bristle number were mapped to the X and third chromosome of Drosophila melanogaster. Lines divergent for high and low abdominal bristle number were created by 25 generations of artificial selection from a large base population, with an intensity of 25 individuals of each sex selected from 100 individuals of each sex scored per generation. Isogenic chromosome substitution lines in which the high (H) X or third chromosome were placed in an isogenic low (L) background were derived from the selection lines and from the 93 recombinant isogenic (RI) HL X and 67 RI chromosome 3 lines constructed from them. Highly polymorphic neutral roo transposable elements were hybridized in situ to the polytene chromosomes of the RI lines to create a set of cytogenetic markers. These techniques yielded a dense map with an average spacing of 4 cM between informative markers. Two factors with large effects on abdominal bristle number were mapped on the X chromosome and five factors on the third chromosome. One factor with a large effect on sternopleural bristle number was mapped to the X and two were mapped to the third chromosome; all factors with sternopleural effects corresponded to those with effects on abdominal bristle number. Two of the chromosome 3 factors with large effects on abdominal bristle number were also associated with reduced viability. Significant sex-specific effects and epistatic interactions between mapped factors of the same order of magnitude as the additive effects were observed. All factors mapped to the approximate positions of likely candidate loci previously characterized by mutations with large effects on bristle number. 55 refs., 4 figs., 7 tabs.

  11. High-resolution whole-organ mapping with SNPs and its significance to early events of carcinogenesis.

    PubMed

    Tuziak, Tomasz; Jeong, Joon; Majewski, Tadeusz; Kim, Mi-Sook; Steinberg, Jordan; Wang, Zhi; Yoon, Dong-Sup; Kuang, Tang C; Baggerly, Keith; Johnston, Dennis; Czerniak, Bogdan

    2005-05-01

    We attempted to identify deleted segments in two model tumor suppressor gene loci on chromosomes 13q14 and 17p13 that were associated with clonal expansion of in situ bladder preneoplasia using single nucleotide polymorphisms (SNPs)-based whole-organ histologic and genetic mapping. For mapping with SNPs, the sequence-based maps spanning approximately 27 and 5 Mb centered around RB1 and p53, respectively, were assembled. The integrated gene and SNP maps of the regions were used to select 661 and 960 SNPs, which were genotyped by pyrosequencing. Genotyping of SNPs was performed on DNA samples corresponding to histologic maps of the entire bladder mucosa in human cystectomy specimens with invasive urothelial carcinoma. By using this approach, we have identified deleted regions associated with clonal expansion of intraurothelial neoplasia; which ranged from 0.001 to 4.3 Mb (average 0.67 Mb) and formed clusters of discontinuous deleted segments. The high resolution of such maps is a prerequisite for future positional targeting of genes involved in early phases of bladder neoplasia. This approach also permits analysis of the overall genomic landscape of the involved region and discloses that a unique composition of noncoding DNA characterized by a high concentration of repetitive sequences may predispose to deletions.

  12. High-resolution ammonia mapping of the very young protostellar core Chamaeleon-MMS1

    NASA Astrophysics Data System (ADS)

    Väisälä, M. S.; Harju, J.; Mantere, M. J.; Miettinen, O.; Sault, R. S.; Walmsley, C. M.; Whiteoak, J. B.

    2014-04-01

    Aims: The aim of this study is to investigate the structure and kinematics of the nearby candidate first hydrostatic core Cha-MMS1. Methods: Cha-MMS1 was mapped in the NH3(1,1) line and the 1.2 cm continuum using the Australia Telescope Compact Array (ATCA). The angular resolution of the ATCA observations is 7″ (~1000 AU), and the velocity resolution is 50 m s-1. The core was also mapped with the 64 m Parkes Telescope in the NH3(1,1) and (2,2) lines. Observations from Herschel Space Observatory and Spitzer Space Telescope were used to help interpretation. The ammonia spectra were analysed using Gaussian fits to the hyperfine structure. A two-layer model was applied in the central parts of the core where the ATCA spectra show signs of self-absorption. Results: A compact high column density core with a steep velocity gradient (~20 km s-1 pc-1) is detected in ammonia. We derive a high gas density (~106 cm-3) in this region, and a fractional ammonia abundance compatible with determinations towards other dense cores (~10-8). This suggests that the age of the high density core is comparable to the freeze-out timescale of ammonia in these conditions, on the order of 104 years. The direction of the velocity gradient agrees with previous single-dish observations, and the overall velocity distribution can be interpreted as rotation. The rotation axis goes through the position of a compact far-infrared source detected by Spitzer and Herschel. The specific angular momentum of the core, ~10-3km s-1 pc, is typical for protostellar envelopes. A string of 1.2 cm continuum sources is tentatively detected near the rotation axis. The ammonia spectra suggest the presence of warm embedded gas in its vicinity. An hourglass-shaped structure is seen in ammonia at the cloud's average LSR velocity, also aligned with the rotation axis. Although this structure resembles a pair of outflow lobes the ammonia spectra show no indications of shocked gas. Conclusions: The observed ammonia

  13. Inclusion of high resolution MODIS maps on a 3D tropospheric water vapor GPS tomography model

    NASA Astrophysics Data System (ADS)

    Benevides, Pedro; Catalao, Joao; Nico, Giovanni; Miranda, Pedro M. A.

    2015-10-01

    Observing the water vapor distribution on the troposphere remains a challenge for the weather forecast. Radiosondes provide precise water vapor profiles of the troposphere, but lack geographical and temporal coverage, while satellite meteorological maps have good spatial resolution but even poorer temporal resolution. GPS has proved its capacity to measure the integrated water vapor in all weather conditions with high temporal sampling frequency. However these measurements lack a vertical water vapor discretization. Reconstruction of the slant path GPS observation to the satellite allows oblique water vapor measurements. Implementation of a 3D grid of voxels along the troposphere over an area where GPS stations are available enables the observation ray tracing. A relation between the water vapor density and the distanced traveled inside the voxels is established, defining GPS tomography. An inverse problem formulation is needed to obtain a water vapor solution. The combination of precipitable water vapor (PWV) maps obtained from MODIS satellite data with the GPS tomography is performed in this work. The MODIS PWV maps can have 1 or 5 km pixel resolution, being obtained 2 times per day in the same location at most. The inclusion of MODIS PWV maps provides an enhanced horizontal resolution for the tomographic solution and benefits the stability of the inversion problem. A 3D tomographic grid was adjusted over a regional area covering Lisbon, Portugal, where a GNSS network of 9 receivers is available. Radiosonde measurements in the area are used to evaluate the 3D water vapor tomography maps.

  14. Evaluation of eelgrass beds mapping using a high-resolution airborne multispectral scanner

    USGS Publications Warehouse

    Su, H.; Karna, D.; Fraim, E.; Fitzgerald, M.; Dominguez, R.; Myers, J.S.; Coffland, B.; Handley, L.R.; Mace, T.

    2006-01-01

    Eelgrass (Zostera marina) can provide vital ecological functions in stabilizing sediments, influencing current dynamics, and contributing significant amounts of biomass to numerous food webs in coastal ecosystems. Mapping eelgrass beds is important for coastal water and nearshore estuarine monitoring, management, and planning. This study demonstrated the possible use of high spatial (approximately 5 m) and temporal (maximum low tide) resolution airborne multispectral scanner on mapping eelgrass beds in Northern Puget Sound, Washington. A combination of supervised and unsupervised classification approaches were performed on the multispectral scanner imagery. A normalized difference vegetation index (NDVI) derived from the red and near-infrared bands and ancillary spatial information, were used to extract and mask eelgrass beds and other submerged aquatic vegetation (SAV) in the study area. We evaluated the resulting thematic map (geocoded, classified image) against a conventional aerial photograph interpretation using 260 point locations randomly stratified over five defined classes from the thematic map. We achieved an overall accuracy of 92 percent with 0.92 Kappa Coefficient in the study area. This study demonstrates that the airborne multispectral scanner can be useful for mapping eelgrass beds in a local or regional scale, especially in regions for which optical remote sensing from space is constrained by climatic and tidal conditions. ?? 2006 American Society for Photogrammetry and Remote Sensing.

  15. Mapping of odor-related neuronal activity in the olfactory bulb by high-resolution 2-deoxyglucose autoradiography

    SciTech Connect

    Lancet, D.; Greer, C.A.; Kauer, J.S.; Shepherd, G.M.

    1982-01-01

    The spatial distribution of odor-induced neuronal activity in the olfactory bulb, the first relay station of the olfactory pathway, is believed to reflect important aspects of chemosensory coding. We report here the application of high-resolution 2-deoxyglucose autoradiography to the mapping of spatial patterns of metabolic activity at the level of single neurons in the olfactory bulb. It was found that glomeruli, which are synaptic complexes containing the first synaptic relay, tend to be uniformly active or inactive during odor exposure. Differential 2-deoxyglucose uptake was also observed in the somata of projection neurons (mitral cells) and interneurons (periglomerular and granule cells). This confirms and extends our previous studies in which odor-specific laminar and focal uptake patterns were revealed by the conventional x-ray film 2-deoxyglucose method due to Sokoloff and colleagues (Sokoloff, L., Reivich, M., Kennedy, C., DesRosiers, M. H., Patlak, C. S., Pettigrew, K. D., Sakurada, O. and Shinohara, M. (1977) J. Neurochem. 28, 897-916). Based on results obtained by the two methods, it is suggested that the glomerulus as a whole serves as a functional unit of activity. The high-resolution results are interpreted in terms of the well-characterized synaptic organization of the olfactory bulb and also serve to illustrate the capability of the 2-deoxyglucose autoradiographic technique to map metabolic activity in single neurons of the vertebrate central nervous system.

  16. Cold climate mapping using satellite high resolution thermal imagery. [weather forecasting improvement

    NASA Technical Reports Server (NTRS)

    Bartholic, J. F.; Sutherland, R. A.

    1977-01-01

    In an attempt to improve cold climate mapping and freeze forecasting techniques, thermal imagery from the NOAA-2 and -3 satellites and the Synchronous Meteorological Satellite (SMS) were obtained and analyzed. Enhanced image transparencies showed detailed temperature patterns over the peninsula of Florida. The analysis was superior to hand-drawn isotherms drawn from the 300 to 500 thermograph stations presently in use. Satellite data on several cold nights with similar synoptic conditions showed that similar cold patterns existed. Thus, cold climate mapping is possible.

  17. High-Resolution Mapping of the Drosophila Fourth Chromosome Using Site-Directed Terminal Deficiencies

    PubMed Central

    Sousa-Neves, Rui; Lukacsovich, Tamas; Mizutani, Claudia Mieko; Locke, John; Podemski, Lynn; Marsh, J. Lawrence

    2005-01-01

    For more than 80 years, the euchromatic right arm of the Drosophila fourth chromosome (101F-102F) has been one of the least genetically accessible regions of the fly genome despite the fact that many important genes reside there. To improve the mapping of genes on the fourth chromosome, we describe a strategy to generate targeted deficiencies and we describe 13 deficiencies that subdivide the 300 kb between the cytological coordinates 102A6 and 102C1 into five discrete regions plus a 200-kb region from 102C1 to 102D6. Together these deficiencies substantially improve the mapping capabilities for mutant loci on the fourth chromosome. PMID:15466427

  18. Cold climate mapping using satellite high resolution thermal imagery. [weather forecasting improvement

    NASA Technical Reports Server (NTRS)

    Bartholic, J. F.; Sutherland, R. A.

    1977-01-01

    In an attempt to improve cold climate mapping and freeze forecasting techniques, thermal imagery from the NOAA-2 and -3 satellites and the Synchronous Meteorological Satellite (SMS) were obtained and analyzed. Enhanced image transparencies showed detailed temperature patterns over the peninsula of Florida. The analysis was superior to hand-drawn isotherms drawn from the 300 to 500 thermograph stations presently in use. Satellite data on several cold nights with similar synoptic conditions showed that similar cold patterns existed. Thus, cold climate mapping is possible.

  19. High-resolution mapping of global surface water and its long-term changes

    NASA Astrophysics Data System (ADS)

    Pekel, Jean-François; Cottam, Andrew; Gorelick, Noel; Belward, Alan S.

    2016-12-01

    The location and persistence of surface water (inland and coastal) is both affected by climate and human activity and affects climate, biological diversity and human wellbeing. Global data sets documenting surface water location and seasonality have been produced from inventories and national descriptions, statistical extrapolation of regional data and satellite imagery, but measuring long-term changes at high resolution remains a challenge. Here, using three million Landsat satellite images, we quantify changes in global surface water over the past 32 years at 30-metre resolution. We record the months and years when water was present, where occurrence changed and what form changes took in terms of seasonality and persistence. Between 1984 and 2015 permanent surface water has disappeared from an area of almost 90,000 square kilometres, roughly equivalent to that of Lake Superior, though new permanent bodies of surface water covering 184,000 square kilometres have formed elsewhere. All continental regions show a net increase in permanent water, except Oceania, which has a fractional (one per cent) net loss. Much of the increase is from reservoir filling, although climate change is also implicated. Loss is more geographically concentrated than gain. Over 70 per cent of global net permanent water loss occurred in the Middle East and Central Asia, linked to drought and human actions including river diversion or damming and unregulated withdrawal. Losses in Australia and the USA linked to long-term droughts are also evident. This globally consistent, validated data set shows that impacts of climate change and climate oscillations on surface water occurrence can be measured and that evidence can be gathered to show how surface water is altered by human activities. We anticipate that this freely available data will improve the modelling of surface forcing, provide evidence of state and change in wetland ecotones (the transition areas between biomes), and inform water

  20. High-Resolution Copy-Number Variation Map Reflects Human Olfactory Receptor Diversity and Evolution

    PubMed Central

    Khen, Miriam; Gonzaga-Jauregui, Claudia; Kim, Philip M.; Urban, Alexander Eckehart; Snyder, Michael; Gerstein, Mark B.; Lancet, Doron; Korbel, Jan O.

    2008-01-01

    Olfactory receptors (ORs), which are involved in odorant recognition, form the largest mammalian protein superfamily. The genomic content of OR genes is considerably reduced in humans, as reflected by the relatively small repertoire size and the high fraction (∼55%) of human pseudogenes. Since several recent low-resolution surveys suggested that OR genomic loci are frequently affected by copy-number variants (CNVs), we hypothesized that CNVs may play an important role in the evolution of the human olfactory repertoire. We used high-resolution oligonucleotide tiling microarrays to detect CNVs across 851 OR gene and pseudogene loci. Examining genomic DNA from 25 individuals with ancestry from three populations, we identified 93 OR gene loci and 151 pseudogene loci affected by CNVs, generating a mosaic of OR dosages across persons. Our data suggest that ∼50% of the CNVs involve more than one OR, with the largest CNV spanning 11 loci. In contrast to earlier reports, we observe that CNVs are more frequent among OR pseudogenes than among intact genes, presumably due to both selective constraints and CNV formation biases. Furthermore, our results show an enrichment of CNVs among ORs with a close human paralog or lacking a one-to-one ortholog in chimpanzee. Interestingly, among the latter we observed an enrichment in CNV losses over gains, a finding potentially related to the known diminution of the human OR repertoire. Quantitative PCR experiments performed for 122 sampled ORs agreed well with the microarray results and uncovered 23 additional CNVs. Importantly, these experiments allowed us to uncover nine common deletion alleles that affect 15 OR genes and five pseudogenes. Comparison to the chimpanzee reference genome revealed that all of the deletion alleles are human derived, therefore indicating a profound effect of human-specific deletions on the individual OR gene content. Furthermore, these deletion alleles may be used in future genetic association studies of

  1. High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation

    PubMed Central

    Ozdemir, Anil; Fisher-Aylor, Katherine I.; Pepke, Shirley; Samanta, Manoj; Dunipace, Leslie; McCue, Kenneth; Zeng, Lucy; Ogawa, Nobuo; Wold, Barbara J.; Stathopoulos, Angelike

    2011-01-01

    Cis-regulatory modules (CRMs) function by binding sequence specific transcription factors, but the relationship between in vivo physical binding and the regulatory capacity of factor-bound DNA elements remains uncertain. We investigate this relationship for the well-studied Twist factor in Drosophila melanogaster embryos by analyzing genome-wide factor occupancy and testing the functional significance of Twist occupied regions and motifs within regions. Twist ChIP-seq data efficiently identified previously studied Twist-dependent CRMs and robustly predicted new CRM activity in transgenesis, with newly identified Twist-occupied regions supporting diverse spatiotemporal patterns (>74% positive, n = 31). Some, but not all, candidate CRMs require Twist for proper expression in the embryo. The Twist motifs most favored in genome ChIP data (in vivo) differed from those most favored by Systematic Evolution of Ligands by EXponential enrichment (SELEX) (in vitro). Furthermore, the majority of ChIP-seq signals could be parsimoniously explained by a CABVTG motif located within 50 bp of the ChIP summit and, of these, CACATG was most prevalent. Mutagenesis experiments demonstrated that different Twist E-box motif types are not fully interchangeable, suggesting that the ChIP-derived consensus (CABVTG) includes sites having distinct regulatory outputs. Further analysis of position, frequency of occurrence, and sequence conservation revealed significant enrichment and conservation of CABVTG E-box motifs near Twist ChIP-seq signal summits, preferential conservation of ±150 bp surrounding Twist occupied summits, and enrichment of GA- and CA-repeat sequences near Twist occupied summits. Our results show that high resolution in vivo occupancy data can be used to drive efficient discovery and dissection of global and local cis-regulatory logic. PMID:21383317

  2. High-resolution mapping of global surface water and its long-term changes.

    PubMed

    Pekel, Jean-François; Cottam, Andrew; Gorelick, Noel; Belward, Alan S

    2016-12-15

    The location and persistence of surface water (inland and coastal) is both affected by climate and human activity and affects climate, biological diversity and human wellbeing. Global data sets documenting surface water location and seasonality have been produced from inventories and national descriptions, statistical extrapolation of regional data and satellite imagery, but measuring long-term changes at high resolution remains a challenge. Here, using three million Landsat satellite images, we quantify changes in global surface water over the past 32 years at 30-metre resolution. We record the months and years when water was present, where occurrence changed and what form changes took in terms of seasonality and persistence. Between 1984 and 2015 permanent surface water has disappeared from an area of almost 90,000 square kilometres, roughly equivalent to that of Lake Superior, though new permanent bodies of surface water covering 184,000 square kilometres have formed elsewhere. All continental regions show a net increase in permanent water, except Oceania, which has a fractional (one per cent) net loss. Much of the increase is from reservoir filling, although climate change is also implicated. Loss is more geographically concentrated than gain. Over 70 per cent of global net permanent water loss occurred in the Middle East and Central Asia, linked to drought and human actions including river diversion or damming and unregulated withdrawal. Losses in Australia and the USA linked to long-term droughts are also evident. This globally consistent, validated data set shows that impacts of climate change and climate oscillations on surface water occurrence can be measured and that evidence can be gathered to show how surface water is altered by human activities. We anticipate that this freely available data will improve the modelling of surface forcing, provide evidence of state and change in wetland ecotones (the transition areas between biomes), and inform water

  3. High-resolution mapping of the NO2 spatial distribution over Belgian urban areas based on airborne APEX remote sensing

    NASA Astrophysics Data System (ADS)

    Tack, Frederik; Merlaud, Alexis; Iordache, Marian-Daniel; Danckaert, Thomas; Yu, Huan; Fayt, Caroline; Meuleman, Koen; Deutsch, Felix; Fierens, Frans; Van Roozendael, Michel

    2017-05-01

    -scale variability, can be mapped accurately with high spatial resolution and in a relatively short time frame, and the contributing emission sources can be resolved. High-resolution quantitative information about the atmospheric NO2 horizontal variability is currently rare, but can be very valuable for (air quality) studies at the urban scale.

  4. Validating a high-resolution digital soil map for precision agriculture across multiple fields

    USDA-ARS?s Scientific Manuscript database

    Digital soil mapping (DSM) for precision agriculture (PA) management is aimed at developing models that predict soil properties or classes using legacy soil data, sensors, and environmental covariates. The utility of DSM for PA is based on its ability to provide useful spatial soil information for o...

  5. Regional validation of a high-resolution digital soil map using soil profile attributes

    USDA-ARS?s Scientific Manuscript database

    Digital soil mapping (DSM) for precision agriculture (PA) management is aimed at developing models that predict soil properties or classes using legacy soil data, sensors, and environmental covariates. The utility of DSM for PA centers on its ability to provide soil information to optimize crop yiel...

  6. High-resolution carbon mapping on the million-hectare Island of Hawaii

    Treesearch

    Gregory P. Asner; R. Flint Hughes; Joseph Mascaro; Amanda L. Uowolo; David E. Knapp; James Jacobson; Ty Kennedy-Bowdoin; John K . Clark

    2011-01-01

    Current markets and international agreements for reducing emissions from deforestation and forest degradation (REDD) rely on carbon (C) monitoring techniques. Combining field measurements, airborne light detection and ranging (LiDAR)-based observations, and satellite-based imagery, we developed a 30-meter-resolution map of aboveground C density spanning 40 vegetation...

  7. A HYBRID HIGH RESOLUTION IMAGE CLASSIFICATION METHOD FOR MAPPING EELGRASS DISTRIBUTIONS IN YAQUINA BAY ESTUARY, OREGON

    EPA Science Inventory

    False-color infrared aerial photography of the Yaquina Bay Estuary, Oregon was acquired at extreme low tides and digitally orthorectified with a ground pixel resolution of 20 cm to provide data for intertidal vegetation mapping. Submerged, semi-exposed and exposed eelgrass mead...

  8. High resolution mapping of modified DNA nucleobases using excision repair enzymes

    PubMed Central

    Bryan, D. Suzi; Ransom, Monica; Adane, Biniam; York, Kerri

    2014-01-01

    The incorporation and creation of modified nucleobases in DNA have profound effects on genome function. We describe methods for mapping positions and local content of modified DNA nucleobases in genomic DNA. We combined in vitro nucleobase excision with massively parallel DNA sequencing (Excision-seq) to determine the locations of modified nucleobases in genomic DNA. We applied the Excision-seq method to map uracil in E. coli and budding yeast and discovered significant variation in uracil content, wherein uracil is excluded from the earliest and latest replicating regions of the genome, possibly driven by changes in nucleotide pool composition. We also used Excision-seq to identify sites of pyrimidine dimer formation induced by UV light exposure, where the method could distinguish between sites of cyclobutane and 6-4 photoproduct formation. These UV mapping data enabled analysis of local sequence bias around pyrimidine dimers and suggested a preference for an adenosine downstream from 6-4 photoproducts. The Excision-seq method is broadly applicable for high precision, genome-wide mapping of modified nucleobases with cognate repair enzymes. PMID:25015380

  9. A high resolution radiation hybrid map of wheat chromosome 4A

    USDA-ARS?s Scientific Manuscript database

    Bread wheat has a large and complex allohexaploid genome with low recombination level at chromosome centromeric and peri-centromeric regions. This significantly hampers ordering of markers, contigs of physical maps and sequence scaffolds and impedes obtaining of high-quality reference genome sequenc...

  10. A HYBRID HIGH RESOLUTION IMAGE CLASSIFICATION METHOD FOR MAPPING EELGRASS DISTRIBUTIONS IN YAQUINA BAY ESTUARY, OREGON

    EPA Science Inventory

    False-color infrared aerial photography of the Yaquina Bay Estuary, Oregon was acquired at extreme low tides and digitally orthorectified with a ground pixel resolution of 20 cm to provide data for intertidal vegetation mapping. Submerged, semi-exposed and exposed eelgrass mead...

  11. 4 Vesta in Color: High Resolution Mapping from Dawn Framing Camera Images

    NASA Technical Reports Server (NTRS)

    Reddy, V.; LeCorre, L.; Nathues, A.; Sierks, H.; Christensen, U.; Hoffmann, M.; Schroeder, S. E.; Vincent, J. B.; McSween, H. Y.; Denevi, B. W.; hide

    2011-01-01

    Rotational surface variations on asteroid 4 Vesta have been known from ground-based and HST observations, and they have been interpreted as evidence of compositional diversity. NASA s Dawn mission entered orbit around Vesta on July 16, 2011 for a year-long global characterization. The framing cameras (FC) onboard the Dawn spacecraft will image the asteroid in one clear (broad) and seven narrow band filters covering the wavelength range between 0.4-1.0 microns. We present color mapping results from the Dawn FC observations of Vesta obtained during Survey orbit (approx.3000 km) and High-Altitude Mapping Orbit (HAMO) (approx.950 km). Our aim is to create global color maps of Vesta using multi spectral FC images to identify the spatial extent of compositional units and link them with other available data sets to extract the basic mineralogy. While the VIR spectrometer onboard Dawn has higher spectral resolution (864 channels) allowing precise mineralogical assessment of Vesta s surface, the FC has three times higher spatial resolution in any given orbital phase. In an effort to extract maximum information from FC data we have developed algorithms using laboratory spectra of pyroxenes and HED meteorites to derive parameters associated with the 1-micron absorption band wing. These parameters will help map the global distribution of compositionally related units on Vesta s surface. Interpretation of these units will involve the integration of FC and VIR data.

  12. Mapping of Impervious Surfaces and Green Vegetation Fraction in Urban Areas Using High-Resolution Optical- and SAR- Data

    NASA Astrophysics Data System (ADS)

    Mack, Benjamin; Becker, Frauke; Menz, Gunther

    2010-12-01

    Impervious surfaces (IS) and vegetated surfaces (VS) are two important variables for urban planning. Both are related to surface biophysical processes (e. g. urban heat island) and the quality of life in urban environments. The new generation of spatially very high resolution satellite sensors (e.g. RapidEye, or TerraSAR-X) show promising capabilities to extract these variables in relevant detail and hence to overcome some of the limitations using traditional approaches. In this study, we show a simple workflow for the synergistic use of high-resolution optical and SAR data for the retrieval of detailed information of IS and VS. Here, the focus is on the processing step of vegetation extraction. Three approaches - linear Spectral Mixture Analysis, per-pixel, and segment-oriented classification - are compared. It will also be analyzed if an explicit shadow analysis leads to a significant improvement of the products.

  13. High-resolution AUV mapping of the 2015 flows at Axial Seamount, Juan de Fuca Ridge

    NASA Astrophysics Data System (ADS)

    Paduan, J. B.; Chadwick, W. W., Jr.; Clague, D. A.; Le Saout, M.; Caress, D. W.; Thomas, H. J.; Yoerger, D.

    2016-12-01

    Lava flows erupted in April 2015 at Axial Seamount were mapped at 1-m resolution with the AUV Sentry in August 2015 and the MBARI Mapping AUVs in July 2016 and observed and sampled with ROVs on those same expeditions. Thirty percent of terrain covered by new flows had been mapped by the MBARI AUVs prior to the eruption. Differencing of before and after maps (using ship-collected bathymetry where the AUV had not mapped before) allows calculation of extents and volumes of flows and shows new fissures. The maps reveal unexpected fissure patterns and shifts in the style of flow emplacement through a single eruption. There were 11 separate flows totaling 1.48 x 108 m3 of lava erupted from numerous en echelon fissures over 19 km on the NE caldera floor, on the NE flank, and down the N rift zone. Flows in and around the caldera have maximum thicknesses of 5-19 m. Most erupted as sheet flows and spread along intricate channels that terminated in thin margins. Some utilized pre-existing fissures. Some flows erupted from short fissures, while at least two longer new fissures produced little or no lava. A flow on the upper N rift has a spectacular lava channel flanked by narrow lava pillars supporting a thin roof left after the flow drained. A shatter ring still emanating warm fluid is visible in the map as a 15-m wide low cone. Hundreds of exploded pillows were observed but are not discernable in the bathymetry. The northern-most three flows deep on the N rift are similar in area to the others but comprise the bulk of the eruption volume. Differencing of ship-based bathymetry shows only these flows. Near the eruptive fissures they are sheet flows, but as they flowed downslope they built complexes of coalesced pillow mounds up to 67-128 m thick. Changes in flow morphology occurred through the course of the eruption. Large pillow mounds had molten cores that deformed as the eruption progressed. One flow began as a thin, effusive sheet flow but as the eruption rate decreased, a

  14. A gene-derived SNP-based high resolution linkage map of carrot including the location of QTL conditioning root and leaf anthocyanin pigmentation.

    PubMed

    Cavagnaro, Pablo F; Iorizzo, Massimo; Yildiz, Mehtap; Senalik, Douglas; Parsons, Joshua; Ellison, Shelby; Simon, Philipp W

    2014-12-16

    Purple carrots accumulate large quantities of anthocyanins in their roots and leaves. These flavonoid pigments possess antioxidant activity and are implicated in providing health benefits. Informative, saturated linkage maps associated with well characterized populations segregating for anthocyanin pigmentation have not been developed. To investigate the genetic architecture conditioning anthocyanin pigmentation we scored root color visually, quantified root anthocyanin pigments by high performance liquid chromatography in segregating F2, F3 and F4 generations of a mapping population, mapped quantitative trait loci (QTL) onto a dense gene-derived single nucleotide polymorphism (SNP)-based linkage map, and performed comparative trait mapping with two unrelated populations. Root pigmentation, scored visually as presence or absence of purple coloration, segregated in a pattern consistent with a two gene model in an F2, and progeny testing of F3-F4 families confirmed the proposed genetic model. Purple petiole pigmentation was conditioned by a single dominant gene that co-segregates with one of the genes conditioning root pigmentation. Root total pigment estimate (RTPE) was scored as the percentage of the root with purple color.All five anthocyanin glycosides previously reported in carrot, as well as RTPE, varied quantitatively in the F2 population. For the purpose of QTL analysis, a high resolution gene-derived SNP-based linkage map of carrot was constructed with 894 markers covering 635.1 cM with a 1.3 cM map resolution. A total of 15 significant QTL for all anthocyanin pigments and for RTPE mapped to six chromosomes. Eight QTL with the largest phenotypic effects mapped to two regions of chromosome 3 with co-localized QTL for several anthocyanin glycosides and for RTPE. A single dominant gene conditioning anthocyanin acylation was identified and mapped.Comparative mapping with two other carrot populations segregating for purple color indicated that carrot anthocyanin

  15. High Resolution Mapping of Soils and Landforms for the Desert Renewable Energy Conservation Plan (DRECP)

    NASA Technical Reports Server (NTRS)

    Potter, Christopher S.; Li, Shuang

    2014-01-01

    The Desert Renewable Energy Conservation Plan (DRECP), a major component of California's renewable energy planning efforts, is intended to provide effective protection and conservation of desert ecosystems, while allowing for the sensible development of renewable energy projects. This NASA mapping report was developed to support the DRECP and the Bureau of Land Management (BLM). We outline in this document remote sensing image processing methods to deliver new maps of biological soils crusts, sand dune movements, desert pavements, and sub-surface water sources across the DRECP area. We focused data processing first on the largely unmapped areas most likely to be used for energy developments, such as those within Renewable Energy Study Areas (RESA) and Solar Energy Zones (SEZs). We used imagery (multispectral and radar) mainly from the years 2009-2011.

  16. High resolution sub-millimetre mapping of starburst galaxies: Comparison with CO emission

    NASA Technical Reports Server (NTRS)

    Smith, P. A.; Brand, P. W. J. L.; Puxley, Phil J.; Mountain, C. M.; Nakai, Naomasa

    1990-01-01

    Researchers present first results from a program of submillimeter continuum mapping of starburst galaxies, and comparison of their dust and CO emission. This project was prompted by surprising results from the first target, the nearby starburst M82, which shows in the dust continuum a morphology quite unlike that of its CO emission, in contrast to what might be expected if both CO and dust are accurately tracing the molecular hydrogen. Possible explanations for this striking difference are discussed. In the light of these results, the program has been extended to include sub-mm mapping of the nearby, vigorously star forming spirals, M83 and Maffei 2. The latter were also observed extensively in CO, in order to study excitation conditions in its central regions. The James Clerk Maxwell Telescope was used in these studies.

  17. Spotlight-Mode Synthetic Aperture Radar Processing for High-Resolution Lunar Mapping

    NASA Technical Reports Server (NTRS)

    Harcke, Leif; Weintraub, Lawrence; Yun, Sang-Ho; Dickinson, Richard; Gurrola, Eric; Hensley, Scott; Marechal, Nicholas

    2010-01-01

    During the 2008-2009 year, the Goldstone Solar System Radar was upgraded to support radar mapping of the lunar poles at 4 m resolution. The finer resolution of the new system and the accompanying migration through resolution cells called for spotlight, rather than delay-Doppler, imaging techniques. A new pre-processing system supports fast-time Doppler removal and motion compensation to a point. Two spotlight imaging techniques which compensate for phase errors due to i) out of focus-plane motion of the radar and ii) local topography, have been implemented and tested. One is based on the polar format algorithm followed by a unique autofocus technique, the other is a full bistatic time-domain backprojection technique. The processing system yields imagery of the specified resolution. Products enabled by this new system include topographic mapping through radar interferometry, and change detection techniques (amplitude and coherent change) for geolocation of the NASA LCROSS mission impact site.

  18. A high-resolution genetic map of mouse chromosome 5 encompassing the reeler (rl) locus

    SciTech Connect

    Beckers, M.C.; Bar, I.; Huynh-Thu, T.

    1994-10-01

    Using interspecific crosses between BALB/c and Mus spretus (SEG) mice, the murine reeler (rl) gene was mapped to the proximal region of chromosome 5 between the hepatocyte growth factor gene (Hgf) and the D5Mit66 microsatellite. The following order was defined: (centromere) - Cch12a/Hgf-D5Mit1-D5Nam1/D5-Nam2-rl/D5Mit61-D5Mit72-Xmv45-Htr5a-Peplb-D5Nam3-D5Mit66. Estimated distances between reeler and the nearest flanking markers D5Nam1 and D5Mit72 are 1.5 and 1.0 cM, respectively (95% confidence level), suggesting that the region could be physically mapped using a manageable number of YAC clones.

  19. High-resolution spatial mapping of changes in the neurochemical profile after focal ischemia in mice.

    PubMed

    Alf, Malte F; Lei, Hongxia; Berthet, Carole; Hirt, Lorenz; Gruetter, Rolf; Mlynarik, Vladimir

    2012-02-01

    After ischemic stroke, the ischemic damage to brain tissue evolves over time and with an uneven spatial distribution. Early irreversible changes occur in the ischemic core, whereas, in the penumbra, which receives more collateral blood flow, the damage is more mild and delayed. A better characterization of the penumbra, irreversibly damaged and healthy tissues is needed to understand the mechanisms involved in tissue death. MRSI is a powerful tool for this task if the scan time can be decreased whilst maintaining high sensitivity. Therefore, we made improvements to a (1)H MRSI protocol to study middle cerebral artery occlusion in mice. The spatial distribution of changes in the neurochemical profile was investigated, with an effective spatial resolution of 1.4 μL, applying the protocol on a 14.1-T magnet. The acquired maps included the difficult-to-separate glutamate and glutamine resonances and, to our knowledge, the first mapping of metabolites γ-aminobutyric acid and glutathione in vivo, within a metabolite measurement time of 45 min. The maps were in excellent agreement with findings from single-voxel spectroscopy and offer spatial information at a scan time acceptable for most animal models. The metabolites measured differed with respect to the temporal evolution of their concentrations and the localization of these changes. Specifically, lactate and N-acetylaspartate concentration changes largely overlapped with the T(2)-hyperintense region visualized with MRI, whereas changes in cholines and glutathione affected the entire middle cerebral artery territory. Glutamine maps showed elevated levels in the ischemic striatum until 8 h after reperfusion, and until 24 h in cortical tissue, indicating differences in excitotoxic effects and secondary energy failure in these tissue types. Copyright © 2011 John Wiley & Sons, Ltd.

  20. High-resolution genetic mapping of rice bacterial blight resistance gene Xa23.

    PubMed

    Wang, Chunlian; Fan, Yinglun; Zheng, Chongke; Qin, Tengfei; Zhang, Xiaoping; Zhao, Kaijun

    2014-10-01

    Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is the most devastating bacterial disease of rice (Oryza sativa L.), a staple food crop that feeds half of the world's population. In management of this disease, the most economical and effective approach is cultivating resistant varieties. Due to rapid change of pathogenicity in the pathogen, it is necessary to identify and characterize more host resistance genes for breeding new resistant varieties. We have previously identified the BB resistance (R) gene Xa23 that confers the broadest resistance to Xoo strains isolated from different rice-growing regions and preliminarily mapped the gene within a 1.7 cm region on the long arm of rice chromosome 11. Here, we report fine genetic mapping and in silico analysis of putative candidate genes of Xa23. Based on F2 mapping populations derived from crosses between Xa23-containing rice line CBB23 and susceptible varieties JG30 or IR24, six new STS markers Lj36, Lj46, Lj138, Lj74, A83B4, and Lj13 were developed. Linkage analysis revealed that the new markers were co-segregated with or closely linked to the Xa23 locus. Consequently, the Xa23 gene was mapped within a 0.4 cm region between markers Lj138 and A83B4, in which the co-segregating marker Lj74 was identified. The corresponding physical distance between Lj138 and A83B4 on Nipponbare genome is 49.8 kb. Six Xa23 candidate genes have been annotated, including four candidate genes encoding hypothetical proteins and the other two encoding a putative ADP-ribosylation factor protein and a putative PPR protein. These results will facilitate marker-assisted selection of Xa23 in rice breeding and molecular cloning of this valuable R gene.

  1. Time-Evolution and Thermal Mapping of Io's Loki Patera at High Resolution

    NASA Astrophysics Data System (ADS)

    de Kleer, Katherine R.; Skrutskie, Michael F.; Leisenring, Jarron; de Pater, Imke; Davies, Ashley; Conrad, Al; Caleb Resnick, Aaron; Hinz, Philip; Defrère, Denis; Veillet, Christian

    2016-10-01

    Observations of Loki Patera with Keck, Gemini N, and the Large Binocular Telescope have yielded a wealth of information in the past several years. Observations with adaptive optics at the Keck and Gemini N telescopes have captured multiple brightening events since 2009. High-cadence observations of the three most recent events place constraints on the thermal properties of the magma and indicate a dependency of the observed intensity on either viewing geometry or mean anomaly. Large Binocular Telescope Interferometer (LBTI) observations during a Europa mutual event have yielded the first-ever temperature map of the entire patera floor at high spatial resolution. M-band (4.7-micron) images were recorded during the event at a cadence of 123 milliseconds, corresponding to a spatial resolution of 10 km across the entire ~200-km patera. This represents a factor of 40 improvement over the spatial resolution achieved by standard adaptive optics imaging with a 10-m telescope at this wavelength. A map of the lava age distribution within the patera is derived from the temperature map using models for cooling basaltic lavas, and the resurfacing rate is calculated. This age distribution, as well as the locations of emission derived from the Keck and Gemini N observations, suggests that resurfacing proceeds in a clockwise direction, contrary to previous findings. All data are consistent with resurfacing by an overturn front on a magma sea, but other resurfacing mechanisms are not ruled out.

  2. Mapping cardiac fiber orientations from high-resolution DTI to high-frequency 3D ultrasound

    NASA Astrophysics Data System (ADS)

    Qin, Xulei; Wang, Silun; Shen, Ming; Zhang, Xiaodong; Wagner, Mary B.; Fei, Baowei

    2014-03-01

    The orientation of cardiac fibers affects the anatomical, mechanical, and electrophysiological properties of the heart. Although echocardiography is the most common imaging modality in clinical cardiac examination, it can only provide the cardiac geometry or motion information without cardiac fiber orientations. If the patient's cardiac fiber orientations can be mapped to his/her echocardiography images in clinical examinations, it may provide quantitative measures for diagnosis, personalized modeling, and image-guided cardiac therapies. Therefore, this project addresses the feasibility of mapping personalized cardiac fiber orientations to three-dimensional (3D) ultrasound image volumes. First, the geometry of the heart extracted from the MRI is translated to 3D ultrasound by rigid and deformable registration. Deformation fields between both geometries from MRI and ultrasound are obtained after registration. Three different deformable registration methods were utilized for the MRI-ultrasound registration. Finally, the cardiac fiber orientations imaged by DTI are mapped to ultrasound volumes based on the extracted deformation fields. Moreover, this study also demonstrated the ability to simulate electricity activations during the cardiac resynchronization therapy (CRT) process. The proposed method has been validated in two rat hearts and three canine hearts. After MRI/ultrasound image registration, the Dice similarity scores were more than 90% and the corresponding target errors were less than 0.25 mm. This proposed approach can provide cardiac fiber orientations to ultrasound images and can have a variety of potential applications in cardiac imaging.

  3. High resolution Moho topography map beneath Iberia and Northern Morocco from RF analysis

    NASA Astrophysics Data System (ADS)

    de Lis Mancilla, Flor; Diaz, Jordi

    2013-04-01

    The Topoiberia-Iberarray broad-band seismic network has covered in three successive legs the Iberian Peninsula and the Northern part of Morocco, allowing to acquire new seismological data with unprecedented resolution and coverage. One of the classical approaches used to infer information on the structure of the crust using passive seismic data is the inspection of the P-to-S conversions at the main discontinuities. In particular, the application of the H-K technique allows to evaluate the thickness and the mean Vp/Vs ratio for the crust beneath each available station. In this contribution, we benefit from the dense Topoiberia-Iberarray seismic network, with stations distributed on a regular 60 x 60 km grid, to obtain a detailed map of the Moho topography and the Vp/Vs variations beneath Iberia and Northern Morocco. This region show a great geodynamical diversity, including, North to South, crustal imbrication in the Pyrenean range, a large and relatively undisturbed Variscan Massif in the center of Iberia and areas of complex and still not completely understood geodynamics in the Alboran domain and the Atlas range. Beneath Northern Morocco, strong lateral variations of the crustal thickness are observed, depicting three domains: a previously unidentified thick crust (reaching at least 45 km) beneath the Rif, a thinned crust region beneath NE Morocco, with depths ranging from 22 to 30 km, and a region of 27-34 km thick crust in the Atlas domain and its foreland regions. Vp/Vs ratios show normal values close to 1.75 for most stations except for the Atlas domain, where several stations give low Vp/Vs ratios of around 1.71. Beneath Southern Iberia, the Moho show also significant variations. The highest values of crustal thickness in this region, reaching 46 km, are found under the External zones of the Betic range, near the contact with the Alboran Domain. Southeastern Iberia is affected by significant crustal thinning (from 19 km to 30 km) occurring over a short

  4. Mapping high-resolution soil moisture and properties using distributed temperature sensing data and an adaptive particle batch smoother

    NASA Astrophysics Data System (ADS)

    Dong, Jianzhi; Steele-Dunne, Susan C.; Ochsner, Tyson E.; Hatch, Christine E.; Sayde, Chadi; Selker, John; Tyler, Scott; Cosh, Michael H.; van de Giesen, Nick

    2016-10-01

    This study demonstrated a new method for mapping high-resolution (spatial: 1 m, and temporal: 1 h) soil moisture by assimilating distributed temperature sensing (DTS) observed soil temperatures at intermediate scales. In order to provide robust soil moisture and property estimates, we first proposed an adaptive particle batch smoother algorithm (APBS). In the APBS, a tuning factor, which can avoid severe particle weight degeneration, is automatically determined by maximizing the reliability of the soil temperature estimates of each batch window. A multiple truth synthetic test was used to demonstrate the APBS can robustly estimate soil moisture and properties using observed soil temperatures at two shallow depths. The APBS algorithm was then applied to DTS data along a 71 m transect, yielding an hourly soil moisture map with meter resolution. Results show the APBS can draw the prior guessed soil hydraulic and thermal properties significantly closer to the field measured reference values. The improved soil properties in turn remove the soil moisture biases between the prior guessed and reference soil moisture, which was particularly noticeable at depth above 20 cm. This high-resolution soil moisture map demonstrates the potential of characterizing soil moisture temporal and spatial variability and reflects patterns consistent with previous studies conducted using intensive point scale soil moisture samples. The intermediate scale high spatial resolution soil moisture information derived from the DTS may facilitate remote sensing soil moisture product calibration and validation. In addition, the APBS algorithm proposed in this study would also be applicable to general hydrological data assimilation problems for robust model state and parameter estimation.

  5. ­­­­High-Resolution Mapping of Kick`em Jenny Submarine Volcano and Associated Landslides

    NASA Astrophysics Data System (ADS)

    Ruchala, T. L.; Carey, S.; Hart, L.; Chen, M.; Scott, C.; Tominaga, M.; Dondin, F. J. Y.; Fujii, M.

    2016-02-01

    To understand the physical and geological processes that drive the volcanism and control the morphology of Kick`em Jenny (KEJ) volcano, the only active submarine volcano in the in the Lesser Antilles volcanic arc, we conducted near-source, high-resolution mapping of KEJ and its subsurface using the Remotely Operated Vehicle (ROV) Hercules during cruise NA054 of the E/V Nautilus (Sept.-Oct. 2014). Shipboard bathymetric data (EM302 system) and slope analysis maps were used to decipher the detailed seafloor morphology surrounding KEJ. Multiple generations of submarine landslides and canyons were observed, suggesting the area has been hosting dynamic sediment transport systems at multiple scales over time. Some of them might have been associated by past eruptions. Clear contacts between partially lithified carbonate sediments and volcanic formations were identified from ROV videos at the middle of the landslide slope face. Detailed observations of facies on these exposures provide constraints on the time intervals between landslide events along the western slope of KEJ. ROV video imagery also identified outcrops of columnar basalts located in the middle of the landslide deposits. These are similar in appearance to those observed in the KEJ crater during previous ROV dives, indicating a possible travel distance of volcanic materials from the crater region along landslide path. High-resolution photo mosaics, bathymetry, and magnetic data acquired by ROV Hercules were used to investigate geological processes and the possible volcanic source of landslide material within the KEJ crater. Mapping in the northwestern part of the crater floor revealed distinctive regions, including (i) microbial mats, (ii) active hydrothermal vent sites; (iii) landforms curved by channelized bottom current where seafloor is outcropped; and (iv) coarse scree the distribution of which may correlate with the distance from the crater rim. Near-bottom magnetic profiles show coherent magnetic

  6. High-Resolution AUV Mapping Reveals Structural Details of Submarine Inflated Lava Flows

    NASA Astrophysics Data System (ADS)

    Paduan, J.; Clague, D. A.; Caress, D. W.; Thomas, H.; Thompson, D.; Conlin, D.

    2009-12-01

    The MBARI mapping AUV D. Allan B. has now been used to map volcanic terrain at mid-ocean ridges, back-arc spreading centers, and seamounts. These include the summit caldera and upper south rift zone at Axial Volcano, the summit of Davidson Seamount, the Endeavour hydrothermal fields, the Northeast Lau Spreading Center and West Mata Volcano, and, most recently, the CoAxial, North Cleft and North Gorda historic eruption sites on the Juan de Fuca and Gorda Ridges. ROV and submersible dives at most of these sites have provided groundtruth for the textures and features revealed in the roughly 1-m resolution maps. A prominent feature in the maps from four of the sites are inflated flows that did not deflate or drain. These resemble subaerial tumuli but differ in being located on level terrain, apparently atop or very near eruptive vents instead of being in the distal portions of flows. The largest inflated flow at Axial Volcano is on the caldera floor. The main part is 500 by 300 m, and up to 30 m high, with a lobe that extends another 750 m in a sinuous path. It and two nearby, medium-sized inflated flows were first described from sidescan imagery and a submersible dive by Appelgate and Embley (Bull. Volcanol., 54, 447-458, 1992). The AUV maps show clearly the smooth, gently domed relief of the large inflated flow and its sinuous shape on the seafloor, the medium-sized nearby inflated flows, and several additional smaller ones. Particularly striking is a network of 4 to 10 m deep cracks along the crest of each inflation. The cracks occur 30 to 50 m from the margins on all sides of the wider parts of the inflated flows, and become medial cracks along the entire length of the narrow parts, which are nearly triangular in cross-section. An inflation pit 35 m in diameter has a depth equal to the surrounding lava fields. ROV Doc Ricketts dove on these flows in August 2009 and photographed the deeply cracked, uplifted, once flat-lying lineated and ropy sheet flows that form

  7. The Value of High Resolution Forest Canopy Maps for Implementing Carbon Sequestration Programs in Maryland

    NASA Astrophysics Data System (ADS)

    Brown, M. E.; Abbott, P. C.; Hittich, R.; Dubayah, R.

    2015-12-01

    As part of the NASA Carbon Monitoring System (CMS) Program, the University of Maryland has produced 1m resolution forest canopy cover and height maps that have been provided to the State of Maryland. The project used existing, wall-to-wall airborne lidar coverage combined with other remote sensing and field datasets to produce countywide maps of carbon stocks and their uncertainties at 30 m resolution as well as the 1m canopy maps. In this paper, we examine what purposes we identified for the data for decision making in climate mitigation, what use it has already seen, and what potential there is in the future for using the data. The State of Maryland has three programs focused on maintaining or increasing forest cover as part of its Greenhouse Gas Emissions Reduction Program (GHGRP) program enacted in 2012, including Woodland Incentive Program (WIP), the Lawn to Woodland Initiative (L2W), and the Environmental Quality Incentives Program (EQIP). Forest canopy data from CMS were examined the prospects for both adoption and carbon sequestration of these three initiatives, and their effects on the overall success of the GHGRP. We found that it was difficult it is to pin down "value" that is directly attributable to the data, although we found the data to be important in recognizing the nature and extent of the carbon problem, and in identifying potential solutions to addressing the problem. As in many decision-making contexts, having high quality, accurate data on forest cover is necessary but not sufficient for effective, affordable programs that lead to carbon sequestration in the state.

  8. Nationwide high-resolution mapping of hazards in the Philippines (Plinius Medal Lecture)

    NASA Astrophysics Data System (ADS)

    Lagmay, Alfredo Mahar Francisco A.

    2015-04-01

    The Philippines being a locus of typhoons, tsunamis, earthquakes, and volcanic eruptions, is a hotbed of disasters. Situated in a region where severe weather and geophysical unrest is common, the Philippines will inevitably suffer from calamities similar to those experienced recently. With continued development and population growth in hazard prone areas, it is expected that damage to infrastructure and human losses would persist and even rise unless appropriate measures are immediately implemented by government. Recently, the Philippines put in place a responsive program called the Nationwide Operational Assessment of Hazards (NOAH) for disaster prevention and mitigation. The efforts of Project NOAH are an offshoot of lessons learned from previous disasters that have inflicted massive loss of lives and costly damage to property. Several components of the NOAH program focus on mapping of landslide, riverine flood and storm surge inundation hazards. By simulating hazards phenomena over IFSAR- and LiDAR-derived digital terrain models (DTMs) using high-performance computers, multi-hazards maps of 1:10,000 scale, have been produced and disseminated to local government units through a variety of platforms. These detailed village-level (barangay-level) maps are useful to identify safe evacuation sites, planning emergency access routes and prepositioning of search and rescue and relief supplies during times of crises. They are also essential for long-term development planning of communities. In the past two years, NOAH was instrumental in providing timely, site-specific, and understandable hazards information to the public, considered as best practice in disaster risk reduction management (DRR). The use of advanced science and technology in the country's disaster prevention efforts is imperative to successfully mitigate the adverse impacts of natural hazards and should be a continuous quest - to find the best products, put forth in the forefront of battle against

  9. High Resolution of Quantitative Traits into Multiple Loci via Interval Mapping

    PubMed Central

    Jansen, R. C.; Stam, P.

    1994-01-01

    A very general method is described for multiple linear regression of a quantitative phenotype on genotype [putative quantitative trait loci (QTLs) and markers] in segregating generations obtained from line crosses. The method exploits two features, (a) the use of additional parental and F(1) data, which fixes the joint QTL effects and the environmental error, and (b) the use of markers as cofactors, which reduces the genetic background noise. As a result, a significant increase of QTL detection power is achieved in comparison with conventional QTL mapping. The core of the method is the completion of any missing genotypic (QTL and marker) observations, which is embedded in a general and simple expectation maximization (EM) algorithm to obtain maximum likelihood estimates of the model parameters. The method is described in detail for the analysis of an F(2) generation. Because of the generality of the approach, it is easily applicable to other generations, such as backcross progenies and recombinant inbred lines. An example is presented in which multiple QTLs for plant height in tomato are mapped in an F(2) progeny, using additional data from the parents and their F(1) progeny. PMID:8013917

  10. High-Resolution Mapping of Thermal History in Polymer Nanocomposites: Gold Nanorods as Microscale Temperature Sensors.

    PubMed

    Kennedy, W Joshua; Slinker, Keith A; Volk, Brent L; Koerner, Hilmar; Godar, Trenton J; Ehlert, Gregory J; Baur, Jeffery W

    2015-12-23

    A technique is reported for measuring and mapping the maximum internal temperature of a structural epoxy resin with high spatial resolution via the optically detected shape transformation of embedded gold nanorods (AuNRs). Spatially resolved absorption spectra of the nanocomposites are used to determine the frequencies of surface plasmon resonances. From these frequencies the AuNR aspect ratio is calculated using a new analytical approximation for the Mie-Gans scattering theory, which takes into account coincident changes in the local dielectric. Despite changes in the chemical environment, the calculated aspect ratio of the embedded nanorods is found to decrease over time to a steady-state value that depends linearly on the temperature over the range of 100-200 °C. Thus, the optical absorption can be used to determine the maximum temperature experienced at a particular location when exposure times exceed the temperature-dependent relaxation time. The usefulness of this approach is demonstrated by mapping the temperature of an internally heated structural epoxy resin with 10 μm lateral spatial resolution.

  11. A multi-plate velocity-map imaging design for high-resolution photoelectron spectroscopy.

    PubMed

    Kregel, Steven J; Thurston, Glen K; Zhou, Jia; Garand, Etienne

    2017-09-07

    A velocity map imaging (VMI) setup consisting of multiple electrodes with three adjustable voltage parameters, designed for slow electron velocity map imaging applications, is presented. The motivations for this design are discussed in terms of parameters that influence the VMI resolution and functionality. Particularly, this VMI has two tunable potentials used to adjust for optimal focus, yielding good VMI focus across a relatively large energy range. It also allows for larger interaction volumes without significant sacrifice to the resolution via a smaller electric gradient at the interaction region. All the electrodes in this VMI have the same dimensions for practicality and flexibility, allowing for relatively easy modifications to suit different experimental needs. We have coupled this VMI to a cryogenic ion trap mass spectrometer that has a flexible source design. The performance is demonstrated with the photoelectron spectra of S(-) and CS2(-). The latter has a long vibrational progression in the ground state, and the temperature dependence of the vibronic features is probed by changing the temperature of the ion trap.

  12. A multi-plate velocity-map imaging design for high-resolution photoelectron spectroscopy

    NASA Astrophysics Data System (ADS)

    Kregel, Steven J.; Thurston, Glen K.; Zhou, Jia; Garand, Etienne

    2017-09-01

    A velocity map imaging (VMI) setup consisting of multiple electrodes with three adjustable voltage parameters, designed for slow electron velocity map imaging applications, is presented. The motivations for this design are discussed in terms of parameters that influence the VMI resolution and functionality. Particularly, this VMI has two tunable potentials used to adjust for optimal focus, yielding good VMI focus across a relatively large energy range. It also allows for larger interaction volumes without significant sacrifice to the resolution via a smaller electric gradient at the interaction region. All the electrodes in this VMI have the same dimensions for practicality and flexibility, allowing for relatively easy modifications to suit different experimental needs. We have coupled this VMI to a cryogenic ion trap mass spectrometer that has a flexible source design. The performance is demonstrated with the photoelectron spectra of S- and CS2 -. The latter has a long vibrational progression in the ground state, and the temperature dependence of the vibronic features is probed by changing the temperature of the ion trap.

  13. A high-resolution map of the chromosomal region surrounding the nude gene

    SciTech Connect

    Blackburn, C.C.; Griffith, J.; Morahan, G.

    1995-03-20

    The nude mutation produces the apparently disparate phenotypes of hairlessness and congenital thymic aplasia. These pleiotropic defects are the result of a single, autosomal recessive mutation that was previously mapped to a 9-cM region of murine chromosome 11 bounded by loci encoding the acetylcholine receptor P subunit and myeloperoxidase. In this study, exclusion mapping of a panel of congenic nude strains was used to place the nude locus between the microsatellite loci D11Nds1 and D11Mit8. The relative distance from nude to each of these loci was determined by analyzing a large segregating cross. Thus, nude lies 1.4 cM distal to D11Nds1 and is 0.5 cM proximal to D11Mit8. Mice that carried recombinational breakpoints between D11Nds1 and D11Mit8 were further analyzed at the loci Evi-2 and D11Mit34, which placed nu 0.2 cM proximal to these markers. D11Nds1 and Evi-2/D11Mit34 thus define the new proximal and distal boundaries, respectively, for the nu interval. We also report the typing of the above microsatellite markers in the AKXD, AKXL, BXD, CXB, and BXH recombinant inbred strains, which confirmed the relative order and separation of loci in this region. 47 refs., 3 figs., 1 tab.

  14. A high resolution CO map of the inner region of M51

    NASA Astrophysics Data System (ADS)

    Aalto, S.; Huettemeister, S.; Scoville, N. Z.; Thaddeus, P.

    M51, the Whirlpool galaxy, is the closest `Grand design' spiral. Seen almost face-on, it is an excellent target for structural studies. We present a sensitive mosaic map of the inner ~2.5', taken at OVRO in the J = 1 - 0 of CO. The resolution, 2.5' ', is the highest ever obtained in a molecular line in this galaxy. We just resolve the circumnuclear disk in the very center of M51, which has been interpretated as a low luminosity AGN. We investigate the differences in gas and cloud properties in the circumnuclear disk, where the gas is dense, the `diffuse' region less than 1kpc distant from the nucleus, which may still be affected by its proximity to the center, the spiral arms and the interarm region. In the spiral arms, evidence of streaming motions, likely due to spiral density waves, is seen with unprecedented clarity. Position-velocity plots indicate that individual clouds are participating in the general motions as bound entities. Arm bifurcations, possibly due to secondary peaks of the density wave, are indicated. Our naturally weighted, most sensitive map reveals bridge-like structures connecting spiral arms. Reversals in the velocity structure along the most prominent bridge suggests that gas is moving off the spiral arm, giving insight into a possible formation mechanism for interarm clouds.

  15. High-resolution linkage-disequilibrium mapping of the cartilage-hair hypoplasia gene

    SciTech Connect

    Sulisalo, T.; Klockars, J.; Chapelle, A. de la; Kaitila, I. |; Maekitie, O.; Sistonen, P.; Francomano, C.A.

    1994-11-01

    We recently assigned the gene for an autosomal recessive skeletal dysplasia, cartilage-hair hypoplasia (CHH), to 9p21-p13 in Finnish and Amish families. An association was observed between CHH and alleles at D9S163 in both family series, suggesting that these loci are in linkage disequilibrium and close to each other. Here we extended these studies by exploiting the linkage-disequilibrium information that can be obtained from families with a single affected child, and we studied 66 Finnish CHH families with seven microsatellite markers. The analysis based on the Luria and Delbrueck (1943) method and adapted to the study of human founder populations suggests that the distance between CHH and D9S163 is {approximately}0.3 cM. An eight-point linkage analysis modified to take advantage of all possible information in 15 Finnish and 17 Amish families was capable of narrowing the likely location of CHH to within an interval of 1.7 cM on a male map. The peak lod score of 54.92 was attained 0.03 and 0.1 cM proximal to D9S163 on the male and female maps, respectively. These results confirm the power of genetic resolution, that lies in the study of linkage disequilibrium in well-defined founder populations with one major ancestral disease mutation. 21 refs., 4 figs., 3 tabs.

  16. High-resolution spectral mapping of a lensed high power laser bar

    NASA Astrophysics Data System (ADS)

    Gannon, Caleb D.; Koenning, Tobias; Patterson, Steve G.; Leisher, Paul O.

    2014-03-01

    Alkali gas lasers based on rubidium vapor have an extremely narrow absorption band (<0.01 nm at STP) at 780 nm. Diode-pumped alkali lasers (DPALs) require high-power diode arrays having emission spectra which are closely matched to this absorption peak. There are several methods which can be used for narrowing and stabilizing the output spectrum of a diode laser bar including external locking via a volumetric holographic grating (VHG). While this approach offers several advantages over internal stabilization techniques, the effect of pointing error arising from bar smile can be detrimental to the locked performance of the lensed array. In order to investigate the effect of smile on wavelength locking, a system capable of mapping the emission spectrum of the lensed diode laser bar was developed. The approach utilizes an imaging system and spatial filter to couple light from individual emitters of the lensed array into a commercial optical spectrum analyzer. This approach offers a larger dynamic range than traditional spectral mapping techniques, with a resolved signal to noise ratio in excess of 60 dB. Results from the characterization of a VHG-locked 780 nm laser bar array will be presented.

  17. Methionine synthase: high-resolution mapping of the human gene and evaluation as a candidate locus for neural tube defects.

    PubMed

    Brody, L C; Baker, P J; Chines, P S; Musick, A; Molloy, A M; Swanson, D A; Kirke, P N; Ghosh, S; Scott, J M; Mills, J L

    1999-08-01

    Periconceptual folate supplementation has been found to prevent the occurrence of many neural tube defects (NTDs). Consequently, genetic variation in folate metabolism genes is expected to contribute to the risk for neural tube defects. Methionine synthase catalyzes the vitamin B(12)-dependent conversion of homocysteine and 5-methyltetrahydrofolate to methionine and tetrahydrofolate. The observation that homocysteine and vitamin B(12) levels are independent predictors of NTD risk suggested that methionine synthase could be a candidate gene for NTDs. To assess the role of the MS gene in NTDs, we performed high-resolution physical mapping of the MS locus, isolated highly polymorphic markers linked to the MS gene, and tested for an association between specific MS alleles and NTDs. We mapped the MS gene to a position between 909 and 913 cR(10000) on chromosome 1 by radiation hybrid mapping. Polymorphic markers D1S1567 and D1S1568 map to locations no more than 900 and 194 kb from the MS gene, respectively. The segregation of these polymorphic markers was measured in 85 Irish NTD families. No allele of either marker showed a significant association with NTDs using the transmission disequilibrium test. A lack of association was also observed for the D1919G missense mutation within the gene. Our results suggest that inherited variation in the MS gene does not contribute to NTD risk in this population.

  18. A high-resolution cat radiation hybrid and integrated FISH mapping resource for phylogenomic studies across Felidae.

    PubMed

    Davis, Brian W; Raudsepp, Terje; Pearks Wilkerson, Alison J; Agarwala, Richa; Schäffer, Alejandro A; Houck, Marlys; Chowdhary, Bhanu P; Murphy, William J

    2009-04-01

    We describe the construction of a high-resolution radiation hybrid (RH) map of the domestic cat genome, which includes 2662 markers, translating to an estimated average intermarker distance of 939 kilobases (kb). Targeted marker selection utilized the recent feline 1.9x genome assembly, concentrating on regions of low marker density on feline autosomes and the X chromosome, in addition to regions flanking interspecies chromosomal breakpoints. Average gap (breakpoint) size between cat-human ordered conserved segments is less than 900 kb. The map was used for a fine-scale comparison of conserved syntenic blocks with the human and canine genomes. Corroborative fluorescence in situ hybridization (FISH) data were generated using 129 domestic cat BAC clones as probes, providing independent confirmation of the long-range correctness of the map. Cross-species hybridization of BAC probes on divergent felids from the genera Profelis (serval) and Panthera (snow leopard) provides further evidence for karyotypic conservation within felids, and demonstrates the utility of such probes for future studies of chromosome evolution within the cat family and in related carnivores. The integrated map constitutes a comprehensive framework for identifying genes controlling feline phenotypes of interest, and to aid in assembly of a higher coverage feline genome sequence.

  19. A High-Resolution Cat Radiation Hybrid and Integrated FISH Mapping Resource for Phylogenomic Studies across Felidae

    PubMed Central

    Davis, Brian W.; Raudsepp, Terje; Wilkerson, Alison J. Pearks; Agarwala, Richa; Schäffer, Alejandro A.; Houck, Marlys; Ryder, Oliver A.; Chowdhdary, Bhanu P.; Murphy, William J.

    2008-01-01

    We describe the construction of a high-resolution radiation hybrid (RH) map of the domestic cat genome, which includes 2,662 markers, translating to an estimated average intermarker distance of 939 kilobases (Kb). Targeted marker selection utilized the recent feline 1.9x genome assembly, concentrating on regions of low marker density on feline autosomes and the X chromosome, in addition to regions flanking interspecies chromosomal breakpoints. Average gap (breakpoint) size between cat-human ordered conserved segments is less than 900 Kb. The map was used for a fine-scale comparison of conserved syntenic blocks with the human and canine genomes. Corroborative fluorescence in situ hybridization (FISH) data were generated using 129 domestic cat BAC-clones as probes, providing independent confirmation of the long-range correctness of the map. Cross-species hybridization of BAC probes on divergent felids from the genera Profelis (serval) and Panthera (snow leopard) provides further evidence for karyotypic conservation within felids, and demonstrates the utility of such probes for future studies of chromosome evolution within the cat family and in related carnivores. The integrated map constitutes a comprehensive framework for identifying genes controlling feline phenotypes of interest, and to aid in assembly of a higher coverage feline genome sequence. PMID:18951970

  20. High-resolution myocardial perfusion mapping in small animals in vivo by spin-labeling gradient-echo imaging.

    PubMed

    Kober, Frank; Iltis, Isabelle; Izquierdo, Marguerite; Desrois, Martine; Ibarrola, Danielle; Cozzone, Patrick J; Bernard, Monique

    2004-01-01

    An ECG and respiration-gated spin-labeling gradient-echo imaging technique is proposed for the quantitative and completely noninvasive measurement and mapping of myocardial perfusion in small animals in vivo. In contrast to snapshot FLASH imaging, the spatial resolution of the perfusion maps is not limited by the heart rate. A significant improvement in image quality is achieved by synchronizing the inversion pulse to the respiration movements of the animals, thereby allowing for spontaneous respiration. High-resolution myocardial perfusion maps (in-plane resolution=234 x 468 microm2) demonstrating the quality of the perfusion measurement were obtained at 4.7 T in a group of seven freely breathing Wistar-Kyoto rats under isoflurane anesthesia. The mean perfusion value (group average +/- SD) was 5.5 +/- 0.7 ml g(-1)min(-1). In four animals, myocardial perfusion was mapped and measured under cardiac dobutamine stress. Perfusion increased to 11.1 +/- 1.9 ml g(-1)min(-1). The proposed method is particularly useful for the study of small rodents at high fields.

  1. High-resolution aeromagnetic data, a new tool for mapping intrabasinal faults: Example from the Albuquerque basin, New Mexico

    USGS Publications Warehouse

    Grauch, V.J.S.

    2001-01-01

    High-resolution aeromagnetic surveys flown over the Albuquerque basin, New Mexico, demonstrate that aeromagnetic methods can successfully map concealed and poorly exposed faults in sediment-filled basins. This is the first known use of aeromagnetic data as an aid to surficial mapping and hydrogeologic studies in a basin. Aeromagnetic maps show detailed fault patterns within the basin fill that revise the structural view of the basin. Concealed faults are more numerous and more closely spaced than expected. The Hubbell Springs fault is the central splay of three generally north-striking fault splays that can be traced for nearly 50 km. The splays converge on the north and may represent the southern extension of the Tijeras fault, contradicting the proposed southwest extension of the Tijeras fault across the basin. In profile view, the linear aeromagnetic anomalies associated with faults show a variety of signatures. One signature has potential for mapping fault-controlled sedimentation in the subsurface because it identifies increases in magnetic, likely coarse-grained, material in the hanging walls of faults.

  2. High-resolution three-dimensional macromolecular proton fraction mapping for quantitative neuroanatomical imaging of the rodent brain in ultra-high magnetic fields.

    PubMed

    Naumova, Anna V; Akulov, Andrey E; Khodanovich, Marina Yu; Yarnykh, Vasily L

    2017-02-15

    A well-known problem in ultra-high-field MRI is generation of high-resolution three-dimensional images for detailed characterization of white and gray matter anatomical structures. T1-weighted imaging traditionally used for this purpose suffers from the loss of contrast between white and gray matter with an increase of magnetic field strength. Macromolecular proton fraction (MPF) mapping is a new method potentially capable to mitigate this problem due to strong myelin-based contrast and independence of this parameter of field strength. MPF is a key parameter determining the magnetization transfer effect in tissues and defined within the two-pool model as a relative amount of macromolecular protons involved into magnetization exchange with water protons. The objectives of this study were to characterize the two-pool model parameters in brain tissues in ultra-high magnetic fields and introduce fast high-field 3D MPF mapping as both anatomical and quantitative neuroimaging modality for small animal applications. In vivo imaging data were obtained from four adult male rats using an 11.7T animal MRI scanner. Comprehensive comparison of brain tissue contrast was performed for standard R1 and T2 maps and reconstructed from Z-spectroscopic images two-pool model parameter maps including MPF, cross-relaxation rate constant, and T2 of pools. Additionally, high-resolution whole-brain 3D MPF maps were obtained with isotropic 170µm voxel size using the single-point synthetic-reference method. MPF maps showed 3-6-fold increase in contrast between white and gray matter compared to other parameters. MPF measurements by the single-point synthetic reference method were in excellent agreement with the Z-spectroscopic method. MPF values in rat brain structures at 11.7T were similar to those at lower field strengths, thus confirming field independence of MPF. 3D MPF mapping provides a useful tool for neuroimaging in ultra-high magnetic fields enabling both quantitative tissue

  3. History of the clay-rich unit at Mawrth Vallis, Mars: High-resolution mapping of a candidate landing site

    NASA Astrophysics Data System (ADS)

    Loizeau, D.; Mangold, N.; Poulet, F.; Bibring, J.-P.; Bishop, J. L.; Michalski, J.; Quantin, C.

    2015-11-01

    The Mawrth Vallis region is covered by some of the largest phyllosilicate-rich outcrops on Mars, making it a unique window into the past history of Mars in terms of water alteration, potential habitability, and the search for past life. A landing ellipse had been proposed for the Curiosity rover. This area has been extensively observed by the High Resolution Imaging Science Experiment and the Compact Reconnaissance Imaging Spectrometer for Mars, offering the possibility to produce geologic, structural, and topographic maps at very high resolution. These observations provide an unprecedented detailed context of the rocks at Mawrth Vallis, in terms of deposition, alteration, erosion, and mechanical constraints. Our analyses demonstrate the presence of a variety of alteration environments on the surface and readily accessible to a rover, the presence of flowing water at the surface postdating the formation of the clay-rich units, and evidence for probable circulation of fluids in the rocks at different depths. These rocks undergo continuous erosion, creating fresh outcrops where potential biomarkers may have been preserved. The diversity of aqueous environments over geological time coupled to excellent preservation properties make the area a very strong candidate for future robotic investigation on Mars, like the NASA Mars 2020 mission.

  4. High-resolution physical mapping in Pennisetum squamulatum reveals extensive chromosomal heteromorphism of the genomic region associated with apomixis.

    PubMed

    Akiyama, Yukio; Conner, Joann A; Goel, Shailendra; Morishige, Daryl T; Mullet, John E; Hanna, Wayne W; Ozias-Akins, Peggy

    2004-04-01

    Gametophytic apomixis is asexual reproduction as a consequence of parthenogenetic development of a chromosomally unreduced egg. The trait leads to the production of embryos with a maternal genotype, i.e. progeny are clones of the maternal plant. The application of the trait in agriculture could be a tremendous tool for crop improvement through conventional and nonconventional breeding methods. Unfortunately, there are no major crops that reproduce by apomixis, and interspecific hybridization with wild relatives has not yet resulted in commercially viable germplasm. Pennisetum squamulatum is an aposporous apomict from which the gene(s) for apomixis has been transferred to sexual pearl millet by backcrossing. Twelve molecular markers that are linked with apomixis coexist in a tight linkage block called the apospory-specific genomic region (ASGR), and several of these markers have been shown to be hemizygous in the polyploid genome of P. squamulatum. High resolution genetic mapping of these markers has not been possible because of low recombination in this region of the genome. We now show the physical arrangement of bacterial artificial chromosomes containing apomixis-linked molecular markers by high resolution fluorescence in situ hybridization on pachytene chromosomes. The size of the ASGR, currently defined as the entire hemizygous region that hybridizes with apomixis-linked bacterial artificial chromosomes, was estimated on pachytene and mitotic chromosomes to be approximately 50 Mbp (a quarter of the chromosome). The ASGR includes highly repetitive sequences from an Opie-2-like retrotransposon family that are particularly abundant in this region of the genome.

  5. A flat Universe from high-resolution maps of the cosmic microwave background radiation

    PubMed

    de Bernardis P; Ade; Bock; Bond; Borrill; Boscaleri; Coble; Crill; De Gasperis G; Farese; Ferreira; Ganga; Giacometti; Hivon; Hristov; Iacoangeli; Jaffe; Lange; Martinis; Masi; Mason; Mauskopf; Melchiorri; Miglio; Montroy; Netterfield

    2000-04-27

    The blackbody radiation left over from the Big Bang has been transformed by the expansion of the Universe into the nearly isotropic 2.73 K cosmic microwave background. Tiny inhomogeneities in the early Universe left their imprint on the microwave background in the form of small anisotropies in its temperature. These anisotropies contain information about basic cosmological parameters, particularly the total energy density and curvature of the Universe. Here we report the first images of resolved structure in the microwave background anisotropies over a significant part of the sky. Maps at four frequencies clearly distinguish the microwave background from foreground emission. We compute the angular power spectrum of the microwave background, and find a peak at Legendre multipole Ipeak = (197 +/- 6), with an amplitude delta T200 = (69 +/- 8) microK. This is consistent with that expected for cold dark matter models in a flat (euclidean) Universe, as favoured by standard inflationary models.

  6. High-resolution global maps of 21st-century forest cover change

    USGS Publications Warehouse

    Hansen, M.C.; Potapov, P.V.; Moore, R.; Hancher, M.; Turubanova, S.A.; Tyukavina, A.; Thau, D.; Stehman, S.V.; Goetz, S.J.; Loveland, T.R.; Kommareddy, A.; Egorov, Alexey; Chini, L.; Justice, C.O.; Townshend, J.R.G.

    2013-01-01

    Quantification of global forest change has been lacking despite the recognized importance of forest ecosystem services. In this study, Earth observation satellite data were used to map global forest loss (2.3 million square kilometers) and gain (0.8 million square kilometers) from 2000 to 2012 at a spatial resolution of 30 meters. The tropics were the only climate domain to exhibit a trend, with forest loss increasing by 2101 square kilometers per year. Brazil’s well-documented reduction in deforestation was offset by increasing forest loss in Indonesia, Malaysia, Paraguay, Bolivia, Zambia, Angola, and elsewhere. Intensive forestry practiced within subtropical forests resulted in the highest rates of forest change globally. Boreal forest loss due largely to fire and forestry was second to that in the tropics in absolute and proportional terms. These results depict a globally consistent and locally relevant record of forest change.

  7. High-resolution global maps of 21st-century forest cover change.

    PubMed

    Hansen, M C; Potapov, P V; Moore, R; Hancher, M; Turubanova, S A; Tyukavina, A; Thau, D; Stehman, S V; Goetz, S J; Loveland, T R; Kommareddy, A; Egorov, A; Chini, L; Justice, C O; Townshend, J R G

    2013-11-15

    Quantification of global forest change has been lacking despite the recognized importance of forest ecosystem services. In this study, Earth observation satellite data were used to map global forest loss (2.3 million square kilometers) and gain (0.8 million square kilometers) from 2000 to 2012 at a spatial resolution of 30 meters. The tropics were the only climate domain to exhibit a trend, with forest loss increasing by 2101 square kilometers per year. Brazil's well-documented reduction in deforestation was offset by increasing forest loss in Indonesia, Malaysia, Paraguay, Bolivia, Zambia, Angola, and elsewhere. Intensive forestry practiced within subtropical forests resulted in the highest rates of forest change globally. Boreal forest loss due largely to fire and forestry was second to that in the tropics in absolute and proportional terms. These results depict a globally consistent and locally relevant record of forest change.

  8. High-resolution mapping and genetic characterization of the Lazy-2 gravitropic mutant of tomato

    NASA Technical Reports Server (NTRS)

    Behringer, F. J.; Lomax, T. L.

    1999-01-01

    Mutation of the Lazy-2 (Lz-2) gene in tomato (Lycopersicon esculentum mill.) produces a phytochrome-dependent reversal of shoot gravitropism, providing a unique genetic resource for investigating how signals from light modulate gravitropism. We mapped the Lz-2 gene using RFLPs and a PCR-based technique to assess the feasibility of positional cloning. Analysis of a 1338 plant backcross population between L. esculentum and L. pennellii placed Lz-2 within a 1.2 cM interval on chromosome 5, 0.4 cM from TG504-CT201A interval. The inabililty to resolve these markers indicates that Lz-2 resides in a centromeric region in which recombination is highly suppressed. Lazy-2 is tightly linked to but does not encode the gene for ACC4, an enzyme involved in ethylene biosynthesis. We also observed that Lz-2 is partially dominant under certain conditions and stages of development.

  9. Mapping Coral-Algal Dynamics in a Seasonal Upwelling Area Using Spaceborne High Resolution Sensors

    NASA Astrophysics Data System (ADS)

    Pauly, Klaas; Goossens, Rudi; De Clerck, Olivier

    2010-12-01

    PROBA/CHRIS is one of the first satellite sensors to offer both high spatial and spectral resolutions. We explored the potential of this sensor to map the dynamics of seaweed and coral cover in an area influenced by seasonal upwelling in the Arabian Sea. Quantitative field assessments coincided with image acquisitions. After removal of sensor noise and atmospheric effects, maximum likelihood supervised classification yielded a tau accuracy of 64.09 for the summer monsoon dataset. Clearer waters and a lower spatial heterogeneity in the winter monsoon dataset resulted in a tau accuracy of 71.45. Post-classification comparison and vegetation indices illustrated the conspicuous turnover from dense macroalgal stands covering nearly all coral communities during summer to bare rock or turf communities during winter, with coral becoming the predominant bottom type. These results were further analysed using a novel maximum entropy sub-pixel approach and were shown to consistently outperform results from Landsat 7 ETM+ imagery.

  10. High-resolution genome-wide mapping of the primary structure of chromatin.

    PubMed

    Zhang, Zhenhai; Pugh, B Franklin

    2011-01-21

    The genomic organization of chromatin is increasingly recognized as a key regulator of cell behavior, but deciphering its regulation mechanisms requires detailed knowledge of chromatin's primary structure-the assembly of nucleosomes throughout the genome. This Primer explains the principles for mapping and analyzing the primary organization of chromatin on a genomic scale. After introducing chromatin organization and its impact on gene regulation and human health, we then describe methods that detect nucleosome positioning and occupancy levels using chromatin immunoprecipitation in combination with deep sequencing (ChIP-Seq), a strategy that is now straightforward and cost efficient. We then explore current strategies for converting the sequence information into knowledge about chromatin, an exciting challenge for biologists and bioinformaticians. Copyright © 2011 Elsevier Inc. All rights reserved.

  11. A Flat Universe from High-Resolution Maps of the Cosmic MicrowaveBackground Radiation

    SciTech Connect

    de Bernardis, P.; Ade, P.A.R.; Bock, J.J.; Bond, J.R.; Borrill,J.; Boscaleri, A.; Coble, K.; Crill, B.P.; De Gasperis, G.; Farese, P.C.; Ferreira, P.G.; Ganga, K.; Giacometti, M.; Hivon, E.; Hristov, V.V.; Iacoangeli, A.; Jaffe, A.H.; Lange, A.E.; Martinis, L.; Masi, S.; Mason,P.; Mauskopf, P.D.; Melchiorri, A.; Miglio, L.; Montroy, T.; Netterfield,C.B.; Pascale, E.; Piacentini, F.; Pogosyan, D.; Prunet, S.; Rao, S.; Romeo, G.; Ruhl, J.E.; Scaramuzzi, F.; Sforna, D.; Vittorio, N.

    2000-04-28

    The blackbody radiation left over from the Big Bang has been transformed by the expansion of the Universe into the nearly isotropic 2.73 K Cosmic Microwave Background. Tiny inhomogeneities in the early Universe left their imprint on the microwave background in the form of small anisotropies in its temperature. These anisotropies contain information about basic cosmological parameters, particularly the total energy density and curvature of the universe. Here we report the first images of resolved structure in the microwave background anisotropies over a significant part of the sky. Maps at four frequencies clearly distinguish the microwave background from foreground emission. We compute the angular power spectrum of the microwave background, and find a peak at Legendre multipole {ell}{sub peak} = (197 {+-} 6), with an amplitude DT{sub 200} = (69 {+-} 8){mu}K. This is consistent with that expected for cold dark matter models in a flat (euclidean) Universe, as favored by standard inflationary scenarios.

  12. A high-resolution land-use map; Nogales, Sonora, Mexico

    USGS Publications Warehouse

    Norman, Laura M.; Villarreal, Miguel L.; Wallace, Cynthia S.A.; Gil Anaya, Claudia Z.; Diaz Arcos, Israel; Gray, Floyd

    2010-01-01

    The cities of Nogales, Sonora, and Nogales, Arizona, are located in the Ambos Nogales Watershed, a topographically irregular bowl-shaped area with a northward gradient. Throughout history, residents in both cities have been affected by flooding. Currently, the primary method for regulating this runoff is to build a series of detention basins in Nogales, Sonora. Additionally, the municipality also is considering land-use planning to help mitigate flooding. This paper describes the production of a 10-meter resolution land-use map, derived from 2008 aerial photos of the Nogales, Sonora Watershed for modeling impacts of the detention basin construction and in support of an ?Early Warning Hazard System? for the region.

  13. Building high-resolution synthetic lethal networks: a 'Google map' of the cancer cell.

    PubMed

    Paul, James M; Templeton, Shaina D; Baharani, Akanksha; Freywald, Andrew; Vizeacoumar, Franco J

    2014-12-01

    The most commonly used therapies for cancer involve delivering high doses of radiation or toxic chemicals to the patient that also cause substantial damage to normal tissue. To overcome this, researchers have recently resorted to a basic biological concept called 'synthetic lethality' (SL) that takes advantage of interactions between gene pairs. The identification of SL interactions is of considerable therapeutic interest because if a particular gene is SL with a tumor-causing mutation, then the targeting that gene carries therapeutic advantages. Mapping these interactions in the context of human cancer cells could hold the key to effective, targeted cancer treatments. In this review, we cover the recent advances that aim to identify these SL interactions using unbiased genetic screens.

  14. High-resolution reflecting time-of-flight momentum and energy mapping system

    SciTech Connect

    Wang Chao; Kang Yifan; Weaver, Larry; Chang Zenghu

    2009-07-15

    A new system to map electron momentum and energy is proposed. A reflecting electrode is introduced into a time-of-flight (TOF) system whose decelerating electric field sends all the electrons back to a position-sensitive detector close to but behind the source of the electrons. The longer flying distance that results makes it possible to significantly improve the energy-resolved performance, especially in the higher energy region. The dependence of the new TOF system on its characteristic parameters is analyzed, along with its application to attosecond streak cameras. Experimental results verified a relative energy resolution better than 0.2 eV for 22 eV electrons and also revealed the availability of the improved relative energy resolution smaller than 1.0% for electron energy ranging from 30 to 40 eV.

  15. High resolution genome-wide mapping of the primary structure of chromatin

    PubMed Central

    Zhang, Zhenhai; Pugh, B. Franklin

    2011-01-01

    The genomic organization of chromatin is increasingly recognized as a key regulator of cell behavior, but deciphering its regulation mechanisms requires detailed knowledge of chromatin’s primary structure - the assembly of nucleosomes throughout the genome. This Primer explains the principles for mapping and analyzing the primary organization of chromatin on a genomic scale. After introducing chromatin organization and its impact on gene regulation and human health, we then describe methods that detect nucleosome positioning and occupancy levels using chromatin-immunoprecipitation in combination with deep sequencing (ChIP-Seq), a strategy that is now straightforward and cost-efficient. We then explore current strategies for converting the sequence information into knowledge about chromatin, an exciting challenge for biologists and bioinformaticians. PMID:21241889

  16. High-resolution mapping and genetic characterization of the Lazy-2 gravitropic mutant of tomato

    NASA Technical Reports Server (NTRS)

    Behringer, F. J.; Lomax, T. L.

    1999-01-01

    Mutation of the Lazy-2 (Lz-2) gene in tomato (Lycopersicon esculentum mill.) produces a phytochrome-dependent reversal of shoot gravitropism, providing a unique genetic resource for investigating how signals from light modulate gravitropism. We mapped the Lz-2 gene using RFLPs and a PCR-based technique to assess the feasibility of positional cloning. Analysis of a 1338 plant backcross population between L. esculentum and L. pennellii placed Lz-2 within a 1.2 cM interval on chromosome 5, 0.4 cM from TG504-CT201A interval. The inabililty to resolve these markers indicates that Lz-2 resides in a centromeric region in which recombination is highly suppressed. Lazy-2 is tightly linked to but does not encode the gene for ACC4, an enzyme involved in ethylene biosynthesis. We also observed that Lz-2 is partially dominant under certain conditions and stages of development.

  17. High-resolution mapping of the spatial organization of a bacterial chromosome.

    PubMed

    Le, Tung B K; Imakaev, Maxim V; Mirny, Leonid A; Laub, Michael T

    2013-11-08

    Chromosomes must be highly compacted and organized within cells, but how this is achieved in vivo remains poorly understood. We report the use of chromosome conformation capture coupled with deep sequencing (Hi-C) to map the structure of bacterial chromosomes. Analysis of Hi-C data and polymer modeling indicates that the Caulobacter crescentus chromosome consists of multiple, largely independent spatial domains that are probably composed of supercoiled plectonemes arrayed into a bottle brush-like fiber. These domains are stable throughout the cell cycle and are reestablished concomitantly with DNA replication. We provide evidence that domain boundaries are established by highly expressed genes and the formation of plectoneme-free regions, whereas the histone-like protein HU and SMC (structural maintenance of chromosomes) promote short-range compaction and the colinearity of chromosomal arms, respectively. Collectively, our results reveal general principles for the organization and structure of chromosomes in vivo.

  18. High-resolution genetic mapping of mammalian motor activity levels in mice.

    PubMed

    Kas, M J H; de Mooij-van Malsen, J G; de Krom, M; van Gassen, K L I; van Lith, H A; Olivier, B; Oppelaar, H; Hendriks, J; de Wit, M; Groot Koerkamp, M J A; Holstege, F C P; van Oost, B A; de Graan, P N E

    2009-02-01

    The generation of motor activity levels is under tight neural control to execute essential behaviors, such as movement toward food or for social interaction. To identify novel neurobiological mechanisms underlying motor activity levels, we studied a panel of chromosome substitution (CS) strains derived from mice with high (C57BL/6J strain) or low motor activity levels (A/J strain) using automated home cage behavioral registration. In this study, we genetically mapped the expression of baseline motor activity levels (horizontal distance moved) to mouse chromosome 1. Further genetic mapping of this trait revealed an 8.3-Mb quantitative trait locus (QTL) interval. This locus is distinct from the QTL interval for open-field anxiety-related motor behavior on this chromosome. By data mining, an existing phenotypic and genotypic data set of 2445 genetically heterogeneous mice (http://gscan.well.ox.ac.uk/), we confirmed linkage to the peak marker at 79 970 253 bp and refined the QTL to a 312-kb interval containing a single gene (A830043J08Rik). Sequence analysis showed a nucleotide deletion in the 3' untranslated region of the Riken gene. Genome-wide microarray gene expression profiling in brains of discordant F(2) individuals from CS strain 1 showed a significant upregulation of Epha4 in low-active F(2) individuals. Inclusion of a genetic marker for Epha4 confirmed that this gene is located outside of the QTL interval. Both Epha4 and A830043J08Rik are expressed in brain motor circuits, and similar to Epha4 mutants, we found linkage between reduced motor neurons number and A/J chromosome 1. Our findings provide a novel QTL and a potential downstream target underlying motor circuitry development and the expression of physical activity levels.

  19. High Resolution Mapping of Bactericidal Monoclonal Antibody Binding Epitopes on Staphylococcus aureus Antigen MntC

    PubMed Central

    Gribenko, Alexey V.; Parris, Kevin; Mosyak, Lidia; Li, Sheng; Handke, Luke; Hawkins, Julio C.; Severina, Elena; Matsuka, Yury V.; Anderson, Annaliesa S.

    2016-01-01

    The Staphylococcus aureus manganese transporter protein MntC is under investigation as a component of a prophylactic S.aureus vaccine. Passive immunization with monoclonal antibodies mAB 305-78-7 and mAB 305-101-8 produced using MntC was shown to significantly reduce S. aureus burden in an infant rat model of infection. Earlier interference mapping suggested that a total of 23 monoclonal antibodies generated against MntC could be subdivided into three interference groups, representing three independent immunogenic regions. In the current work binding epitopes for selected representatives of each of these interference groups (mAB 305-72-5 – group 1, mAB 305-78-7 – group 2, and mAB 305-101-8 – group 3) were mapped using Hydrogen-Deuterium Exchange Mass Spectrometry (DXMS). All of the identified epitopes are discontinuous, with binding surface formed by structural elements that are separated within the primary sequence of the protein but adjacent in the context of the three-dimensional structure. The approach was validated by co-crystallizing the Fab fragment of one of the antibodies (mAB 305-78-7) with MntC and solving the three-dimensional structure of the complex. X-ray results themselves and localization of the mAB 305-78-7 epitope were further validated using antibody binding experiments with MntC variants containing substitutions of key amino acid residues. These results provided insight into the antigenic properties of MntC and how these properties may play a role in protecting the hostagainst S. aureus infection by preventing the capture and transport of Mn2+, a key element that the pathogen uses to evade host immunity. PMID:27689696

  20. High Resolution Mapping of Bactericidal Monoclonal Antibody Binding Epitopes on Staphylococcus aureus Antigen MntC.

    PubMed

    Gribenko, Alexey V; Parris, Kevin; Mosyak, Lidia; Li, Sheng; Handke, Luke; Hawkins, Julio C; Severina, Elena; Matsuka, Yury V; Anderson, Annaliesa S

    2016-09-01

    The Staphylococcus aureus manganese transporter protein MntC is under investigation as a component of a prophylactic S.aureus vaccine. Passive immunization with monoclonal antibodies mAB 305-78-7 and mAB 305-101-8 produced using MntC was shown to significantly reduce S. aureus burden in an infant rat model of infection. Earlier interference mapping suggested that a total of 23 monoclonal antibodies generated against MntC could be subdivided into three interference groups, representing three independent immunogenic regions. In the current work binding epitopes for selected representatives of each of these interference groups (mAB 305-72-5 - group 1, mAB 305-78-7 - group 2, and mAB 305-101-8 - group 3) were mapped using Hydrogen-Deuterium Exchange Mass Spectrometry (DXMS). All of the identified epitopes are discontinuous, with binding surface formed by structural elements that are separated within the primary sequence of the protein but adjacent in the context of the three-dimensional structure. The approach was validated by co-crystallizing the Fab fragment of one of the antibodies (mAB 305-78-7) with MntC and solving the three-dimensional structure of the complex. X-ray results themselves and localization of the mAB 305-78-7 epitope were further validated using antibody binding experiments with MntC variants containing substitutions of key amino acid residues. These results provided insight into the antigenic properties of MntC and how these properties may play a role in protecting the hostagainst S. aureus infection by preventing the capture and transport of Mn2+, a key element that the pathogen uses to evade host immunity.

  1. Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine

    PubMed Central

    Wang, Minghui; Londo, Jason P.; Acharya, Charlotte B.; Mitchell, Sharon E.; Sun, Qi; Reisch, Bruce; Cadle-Davidson, Lance

    2015-01-01

    Genotyping by sequencing (GBS) provides opportunities to generate high-resolution genetic maps at a low genotyping cost, but for highly heterozygous species, missing data and heterozygote undercalling complicate the creation of GBS genetic maps. To overcome these issues, we developed a publicly available, modular approach called HetMappS, which functions independently of parental genotypes and corrects for genotyping errors associated with heterozygosity. For linkage group formation, HetMappS includes both a reference-guided synteny pipeline and a reference-independent de novo pipeline. The de novo pipeline can be utilized for under-characterized or high diversity families that lack an appropriate reference. We applied both HetMappS pipelines in five half-sib F1 families involving genetically diverse Vitis spp. Starting with at least 116,466 putative SNPs per family, the HetMappS pipelines identified 10,440 to 17,267 phased pseudo-testcross (Pt) markers and generated high-confidence maps. Pt marker density exceeded crossover resolution in all cases; up to 5,560 non-redundant markers were used to generate parental maps ranging from 1,047 cM to 1,696 cM. The number of markers used was strongly correlated with family size in both de novo and synteny maps (r = 0.92 and 0.91, respectively). Comparisons between allele and tag frequencies suggested that many markers were in tandem repeats and mapped as single loci, while markers in regions of more than two repeats were removed during map curation. Both pipelines generated similar genetic maps, and genetic order was strongly correlated with the reference genome physical order in all cases. Independently created genetic maps from shared parents exhibited nearly identical results. Flower sex was mapped in three families and correctly localized to the known sex locus in all cases. The HetMappS pipeline could have wide application for genetic mapping in highly heterozygous species, and its modularity provides opportunities to

  2. Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine.

    PubMed

    Hyma, Katie E; Barba, Paola; Wang, Minghui; Londo, Jason P; Acharya, Charlotte B; Mitchell, Sharon E; Sun, Qi; Reisch, Bruce; Cadle-Davidson, Lance

    2015-01-01

    Genotyping by sequencing (GBS) provides opportunities to generate high-resolution genetic maps at a low genotyping cost, but for highly heterozygous species, missing data and heterozygote undercalling complicate the creation of GBS genetic maps. To overcome these issues, we developed a publicly available, modular approach called HetMappS, which functions independently of parental genotypes and corrects for genotyping errors associated with heterozygosity. For linkage group formation, HetMappS includes both a reference-guided synteny pipeline and a reference-independent de novo pipeline. The de novo pipeline can be utilized for under-characterized or high diversity families that lack an appropriate reference. We applied both HetMappS pipelines in five half-sib F1 families involving genetically diverse Vitis spp. Starting with at least 116,466 putative SNPs per family, the HetMappS pipelines identified 10,440 to 17,267 phased pseudo-testcross (Pt) markers and generated high-confidence maps. Pt marker density exceeded crossover resolution in all cases; up to 5,560 non-redundant markers were used to generate parental maps ranging from 1,047 cM to 1,696 cM. The number of markers used was strongly correlated with family size in both de novo and synteny maps (r = 0.92 and 0.91, respectively). Comparisons between allele and tag frequencies suggested that many markers were in tandem repeats and mapped as single loci, while markers in regions of more than two repeats were removed during map curation. Both pipelines generated similar genetic maps, and genetic order was strongly correlated with the reference genome physical order in all cases. Independently created genetic maps from shared parents exhibited nearly identical results. Flower sex was mapped in three families and correctly localized to the known sex locus in all cases. The HetMappS pipeline could have wide application for genetic mapping in highly heterozygous species, and its modularity provides opportunities to

  3. Reducing Uncertainties in Satellite-derived Forest Aboveground Biomass Estimates using a High Resolution Forest Cover Map

    NASA Astrophysics Data System (ADS)

    Zhang, G.; Ganguly, S.; Nemani, R. R.; Milesi, C.; Basu, S.; Kumar, U.

    2014-12-01

    Several studies to date have provided an extensive knowledge base for estimating forest aboveground biomass (AGB) and recent advances in space-based modeling of the 3-D canopy structure, combined with canopy reflectance measured by passive optical sensors and radar backscatter, are providing improved satellite-derived AGB density mapping for large scale carbon monitoring applications. A key limitation in forest AGB estimation from remote sensing, however, is the large uncertainty in forest cover estimates from the coarse-to-medium resolution satellite-derived land cover maps (present resolution is limited to 30-m of the USGS NLCD Program). The uncertainties in forest cover estimates at the Landsat scale result in high uncertainties for AGB estimation, predominantly in heterogeneous forest and urban landscapes. We have successfully developed an approach using a machine learning algorithm and High-Performance-Computing with NAIP air-borne imagery data for mapping tree cover at 1-m over California and Maryland. In a comparison with high resolution LiDAR data available over selected regions in the two states, we found our results to be promising both in terms of accuracy as well as our ability to scale nationally. The generated 1-m forest cover map will be aggregated to the Landsat spatial grid to demonstrate differences in AGB estimates (pixel-level AGB density, total AGB at aggregated scales like ecoregions and counties) when using a native 30-m forest cover map versus a 30-m map derived from a higher resolution dataset. The process will also be complemented with a LiDAR derived AGB estimate at the 30-m scale to aid in true validation.

  4. High-resolution mapping of architectural DNA binding protein facilitation of a DNA repression loop in Escherichia coli

    PubMed Central

    Becker, Nicole A.; Maher, L. James

    2015-01-01

    Double-stranded DNA is a locally inflexible polymer that resists bending and twisting over hundreds of base pairs. Despite this, tight DNA bending is biologically important for DNA packaging in eukaryotic chromatin and tight DNA looping is important for gene repression in prokaryotes. We and others have previously shown that sequence nonspecific DNA kinking proteins, such as Escherichia coli heat unstable and Saccharomyces cerevisiae non-histone chromosomal protein 6A (Nhp6A), facilitate lac repressor (LacI) repression loops in E. coli. It has been unknown if this facilitation involves direct protein binding to the tightly bent DNA loop or an indirect effect promoting global negative supercoiling of DNA. Here we adapt two high-resolution in vivo protein-mapping techniques to demonstrate direct binding of the heterologous Nhp6A protein at a LacI repression loop in living E. coli cells. PMID:26039992

  5. High-resolution mapping of architectural DNA binding protein facilitation of a DNA repression loop in Escherichia coli.

    PubMed

    Becker, Nicole A; Maher, L James

    2015-06-09

    Double-stranded DNA is a locally inflexible polymer that resists bending and twisting over hundreds of base pairs. Despite this, tight DNA bending is biologically important for DNA packaging in eukaryotic chromatin and tight DNA looping is important for gene repression in prokaryotes. We and others have previously shown that sequence nonspecific DNA kinking proteins, such as Escherichia coli heat unstable and Saccharomyces cerevisiae non-histone chromosomal protein 6A (Nhp6A), facilitate lac repressor (LacI) repression loops in E. coli. It has been unknown if this facilitation involves direct protein binding to the tightly bent DNA loop or an indirect effect promoting global negative supercoiling of DNA. Here we adapt two high-resolution in vivo protein-mapping techniques to demonstrate direct binding of the heterologous Nhp6A protein at a LacI repression loop in living E. coli cells.

  6. Drawing a high-resolution functional map of adeno-associated virus capsid by massively parallel sequencing.

    PubMed

    Adachi, Kei; Enoki, Tatsuji; Kawano, Yasuhiro; Veraz, Michael; Nakai, Hiroyuki

    2014-01-01

    Adeno-associated virus (AAV) capsid engineering is an emerging approach to advance gene therapy. However, a systematic analysis on how each capsid amino acid contributes to multiple functions remains challenging. Here we show proof-of-principle and successful application of a novel approach, termed AAV Barcode-Seq, that allows us to characterize phenotypes of hundreds of different AAV strains in a high-throughput manner and therefore overcomes technical difficulties in the systematic analysis. In this approach, we generate DNA barcode-tagged AAV libraries and determine a spectrum of phenotypes of each AAV strain by Illumina barcode sequencing. By applying this method to AAV capsid mutant libraries tagged with DNA barcodes, we can draw a high-resolution map of AAV capsid amino acids important for the structural integrity and functions including receptor binding, tropism, neutralization and blood clearance. Thus, Barcode-Seq provides a new tool to generate a valuable resource for virus and gene therapy research.

  7. High Resolution Mapping of QTLs for Heat Tolerance in Rice Using a 5K SNP Array.

    PubMed

    Ps, Shanmugavadivel; Sv, Amitha Mithra; Prakash, Chandra; Mk, Ramkumar; Tiwari, Ratan; Mohapatra, Trilochan; Singh, Nagendra Kumar

    2017-12-01

    Heat stress is one of the major abiotic threats to rice production, next to drought and salinity stress. Incidence of heat stress at reproductive phase of the crop results in abnormal pollination leading to floret sterility, low seed set and poor grain quality. Identification of QTLs and causal genes for heat stress tolerance at flowering will facilitate breeding for improved heat tolerance in rice. In the present study, we used 272 F8 recombinant inbred lines derived from a cross between Nagina22, a well-known heat tolerant Aus cultivar and IR64, a heat sensitive popular Indica rice variety to map the QTLs for heat tolerance. To enable precise phenotyping for heat stress tolerance, we used a controlled phenotyping facility available at ICAR-Indian Institute of Wheat and Barley Research, Karnal, India. Based on 'days to 50% flowering' data of the RILs, we followed staggered sowing to synchronize flowering to impose heat stress at uniform stage. Using the Illumina infinium 5K SNP array for genotyping the parents and the RILs, and stress susceptibility and stress tolerance indices (SSI and STI) of percent spikelet sterility and yield per plant (g), we identified five QTLs on chromosomes 3, 5, 9 and 12. The identified QTLs explained phenotypic variation in the range of 6.27 to 21. 29%. Of these five QTLs, two high effect QTLs, one novel (qSTIPSS9.1) and one known (qSTIY5.1/qSSIY5.2), were mapped in less than 400 Kbp genomic regions, comprising of 65 and 54 genes, respectively. The present study identified two major QTLs for heat tolerance in rice in narrow physical intervals, which can be employed for crop improvement by marker assisted selection (MAS) after development of suitable scorable markers for breeding of high yielding heat tolerant rice varieties. This is the first report of a major QTL for heat tolerance on chromosome 9 of rice. Further, a known QTL for heat tolerance on chromosome 5 was narrowed down from 23 Mb to 331 Kbp in this study.

  8. Mapping of photoreceptor dysfunction using high resolution three-dimensional spectral optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Sikorski, B. L.; Szkulmowski, M.; Kałużny, J. J.; Bajraszewski, T.; Kowalczyk, A.; Wojtkowski, M.

    2008-02-01

    The ability to obtain reliable information on functional status of photoreceptor layer is essential for assessing vision impairment in patients with macular diseases. The reconstruction of three-dimensional retinal structure in vivo using Spectral Optical Coherence Tomography (Spectral OCT) became possible with a recent progress of the OCT field. Three-dimensional data collected by Spectral OCT devices comprise information on light intensity back-reflected from the junction between photoreceptor outer and inner segments (IS/OS) and thus can be used for evaluating photoreceptors impairment. In this paper, we introduced so called Spectral OCT reflectivity maps - a new method of selecting and displaying the spatial distribution of reflectivity of individual retinal layers. We analyzed the reflectivity of the IS/OS layer in various macular diseases. We have measured eyes of 49 patients with photoreceptor dysfunction in course of age-related macular degeneration, macular holes, central serous chorioretinopathy, acute zonal occult outer retinopathy, multiple evanescent white dot syndrome, acute posterior multifocal placoid pigment epitheliopathy, drug-induced retinopathy and congenital disorders.

  9. High-resolution mapping of the gene for cystinosis, using combined biochemical and linkage analysis

    SciTech Connect

    Jean, G.; Fuchshuber, A.; Gribouval, O.

    1996-03-01

    Infantile nephropathic cystinosis is an autosomal recessive disorder characterized biochemically by an abnormally high intracellular content of free cystine in different organs and tissues due to a transport defect of cystine through the lysosomal membrane. Affected children present with the Fanconi syndrome and usually develop progressive renal failure within the 1st decade of life. Measurement of free cystine in purified polymorphonuclear leukocytes provides an accurate method for diagnosis and detection of heterozygous carriers previously determined by their leukocyte cystine content in the linkage analysis. This approach allowed us to obtain highly significant results, confirming the localization of the cystinosis gene locus recently mapped to the short arm of chromosome 17 by the Cystinosis Collaborative Research Group. Crucial recombination events allowed us to refine the interval of the cystinosis gene to a genetic distance of 1 cM. No evidence of genetic heterogeneity was found. Our results demonstrate that the use of the previously determined phenotypes of heterozygous carriers in linkage analysis provides a reliable method for the investigation of simplex families in autosomal recessive traits. 25 refs., 4 figs., 1 tab.

  10. High-Resolution Air Pollution Mapping with Google Street View Cars: Exploiting Big Data.

    PubMed

    Apte, Joshua S; Messier, Kyle P; Gani, Shahzad; Brauer, Michael; Kirchstetter, Thomas W; Lunden, Melissa M; Marshall, Julian D; Portier, Christopher J; Vermeulen, Roel C H; Hamburg, Steven P

    2017-06-20

    Air pollution affects billions of people worldwide, yet ambient pollution measurements are limited for much of the world. Urban air pollution concentrations vary sharply over short distances (≪1 km) owing to unevenly distributed emission sources, dilution, and physicochemical transformations. Accordingly, even where present, conventional fixed-site pollution monitoring methods lack the spatial resolution needed to characterize heterogeneous human exposures and localized pollution hotspots. Here, we demonstrate a measurement approach to reveal urban air pollution patterns at 4-5 orders of magnitude greater spatial precision than possible with current central-site ambient monitoring. We equipped Google Street View vehicles with a fast-response pollution measurement platform and repeatedly sampled every street in a 30-km(2) area of Oakland, CA, developing the largest urban air quality data set of its type. Resulting maps of annual daytime NO, NO2, and black carbon at 30 m-scale reveal stable, persistent pollution patterns with surprisingly sharp small-scale variability attributable to local sources, up to 5-8× within individual city blocks. Since local variation in air quality profoundly impacts public health and environmental equity, our results have important implications for how air pollution is measured and managed. If validated elsewhere, this readily scalable measurement approach could address major air quality data gaps worldwide.

  11. High-resolution radiation mapping to investigate FDNPP derived contaminant migration.

    PubMed

    Martin, P G; Payton, O D; Yamashiki, Y; Richards, D A; Scott, T B

    2016-11-01

    As of March 2016, five years will have passed since the earthquake and ensuing tsunami that crippled the Fukushima Daiichi Nuclear Power Plant on Japan's eastern coast, resulting in the explosive release of significant quantities of radioactive material. Over this period, significant time and resource has been expended on both the study of the contamination as well as its remediation from the affected environments. Presented in this work is a high-spatial resolution foot-based radiation mapping study using gamma-spectrometry at a site in the contaminated Iitate Village; conducted at different times, seventeen months apart. The specific site selected for this work was one in which consistent uniform agriculture was observed across its entire extent. From these surveys, obtained from along the main northwest trending line of the fallout plume, it was possible to determine the rate of reduction in the levels of contamination around the site attributable to the natural decay of the radiocesium, remediation efforts or material transport. Results from the work suggest that neither the natural decay of radiocesium nor its downward migration through the soil horizons were responsible for the decline in measured activity levels across the site, with the mobilisation of contaminant species likely adhered to soil particulate and the subsequent fluvial transport responsible for the measurable reduction in activity. This transport of contaminant via fluvial methods has already well studied implications for the input of contaminant material entering the neighbouring Pacific Ocean, as well as the deposition of material along rivers within previously decontaminated areas.

  12. High-resolution mapping of the gene for cystinosis, using combined biochemical and linkage analysis.

    PubMed

    Jean, G; Fuchshuber, A; Town, M M; Gribouval, O; Schneider, J A; Broyer, M; van't Hoff, W; Niaudet, P; Antignac, C

    1996-03-01

    Infantile nephropathic cystinosis is an autosomal recessive disorder characterized biochemically by an abnormally high intracellular content of free cystine in different organs and tissues due to a transport defect of cystine through the lysosomal membrane. Affected children present with the Fanconi syndrome and usually develop progressive renal failure within the 1st decade of life. Measurement of free cystine in purified polymorphonuclear leukocytes provides an accurate method for diagnosis and detection of heterozygous carriers. In order to localize the gene locus for cystinosis we performed linkage analysis in 18 cystinosis families. However, since 17 of these were simplex families, we decided to include the phenotypes of the heterozygous carriers previously determined by their leukocyte cystine content in the linkage analysis. This approach allowed us to obtain highly significant results, confirming the localization of the cystinosis gene locus recently mapped to the short arm of chromosome 17 by the Cystinosis Collaborative Research Group. Crucial recombination events allowed us to refine the interval of the cystinosis gene to a genetic distance of 1 cM. No evidence of genetic heterogeneity was found. Our results demonstrate that the use of the previously determined phenotypes of heterozygous carriers in linkage analysis provides a reliable method for the investigation of simplex families in autosomal recessive traits.

  13. Quantitative high-resolution mapping of phenanthrene sorption to black carbon particles.

    PubMed

    Obst, Martin; Grathwohl, Peter; Kappler, Andreas; Eibl, Oliver; Peranio, Nicola; Gocht, Tilman

    2011-09-01

    Sorption of hydrophobic organic contaminants such as polycyclic aromatic hydrocarbons (PAHs) to black carbon (BC) particles has been the focus of numerous studies. Conclusions on sorption mechanisms of PAH on BC were mostly derived from studies of sorption isotherms and sorption kinetics, which are based on batch experiments. However, mechanistic modeling approaches consider processes at the subparticle scale, some including transport within the pore-space or different spatial pore-domains. Direct evidence based on analytical techniques operating at the submicrometer scale for the location of sorption sites and the adsorbed species is lacking. In this work, we identified, quantified, and mapped the sorption of PAHs on different BC particles (activated carbon, charcoal and diesel soot) on a 25-100 nm scale using scanning transmission X-ray microscopy (STXM). In addition, we visualized the pore structure of the particles by transmission electron microscopy (TEM) on the 1-10 nm-scale. The combination of the chemical information from STXM with the physical information from TEM revealed that phenanthrene accumulates in the interconnected pore-system along primary "cracks" in the particles, confirming an adsorption mechanism.

  14. Euro-Maps 3D- A Transnational, High-Resolution Digital Surface Model For Europe

    NASA Astrophysics Data System (ADS)

    Uttenthaler, A.; Barner, F.; Hass, T.; Makiola, J.; d'Angelo, P.; Reinartz, P.; Carl, S.; Steiner, K.

    2013-12-01

    Euro-Maps 3D is a homogeneous 5 m spaced digital surface model (DSM) semi-automatically derived by Euromap from 2.5 m in-flight stereo data provided by the Indian IRS-P5 Cartosat-1 satellite. This new and innovative product has been developed in close co- operation with the Remote Sensing Technology Institute (IMF) of the German Aerospace Center (DLR) and is being jointly exploited. The very detailed and accurate representation of the surface is achieved by using a sophisticated and well adapted algorithm implemented on the basis of the Semi-Global Matching approach. In addition, the final product includes detailed flanking information consisting of several pixel-based quality and traceability layers also including an ortho layer. The product is believed to provide maximum accuracy and transparency. The DSM product meets and exceeds HRE80 qualification standards. The DSM product will be made available transnational in a homogeneous quality for most parts of Europe, North Africa and Turkey by Euromap step-by-step. Other areas around the world are processed on demand.

  15. Estimating High-Resolution Directional Clutter Maps in Forested Terrain Using Airborne Lidar Data

    DTIC Science & Technology

    2008-12-01

    SNR ) levels for each SV and position solution statistics at each site were then analyzed and compared with the base station data. These SNR values...spatial neighborhood in which lidar returns are from objects likely to affect the SNR of the GPS signal. We compute the number of ALSM points...lidar returns. The ALSM point densities in the Fresnel zone were then compared to the SNR levels of each SV. Fig. 2 A diagram of Fresnel

  16. Comparing landslide inventory maps

    NASA Astrophysics Data System (ADS)

    Galli, Mirco; Ardizzone, Francesca; Cardinali, Mauro; Guzzetti, Fausto; Reichenbach, Paola

    Landslide inventory maps are effective and easily understandable products for both experts, such as geomorphologists, and for non experts, including decision-makers, planners, and civil defense managers. Landslide inventories are essential to understand the evolution of landscapes, and to ascertain landslide susceptibility and hazard. Despite landslide maps being compiled every year in the word at different scales, limited efforts are made to critically compare landslide maps prepared using different techniques or by different investigators. Based on the experience gained in 20 years of landslide mapping in Italy, and on the limited literature on landslide inventory assessment, we propose a general framework for the quantitative comparison of landslide inventory maps. To test the proposed framework we exploit three inventory maps. The first map is a reconnaissance landslide inventory prepared for the Umbria region, in central Italy. The second map is a detailed geomorphological landslide map, also prepared for the Umbria region. The third map is a multi-temporal landslide inventory compiled for the Collazzone area, in central Umbria. Results of the experiment allow for establishing how well the individual inventories describe the location, type and abundance of landslides, to what extent the landslide maps can be used to determine the frequency-area statistics of the slope failures, and the significance of the inventory maps as predictors of landslide susceptibility. We further use the results obtained in the Collazzone area to estimate the quality and completeness of the two regional landslide inventory maps, and to outline general advantages and limitations of the techniques used to complete the inventories.

  17. High Resolution Stratigraphic Mapping in Complex Terrain: A Comparison of Traditional Remote Sensing Techniques with Unmanned Aerial Vehicle - Structure from Motion Photogrammetry

    NASA Astrophysics Data System (ADS)

    Nesbit, P. R.; Hugenholtz, C.; Durkin, P.; Hubbard, S. M.; Kucharczyk, M.; Barchyn, T.

    2016-12-01

    Remote sensing and digital mapping have started to revolutionize geologic mapping in recent years as a result of their realized potential to provide high resolution 3D models of outcrops to assist with interpretation, visualization, and obtaining accurate measurements of inaccessible areas. However, in stratigraphic mapping applications in complex terrain, it is difficult to acquire information with sufficient detail at a wide spatial coverage with conventional techniques. We demonstrate the potential of a UAV and Structure from Motion (SfM) photogrammetric approach for improving 3D stratigraphic mapping applications within a complex badland topography. Our case study is performed in Dinosaur Provincial Park (Alberta, Canada), mapping late Cretaceous fluvial meander belt deposits of the Dinosaur Park formation amidst a succession of steeply sloping hills and abundant drainages - creating a challenge for stratigraphic mapping. The UAV-SfM dataset (2 cm spatial resolution) is compared directly with a combined satellite and aerial LiDAR dataset (30 cm spatial resolution) to reveal advantages and limitations of each dataset before presenting a unique workflow that utilizes the dense point cloud from the UAV-SfM dataset for analysis. The UAV-SfM dense point cloud minimizes distortion, preserves 3D structure, and records an RGB attribute - adding potential value in future studies. The proposed UAV-SfM workflow allows for high spatial resolution remote sensing of stratigraphy in complex topographic environments. This extended capability can add value to field observations and has the potential to be integrated with subsurface petroleum models.

  18. OnEarth: An Open Source Solution for Efficiently Serving High-Resolution Mapped Image Products

    NASA Astrophysics Data System (ADS)

    Thompson, C. K.; Plesea, L.; Hall, J. R.; Roberts, J. T.; Cechini, M. F.; Schmaltz, J. E.; Alarcon, C.; Huang, T.; McGann, J. M.; Chang, G.; Boller, R. A.; Ilavajhala, S.; Murphy, K. J.; Bingham, A. W.

    2013-12-01

    This presentation introduces OnEarth, a server side software package originally developed at the Jet Propulsion Laboratory (JPL), that facilitates network-based, minimum-latency geolocated image access independent of image size or spatial resolution. The key component in this package is the Meta Raster Format (MRF), a specialized raster file extension to the Geospatial Data Abstraction Library (GDAL) consisting of an internal indexed pyramid of image tiles. Imagery to be served is converted to the MRF format and made accessible online via an expandable set of server modules handling requests in several common protocols, including the Open Geospatial Consortium (OGC) compliant Web Map Tile Service (WMTS) as well as Tiled WMS and Keyhole Markup Language (KML). OnEarth has recently transitioned to open source status and is maintained and actively developed as part of GIBS (Global Imagery Browse Services), a collaborative project between JPL and Goddard Space Flight Center (GSFC). The primary function of GIBS is to enhance and streamline the data discovery process and to support near real-time (NRT) applications via the expeditious ingestion and serving of full-resolution imagery representing science products from across the NASA Earth Science spectrum. Open source software solutions are leveraged where possible in order to utilize existing available technologies, reduce development time, and enlist wider community participation. We will discuss some of the factors and decision points in transitioning OnEarth to a suitable open source paradigm, including repository and licensing agreement decision points, institutional hurdles, and perceived benefits. We will also provide examples illustrating how OnEarth is integrated within GIBS and other applications.

  19. High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus

    DOE PAGES

    Muchero, Wellington; Guo, Jianjun; Difazio, Stephen P.; ...

    2015-01-23

    We report the identification of six genetic loci and the allelic-variants associated with Populus cell wall phenotypes determined independently using pyrolysis Molecular Beam Mass Spectrometry (pyMBMS), saccharification assay and wet chemistry in two partially overlapping populations of P. trichocarpa genotypes sampled from multiple environments in the Pacific Northwest of North America. All 6 variants co-located with a quantitative trait locus (QTL) hotspot on chromosome XIV for lignin content, syringyl to guaiacyl (S/G) ratio, 5- and 6- carbon sugars identified in an interspecific P. trichocarpa x P. deltoides pseudo-backcross mapping pedigree. Genomic intervals containing an amino acid transporter, a MYB transcriptionmore » factor, an angustifolia CtBP transcription factor, a copper transport protein ATOX1-related, a Ca2+ transporting ATPase and a protein kinase were identified within 5 QTL regions. Each interval contained single nucleotide polymorphisms (SNPs) that were significantly associated to cell-wall phenotypes, with associations exceeding the chromosome-wise Bonferroni-adjusted p-values in at least one environment. cDNA sequencing for allelic variants of 3 of the 6 genes identified polymorphisms leading to premature stop codons in the MYB transcription factor and protein kinase. On the other hand, variants of the Angustifolia CtBP transcription factor exhibited a polyglutamine (PolyQ) length polymorphism. Results from transient protoplast assays suggested that each of the polymorphisms conferred allelic differences in activation of cellulose, hemicelluloses and lignin pathway marker genes, with truncated and short PolyQ alleles exhibiting significantly reduced marker gene activation. Genes identified in this study represent novel targets for reducing cell wall recalcitrance for lignocellulosic biofuels production using plant biomass.« less

  20. High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus

    SciTech Connect

    Muchero, Wellington; Guo, Jianjun; Difazio, Stephen P.; Chen, Jay; Ranjan, Priya; Slavov, Gancho; Gunter, Lee E.; Jawdy, Sara; Bryan, Anthony C.; Sykes, Robert; Ziebell, Angela L.; Klapste, Jaroslav; Porth, Ilga; Skyba, Oleksandr; Unda, Faride; El-Kassaby, Yousry; Douglas, Carl; Mansfield, Shawn; Martin, Joel; Schackwitz, Wendy; Evans, Luke M.; Czarnecki, Olaf; Tuskan, Gerald A.

    2015-01-23

    We report the identification of six genetic loci and the allelic-variants associated with Populus cell wall phenotypes determined independently using pyrolysis Molecular Beam Mass Spectrometry (pyMBMS), saccharification assay and wet chemistry in two partially overlapping populations of P. trichocarpa genotypes sampled from multiple environments in the Pacific Northwest of North America. All 6 variants co-located with a quantitative trait locus (QTL) hotspot on chromosome XIV for lignin content, syringyl to guaiacyl (S/G) ratio, 5- and 6- carbon sugars identified in an interspecific P. trichocarpa x P. deltoides pseudo-backcross mapping pedigree. Genomic intervals containing an amino acid transporter, a MYB transcription factor, an angustifolia CtBP transcription factor, a copper transport protein ATOX1-related, a Ca2+ transporting ATPase and a protein kinase were identified within 5 QTL regions. Each interval contained single nucleotide polymorphisms (SNPs) that were significantly associated to cell-wall phenotypes, with associations exceeding the chromosome-wise Bonferroni-adjusted p-values in at least one environment. cDNA sequencing for allelic variants of 3 of the 6 genes identified polymorphisms leading to premature stop codons in the MYB transcription factor and protein kinase. On the other hand, variants of the Angustifolia CtBP transcription factor exhibited a polyglutamine (PolyQ) length polymorphism. Results from transient protoplast assays suggested that each of the polymorphisms conferred allelic differences in activation of cellulose, hemicelluloses and lignin pathway marker genes, with truncated and short PolyQ alleles exhibiting significantly reduced marker gene activation. Genes identified in this study represent novel targets for reducing cell wall recalcitrance for lignocellulosic biofuels production using plant biomass.

  1. HIGH RESOLUTION NEAR-INFRARED SURVEY OF THE PIPE NEBULA. I. A DEEP INFRARED EXTINCTION MAP OF BARNARD 59

    SciTech Connect

    Roman-Zuniga, Carlos G.; Alves, Joao F.; Lada, Charles J.

    2009-10-10

    We present our analysis of a fully sampled, high resolution dust extinction map of the Barnard 59 complex in the Pipe Nebula. The map was constructed with the infrared color excess technique applied to a photometric catalog that combines data from both ground and space based observations. The map resolves for the first time the high density center of the main core in the complex, which is associated with the formation of a small cluster of stars. We found that the central core in Barnard 59 shows an unexpected lack of significant substructure consisting of only two significant fragments. Overall, the material appears to be consistent with being a single, large core with a density profile that can be well fit by a King model. A series of NH{sub 3} pointed observations toward the high column density center of the core appear to show that the core is still thermally dominated, with subsonic non-thermal motions. The stars in the cluster could be providing feedback to support the core against collapse, but the relatively narrow radio lines suggest that an additional source of support, for example, a magnetic field, may be required to stabilize the core. Outside the central core our observations reveal the structure of peripheral cores and resolve an extended filament into a handful of significant substructures whose spacing and masses appear to be consistent with Jeans fragmentation.

  2. Cold-seep habitat mapping: High-resolution spatial characterization of the Blake Ridge Diapir seep field